Handbook of Chem Office

Contents
Introduction Using Documents .................................................... 12

Setting the Default Document Location ...........12
About ChemDraw ..................................................... 1 Creating a Document ........................................12
What’s New in ChemDraw 7 .................................... 1 Creating a New Document ........................... 12
For Users of ChemDraw 5 ..................................1 Creating a Document Using a
For Users of ChemDraw 5 and 6 ........................1 Style Sheet or Stationery Pad....................... 12
About This User’s Guide........................................... 2 Opening a Document ........................................13
Setting the Default Open File Format .......... 13
Conventions............................................................... 2
Saving Changes Automatically .........................13
Additional Information.............................................. 3
Reversing and Repeating Actions .....................14
Quick Reference Card .........................................3 Undoing Actions .......................................... 14
Online Help .........................................................3 Redoing Actions........................................... 14
Online Help .................................................... 3 Repeating Actions ........................................ 14
ToolTips ......................................................... 3 Discarding Recent Changes to a Document ......15
Context-sensitive Help (Windows)................ 3 Saving Documents ............................................15
CambridgeSoft Web Pages .................................3 Setting the Default Save File Format ........... 15
Installation and System Requirements ...................... 4 Saving a Document with a
Windows Requirements ......................................4 Different Name or Location......................... 16
Macintosh Requirements ....................................4 Saving a Document in a
Different File Format ................................... 16
Chapter 1: ChemDraw Basics Closing a Document ..........................................16
Accessing Documents Quickly ............................... 17
Overview ................................................................... 5 The ChemDraw Items Folder ............................17
Starting ChemDraw................................................... 5 The Open Special Submenu ..............................17
ChemDraw’s Graphical User Interface (GUI) .......... 5 The Window Menu ...........................................17
The Tools Palette ................................................7 Printing .................................................................... 18
Showing and Hiding Palettes ......................... 8 Printing Background Color ...............................18
Macintosh Print Preferences .............................18
Docking and Undocking Palettes................... 8
Optimize Pictures for High-Resolution
Tearing Off Palettes ....................................... 8
Non-PostScript Printing (Macintosh)........... 18
Setting the Default Tool................................. 8 Include PostScript (Macintosh).................... 19
Toolbars ..............................................................9 Include ChemDraw Laser Prep
Docking and Undocking Toolbars ................. 9 (Macintosh) .................................................. 19
The Status Bar or Message Area Scripts (Macintosh) ................................................. 19
(Windows) ..........................................................9 Closing ChemDraw ................................................. 19
Customizing ChemDraw ........................................... 9
Setting Preferences .............................................9 Chapter 2: Tutorials
Document and Object Settings .........................10
Default Style Sheet or Stationery Pad.......... 10 Overview ................................................................. 21
Saving Customized Settings as Tutorial 1: Reaction Schemes ................................. 21
Style Sheets or Stationery Pads.................... 10 Tutorial 2: Drawing an Intermediate ....................... 28
Tutorial 3: Using Rings ........................................... 32
Applying Document Settings From
Tutorial 4: Fischer Projections ................................ 35
Other Documents ......................................... 11
Tutorial 5: Perspective Drawings ............................ 40
Applying Object Settings from Tutorial 6: Newman Projections ............................. 44
Other Documents ......................................... 11 Tutorial 7: Showing Stereochemistry...................... 47
ChemDraw Contents • i
Chapter 3: Chapter 4:
Drawing Chemical Structures Drawing Captions and Atom Labels
Overview ................................................................. 49 Creating Text........................................................... 65
Drawing Settings..................................................... 49 Formatting Text....................................................... 65
Displaying the Info Window................................... 52 Setting the Baseline Style .................................66
Contents
Drawing Bonds ....................................................... 52 Specifying Line Spacing ...................................66

Setting the Default Tool ...................................53 Aligning Text ....................................................66
Drawing Constrained Bonds .............................53 Captions ....................................................... 66
Drawing with Fixed Lengths ....................... 53 Atom Labels................................................. 67
Drawing with Fixed Angles ......................... 53 Automatic Alignment................................... 67
Toggling Fixed Lengths and Fixed Angles.. 53 Changing the Default Caption or
Dative Bonds and Wedged Bonds ....................53 Atom Label Text Format ..................................68
Adding a Bond by Clicking ..............................54 Specifying Document Settings for
Adding Bonds by Dragging ..............................54 New Text...................................................... 68
Changing the Highlight Box Size .....................54 Setting an Individual Text Format
Multiple Bonds ................................................55 Before Typing .............................................. 69
Double Bonds .............................................. 55 Changing the Spacing of
Double Either Bonds.................................... 55 Individual Text Objects................................ 69
Triple Bonds ................................................ 55 Fractional Character Widths (Macintosh).... 69
Quadruple Bonds ......................................... 55 Coloring Text ....................................................69
Drawing Rings ........................................................ 56 Creating Captions.................................................... 70
Drawing a Ring .................................................56 Changing the Caption Width ............................70
Drawing a Ring by Clicking .............................56 Editing a Caption ..............................................70
Drawing Cyclohexane Chair Rings ..................57 Adding Chemical Names ........................................ 71
Drawing Resonance Delocalized Rings ...........57 Labeling Atoms with the Text Tool ........................ 72
Drawing Cyclopentadiene and Specifying the Margin Width ...........................72
Benzene Rings ..................................................57 Editing Atom Labels .........................................72
Drawing Acyclic Chains ......................................... 58 Deleting an Atom Label ....................................73
Drawing Chains ................................................58 Labeling Atoms with HotKeys................................ 73
Adding Chains ..................................................58 Method 1: Labeling the last atom drawn ..........73
Changing Chain Direction ................................59 Method 2: Labeling an atom by pointing .........73
Editing Bonds.......................................................... 59 Method 3: Labeling an atom with
Changing Bond Types ......................................59 a selection tool ..................................................73
Changing Double Bonds ...................................59 Method 4: Labeling multiple atoms ..................73
Changing Orientation of Wedged and Hard-Coded HotKeys .......................................74
Dative Bonds ....................................................60 Creating HotKeys .............................................74
Changing Alignment of Double Bonds ............60 Labeling Atoms With a Bond or Ring Tool............ 75
Moving Atoms ..................................................60 Repeating an Atom Label........................................ 75
Changing Bond Crossings ................................61 Numbering Atoms................................................... 75
Changing the Bond Order .................................61 Showing and Hiding Atom Numbers ...............76
Automatic Warnings ............................................... 62 Editing Atom Numbers .....................................77
Automatic Drawing—Structures from Positioning Atom Number Indicators ...............77
Chemical Names ..................................................... 63 Typing Non-Roman Text ........................................ 78
Converting Names to Structures .......................63 Creating a New Line and Closing Text Boxes........ 78
Inserting Names ........................................... 63 Using the Text Tool with the Lasso Tool................ 79
Paste Special ................................................ 64 Using Bitmap Fonts When Available
Converting Captions to Structures ....................64 (Macintosh) ............................................................. 79
ii • Contents CambridgeSoft
Chapter 5: Drawing Orbitals, Chapter 6: Manipulating Drawings
Symbols, Arrows, Arcs, and Other
Shapes Overview ................................................................. 95
Using a Selection Tool ............................................ 95
Overview ................................................................. 81 Selecting Objects with the Lasso Tool ..............95
The Orbital Tool Palette.......................................... 81 Selecting Objects with the Marquee Tool .........95
s-orbitals ............................................................82 Toggling Between Selection Tools ...................96
Sigma Orbitals ..................................................82 Toggling Between Other Tools .........................96
Single Lobe Orbitals .........................................82 Selecting Objects by Clicking ...........................96
p-orbitals ...........................................................83 Setting the Highlight Box Tolerance ................96
Hybrid Orbitals .................................................83 Selecting Entire Structures ................................97
d-orbitals ...........................................................83 Making Multiple Selections ..............................97
dz2-orbitals .......................................................83 Removing Objects from the Selection ..............97
The Chemical Symbols Tool................................... 84 Selecting All Objects ........................................97
H-dot and H-dash ..............................................84 Deselecting All Objects ....................................97
Lone Pair ...........................................................84 Deleting Objects ................................................97
Radical ..............................................................85 Moving Objects .................................................98
Radical Cation and Radical Anion ....................85 Using the Clipboard ..........................................98
Charge Symbols ................................................85 Cutting.......................................................... 98
Rotating a Symbol ............................................86 Pasting.......................................................... 98
Selecting Tools From a Palette................................ 86 Moving Atoms ..................................................99
The Arrow Tool....................................................... 86 Duplicating Objects ..........................................99
Selecting an Arrow ...........................................86 Rotating Objects .................................................... 100
Drawing an Arrow ............................................86 Reflecting Objects Through Planes....................... 101
Editing an Arrow ..............................................87 Flipping Objects ......................................... 101
The Drawing Elements Tool ................................... 87 Creating Mirror Images.............................. 101
Selecting a Drawing Element ...........................87 Resizing Objects.................................................... 101
Drawing Boxes .................................................87 The Resize Handle ..........................................101
Drawing Circles and Ovals ...............................88 Scaling Objects ...............................................102
Resizing or Rotating Drawing Elements ..........88 Distorting a Selection ......................................102
Distorting Circle and Ovals ..............................88 Joining Objects ...................................................... 103
Drawing Lines ...................................................88 Setting the Maximum Distance Tolerance ......103
The Brackets Tool ................................................... 89 Grouping Objects .................................................. 104
Drawing Single Brackets ..................................89 Ungrouping Objects ........................................104
Drawing Paired Brackets ..................................89 Creating Integral Groups .................................104
Drawing Daggers ..............................................89
Framing Objects ...................................................... 89 Chapter 7:
The Arc Tool ........................................................... 90 Advanced Drawing Techniques
Drawing Arcs ....................................................90
Editing Arcs ......................................................90 Overview ............................................................... 105
The Pen Tool ........................................................... 90 Using Nicknames .................................................. 105
Drawing Bézier Curves by Dragging ................91 Applying Nicknames ......................................105
Drawing Segments by Clicking ........................91 Defining Nicknames .......................................106
Editing a Curve .................................................92 Troubleshooting Nicknames ...........................107
Changing the Shape of a Curve.................... 92 Viewing Nicknames ........................................108
Adding a Segment........................................ 92 Deleting Nicknames .............................................. 108
Deleting a Segment ...................................... 93 Contracting Labels ................................................ 108
Applying a Style to a Shape ..............................93 Expanding Labels .................................................. 109
Filled and Closed Styles............................... 93 Using Multi-Center Bonds .................................... 109
Shaded Style................................................. 93 Creating a Multi-Center Bond ........................109
Plain Style .................................................... 93 Viewing Attachment Points ............................110
ChemDraw Contents • iii

Multi-Attached Labels .......................................... 111 Chapter 9:
Adding Bonds to an Atom Label ....................111 Drawing Query Structures
Using Clean Up Structure ..................................... 111
Using Variable Attachment Positions ................... 112 What Are Query Structures? ................................. 131
Working with Color .............................................. 113 Atom Properties .................................................... 131
Coloring Objects .............................................114 Viewing Atom Property Values ......................132
Contents
Displaying the Color Palette ...........................114 Removing Atom Properties ............................132

Customizing the Color Palette .......................115 Atom Property Options ...................................133
Windows Color Settings .................................115 Substituents ................................................ 133
Adding or Customizing Implicit Hydrogens .................................... 134
Windows Colors ........................................ 116 Ring Bond Count ............................................134
Macintosh Color Settings ...............................116 Unsaturation ....................................................134
Adding or Customizing Reaction Change .............................................135
Macintosh Colors ....................................... 117 Reaction Stereo ...............................................135
Removing Colors ............................................117 Translation ......................................................135
Abnormal Valence ..........................................136
Templates and Color .......................................117
Bond Properties..................................................... 136
Saving Color Palette Settings .........................117
Viewing Bond Property Values ......................137
Drawing With Templates ...................................... 117
Removing Bond Properties .............................137
The Templates Tool ........................................118 Bond Property Options ...................................137
Choosing a Template ......................................118
Bond Types ................................................ 137
Using Templates .............................................118 Topology .................................................... 138
Drawing a Template................................... 118
Reaction Center.......................................... 139
Fusing a Template With an Query Tools Palette............................................... 139
Existing Structure ...................................... 118
Query Indicators.................................................... 139
Drawing with the Same Template ............. 119 Viewing Query Indicators.......................... 139
Creating Templates and Template Documents ..... 119
Hiding Query Indicators ............................ 139
Creating Templates .........................................119 Removing Query Indicators....................... 140
Orientation of Templates ................................120
Positioning Query Indicators ..................... 140
Resizing Template Panes ................................120 Drawing Stereochemical Symbols ........................ 140
Template Panels ..............................................120
Drawing Free Sites................................................ 140
Saving Template Documents ..........................121 Generic Nicknames ............................................... 141
Chapter 8: Working With Structures Element Lists......................................................... 142
Element Not-Lists ................................................. 142
Overview ............................................................... 123 Link Nodes ............................................................ 143
Checking Chemistry.............................................. 123 Representing Polymers and
Check Structure ..............................................123 Other Repeating Units........................................... 143
Check Structure when Copying to Setting Bracket Properties ..............................143
Clipboard or Exporting ...................................124 Bracket Usage .................................................144
Viewing Analysis Information.............................. 124 Structure-based Polymer Representations . 144
Viewing Chemical Properties ............................... 125 Source-based Polymer Representations..... 145
Showing Stereochemistry ..................................... 126 Repeat Pattern .................................................146
Stereochemistry Indicators .............................127 Flip Type .........................................................146
Hiding Indicators ....................................... 127 Exporting Bracket Properties ..........................146
Removing Indicators.................................. 127
Alternative Groups ................................................ 147
Positioning Indicators ................................ 127
Defining an Alternative Group .......................147
Converting Structures to 3D ................................. 128
Spectrum-Structure Assignments.......................... 128 Defining Attachment Points ...........................148
Assigning Structures to Spectra ......................128 Multiple Attachment Points ............................148
Viewing Spectral Assignments .......................129 Showing Attachment Rank Indicators ............149
Removing Spectral Assignments ....................129 Attachment Point Numbering .........................149
NMR Shift Information—ChemNMR Pro .......... 129 Anonymous Alternative Groups ........................... 150
iv • Contents CambridgeSoft
Atom-to-Atom Mapping ....................................... 150 Creating Tables ..................................................... 164
Always Display and Print Atom Mapping ......151 Creating Tables with the Table Tool ..............164
Automatic Mapping ........................................151 Creating Tables with the Text Tool ................167
Manual Mapping .............................................151 Creating the First Row
Clearing Reaction Mapping ............................152 (column headings)...................................... 167
Exporting Reaction Mapping ..........................152 Creating a New Row .................................. 167
Export Compatibility............................................. 152 Adjusting Row or Column Spacing ........... 168
Moving Around In Tables.......................... 168
Chapter 10: Inserting a New Row.................................. 168
Working with Page Layout
Chapter 11: Sharing Information
Overview ............................................................... 155
Controlling the Drawing Area............................... 155 Overview ............................................................... 169
Setting up Pages .................................................... 155 Transferring Between ChemDraw Documents ..... 169
Paged Document Setup ...................................156 Using the Clipboard ........................................169
Poster Documents Setup .................................156 Copying ...................................................... 169
Creating Headers and Footers .........................157 Cutting........................................................ 169
Page Setup ............................................................. 157 Pasting........................................................ 169
Page Orientation .............................................158 Using the Drag-and-Drop Feature ..................170
Reduce or Enlarge ...........................................159 Autoscaling .....................................................170
Saving Page Setup Settings .............................159 Bonds ..............................................................171
35mm Slide Boundary Guides .............................. 159 Atom Labels ....................................................171
Changing Perspectives .......................................... 159 Captions ..........................................................171
Magnifying with the View Menu ...................159 Non-bond Objects and Color ..........................171
Magnify ...................................................... 159 Pasting to an Empty Document Window ........172
Actual Size ................................................. 160 Transferring ChemDraw Documents
Reduce........................................................ 160 Across Platforms ................................................... 172
Fit to Window ............................................ 160 Transferring from Macintosh to Windows .....172
Using the Magnification Control ............... 160 Transferring from Windows to Macintosh .....173
Arranging Objects ................................................. 161 Transferring Files to
Using Rulers ...................................................161 ChemDraw/Plus 3.1 for the Macintosh...... 173
Showing Rulers ...............................................161 Embedding Objects (Windows) ............................ 173
Hiding Rulers ..................................................161 Inserting Graphics or Objects from Other
Using the Crosshair .........................................161 Applications ....................................................174
Displaying the Crosshair .................................162 Inserting Reference Numbers in
Moving the Crosshair ......................................162 Microsoft Word ...............................................174
Aligning Objects using the Crosshair .............162 Transferring PostScript (Macintosh) ..................... 175
Hiding the Crosshair .......................................162 Importing and Exporting ....................................... 176
Centering on a Page ........................................163 Exporting Using the Clipboard .......................176
Aligning Objects .............................................163 SMILES and SMIRKS Strings .......................177
Distributing Objects ........................................163 Creating SMILES Strings .......................... 177
Front to Back Ordering ...................................164 Pasting SMILES from Clipboard............... 178
Send to Back .............................................. 164 Creating SLN Strings ................................. 178
Bring to Front............................................. 164
ChemDraw Contents • v
Exporting and Importing Using File Formats ....... 178 Chapter 12: Accessing the
Bitmap (.bmp) Export Only ............................179 CambridgeSoft Web Site
ChemDraw Template (*.ctp, *.ctr) .................179
ChemDraw (*.cdx) .........................................179 Online Menu Overview......................................... 185
ChemDraw XML (*.xml) ...............................179 Finding Chemical Suppliers on ChemStore.com .. 185
ChemDraw 3.5 (*.chm) ..................................179 Finding Information on ChemFinder.com ............ 185
Contents
ChemDraw 2.0 and Finding ACX Structures and Numbers ................. 186
ChemDraw 2.1 (*.chm) Import Only .............179 ACX Structures ...............................................186
ChemDraw Stationery/Style Sheet (*.cds) .....179 ACX Numbers ................................................186
Connection Table (*.ct) ..................................180 Browsing ChemStore.com .................................... 186
DARC-F1 Format (*.f1d) ...............................180 Browsing CambridgeSoft.com ............................. 187
DARC-F1 Query (*.f1q) .................................180 Accessing the Online ChemDraw User’s Guide... 187
Encapsulated PostScript (Text) (Macintosh) Accessing CambridgeSoft Technical Support ...... 188
PostScript, *.eps (Windows) Export Only ......180 Registering Online ................................................ 189
Encapsulated PostScript (Mac) (Macintosh) Using the ChemOffice SDK.................................. 189
and PostScript with Preview (Windows) ........180
GIF Image (*.gif) Export Only .......................180 Appendix A:
ISIS/SKC and ISIS/TGF .................................181 The Chemistry of ChemDraw ....... 191
ISIS/Reactions (*.rxn) ....................................181
JDX (*.jdx, *.dx) Import Only .......................181
Appendix B: Technical
MDL MolFile (*.mol) .....................................181
Molecular Simulations MolFile (*.msm) .......182 Support ............................................................ 203
PICT (Macintosh) ...........................................182
PICT scaled 4X (Macintosh) ..........................182 Appendix C: Document
PNG file (*.png) Export Only ........................182 Settings ........................................................... 207
SMD (*.smd) ..................................................183
SPC (.*spc) Import Only ................................183 Appendix D: Automation .................. 213
Template Style Sheet (*.cts) ...........................183
Windows Metafile (Windows Only)
(*.wmf) ...........................................................183
Appendix E: How ChemNMR Pro
TIFF file (*.tif) Export Only ...........................183 Works ................................................................ 215
Resolution ................................................. 183
Color .......................................................... 183 Appendix F: How ChemProp
Compression .............................................. 184 Works ................................................................ 217
Setting TIFF options .................................. 184
Appendix G: Chemistry File
Formats ........................................................... 219
Index
vi • Contents CambridgeSoft
Introduction
About ChemDraw For Users of ChemDraw 5
ChemDraw is a tool to enable professional ChemDraw 6 included the following changes:
scientists, science students, and scientific authors to • Modifier key is Alt instead of Ctrl—key
communicate chemical structures. It is designed to combinations that previously used the Ctrl key
work according to conventions we found most now require the Alt key
intuitive for such users. Our goal has been to make
ChemDraw as easy to use as possible while • Shortcut menus—when you right-click an
providing superior drawing quality. object a menu is displayed offering quick access
to ChemDraw commands
What’s New in
For Users of ChemDraw 5 and 6
ChemDraw 7 Some features have been relocated in
ChemDraw 7 is enhanced by the following features: ChemDraw 7.0. The following table shows the new
location.
• User interface reorganization—includes tabbed
dialog boxes, docking toolbars and tear-off
Feature ChemDraw 6 ChemDraw 7
palettes
• Chemical Properties, Info, and Analysis Analyze Structure menu View menu,
windows—display data about chemical Structure or toolbar Show Analysis
properties and drawing parameters as you draw window
• Per-object drawing settings—allows you to edit
the settings of only selected objects Caption Text File menu Object menu,
• Table Tool—create tables by clicking and Settings Settings,
dragging Captions tab
• Atom Numbering—add sequential indicators to
atoms Chemical Structure menu View menu,
Properties or toolbar Show Chemical
• BioArt—templates for drawing biological
Properties
structures
window
• Brackets—enhanced functions enable you to
draw chemically significant brackets to
CLogP CLogP menu View menu,
represent polymers and other repeating units
(6.0.2 or later) Show Chemical
• On Windows, in-place editing of objects in any Properties
application window
• On Windows, reference numbers in Microsoft
Word
• On the Mac, compatibility with MacOS X
ChemDraw 7 Introduction • 1
What’s New in ChemDraw 7
Feature ChemDraw 6 ChemDraw 7 Feature ChemDraw 6 ChemDraw 7
Color Palette File menu Color menu or Add or delete Tools menu Edit menu
Document Template rows
Administrator
Settings dialog or columns

box
NMR Estimate or Structure menu
Document File menu File Menu, estimates Scripts menu
Setup Document
Settings, Layout Tools menu Tools menu View menu
and Footer tabs items
Drawing File menu File menu,

Settings Document About This User’s Guide
Settings,
This user’s guide contains information for the
Drawing tab
Windows and Macintosh platforms. Illustrations are
taken from Windows, except when the Macintosh
Label Text File Menu File menu, version differs.
Settings Document
Settings, Atom This guide assumes you are familiar with your
Labels tab computer’s operating system. For details about
using your operating system, refer to the user
documentation provided with that system.
m/e values Status bar View menu,
Show Analysis
window
Conventions
The following notations are used throughout this
Positioning Status bar View menu, user’s guide:
and size Show Info
The Ultra symbol indicates that a
information window, or in
drawing area ChemDraw feature is available in CS ChemDraw
Ultra only.
Fixed lengths Tools menu Object menu The Pro symbol indicates that a feature is
and angles available in CS ChemDraw Pro. Features available
in CS ChemDraw Pro are also included in CS
Format Text menu File menu, ChemDraw Ultra.
Document
Features that are available in CS ChemDraw Std are
Settings,
not indicated by a symbol.
Captions and
Atom Labels tab
NOTE: Notes such as this are used to highlight
information supplemental to the main text.
2 • Introduction CambridgeSoft
About This User’s Guide
Additional Information ToolTips
To access ToolTips:
Additional ChemDraw information is available in
• Point at an item in a Toolbar or Tool palette.
the following formats:
A description of the item appears.
• A Quick Reference Card.
• Online Help. The type of online Help available
depends on the platform you are using.
• CambridgeSoft Web Pages.
Context-sensitive Help (Windows)
Quick Reference Card
To access context-sensitive help:
The ChemDraw Quick Reference Card is located in
the back of the manual. The card provides 1. Press Shift+F1.
summaries of ChemDraw commands and features.
2. Click any menu item or tool.
Use the Quick Reference Card as you perform the
tutorials in “Chapter 2: Getting Started Tutorials” Information about the selected item appears.
because the card contains information about the
elements of the interface. CambridgeSoft Web Pages
The following table contains the addresses of
Online Help ChemDraw-related web pages.
ChemDraw provides the following types of online
information: For Access …
information
• Online Help—An online version of this guide. about …
• ToolTips—Displays a short description of user Technical http://www.cambridgesoft.com/
interface objects. Support support/
• Context-sensitive Help (Windows)—
Displays Help topics related to user interface ChemDraw http://doc.cambridgesoft.com/
objects. Plugin
Online Help ChemDraw for http://java.cambridgesoft.com/

Java
To access the online Help:
Windows: Software http://sdk.cambridgesoft.com/
Developer’s kit
• From the Help menu, choose Contents.
Macintosh: Active X http://sdk.cambridgesoft.com/
control
• From the Help menu, choose CS ChemDraw
Help. Purchasing http://store.cambridgesoft.com/
A web browser is required to view the Help. CambridgeSoft
You can use Internet Explorer version 4.0 or products and
later or Netscape Navigator version 4.0 or later. chemicals
ChemDraw 7 Introduction • 3
Additional Information
Installation and System
Requirements
Administrator
To install ChemDraw, see the “Read Me First”

document that came with your software. Late
breaking information about installation is contained
in the Read Me file (Macintosh) or Install.txt
(Windows) on the installation CD-ROM.
Windows Requirements
• Windows 95, 98, 2000, Me, XP, or NT
• Disk Space:
• Std: 30 MB
• Pro: 40 MB
• Ultra: 70 MB
Macintosh Requirements
• MacOS 8.6–9.1, MacOS X 10.1
• Disk Space:
• Std: 8 MB
• Pro: 32 MB
• Ultra: 55 MB
Installation and System Requirements
Chapter 1: ChemDraw Basics
Overview ChemDraw’s Graphical
The information required to begin using ChemDraw User Interface (GUI)
includes how to do the following:
ChemDraw’s graphical user interface (GUI) is the
• Start ChemDraw part of the application that you interact with.
• Identify the parts of the ChemDraw interface Although the Macintosh and Windows versions
differ, the essential ChemDraw GUI consists of a the
• Customize parts of the user environment
same elements.
• Create, open, and save documents
• Set printing preferences
Starting ChemDraw
You can start the ChemDraw application in the
following ways:
Macintosh:
• From the desktop, double-click the ChemDraw
application icon.
• Click the ChemDraw application and choose
Open from the File menu.
Microsoft Windows:
• On the desktop, double-click the ChemDraw
application icon
• From the Start menu, choose ChemDraw.
ChemDraw opens and a new document is
created.
ChemDraw 7 Chapter 1: ChemDraw Basics • 5

Starting ChemDraw
The Windows version of ChemDraw is shown below.
Magnification Minimize Maximize

Toolbar
Control Button Button
Administrator
Title Bar
Close
Menu Bar Button
Main Tools
Palette
Scroll
Bars
Document Window
Status Bar Resize
The Macintosh OS 9 version of ChemDraw is shown below.
Menu Bar Magnification Control Zoom Collapse/Expand
Title Bar
Close Box
Tools Palette
Scroll Bars
Document Window
Resize
6 • Chapter 1: ChemDraw Basics CambridgeSoft

ChemDraw’s Graphical User Interface (GUI)
The Tools Palette The following table describes the functions of the
Main tools.
ChemDraw provides the Main Tools palette to
enable you to create and manipulate drawings. The
Tool Description
Windows version of the Main Tools palette is shown
below.
Selection Lasso—select objects by dragging
around them.
Lasso Marquee Marquee—select objects by dragging
Solid Bond Eraser diagonally across them.
Multiple Bonds Text Objects that are selected can be further

Dashed Bond Pen
manipulated using menu commands.
Hashed Bond Arrows

Bond Draw single, double, and triple bonds
Hashed Wedged Bond Orbitals of various types.
Bold Bond Drawing Elements
Eraser Delete objects.
Bold Wedged Bond Brackets
Hollow Wedged Bond Chemical Symbols Multiple Draw double, triple, and quadruple
Wavy bond Arcs Bonds bonds of various types.
Table Query Tools
Text Create atom labels and captions.
Acyclic Chain Templates
Cyclopropane Ring Cyclobutane Ring Pen Draw freehand shapes such as custom
Cyclopentane Ring
arrows and orbitals.
Cyclohexane Ring
Cycloheptane Ring Cyclooctane Ring

Arrow Draw arrows. Arrows of different
Cyclohexane Chair (1) Cyclohexane Chair (2) types can be selected from the Arrow
Cyclopentadiene Ring
Tools palette.
Benzene Ring
Orbital Draw orbitals. Orbitals of different

types can be selected from the Orbital
Tools palette.
Drawing Draw annotations that lack chemical

Elements significance, such as boxes and lines.
Drawing Elements of different types
can be selected from the Drawing
Element Tools palette.

Docking and Undocking Palettes
Tool Description
The tools palettes can be docked or undocked.
Docked toolbars are attached to the left edge of the
Brackets Draw brackets, parentheses, and
ChemDraw window. Undocked palettes can float
Administrator
braces.
anywhere in the ChemDraw screen.
Chemical Draw chemically significant symbols To dock a tool palette:

Symbols such as charges, radicals, and lone • Double-click the palette background or drag the
pairs. palette to the left edge of the ChemDraw screen.
To undock a palette:
Arc Draw arcs. Arcs of different degrees
can be selected from the Arc tool’s • Drag the palette into the position you want.
palette.
Tearing Off Palettes
Acyclic Draw chains of any length. Some tools have palettes extending from them,
Chain indicated by an arrow on the tool button. You can
“tear off” the palette and place it anywhere in the
Query Draw stereochemical flags, indicate ChemDraw screen. You cannot dock torn off
Tools free sites, alternative groups and palettes.
correspondences between atoms in
query structures. To tear off a palette:
• Click its title bar.
Templates Draw structures with templates stored
You can drag the palette to reposition it.
in template documents. Templates can
be selected from the Templates tools You can also show or hide a palette by selecting it
palette. from the View menu.
Rings Quickly draw common structural Setting the Default Tool

components. You can set which tool is automatically selected
when you open documents in the Preferences dialog
Showing and Hiding Palettes box.
To show or hide a tools palette: To set the default tool:

• From the View menu, choose the palette to 1. From the File menu, choose Preferences.
show or hide.
The Preferences dialog box appears.
A check mark appears next to palettes that are
2. Click Open/Save.
shown.

3. In the Opening Files section, click the Default To dock a toolbar:
Tool to be automatically selected when you
• Double-click the toolbar background or drag
open a document.
the palette to the top edge of the ChemDraw
screen.
To undock a toolbar:
• Drag the palette into the position you want.
The Status Bar or Message

Area (Windows)
The status bar or message area displays information
about the menu you are using.
Customizing ChemDraw
You can customize ChemDraw by configuring
Preferences and Document Settings.
Preferences allow you to change the default
behavior of certain options that apply to every open
Toolbars document. Document Settings allow you to change
ChemDraw toolbars contain buttons and lists that the default behavior of options that will affect only
provide shortcuts for menu commands. You can the active document.
choose whether to display or hide the toolbars as
follows: Setting Preferences
• From the View menu, choose one of the Preferences affect the way the ChemDraw
following toolbars: application works, regardless of the document with
which you are working.
• General Toolbar
To open the Preferences dialog box:
• Style Toolbar
• Object Toolbar • From the File menu, choose Preferences.
A check mark appears next to the item when the

toolbar is displayed.
Docking and Undocking Toolbars

The toolbars can be docked or undocked. Docked
toolbars are attached to the top edge of the
ChemDraw window. Undocked toolbars can float
anywhere in the ChemDraw screen.

The Preferences dialog box appears: You can apply document settings in the following
ways:
• Customize settings for the entire document
using the Document Settings dialog box
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• Apply settings to the entire current document

from an existing document
• Apply settings to selected objects in the current
document from an existing document
Default Style Sheet or Stationery Pad

When you open ChemDraw, the last Style Sheet or
Stationery Pad used opens as the default. If you
choose another Style Sheet or Stationery Pad, that
Windows Preferences
file becomes the default.
To view the default Style Sheet or Stationery Pad:
To restore the CambridgeSoft default settings: • Click the File menu.
• Click Use Defaults. The “New” menu item displays the name of the
Style Sheet or Stationery Pad.
Document and Object Settings
Saving Customized Settings as Style
Document and object settings are user-definable
settings that are applied to the current document.
Sheets or Stationery Pads
Settings include: Every new document created with ChemDraw uses
a Style Sheet (Windows) or Stationery Pad
• Drawing settings—set drawing options such as (Macintosh) to obtain its document settings. Style
the fixed length used to draw bonds Sheets and Stationery Pads can also contain
• Caption and label text settings—set text options predefined objects. When you create a new
such as the font used for atom labels and document, you actually create an untitled copy of
captions the Style Sheet or Stationery Pad. Any changes you
• Color settings—set available colors for objects make to the copy of the Style Sheet does not affect
and the document background the Style Sheet or Stationery Pad itself.
• Print/Page Setup—set options such as the page You can create a Style Sheet or Stationery Pad with
size used and footers your own customized setting by saving it as a .cds
file. If you store the .cds file in the ChemDraw Items
folder, it appears in the Open Special menu so you
can access it from the File menu.

To save a document’s setting as a Style Sheet or To apply the document settings from a document or
Stationery Pad: not listed in the menu:
1. In the document whose settings you want to 1. From the Apply Document Settings from
save, from the File menu, choose Save As. submenu, choose Other.
The Save As dialog box appears. The following dialog box appears.
2. Open the appropriate folder and select a

ChemDraw document, Style Sheet, or
Stationery Pad.
2. Name the file and choose .cds as the type. 3. Click Open.
3. To save the file in the ChemDraw items folder,
Applying Object Settings from Other
click Go To ChemDraw Items.
Documents
4. Click Save.
You can apply settings from another document to
selected objects in the current document. You can
Applying Document Settings From
apply the chosen settings to the selected objects
Other Documents
only, or to all new objects drawn in the current
To apply document settings to the active window document.
that are contained in a different document:
To apply object settings:
• On the File menu point to Apply Document
Settings from, and then choose the document 1. Select the object.
from which to apply the settings. 2. On the Object menu, point to Apply Object
The settings in the active document window Settings from, and then choose the document
change to those found in the Style from which to apply the settings.
Sheet/Stationery Pad that you choose. The following dialog box appears:

3. Take the appropriate action:
If you want to apply the Then click …

settings to the …
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selected object only No
selected object and any new Yes

objects you draw
The settings are applied.
Using Documents
Documents are the ChemDraw work space where
you create and manipulate structures. You can create
a new document or open an existing document and If Use Documents Location is not selected, the first
edit it. time you use the Open dialog box your Documents
folder is shown. Subsequent uses show the last
Setting the Default Document directory used.
Location Creating a Document

You can set what file location is shown in the Open You can create a new, blank document using the
dialog box by using the Preferences dialog box. ChemDraw default settings, or use a Style Sheet
(Windows) or Stationery Pad (Macintosh) with
To set the default location:
customized settings.
1. From the File menu, choose Preferences.
Creating a New Document
To create a document:
2. Click Open/Save.
• From the File menu, click New Document.
3. Click Use Documents Location and type or
browse to the location to use.
Creating a Document Using a Style
Sheet or Stationery Pad
To create a new document using a different Style
Sheet:
1. From the File menu, click Open Special.

2. Choose a Style Sheet or Stationery Pad from
the list.
A new document is created with the settings
(and objects) stored in the Style Sheet or
Stationery Pad.

Using Documents
ChemDraw provides pre-defined Style Sheets and .
Stationery Pads located in the ChemDraw Items

folder. For example, the ACS Document 1996 is
configured to create documents that are set with the
bond lengths, bond width, spacing, and fonts used in
the 2-column format of all American Chemical
Society journals. For a list of the settings stored in
these documents, see “Appendix C: Document
Settings.”
Opening a Document
To open a document:
• From the File menu, do one of the following:
• Choose Open, and in the Open dialog box,
select the name and location of the file and
then click Open or OK. If Use Default File Format is not selected, the first
• Choose the document from the list of time you use the Open dialog box the ChemDraw
previously opened documents at the bottom format is shown. Subsequent uses show the last
of the menu. format used.
Setting the Default Open File Format Saving Changes Automatically

You can set what file format is selected by default in You can configure ChemDraw to save changes to a
the Open dialog box. document automatically at the time interval you set.
To set the default file format: To set the frequency at which ChemDraw
automatically saves your changes:
2. Click Open/Save.
2. Click Open/Save.
3. In the Opening Files section, click Use Default
File Format and choose the format you want
from the list

Using Documents
3. Click Autosave Every and type or select the For example, if you draw cyclohexane, create an
minutes to use. atom label text box, type a label, and select and
rotate the structure, you will be able to remove the
actions as follows:
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1. Remove the rotation.

2. Remove atom label.
3. Remove the ring.
At each step, the text of the Undo command
indicates the action being removed.
Redoing Actions
When you undo an action, the Redo command
becomes active so you can reverse the effect of the
Undo command.
To redo the last action undone:
• From the Edit menu, choose Redo.
The time starts counting down after the first change The last action undone is reinstated. The Undo
is made. command changes to reflect that action. The
Redo command changes to reflect the next
Reversing and Repeating action that can be redone.
Actions
ChemDraw keeps track of the actions you perform.
Repeating Actions
You can reverse actions one at a time by choosing If an action is repeatable, the name of the action
the Undo command. The number of actions that can appears next to the Repeat command on the Edit
be undone or redone is limited only by the amount Menu.
of memory (RAM and virtual memory) available for To repeat an action:
use by ChemDraw. When you save your document
the Undo queue is reset and starts over. • From the Edit menu, choose Repeat.
The last action performed is repeated.
Undoing Actions
To undo the last action performed:
• From the Edit menu, choose Undo.
The last action performed is reversed. The Redo
command changes to reflect the undone action.
The Undo command changes to reflect the next
action you can undo.

Using Documents
Discarding Recent Changes to 4. Click Save or OK to create the file.
a Document The title of the document window changes to

name of the saved file. The file name is added
To retrieve the last saved version of a file: to the bottom of the File menu.
• From the File menu, choose Revert.
CAUTION
All changes made to the file since it was saved
last are discarded and the previous version of ChemDraw uses the .cdx file format to store chemical
information accurately with a structure drawing. Other
the file appears.
file formats may be capable of storing a picture of your
drawing, but they might lose chemically relevant
NOTE: You can use the Undo command in the Edit information about the structure. For example, if you
menu to remove each individual action since the last save a ChemDraw drawing in the .eps file format, you
save. will store only a picture of the structure without storing
the chemical significance of the connections between
atoms and bonds.
Saving Documents
To save a ChemDraw document in the default To save a document that has previously been saved:
ChemDraw cdx file format: • From the File menu, choose Save.
1. From the File menu, choose Save As. The contents of the file are updated to reflect the
information currently in the window without
The Save As dialog box appears. The
displaying the Save As dialog box.
appearance of the dialog box depends on the
platform you are using. Setting the Default Save File Format
2. Choose a folder in which to store the file. You can set what file format is selected by default in
3. Type a file name in the File name (Windows) or the Save As dialog box.
Save As (Macintosh) text box.
To set the default file format:
MacOS 9 allows you to type up to 255
characters for a file name, including spaces. For 1. From the File menu, choose Preferences.
example: “my first structure in ChemDraw”. The Preferences dialog box appears.
The Windows operating system allows you to 2. Click Open/Save.
type up to 255 characters for a file name,
including the entire path of directories in which
the file is stored.

Using Documents
3. In the Saving Files section, click Use Default 3. Type a new file name.
File Format and choose the format you want 4. Click Save or OK.
from the list.
Saving a Document in a Different File
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Format
To save a ChemDraw document in another file
format:
1. From the File menu, choose Save As.

The Save As dialog box appears.
2. Select a folder in which to save the document.
3. Type a file name in the in the File name
(Windows) or Save As (Macintosh) box.
4. Select a file format from the File Format or
Save as Type list.
NOTE: When you select some formats, the Options

button becomes active. Click it to open a dialog box
If Use Default File Format is not selected, the first for setting options specific to these formats. For
time you use the Save dialog box, the ChemDraw more information about these options, see “Chapter
format is shown. Subsequent uses show the last 11: Sharing Information.”
format used.
5. Click Save or OK.
Saving a Document with a Different If you type a name that already exists in the same
Name or Location directory, the existing document is replaced. If you
You can save a copy of your document under a do not want to replace the original ChemDraw
different name, location, or file format. Saving a document, use a different name. For information
copy under a different name or location is useful for about other file formats, see “Chapter 11: Sharing
keeping earlier revisions of your document. Saving Information.”
a file as a different format is useful for creating Style
Sheets or Stationery Pads and for exporting
Closing a Document
information to other applications. To close a ChemDraw document:
To save a copy of a ChemDraw document under a • From the File menu, choose Close.
different name or in a different location: If the document contains unsaved information, you
are prompted to save the file.
2. Choose a new location in which to save the
document.

Using Documents
Accessing Documents
Quickly
You can quickly access ChemDraw documents by
placing them in the ChemDraw Items folder and
then selecting them from the Open Special menu.
You can quickly access open documents by using
the Window menu.
The ChemDraw Items Folder

The ChemDraw Items Folder is usually located in
the same folder as your ChemDraw application. It
contains Stationery Pad files, Template documents,
the ChemDraw Preferences file, scripts, ChemDraw
HotKeys file, the ChemDraw Nicknames file, the
isotopes file (which contains the isotopes and 4. Click OK.
elements ChemDraw uses), and the generic
nicknames file. In ChemDraw Pro, it also contains The Open Special Submenu
Template documents and Template Stationery Pads.
To select documents from the ChemDraw Items
If you want the ChemDraw Items folder to reside in
a different directory, you can specify the path. folder:
To change the path to the ChemDraw Items folder: • On the File menu, point to Open Special, and
select the file to open.
The Open Special submenu, listing documents
The Preferences dialog box appears. that you commonly use, appears.
2. Click Open/Save.
3. In the ChemDraw Items Location box, type the The Window Menu
path or click Browse, select the location, and
The Window menu lists all open ChemDraw and
then click OK.
Template documents. The document you choose
from the Windows menu becomes the active
window.

Accessing Documents Quickly
Printing QuickDraw is the graphical format that is supported
by the Macintosh Operating System. Every printer
ChemDraw uses the standard system commands to that supports the MacOS can convert QuickDraw
print ChemDraw documents. The options that you representations into printed output. However,
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have available to you depend on the printer that you QuickDraw does not support some features (for
are using. Refer to your printer’s documentation for example, high-resolution printing) that are available
more information. only on some printers.
In general, to print a ChemDraw document: If you are transferring information to another

application from which you print ChemDraw
1. From the File menu, choose Page Setup. pictures, you should consider including PostScript
2. Make all appropriate selections for the printer commands and the ChemDraw LaserPrep File with
you are using and click OK. the pictures. For information about special situations
3. From the File menu, choose Print. to consider, see “Transferring PostScript
(Macintosh)” on page 175.
4. Make your selections in the Print dialog box
and click OK.
Optimize Pictures for High-Resolution
To print a document from the Explorer or from the Non-PostScript Printing (Macintosh)
Finder: The Macintosh High Resolution Clipboard supports
1. Select the document you want to print. high-resolution printers. Most applications support
the High Resolution Clipboard. Because this was
2. From the File menu, choose Print.
not always the case in the past, this preference
The ChemDraw application is opened and the continues to be available for users to turn off if an
Print dialog box appears. application being used does not support the High
3. Make your selections in the Print dialog box Resolution Clipboard.
and click OK.
If you are unsure if the application uses a High
Printing Background Color Resolution Clipboard, try transferring pictures with
this check box selected and deselected, and see
Print Background Color controls whether the which picture prints with higher quality.
Background Color contained in your ChemDraw
document is printed. If you are printing to a non-PostScript printer,
deselect Include ChemDraw LaserPrep and
To change whether the Background color is printed:
Include PostScript to reduce the size of each
1. From the File menu, choose Preferences. picture. Do not deselect this option if the document
will ever be printed to a PostScript printer.
2. Click Print Background Color.
3. Click OK. Printers that use the PostScript page definition
language use the PostScript representation. The
Macintosh Print Preferences PostScript representation describes objects by using
mathematical shapes that can be precisely imaged at
When you print a document, ChemDraw creates
whatever resolution is used by your printer. The
both a QuickDraw representation and a PostScript PostScript representation created by ChemDraw is
representation of the document’s contents.

Printing
composed of two parts, the PostScript commands 3. Click OK.
and the ChemDraw Laser Prep. The ChemDraw
Laser Prep contains specific instructions that enable NOTE: When you select Include ChemDraw Laser
the printer to interpret the PostScript commands Prep, you should also select Include PostScript.
contained in a ChemDraw document.
For more information, see “Transferring PostScript
Include PostScript (Macintosh) (Macintosh)” on page 175.
To transfer ChemDraw pictures to another

document that will be printed on a PostScript
Scripts (Macintosh)
printer: The Scripts menu contains scripts that you can use
to perform tasks within ChemDraw or between
ChemDraw and another scriptable application.
2. Click Include PostScript.
Scripts, found in the Scripts menu, are created using
3. Click OK. Apple’s Script Editor application. With the proper
When Include PostScript is deselected, no script extensions in conjunction with Apple’s Script
PostScript commands are generated. This usually Editor application, you can create scripts using the
results in lower quality printing, particularly of AppleScript™ scripting language and add scripts to
drawings cut and pasted into other applications. the Scripts menu by placing them in the ChemDraw
However, because the representation used for
Folder.
printing when Include PostScript is not selected is
the same as that used for drawing to the screen,
better correspondence between the screen and NOTE: Scripts not stored within the ChemDraw
printed output may be observed. Folder are not accessible from the Scripts menu.
For more information, see “Transferring PostScript

For more information about AppleScript™ and the
(Macintosh)” on page 175.
Script Editor application see your system manuals.
Include ChemDraw Laser Prep
(Macintosh) Closing ChemDraw
Selecting the include ChemDraw Laser Prep allows To close the ChemDraw application:
you to print to a printer that cannot be initialized
• From the File menu, choose Exit ChemDraw
using ChemDraw. If you create drawings with this
(Windows) or Quit ChemDraw (Macintosh).
option off, they will not print on PostScript printers
without the use of ChemDraw. If you have unsaved document windows open,
you are prompted to save them before you can
To Include ChemDraw Laser Prep: close the application.
2. Click Include ChemDraw Laser Prep.

Scripts (Macintosh)
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Closing ChemDraw
Chapter 2: Tutorials
Overview 3. Type tut1.cdx in the appropriate text box.
4. Select a folder in which to save the file.
The tutorials are designed to teach you the
5. Click Save.
fundamental drawing techniques available in
ChemDraw. Before you begin, you may want to 6. From the View menu, choose Show General
review “Conventions” on page 2 to familiarize Toolbar.
yourself with the terminology used in the tutorials. 7. From the View menu, choose Show Info
You may also want to use your Quick Reference Window.
Card while you perform the tutorials.
The Info window appears and displays drawing
ChemDraw automatically checks for correct parameters as you draw.
chemical syntax as you draw. If ChemDraw finds a
potential problem, a red box is displayed around the
erroneous object. The red box is displayed on screen
only and does not print.
To disable the automatic error checking on a specific
object:
• Right-click the object and deselect Display
Warnings.
Tutorial 1: Reaction
Schemes 8. Click the Object menu and make sure there is a
In this tutorial, you will draw the following check mark next to the Fixed Lengths and
(simplified) reaction scheme: Fixed Angles commands. If either command is
not checked, choose it.
O O
OH
NOTE: Applying fixed lengths and fixed angles
enables you to create structures with consistent
OH bond lengths and angles. The fixed length dimension
2-propanone 4-hydroxy-4-methyl-2-pentanone
2 moles 1 mole is set in the Drawing Settings dialog box. The fixed
angle dimension increments angles by 15 degrees.
Create a ChemDraw Document:
1. Start ChemDraw.
ChemDraw 7 Chapter 2: Tutorials • 21

Tutorial 1: Reaction Schemes
Create a bond: Change a single bond into a double bond:
1. Click the Solid Bond tool . 1. Point to the atom shown below and hold the
2. Position the pointer (+) anywhere in the mouse button down.
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document window and click.

The bond is extended to its fixed length at a
30-degree angle.
2. Drag as shown below over the existing single

bond. Release the mouse button.
Add a second bond:
1. Point to the right atom of the bond.
2. Click the atom to add a bond. Add labels to the structure:

A second bond is drawn, forming a 120-degree 1. Point to the atom shown below.
angle between the bonds.
NOTE: The angle used when clicking to add

bonds is controlled by the Chain Angle setting 2. Double-click the atom.
in the Drawing Settings dialog box in the File
menu. If this bond angle cannot be established,
the next smaller and logical bond angle is used.
Add a third bond:
1. Continue pointing to the atom shown below.

.
3. Type an uppercase O in the text box that
appears.
.
2. Click the atom to add a bond.
22 • Chapter 2: Tutorials CambridgeSoft

4. Close the text box by doing one of the
following: NOTE: When you create a copy as shown above
you can drag it anywhere in the document window.
• Click in an empty area of the window. If you want the copy to remain aligned with the
• Click another tool. original, hold Shift while dragging.
Next, you duplicate a structure and then create
another structure from the duplicate. Modify the duplicated structure:
Duplicate the structure: 1. Click the Solid Bond tool .

2. Point, in the copied structure, to the atom shown
1. Click the Lasso tool .
below and click.
The last structure drawn is automatically
selected. O
2. Point over the Selection Rectangle.
Add several bonds to a single atom:
1. Point to the atom shown below.

3. Press and hold Ctrl (Windows) or Option
(Macintosh). O
The hand pointer with a plus sign indicates that

you are in the duplication mode of a selection
tool.
2. Click the atom three times, allowing a pause
between each click.
NOTE: If you click too fast, the click is

interpreted either as a double-click, which
4. Drag the Selection Rectangle to the right. opens a text box or a triple-click, which
duplicates your last atom label.
A copy of the structure appears as you begin

drag. The original structure remains in its
position. Release the mouse button when the
copy is clear of the original.

Create an atom label using HotKeys. HotKeys are In the following steps, you use a different method
keys on your keyboard that are linked to specific for selecting structures and then separate the
atom labels. For more information about HotKeys, structures to make room for an arrow.
see “Labeling Atoms with HotKeys” on page 73.
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1. Click the Marquee tool .

NOTE: Alternatively, you can select the Lasso
O tool and hold Alt to use the Marquee tool.
The last object drawn is selected.

Drag the selection to make room for an arrow:
2. Type O or o.
• Press Shift to maintain the alignment of the
structure and drag the Selection Rectangle to
O the right.
OH
When you use HotKeys that represent a single
element, the correct number of hydrogen atoms is
Add arrows to the reaction scheme.
added to the label.
1. Click the Arrow tool to display the Arrow
Align the structures:
palette.
1. Select the structures.
NOTE: The triangle in the lower right corner
2. On the Object menu, point to Align, and then
of the Arrow icon indicates it contains a palette.
choose T/B centers.
You structures should appear as shown below. 2. Click and hold the palette title bar and drag the
palette to the location you want.
O O
OH

3. Click the arrow shown below.
NOTE: If you need to change the length (or the
angle relative to the X-axis) of the arrow:
1. Hold Shift and point to the arrowhead
(a highlight box appears when you are
pointing correctly).
2. Drag the arrowhead to the length (and angle)
you want.
Use the Text tool to add line formula or other

captions for representing reagents and reactions.
Insert text in the drawing:
1. Click the Text tool .

4. After the arrow is selected, release the mouse 2. Point above the arrow. A text insertion point
button. appears as shown below.
NOTE: The arrow you choose from the palette O O

becomes the default arrow type. To change the
arrow type, display the arrow palette and select
the arrow type you want. OH
Draw the arrow you selected: 3. Click to create a text box.
1. Point after the first structure and hold down the

O O
mouse button.
O O
OH
4. Type OH.
OH
O O
2. Drag the Arrow to the length you want. Release
the mouse button.
OH
O O
NOTE: If you want to realign the caption,
select a selection tool and drag the caption.
OH

Add a charge symbol using the specialized symbols To group objects:
available in the Chemical Symbols tool palette:
1. Click a Selection tool, the Lasso or
1. Click the Chemical Symbol tool . Marquee .
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2. Click the circled negative charge symbol 2. Hold Shift and click the arrow, the OH caption,
shown below. and the charge symbol.
3. Point to the center of the OH label.

The Shift key allows you to add objects to a
selection without deselecting other objects.
O O
OH NOTE: If you click a selected object while
holding Shift, that object is deselected.
OH
3. From the Object menu, choose Group.
4. Click to add the charge symbol.
O O
NOTE: You can select individual objects
OH within a group by clicking them.
OH Use the Text tool to create a caption containing the

name and amount of reactant, and then center the
NOTE: If you hold the mouse button down caption under the structure.
after depositing the symbol, you can rotate the
symbol around the label in a fixed position by 1. Click the Text tool .
dragging it.
2. Point below the first structure.
Objects added from the Chemical Symbols palette O

are automatically associated with the structure they
are closest to.
Some objects, such as arrows, are not associated
automatically. You can manually group objects
using the Group command. You can then select the
grouped objects to manipulate or move them
together.

3. Click to create a text box. The default cursor is 3. Type 2 moles.
flush left.
O
O
2-propanone
2 moles
4. From the Text menu, choose Centered. Create an aligned caption for the other structure.
O 1. Press Tab to create another Text box that is
aligned adjacent to the first.
The cursor moves to the center of the text box.

2-propanone
Type the caption: 2 moles
1. Type 2-propanone.
NOTE: You can use the Tab key in the caption
O mode of the text tool to create multiple aligned
captions with the same font, font size, style, and
justification as the previous caption.
2. Type 4-hydroxy-4-methyl-2-pentanone, press

2-propanone Enter or Return, and then type 1 mole.
2. Press Enter or Return to insert a new line. If your captions are not aligned properly beneath the
structures you can move them using a selection tool.
O
1. Click a Selection tool (Lasso or Marquee).
The text box is automatically selected because
it is the last object drawn.
NOTE: The object that is automatically selected is

2-propanone
set in the Preferences dialog box.

2. Press the Left or Right Arrow key to center the
caption beneath its structure. This method
Tutorial 2: Drawing an
maintains the alignment created by the Tab key. Intermediate
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To complete the drawing, add a shadowed box In this tutorial you will draw the following
around the scheme: intermediate structure starting from a ring and then
add arrows with customized shapes using the Pen
1. Click the Drawing Elements tool .
tool.
2. Select the shadowed box from the palette of O-

drawing elements. OH
Create a new ChemDraw document:
3. Point to the upper left corner of the reaction 1. From the File menu, choose New Document.
scheme. Hold the down the mouse button and 2. From the File menu, choose Save As.
drag diagonally downward to the right to draw
3. Type tut2.cdx in the appropriate text box.
the box.
5. Click Save.
Draw a ring:
O O
OH
1. Click the Cyclohexane Ring tool .
OH 2. Point in the document window. The
2-propanone 4-hydroxy-4-methyl-2-pentatone Cyclohexane cursor appears.
2 moles 1 mole
3. Click to add a ring.
Save and close the document:
1. From the File menu, choose Save.

Your document is saved.
2. From the File menu, choose Close.

Tutorial 2: Drawing an Intermediate
Delete an atom and its bonds from the ring: Add second and third bonds:
1. Click the Eraser tool . 1. Point to the atom shown below and click to add
2. Point to the atom shown below. another bond.
2. Add a third bond by dragging to make sure it

has the desired orientation:
NOTE: You can delete a bond individually by
a. Continue pointing to C4.
pointing at the center of the bond and clicking.
3. Click the atom.
b. Hold the mouse button and drag diagonally

upward toward the right.
Add a bond:
1. Click the Solid Bond tool .

c. When the bond is oriented, release the mouse

button to deposit the bond.
Create a double bond:

3. Click to add a bond.

2. Drag diagonally downward over the existing 2. Double-click the atom to open a text box.
bond to create a double bond.
Administrator
3. Type O and then type “-”.

Change the orientation of the double bond:
1. Point to the center of the double bond. O-
Label an atom with “OH”:

2. Click the bond twice to move the second line to 1. Point to the atom shown below.
the outside.
The bond moves to the inside on the first click O-
and to the outside on the second click.
2. Double-click the atom to open a text box.
O-
NOTE: You can move a double bond by

clicking it when a bond tool is selected. The
cursor corresponding to the bond tool that is
selected appears.
3. Type OH.
Next you will add an arrow that is not included in the
Add an atom label:
arrow palette to indicate electron flow.
1. Point to the atom to label shown below.
To create a customized arrow using the Pen tool.
1. Click the Pen tool .

2. From the Curves menu, choose Arrow at End.

3. Point near the double bond where you want to 6. Drag upward to create a curve segment.
indicate the start of electron flow.
O-
-
O OH
OH
4. Drag downward and to the left. Release the

mouse button.
Refine the shape of the arrow:
-
O
1. Point to the handle pointing away from and to
OH the right of the curve. This is a tangent handle
that controls the tangent of the curve that it
touches.
The hand with a “+” cursor indicates that you

2. Drag the handle upward to the right to make the
are in the editing mode of the Pen tool.
arrowhead point more inward.
5. Position the cursor where you want the
arrowhead to appear.
O-
OH
3. Press Esc when you are finished.

4. Create additional arrows as described above to Create a ring:
complete the intermediate as shown below.
O- 2. Point in an empty area of a document window.
Administrator
OH
NOTE: If you want to magnify the entire document

so you can see arrows or other objects that are in
small places, choose Magnify from the View menu.
Fuse a second ring to the first:

1. Point to the center of lower right bond in the
ring.
Tutorial 3: Using Rings

In this tutorial you will draw more complex
structures by using rings.
2. Click to fuse another ring.
O
CH
Open a new ChemDraw document:
1. From the File menu, choose New Document.

5. Click Save.

Fuse a third ring: 2. Click to fuse another ring.
1. Point to the bond shown below.
2. Click to fuse another ring. Your document

should contain the structure shown below. Remove atoms and their bonds from the ring using
the Eraser tool:
1. Click the Eraser tool .

Fuse a fourth ring:
1. Point to the bond shown below.
A highlight box appears on the atom to be

removed.
3. Click to delete the atom and its bonds.

4. Click each of the atoms shown below to delete 3. Drag upward to draw a double bond.
the bonds.
Administrator
Add another double bond:
The resulting structure is shown below.
2. Right-click, point to Double, and then choose

Plain.
Realign the double bond so it is centered:
Add double bonds to the structure: 1. Point to the center of the upper double bond.

2. Point to the atom indicated below.
2. Right-click, point to Bond position, and then

choose Centered.

Add a carbon atom label: 2. Press the o key on your keyboard. “o” is a
Hotkey assigned to the atom label “O”.
O
CH
2. Press the c key on your keyboard. “c” is a

HotKey assigned to the atom label “C”. Save and close the document.
The CH atom label appears with the correct 1. From the File menu, choose Save.
number of hydrogen atoms.
CH
Tutorial 4: Fischer
Projections
This tutorial demonstrates creating a Fischer
projection of glucose (shown below) by drawing a
linear series of bonds. You can also create the same
Add an oxygen atom label to complete the structure: drawing using a template.
CHO
H OH
HO H
CH
H OH
H OH
CH2OH

Tutorial 4: Fischer Projections
Create document from a template by opening the Add a second bond:
appropriate document template:
1. Point to the lower atom.
1. From File menu, point to Open Special, and
Administrator
then choose ACS Document 1996.

The new document created is based on a Style
Sheet (Windows), or Stationery Pad
2. Drag downward to draw the second bond.
(Macintosh).
NOTE: These special documents allow you to have

pre-configured settings for different tasks. In this
example, the ACS template provides the required
settings for structures to be published in all ACS
journals:
• One-column layout (Page Setting)
• Bonds with a Fixed length of 0.2 inches
3. Repeat step 1 and step 2 three times to draw a
(Drawing Setting)
• Atom Labels in Times font (Text Setting) total of five bonds.

5. Click Save.
Draw the first bond:

2. Point in the document window. Drag downward
vertically to draw the first bond.
NOTE: When you drag the pointer along the length

of the bonds, the pointer alternates between an
arrow and a cross. The arrow indicates you are
pointing over the center of a bond, and the cross
indicates you are pointing to an atom.

Add horizontal bonds to the second atom in the Add bonds to the next three carbon atoms:
string of bonds you created:
1. Point to C3 and click the atom to add a
• Point to C2 and click the atom to add a perpendicular bond.
perpendicular bond.
2. Continue pointing to C3 and click the atom to

Add a horizontal bond in the opposite direction: add a perpendicular bond in the opposite
direction.
• Continue pointing to C2 and click the atom to
add a perpendicular bond in the opposite
direction.
3. Repeat step 1 and step 2 for the fourth (C4)

and fifth (C5) atoms.

Add labels to C1 and C6:
CHO
1. Point to C1.
Administrator
5. Click outside the text box to deselect it.
2. Double-click C1 to create a text box, then type Add the H and OH labels:
CHO.
CHO
CH2OH
3. Point to C6.
2. Type h to label the atom with hydrogen.
CHO
4. Click C6 to create a text box, then type CH2OH. CH2OH

3. Double-click the remaining hydrogen atoms The Analysis window appears. You can drag the
shown below. The atoms are labeled with the window to any position.
same symbol.
CHO
CH2OH 3. Click Paste to paste the information as a

caption below the structure.
4. Label the remaining atoms by typing o to label
them with OH. The result should appear as CHO
shown below.
H OH
CHO
HO H
H OH H OH
HO H H OH
CH2OH
H OH
C6H12O6
Exact Mass: 180.06
H OH Mol. Wt.: 180.16
m/e: 180.06 (100.0%), 181.07 (7.1%), 182.07 (1.4%)
CH2OH C, 40.00; H, 6.71; O, 53.29

View the basic properties of the structure you drew
and paste the information into your document:
1. Click a selection tool to automatically select the
last structure drawn. If the structure is not
selected, double-click the structure.
2. From the View menu, choose Analysis
Window.

Tutorial 5: Perspective Rotate the ring:
1. From the Edit menu, choose Select All.

Drawings
Administrator
In this tutorial you will learn how to create a

perspective drawing by drawing the following
α-D-glucose as a Haworth projection.
CH2OH
O 2. Point to the upper right corner of the Selection
OH
Rectangle (the Rotation handle).
OH OH
OH
Create a new document using the ChemDraw

default style:
1. From File menu, point to Open Special, and

then choose New Document.
NOTE: The cursor changes to a curved
double-sided arrow to indicate the rotation mode of
4. Select a folder in which to save the file. a selection tool is activated.
5. Click Save.
3. Drag the Rotation handle to the right about 30
Draw a ring: degrees. The amount of rotation is displayed on
the screen and in the Info window.
2. Point in an empty area of a document window.
Even though Fixed Angles is on, the angle is not

constrained. The Fixed Angles feature constrains
angles only when they are being drawn. For
example, if you created this ring by dragging instead
of clicking, the angle would be constrained when
Fixed Angles is on.

Tutorial 5: Perspective Drawings
Change cyclohexane to tetrahydropyran: 5. Drag downward to create another bond.
1. Click outside the structure to deselect it. O

2. Point to the atom indicated below.
6. Repeat for the atoms indicated by the arrows

3. Type o. below.
Add vertical bonds:
1. Click the Solid Bond tool . The result appears as shown below.
2. Point to the atom shown below. O
3. Drag upward to create a bond.

Draw one bond upward at C5:

O
O
4. Point to C1 again.

2. Hold the mouse button and drag upward. Distort the structure to change its aspect ratio to give
the perspective of viewing the structure along the
Z-axis.
Administrator
1. Click the Lasso tool .
O 2. Point to the Resize handle (lower right corner)

and press Shift.
Resize handle
For the downward bond for C5, you must turn Fixed
Lengths off or the bond will be joined to the upward
bond of C3.
You can temporarily disable Fixed Lengths using a NOTE: The cursor changes to a cross with
modifier key: arrows at each end indicating the distortion
function of a selection tool.
3. Drag upwards until you have distorted the

structure to about 50%, as shown on the screen
O or in the Info window.
2. Hold down the mouse button, press Alt or

Option and drag downward from C5. Stop
dragging about half the distance to the upward
bond on C3.

Next, you create OH labels. Because this label is Add the CH2OH label:
repeatedly used, you will learn how to repeat a label.
1. Triple-click the upper atom of C5.
Only labels created by opening a text box are
repeatable. 2. Press Enter to open the atom label text box and
type CH2 before the OH.
1. Select the Solid Bond tool, point to the atom
shown below and double-click to open a text CH2OH
box. O
OH
OH OH
O OH
NOTE: The Enter HotKey opens a text box for

the last atom labeled. The definition for this
2. Type OH, move the pointer to the next atom as
particular HotKey cannot be changed.
shown, and triple-click to repeat the atom label.
Change the type of the front bonds:

O
1. Click the Bold Bond tool .
OH 2. Point to the center of the bond shown below.
The cursor changes to a bold arrow as you point
3. Triple-click the remaining atoms (as shown at the bond.
below) to repeat the OH label.
CH2OH
O
O OH
OH
OH OH
OH OH
OH
OH
3. Click to change to the new bond type.
NOTE: If you find it difficult to place the labels
CH2OH
because of the size of the drawing, choose
O
Magnify from the View menu. OH
OH OH
OH

4. Click the Solid Wedge bond tool .
Tutorial 6: Newman
5. Point to each of the bonds shown below.
Projections
CH2OH
Administrator
O This tutorial demonstrates how to draw a Newman

OH
projection. You can also create the same drawing
OH OH using a template.
OH
6. For each bond, point slightly off center in the

direction that you want the wide end of the
wedge to be oriented and click.
NOTE: If you move the pointer too far, the

highlight box disappears. Choose Magnify from Create a ChemDraw document:
the View menu if you find it difficult to place the
pointer. 1. From the File menu, choose New Document.
The resulting structure is shown below.
CH2OH 4. Select a folder in which to save the file.
O
OH 5. Click Save.
OH OH Create the first bond:

OH
NOTE: If the wedge is pointed in the wrong 2. Point in the document window and drag
direction, click the bond again to flip its downward to create the first bond.
orientation.

2. From the File menu, choose Close. 3. Continue pointing at the lower atom and click
again to add a second bond.

Tutorial 6: Newman Projections
4. Continue pointing at the same atom and click 2. Point to the central atom of the lower fragment.
again to add a third bond.
5. Click the Lasso tool . NOTE: When connecting existing atoms, the
Fixed Length and Fixed Angles commands are
The last structure you drew is automatically ignored.
selected.
6. Point within the Selection rectangle and hold 3. Click and drag to the central atom of the upper
Ctrl (Windows) or Option (Macintosh). fragment.
4. Release the mouse button when the highlight
box over the central atom appears.
7. Hold the mouse button and drag a copy of the

structure diagonally upward to the right of the
original.
In this step, you will use the Orbital tool to draw the
hollow circle that is particular to Newman
Projections rather than an orbital.
1. Click the Orbital tool .

2. Click the unfilled s orbital.
8. Release the mouse button and depressed key

when the copy is positioned.
Add a bond between the duplicated structures:
1. Click the Solid Bond tool . 3. Point to the left center carbon and drag outward.

The size of the orbital is constrained just like Rotate the selection:
bonds. The constraint is based on a percentage
1. Double-click the Rotation handle in the upper
of the Fixed Length setting in the Drawing
Settings dialog box. right of the Selection Rectangle to open the
Administrator
Rotate dialog box.
NOTE: Orbitals are not automatically 2. Type 180 in the text box, click degrees CW, and
grouped with the closest structure. If you want then click Rotate.
to group the orbital with the existing structure
so you can move them as a unit, choose Group
from the Object menu.
Move part of the structure to the front to overlap the

orbital:
Change the layering of the structure so that the
1. Click the Marquee tool . selection is in front:
2. Point above the structure and drag around the • From the Object menu, choose Bring to Front.
upper fragment to select the three bonds.
Orient the front part of the structure to create a
Newman projection.
1. Point within the Selection Rectangle until the

pointer changes to a hand.
NOTE: Only bonds that are completely within the

Lasso area are selected. Do not select the bond
connecting the two fragments. Alternately, you can
Shift+click on each bond separately.

2. Drag the selection until the central atom of the 2. Click in the document window and drag
selection is centered within the orbital. downward to create the first bond.
3. Continue pointing at the lower atom and click

again to add a second bond.
3. Release the mouse button and click outside the
Selection Rectangle to deselect the structure.

4. Continue pointing at the same atom and click
again to add a third bond.
Tutorial 7: Showing
Stereochemistry
This tutorial demonstrates using stereochemistry
5. Point to the atom shown below and click.
markers and the flip command.
Create a new document.
1. From the File menu, choose New Document.

3. Type tut7.cdx in the appropriate text box. 6. Point to the atom shown below and click twice
to create two bonds.
5. Click Save.
Draw the following structure:
O
7. Pointing to the bond shown below, right-click,
point to Double, and then choose Plain.
OH
NH2

Tutorial 7: Showing Stereochemistry
8. Click the Wedged Bond tool, point to the atom Display the stereochemical markers.
below, and then click.
1. Select the entire structure with the Lasso or
Marquee.
Administrator
2. From the Object menu, choose Show

Stereochemistry.
The S marker appears.
Add atom labels.
O
1. With the Text tool, click the atom shown below,
and then type NH2 in the text box that appears.
(S)
OH
NH2
3. Select the structure and from the Object menu,
choose Flip Horizontal.
The R marker appears.
2. With the Text tool, click the atom shown below,
and then type O in the text box that appears. O
(R)
HO
NH2
4. With the structure selected, simultaneously

NH2 hold Alt or Option and click the Object menu.
3. With the Text tool, click the atom shown below, Choose Rotate 180° Vertical.
and then type OH in the text box that appears.
NH2
O
HO
(R)
O
NH2 The Wedged bond becomes hashed and the (R)
stereochemistry is preserved.


Tutorial 7: Showing Stereochemistry
Chapter 3:
Drawing Chemical Structures
Overview The drawing settings are described in the following
table:
ChemDraw provides the following tools for drawing
chemical structures: Adjust this If you want to …
• Bond tools setting …
• Ring tools
Chain Angle Set the angle (from 1 to 179
• An acyclic chain tool degrees) between bonds created by
• Automatic error checking the Acyclic chain tool or modified
by the Clean Up Structure
• In ChemDraw Ultra, the ability to draw command.
structures automatically from chemical names
For more information see,
Drawing Settings “Drawing Acyclic Chains” on page
58 and “Using Clean Up Structure”
Drawing settings are document settings that affect on page 111.
how bonds and other objects are drawn. You can
configure the drawing settings for an entire Bond Set the distance between the lines
document or for a particular object as follows: Spacing in double or triple bonds. The
distance is set either as:
• For the entire document, in the Document
Settings dialog box. • The percent of the length of
• For an object, in the Object Settings dialog box. the bond (between 1 and 100).
This allows for proportional
Changes made to the drawing settings affect the
spacing to be used if different
active document window only. Drawing settings can
bond lengths are used in the
be saved in Style Sheets/Stationery Pads. drawing.
For information on applying settings from other
documents to your document or specific objects, see
“Document and Object Settings” on page 10.
10% 14% 18%
• An absolute value you choose
in the units specified for your
document.
ChemDraw 7 Chapter 3: Drawing Chemical Structures • 49

Drawing Settings
Adjust this If you want to … Adjust this If you want to …
setting … setting …
Administrator
Fixed Length Constrain the length of the bonds Margin Change the amount of space
drawn to the length you specify Width surrounding all atom labels that
when the Fixed Lengths command will erase portions of the bonds to
in the Object menu is selected (a which they are attached. The
check mark is next to it). This also margin width also determines the
adjusts the preferred bond length amount of white space surrounding
for structures modified by the the front bonds in a bond crossing.
Clean Up Structure command.
For more information, see
For more information see “Creating Atom Labels” on page
“Drawing with Fixed Lengths” on 75 and “Changing Bond
page 58 and “Using Clean Up Crossings” on page 68.
Structure” on page 118.
Hash Spacing Set the spacing between the hashed
Bold Width Set the width of the line used when lines used when wedged hashed
bold and wedge bonds are drawn. bonds, hashed bonds, dashed
The Bold Width setting must be bonds, dashed arrows, or dashed
greater than the Line Width setting. curves are drawn.
The end of a wedge is 1.5 times the
bold width.
2 Point 4 Point 8 Point
2 Point 4 Point 8 Point Color Change the color in of selected

objects. For more information, see
“Customizing the Color Palette”
Line Width Set the width of all bonds, lines,
on page 115.
and arrowheads in the drawing.
Units Set the units used in the Object

Settings dialog box to centimeters,
inches, points, or picas.
0.5 Point 1 Point 1.5 Point

Atom and Set which indicators you want to
Bond display in your drawings. For more
Indicators information about using indicators,
see “Numbering Atoms” on page
75 and “Showing Stereochemistry”
on page 126.
50 • Chapter 3: Drawing Chemical Structures CambridgeSoft

Drawing Settings
To configure the drawing settings for an entire To configure the drawing settings for a selected
document: object:
1. From the File menu, choose Document
1. Select the object.
Settings.
2. From the Object menu, choose Object
The Document settings dialog box appears.
Settings.
The Object Settings dialog box appears with the
Drawing tab displayed.
2. Click the Drawing tab and configure the

settings.
3. Configure the settings and click OK.

The settings you chose are applied to the
selected object only.
3. Click OK when you are finished.

The settings you chose are applied to the entire
document.

Drawing Settings
Displaying the Info Value Description
Window
Other Angle:
Administrator
As you draw structures, you can view drawing

parameter information in the Info window. • Angle the bond being drawn makes
with the x-axis
To display the Info window:
• Angle of rotation
• From the View menu, choose show Info
Window. • Direction of dragged object
The Info window appears.

Dist:
• Length of bond being drawn

• Distance selected object was
dragged
%—Amount of scaling
Drawing Bonds
The Main Tools palette contains the bond tools
shown below:
The table below shows some of the measurements
the values can represent. Solid Bond
Value Description Multiple Bonds
Dashed Bond
Pointer • X,Y—Current location of pointer
Hashed Bond
• dX—Amount dragged object has
moved horizontally Hashed Wedged Bond
• dY—Amount dragged object has
Bold Bond
moved vertically
Bold Wedged Bond
Selection • X,Y—Position of area shown in the
following graphic: Hollow Wedged Bond
• W—Width of selected object
Wavy Bond
• H—Height of selected object

Displaying the Info Window
Setting the Default Tool Drawing with Fixed Angles
You can set the default for new documents in the To draw bonds with constrained angles that are
Preferences to the Last Used, Lasso, Marquee, or multiples of 15 degrees relative to the X-axis:
Plain Bond.
1. From the Object menu, choose Fixed Angles.
To set the default tool:
A check mark appears next to the Fixed Angles
1. From the File menu, choose Preferences. command indicating that it is on.
2. Click the Open/Save tab. 2. Click a bond tool.
3. In the Opening Files section, click the default 3. Drag from one end of the bond to the other in a
tool to use. document window.
4. Move the end of the bond to other angles.
Drawing Constrained Bonds The Info Window shows that the bond angle is
You can draw any bond length and create any angle constrained to 15-degree increments.
relative to the X-axis. The Info Window displays the
bond length and angle as you drag the bond. Toggling Fixed Lengths and Fixed
However, you can draw bonds that are constrained Angles
to: If Fixed Lengths or Fixed Angles are selected, you
• A fixed length can temporarily deselect them.
• A fixed angle relative to the X-axis To toggle Fixed Lengths and Fixed Angles:
• Press Alt or Option and drag from one end of a
Drawing with Fixed Lengths
bond to the other end in the document window.
To draw bonds that are constrained to a fixed length:
1. From the Object menu, choose Fixed Lengths.

Dative Bonds and Wedged
A check mark appears next to the Fixed Lengths
Bonds
command indicating that it is selected. All the Dative bonds and wedged bonds are drawn with a
bonds drawn are constrained to the fixed length fixed orientation in a document window.
specified in the Drawing Settings dialog box.
To draw a dative bond:
2. Click a bond tool.
1. Click the Dative Bond tool.
3. Drag from one end of the bond to the other.
2. Drag from the positive to the negative end
The Info Window displays the bond length.
(arrow head) of the dative bond.

Drawing Bonds
To draw a wedged bond: Adding Bonds by Dragging
1. Click one of the wedged bond tools. To control the orientation of bonds that you draw,
2. Drag from the narrow end of the wedged bond you can add bonds by dragging.
Administrator
to the wide end of the wedged bond. By using this dragging method for drawing the
bond, you can control the orientation of the other
end of the bond.
To add a bond by dragging:
To change the orientation of the dative or wedged 1. Click a bond tool.

bond: 2. Point to an atom.
• Click the center of the dative or wedge bond
using the appropriate tool.
The orientation of the bond is inverted. A highlight box appears over the atom
indicating where the bond will be joined.
Adding a Bond by Clicking
3. Drag from the atom at which you are pointing to
To quickly add a fixed length bond: the end of the new bond.

A new bond is drawn and joined to the atom
2. Click an atom. where the highlight box appeared.
A new bond is drawn and joined to the atom you

clicked.
Changing the Highlight Box

Size
Bonds drawn by this method are always drawn using
the Fixed Length specified in the Drawing Settings The size of highlight box is controlled by the
dialog box. The angle that the deposited bond makes Tolerance value in the Preferences dialog box. With
with its nearest neighbor is equal to the Chain Angle the default Tolerance setting of 5 pixels, the
set in the Drawing Settings dialog box. If this angle highlight box appears on atoms if the pointer is
cannot be established, a smaller angle is used. located in a square region 10 pixels on a side or +/-
5 pixels from the atom.
To change the Tolerance:

2. On the General tab, select or type the tolerance,
and then click OK.

Drawing Bonds
Multiple Bonds Double Bonds
The Multiple Bond tool on the Main toolbar To draw a double bond:
includes the following palette.
1. Click the Solid, Dashed, or Bold bond tool.
2. Drag over an existing bond from one end of the
bond to the other end.
You can use the tools on the Multiple Bond palette

A double bond is created.
to create the following multiple bonds:
Double
Bold Double
Double Either Bonds
Tautomeric To draw a double either bond:
1. Draw a double bond using the Wavy Bond tool.

Aromatic
2. Point to the center of the double bond and click.
Triple Bonds
Double Either
You can draw a triple bond by drawing another
Dative single bond on top of a double bond. All bonds in a
triple bond are solid bonds.
Triple To draw a triple bond:
1. Click any bond tool.

Quadruple
2. Drag from one end of an existing double bond
to the other.
Quadruple Bonds
NOTE: You can also draw multiple bonds by
right-clicking over a bond and selecting the bond To draw a quadruple bond:
type from the shortcut menu or by using the bond
properties dialog box. For more information, see 1. Click any bond tool.
“Bond Properties” on page 136. 2. Drag from one end of an existing triple bond to
the other.
The triple bond changes to a quadruple bond.

Drawing Bonds
To change a quadruple bond into a single bond: The cyclohexane tool is shown below:
1. Click any bond tool.

2. Drag from one end of an existing quadruple
Administrator
3. Drag from the beginning to the end of the first

bond to the other.
bond.
The quadruple bond changes into a single bond
corresponding to the tool used to draw over the
bond.
NOTE: You can also use the Eraser tool to reduce

the bond order. For more information, see “Deleting When you point in a document window, the
Objects” on page 97. pointer changes to a ring tool pointer. The
highlight box on the ring tool pointer indicates
Drawing Rings the atom that is drawn first. The bond directly
below the highlight box is the bond that is
The Main Tools palette contains the following ring drawn first.
tools that enable you to draw ring sizes and types:
First atom drawn
Cyclopropane Cyclobutane
First bond
Cyclopentane Cyclohexane
drawn
Cycloheptane Cyclooctane
Cyclohexane Chair (1) Cyclohexane Chair (2)
Cyclopentadiene Benzene
Drawing a Ring by Clicking
To quickly draw a ring:
Drawing a Ring
• Click a ring tool, and then click in a document
If Fixed Lengths is on when you draw a ring, the
window.
length of each bond in the ring is automatically set
to the fixed length. If Fixed Angles is on, the angle A ring appears in a document window centered
the first bond in the ring makes with the X-axis is around the pointer. The ring is drawn using the
restricted to 15-degree increments. For more Fixed Length specified in the Drawing Settings
information, see “Drawing Constrained Bonds” on dialog box. The ring is deposited in the
page 53. orientation shown on the ring tool icon.
If you click an atom, the ring is fused to that atom.
To draw a ring:
1. Click a ring tool.

2. Position the pointer in a document window.

Drawing Rings
If you click a bond, the ring is fused to that bond. Drawing Resonance
Delocalized Rings
Any of the ring tools, except the cyclohexane chairs,
can be drawn in a resonance delocalized form.
To draw a resonance delocalized ring:

If you click an atom in a ring, a spiro linkage is
formed. 1. Click a ring tool.
2. Press Ctrl or Command and drag or click to
draw the ring.
A circle appears inside the ring.
Drawing Cyclohexane Chair

Rings
You can draw Cyclohexane chair rings in two NOTE: The circle is automatically grouped with
orientations: horizontal and vertical.When you draw the ring when drawn. For more information on
grouping objects, see “Grouping Objects” on page
a cyclohexane chair ring by clicking, the chair is
104.
drawn in a horizontal orientation.
To orient a cyclohexane chair ring to a vertical

Drawing Cyclopentadiene and
orientation:
Benzene Rings
1. Click one of the Cyclohexane Chair Ring
The double bonds in the cyclopentadiene or benzene
tools.
ring tools can be drawn in either of two forms.
2. Click+drag in the structure to the orientation
you want. When you draw a cyclopentadiene or benzene ring a
double bond is drawn first. The Cyclopentadiene
and Benzene Ring tool pointers indicate this
orientation.
To shift the orientation so the first bond drawn is a
single bond, do one of the following:
• Shift+drag from the beginning of the first
Vertical Orientation
single bond to the end of the single bond.
Horizontal Orientation
• Shift+click in a document window to draw the
bond with a Fixed Length.

Drawing Rings
In the figure below, the arrow indicates the direction Adding Chains
in which the first bond is drawn.
To add an acyclic chain to an existing atom:
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1. Click the Acyclic Chain tool.

2. Point to the atom to which you want to attach
the chain.
Drawing Acyclic Chains

You can draw long hydrocarbon chains with the 3. Drag in the direction you want the chain to
Acyclic Chain tool . grow.
Drawing Chains 2
To draw an acyclic chain:
1. Click the Acyclic Chain tool.

To specify a chain length:
2. Drag in the direction you want the chain to grow
in a document window. 1. Click the Acyclic Chain tool.
2. Click an existing atom or an empty area in a
5 document window.
The Add Chain dialog box appears.
A number appears at the end of the chain

indicating how many atoms you have drawn.
When Fixed Lengths is on, the pointer on the acyclic
chain can be dragged to make any angle relative to
the X-axis. At a constant chain length, the positions
of the first bond and all subsequent odd-numbered
atoms depend on the direction you drag. Before 3. Type the number of bonds in the chain.
releasing the mouse button, this position can be
4. Click Add.
changed by dragging in the opposite direction.
When Fixed Angles is on, the angle the acyclic To add another chain of the same length anywhere in
chain makes relative to the X-axis is constrained to a document window:
15-degree increments. • Alt+click or Option+click an existing atom or
click in an empty area within the document
window.

Drawing Acyclic Chains
Changing Chain Direction Changing Double Bonds
To change the direction of the chain as you draw: To change one type of double bond to another:
• Press Alt or Option while drawing chains in the
1. Click the Bold, Dashed, or Solid Bond tool.
direction you want.
2. Point to one of the bonds in the double bond.
Editing Bonds 3. Click the bond.
You can modify the appearance of chemical

structures by:
• Changing bond types
• Changing bond alignment and orientation
The double bond changes to the new bond type.
• Moving atoms One of the bonds in the double bond is always a
• Layering bonds solid or dashed bond.
• Changing the bond order
NOTE: If you click a tautomeric bond
(solid/dashed) a second time with the dashed bond
Changing Bond Types tool, you create an aromatic double bond
To change a single bond from one type to another: (dashed/dashed).

2. Point at the center of an existing bond and click.
The bond that you click changes to the new

bond type.

Editing Bonds
Changing Orientation of To change the alignment of a double bond:
Wedged and Dative Bonds 1. Click the bond tool used to create the existing
When you draw or change a bond to a wedged or double bond.
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dative bond, the orientation of the bond is chosen 2. Do one of the following:
appropriately. • Click the center of the double bond.
To change the orientation: The alignment changes. Click the center of
• Click the dative or wedged bond with the tool the double bond again to change to the next
used to create it. alignment.
• Right-click or Control-click, point to Bond
CO2H Position, and then choose the alignment.
Moving Atoms
H
HO You can use any of the bond tools to move an atom
CH3 within acyclic or cyclic structures. You cannot use a
The dative or wedged bond is changed to the ring tool.
opposite orientation. To move an atom in a chemical structure:

CO2H
2. Point at the atom to move.
A highlight box appears over the atom.
H
HO
CH3
Changing Alignment of Double
Bonds
The bonds in a double bond can have any one of 3. Shift+drag the atom.
three alignments relative to other bonds:
• Above
• Below
• Centered
You can convert ring types by dragging one atom on

top of an adjacent atom. For example, you can use
this method if you want to convert a 6-membered
ring into a 5-membered ring.

Editing Bonds
To convert ring types: The bond appears in front.
1. With a bond tool selected, point to an atom and

Shift-Drag.
NOTE: You can also layer bonds using the Bring to

Front and Send to Back commands. For more
information, see “Front to Back Ordering” on page
2. Release when one atom is on top of the other. 164.
NOTE: You can magnify your view to make

changing the bond layering easier. For more
information, see “Changing Perspectives” on page
153.
The bond between the atoms disappears.
NOTE: You can also move atoms using a selection Changing the Bond Order
tool. For more information see “Moving Objects”
on page 98. You can reduce or increase the order of bonds in a
structure by using the Bond Properties dialog box or
with the shortcut menus as follows.
Changing Bond Crossings
To reduce the bond order:
When one bond crosses another, white space is used
to indicate which bond is in front of the other. 1. Point to the bond to change and Right-click
(Windows) or Control-click (Macintosh).
To change which bond is in front:
2. Choose the appropriate bond type from the
1. Click any bond tool. shortcut menu that appears.
2. Double-click the bond to bring it to the front.
NOTE: You can also use the eraser tool to reduce
the bond order. For more information, see “Deleting
Objects” on page 97.

Editing Bonds
Automatic Warnings The Display tab appears.
ChemDraw automatically checks for correct

chemical syntax as you draw. If ChemDraw finds a
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potential problem, a red box is displayed around the

questionable object. The red box is displayed on
screen only and does not print.
To enable the automatic display of chemical
warnings:
• On the View menu, choose Show Chemical
Warnings.
This setting applies to all documents.
To view a description of the problem, do one of the
following:
• Right-click on the warning and choose Explain
This Warning. 3. In the Chemical Warnings section, click the
• Select the structure and from the Structure types of warnings you want to display.
menu, choose Check Structure. To disable the automatic error checking on a specific
For more information, see “Checking object:
Chemistry” on page 123. • Right-click the object and deselect Display
To select which types of chemical warnings to Warnings.
display: When Display Warnings is deselected for an object:
1. From the File menu, choose Preferences. • Red boxes are not displayed for questionable
objects.
2. Click Display.
• Problems are not reported by the Check
Structure command. For more information on
the Check Structure commands, see “Check
Structure” on page 123.

Automatic Warnings
Automatic Inserting Names
Drawing—Structures For example, to insert 2-bromobenzoic acid:
1. From the ChemDraw Ultra Structure menu,

from Chemical Names choose Convert Name to Structure.
In ChemDraw Ultra only, you can draw a structure The Insert Structure dialog box appears.
automatically from a chemical name, by using the
2. Type 2-bromobenzoic acid.
Convert Name to Structure feature, a name
interpreter.
ChemDraw Ultra Name-to-Structure recognizes
most organic nomenclature. Most inorganic
chemistry is also recognized, especially when the
rules closely match those for organic chemistry.
The following are not supported:
• Coordination complexes NOTE: You can also copy a name to the
• Polyboranes clipboard and then type Crtl+V (Windows) or
Command+V (Macintosh) to paste the name
• Polymers into the dialog box.
• Some highly-bridged ring systems, including
fullerenes and porphyrins/porphines 3. Click OK.
• Some stereochemistry designators: +, -, +/-, +-, The molecular structure and name appear in the
D, L, DL, endo, exo, syn, anti, r, t, c drawing area.
Although some trade names are supported, Br
Name-to-Structure is not intended to interpret trade
or common names. A chemical database, such as O
chemfinder.com, is more appropriate for obtaining
structures for trade or common names.
OH
Converting Names to 2-bromobenzoic acid
Structures
You can insert a name as a structure in the document
window by using the
• Insert Structure dialog box
• Paste Special command

Automatic Drawing—Structures from Chemical Names
Paste Special
The Paste Special command allows you to paste
names copied to the clipboard from other
applications as a structure in ChemDraw.
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To paste a name copied to the clipboard from

another application:
1. Click in the document window.

2. From the Edit menu, point to Paste Special,
and then choose Name as Structure.
The structure appears in your document.
Converting Captions to
Structures
If a caption is already present in the drawing area
you can convert it to a structure as follows:
1. Select the caption.
2. From the ChemDraw Ultra Structure menu,

choose Convert Name to Structure.
The molecular structure and name appear in the
drawing area.

Automatic Drawing—Structures from Chemical Names
Chapter 4:
Drawing Captions and Atom Labels
Creating Text Formatting Text
ChemDraw enables you to create the following Text settings affect how captions and atom labels for
types of text: the current document are drawn and formatted. Text
settings include:
• Caption text—Create annotations, chemical
names, chemical formulas, page titles, and • Font
information in tables. • Font size
OH • Font style
• Baseline style
• Line spacing
Caption Text • Alignment
Phenol The text settings are described in the following
• Atom label text—Identify atoms and sections.
substructures by their chemical symbols and Changing the Text Settings in the Document
formulas. Settings dialog box affects the current document
OH
only. You can also change settings for individual
Atom Label
objects by using the Object Settings dialog box or
Text
the Text menu.
To display the document text settings for captions

and atom labels:
You create and edit caption and atom label text with
the Text tool. You set the text format in the
Settings.
Document Settings or Object Settings dialog box.
2. In the Document Settings dialog box, click
ChemDraw does not install its own fonts. If a Captions or Atom Labels.
ChemDraw document contains fonts that are not
available on a particular computer, they are
substituted with available fonts.
You can also use HotKeys to quickly label atoms.
For more information see “Labeling Atoms with
HotKeys” on page 73.
ChemDraw 7 Chapter 4: Drawing Captions and Atom Labels • 65

Formatting Text
The Windows Captions tab containing the text If the captions you select have more than one style,
settings is shown below. a hyphen appears next to each style that is applied to
a portion of the selection. A check mark appears
next to each style that applies to all of the selected
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text. Choosing a style, except Plain, adds the new

style to all of the selected captions. Previously
applied styles are not affected.
Specifying Line Spacing

You can specify the three types of line spacing:
• Automatic—Consistently spaced lines of text
based on the height of the tallest character in the
entire caption. This is the default line spacing.
• Variable—Lines of text with different spacing
based on the tallest character and the lowest
descender in each line.
• Fixed—Consistently spaced lines using a
3. Change the settings if desired. The options are spacing that you specify.
described in the following sections.
4. Click OK.
Aligning Text
The formatting is applied to the current You can set the alignment of captions and atom
document. labels to justify text to suit your needs. The options
available depend on whether you are aligning
Setting the Baseline Style captions or atom labels.
You can specify the following baseline styles: Captions

• Superscript—Reduces the text size by about You specify the caption justification and line
25 percent and raises its baseline. spacing on the Captions tab of the Object Settings
• Subscript—Reduces the text by about dialog box. All text in a single caption must have the
25 percent and lowers the baseline. same Justification and Line Spacing.
• Formula—Formats in a way that is appropriate
for most formulas.
You can apply several styles to the same selected
caption. You can also apply multiple styles to
different portions of a single caption.
66 • Chapter 4: Drawing Captions and Atom Labels CambridgeSoft

Formatting Text
There are four available justifications: Examples of the atom label justifications are shown
below.
• Flush Left—creates left-justified caption text.
OMe RNH
CH2
N
• Centered—creates centered caption text.
Stacked Above Centered
• Flush Right—creates right-justified caption

text. N N
CH2 H2C
OMe MeO
Flush Left Flush Right
• Justified—creates right-left justified caption Automatic Alignment

text.
When you justify Atom labels automatically,
ChemDraw breaks the label into tokens. A token
consists of an uppercase letter followed by any
numbers or lowercase letters. The first token is
attached to the atom and the rest of the label appears
Atom Labels without obscuring other parts of the chemical
Use the Centered, Flush Left, Flush Right, Stacked structure.
Above, Automatic, or Best Initial Position
For example, to create N-methylpiperidine, label an
justifications to create labels that identify atoms and
atom in cyclohexane with the atom label “NCH3”,
functional groups in your chemical structure without
which contains the three tokens, “N” and “C” and
obscuring any bonds or other atom labels.
“H3”. If you label C3, the tokens are placed from left
to right because there are bonds to the left of the
atom.
NCH3

Formatting Text
If you label C5, the tokens are placed from right to Changing the Default Caption
left because there are bonds to the right of the atom:
or Atom Label Text Format
Each new caption or atom label uses default
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document settings for the font, size, and style of

H3CN captions and atom labels. You can change the format
by:
In ChemDraw Pro, you can force an entire
multi-atom label to be a token by defining it as a • Changing the document settings for subsequent
Nickname. This prevents the label from flipping drawings in the current document.
when applied to the left side of a structure. • Choosing a new format for an individual
For example, if you define the Nickname “CH3”, caption or label from the Text menu or toolbar
and label C5 with the combined label and nickname before you type.
“NCH3”, the final orientation is “CH3N” instead of • Selecting text and applying a new format to an
“H3CN”. In this case, the Nickname, “CH3”, is a individual label after you type.
token. For more examples, see “Using Nicknames”
on page 105. Specifying Document Settings for New
If you label C1, the second and third tokens are
Text
placed above the first token since there are bonds To specify the text settings for new captions and
below the atom. atom labels in the current document:
CH3 1. From the File menu, choose Document

N Settings.
2. In the Document Settings dialog box, click
Captions or Atom Labels.
If you label C4, the second and third tokens are 3. Click the appropriate options.
placed below the first token. 4. Click OK.
These settings affect all new captions or atom labels
in the current document. To use these settings in new
documents save them in a Style Sheet or Stationery
N Pad. For more information, see “Saving Customized
CH3 Settings as Style Sheets or Stationery Pads” on page
10.

Formatting Text
Setting an Individual Text Format 5. To apply the settings to all subsequent drawings
Before Typing as well, click Set Defaults for Document.
You can set the text format for an individual caption 6. Click OK.
or atom label before you type. The format change is To change only a part of a single caption you must
applied to the current text only. use the Text tool:
To set the text format before you type: • Select part of the caption with the Text tool.
1. Click the Text tool and then click in the To specify a font and size for selected text, do one of
document window. the following:
A text box appears. • Right-click and choose the font and size from
the menu.
2. Set the text format in one of the following ways:
• From the Style Toolbar, select the font and size
• From the Text menu, choose the format
from the drop-down menus.
options.
• From the Style toolbar, choose the format Fractional Character Widths
options. (Macintosh)
3. Type the text in the text box. On the Macintosh, you can choose to have the
The format is applied to the typed text. Any spacing between characters as to close to
subsequent text you type is formatted according proportional as possible. If you are printing to a
PostScript printer, this option improves the font
to the default document settings for the current
appearance.
document.
To set fractional widths:
Changing the Spacing of Individual
Text Objects 1. From the File menu, choose Document
Settings.
You can change the text settings for an specific
2. In the Document Settings dialog box, click the
caption or atom. The setting change is applied to the
Footer tab.
selected object only. You can also choose whether to
have the settings applied to the selected text and to 3. Click Fractional Widths.
all subsequent text you type.
Coloring Text
To change the text settings for a specific caption or
You can color captions and atom labels before or
atom label:
after they are typed, and as a whole or in part.
1. Select the text to change with a selection tool.
To color a caption or atom label:
2. From the Object menu, choose Object
Settings. 1. Select the Text tool.
3. In the Object Settings dialog box, click 2. Click in the position where you want to place
Captions or Atom Labels. the text.
3. From the Color menu, choose a color.
4. Click the appropriate options.
4. Type the caption or atom label.

Formatting Text
To color individual characters: You can also click outside the Caption text box
in a document window to close the current
1. Select part of an existing caption or atom label
Caption text box and open a new Caption text
using the Text tool. box.
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2. From the Color menu, choose a color.

NOTE: You can verify the chemical significance of
NOTE: Macintosh: Captions that contain multiple captions using the Check Structure command. For
colors change to the foreground color when rotated. more information, see “Check Structure” on page
However, all colors contained in the caption are 123. You must format the captions in Formula style
printed. to use these commands. For more information see
“Changing the Default Caption or Atom Label Text
Format” on page 68.
To color several captions or atom labels at once:
1. Select the captions or atom labels using a

selection tool.
Changing the Caption Width
2. From the Color menu, choose a color. To change the width of a caption:
1. Select a caption using the Text tool.

Creating Captions
The Caption text box appears around the
The format of any new captions you create are caption. The right side of the text box contains
specified in the Captions Settings tab of the a Resize handle.
Document Settings dialog box. To change the
settings before you type, see “Formatting Text” on Resize handle
page 65.
To create a caption: 2. Drag the Resize handle.

The point at which the text wraps is adjusted as
you drag the Resize handle.
2. Point in an empty space in a document window.
A caption text box with a flashing insertion Editing a Caption
point appears.
To open a caption for editing:

2. Point at a caption and click to open the text box.
3. Type a caption.
The text box widens as you type to
accommodate the caption.
4. To create a new line, press Enter or Return. The caption text is highlighted.

Creating Captions
To change all of the highlighted text within an open • Isotopic variation, charged carbon atoms,
text box: radicals and multi-component species are
ignored
• Type the new caption text over the highlighted
text. • The set of heavy atoms for an organic
component is confined to: Hg, B, C, N, O, F, Si,
P, S, Cl, Ge, As, Se, Br, Sn, Sb, Te, I, Pb, Bi
To insert the name of a structure into your drawing:

The highlighted text disappears as you type the
new caption. 1. Select the drawing for which you want to insert
a name.
If not all the text is highlighted and you want to
select all of the caption text:
• From the Edit menu, choose Select All.
To change part of the caption text: 2. From the Structure menu, choose Convert
• Drag the insertion point over a part of the Structure to Name.
caption.
Adding Chemical
Cyclohexane
Names
The name of the structure appears as a caption
In ChemDraw Ultra only, you can insert the name of under your drawing.
a selected structure as a caption using the Convert
The chemical naming features are provided by
Structure to Name command from the Structure
AutoNom. To view information about Autonom:
menu.
• From the Structure menu, choose About
The conversion of a structure to a name is limited by
AutoNom.
the following:
• Stereochemical information is ignored
• Structures must contain fewer than 125 atoms
(excluding implicit hydrogens)
• Rings and chains must contain fewer than 44
atoms

Adding Chemical Names
Labeling Atoms with the You can also click outside the current Atom Label
text box on another unlabeled atom to open a new
Text Tool Atom Label text box.
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The format of any new atom labels you create are

NOTE: You can use HotKeys to label an atom
specified in the Atom Labels tab of the Document
instead of using the Text tool. You can also label
Settings dialog box. To change the settings before atoms using Nicknames that are text representations
you type, see “Formatting Text” on page 65. of substructures. For more information, see
“Labeling Atoms with HotKeys” on page 73 and
To place an atom label on an atom:
“Using Nicknames” on page 105.
2. Point to an atom. Specifying the Margin Width
The pointer changes when it is positioned You can adjust the white space surrounding the atom
correctly over an atom to indicate that you will label can so some of the attached bond is hidden.
create an atom label rather than a caption.
Cl Cl
0.278 pt 0.6 pt
To adjust the white space:

3. Click the atom. 1. From the File menu, choose Document
An Atom Label text box appears over the atom. Settings.
The Object Settings dialog box appears.
2. On the Drawing tab, type a new Margin Width
value.
3. Click OK.
4. The margin width is applied to all subsequent
4. Type an atom label.
drawings
Numbers are automatically subscripted. The
justification you choose determines how the Editing Atom Labels
letters in an atom label are positioned on a bond.
Numbers, leading open parentheses, and To edit an atom label:
trailing closed parentheses are ignored in the 1. Click an existing label using the Text tool or
positioning of atom labels. For more double-click using a bond or ring tool.
information, see “Atom Labels” on page 67.
The highlighted atom label text appears within
5. Close the Atom Label text box. the Atom Label text box.

Labeling Atoms with the Text Tool
2. Type the new atom label text over the Method 2: Labeling an atom by
highlighted text.
pointing
If all the text is not highlighted, and you want to
select all of the atom label: 1. Using a bond tool or the Text tool, position the
• From the Edit menu, choose Select All. pointer over an atom.
To edit part of the atom label:
1. Drag the insertion point over part of the atom

A highlight box appears over the atom.
label.
2. Press a HotKey, for example, “c”.
2. Type the new characters.
3. Close the Atom Label text box. H3C
Deleting an Atom Label The label is added to the atom highlighted. If

To delete an atom label, leaving the underlying the label is a single element, such as “C”, then
bonds unchanged, do one of the following: the appropriate number of hydrogen atoms are
added to the label.
• Click the Eraser tool and then click the atom
label.
Method 3: Labeling an atom
• With the atom label selected, press the spacebar with a selection tool
or delete HotKey.
1. Using a selection tool, position the pointer over
Labeling Atoms with an atom.
Highlight boxes appear over the atom.
HotKeys
Use ChemDraw HotKeys to quickly label atoms and
apply atom properties. The file CS ChemDraw
Hotkeys in the ChemDraw Items folder contains the 2. Press a HotKey, for example, “c”.
HotKeys provided with ChemDraw. You can add or
change HotKeys by editing the file in a text editor. C
Use the following methods to label an atom with a H2
HotKey.
Method 4: Labeling multiple
Method 1: Labeling the last atoms
atom drawn 1. Select several atoms using a selection tool.
1. Draw a bond.
2. Press a HotKey.
The last atom drawn is labeled. Each time you 2. Press a HotKey, for example, “c”.
draw a bond, the last atom drawn is the HotKey
atom.

Labeling Atoms with HotKeys
The selected atoms are labeled.
HotKey Function
H 3C
C c Centers the double bond to which
H2
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you are pointing.

The element or label associated with the
l Positions the double bond to which
HotKey is added to the structure.
you are pointing to the left.
Hard-Coded HotKeys r Positions the double bond to which
You cannot edit hard-coded HotKeys. The following you are pointing to the right.
table contains a list of hard-coded HotKeys:
Creating HotKeys
HotKey Function To add or edit ChemDraw HotKeys:
Enter or
• Open the CS ChemDraw Hotkeys file in the
Opens the atom label text box.
Return ChemDraw Items folder.
space
The CS ChemDraw HotKeys.txt file appears.
Removes an atom label.
/ (slash) Displays the Atom Properties dialog

box when pointing to an atom or the
Bond Properties dialog box when
pointing to a bond.
= (equal) Displays the List Nickname dialog

box.
. (period) Adds an attachment point.
' (apostrophe) Adds an atom number.

Delete Deletes selected objects.
1 When pointing to a bond, changes
the bond to single.
the bond to double.
the bond to triple.
f Send bond to which you are You can use any uppercase or lowercase
pointing to the front of the drawing. alphanumeric key as a HotKey with the exception of
b Send bond to which you are the hard coded HotKeys listed previously. If a
pointing to the front of the drawing. capital and lowercase HotKey do not exist, the

Labeling Atoms with HotKeys
HotKey is assigned to both. If a key is used more An atom text label appears over the atom.
than once in the file, the one closer to the end of the
file takes precedence.
To add a HotKey:
1. Add a new line and type the key you want to

use. 3. Type the text.
2. Type a space.
Repeating an Atom
3. Type the letters to associate with the HotKey.
HotKeys defined for single elements always
Label
result in the adding of the appropriate number You can repeat an atom label using the text, bond, or
of hydrogen atoms. ring tools.
4. Save and close the HotKeys file. To label several atoms with the same text using the
Text tool:
To create a new HotKeys file:
1. Click the Text tool.
1. Create a text file named CS ChemDraw
Hotkeys. 2. Label a single atom.
2. Save the file in the ChemDraw Items folder. 3. Double-click another atom to repeat the
previous label.
3. Click OK or Save.
To label several atoms with the same text using a
Labeling Atoms With a bond, ring, or Acyclic Chain tool:
Bond or Ring Tool 1. Click the tool.

2. Triple-click an atom to repeat the previous
To avoid switching back and forth between tools,
you can label atoms with a bond or ring tool. label.
To label an atom using a bond or ring tool: Numbering Atoms

1. Click the Bond or Ring tool. You can add sequential numbering indicators to the
2. Point to an atom and double-click. atoms in a structure. ChemDraw recognizes the
following types of indicators:
• Numbers (1, 2, 3, and so on)
• Text ending with a number (atom1)
• Greek letters in the Symbol font
• Letters (a, b, c, and so on)
The default indicator is numbers.

Labeling Atoms With a Bond or Ring Tool
Showing and Hiding Atom To number individual atoms, do one of the
following:
Numbers
To add atom numbering to an entire structure: If you want to … Then…
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1. Select the structure.

show a previously • Select the atom,
2. Do one of the following: assigned atom right-click, and
number. choose Show Atom
If you want to … Then… Number.
A previously assigned
show previously • Right-click, point to number is displayed.
assigned atom Atom, and then click
numbers. Show Atom Number. • Type the HotKey '
assign an atom
number (apostrophe).
Any previously assigned
numbers remain The atoms are numbered
unchanged. in the sequence you
choose.
assign new atom • Type the HotKey '
To hide atom numbering in a structure:
numbers. (apostrophe).
The atoms in the structure
are numbered 2. Right-click, point to Atom, and then deselect
sequentially. Show Atom Number.
To hide an individual atom number:
6
• Select the atom, right-click, and then choose
5 1 Hide Indicator.
To remove an atom number indicator:
4 2
• Click the indicator with the Eraser tool.
3

Numbering Atoms
Editing Atom Numbers The Position Indicators dialog box appears.
You can edit the text and style of atom number

indicators. If you change the atom number text, any
other atom number indicators in the structure are
updated accordingly.
To edit atom number text:
1. Click the Text tool.

2. Do one of the following:
• Select the atom number indicator and type
the changes. 2. Click the appropriate Position option, and type
• Double-click the atom number indicator to a value:
change to the next character in the sequence.
To edit the atom number style: To position … Type a value for
Position …
• Select the atom number indicator, right click,
and then choose the appropriate option.
from the atom or bond by angle or by clock
center to the indicator
Positioning Atom Number center
Indicators
Atom number indicators are positioned from the atom or bond by offset—
automatically and move appropriately if a structure center to bottom left of horizontal and
is modified. You can reposition them by dragging indicator baseline vertical
them to the desired position or with the Indicator
Position dialog box. at specified coordinates absolute—
horizontal and
To reposition an indicator numerically: vertical
1. Right-click the indicator to move and choose
Position.

Numbering Atoms
Typing Non-Roman Text Creating a New Line and
ChemDraw uses standard methods for entering all Closing Text Boxes
types of text, including the Greek characters and
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other symbols commonly used in chemistry. The default way to create a new line in a caption text
box is to press Enter or Return. To close the text box,
To enter Greek characters: you click outside the text box or select another tool.
1. Click in a text box with the text tool. You can change the default and use Enter or Return
2. On the Style toolbar, choose Symbol from the to close the text box and press Alt+Enter or
font menu. Option+Return to create a new line by doing the
following:
3. Type the text. For example, an “a” is a
lower-case alpha, a “P” is a capital pi. 1. From the File menu, choose Preferences.
To enter additional non-Greek text in the same text 2. On the General tab, choose the appropriate
box: option:
• On the Style toolbar, choose the previously
selected font. To change the Select …
default for …
To enter a degree symbol:
Atom Label text Require Alt+Enter to
1. Click in a text box with the text tool.
Create New Line in Atom
2. Take the appropriate action: Labels.
If you’re Then … Caption text Require Alt+Enter to

using …
Create New Line in
Macintosh • Press Option+Shift+8. Captions.
Windows 1. Press Num Lock. 3. Click OK.
2. Press ALT.
3. Type 0, 1, 7, 6 using the

keypad.
4. Release ALT.
NOTE: The characters available differ in different

fonts. A list of all characters available in each font
how to type them is available in the KeyCaps menu
item of the Macintosh Apple menu or the Character
Map application in the Windows Accessories.

Creating a New Line and Closing Text Boxes
Using the Text Tool with For accurate correspondence between what you see
on the screen and what is printed:
the Lasso Tool • Deselect Use Bitmap Fonts When Available.
The Text tool used in conjunction with a selection This change affects all documents.
tool enables you to perform additional edits, such as
simultaneously changing several captions or atom
labels. For more information about selection tools,
see “Chapter 7: Advanced Drawing Techniques”
You can toggle between the Text tool and the Lasso
tool as follows:
• Press Ctrl+Alt+Tab or
Command+Option+Tab.
The text box is automatically selected when you
switch to the lasso tool.
To switch from the Lasso tool to the Text tool when
a caption or atom label is selected:
• Press Ctrl+Alt+Tab or
Command+Option+Tab.
The Text tool is selected and the text box is
opened for editing.
Using Bitmap Fonts

When Available
(Macintosh)
When text appears in a document on the screen, it
can appear using either a bitmap or a TrueType font.
To use bitmap fonts if they are available:

2. Select Use Bitmap Fonts When Available.
Text drawn using Bitmap fonts looks better and
appears more quickly than text drawn using
TrueType fonts. However, the size and position of
text drawn using Bitmap fonts change somewhat
when printed.

Using the Text Tool with the Lasso Tool
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Using Bitmap Fonts When Available (Macintosh)
Chapter 5: Drawing Orbitals, Symbols,
Arrows, Arcs, and Other Shapes
Overview The Orbital Tool Palette
ChemDraw provides the following tools that enable Use the Orbital tool palette to add orbitals to your
you to add chemical symbols and shapes to your chemical structures. You draw orbitals so that the
documents: node appears first. Depending on the orbital type,
available fill patterns are:
• Orbital tool—to draw orbitals
• Chemical Symbols tool—to draw charges, • Background color
radicals, and other symbols • Shaded
• Arrow tool—to draw arrows • Solid color
• Drawing Elements tool—to draw boxes, You can modify the fill patterns with the Color
circles, and lines menu.
• Brackets tool—to draw brackets, braces, Display the Info window to view the orbital’s length
parentheses, and daggers and angle relative to the X-axis while you draw it.
• Add Frames command—to enclose drawings You can constrain the length and angle of an orbital
in rectangles, brackets, parentheses, or braces by selecting Fixed Lengths and Fixed Angles on the
Object menu.
• Arc tool—to draw arcs
• Pen tool—to draw freehand shapes
NOTE: Orbitals are not normally part of the
You can use the tool palettes as extensions of the structure they are drawn near and are not selected
Main tools palette. Or you can tear them off and when you double-click a bond, atom, or atom label
place them anywhere on your screen. with a selection tool. To group the orbitals with the
structure, use the Group command from the Object
To display the Orbital tools, do one of the following: menu. For more information, see “Grouping
• From the View menu, point to Toolbars, and Objects” on page 104.
then choose the palette to display. The palette
stays open and you can drag it to where you
want.
• On the Main Tools palette, click the Orbital tool
and point to the orbital you want.
The following procedures use the Orbital tools from
the Main Tools palette.
ChemDraw 7 Chapter 5: Drawing Orbitals, Symbols, Arrows, Arcs, and Other Shapes • 81
The Orbital Tool Palette
s-orbitals Single Lobe Orbitals
The s-orbital tools are shown below: Single lobe orbitals are commonly used for
indicating a lone pair. The single lobe orbital tools
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are shown below:
To draw an s-orbital:
1. Hold down the mouse button over the Orbital

tool and drag to select the s-orbital tool To draw a single lobe orbital:
from the palette. 1. Hold down the mouse button over the Orbital
2. Point to an atom where the orbital will be tool and drag to select the single lobe
centered. orbital tool from the palette.
2. Point to an atom where the narrow end of the
orbital is to be attached.
3. Drag outward.
3. Drag from the narrow end of the lobe to its wide

end.
Sigma Orbitals
The σ-orbital tools are shown below:
To draw a σ-orbital:

tool and drag to select the σ-orbital tool
from the palette.
2. Point where the orbital will be centered.
3. Drag outward along the long axis of the orbital.
82 • Chapter 5: Drawing Orbitals, Symbols, Arrows, Arcs, and Other Shapes CambridgeSoft
p-orbitals
The p-orbital tools are shown below:
To draw a p-orbital: d-orbitals

1. Hold down the mouse button over the Orbital The d-orbital tools are shown below:
tool and drag to select the p-orbital tool
from the palette.
2. Point to an atom where the node of the orbital is
to be attached. To draw a d-orbital:

tool and drag to select the d-orbital tool
from the palette.
3. Drag from the orbital node to the wide end of
the filled lobe. to be attached.
3. Drag from the center of the orbital to the wide
end of a filled lobe.
Hybrid Orbitals
The hybrid-orbital tools are shown below:
dz2-orbitals
The dz orbital tools are shown below:
2-
To draw a hybrid orbital:

tool and drag to select the hybrid-orbital
tool from the palette. To draw a dz orbital:
2-

to be attached.
tool and drag to select the dz2-orbital tool
3. Drag from the orbital node to the wide end of from the palette.
the major lobe of the orbital.
2. Point to an atom where the node of the orbital
will be attached.
3. Drag from the center of the orbital to the wide To represent a hydrogen atom that is directed
end of a lobe. backwards into the plane away from you along the
Z-axis, use the H-dash symbol . You can draw
H-dots and H-dashes only by clicking atoms.
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To draw an H-dot or an H-dash:
1. Hold down the mouse button over the

Chemical Symbols tool and drag to select
the symbol from the palette.
The Chemical Symbols 2. Point to the atom.
Tool O
Use the Chemical Symbols tool to add
chemical symbols to your structure. When you click
O
the Chemical Symbols tool, the following palette
appears:
O
3. Click the atom.
If you click an atom and then click the Symbol tool, O

the charge, radical, or free site symbols are created
at a fixed distance from the atom they are associated
H-dot symbol
with. If you immediately drag the symbol to any O
position around an atom, it remains at that fixed Lone Pair

distance. You can, however, select a symbol
separately and move it anywhere or resize it. Use the lone pair symbol to indicate a lone
pair of electrons common in Lewis structure
When you attach a symbol to an atom, it remains at representations.
a fixed distance from the central character of the
atom label. To draw a lone pair:

H-dot and H-dash
To represent a hydrogen atom that is coming out of the lone pair from the palette.
the plane toward you along the Z-axis, use the H-dot
2. Point to the atom where you want the lone pair
symbol .
located and drag in the appropriate direction to
position it.
3. Release the mouse button.
The Chemical Symbols Tool
The lone pair is offset from the atom at a fixed 3. Drag from the charge portion of the symbol to
position. the radical portion of the symbol.
To quickly deposit a radical cation or radical anion
symbol in a horizontal orientation:
OH • Click to deposit the symbol.
Charge Symbols
To deposit a lone pair symbol in a horizontal
orientation: Use the charge symbols shown below to represent
charges on structures.
• Click in a document window.
To change the orientation:
• Click and drag the symbol to the desired
orientation.
To draw a charge and associate it with a structure:
Radical
Use the radical symbol to indicate a single Chemical Symbols tool and drag to
non-bonded electron. select the charge symbol from the palette.
To draw a radical symbol: 2. Click to the atom to which you want the charge
to correspond.
NH3
the radical from the palette.
O
2. Point to the atom where you want the radical H2N
symbol to appear. H OH
3. Click to draw the symbol.

The number of hydrogen atoms increases or
decreases as appropriate for the addition of the
Radical Cation and Radical charge.
Anion
NH3
Use the charge radical symbols to represent
O
radicals that are charged. H3N
H OH
To draw a radical cation or radical anion symbol:

the symbol from the palette.
2. Point to the atom where you want the symbol to
appear.
The Chemical Symbols Tool
Rotating a Symbol The Arrow Tool
With the exception of the charge and the radical
Use the Arrow tool to add arrows to show the
symbols, you can rotate the symbols by selecting conversion of reactants to products and to indicate
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and dragging the Rotation handle on the Selection

electron flow.
Rectangle. All symbols are rotated around the same
end from which they were originally drawn. For
NOTE: Use the Pen tool to make customized
example, the radical cation symbol is rotated and
arrows. For more information, see“The Pen Tool”
resized from the charge. The Info window shows the
on page 90.
angle that one of the ends of a symbol makes with
the X-axis as you rotate symbols.
Selecting an Arrow
To rotate a chemical symbol:
To select an arrow:
1. Select the chemical symbol with a selection
• Hold down the mouse button over the Arrow
tool.
tool and drag to select the arrow type from
2. Drag the Rotation handle on the chemical the palette.
symbol.
For more information about rotating and resizing,
see “Rotating Objects” on page 100.
Selecting Tools From a

Palette
Some tools have a palette containing different types
of that tool. A tool palette is indicated by a in the
lower right corner of the tool. When you choose a
tool type from the palette, it becomes the default
tool. To use a different tool type, select it. Drawing an Arrow
To select a tool and use its default tool type: To draw an arrow:
• Click the tool’s icon to select it.
1. Click the Arrow tool .
To choose a different tool type from the palette: 2. Point in the document where you want the
beginning of the arrow to appear.
1. Point to the tool’s icon and hold down the
mouse button. 3. Drag to where you want the arrowhead to be.
The palette appears.

2. Drag to select an tool type from the palette.
3. Release the mouse button over the object you
want to select.
Selecting Tools From a Palette
Editing an Arrow Some drawing element types are available with fill
patterns: hollow (no fill pattern), gray, and black.
To lengthen, shorten, or rotate an arrow: You can change the type of box, circle, or oval using
the Curves menu.
1. Click the Arrow tool .
2. Press Shift and point to the head of the arrow.
The Info window indicates the length and angle
relative to the X-axis while you use any of the
A highlight box appears over the head of the drawing element types.
arrow.
3. Drag the arrowhead. Selecting a Drawing Element
The arrow is resized and rotated relative to its end. To select a Drawing Element:
The Info window shows the change in length and the
• Hold down the mouse button over the Drawing
angle the arrowhead makes with the X-axis as you
Elements tool and drag to select the
drag.
element from the palette.
You can resize and rotate an arrow using a selection
tool by dragging the Resize or Rotation handle on
the Selection rectangle. The resize or rotation occurs
around the center of the Selection rectangle. The
Info window indicates the percentage enlarged or
reduced when you drag the Resize handle and the
number of degrees rotated when you drag the
Rotation handle.
You cannot change the aspect ratio of arrows. For Drawing Boxes
more information, see “Rotating Objects” on page
To draw a box:
100 and “Resizing Objects” on page 101.
1. Select one of the box tools shown below.
The Drawing Elements
Tool
The Drawing Elements tool provides shapes you can
add to your drawing. 2. Point where you want a corner of the box to be
located.
Drawing elements are not a part of the structure they
3. Drag from one corner of the box diagonally to
are drawn near. If you double-click on a bond, atom,
or atom label with a drawing tool, they are not the opposite corner.
selected. To group drawing elements with a
structure, use the Group command in the Object
menu. For more information, see “Grouping
Objects” on page 104.
The Drawing Elements Tool
Drawing Circles and Ovals To scale atom labels when resizing:
• Hold Control (Windows) or Command
To draw a circle or oval:
(Macintosh) while dragging to resize.
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1. Select one of the circle or oval tools shown

below. Distorting Circle and Ovals
You can distort circles and ovals (Shift+dragging the
Resize handle) to convert them into an equivalent
closed curve. You can distort gray shaded circles and
ovals to convert these objects to solid filled curves
2. Point where you want the center of the circle to with fill the same color as the curve. You can also
be located. distort boxes and closed brackets.
3. Drag outward from the center.
The remaining Drawing Element types cannot be
distorted. For more information, see “Rotating
Resizing or Rotating Drawing Objects” on page 100 and “Resizing Objects” on
Elements page 101.
A drawing element is resized or rotated from the
same point that it was originally drawn. For Drawing Lines
example, a shadowed box is resized from the corner Lines drawn with the line tool differ in two
where the plain edges meet. significant ways from bonds drawn with the bond
tools:
You cannot rotate Boxes, Brackets, or Daggers.
When a box or closed bracket is rotated along with • They are not included in chemical interpretation
objects within its borders, the area of the box or of the drawing
closed bracket increases to accommodate the • Lines that cross appear solid
rotation of the contained objects.
To draw using a line tool:
To resize or rotate a drawing element:
1. Select a line tool.
1. Select the Drawing Element tool.
2. Press Shift and point to an end or edge of a
drawing element.
A highlight box appears.
3. Drag the object to the new size or orientation.
The Info window shows the percentage
enlarged or reduced when you drag the Resize 2. Point where you want the line to start.
handle and the number of degrees the object 3. Drag from one end of the line to the other end.
rotates when you drag the Rotation handle.
The Drawing Elements Tool
The Brackets Tool Drawing Daggers
Brackets includes braces {}, brackets [], and To draw a dagger:
parentheses ().
1. Select a dagger tool.
To select a Bracket tool:
• Hold down the mouse button over the Brackets
tool and drag to select a tool from the
palette.
2. Point where you want the symbol to be located.
Drawing Single Brackets 3. Click to deposit the dagger.
A single bracket can be drawn in any orientation.
NOTE: The size of the dagger symbol is
To draw a single bracket: proportional to the Atom Label font size specified in
the Text Settings dialog box.
1. Select a single bracket tool.
Framing Objects
2. Point where you want the bracket to start. You can enclose your drawings or group structures
with a rectangle, brackets, parentheses, or braces.
3. Drag from one end of the bracket to the other
end. To enclose your object:
Drawing Paired Brackets 1. Select the drawing to enclose.
Paired brackets can only be placed in a vertical 2. On the Object menu, point to Add Frame, and
orientation. A rectangle or box defines their then choose the type of frame to add.
position. The frame you selected is inserted in your
drawing.
To draw a paired brackets:
1. Select a paired bracket tool.
2. Point where you want a corner of the bracket to

be located.
3. Drag from one corner of the box diagonally to
the opposite corner.
The Brackets Tool
The Arc Tool You can resize and rotate an arc by dragging the
Resize or Rotation handle on the Selection
Use the Arc tool to draw solid or dashed arcs of rectangle. The resize or rotation occurs around the
different angles: 90°, 120°, 180°, and 270°. center defined by the Selection rectangle. When you
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drag the Resize handle, the Info window indicates

the percentage enlarged or reduced. When you drag
the Rotation handle, the Info window indicates the
degree rotated. For more information, see “Rotating
Objects” on page 100 and “Resizing Objects” on
Drawing Arcs page 101.
Where you access the arc tool depends on which

level of ChemDraw you are using.
The Pen Tool
To draw an arc: Use the Pen tool to draw shapes that are not provided
in the Arrow, Orbital, or Drawing Elements palettes.
1. Do one of the following: For example, you can draw irregularly shaped
• In ChemDraw Std, hold down the mouse arrows, curves depicting graphs or reaction
button over the Drawing Elements tool coordinate diagrams, and other irregularly shaped
and drag to select the angle from the palette. solids.
• In ChemDraw Pro or Ultra, hold down the The Pen tool has two modes:
mouse button over the Arc tool and
drag to select the angle from the palette. • Drawing—Used to create shapes. The hand
2. Drag from the left edge of the arc to the
cursor appears with a “+” sign inside.
clockwise end of the arc in a document window. • Edit—Used to edit shapes. In drawing mode,
The Info window shows the length between the press Esc or select a tool to enter edit mode.
ends, and the angle the clockwise end makes Some examples of shapes that you can draw using
with the X-axis while you draw an arc. the Pen tool are shown below.
Editing Arcs
To resize or rotate an arc using the Arc tool:
1. Select the Arc tool.

2. Press Shift and point to the clockwise end of the
arc. Customized orbitals Unique arrows
A highlight box appears.
3. Drag the clockwise end of the arc.
The arc is resized and rotated relative to the end
from which it was drawn. The Info window
indicates the distance between the ends of the arc
and the angle the clockwise end makes with the
Curves and axes Geometric shapes
X-axis.
The Arc Tool
To toggle between a selection tool and the Pen tool Direction points appear on the direction line. Use the
do one of the following: direction points to adjust the curve from that point.
• Press Ctrl+Alt+Tab (Windows) or
Command+Tab (Macintosh). Direction Point
• Click a selection tool.
Direction Line
The last drawn curve and a selection tool are
selected.
Drawing Bézier Curves by

Dragging
A Bézier curve is a curve that is calculated to
Drawing Segments by Clicking
connect separate points into a smooth line.You can You can draw shapes with corners by clicking
draw Bézier curves with the Pen tool by clicking and repeatedly in an outline of the shape you want.
dragging repeatedly to create curved segments.
To draw segments:
To draw a Bezier Curve:
1. Select the Pen tool.
1. Select the Pen tool. 2. Point to where you want the beginning of the
2. Point to where you want the beginning of the curve to appear.
curve to appear and click. 3. Click to deposit an anchor point.
An anchor point appears.
3. Move the cursor to another position.
4. Hold down the mouse button and drag to create 4. Move the cursor and click again to add a second
an arc. point.
5. Continue until you have the curve you want.
Anchor Point
6. Press Esc or click another tool.

A direction line appears tangentially to the curve.
Use the direction line to control the “curviness” of NOTE: To place the fewest strategically placed
the segment. The slope of the direction line control points for obtaining the smoothest curve,
determines the slope of the curve. The length of the work in a magnified view.
direction line determines the height of the curve.
The Pen Tool
Editing a Curve 2. Drag the direction lines to create the shape you
want.
You can edit a curve by selecting it and manipulating
it with the direction lines.
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To select an existing curve:
1. Select the Pen tool.

2. Point at the center of the curve.
A highlight box appears when you are
positioned correctly. Alternatively, you can Ctrl-Shift-Click a direction
point and move it.
Adding a Segment
To extend an existing curve by adding a segment:
3. Click the highlight box to select the curve.
1. Select the Pen tool and click the existing curve
The direction lines appear.
you want to edit.
2. Point to the endpoint of a curve until the cursor
appears as a hand.
Changing the Shape of a Curve

3. Alt+click the endpoint.
Use the endpoints of the direction lines to increase
or decrease the breadth of the curve or change its The cursor appears as a hand with a “+” sign
direction. inside.
To change the shape of a curve:
1. Select the Pen tool and click the existing curve

you want to edit.
4. Click and drag to connect more segments to

your curve.
The Pen Tool
Deleting a Segment The following illustration shows the shape above
To delete a curve segment: with the Filled and Closed styles applied.
• In the edit mode of the Pen tool, Alt+Shift+click

the control point where you want to delete a
curve segment.
The cursor appears as the Eraser tool before you
click.
You can also delete entire curves using a selection Shaded Style
tool and the Eraser tool. You can apply shading to any curve, however the
shaded style works best with convex or slightly
Applying a Style to a Shape concave shapes. Shading may not appear as desired
in extremely concaved shapes.
All curves are drawn with the last curve style chosen
until you change the selections. Certain styles are The illustration below shows shapes with the Plain
mutually exclusive. For example, if you choose style applied.
Closed, you cannot also choose Arrow at Start.
You can use the Doubled style to represent cell
membranes. The lines are separated by twice the
Bold Width setting for the drawing. Doubled lines
cannot be dashed or include arrows.
To apply a style to a curve: The following illustration shows the above shapes
1. Select a curve using either the Pen tool or a with the Shaded style applied.
selection tool.
2. From the Curves menu, choose a style.
Filled and Closed Styles

The illustration below shows a shape with the Plain
style applied.
Plain Style
To remove all styles from a curve:
• With a curve selected, from the Curves menu,
choose Plain.
The Pen Tool
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The Pen Tool
Chapter 6: Manipulating Drawings
Overview Selecting Objects with the
The Lasso or Marquee tools enable you to select
Lasso Tool
objects to edit. You can select objects individually or Use the Lasso tool to make freehand selection of
as groups. You can then duplicate, move, resize, irregular areas.
rotate, or delete the selected objects.
To select objects using the Lasso tool:
Using a Selection Tool 1. Select the Lasso tool .
You can use the Lasso or the Marquee selection tool 2. Press the mouse button while the pointer is not
to select all objects. You use the Lasso to select over any object.
objects freehand and the Marquee to select 3. Drag around a portion of a chemical structure or
rectangular regions. other object.
You can set ChemDraw so that the last object drawn
to selected when you click the Lasso tool.
To set this option:

2. On the General tab, select Automatically
Select Recent Objects When Choosing
Lasso. As you drag, a line appears which defines the
Selection area. Bonds, structures, or other
When you click the Lasso tool, a selection
objects are selected only if they are entirely
rectangle appears around the last object drawn.
within this area. The end points of the Lasso are
automatically connected when you release the
mouse button.
Selecting Objects with the

Marquee Tool
Use the Marquee tool to select objects and structures
within a rectangular area.
To select objects using the Marquee tool:
1. Select the Marquee tool .

The pointer becomes a Marquee.
ChemDraw 7 Chapter 6: Manipulating Drawings • 95

Using a Selection Tool
2. Drag diagonally across the chemical structures Selecting Objects by Clicking
or other objects.
To select an object by clicking:
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1. Select the Lasso or the Marquee tool.

2. Point to an object in a document window.
As you drag, a rectangle appears which defines

the Selection area. Bonds and other objects are A highlight box appears over the selected
selected only if they are entirely within the object. If you point at a bond, the highlight box
rectangle. appears over the length of the bond.
You can use the Marquee to select several objects at 3. Click the object.
once if they can be surrounded by a rectangle.
Toggling Between Selection

Tools
The selected objects appear within the Selection
You can set one selection tool to behave like the Rectangle and the cursor changes to a hand.
other as follows:
• Click the Lasso or Marquee tool and NOTE: If the bond or other object is part of a group
press Alt or Option. you can select it as an individual object. For more
information, see “Grouping Objects” on page 104.
Toggling Between Other Tools
To quickly switch to a selection tool from another Setting the Highlight Box
tool: Tolerance
• Press Ctrl+Alt+Tab (Windows) or You determine the size of the highlight box and how
Command+Option+Tab (Macintosh). close you must get to activate an object by setting
A selection tool and the last drawn object are the Tolerance. The standard setting for the Tolerance
selected. is 5 pixels. At this setting, the highlight box appears
on bonds if the pointer is located 5 pixels or less
To switch from a selection tool to the last drawing
from any point on the bond.
tool used:
To set the Tolerance:
• Press Ctrl+Alt+Tab (Windows) or
Command+Tab (Macintosh). 1. From the File menu, choose Preferences.
2. Select or type the tolerance.
This change affects all documents.
96 • Chapter 6: Manipulating Drawings CambridgeSoft

Selecting Entire Structures NOTE: Objects may appear within the borders of
To select an entire chemical structure: the Selection rectangle, but not be selected. Only
objects that are shimmering are selected.
• Using a selection tool, double-click a bond or
atom within the structure.
Selecting All Objects
To select all objects within a document window:
Deselecting All Objects

The entire chemical structure is selected.
To deselect all selected objects, do one of the
following:
• Click in any empty area in a document window
that is outside the Selection rectangle.
• Press Esc.
If the chemical structure or other object is part of a • Select a different tool.
group, the entire group is selected. For more • Select another object without holding down
information, see “Grouping Objects” on page 104. Shift.
Making Multiple Selections The selected objects are deselected.
To make multiple selections or add more objects to Deleting Objects

the selection:
To delete selected objects, do one of the following:
• Press Shift and select the other objects.
• Press Delete.
You can add objects to the Selection by clicking,
• Press Backspace.
double-clicking, or by using the selection tools.
• From the Edit menu, choose Clear.
Removing Objects from the • Use the Eraser tool:
Selection a. Click the Eraser tool.
To remove an object from the selection: b. Click a single, double, or triple bond.
• Press Shift and select an object contained
within the Selection rectangle by clicking,
double-clicking, or with a selection tool.
The object is removed from the selection.

The bond order is reduced by one. To move selected objects a small distance using the
Arrow keys:
• Press an arrow key while an object is selected.
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The selected object moves 1 point in the

direction of the arrow.
Moving Objects To move in a larger increment, for example, to the
right:
To move an object:
• Press Alt+Right Arrow.
1. Select the object using a selection tool. The selected objects move 10 points in the
2. Point within the border of the Selection direction of the arrow. These small incremental
rectangle. movements are often useful for aligning
objects.
For more information about aligning objects, see
“Chapter 10: Working with Page Layout.”
Using the Clipboard

Use the Clipboard to remove the objects contained
3. Drag the object. in the Selection rectangle for later use. You can paste
the copy from the Clipboard to another position in
the same document, to another ChemDraw
document, or to a different type of document.
Cutting
To use the clipboard:
1. Select the object with a Selection tool.

To constrain the movement to the horizontal or
vertical direction: 2. From the Edit menu, choose Cut.
The object is transferred to the Clipboard and
• Shift+drag the selected objects. deleted from a document window.
Pasting
To paste a copy of the contents of the Clipboard into
a document window:
1. Click a Selection tool.

2. From the Edit menu, choose Paste.
For information about transferring ChemDraw
pictures to other types of documents see
“Autoscaling” on page 170.

Moving Atoms Duplicating Objects
You can move the atoms within a chemical structure To duplicate objects with a selection tool:
using a selection tool.
1. Click a selection tool.
To move a single atom:
2. Select the objects.
1. Point to an atom using a selection tool.
3. Ctrl or Option+drag to create a copy and

2. Drag the atom. position it.
A copy of the selected objects is moved to the

The bonds connected to the atom stretch. new position.
To move multiple atoms:
To duplicate the selected objects and constrain the
• Select only the bonds that have atoms on both positioning of the copy to the same position as the
ends that you want to move. original objects:
The unselected bonds that are attached to the 1. Select a selection tool.
selected atoms are stretched.
2. Select the objects.
NOTE: You can also move atoms using the bond 3. Shift+Ctrl+drag or Option+Command+drag
tool that was used to draw the atom. For more to create a copy and position it.
information, see “Moving Atoms” on page 60. To place a copy of an object on the Clipboard:
1. Select the objects using a selection tool.

2. From the Edit menu, choose Copy.
A copy of the object is placed on the Clipboard.
You can transfer the copy on the Clipboard by the
pasting it to the current document, another
ChemDraw document, or a different document type.

For information about transferring ChemDraw
pictures to other types of documents see NOTE: Captions and atom labels that contain
“Autoscaling” on page 170. multiple colors change to the foreground color when
rotated. However, all colors contained in the
captions are printed.
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Rotating Objects
To rotate objects: To rotate the selected objects a specified number of
degrees:
1. Select the objects to rotate using a selection
tool. 1. Do one of the following:
The Rotation handle is located on the upper • From the Object menu, choose Rotate.
right corner of the selection rectangle • Double-click the rotation handle.
The Rotate Objects dialog box appears.
Rotation handle
2. Drag the Rotation handle clockwise or

counterclockwise. 2. Type a whole number and click degrees CW
for a clockwise rotation or degrees CCW for
counterclockwise rotation.
3. If you want to rotate the atom label text, click
Rotate Atom Labels.
The screen and Info window indicate the 4. Click Rotate.

magnitude of the rotation around the center of Objects are rotated around the center of the
the Selection rectangle. Selection rectangle.
By default, atom labels do not rotate with the
To repeat the same rotation on any object in the
structure.
document window:
To rotate an atom label with a structure:
1. Immediately after performing a rotation, select
• Press Ctrl or Command while dragging the the other objects to rotate.
structure.
2. From the Edit menu, choose Repeat Rotate.
If a single atom is unselected when a structure is
rotated, the structure rotates around the unselected
atom.

Rotating Objects
Reflecting Objects To create a mirror image:
1. Draw a structure with defined stereochemistry,

Through Planes for example, wedged bonds.
You can reflect structures through planes 2. Make a copy of the structure.
perpendicular to the X-axis or Y-axis using a
a. Select the structure
selection tool. Used with duplicating, you can create
mirror images of chemical structures for b. Alt+Drag the structure.
representing racemic mixtures and other 3. While the structure is selected, from the Object
stereoisomers. menu, choose Flip Horizontal or Flip Vertical.
Flipping Objects Resizing Objects

To reflect an object through a plane perpendicular to You can resize objects by dragging the resize handle
the X-axis: of a selected object or by scaling. If all objects in the
document window are part of the selection, after you
1. Select the objects to reflect. resize, a message appears asking whether you want
to change the document settings for that document.
If you do so, all subsequent bonds, atom labels, and
captions are drawn using the new settings.
The Resize Handle

To resize an object or collection of objects:
2. From the Object menu, choose Flip Horizontal.
1. Select the objects to resize.
The resize handle is located in the lower right
corner of the selection rectangle.
Atom labels and captions do not flip along with the

object.
Resize handle
To reflect an object through a plane perpendicular to
the Y-axis:
2. Point to the Resize handle.
1. Select the objects to reflect.
The cursor becomes a double-headed arrow.
2. From the Object menu, choose Flip Vertical.
Creating Mirror Images

You can create mirror images from structures with
defined stereochemistry by duplicating the structure
and then flipping it.

Reflecting Objects Through Planes
3. Drag the resize handle until the object is the size To scale bonds so that the Fixed Length becomes the
you want. new median bond length:
The screen and Info window indicate the 1. Select the top option.
percentage enlarged or reduced.
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The fixed length presently in the Drawing

Settings dialog is shown in parentheses at the
end of the line for this button.
2. Click Scale.
To scale the bonds to a new fixed length that you

specify:
1. Select the middle option.

Scaling Objects 2. Type the new median bond length in the box to
the right of the button.
To resize objects with the Scale command:
3. The current median bond length for the
1. Select the objects to scale. selection is shown in the highlighted text box
when the dialog box initially appears.
4. Click Scale.
• From the Object menu, choose Scale.
• Double-click the Resize handle. To scale objects by a percentage:
The Scale Objects dialog box appears. 1. Click Scale by.

2. Type the percentage in the box to the right of the
button.
3. Click Scale.
This is the only available option when the selection
does not contain any atoms or bonds.
Distorting a Selection
In most cases, when you resize an object, the aspect
ratio of the object (the ratio of the height to width)
Use the first two options in the Scale Objects dialog
does not change. However, it is possible to change
box to scale all selected objects so that the median
the aspect ratio (distort) of certain objects including
selected bond has a specified length based on the chemical structures, circles, boxes, and ovals.
following scale factor:
To distort an object in the horizontal or vertical
new median bond length direction:
scale factor =
current median bond length
1. Select the object and Shift+drag the Resize
handle.
Shift modifies the resize operation so that you
can distort objects along the X-axis or Y-axis.
2. Drag the Resize handle in the desired direction.

Resizing Objects
Joining Objects 2. Select both chemical structures.
3. From the Object menu, choose Join.
Use the Join command in the Object menu to fuse
two chemical structures together. Once structures
are joined they can be easily selected by
double-clicking.
Objects to be joined must be positioned close
enough to be within the Tolerance setting specified
in the Preferences dialog box. For information about
setting the tolerance, see “Setting the Maximum NOTE: When you join two differently colored
Distance Tolerance” on page 103. bonds or atom labels, the color of the front object
becomes the color of the resulting joined object.
To join chemical structures along the length of a When you join two atoms that are labeled, the front
bond: atom label becomes the atom label of the resulting
atom. For more information about front to back
1. Position the structures to join so the bonds you
ordering of objects, see “Chapter 10: Working with
want to join are nearly overlapping (within Page Layout.”
tolerance).
2. Select the chemical structures to join.
Setting the Maximum Distance
Tolerance
The maximum distance required between two atoms
for joining to occur is controlled by the Tolerance
3. From the Object menu, choose Join. setting in the Preferences dialog box. For example,
The structures are joined. if the setting for the Tolerance is 5 pixels, then two
atoms are joined if they are within 5 pixels of each
other.
To change the Tolerance:

To join chemical structures at one atom to create a
spiro linkage: 2. On the General tab, select or type the
Tolerance.
1. Position the two chemical structures so two
atoms nearly overlap.
.

Joining Objects
Grouping Objects To select an individual object within a group:
• Click the object using a selection tool.
You can group a number of objects drawn
separately. Grouping creates an association between The object is selected, not the group.
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objects so they can be easily selected. You can select

all grouped objects can by double-clicking with a
selection tool. Objects within a group can be
selected individually and manipulated while still
remaining part of the group.
If you want to group objects so that the individual
objects in the group cannot be accessed, you can Ungrouping Objects
create an Integral group. When you select any object
in an Integral group, the entire group is selected. To To ungroup objects that are grouped:
access an individual object in an Integral group, you
1. Double-click a group using a selection tool.
must ungroup them.
2. From the Object menu, choose Ungroup.
Grouping does not lock the position or orientation of
objects. Grouped objects maintain their relative All the objects previously grouped become
positions when they are centered on the page, individual objects.
aligned or distributed.
Creating Integral Groups
Atoms and bonds making up a single chemical
To create a group in which individual objects cannot
structure are always grouped. If you group part of a
be accessed:
structure with other objects, the resulting group
contains the entire structure. If you add atoms or 1. Select the objects to group using a selection
bonds to a grouped structure, the new atoms and tool.
bonds are part of the group.
To group several objects: 3. With the group selected, right-click, point to
Group, and then click Integral.
1. Select the objects to group using a selection
tool. To ungroup objects in an Integral group:
1. Select the Integral group.
To select grouped objects:
2. Right-click, point to Group, and then deselect
• Double-click the grouped objects using a Integral.
selection tool.

Grouping Objects
Chapter 7:
Advanced Drawing Techniques
Overview You can use Generic Nicknames when drawing
query structures. For more information, see
ChemDraw provides advanced drawing features that “Generic Nicknames” on page 141.
allow you to:
Applying Nicknames
• Label functional groups with Nicknames
• Expand Nicknames To use a Nickname to label an atom:
• Add bonds to specific characters in atom labels 1. Create a structure. 2 3
• Create bonds whose attachment is not explicitly

defined
• Color objects
• Draw with Templates
Using Nicknames NHOH
2. Double-click an atom with a bond tool or click

Nicknames allow you to create short names for
an atom with the Text tool.
functional groups to use as an atom label or part of a
label. When an atom is labeled with a Nickname, the An atom label text box appears.
chemical significance of the expanded structure is
retained.
Commonly used Nicknames, such as Me, Et, and Ph
are provided with ChemDraw in the ChemDraw
Nicknames file located in your ChemDraw Items
folder. You can add to or delete from this list.
You can assign HotKeys to Nicknames. For
NHOH
example, in the Nicknames and HotKeys provided
with ChemDraw, the HotKey, “4” labels an atom
with “Ph” which is a Nickname representing a
phenyl group. For more information, see “Labeling
Atoms with HotKeys” on page 73.
ChemDraw 7 Chapter 7: Advanced Drawing Techniques • 105

Using Nicknames
3. Type a Nickname label such as “Et”. Defining Nicknames
Et To define your own Nicknames, you must have
ChemDraw Pro.
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You can define Nicknames with one or two

attachment points. The attachment points must be
single bonds.
To define a new Nickname:

NHOH
1. Create a structure containing the functional

To select a Nickname to apply to an atom using a
group you want to define as a Nickname.
HotKey:
2. Select the functional group.
1. Point to an atom.
You must indicate the connection point for the
2. Press the HotKey “=”. functional group by selecting the new fragment
The Choose Nickname dialog box appears. without the bond connected to the attachment point.
NOTE: If stereochemistry is indicated in a

structure that you are defining as a Nickname, the
stereochemistry is retained.
3. From the Structure menu, choose Define

Nickname.
The number of connection points is shown by
3. Select a Nickname from the list.
radicals in the Formula. You can have only one
4. Click OK. or two connection points in a nickname.
NOTE: Nicknames are tokens and do not flip

orientation when applied to the left side of a
structure when using Automatic Justification. For
example, in the absence of a defined Nickname, the
label “OTHP” appears as “PHTO” when applied
to the left side of a structure. However, since the
Nickname “THP” is defined, the label appears as 4. Type a short name for the Nickname.
“THPO”. For more information, see “Aligning
Text” on page 66. 5. Click OK.
The Nickname is defined.
If you use a Nickname that is the same as an element
name, a message indicates that the element is
replaced with the Nickname. For example, using Ac
106 • Chapter 7: Advanced Drawing Techniques CambridgeSoft

Using Nicknames
for an acetyl group replaces the element Actinium. In the example below, the sulfonamide group is
The Check Structure command recognizes the label attached to an unselected bond, which defines a
as an acetyl group rather than Actinium. bond from sulfur as the connection point for the
group. This allows you to define a Nickname.
ChemDraw provides the following default
Nickname/Element conflicts:
Symbol Nickname Element

Ac Acetyl Actinium
Am Amyl Americium
Np para- Neptunium You must leave a bond unselected for each
Nitrophenyl
connection point. You cannot define more than two
Pr Propyl Praeseodymium connection points or one attachment point on a
single atom in a nickname.
To remove the overriding Nicknames, choose List
Nicknames from the File menu and delete the
overriding Nickname definition. For more
information, see “Deleting Nicknames” on page
115.
Troubleshooting Nicknames
If the command Define Nicknames is dimmed,
check for the following:
• A connection point is not present
• More than 2 connection points are defined
• The connection point is not a single bond
In the example below, the functional group was
incorrect definitions correct definitions
drawn and the entire group selected. Because there
is no atom that indicates a connection point, you
cannot define a Nickname. The definition in the figure below was used for the
amino acid, Ala. The unselected bond at each end of
the structure indicates the connection points—
Nitrogen on the left and Carbon on the right.

Using Nicknames
You can draw a peptide chain by:
Contracting Labels
• Stringing Nicknames together.
You can compress an area of a structure and replace
it with a text label by using the Contract Label
H Gly Ala OH
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command. Contracted labels are similar to

• Stringing Nicknames together in an atom label Nicknames, but they are for one-time use only, in the
as long as there is a bond attached. current document.
H GlyAlaOH To create a contracted label:

• Stringing Nicknames together and not 1. Select the area of the structure to contract.
including bonds.
HGlyAlaOH
Viewing Nicknames
To view the list of defined Nicknames: 2. From the Structure menu, choose Contract
Label.
• From the File menu, choose List Nicknames.
The Contract Label dialog box appears.
The List Nickname dialog box appears.
3. Type a label for the contracted structure and

click OK.
To insert a nickname into your document:
The label replaces the selected portion of the
1. Select the nickname. structure.
2. Click Insert.
The nickname appears in your document. NOTE: If the area of the structure you contract
contains errors, an error dialog box appears. Click
Ignore to view any other errors. Click Ignore All to
Deleting Nicknames ignore all errors or Stop to end the contract process.
To delete a Nickname:
molecule
1. From the File menu, choose list Nicknames.
2. Select the Nickname that you want to delete
from the list.
3. Click Delete.
The Nickname is removed from the list.

Deleting Nicknames
Expanding Labels Using Multi-Center
If your structures contain defined nicknames, long Bonds
atom labels, or contracted labels, ChemDraw can
restore your structures to the fully expanded form. You can draw, with chemical significance,
polyhapto structures, for example, ferrocene
Contracted Form
((Cp)2Fe).
Ph CH2 CH2CHCH3
CH3
Expanded Form Fe
Creating a Multi-Center Bond

When you expand a label containing a divalent To create a multi-center attachment point:
nickname, for example HAlaOH, the first 1. Select the structure whose center you want
attachment is to the character left of the nickname defined as a multi-center attachment point.
(H). The second attachment is to the character right
2. From the Structure menu, choose Add
of the nickname (OH).
Multi-Center Attachment.
To expand atom labels: An asterisk is displayed with the fragment to
1. Select a selection tool.
show that it contains a multi-center node.
2. Select the label to expand or double-click the

structure to expand all possible labels.
The asterisk is not visible once a bond is drawn to it.

You can view the attachment point with a bond or
3. From the Structure menu, choose Expand selection tool. For more information, see “Viewing
Label. Attachment Points” on page 110.
Your structure is redrawn in its expanded form.

Expanding Labels
To draw a bond to a multi-center attachment point: Viewing Attachment Points
1. Click the Bond tool. After you draw a bond from the multi-center
2. Point to the asterisk and either click or drag to attachment point, the asterisk disappears. You can
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create a bond. verify the node is present with a bond or a selection

tool. This provides a way to check the definition of
a pre-existing multi-center attachment point.
To view a node with a selection tool:
• Select the selection tool and position the cursor
over to attachment point.
The attachment node is highlighted.
Fe
To make the bond in ferrocene appear that it is
coming from within the ring:
1. Double-click the wedged bond to make it come

To view a node with a bond tool:
forward.
• Select the bond tool and position the cursor over
2. Select the downward bond.
the attachment point.
3. Double-click on the cyclopentadienyl ring with
The attachment node and all the atoms it
a selection tool.
represents are highlighted.
The entire structure, including the single bond,
is selected. The Cp ring and the single bond are
associated as one structural unit because
ChemDraw recognizes the bond between them.
Fe
NOTE: For the best looking structure, you may to
draw a longer than normal bond. You can toggle the
Fixed Length command by pressing Ctrl +L
(Windows) or Command +L (Macintosh).

Using Multi-Center Bonds
Multi-Attached Labels 4. Click and drag from the atom label to draw your
bonds.
Multi-attached atom labels enable you to draw
chemical structures more efficiently by allowing
Ph CH2 CH2CHCH3
you to attach bonds anywhere along an atom label.
H2 You can determine the orientation of the resulting

C
bond by dragging. If you click to add a bond, there
CH2
are several preferential orientations for the resulting
NH bond as outlined below.
O
• Adding from the end of an atom label creates
CH3
bonds that are preferentially horizontal.
Expanded structure • Adding from the middle of an atom label
creates bonds that are preferentially vertical.
O
• Adding from the start of an atom label creates
CH2CH2NHCCH3 bonds that try to attain the chain angle setting in
the Drawing Settings dialog box. If that angle
cannot be attained, the next best angle is used.
Compact structure with multi-attached atom labels

Using Clean Up
Adding Bonds to an Atom Structure
Label The Clean Up Structure command is used to neaten
the appearance of molecules by regularizing bond
To add bonds to an atom labels: lengths and angles. Graphic objects such as arrows
and aromatic circles are not affected. Use Clean Up
1. Draw the structure and attach any necessary
Structure to redraw structures that you may have
atom label.
drawn freehand or to neaten structures that you may
2. Select a Bond tool. have imported from another application.
3. Position the cursor where you want to attach
Clean Up Structure may not create the best structure.
additional bonds.
Most structures have many “clean” forms, a
The selected part of the atom label is problem that is particularly noticeable with
highlighted. straight-chain alkanes.
If you select only part of a structure when you
choose Clean Up Structure, the other atoms and
bonds are not be affected.

Multi-Attached Labels
To use Clean Up Structure:
NOTE: For some compounds, the Clean Up
Structure command produces a structure that 1. Select the structure or part of the structure you
extends beyond the bounds of the page. To view the want to clean up with a selection tool.
entire structure, scale the structure or increase the
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size of the printed page. For more information, see

“Resizing Objects” on page 101 and “Setting up
Pages” on page 155.
General Rules for Clean Up Structure are:

2. From the Structure menu, choose Clean Up
• The Fixed Length setting in the Drawing Structure.
Settings dialog determines optimum bond
lengths.
• A given ring is redrawn only if all of its bonds
are selected.
• Multi-attached atom labels and variable NOTE: Clean Up Structure does not position
attachment points cannot be cleaned. molecules relative to other objects. Overlap may
• Multi-center bonds cannot be cleaned. occur.
• Structures are rotated so that as many bonds as

possible are directed at a multiple of 15 degrees. Using Variable
• Clean Up Structure preserves stereochemical
meaning rather than the precise identity of any
Attachment Positions
wedged or hashed bonds, as shown below. You can use the Add Variable Attachment command
to draw different positional isomers of a compound
using an abbreviated notation that retains chemical
significance.
OH
Cl
For example, you can draw explicitly the three
isomers of dibromobenzene shown below.
O
O Br Br Br
HO Cl
Br
Before After
Br
Br
o-Dibromobenzene m-Dibromobenzene p-Dibromobenzene

Using Variable Attachment Positions
You can express all three isomers as a single parent To verify that the node is present, do one of the
structure by using a variable attachment. following:
• Click a Selection tool and place the pointer on
Br
the attachment point.
The attachment node is highlighted.
Br
Br
To use variable attachment:
1. Draw the structural fragment to which you want

to assign a variable attachment node.
• Click a Bond tool and place the pointer on the
2. Select the fragment using a selection tool.
attachment point.
3. From the Structure menu, choose Add
The attachment node and the atoms it represents
Variable Attachment.
are highlighted.
An asterisk appears in the center of your
fragment. Br
Br
For more information about viewing the attachment

You can treat this attachment node as you would points, see “Viewing Attachment Points” on page
treat the end of a normal bond. 110.
1. Click a Bond tool.

Working with Color
2. Point to the asterisk and drag to draw a bond.
With the color capabilities of ChemDraw, you can
Br create full color presentations of your chemical
drawings to appear on your monitor, print on a color
printer, or create 35mm slides using a film printer.
Most computers can display any of 16 million
colors, but the number of colors that can appear at
NOTE: In the example above, Fixed Lengths was any one time may be limited by the particular
disabled using Shift, so a bond could be drawn monitor and display card installed in your computer.
extending further from the ring.
In ChemDraw, you can choose from a palette
consisting of a Background Color, a Foreground
After you draw a bond from the attachment
Color, and up to twenty additional colors for any
node, the asterisk disappears. given drawing. A palette is stored in every document

Working with Color
and Style Sheet/Stationery Pad. You can use Style Displaying the Color Palette
Sheets/Stationery Pads to create a series of
documents with the same color scheme. You can use the color palette to specify the color of
objects and text in the document within the active
Using color you can:
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window.
• Color atoms and bonds in a mostly
black-on-white drawing to highlight areas of To view the Color palette:
interest.
• Color parts of a structure in a reaction scheme Settings.
to indicate where starting materials end up in
2. Click the Colors tab.
the products of a complicated mechanism.
• Use colored boxes and circles to highlight
atoms or molecules.
• Create slides that are easier to view by using
light objects on a dark background.
Coloring Objects
Any object that you can select with a selection tool
can be colored. You can color individual bonds, part
or all of a chemical structure, or objects such as
boxes, curves, arrows, orbitals and reaction
mechanism symbols.
The border of objects that are shaded or filled, such
as white filled s-orbitals in the Orbitals palette, are
the same color as the shading or fill. The border of
objects that are hollow, such as circles and hollow
Use the Color tab to specify the following colors:
boxes in the Drawing Elements palette can be
colored, but the inside of the object cannot. • Background Color—Fills the background of
the current document in the active window.
To color an object:
• Foreground Color—Default color used when
1. Select the object in a document window with a you draw a new object.
selection tool.
• Other Colors—Colors available in the Color
2. Do one of the following: Menu for changing the color of individual
• From the Color menu, choose a color. objects. The colors are represented in the same
• In the Object Settings dialog box, on the order that they appear in the Color menu.
Drawing tab, click the Color button , and You can customize the Color menu. Colors can be
select the color from the menu that appears. added, or existing colors can be changed. Changing
• On the Style toolbar, click the Color button a color, for example Other #2, changes all objects
, and select the color from the menu that that are using the color.
appears.

Working with Color
NOTE: If you select an individual or grouped
Windows Color Settings
object that contains multiple colors, there is a check To change the palette of colors used in the current
mark next to each of the colors in the Color menu. document:
The purpose of the check marks is to alert you that a
change would affect more than one color. 1. From the File menu, choose Document
Settings.
Customizing the Color Palette The Document Settings dialog box appears.
You can add, remove, or change the default 2. Click the Colors tab.
foreground and background color and specify the
other colors available for coloring objects.
Changes made to the color palette affect the current
document only. You can save Color Palette settings
in a Style Sheet/Stationery Pad. For more
information, see “Saving Customized Settings as
Style Sheets or Stationery Pads” on page 10.
A summary of each of the options is described in the
following table.
Option Description
New Color Add a new color box and set its

color using the Color Picker or
Color Wheel dialog box.
3. Double-click the color to change.
The Color dialog box appears.
Remove Color Delete a color box that you have
selected in the left side of the
dialog box. Any objects using
the removed color are changed
to the Foreground color.
Set Color Change the color associated

with a color box that you have
selected in the left side of the
dialog box. Any objects using
the old color are changed to the
new color.

Working with Color
4. Click a color box in the Basic Colors or the Macintosh Color Settings
Custom Colors section.
A highlighted border appears around the color To change the palette of colors used in the current
you select. document:
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5. Click OK. 1. From the File menu, choose Document

The color is changed to the new color and added Settings.
to the Color menu. The Document Settings dialog box appears.
2. Click the Colors tab.
Adding or Customizing Windows
Colors
To add colors or create customized colors:
1. In the Color dialog box, click Define Custom

Colors.
Color Refiner box Luminosity box
3. Click New Color.

The Color Picker dialog box appears.
Color Wheel
2. Click a color in the Color Refiner box to set the

hue and saturation.
The pointer turns into a Crosshair when you
click. You can drag to a different region to
change the hue and saturation.
3. Click in the Luminosity box to set the
brightness of the color.
4. If necessary, change the hue, saturation,
4. Click a color to change to in the Color Wheel.
luminosity, and RGB components by typing the
values in the text boxes. For more information about the Macintosh
Color Wheel, refer to your System
5. Click Add to Custom Colors.
documentation.

Working with Color
5. Click OK. Templates and Color
The new color appears in the Colors tab in place The background and foreground colors used in a
of the original color and is added to the color template from the template pop-up palette are not
menu. used when the template is drawn in a document
window. However, any other colors used in the
Adding or Customizing Macintosh template are added to the color palette of the current
Colors document if they are not already present. This is part
To add a new color to the Color menu: of the autoscale feature. For more information, see
1. On the Color tab, click New Color or Set Other
Color. Saving Color Palette Settings
The Color Picker dialog box appears. You can save the Color Palette in a Style Sheet or
2. Click a color in the Color Wheel. Staionery Pad. The Color Palette is saved in addition
to other document settings such as Page Setup
3. If necessary, adjust the hue, saturation,
settings, Text settings, and Drawing settings.
brightness, and RGB components by typing the
values in
4. Click OK.
Drawing With Templates
Template documents are collections of structures
The new color is added to the list of Other
Colors. organized by structural type or functionality. A
structure in a Template document is named a
Removing Colors template. Use an existing template instead of
drawing the structure to shorten the time required to
To remove a color from the Color menu: create documents.
1. Click the color you want to remove. The Template documents distributed with
ChemDraw are stored in the ChemDraw Items
A highlight box appears around the color.
folder in the same folder as the ChemDraw
2. Click Remove Color. application.
The color disappears from the list of other
colors. Objects that were drawn in the removed NOTE: In ChemDraw Pro, you can define
color are changed to the Foreground color your own commonly used structures as templates.
Any Template documents in the ChemDraw Folder
are listed in the Windows menu (Macintosh) or Open
Special on the File menu (Windows).

The Templates Tool When you display the Template palette that was last
used, a blinking box appears around the currently
The Templates tool contains a palette from which selected template until you drag to another template.
you can select different types of structures or
Using Templates
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objects. The Templates tool has two levels:

• The first level displays the available Template When you draw with templates, the first bond drawn
documents. determines the position of the template in a
• The second level displays the templates within document window. All remaining bonds are drawn
each Template document. counterclockwise. The most nearly vertical bond on
the far-left atom is drawn first, from top to bottom.
If there are two equivalent bonds, the atoms that are
at a lower position are used to draw the first bond.
Drawing direction of template structures
Templates are automatically scaled to the document

settings of the current document in the active
window. For more information, see “Autoscaling”
on page 170.
NOTE: In ChemDraw Pro the pop-up menu
is segmented if any Template documents are open for After a template is drawn in a document window, the
editing. The upper segment contains Template structures or objects can be manipulated by standard
documents that are currently open for editing. drawing and editing methods.
Drawing a Template
Choosing a Template To draw a template:
To choose a template from the Template palette: • Click in a document window.
1. Hold down the mouse button over the The template is drawn centered around the
Templates tool . pointer in the orientation that it appears in the
A menu listing the Template documents Templates palette.
appears.
Fusing a Template With an Existing
2. Point to a Template document name.
Structure
A palette containing the available templates
appears. To draw a template and fuse it with an existing
structure:
3. Choose a template from the palette.
• Click an existing bond in a document window.

To deposit a template and create a spiro-linkage with
an existing structure:
• Click an existing atom in a document window. Pane
To draw a template in a document window and
control the size and orientation: Template Panel
• Drag from the beginning of the first bond in the
template to the end of the first bond. Resize
When you drag upwards the bulk of the Handle
template is drawn to the left, and when you drag
downwards the bulk of the template is drawn to Drawing Area
the right. Templates must contain at least one
bond in order to be drawn by the dragging
method.
Drawing with the Same Template

The templates you define are not limited to atoms
To draw another template of the same type: and bonds. Templates can contain any ChemDraw
objects such as captions, boxes, arcs, orbitals,
1. Click the Templates tool . arrows, reaction mechanism symbols, and curves.
2. Draw the template in a document window. The ChemDraw objects in Template documents can
be colored. However, the colors do not appear in the
Creating Templates Templates tool palette. You can paste pictures from
other applications into a Template pane. Pasted
and Template objects are scaled to the current Template document
Documents settings. For more information, see “Autoscaling”
on page 170.
In ChemDraw Pro you can create new templates and
add them to existing Template documents or create Creating Templates
new Template documents.
To create a new template:
To create a new Template document:
1. Select a Template pane by clicking it.
• On the File menu, point to Open Special, and
then choose New Templates. 2. Draw a structure or object in the drawing area of
A new and untitled Template window appears. The the Template window.
Template window is similar to a document window. The structure appears in the Template pane as
The Template window is divided into two halves by you draw. The tools in the Tools palette are used
a moveable, horizontal line: to draw a template in the drawing area of the
• Template panel—Top half of the window Template window exactly as they are used to
consists of individual panes where newly draw structures in the drawing area of a
created templates appear. document window.
• Drawing area—Bottom half of the window To select a different Template pane:
where you can draw new templates.
• Click another Template pane.

Creating Templates and Template Documents
When you select a Template pane, the contents Resizing Template Panes
of the pane appear in the drawing area.
To resize the Template panes in the Template panel:
• Drag the Resize handle on the lower right
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corner of the Template panel.

The percentage the block of Template panes is
enlarged or reduced appears in the Info window.
Template Panels
To increase the size of the Template panel:
Drag the Template dividing line.
To add a row of panes to the Template panel:
Select a Template pane.
From the Edit menu, choose Add Row Before or
As you define templates they become available for Add Row After.
use in your document without having to save the The new row is added before or after the Template
Template document. pane you selected.
To view the newly-defined Template: To add a column to the Template panel:
• Point at the Templates tool and hold Select a Template pane.
down the mouse button.
From the Edit menu, choose Add Column Before or
The name of the new Template document Add Column After.
appears in the menu.
The new column is added to the right or left of the
Template pane you selected.
Orientation of Templates
To delete a row of Template panes from the
To make the templates that you create as easy to
Template panel:
draw with as possible, it is recommended that you
orient your structures so that the bond that Select a Template pane in the row you want to
establishes the position of the template, for example, delete.
the bond used for fusing is left and vertical. The From the Edit menu, choose Delete Row.
most vertical left bond is drawn first. For examples,
To delete a column of Template panes from the
see “Using Templates” on page 118.
Template panel:
Select a Template pane in the column you want to
delete.
From the Edit menu, choose Delete Column.
The column is removed and all other columns
are moved to the left.

Saving Template Documents
To save a Template document and have it available
in the Template pop-up menu and the Window
menu:

Saving a Template document in the ChemDraw
Items folder makes it accessible in the Open
Special submenu and in the Templates tools
palette.
2. Type a name for the Template document and
click OK or Save.

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Chapter 8: Working With Structures
Overview Each label in the structure is checked.
sequentially. When a label is incorrect, a
You can perform the following functions on the message window appears.
structures you create:
• Check a structure to identify valence and label
errors
• View analysis information about a structure
• Display the chemical properties for a structure
• Assign Atom-to-Atom mapping
• In ChemDraw Pro, show stereochemistry and
calculate chemical properties
• In ChemDraw Ultra, assign structures to spectra
and calculate NMR Shift information
Checking Chemistry To continue checking the structure when a message

appears:
The Check Structure command identifies valence
and label errors in your structure. • Click Ignore.
To ignore all subsequent errors in a structure:
Check Structure
• Click Ignore All.
You can check the chemistry of a selected structure,
To stop checking a structure when a message
part of a structure, or caption (in Formula style) with
appears:
the Check Structure command. The structure is
checked using normal valences and elements, and • Click Stop.
defined Nicknames. The check ends and the atom that is causing the
To check the valences of all selected atoms in a problem is selected.
structure:
O
1. Select a structure, part of a structure, or caption

with a selection tool.
2. From the Structure menu, choose Check
Structure.
ChemDraw 7 Chapter 8: Working With Structures • 123

Checking Chemistry
Check Structure when Copying The Decimals setting applies to Exact Mass,
Molecular Weight, and m/e only.
to Clipboard or Exporting
The following table describes the analysis
To have ChemDraw perform a check structure properties.
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analysis on any structure copied to the Clipboard:

Property Description
2. Click the Check Structure When Copying to Formula The molecular formula showing the
Clipboard or Exporting check box. exact number of atoms of each
element in the molecule and charges,
radicals, and isotopes.
Viewing Analysis Exact Mass The exact molecular mass of the

structure, where atomic masses of
Information each atom are based on the most
The Analysis window displays the chemical common isotope for the element.
formula, exact mass, molecular weight, m/e, and
Molecular The average molecular mass of the
elemental analysis for the entire document, a
Weight structure, where atomic masses are
structure, part of a structure, or a caption in Formula
based on the average of all isotope
style. masses for the element.
To view analysis information:
m/e Mass/charge, where charge =1. The
• From the View menu, choose Show Analysis weights of the most common isotopes
Window. and a graphical representation of the
The Analysis window appears. isotopic abundance is shown.
The molecular weight shown takes
the isotopes for each atom and their
natural abundance into account.
Where there is more than one
abundant isotope, ChemDraw
computes multiple molecular
weights. Low abundance
combinations (whether because the
isotope is in low abundance or
because it includes many moderate-
abundance contributions) are not
Values for selected objects in the document window taken into account.
are shown. If nothing is selected in your document, NOTE: You cannot paste the graph
values for the entire document are shown. in a document.
You can have this window open as you draw in the Elemental The percent by weight of each
document. It shows the current values as you draw. Analysis element in the structure.
124 • Chapter 8: Working With Structures CambridgeSoft

Viewing Analysis Information
To paste information about a structure as a caption: Viewing the Chemical
1. Click the check boxes for the information that Properties Window
you want to paste.
To view predicted properties for a selected structure:
NOTE: You cannot paste the m/e graph.
1. Select the structure to analyze.
2. Click Paste. 2. From the View menu, choose Show Chemical
The information appears as a multiline caption Properties Window.
below the structure. You can edit this information The Chemical Properties window appears.
with the text tool.
Br
Cl Cl
C6H3BrCl2
Exact Mass: 223.88
Mol. Wt.: 225.90
m/e: 225.88 (100.0%), 223.88 (62.0%), 227.87
(44.9%), 226.88 (6.7%), 229.87 (6.2%), 224.88 (4.1%),
228.88 (3.0%)
C, 31.90; H, 1.34; Br, 35.37; Cl, 31.39
The following basic values are displayed.
Viewing Chemical Property Description

Properties Boiling Point The boiling point for the
ChemDraw Ultra, using an add-on, structure. Reported in Kelvin
CS ChemProp Pro, calculates predicted values for at 1 atm.
the physical and thermodynamic properties of a
selected structure of up to 100 atoms. You can view Melting Point The melting point for the
structure. Reported in Kelvin
the values in the Chemical Properties window.
at 1 atm.
The properties are calculated using the most reliable
methods for calculation for the given structure. Critical The temperature above which
Log P and MR values based on literature values Temperature the gas form of the structure
rather than a calculation are included in the report cannot be liquefied, no matter
file. the applied pressure (Tc).
Reported in Kelvin.

Viewing Chemical Properties
To paste the basic properties into your document:
• Click Paste.
Critical Pressure The minimum pressure that To create a report and view results for other
must be applied to liquefy the
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fragmentation methods including the Broto,

structure at the critical
Crippern, Viswanadhan, Joback, and Joback/Stein
temperature (Pc). Reported in
methods:
bars.
• Click Report.
Critical Volume The volume occupied at the
compound’s critical When you create a report, a detailed list of
temperature and pressure information used for performing the calculation is
(Vc). Reported in cm3/mol. shown in a text file. The list includes additional
properties and literature references used to perform
Gibbs Energy The Gibbs free energy, ∆G, for the calculation.
the structure. Reported in
kJ/mol at 1 atm and 298.15K.
Showing
LogP The logarithm of the partition
coefficient for
Stereochemistry
n-octanol/water. When the Show Stereochemistry option is selected,
ChemDraw calculates the absolute stereochemistry
MR The Molar Refraction index. for tetrahedral atoms and double bonds according to
the Cahn-Ingold-Prelog (CIP) priority rules. For
Henry’s Law The logarithm of Henry’s law more information about the CIP rules, see
constant (no units). “Stereochemistry” on page 197.
Heat of Formation The heat of formation, ∆Hf, Only tetrahedral and double-bond stereochemistry
for the structure. Reported in are supported, and only non-racemic
kJ/mol at 1 atm and 298.15K. stereochemistry is interpreted. Stereochemical
indicators for aromatic bonds are not shown.
CLogP The n-octanol/water partition
coefficient based on ChemDraw calculates and displays the following
established chemical stereochemical terms:
interactions.
• (R), (S)—Standard tetrahedral stereochemistry
CMR Molar refractivity calculated • (r), (s)—Tetrahedral stereochemistry
for a specific algorithm and determined by other stereochemical centers.
from fragment-based methods For example: cis-decalin and myo-inositol.
developed by the Medicinal
• (E), (Z)—Standard double-bond
Chemistry Project and
stereochemistry
BioByte.
The atom label settings determine the font style and
size of the terms.

Showing Stereochemistry
Stereochemistry Indicators Positioning Indicators
To show the stereochemistry of a structure: Stereochemistry indicators are positioned
automatically and move appropriately if a structure
• Select a structure, right-click, and then click is modified. You can reposition them by dragging
Show Stereochemistry. them to the desired position or with the Indicator
The stereocenters are marked as shown in the Position dialog box.
following example.
To reposition an indicator numerically:
1. With a selection tool, click the indicator to

move.
2. Right-click and choose Position.
(R)
The Position Indicator dialog box appears.
(R)
(R)
H
(S) (S)
(R) (S)
H H
(S)
HO (Z)
cholesterol
If you make changes to the drawing that affect the

stereochemistry, the stereochemistry is recalculated.
Hiding Indicators
3. Click the appropriate Position option, and type
To hide an individual indicator: a value:
1. Select the indicator to hide.

To Position … Type a value for
2. Right-click and choose Hide Indicator. the position by…
Removing Indicators from the atom or bond angle, in degrees

To delete an indicator: center to indicator center or
clock, in clock time
1. Click the indicator.
2. Click the eraser tool and then click the from the atom or bond offset, horizontal
indicator. center to bottom left of and vertical
indicator baseline
at specified coordinates absolute, horizontal

and vertical

Showing Stereochemistry
Converting Structures Spectrum-Structure
to 3D Assignments
ChemDraw Ultra enables you to assign structures to
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You can convert a two-dimensional structure drawn spectra.You can then display the structure associated
in ChemDraw to a three-dimensional structure. To with a specific peak by placing the pointer on that
use this feature, you must have CambridgeSoft peak.
Chem3D installed on your computer.
Assigning Structures to
To convert a structure to 3D:
Spectra
1. Select the structure to convert.
To assign structures to a spectrum:
2. From the Edit menu, choose Get 3D Model.
The 3D structure appears in the document 1. Open a spectral file.
window. 2. Draw the structure or structures you want to
assign to the spectrum.
To edit the 3D structure:
3. Select specific atoms and bonds in the structure.
1. Double-click the 3D structure. 4. Shift-click the peak or peaks to which you want
Chem3D opens. the structure assigned.
The selection rectangle surrounds the selected
2. Edit the structure and close Chem3D when you
objects.
are finished.
The edited structure appears in the ChemDraw
document window.
O
10 8 6 4 2 0
PPM
5. From the Structure menu, choose Make

Spectrum-Structure Assignment.
The selected atoms and bonds in the structure
are associated with the selected spectral peaks.

Converting Structures to 3D
Viewing Spectral Assignments NMR Shift
To view the spectral assignments: Information—
1. Click the Lasso or Marquee tool. ChemNMR Pro
2. Place the pointer over a peak.
ChemNMR Pro is a feature of ChemDraw Ultra
The assigned atoms or bonds are highlighted. only. ChemNMR Pro estimates and displays proton
and carbon-13 chemical shifts in ppm for a selected
molecule.
To view 1H or 13C NMR information:
1. Select the target chemical structure.
2. From the Structure menu, choose 1H-NMR

Shifts or 13C-NMR Shifts.
ChemNMR Pro redraws the molecule with the
estimated shifts and displays the information
Removing Spectral and line spectrum in a new window as shown
Assignments below.
To remove spectrum to structure assignments:
1. Click the Lasso or Marquee tool.

2. Select the objects from which to remove the
assignment.
3. From the Structure menu, choose Clear
Spectrum-Structure Assignment.

NMR Shift Information—ChemNMR Pro
ChemNMR H-1 Estimation
7.01 3.22
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7.02
H 6.39
7.02
7.18 H
6.58
Estimation Quality: blue = good, magenta = medium, red = rough
8 7 6 5 4 3 2 1 0
PPM
Protocol of the H-1 NMR Prediction:
Node Shift Base + Inc. Comment (ppm rel. to TMS)
CH 7.02 7.26 1-benzene

-0.12 1 -C=C
-0.12 1 -C
-0.05 1 -C=C
-0.19 1 -C
0.04 1 -C=C
-0.12 1 -C
-0.05 1 -C=C
-0.20 1 -C
CH2 3.22 1.37 methylene
1.22 1 alpha -1:C*C*C*C*C*C*1
0.63 1 alpha -C=C
H 6.58 5.25 1-ethylene
1.65 1 -1:C*C(R)*C*C*C*C*1 gem
-0.32 1 -C-1:C*C*C*C*C*C*1 trans
H 6.39 5.25 1-ethylene
0.09 1 -1:C*C(R)*C*C*C*C*1 trans
1.05 1 -C-1:C*C*C*C*C*C*1 gem

NMR Shift Information—ChemNMR Pro
Chapter 9:
Drawing Query Structures
What Are Query For more information on query properties, see
“Chapter 11: Sharing Information”, or consult the
Structures? documentation for your chemical database.
Using a query structure to specify properties for

NOTE: You can assign conflicting or nonsensical
atoms and bonds provides an efficient way to search
properties. For example, you can require that one of
chemical databases such as ChemFinder, DARC, the atoms in benzene is not part of any ring, which is
RS3, or ISIS/Base. You can use a query structure to inherently impossible. The results of the search
narrow or broaden your search. depend on the query system used, but usually no
For example, creating a query structure indicating a matches are found.
bond as either double or single might broaden your
search. Indicating atom properties where a particular
atom must have a charge of +3 might narrow your
Atom Properties
search. To assign properties to selected atoms in a structure:
Because ChemDraw is not a chemical database 1. Do one of the following:

application, the interpretation of query structures
• Select a single atom by clicking it with a
involves other programs. Not all databases support
selection tool.
the same query properties. If you use a query
structure containing properties not understood by a • Select multiple atoms by Shift+clicking the
given database, one of the following may happen: atoms.
• An error message appears
• Right-click, point to an atom, point to the
• The unsupported properties are ignored
property you want, and then click the
To use query structures for searching you may do appropriate option.
either of the following:
• From the Structure menu, choose
• Paste the query structure into a database search Properties. On the Atom Properties tab,
window and initiate a search. select the properties to associate with the
• Save the structure in an appropriate file format selected atoms and click OK.
and open the file in the database application. • Point to an atom and press the HotKey “/ ”.
In the Atom Properties dialog box, select the
properties to associate with the selected
atoms. Click OK.
ChemDraw 7 Chapter 9: Drawing Query Structures • 131

Atom Properties
Query indicators appear next to atoms that have Viewing Atom Property Values
associated atom properties.
Except for the three Substituents query properties,
X3 the characters indicate that a given property is
applied, but not the value of that property.
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T *2HS
To find the value of a query property setting:

C R
1. Select the atom.
S
The character that appears depends on which query
properties have been assigned. If more than one • Right-click, point to an atom, and then point
property is assigned, more than one character to the appropriate property.
appears adjacent to the atom. For more information, • From the Structure menu, choose
see “Query Indicators” on page 139. Properties and view the settings on the
The atom property indicators are shown in the Atom Properties tab.
following table.
Removing Atom Properties
Indicator Query Property To remove all atom properties from an atom:
* Substituents: Free Sites (followed 1. Select the atom.
by the number of free sites) 2. From the Structure menu, choose Properties.
U Substituents: Up to (followed by 3. Click Use Defaults.
the maximum number of The atom properties are removed and the
substituents) characters no longer appear.
X Substituents: Exactly (followed by To remove specific atom properties:
the number of substituents)
1. Select the atom.
H Implicit Hydrogens 2. Do one of the following:
R Ring Bond Count • Right-click, point to an atom, point to the

property you want, and then choose the
S Unsaturation appropriate option.
3. From the Structure menu, choose Properties
C Reaction Change
and then click the atom property to remove.
T Reaction Stereo
L Translation
NOTE: The Abnormal Valence atom property does

not provide a visual indicator.
132 • Chapter 9: Drawing Query Structures CambridgeSoft

Atom Properties
Atom Property Options The substituent options are described in the
following table.
The following topics describe the atom properties
you can associate with an atom.
Option Search Result
Substituents
The three Substituents properties specify the Unspecified Default. Search is determined by
the target database. Some
number of substituents that may be bonded to the
databases (including ISIS) find
selected atoms. In ChemDraw, a substituent is
compounds with any substitution
defined as a non-hydrogen atom connected by a at this atom and some databases
bond of any order. (including DARC) find only
For example, in the figure below, the carbonyl compounds with substitution
exactly as drawn.
carbon, indicated by the arrow in propanal, has a
substituent count of two: the alpha carbon and the
aldehyde oxygen. The double bond to the aldehyde Free Sites Finds compounds in which the
oxygen counts as only one substituent and hydrogen selected atoms may contain a
range of substituents up to the
atoms never count as substituents.
number specified plus the
number of bonds as drawn. A
value of zero finds a substituent
O count as drawn. You can also use
the Free Sites symbol in the
Chemical Symbols palette to
apply free sites. For more
H
information, see “Chapter 5:
The substituent count atom property allows you to Drawing Orbitals, Symbols,
specify the number of bonds to an atom in the target Arrows, Arcs, and Other Shapes”
structure. This includes bonds already drawn in the
query structure. Up to Finds compounds in which the
selected atoms may contain a
range of substituents up to the
number specified.
Exactly Finds compounds in which the

selected atoms contain the exact
number of substituents as
specified, up to 15 substituents.

Atom Properties
Implicit Hydrogens
The Implicit Hydrogens property specifies whether
additional, implicit hydrogen atoms may be attached
to the selected atoms. If implicit hydrogen atoms are As drawn Finds compounds in which the
Administrator
not allowed, all valences to that atom must be filled selected atoms reside in the same
by bonds to non-hydrogen atoms. The implicit type and number of rings as drawn.
hydrogen options are described in the following
table. Simple ring Finds compounds in which the
selected atoms is a member of only
Option Search Result one ring (the atom has two ring
bonds).
Allowed Default. Finds compounds

regardless of whether hydrogen Fusion Finds compounds in which the
atoms are attached to the selected selected atoms lies at ring fusions
atoms. (the atom has three ring bonds).
Not allowed Finds compounds with no Spiro or Finds compounds in which the
additional hydrogen atoms higher selected atoms is a member of a
attached to the selected atoms. spiro or higher linkage (the atom
has four or more ring bonds).
Ring Bond Count Unsaturation

The Ring Bond Count specifies the number of bonds
The Unsaturation property specifies whether a
attached to an atom that are part of rings of any size.
multiple bond is attached to the selected atoms. The
For simple cases, this also specifies the maximum
unsaturation options are described in the following
number of rings in which an atom can reside. The
table.
ring bond count options are described in the
following table.
Option Search Result Unspecified Default. Finds compounds

regardless of whether a multiple
Any Default. Finds compounds in bond is attached to the selected
which the selected atoms can be a atoms.
member of any type of ring, or a
member of no ring at all. Must be absent Finds compounds that do not
have a multiple bond attached to
No ring bonds Finds compounds in which the the selected atoms.
selected atoms are acyclic.
Must be Finds compounds that have at
present least one multiple bond (double,
triple or aromatic) attached to the
selected atoms.

Atom Properties
Reaction Change Translation
The Reaction Change property specifies whether a The Translation property specifies what is required
change occurs at selected atoms after a reaction. to match in the structure query and possible database
This property is only meaningful when searching a hits in a Markush DARC query.
database containing chemical reactions. The
reaction change options are described in the The translation options are described in the
following table. following table:
Option Search Result Option Definition

May be Default. Finds all reactions
anything regardless of any change to Equal Default. Matches specific to specific
selected atoms after a reaction. or generic to generic terms.
Must be as Finds all reactions that are Broad Translates specific query atoms to
specified changed at the selected atoms corresponding superatoms in the
exactly as specified by the database.
reaction center property in the
Atom Properties dialog box.
Narrow Translates query superatoms to
corresponding specific atoms or
Reaction Stereo groups in the database.
The Reaction Stereo property specifies that the
selected atoms are stereocenters in a reaction. This Any Translates generic or specific terms
property is only meaningful when searching a to any term.
database containing chemical reactions.
For more information, refer to the Markush DARC
The reaction stereo options are described in the
following table. User Manual.
Any Default. Finds all compounds

regardless of the stereochemistry
at the selected atoms.
Inversion Finds compounds in which the

selected atoms have an inverted
stereo configuration after a
reaction.
Retention Finds compounds whose selected

atoms have an unchanged stereo
configuration after a reaction.

Atom Properties
Abnormal Valence Bond Properties
The Abnormal Valence property specifies whether
selected atoms can have a valence other than To define bond properties of selected bonds in a
structure:
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normal. “Normal” valences for each element are

defined in the Isotopes Table file in the ChemDraw 1. Do one of the following:
Items folder. • Select a bond using a selection tool.
The Abnormal Valence options are described in the • Shift+click to select multiple bonds.
following table.
• Right-click, point to Bond, point to the
property you want, and then choose the
appropriate option.
Not allowed Default. Finds compounds where
the selected atoms only have • From the Structure menu, choose
valences that are normal for that Properties. On the Bond Properties tab,
element. If necessary, hydrogen select the bond properties to associate with
atoms are automatically added to or the selected bonds from the drop-down lists.
removed from the atom before Click OK.
transferring it to the chemical
• Point to an bond and press the HotKey “/ ”.
database. If the Check Structure
In the Bond Properties dialog box, select the
When Copying to Clipboard or
Exporting preference is turned on, properties to associate with the selected
an error message warns of abnormal atoms. Click OK.
valences. Query indicators appear next to bonds that have
associated bond properties.
Allowed Finds compounds with the specific
valence drawn. S/D Any S/D
Rxn S/D
NOTE: If Abnormal Valence is Allowed, any

Any S/D
Invalid Valence messages for those atoms are
ignored automatically by the Check Structure one bond many bonds
command.
The characters that appears depends on which query
properties have been assigned. If more than one
property is assigned, more than one descriptor
appears adjacent to the atoms. For more
information, see “Query Indicators” on page 139.

Bond Properties
The indicators are described in the following table. Removing Bond Properties
Indicator Bond Query Property To remove all bond properties from selected bonds:
1. Select the bonds.

Any Bond Type: Any
2. From the Structure menu, choose Properties.
3. Click Use Defaults.
S/D Bond Type: Single/Double
The bond properties are removed and the
D/A Bond Type: Double/Aromatic indicators are no longer adjacent to the selected
bonds.
S/A Bond Type: Single/Aromatic To remove specific bond properties:
Rng Topology: Ring 1. Select the bond.

Chn Topology: Chain • Right-click, point to the appropriate
property, and then click the property to
Rxn Reaction Center remove.
• From the Structure menu, choose
Viewing Bond Property Values Properties, and then click the bond property
to remove.
The descriptor for the Reaction Center query
property indicates that the property is applied, but Bond Property Options
not the value of the property.
The following are the atom properties that you can
To find the value of a query bond property setting: associate with an atom:
1. Select the bond. Bond Types

2. Do one of the following: This property specifies the bond type of the selected
• Right-click, point to the bond, and then point bonds. The default bond type corresponds to the
to the appropriate property. current type of the bond (single, double, etc.) as
drawn.
• From the Structure menu, choose Bond
Properties, and view the settings of the
drop-down list boxes.

Bond Properties
The Bond Type options are described in the
following table. NOTE: Not all bond types are supported in all file
formats. When an unsupported bond type is saved to
a given file format, it is converted to the closest
Option Search Result equivalent that is supported.
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Single (all) and Finds compounds with the bond

Dative type you select for the selected Topology
bonds. The Topology property specifies the ring
environment of the selected bonds.
Double or Finds compounds whose selected
Double Bold bonds are double. The Topology options are described in the following
table.
Double Either Finds compounds whose selected
bonds are double bonds and have Option Search Result
either cis/trans stereochemical
configuration. Unspecified Default. Finds compounds
regardless of environment.
Aromatic Finds compounds whose selected
bonds are aromatic. Ring Finds compounds where the
selected bonds are part of a
Tautomeric Finds compounds whose selected ring.
bonds are tautomeric.
Chain Finds compounds where the
selected bonds are part of a
Triple Finds compounds whose selected
chain (and are specifically not
bonds are triple.
part of a ring).
Quadruple Finds compounds whose selected
bonds are quadruple.
Any Finds compounds regardless of

the bond type of the selected
bonds.
S/D Finds compounds whose selected

bonds are single or double.
D/A Finds compounds whose selected

bonds are double or aromatic.
S/A Finds compounds whose selected

bonds are single or aromatic.

Bond Properties
Reaction Center Query Tools Palette
The Reaction Center property specifies how the
selected bonds are affected in a reaction. This ChemDraw provides Query tools to enable you to
property is only meaningful when searching a draw query structures.
database containing chemical reactions. To display the Query tools:
The Reaction Center options are described in the • Click .
following table The Query tools palette appears. The Windows
tools are shown below.
Free Site
Unspecified Default. Finds compounds
regardless of whether the selected Reaction
Atom-Atom Absolute
bonds are affected by the reaction. Map Stereochemistry
Relative
Center Finds compounds where the Alternative Stereochemistry
Group
selected bonds are affected by a Racemic
reaction, but the type of change is Stereochemistry
Attachment Point
unspecified.
Query Indicators
Make/Break Finds compounds where the
selected bonds are either broken or You can display small characters to indicate query
created in a reaction. properties you assign to atoms and bonds.
Change Finds compounds where the bond Viewing Query Indicators

order of the selected bonds
To display query indicators for a structure:
changes in a reaction.
• Select a structure to which query indicators are
Make&Chang Finds compounds where the assigned, right-click, point to Atom or Bond,
e selected bonds are formed, broken, and then click Show Query Indicator.
or undergo a change in bond order.
To display query indicators for individual atoms or
Not Center Finds compounds where the bonds:
selected bonds are not part of the
• Select the atom or bond, right-click, and choose
reaction center.
Show Query Indicator.
Not Modified Finds compounds where the
selected bond’s orders do not Hiding Query Indicators
change, but which may or may not
To hide an individual indicator:
be part of the reaction center.
1. Select the indicator to hide.
Unmapped Finds all compounds.
2. Right-click and choose Hide Indicator.

Query Tools Palette
Removing Query Indicators Drawing
To delete a query indicator:
Stereochemical
1. Click the indictor.
Symbols
Administrator
2. Click the eraser tool and then click the

indicator.
ChemDraw provides three types of stereochemical
Positioning Query Indicators flags that indicate that the molecule with which they
Query indicators are positioned automatically and are associated represents one of the following:
move appropriately if a structure is modified. You • Racemic—A racemic mixture.
can reposition them by dragging them to the desired
position or with the Indicator Position dialog box. • Absolute—A pure enantiomer of known
configuration.
To reposition an indicator numerically:
• Relative—A pure enantiomer of unknown
1. With a selection tool, click the indicator to configuration.
move.
The font and size for stereochemical flags is
2. Right-click and choose Position. determined by the default Atom Label size for the
The Position Indicator dialog box appears. document.
To draw a stereochemical flag:
1. On the Query tools palette, click the tool for the

flag you want to use.
2. Position the pointer next to the structure to
which you want to assign the flag.
3. Click to deposit the symbol.
Drawing Free Sites

3. Click the appropriate Position option, and type
a value: Use the Free Sites tool to increment or decrement
the number of free sites in a query structure.
To Position … Type a value for… To increment the number of Free Sites:
from the atom or bond angle, degrees or 1. On the Query tools palette, click the Free Site
center to indicator center clock, o’clock tool .
2. Position the pointer over the atom to which you
from the atom or bond offset, horizontal and want to apply free sites.
center to bottom left of vertical
indicator baseline 3. Click to add the symbol.
4. Continue to click the atom to increment the free
at specified coordinates absolute, horizontal site number.
and vertical

Drawing Stereochemical Symbols
To decrement the number of free sites:
• Hold the Alt key while clicking the atom.
You can also change the free sites by using the Atom
Properties dialog box or the shortcut menu. For
more information see “Atom Properties” on page
131.
Generic Nicknames
Generic nicknames represent a class of elements or
structural moieties. For example:
• “M” can be a generic nickname for all metals
• “X” can represent halides
• “Ary” can represent an aromatic substructure To label an atomic position with a generic nickname,
If you are using a query system that recognizes use the same procedures as labeling an atom:
generic nicknames, you can use these nicknames in 1. Do one of the following:
your ChemDraw query structure.
• Open a text box on an atom position by
You can assign Generic nicknames, like other clicking with the Text tool.
nicknames, to HotKeys. For information on • Double-click on an atom position with a
assigning a HotKey to a nickname, see “Chapter 8:
Bond tool.
Working With Structures”
2. Type the generic nickname.
You cannot define the meaning of a generic
3. Press Return or click outside the text box.
nickname in ChemDraw because generic nicknames
represent multiple (and perhaps an infinite number
X
of) substituents. Generic nicknames have meaning
only in the context of the search system you are
using.
The generic nicknames recognized as chemically
meaningful to ChemDraw are listed in Generic
Nicknames file in the ChemDraw Items folder. For
definitions of the nicknames, see the “Nickname NOTE: If you perform Check Structure on a
Definitions” Help topic. structure with a generic nickname, a message is
To edit the generic nickname files: displayed because the structure contains variable
substituents. If you ignore this message, the generic
• Open the Generic Nicknames file in a text nicknames are ignored and ChemDraw reports the
editor and make your changes. chemical formula, mass, and so on as if the atom
label containing the generic nickname were not
See the provided Generic Nicknames file for
selected.
examples of the correct format as follows.

Generic Nicknames
Element Lists The following example shows a query structure
created to find compounds matching the following
You can define your search query more concisely criteria:
with the element list. By labeling an atom position a. Non-oxygen chalcogenide bonded to another
Administrator
as a list of elements you specify that one of these atom.

elements must match in the structure for which you b. Not necessarily carbon (a generic nickname).
are searching. The elements in the element list must
c. The bond type between the chalcogenide and
be separated by commas. A space after each comma the other atom to be a single or double bond.
and brackets are optional. An example of an element
list is shown below. (b) (a)
[S,Se,Te]
A [S, Se, Te]
S/D
NOTE: An element list may contain only atomic

symbols, plus D (deuterium) and T (tritium).
(c)
To create an element list: The “A” label indicates that the atom may match any
atom except hydrogen. The mark near the bond
1. Open an atom label text box. indicates that the bond has special properties. The
2. Type an open bracket ([) followed by a list of
bond type specified in the Bond Properties dialog
box must be single or double, S/D. The “[S,Se,Te]”
elements separated by commas (Cl, Br, I),
specifies that one of these elements must match in
followed by a close bracket (]).
the target structures.
Element Not-Lists
The element not-list specifies that the elements in
the list match must not match in the structure for
which you are searching. Commas must separate the
elements in the element not-list. A space after each
comma and brackets are optional.
3. Close the text box.
The word NOT must be in all-caps and must be
[Br, I, Cl] followed by a space. Alternatively, the word NOT
may be replaced with a minus sign.
For example:
NO T F,Cl,B r,I [- C, O, N]
NOT[F,Cl,Br,I] [NOT C,O,N]
NOTE: An element not-list may contain only

atomic elements, plus D (deuterium) and T (tritium).

Element Lists
To create an element not-list:
Representing Polymers
1. Open an atom label text box.
and Other Repeating
2. Type an open bracket, the word NOT, and a
space (“[NOT”) followed by a list of elements Units
separated by commas (“Cl, Br, I”), followed by
a close bracket (“]”). Brackets, parentheses, and braces enclose structures
or structural fragments that are to be repeated a
Link Nodes number of times. ChemDraw’s bracket properties
allow you to specify the context and orientation of
You can specify a variable-length chain or ring by the repeating units.
indicating that one of the atoms can be repeated
some number of times using link nodes. To enclose structures with brackets:
Link nodes must have exactly two connecting 1. Click the Bracket tool and choose one of
bonds. The atom label must conform to the the double bracket tools.
following conditions: 2. Click+drag across the structure to draw the
• No more than a single element symbol or a brackets.
generic nickname 3. Do one of the following:
• The last part of the label in the form: number • Right-click or Control-click and choose the
hyphen number, with the number and hyphen appropriate bracket properties from the menu
subscripted that appears.
• Parentheses or braces may be used instead of The bracket properties are described in the
brackets following sections.
• Brackets can be omitted if not needed for
Setting Bracket Properties
clarity, for example with O1-3
You can change the properties of brackets by the
To create a link node: context menus or Bracket Properties dialog box.
1. Open an atom label text box. To use the Bracket Properties dialog box:
2. Type in the following format:
1. Select the structure
[CH2]4-7 2. From the Structure menu, choose Bracket

Properties.

Link Nodes
The following dialog box appears. Bracket Usage
Representations of polymers are either
structure-based or source-based. The type of bracket
Administrator
you use depends on which type of representation

you need. For references, see “Polymer
Representations” on page 198.
Structure-based Polymer
Representations
Structure-based polymer representations enclose
The Flip Type option appears only for brackets with only a portion or a structure within brackets. One or
exactly two crossing bonds, and is disabled in other more bonds cross each of the enclosing brackets.
cases. The crossing bonds “match up”, making the
You can customize the text that appears to the polymer structure more explicit.
bottom right of the bracket for the bracket types You create a structure-based polymer representation
shown below: by enclosing a portion of a structure in brackets with
• Component C—the Component Order must be a bracket type of SRU (n). The subscript “n” is
a non-negative integer, and is displayed as the recommended by IUPAC to notate structure-based
letter “c” followed by that integer (or “c” alone representations of unknown size, but you can edit
if an order of zero is specified). the text using the text tool.
A structure-based representation of
poly(vinyl chloride) is shown below.
Cl
• Multiple Group (#)—the Repeat Count must be
a positive integer.
*
*
n
You can also use the Bracket Usage types

• SRU (n)—the SRU label can be any text. “Crosslink (xl)”, “Graft (grf)”, and “Modification
(mod)” to represent specific types of repeating units
in a structure-based representation, but they are
rarely encountered and using them is discouraged.
You can also edit he text for these Bracket Usage
types directly in the document using the Text tool.
You cannot edit he text displayed for the other
Bracket Usage types.

Representing Polymers and Other Repeating Units
Source-based Polymer represent different specific types of copolymers in a
Representations source-based representation, but they are rarely used
and their use is discouraged.
Source-based polymer representations enclose an
entire discrete chemical substance in brackets. The The bracket type, “Mixture, unordered (mix)” is not
mode of polymerization may be obvious from for polymers, but to represent a collection of
context, or it might be unknown. Source-based substances that may all be present, but not
representations are useful when describing necessarily in known amounts. Bracket type
processes where the starting materials are known, “Component (c)” indicates individual mixture
but the exact structure of the reaction product is not. elements.
You can create a source-based representation by An example is shown below.
enclosing a structure in “Monomer (mon)” brackets.
A source-based representation of poly(vinyl COOH
chloride) is shown below. O O
COOH
c c
Cl
COOH
O O
COOH
c c
mon
Bracket type “Mixture, ordered (f)” is primarily
You can use “Mer (mer)” brackets for components used to describe manufacturing processes, where the
of a copolymer where those individual components ordering of components is a critical part of the
are known not to repeat themselves or alternate with process (and where a different ordering might
the other components. An example is shown below. produce a different final product. As with Unordered
Mixtures, individual elements of an ordered mixture
should be surrounded by brackets with a bracket
O usage of “Component (c)”. Unlike with Unordered
Mixtures, however, components of Ordered
OH OH
HO
Mixtures must represent their ordering. You can do
HO mer
this by editing the “c” label with the text tool to
include a number (“c1”, “c2”, and so on.)
O mer
You use the bracket type, “Multiple Group (#)” to

co
indicate that the enclosed items are repeated a

Copolymers represent substances with more than specific known number of times. Multiple Group
one repeating unit. In general, you can use bracket brackets may enclose entire structures, or may
type “Component (co)”. You can also use enclose a portion of the structures only. You can edit
“Copolymer, alternating (alt)”, “Copolymer, the numeric repeat count with the text tool.
random (ran)”, and “Copolymer, block (blk)” to

Examples follow.
O O *
* * = * O O
hh
O O *
O * * = * O O
Administrator
OH eu
O O
HO * * = mixture of the above, or unknown repeat pattern
Na+ Na+
-O O-
2
Flip Type
For ladder-type polymers (those polymers with two
O
H H
connecting bonds on each side), there is a potential
3 ambiguity in the order of the connections. You can
assign the Flip Type property to resolve that
ambiguity. This property is appropriate only for
O
brackets with exactly two crossing bonds, and is
disabled in other cases.
O 13
14
Because of its prevalence the No Flip type does not
Because Multiple Group brackets represent a
receive any special annotation.
specific repeat count (unlike the unknown repeat
count of the other bracket types), it is possible to H H H H
H
* N * N N N N *
calculate accurate molecular weights (and related *
=
data) for such structures. That data is displayed in
*
the Analysis window as with any other structure. * * *
.
flip
H H H
* N * N N *
*
=
*
* * N N *
H H
Exporting Bracket Properties

Bracket properties are saved in cdx files. They can
be transferred to ISIS/Draw as skc, tgf, or mol files,
Repeat Pattern or from the clipboard. Some constraints are imposed
For simple linear polymers, the repeating units may by ISIS/Draw. For example, the SRU label is
connect head-to-tail or head-to-head (or their repeat truncated to its first character. Bracket properties are
pattern might be a mixture or unknown). You can not saved to any other file format. They are not
also assign this property to brackets. currently recognized by ChemFinder or by the
ChemOffice WebServer.
Because of its prevalence, the Head-to-Tail type is
assumed to be the default Repeat Pattern, and does
not receive any special annotation on the brackets,
as shown below.

Alternative Groups The Alternative Group Title box appears.
You can create a search query that contains variable

functional groups or substructures. Instead of
submitting multiple queries on structures that share
a common substructure, you can submit a single
query with the parent structure. The parent structure
can have attachment points to a list of alternative
groups that you can define.
Alternative groups, sometimes called R-Groups,
3. Type a title, such as R1, in the Alternative
G-Groups, or Generic Groups, are shown below.
Group Title box.
F
G
NH2
NH2
OH 4. Draw the substructure fragments in the
OH Alternative Group box.
Defining an Alternative Group

In ChemDraw Pro, you can create alternative group
definitions (R, G, etc.) that represent a set of
substituents, any one of which will match the query.
To define an alternative group:
1. Click the Alternative Group tool .

2. Click and drag to create an area large enough to
draw the alternative groups.

Alternative Groups
Defining Attachment Points R1
1 R1
Specify where the fragments should bond to the
parent structure at the alternative group label:
Administrator
1 NH2
1. Click the Attachment Point tool .
1 OH
• Click a substructure fragment where you
want to place the attachment point.
1 F
• Point to a substructure fragment where you
want to place the attachment point and press
the HotKey “.”. The number displayed in the attachment point
An attachment point symbol appears. symbol is the attachment rank order. See the
example in “Multiple Attachment Points” on page
148.
Attachment
point symbol Multiple Attachment Points
If you have well-defined multiple attachment points
on your structure fragments, you can perform
searches for specific materials. This type of search is
especially useful for searching for conformationally
similar structures.
3. Repeat step 2 for all fragments.
For example, you want to find the two compounds
below:
NH2 NH2
O
However, you are not interested in the two

When you create a parent compound that contains compounds below:
an alternative group you defined, an attachment
point symbol appears next to the label. The
attachment point number matches that found in the
definition.
NH2 NH2
O

Alternative Groups
By specifying the attachment points order, you can Showing Attachment Rank
exclude the unwanted compounds. The parent
structure below satisfies the necessary requirements.
Indicators
You can hide the attachment rank indicators if
To specify the attachment points order: required. For example, sometimes—particularly in
1. Draw the parent structure shown below. publication-quality drawings—the numbering of
attachment points is implicit and the numbered
attachment rank indicators are superfluous.
R1
NH2
To hide the attachment rank indicators and remove
the numbers from the attachment points:

2. Create an Alternative Group Box labeled “R1”.
2. In the Preferences dialog box, click Display.
3. Deselect Show Attachment Rank Indicators.
R1
The following illustration shows an alternative
group definition and a parent structure with the
attachment rank indicators hidden.
1 2
R1 R1
NH2
1 O 2
3. Draw the structure fragments and label them

with attachment points.
O
When the alternative group definition is
complete, the attachment point symbols appear This change affects all documents.
in the parent compound.
By numbering your attachment points, you have Attachment Point Numbering
unambiguously specified that the methyl group must Numbered attachment points allow you to specify
be adjacent to the amine group. The conformations precisely how the structure fragments are connected
that are not of interest are excluded. to your parent structure.
The numbering of the attachment points is related to
the front to back order of the attachment points.
To set the order of the attachment points:
• Click the ends of the bonds in order.
The last point clicked has the highest number.

Alternative Groups
To change the ordering of the attachment points do To create anonymous alternative groups:
one of the following:
1. Open an atom label text box.
• Click the attachment points with the
2. Type an open bracket “[”followed by a list of
Attachment Point tool.
Administrator
elements, fragments, nicknames, or generic

• Select an attachment point with a selection tool, nicknames separated by commas, followed by a
and from the Object menu, choose Bring to
close bracket “]”.
Front or Send To Back.
The attachment point numbers are highest in the
front.
Atom-to-Atom Mapping
You can create correspondences between atoms in
Anonymous Alternative different structures for use in creating queries for
searching a reaction database.You can assign
Groups atom-to-atom mapping for creating records for a
reaction database and for creating queries for
An anonymous alternative group is a cross between
searching a reaction database. You can assign atom
an element list and an alternative group. Element
mapping in two ways:
lists are restricted to single elements, but
anonymous alternative groups can contain any • Automatic mapping, using the Map Reaction
structure that can be represented by text. Nicknames Atoms command.
and generic nicknames are allowed in anonymous • Manual mapping, using the Reaction
alternative groups. Anonymous alternative groups Atom-Atom Map tool .
are shortcut notation for regular alternative groups,
eliminating the need to specify a name such as “R1”. To be mapped properly, reactions must contain only
one step. Mapping does not support multi-step
You can define your search query more concisely reactions.
with the anonymous alternative group. By labeling
an atom position as a list of substructures you During either type of mapping process, the mapping
algorithm perceives and assigns a reaction center for
specify that one of these substructures must match in
the reactants and products.
the structure for which you are searching. Commas
must separate the items in the anonymous When a reaction map is established, you can point to
alternative group. A space after each comma and the an atom in one structure with the Reaction
brackets are optional. Atom-Atom Map tool selected to highlight the
Examples of anonymous alternative groups follow: mapped atom in the other structure.
[OMe,OPh] [M,B,C]
[OCH3,OH] X,S,Se

Anonymous Alternative Groups
Always Display and Print Atom Manual Mapping
Mapping In situations that require manual mapping of atoms,
you can use the Reaction Atom-Atom Map tool.
To make the symbols always appear and print on the This might be necessary when the automatic
atoms when reaction mapping has been performed: mapping is applied to complicated reactions. In
these cases you can manually readjust the reaction
mapping.
2. In the Preferences dialog box, click Display.
The following figure shows how to amend the initial
3. Select Always Display and Print Reaction
mapping by using the Reaction Atom-Atom Map
Mapping.
tool.
4. Click OK.
Rxn
7 7
Deselect Always Display and Print Atom Mapping O OH
to show the symbols only when you select the
Reaction Atom-Atom Map tool. When this option is 6 6
∆
1 5 1 5 Rxn
deselected, atom mapping symbols do not print,
even though a reaction map has been created.
2 4 2 4
3 3
Automatic Mapping
When you perform manual mapping with the
To automatically create a reaction map: Reaction Atom-Atom Map tool, you can suppress
automatic re-mapping of atoms other than your
1. Draw the reaction you want to map. For target atom.
example:
To suppress automatic re-mapping:
OSiMe 3
O O
+
Ph
Ph
2. On the General tab, select Automatic Reaction
O
Mapping.
2. Select the reactants and products in the reaction. 3. Click OK.
3. From the Structure menu, choose Map
Reaction Atoms.
To use the Reaction Atom-Atom Map tool to
supplement the automatic mapping:
OSiMe3
O O
Rxn
+ Rxn Rxn
1. Click the Reaction Atom-Atom Map tool .
Ph Rxn
Ph Rxn Rxn
Rxn
2. Point to the atom in the reactant whose mapping
O you want to establish. For example, in the
The symbol “Rxn” appears next to the bonds in following drawing you would point to the
the reactant and product that are perceived by acyclic carbon adjacent to the ether oxygen.
the algorithm as being modified by the reaction.
These symbols are bond properties that are
automatically applied. For more information
about the Reaction Center bond property, see
“Bond Properties” on page 136.

3. Drag from the reactant atom to the
corresponding product atom.
Export Compatibility
Because query properties are only useful in a
7
Rxn
7 chemical database, you must transfer your structures
Administrator
O OH
from ChemDraw into your search system. Not all
6 6
file formats support the same query properties and
1 5 5 Rxn
1
not all chemical databases support the same file
formats. Consult the documentation for your
2 4 2 4
3
database to see which file formats are supported.
3
The remaining atoms are automatically mapped The following table lists the query properties that
based on the manual mapping you performed. ChemDraw writes to ISIS (SKC, TGF, and
Clipboard) and DARC (F1, F1-Query, and
Rxn
1
1
Clipboard) file formats. All query properties are
Rxn Rxn
8 8
O 9
OH 9 written to the ChemDraw (CDX) file format. CDX
Rxn Rxn is the preferred format to use to retain all query
2
7
6
10
2
7
6
10
Rxn
properties in a drawing.
11 11
3 5
Exported ISIS DARC Mol Rxn
3 5
4 4
Query F1-
Properties Query
You can continue to set or change the mapping for
other atoms in the reaction if necessary until you get Atom Properties
exactly the mapping you want. For this example Substituents
additional manual mapping is not necessary.
Unspecified X X X X
Clearing Reaction Mapping Free Sites b X b b
a c a a
To clear all reaction mapping: Up to
Exactly Xd Xd Xd
1. Select the structures whose mapping you want
to remove. Implicit Hydrogens
2. From the Structure menu, choose Clear Not allowed X X X X
Reaction Map.
Allowed X X X X
Exporting Reaction Mapping Ring Bond Count
Reaction mapping and reaction center perception Any X X X
information are stored in the native ChemDraw file
No ring bonds X X X
format (*.cdx) for reopening in ChemDraw and the
ISIS Reaction file format for transfer to other As drawn X X X
applications that read atom mapping, such as
Simple ring X X X
ChemFinder and ISIS/Base. You can also copy
mapped reactions to these same applications using Fusion X X X
the Clipboard.

Exported ISIS DARC Mol Rxn Exported ISIS DARC Mol Rxn
Query F1- Query F1-
Properties Query Properties Query
Spiro or higher X X X Wedged X X X X

Hashed
Unsaturation
Bold X f f f
Unspecified X X X
Wedged X X X X
Must be absent
Wavy X g X X
X
Must be present X X X
Hollow f f f f
Reaction Change
Wedged
May be X X h h h h
Dative
anything
Double Xi X Xi Xi
Must be as X X
specified Double Either X X X X
j j j j
Reaction Stereo Double Bold
Any X X Aromatic X Xk X X
X X l l l l
Inversion Tautomeric
Retention X X Triple X X X X
r r r r
Translation Quadruple
Equal X Any X Xm X X
Broad X S/D X X X X
Any X D/A X X X X
Narrow X S/A X X X X
Abnormal Valence Topology

Not Allowed X X X X Unspecified X X X X
Allowed X X X X Ring X X X X
Bond Properties Chain X X X X
Bond Type Reaction Center

Single X X X X Unspecified X X X
Dashed X e X X Center X X X
Hashed e e e e Make/Break X X X
Change X X X

f
Converted to Wedged
Exported ISIS DARC Mol Rxn
Query F1- g
Converted to Racemic
Properties Query h Converted to a Single, with a positive charge
Administrator
Make&Change X X X applied to that atom at the base of the dative bond

Not Center X X X and a negative charge applied to the atom at the
point of the dative bond
Other Query Attributes
i Interpreted by ISIS as unspecified cis/trans
Generic Xn Xo Xn Xn
stereochemistry
Nicknames
j Converted to Double
Element Lists Xpu X Xpu Xpu
k
Element Not- Xp X Xp Xp
Converted to Normalized
Lists l
Converted to S/D
Alternative X q Xs
X m Converted to Undefined
Groups
n
t t t
Only M, X, Q, A; others written as aliases
Anonymous
o
Alternative Extensive list — see DARC manual
Groups p
Truncated to the first 5 elements
v v v
Link Nodes q
Converted to G-Groups and possibly renamed;
Bracket X X X only 20 supported in one file.
properties
r
Converted to single.
Atom-Atom X X X
s
mapping An RGFile will be created automatically.
t
Variable Converted to non-anonymous alternative groups.
Attachment u Lists of greater than 5 elements converted to
Positions
alternative groups.
a Converted to the appropriate number of exact v
The low end of the repeat range is always treated
substituents
as 1.
b
Free Sites counts of zero translated to
“Substitution as drawn”; all other Free Sites values
written as substitution counts equal to the total
current valence plus the free sites value.
c Converted to the appropriated number of Free
Sites
d
Substituent counts of greater than 5 are translated
to “6 or more”
e
Converted to Wedged Hashed

Chapter 10:
Working with Page Layout
Overview The size of drawing area displayed depends on the
size and resolution of your monitor. In some cases
The presentation quality of your ChemDraw you can see the entire document.
document is determined by how well the chemical
structures and other objects are placed on the page If you magnify a document, the drawing area size
(layout). Effective layout of a drawing includes and drawing objects become bigger. If you increase
proper alignment of chemical structures and other the magnification so that the page size becomes
objects, appropriate page size, and page orientation. bigger than the screen, scroll bars become available.
The page layout tools include: setup of the page and
the use of the ruler, and the grouping, layering,
aligning, and distributing commands. You can also
Setting up Pages
organize information on the page using tables. You can create two types of documents:
Controlling the Drawing Pages—A single document containing one or more

sheets, each of which is printed on a single piece of
Area paper.
The size of a document window is not necessarily Posters—A single large document, composed of as
the same as the size of the drawing area of the page. many pieces of paper as necessary.
A document window, in most cases, actually covers
only a portion of the drawing area.
The following options allow you to set the drawing
area displayed on your screen.
• Document Settings and Page Setup from the
File menu allow you to set the size and
orientation of the page, margins, headers,
footers, and the document type and size.
• View menu options: Actual Size, Fit to
Window, Magnify, and Reduce.
• Magnification Controls: enlarge and reduce
• Dragging to enlarge the drawing area.
• Windows: Point to a border or corner of a
document window and drag to resize.
• Macintosh: Drag the Size box in the lower
right corner of the document window.
ChemDraw 7 Chapter 10: Working with Page Layout • 155

Controlling the Drawing Area
Paged Document Setup Poster Documents Setup
To create a document with one or more page: You can create a poster by creating a single large
drawing area, which will be printed on as many
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1. From the File menu, choose Document separate pages as necessary. When you set the
Settings. document size and how much each page overlaps,
The Document Settings dialog box appears. ChemDraw calculates the number of pages needed
and the margin sizes. You can set registration marks,
which mark the overlap setting on each page, to use
as a guide when assembling the poster from the
separate pages.
To create a poster document:

Settings.
2. On the Layout tab, click Poster.
3. Type the Height, Width, and Page Overlap.
The number of pages and the margin
dimensions are calculated.
4. Select whether to Print Registration Marks.
5. Create Headers and Footers as described in
“Creating Headers and Footers” on page 157.
2. On the Layout tab, ensure Pages is selected.
6. Click OK.
3. Specify the number of pages in the Document
An example of a 19-inch by 14-inch poster,
Size section.
consisting of six 8.5-inch by 11-inch pieces of paper
The size of the pages is determined by the Page with a 1-inch overlap is shown below.
Setup settings. For more information, see “Page
Setup” on page 157. 8.5"
4. Type the Margin settings. 1" 1"
The units of the margins are set in the

11"
Preferences dialog box. The paper size minus
the margins determines the drawing area.
1" 19" X 14" Poster
5. Create Headers and Footers as described in
“Creating Headers and Footers” on page 157.
6. Click OK.
A document is created using your settings.
156 • Chapter 10: Working with Page Layout CambridgeSoft

Setting up Pages
Creating Headers and Footers 6. Position the text horizontally by typing the
characters in the table below. Any text
You create headers and footers in the Document
following these characters is appropriately
Settings dialog box. In poster documents, only one
aligned.
header and footer appear for the entire document.
To create headers and footers: To align the text … Type …
1. From the File menu, choose Document centered &c

Settings.
2. Click the Footer tab. right &r
left (default) &l
Page Setup
The Page Setup parameters that affect the size of the
drawing area are:
• Page size
• Orientation
These parameters are specified in the Page Setup
dialog box. The Page Setup dialog box and the
options available vary depending on the printer you
have chosen. For the Macintosh, the version of the
printer driver for that printer is installed in your
System Folder.
3. Type the value of the position from the edge of
To set the paper size, orientation, and margins:
the page that you want the header or footer to
appear. 1. From the File menu, choose Page Setup.
4. Type the text to appear in the header or footer. The Page Setup dialog box appears. The dialog
5. Type additional information in the Text box box appears slightly different depending on the
from the following table: printer and platform you have.
To include the… Type …
file name &f
page number &p
date printed &d
time printed &t

Page Setup
A Windows dialog box for a typical postscript The available page sizes vary depending on the
printer is shown below. type of printer. Listed below are common sizes
available. The page orientation you choose
determines which of the measurements is height
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and which is width:
Paper Type Dimensions
US Letter 8.5 x 11 inches
US Legal 8.5 x 14 inches
A4 Letter 21 x 29.7 cm
B5 Letter 17.6 x 25 cm
Tabloid 11 x 17 inches
The Macintosh Page Setup dialog box with

International 8.5 x 12 inches
common settings for a LaserWriter is shown
below.
Computer 14 x 11 inches
Page Orientation
To choose the orientation of the page:
• Click the vertical (portrait) or horizontal
(landscape) orientation button.
The orientation of a document window changes
to the orientation you have chosen. This is
evident when the rulers are visible.
2. Select a paper size from the drop-down list.

Page Setup
Reduce or Enlarge To display the 35mm slide boundary lines:
Some printers include an option to reduce or enlarge 1. From the File menu, choose Preferences.
your drawings by a variable percentage (25-400%). 2. Select the Show 35mm Slide Boundary
This option scales all objects and text in the Guides check box.
document window by the percentage specified. This
3. Click the OK button.
is not a change in magnification. The size of objects
is changed relative to the paper size, margins, and Two 35mm Slide Boundary Guides appear in
orientation you have specified. the same orientation you have chosen in the
Page Setup dialog box. These guides appear in
The enlarge or reduce option is useful for changing
every document.
the size of the available drawing area, while keeping
the images on the screen at the normal size when you This preference affects all documents.
are drawing. If your document is set so that the
drawing fills the page on one printer and you use Changing Perspectives
another printer that requires larger margins, the
You can use a close-up view of objects in your
drawing my disappear off the edge of the document
reaction scheme to make sure they are properly
window. You can reduce the size of the drawing with positioned. At times, you may want to reduce your
the reduce option so that it fits in the document view so that you can move groups of objects around
window. the page. You can change the magnification to
perform these functions by using the Magnify and
Saving Page Setup Settings Reduce commands in the View menu or the
You can save Page Setup settings in a Style Sheet or magnification controls.
Stationery Pad. Whenever you open a Style Sheet or
Magnifying with the View Menu
Stationery Pad, these settings are automatically
used. The Page Setup settings are saved in addition When you use the View menu to magnify or reduce,
to the Text settings, Drawing Settings, and the Color the magnification is set to the next higher or lower
Palette. value. You can magnify up to 400% or reduce to
25%.
35mm Slide Boundary Magnify
Guides To magnify using the View menu:
If you make 35mm slides from a hard copy of a
1. Select the object around which you want to
ChemDraw document or from a screen shot, you can
magnify your view.
display boundary lines that appear on your screen
positioned at 7 inches and 10.5 inches to match the
2:3 ratio for the 35 mm slide format. These guides NOTE: If you do not select an object, the last
help you keep your drawing within this region to object drawn is the center point of the
maintain the proper ratio, but are not printed. The magnification.
drawing area of the page must be at least 7 x 10.5
inches for these boundary lines to be visible. 2. From the View menu, choose Magnify.

35mm Slide Boundary Guides
The magnification occurs around the center of Fit to Window
the selected object. The magnification Fit to Window reduces the magnification until the
percentage appears in the Magnification entire page is visible in the document window.
drop-down list.
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To view the entire drawing area in a document

Windows Macintosh window at once:
• From the View menu, choose Fit to Window.
You can continue to magnify your view to a The Magnification control shows the reduction
maximum of 400%. in magnification that was required to have the
entire page appear on the screen.
Actual Size
To return to the actual size from any other Using the Magnification Control
magnification: When you use the Magnification control, you can
• From the View menu, choose Actual Size. display magnifications from 10% to 999% of the
The view is returned to the original size. normal size of your page. The magnification control
allows you to select a specific value.
Reduce To use the Magnification controls:
To reduce the magnification: Windows:
1. Select an object around which you want to • Select a value from the drop-down list
reduce the magnification. or type a value.
Macintosh:
NOTE: If you do not select an object, the last
object drawn is the center point of the Do one of the following:
magnification.
• Select a value from the drop-down list
.
2. From the View menu, choose Reduce.
• Select Other from the drop-down list. In the
The reduction in magnification appears in the
Magnification drop-down list. dialog box that appears, type a value and click
OK.
Windows Macintosh
You can reduce the magnification until the entire

page fits on the screen. In the reduced view, you can
continue to use all of the drawing tools. In particular,
you can use a selection tool to rearrange the drawing
in order to take better advantage of the space
available.

Changing Perspectives
Arranging Objects
This section describes methods for positioning,
Ruler Guides
aligning, and layering objects in a document
window.
Using Rulers
You can use the rulers to position objects a measured
distance away from some reference point or create Ruler guides also appear when you drag selected
objects of an approximate size. The units used for objects. In this case, however, there are two Ruler
the ruler are set in the Preferences dialog box, where guides that bracket the object. With this bracketing
you have the choice of inches, centimeters or points. you can quickly establish the height and width of the
selected objects.
Showing Rulers
To display the rulers:
• From the View menu, choose Show Rulers. Ruler Guides
A check mark appears next to the Show Rulers

command, and the rulers appear along the top
and left edges of a document window.
Hiding Rulers
To Hide the rulers:
• From the View menu, choose Show Rulers.
The check mark disappears.
Using the Crosshair

Use the Crosshair to align objects relative to each
As you move the pointer, Ruler Guides appear other, and to space objects a consistent distance
on each ruler, indicating the position of the apart. The axes of the Crosshair can be moved
pointer. within a document window.

Arranging Objects
Displaying the Crosshair Aligning Objects using the
To show the Crosshair: Crosshair
• From the View menu, choose Show Crosshair. To use the Crosshair to align objects do one of the
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following:
A check mark appears next to the Show
Crosshair command and the Crosshair appear • Move the Crosshair axes and align it with the
within a document window. object.
To assist you in aligning objects, the Crosshair • Select an object and drag it until it is aligned
includes grid lines that extend from the major with either axis of the Crosshair, or a grid line.
division marks on each axis. In either case, if a bond or side of the object is
parallel to one of the axis, it disappears when it is
exactly positioned over a Crosshair axis.
To align another object on the Crosshair:
1. Select a second object.

2. Drag the second object to the Crosshair axis or
grid line and align it to the first.
You can also move selected objects in small
increments to align them with the Crosshair using
You can also show the Rulers while the Crosshair
the Arrow keys available on some keyboards:
are displayed so that you can see the unit
measurement associated with each of the divisions To move 1 point in the direction of an Arrow key:
on the Crosshair axes.
NOTE: 1 point equals 1/72 inch or 0.035 cm.
Moving the Crosshair
• Select the objects and then press an Arrow key.
To move the Crosshair:
To move 10 points using the Arrow key, for
1. Position the pointer where the Crosshair axes example, to the right:
intersect.
• Press Alt+Right Arrow or Option+Right
When the pointer is near to the center of the Arrow.
Crosshair, it changes to an arrow.
2. Drag the Crosshair. Hiding the Crosshair
To constrain the movement of the Crosshair to the To hide the Crosshair:
X- or Y-direction:
• From the View menu, choose Show Crosshair.
• Shift+drag the crosshair. The check mark next to the Show Crosshair
command disappears.

Arranging Objects
Centering on a Page 2. From the Align submenu, choose one of the
Align commands.
To center an object (or group of objects) at the center
of the page:
1. Select the object you want to center using a

selection tool.
2. From the Object menu, choose Center on
Page.
The selected objects move so that the center of
the Selection rectangle is positioned at the If you select only part of a structure or group
center of the page. with a selection tool, only that part is used for
the alignment operation, but the entire structure
Aligning Objects or group is moved.
Use the Align commands to align objects relative to
Distributing Objects
each other. Examples of the types of alignments are
shown on the menu. Use the distribute commands to distribute objects
horizontally or vertically and at an equal distance
apart. For reactants and products with different
shapes, select the parts of the objects to distribute.
To distribute 3 or more objects:
1. Select the 3 or more objects to distribute.
OH
To align two or more objects:
CH2Br
1. Select the objects with a selection tool. 2. On the Object menu, point to Distribute, and
then choose Vertically or Horizontally.
OH
CH2Br
The space between the objects is equalized. The

upper, lower, right, and left positions of objects
in your selection remain unchanged.

Arranging Objects
Front to Back Ordering Creating Tables
The front to back ordering is a useful method for
You can create tables of ChemDraw objects with the
changing the orientation of one object relative to Table tool or tables of text with the Text tool.
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another object within the same picture layer. For

additional information specific to the layering of Creating Tables with the Table
bonds, see “Changing Bond Crossings” on page 61.
Tool
Send to Back Tables created with the Table tool are containers for
drawings and data. To place a structure in a table,
To place one object behind another within a layer:
you can draw it directly in the table, or copy or drag
1. Select the object that you want to send to the it into the table.
back, in this example, the two upper orbitals.
The Table tool enables you to do the following:
• Create and modify tables
• Customize the borders
• Add or delete rows and columns
• Resize the table and its cells manually
• Fit a cell around its contents automatically
2. From the Object menu, choose Send to Back. • Align cell contents
To create a table with the Table tool:
1. On the Main Tools palette, click the Table tool

.
• Click and drag in the document window to
The selected object appears behind all other
create the table.
objects in the same layer.
The default table has two rows and two
Bring to Front columns.
To place one object in front of another within a • Click in the document window, type the
layer: numbers of rows and columns in the Insert
Table dialog box, and then click OK.
1. Select the object that you want to move
forward.
2. From the Object menu, choose Bring to Front.
The selected object now appears in front of all
other objects.

Creating Tables
The table appears in the document window. To customize the borders of the table:
1. With the Table tool selected, point to a border

and right-click or option-click.
The Table Borders dialog box appears.
To resize the rows or columns:
1. Place your pointer on the border to resize.

The pointer changes to a double-headed arrow.
2. In the Setting section, click the borders to which

you want to apply the settings.
3. In the Style section, select the style, color and
2. Drag the border to the desired size. width of the border to apply.
4. In the table diagram, click the borders to
customize.
5. Click OK.

Creating Tables
To make a cell fit around its contents, such as in the 2. Right-click or Option-click and from the menu
table shown below: that appears, choose the appropriate option:
O If you want to … Then choose …

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add an empty row Add Row Before.

above the indicated row
OH
add an empty row Add Row After.
below the indicated row
add an empty column to Add Column Before.

1. Point to a border and right-click.
the left of the indicated
2. Choose Size To Fit Contents. column
The cells resize to fit around the contents.
add an empty column to Add Column After.
O the right of the
indicated column
delete the indicated row Delete Row.

OH
and its contents
delete the indicated Delete Column.

column and its contents
To align all of the objects in the table:

To add rows or columns to the table:
• Point to a border, right-click, point to Align, and
1. Point to the border where you want to add the then choose the alignment you want.
rows or columns. The cell contents shift and stay in a fixed
The arrow appears as shown below. position relative to the cell. The default
alignment is unaligned.

Creating Tables
Creating Tables with the Text To create another column with this same spacing as
the previous:
Tool
• Press Tab.
ChemDraw allows you to create tables of text using
the Tab key with the Text tool. A third caption text box appears.
Creating the First Row (column Creating a New Row

headings) To start a new row that is exactly aligned with the
To create the first row and establish the columns of first:
a table: • Press Tab twice at the end of a row.
1. Click the Text tool. A caption text box appears exactly aligned
under the first caption positioned exactly 20
2. Click in a document window where you want
the table to start. points below the first caption in the first row.
The following diagram illustrates the creation of a
3. Type a caption.
new row.
4. Press Tab.
A second caption box appears. Compound M.W. LogP LD50
tab twice
5. Type a second caption. 1
The second column is placed 20 points To change the spacing between rows as you create
(20/72 inch, 0.71 cm) to the right of the first. the table:
6. Press Tab again to create a third column, and so 1. Select the captions in a row.
on.
2. Move the captions using the arrow keys.
NOTE: The style, font, and size that you set in each For more information on moving objects, see
column are maintained in all the rows that follow. “Moving Objects” on page 98.
To continue and fill in the row with captions:
The following illustration shows the creation of new
• Press Tab to create another caption in the row,
columns using the Tab key.
and then press Tab twice to begin a new row.
Compound M.W. LogP LD50 The spacing between the newest row and the
tab tab tab row directly before it have the same spacing
that you specified between the previous two
To change the spacing between columns one point at
rows.
a time while editing a caption:
1. Select the caption.

2. Move the caption with the arrow keys.
For more information on moving objects, see
“Moving Objects” on page 98.

Creating Tables
Adjusting Row or Column Spacing Inserting a New Row
To use a selection tool to adjust the spacing in a To insert a row:
table: 1. Select a selection tool and select a row of
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1. Select all of the captions with a selection tool. captions.
2. Shift+drag the caption. 2. Shift+drag the selected row.
The movement is constrained to the X-axis or Y-axis Shift constrains the movement to the Y-axis to
so that you can maintain the row or column maintain the column alignment.
alignment. 3. Select the first caption in the row above or
below the space you created.
Moving Around In Tables 4. Shift+Alt+drag or Shift+Option+drag to
To move within an existing table: create a copy of the caption and position it in the
empty space you created.
1. Click the Text tool and select a caption.
The placement of this copied caption sets the
2. Press Alt+Arrow or Option+Arrow to move to
position of the inserted row.
the next caption in the direction of the arrow.
To fill in the inserted row with caption text:
Alternatively, you can use the following key
combinations: 1. Click the Text tool and select the first caption in
the inserted row.
Use … To move …
2. Type new text.
Tab (Windows) right 3. Press Tab to move to the second caption in the
Option+Tab (Macintosh) inserted row, and so on.
Shift+Tab (Windows) left

Option+Shift+Tab (Macintosh)
Alt+Enter (Windows) down

Option+Enter (Macintosh)
Alt+Shift+Enter (Windows) up
Option+Shift+Enter (Macintosh)
To move to the caption above and open it for editing,

do one of the following:
• Press Shift+Alt+Enter or
Shift+Command+Return.
• Press Alt+Up Arrow or Command+Up Arrow.

Creating Tables
Chapter 11: Sharing Information
Overview Cutting
ChemDraw includes many of the standard system To place ChemDraw objects on the Clipboard and
remove the objects from a document window:
commands for transferring information within and
between ChemDraw documents, and between 1. Select the objects to remove with a selection
ChemDraw and documents created using other tool.
applications. You can transfer information using the 2. From the Edit menu, choose Cut.
Clipboard, drag and drop, object embedding, and
The selected objects are placed on the clipboard
file formats.
and removed from a document.
ChemDraw does not install its own fonts. If a
ChemDraw document contains fonts that are not Pasting
available on a particular computer, they are To paste the contents of the Clipboard into a
substituted with fonts that are available. ChemDraw document:
• From the Edit menu, choose Paste while a
Transferring Between selection tool is selected.
ChemDraw Documents The contents of the clipboard are placed in the
center of the active document.
You can use the clipboard or the drag-and-drop If the Clipboard contains ChemDraw structures, the
feature to transfer ChemDraw pictures to other pasted information is scaled to the settings in the
ChemDraw documents. current document. For more information, see
Using the Clipboard
To view the contents of the Clipboard:
You can use the clipboard to copy or cut a
• Take the appropriate action:
ChemDraw object for pasting into another
document.
If you are Then…
Copying using …
To place a copy of a ChemDraw drawing on the

Windows From the desktop, click Start, point
clipboard: to Programs, point to Accessories,
and then choose the Clipboard
1. Select the objects to copy using a selection tool.
Viewer.
A copy of the selected objects is placed on the Macintosh From the Edit menu, choose Show
Clipboard. The selected objects remain in the Clipboard.
document.
ChemDraw 7 Chapter 11: Sharing Information • 169

Transferring Between ChemDraw Documents
See your operating system documentation for To create a clipping file or a scrap file:
information on using the Clipboard.
1. Select an object in a ChemDraw document.
NOTE: You can paste the contents of the Clipboard 2. Drag the selection out of the ChemDraw
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into another application by the same procedure. See document window onto the desktop.
your application documentation for additional A clipping file or a scrap file is created on your
information specific to the application. Macintosh: desktop.
If you are pasting the ChemDraw drawing in a
document from which you are planning to print to a To view the information within a clipping file or a
PostScript printer, see“Transferring PostScript scrap file:
(Macintosh)” on page 175. • Double-click the file’s icon.
A window appears showing the ChemDraw
Using the Drag-and-Drop drawing. Click the close box to close the
Feature clipping file’s window.
You can use the drag-and-drop feature to copy To use the contents of a clipping or scrap file in a
objects to place in other documents. To use this document:
feature in other applications, they must support
drag-and-drop. • Drag the clipping or scrap file into an open
window of an application that supports the
To use the drag-and-drop feature to transfer drag-and-drop feature.
information between ChemDraw documents:
The contents of the clipping or scrap file are
1. Select an object or structure in a ChemDraw copied to the open window. The clipping or
document. scrap file is unchanged.
2. Drag the selection into another ChemDraw
document window.
Autoscaling
The selection is copied to the destination When you transfer ChemDraw objects using the
ChemDraw document. Clipboard or drag and drop from one ChemDraw
document (the source document) to another
To drag and drop a selection to another application: ChemDraw document (the destination document),
1. Select an object or structure in a ChemDraw the objects are automatically scaled to match the
document. document settings of the destination document.
Automatic scaling assures that the objects being
2. Drag the selection into the other application’s
transferred match the settings of the current
document window.
document.
The selection is copied to that application’s
document.
You can also use the drag-and-drop feature to create
clipping files (Macintosh) or scrap files (Windows).
170 • Chapter 11: Sharing Information CambridgeSoft

Bonds Captions
All bonds drawn in the source document using the ChemDraw autoscales captions are autoscaled using
values specified in the Drawing Settings dialog box the ratio of the fixed length in the destination
can be changed to use the Drawing Settings in the document to the fixed length in the source document
destination document. times the caption font size. The font size of the
caption can be any size and is not related to the
Any resized bond in the source document is scaled
setting in the Settings dialog box. This assures that
in the destination document. The scale factor is
captions are always in proportion to the bonds with
based on the ratio of the bond’s length after resizing
which they are pasted.
(source) to the Fixed Length in the Drawing Settings
dialog box (source). This scaling process maintains For example, If the source document has a fixed
the source document proportions in the destination length of 1.0 cm and the destination document has a
document. All values in the Drawing Settings dialog fixed length of 2.0 cm, and the caption you are
box are scaled using this method. pasting is 12 points, then the resulting caption size
after autoscaling is (2.0 cm /1.0 cm) x 12 points = 24
For example, the Fixed Length is set to 1.0 cm in a
points.
source document. A benzene ring is resized in to
200%. The bond length is then 2.0 cm: a ratio of 2.0
Non-bond Objects and Color
cm:1.0 cm or a scale factor of 2. In the destination
document, the Fixed Length set to 1.7 cm. When the All objects that are not affected by settings in the
benzene ring is pasted into the destination Document Settings dialog boxes, such as arrows and
document, the bonds are scaled by a factor of 2 to a boxes, are scaled to maintain the same proportions
final bond length of 3.4 cm. to bonds that were present in the source document.
With the exception of the foreground and
Atom Labels background color, the other colors present in the
Atom labels are scaled the same way as bonds. selection to be pasted are added to the destination
document’s Color Palette if they are not already
For example, in the source document, the atom label
present (up to a maximum of 20 total colors). The
font size is set to 16 points. One or two atom labels
background color in the destination document is
in the source document are resized to 8 points, a
unchanged, and all objects colored using the
ratio of 8:16 or a scale factor of 0.5. The destination
foreground color are changed to match the
document has an atom label font size is set to 14
foreground color in the destination document.
points. When the atom label is pasted into the
destination document, the font size is scaled by a
factor of 0.5 to give a final atom label font size of 7
points.

Pasting to an Empty Document Transferring ChemDraw
Window
Documents Across
If you paste a ChemDraw drawing into an empty
Platforms
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ChemDraw document and the settings between the

documents are different, the Change Settings dialog
Use the following procedures to transfer ChemDraw
box appears:
documents across platforms. From the following
table, determine the versions of the ChemDraw
software between which you want to transfer
documents and then follow the appropriate
instructions.
When you transfer ChemDraw files across
platforms, fonts are not transferred. If a font in the
transferred document is not available, ChemDraw
substitutes fonts for those that are available on the
To change the settings in the destination document
new platform.
to match the settings in the source document:
• Click Change Settings. Transferring from Macintosh to
All of the settings in the destination document Windows
are changed to match those of the source
To be able to open a ChemDraw file created on the
document. All of the colors in the Color Palette
Macintosh in Windows, follow the instructions for
of the destination document are changed to
the appropriate versions shown in the table below.
those specified in the source document.
To scale the objects from the source document to the From To Instructions
settings in the destination document: Mac Windows
Version Version
• Click Don’t Change Settings.
≥ 4.0 ≥ 4.0 Save as ChemDraw and
The settings from the source document are add .cdx to the file
scaled to those in the destination document name.
using the ratios given above.
≥ 4.0 3.x Save as ChemDraw 3.x
and add .chm to the file
NOTE: If the source document was created in a name.
ChemDraw version earlier than 3.0, the name of the
document appears as “Unknown” in the dialog box. ≤ 3.5.x = 3.x Save as ChemDraw and
add .chm to the file
name.

Transferring ChemDraw Documents Across Platforms
Transferring from Windows to 4. From the Control Panels, select
PC Exchange.
Macintosh
5. Select Add.
To be able to open a ChemDraw file created in
6. Change the DOS suffix to .chm.
Windows on the Macintosh, follow the instructions
for the appropriate versions shown in the table 7. In the application selection, find CSC
ChemDraw on your Mac and click once to
below.
highlight the selection.
From To Mac Instructions 8. Change the document type to CHMS.
Windows Version
If you are using a translator other than
Version
PC Exchange, you need to use an editor such as
≥ 4.0 ≥ 4.0 Save as the default ResEdit or Disktop to change the type and creator of
ChemDraw (.cdx). the files being transferred. The type should be
“CHMS” and the creator should be “CHMD.”
≤ 3.5.x ≥ 4.0 Save as ChemDraw
3.x (.chm).
Embedding Objects
≤ 3.5x ≤ 3.x Save as ChemDraw
3.x (.chm) and (Windows)
follow the
instructions in To make changes to ChemDraw drawings that are
“Transferring files pasted in other types of documents, ChemDraw
to ChemDraw/Plus supports the Object Linking and Embedding (OLE)
3.1 for the protocol on Windows. The Windows version of
Macintosh” below. ChemDraw is an OLE server, which means it can
create OLE objects that can be copied and pasted
into other OLE client applications.
Transferring Files to ChemDraw/Plus
3.1 for the Macintosh When a drawing is transferred from ChemDraw into
another document type that supports OLE, you can
Use the following procedure to transfer a open the drawing and edit it from within the client
ChemDraw for Windows file to ChemDraw/Plus 3.1 application.
for the Macintosh. A file translator such as
For example, to edit a ChemDraw drawing inserted
PC Exchange or Apple File Exchange must be
into Microsoft Word for Windows version 6.0 or
running on your Macintosh. later, do one of the following:
To transfer from Windows to ChemDraw/Plus 3.1 • Select a ChemDraw drawing in a Word
for the Macintosh: document and from the Edit menu, point to
CS ChemDraw Drawing Object, and then
1. In ChemDraw for Windows, save the file in the choose Edit.
ChemDraw (.chm) format.
• Double-click a ChemDraw drawing in a Word
2. Insert the disk with the ChemDraw for document.
Windows files into the Mac floppy drive.
The ChemDraw tools and menus replace those
3. If you are using PC Exchange, double click the of Word. Use the ChemDraw tools to edit the
floppy disk icon to display the files. drawing.

Embedding Objects (Windows)
When you have finished making changes: 2. Take the appropriate action:
• Click in another area of the document.

If you want Then …
The Word tools and menus are restored.
to …
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Inserting Graphics or Objects

create a new a. Click Create New.
from Other Applications object
You can insert graphics or documents created in b. Select the Object Type.
other applications into ChemDraw. You can edit c. Click OK.
inserted objects using the ChemDraw Edit menu.
Inserted objects can be resized using the resize
insert an a. Click Create from File.
handles of a selected object. You cannot rotate or
existing
flip inserted objects. graphic b. Type the path or browse
to the object to insert.
To insert an object from another application into
ChemDraw: c. Click OK.
1. From the Edit menu, choose Insert Graphic.
2. In the Open dialog box, select the graphic and Inserting Reference Numbers
click Open. in Microsoft Word
To insert an object from another application into You can assign reference numbers to ChemDraw
ChemDraw: structures that appear in your Microsoft Word
documents to use as a reference. If you delete, add,
1. From the Edit menu, choose Insert Object. or rearrange a structure, you can update the
The Insert Object dialog box appears. references so that they are numbered sequentially.
The first reference is inserted as the number 1, each
subsequent number is added sequentially.
You can edit the reference number text with the Text
tool. If you have different types of reference text,
you are prompted to choose which type to continue
the sequence.
After you have reference numbers associated with
your structures, you can add cross-references to
other structures.
To insert a sequence number:
1. In Word, double-click the structure to number.

ChemDraw tools and menus appear.

Embedding Objects (Windows)
To select a reference sequence:
1. Double-click the structure to add to the

sequence.
2. From the Edit menu, choose Insert Sequence
Number.
The Select one sequence number dialog box
appears.
3. Select the sequence to use and click OK.
4. The next reference in the sequence you chose is
added.
To insert a cross reference to an existing reference:
1. Double-click the reference number of the

2. From the Edit menu, choose Insert Sequence structure to cross reference from.
Number. The Insert Cross-Reference dialog box appears:
A number is added to the document. 2. Click the structure that you want to cross
reference to.
3. Click OK.
The cross reference number is added.
To navigate through the cross-references:
• From the Edit menu, choose Go Forward or Go
Back.
Transferring PostScript
(Macintosh)
To obtain the highest quality drawings possible on a
To edit the reference number:
PostScript printer, ChemDraw creates both a screen
1. Double-click the structure associated with the representation and a PostScript representation of
reference. your drawing. PostScript is a page-definition
2. With the ChemDraw Text tool, edit the language used to describe drawings. Many printers,
reference. including most Apple LaserWriter printers, use
PostScript to create high quality output.
For best print quality under all circumstances, we
recommend that you leave the Include PostScript
and Include ChemDraw Laser Prep preferences

Transferring PostScript (Macintosh)
selected (default) when you copy and paste from To print to a non-PostScript printer:
ChemDraw to other applications. The ChemDraw
Laser Prep option adds approximately 11K to 12K to NOTE: You can also use this procedure to transfer
each drawing, but these options give you the greatest ChemDraw drawings to a drawing program that
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flexibility if you give your document to someone does not use PostScript commands.
else or later want to print it on a PostScript printer.
• Deselect both Include PostScript and Include
If you never plan to print to a PostScript printer or
ChemDraw Laser Prep on the General tab or
never plan to give your document to someone who
the Preferences dialog box.
uses a PostScript printer, you can turn the
preferences off.
Importing and Exporting
To deselect the PostScript preferences:
There are two ways to transfer ChemDraw drawings
1. From the File menu, choose Preferences. to and from other applications:
2. Deselect Include PostScript and Include • Using the Clipboard—The Clipboard is useful
ChemDraw LaserPrep. for transferring part or all of the information
To transfer only a few drawings to another within an active document window between
document: applications on the same computer or a
networked computer.
NOTE: You can also transfer drawings to a • Using different file formats—File formats are
document in a remote location whose printer cannot useful for saving and opening the contents of a
be initialized by ChemDraw. ChemDraw document for transfer to other
chemistry, word processing, and desktop
• In the Preferences dialog box, select Include publication applications.
PostScript and Include ChemDraw Laser
Prep. Exporting Using the Clipboard
The PostScript commands and the ChemDraw ChemDraw includes several formats on the
Laser Prep are transferred with each drawing. Clipboard during a normal copying operation.
The transferred drawings can be printed ChemDraw supports the following formats:
independently of ChemDraw. • ChemDraw 4.0 or later (*.cdx)
If you do not check the Include PostScript • ChemDraw 3.5 (*.chm)
check box when printing to a PostScript printer • PICT (Macintosh only)
ChemDraw sends QuickDraw commands to the
• WMF (*.wmf, Windows only)
printer. For more information, see “Printing
Background Color” on page 18. • PostScript (Macintosh only with appropriate
preferences turned on)
• ISIS/Sketch (SKC)
• MDL MolFile (no arrow is in the selection)
• RXN File (arrow is in the selection)
• DARC F1

Each of these formats is briefly described in the next The SMILES string corresponding to the
section under file formats. trans-2-amino-cyclohexanol molecule is
transferred to the Clipboard.
To export a file using the Clipboard:
NH2
1. Select the structure using a selection tool.
The structure is copied to the Clipboard. For OH
large structures you may see a status bar
indicating the progress. N[C@@H]1[C@H](O)CCCC1
To display the SMILES string:
SMILES and SMIRKS Strings
• Paste the string in a document window.
A SMILES string is a way to describe a chemical
structure in a line of text. Several software packages To view the SMILES string on the clipboard:
use SMILES strings as a way to enter and store • In Windows, on the desktop, click Start, point
chemical structure information. to Programs, then point to Accessories, and
A SMIRKS string is a way to describe chemical choose Clipboard Viewer.
reactions in text. If you select a reaction and use the • On the Macintosh, from the Edit menu, choose
Copy As SMILES command, a SMIRKS string is Show Clipboard.
copied to the clipboard. If you use the Paste Special
When the SMILES string is on the Clipboard, you
SMILES command when a SMIRKS string is on the
can transfer it to another application that can
clipboard, a reaction is pasted into your document.
interpret and manipulate SMILES strings.
SMIRKS allows for agents, which are molecules
If you select more than one structure in ChemDraw,
that do not contribute atoms to the product or accept
and choose Copy SMILES from the Edit menu, the
atoms from the reactants. ChemDraw does not allow
SMILES string for each structure is copied to the
for agents. When you copy a reaction, everything
Clipboard and separated from the previous SMILES
before the arrow is a reactant and everything after
string by a period.
the arrow is a product. When you paste a reaction,
any agents present are moved before the arrow. SMILES supports an alternate notation for aromatic
structures using lowercase letters. ChemDraw
Creating SMILES Strings generates this type of SMILES string for any
structure drawn with explicit aromatic bonds, either
To create the SMILES string for the following
by using the Aromatic bond type in the Atom
structure:
Properties dialog box, or by placing a circle within
1. Select the structure using a selection tool. any ring structure.
2. From the Edit menu, point to Copy As, and then
choose SMILES.

Pasting SMILES from Clipboard Exporting and Importing
If you have a SMILES string, then you can
automatically convert that text string into a
Using File Formats
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ChemDraw structure. Many applications can use the information

contained within a ChemDraw document and saved
To paste a SMILES string as a ChemDraw structure: in one of the other file formats. File formats are
1. Select the SMILES string using the Text tool. available in a pop-up menu at the bottom of the
Open and Save dialog boxes.
3. From the Edit menu, point to Paste Special, To export a file:
and then choose SMILES. 1. From the File menu, choose Save As.
The SMILES string is drawn as a structure. 2. In the Save As dialog box, do the following:
a. Type a name for the file and choose a
NOTE: Pasting SMILES uses the same routines as
the Clean Up structure command. For more location in which to save it.
information, see “Using Clean Up Structure” on b. Select a file format from the bottom of the
page 111. dialog box.
c. Click OK or Save.
Creating SLN Strings A copy of the current document is saved in the
You can copy a ChemDraw structure to the format you specified. The current document
Clipboard as an SLN string for export to a TRIPOS remains unchanged.
application. Some file formats do not support atom labels that
contain nicknames or structural fragments. When
To copy a ChemDraw structure as an SLN string: you save in these formats, ChemDraw automatically
1. Select a structure. expands all atom labels and saves the file using the
expanded form. For more information, see
“Expanding Labels” on page 109.
choose SLN.
The following formats do not support nicknames or
The Structure is copied to the clipboard as an
structural fragments:
SLN String.
• Connection Table
• DARC F1
• DARC F1 Query
• MSI MolFile
C[1]CCCCC@1 • SMD

Exporting and Importing Using File Formats
Bitmap (.bmp) Export Only ChemDraw XML (*.xml)
Bitmap (.bmp) files store raster graphics in an array The cdxml file format is an interpreted version of
of individual bits. Bitmap images are the most cdx that conforms to the XML specification unlike
common format for continuous-tone images. binary cdx format. cdxml is text-based but contains
Because they represent a fixed number of pixels, some data. For information about XML in general,
bitmaps are resolution dependent and may appear see www.xml.org.
jagged and lose detail if they are scaled on-screen or
printed on a higher resolution printer than they were ChemDraw 3.5 (*.chm)
created for. ChemDraw 3.5 file formats are used for saving or
opening ChemDraw documents using the version
ChemDraw Template (*.ctp, 3.5.x of ChemDraw. These documents can also be
*.ctr) opened in versions 3.0, 3.0.1, 3.0.2, and 3.1 of
Use the CD Template file format to save template ChemDraw as long as atom properties are not used
documents that appear in the template pop-up menu. in the files.
ChemDraw (*.cdx) NOTE: When you save a ChemDraw file in one of

these formats, all features specific to later versions
The ChemDraw file format is the native format for
are lost. For example, multi-attached atom labels,
ChemDraw version 4.0 and later. This is a public variable attachment points, and multicenter bonds
tagged file format that stores information about a are not be saved.
ChemDraw structure in a series of data blocks. This
format is designed to be easily generated and
interpreted by other programs. This format ChemDraw 2.0 and ChemDraw
accurately stores anything that can be drawn in 2.1 (*.chm) Import Only
ChemDraw.
ChemDraw 2.0 and ChemDraw 2.1 file formats are
used for opening ChemDraw documents using the
NOTE: Imported drawings saved within a version 2.x file format of ChemDraw for Macintosh.
ChemDraw file created using ChemDraw for
You cannot save files in these formats.
Macintosh are lost when the file is opened using
ChemDraw for Windows. However, all ChemDraw
specific information is preserved. Imported
ChemDraw Stationery/Style
drawings include any graphics pasted into a Sheet (*.cds)
ChemDraw document from another Macintosh
Use ChemDraw Stationery file format to save
application. The same applies for Windows to
document settings and other objects.
Macintosh conversion.

Connection Table (*.ct) To include fonts in Windows EPS files, you must
have Adobe Type Manager (ATM) installed. Only
The Connection Table file format is a simple format ATM fonts are saved in the EPS file.
that saves a list of atom connectivities in terms of an
Encapsulated PostScript (Mac)
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element, serial number, X and Y coordinates, bond

order, and bond type. For more information, see (Macintosh) and PostScript
“Appendix G: Chemistry File Formats.”
with Preview (Windows)
DARC-F1 Format (*.f1d) Macintosh Encapsulated PostScript (Mac) files
The native file format for storing structures in the contain the scalable PostScript representation and
the QuickDraw (PICT) representation of a
Questel DARC system.
ChemDraw drawing that other Macintosh
applications can translate and view.
DARC-F1 Query (*.f1q)
You can open and view ChemDraw drawings saved
The native file format for storing queries in the
in EPS (Mac) file format and PostScript with
Questel DARC system.
Preview in various illustration, desktop publishing,
and desktop presentation applications.
Encapsulated PostScript (Text)
Windows Postscript with Preview files contain the
(Macintosh) scalable PostScript representation and the Windows
PostScript, *.eps (Windows) Metafile (WMF) representation of a ChemDraw
Export Only drawing that other Windows applications can
translate and view.
Encapsulated PostScript (Text) files (EPS (Text)),
To include fonts in Windows EPS files, you must
are ASCII text files containing the scalable
have Adobe Type Manager (ATM) installed. Only
PostScript representation of a ChemDraw drawing
ATM fonts are saved in the EPS file.
that can be opened using other applications and
platforms. No preview is included in this type of All colors are saved in the EPS file except for the
EPS file. Programs that do not support the display of Background color. To save an EPS file with a
raw PostScript can only print, not view an image on colored background, create a large colored rectangle
screen. and choose Send to Back before saving the file.
Use EPS files to share ChemDraw drawings with
desktop publishing applications such as Adobe
GIF Image (*.gif) Export Only
PageMaker and QuarkXPress. Graphics interface format (GIF) is useful for
working with the hypertext markup language
All colors are saved in the EPS file except for the (HTML) used in displaying information on the
Background color. To save an EPS file with a World Wide Web. A GIF image can be displayed
colored background, create a large colored directly on a Web page rather than having to
rectangular box using the Drawing Elements tool download the drawing for viewing in a Helper
and choose Send to Back before saving the file. For application.
more information, see “Drawing Boxes” on page 87
and “Working with Color” on page 113. ChemDraw saves GIF files according to the GIF 89a
specifications with transparent backgrounds.

ISIS/SKC and ISIS/TGF NOTE: You cannot save a reaction with an
You can save a ChemDraw document in an ISIS file intermediate step accurately in the RXN file format.
format for export to an ISIS application, or import a
file created by an ISIS application into ChemDraw. Molecules whose centers are behind or above the tip
of the arrow are considered reactants, and all
ChemDraw Pro provides two ISIS file formats:
remaining molecules are products. The reaction
• ISIS/Sketch (*.skc)—For saving files as a arrow can be at any orientation; it does not have to
binary sketch file for transfer to another ISIS be parallel to the x-axis. If a reaction contains
application running on the same operating multiple arrows, then the largest arrow is used as the
system (this format is used on the Clipboard). reaction arrow.
• ISIS/TGF (*.tgf)—For saving as an ASCII text Reaction mapping and reaction center information is
file (a Transportable Graphics File) for transfer stored in the rxn output file.
to ISIS applications on different platforms.
JDX (*.jdx, *.dx) Import
NOTE: When transferring between ChemDraw Only
and ISIS/Draw, if information in a file or on the The Joint Commission on Atomic and Molecular
Clipboard contains only non-bond, unsupported Properties (JCAMP) developed the JDX file format
objects, the information is imported as a WMF
for spectral data. JDX is a public, but not well
(metafile) or PICT graphic. However, if a supported
defined format that has numerous variations.
object, such as a bond, is also in the file or on the
Clipboard, then only the supported object appears. ChemDraw supports many of the more common
spectral variations with uniform x-axis spacing.
ChemDraw also supports Bruker NMR JCAMP
NOTE: Object types in ISIS not supported in data, which is saved with a .dx file extension
ChemDraw, such as polymers, are not transferred.
Object types in ChemDraw not supported in ISIS are When you import JDX files, they appear in the
not transferred. However, in some cases, such as window with a spectrum of a standard size that can
different arrow types, the arrow is converted to the be re-sized by dragging.
most similar form. You can export spectral data as part of a .cdx file
only.
ISIS/Reactions (*.rxn)
MDL MolFile (*.mol)
The ISIS/Reactions format (RXN) is an MDL-
MDL Information Systems, Inc. MolFile (MDL
developed format for storing chemical reaction
MolFile) file format is used by several other
information used by the ISIS family of products and
Windows, Macintosh, and UNIX chemical
others.
databases and drawing applications such as
For single step single or multi-line reactions, ISIS/Draw™, ISIS/Base™, MACCS™, and
ChemDraw uses the point of the reaction arrow as REACCS™.
the dividing line to determine which molecules in a
reaction are reactants and which are products.

ChemDraw Pro provides two MDL MolFile PICT (Macintosh)
formats:
PICT files contain a QuickDraw representation of a
• MDL MolFile (Text) ChemDraw drawing that can be used by various
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• MDL MolFile (Mac) for Macintosh only. This drawing applications. You can save a ChemDraw
file type is saved with an mmol file extension document in the PICT format so it can be opened by
and can be saved and opened with ISIS. one of these other applications. The PICT file format
contains ChemDraw structural information. PICT
MDL MolFile files are ASCII text files that can be
files created by ChemDraw version 6.0 or earlier can
created or edited in common word processing
be reopened and edited by ChemDraw version 6.0.
applications or text editors. Atom and bond property
PICT files created by ChemDraw 6.0 can be edited
information is stored in the MolFile.
by ChemDraw 3.x, but not by earlier versions of
MDL RGFile (*.rgf) file format is used by several ChemDraw.
other chemical databases and drawing applications.
All colors are saved in the PICT file except for the
The MDL File RGFile supports alternate groups
Background color.
whereas an MDL Molfile cannot. When you save a
ChemDraw file that contains alternate groups as an PICT scaled 4X (Macintosh)
MDL MolFile, it is automatically saved as an MDL
PICT scaled 4X files are the same as PICT files,
RGFile.
except that the drawing is four times larger. When
Molecular Simulations these larger files are placed into certain other
applications and shrunk back down to 1/4 size, they
MolFile (*.msm) may provide higher quality output than regular PICT
Molecular Simulations MolFile format is an ASCII files.
text file used by applications such as ChemNote™.
You can save a ChemDraw Pro document in PNG file (*.png) Export Only
Molecular Simulations MolFile format for export to PNG (Portable Network Graphics) format is an
one of these applications. alternative to the GIF format for adding graphics to
web pages. You can save, but not open, files in PNG
NOTE: ChemDraw uses the file extension “.msm” format. The PNG format is fairly new and was
for Molecular Simulations MolFiles rather than the designed to address many of the shortcomings of the
standard “.mol”, used by Molecular Simulation, GIF format. In particular, the PNG file format offers
Inc. ChemDraw recognizes files with the “.mol” file true color images, is less prone to transmission
extension as MDL MolFiles. In addition, the errors and offers a full alpha channel for specifying
extension “.msi” used in earlier versions of background or transparency options.
ChemDraw is no longer recognized in ChemDraw.
To open Molecular Simulations MolFiles that have For additional information about PNG visit:
a “.mol” or “.msi” extension you must first change http://www.boutell.com/boutell/png
the extension to “.msm”.

SMD (*.smd) TIFF file (*.tif) Export Only
Standard Molecular Data (SMD) file format, version TIFF format (Tagged Image File Format) is a high
4.3, is an ASCII text file commonly used by resolution format commonly used for saving
programs that search Chemical Abstracts Databases graphics for importing into desktop publishing
such as STN Express™. You can save your applications on the same or on different computer
platforms. TIFF images can be saved using a variety
ChemDraw document in SMD format and use the
of resolution, color, and compression options. As
file for searching in a Chemical Abstracts database. TIFF images can get rather large, choosing
appropriate options is important. The TIFF format is
SPC (.*spc) Import Only for export only.
The SPC file format was developed by Galactic
Resolution
Industries as part of the GRAMS software, which
reads spectral data from every type of spectrometer Available resolutions range from 72 (computer
and converts them to SPC format. SPC is a monitor) to 1440 dpi (high resolution output). When
well-defined, proprietary, but open standard format choosing a resolution, keep in mind that the size of
for spectral data. the file increase as the square of the resolution.
ChemDraw imports most one-dimensional spectral Color

spc formats. When you import an SPC file, it
appears in the window with a spectrum of a standard You can select from the following color options:
size that can be re-sized by dragging. • Monochrome—Forces all objects to black and
You can export spectral data as part of a .cdx file white.
only. • RGB Indexed—Stores colors using computer
Template Style Sheet monitor style of color encoding.
(*.cts) • CMYK Planar—Uses printing press style of
color encoding. Groups each color type
The Template Style Sheet file format is used for
sequentially. This provides better compression.
saving document settings and row and column
characteristics for creating ChemDraw Template For example:
documents. CCCCCCMMMMMMYYYYYYKKKKK
rather than CMYKCMYKCMYKCMYK. This
Windows Metafile (Windows option produces far better compression than
Only) (*.wmf) using the PackBits compression method.
However, many desktop publishing packages
The Windows Metafile file format saves the Graphic
do not support CMYK Planar files.
Device Interface (GDI) representation of a
ChemDraw drawing. Using the WMF file format • CMYK Contiguous—Uses printing press style
you can transfer ChemDraw drawings to other of color encoding. Stores colors non-
applications, such as Microsoft Word, that support sequentially. For example: CMYKCMYK. The
that WMF file format on the same or different
PackBits compression type provides no
computers rather than using the Clipboard. The
compression for this type of file.
WMF file format contains ChemDraw structural
information.

3. Select the options you want and click OK.
NOTE: If objects in your document are black and
white they are saved black and white regardless of
NOTE: In the Macintosh version you may want to
which Color options you set. If you import drawings
increase the memory allocated to ChemDraw if you
from other applications and want them to print
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are saving large TIFF files.

Black and White you must set the Color option to
Monochrome.
Compression
You can select from the following compression
options:
• PackBits—Used to reduce files size by
encoding repeating bytes of information as
output when using the CMYK Planar color
option. Below is a highly simplified
representation of this compression scheme. For
a line of color information such as:
CCCCCMMMMMYYYYYKKKKK, the
compression yields a smaller file by
representing the information as C46M5Y5K.
• CCITT Group 3—Used for fax transmissions
of images.
• CCITT Group 4—Used for fax transmissions
of images.
• Deflate—Similar to LZW compression. Works
well with all Color and Resolution options.
Setting TIFF options

To set these options:
• Click the Options button in the Save dialog box
to display the following dialog box.

Chapter 12: Accessing the
CambridgeSoft Web Site
Online Menu Overview
You can access different areas of the CambridgeSoft
web site from within ChemDraw with the Online
menu. To use the Online menu, you must have
internet access.
Finding Chemical
Suppliers on
ChemStore.com
Find Suppliers on ChemStore.Com opens the
ChemACX.Com page (ACX—Available Chemical
Exchange) of the CambridgeSoft web site. You can search ChemACX.Com for chemicals by
To access Lookup Suppliers on ChemStore.Com: supplier or by chemical name.
1. In ChemDraw, select the molecule for which to Finding Information on

search.
2. From the Online menu, choose Find Suppliers
ChemFinder.com
on ChemStore.com. Find Information on ChemFinder.com opens
The ChemACX.Com page opens in your ChemFinder.com, where you can search the
browser. For example the ChemACX.com page ChemFinder database for chemical information.
for Benzene is shown below. To access ChemFinder.Com:
1. In ChemDraw, select the molecule for which to

search.
2. From the Online menu, choose Find
Information on ChemFinder.com.
ChemDraw 7 Chapter 12: Accessing the CambridgeSoft Web Site • 185

Finding Chemical Suppliers on ChemStore.com
ChemFinder.com opens in your browser. The 2. Type the ACX registry number.
following page is shown for Benzene. 3. Click OK.
The Structure appears in your document.
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ACX Numbers
To Find an ACX number for a structure:
1. In a ChemDraw document, select the structure

for which you want to find an ACX number.
2. From the Online menu, choose Find ACX
Number from Structure.
The ACX number appears in the Find ACX
Number from Structure dialog box.
You can search for chemical information by, name,

CAS number, molecular formula, or molecular
weight. Follow the links to do substructure queries.
Finding ACX Structures

and Numbers
ChemDraw searches ACX and returns information
about related structures and numbers. You can place
the returned information in your document.
Browsing
ACX Structures ChemStore.com
Browse ChemStore.com opens the ChemStore page
To find an structure that corresponds to an ACX
of the CambridgeSoft web site.
number:
To access Browse ChemStore.com:
Structure from Number. • From the Online menu, choose Browse
ChemStore.com.
The Find Structure from ACX number dialog
box appears.
186 • Chapter 12: Accessing the CambridgeSoft Web Site CambridgeSoft

Finding ACX Structures and Numbers
The ChemStore.Com page opens in your The CambridgeSoft web site in your browser.
browser.
Check the CambridgeSoft web site for new product

You can search ChemStore.Com for chemicals, lab information. You can also get to ChemStore.Com,
supplies, chemistry-related software, and other ChemNews.Com, and other pages through
items you want to buy. You can access CambridgeSoft.Com.
ChemACX.Com, LabEqwip.Com, and other pages
from ChemStore.Com. Accessing the Online
Browsing ChemDraw User’s
CambridgeSoft.com Guide
Browse CS ChemDraw Documentation opens the
Browse CambridgeSoft.com opens the Home page
Technical Support Manuals page where you can
access current and previous versions of the
To access the CambridgeSoft Home Page: ChemDraw User’s Guide.
• From the Online menu, choose Browse
CambridgeSoft.com.

Browsing CambridgeSoft.com
To access the CambridgeSoft Manuals page: The Tech Support page opens in your browser.
1. From the Online menu, choose Browse

CS ChemDraw Documentation.
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2. Click version of the manual to view.

A PDF version of the ChemDraw User’s Guide
appears.
Use the Tech Support page to find answers to
Accessing Frequently Asked Questions (FAQs), the technical
CambridgeSoft support newsletter, documentation, downloads, and
contact a Technical Support Representative.
Technical Support
Browse CS ChemDraw Technical Support opens the
Tech Support page of the CambridgeSoft web site.
To access CS ChemDraw Technical Support:
CS ChemDraw Technical Support.

Accessing CambridgeSoft Technical Support
Registering Online Using the ChemOffice
Register Online opens the ChemClub page of the SDK
CambridgeSoft web site, where you can register
your copy of ChemOffice. The ChemOffice Software Developer’s Kit (SDK)
enables you to customize your applications.
To register online:
To browse the ChemOffice SDK:
1. From the Online menu, choose Register
Online.
ChemOffice SDK.
The CambridgeSoft home page opens in your
The CS ChemOffice SDK page opens in your
browser.
browser.
The ChemOffice SDK page contains

documentation, sample code, and other resources
2. Click the Register tab. for the Application Programming Interfaces (APIs).
3. Click Register Your Software.
4. Register ChemDraw.

Registering Online
Administrator

Using the ChemOffice SDK
Appendix A:
The Chemistry of ChemDraw
Overview ChemDraw’s chemical intelligence can be used as a
sophisticated “spelling” checker for chemical
ChemDraw automatically converts lines, characters, compounds. For example, if you’re investigating
and other symbols into chemically meaningful organic acids, a compound with the structural
figures as you work. This work occurs in the formula CH3COO would probably represent acetic
background, but you can choose to view this acid. Present the same formula in a paper on
chemical data using Check Structure, Analyze transition metal chemistry, and you might be
Structure, and Expand Atom Labels. ChemDraw describing a novel methylated cobalt oxide. If you
also uses this chemical data when exporting to file had asked ChemDraw to interpret it beforehand, you
formats that support only a subset of the notations would have received a message reporting a valence
that ChemDraw does. error, and you might have been prompted either to
add a negative charge or to change the
This appendix describes how ChemDraw interprets
capitalization.
what you draw and how you can help ChemDraw
better interpret what you mean. ChemDraw can offer only suggestions. If you and
your audience understand what you are trying to
ChemDraw’s Chemical depict, then you can ignore ChemDraw’s
suggestions. In many cases, you can teach
Intelligence ChemDraw to understand the notation you’re using.
For more information, see “Applying Nicknames”
ChemDraw was designed as a tool to aid in chemical
communication. Most chemists would understand on page 105.
AcOo-C6H4COOH immediately, whether or not
they recognized it as aspirin. Most computer
programs, however, require what is known as a
“complete connection table,” in this case, a
collection of 21 atoms connected by 5 double bonds
and 16 single bonds in a specific pattern. ChemDraw
takes what makes sense to a chemist and converts it
into what makes sense to another application.
ChemDraw 7 Appendix A: The Chemistry of ChemDraw • 191

Database Conventions Chemical Conventions
Most databases require not only that you draw a The following table describes the chemical
structure in a way that makes sense, but that you conventions understood by ChemDraw.
Administrator
draw it in the way that the database expects it.

Consider ferrocene, which is represented in at least Bond Description
four different ways in major databases:
Single bond, unspecified
stereochemistry.
Fe
Single bond, “down”

Fe Fe
stereochemistry (into the plane of
the paper, away from the viewer),
Fe
from the first drawn atom to the
second drawn atom.
and 3 other isomers
Merck Index Beilstein Single bond, “up” stereochemistry
(out of the plane of the paper,
toward the viewer), from the first
HC CH
drawn atom to the second drawn
HC CH
atom.
CH
Fe
Fe CH Single bond, mixture of “up” and
CH CH “down” stereochemistries in some
CH CH unspecified proportion.
Aldrich MDL ACD

Dative bond. Often used to indicate
polar bonds, such as the N-O bond
A successful search in one database might not in pyridine N-oxide.
produce any hits in another. When in doubt, consult
the documentation for your database, and see if it Double bond, with cis/trans
offers any clues to the conventions used. stereochemistry as drawn.
Double bond, with cis/trans

stereochemistry unknown.
Tautomeric bond, either single or

double according to rules of
tautomerism.
192 • Appendix A: The Chemistry of ChemDraw CambridgeSoft

Database Conventions
When analyzing an atom label, ChemDraw starts at
Aromatic bond, part of a the left and continues to the right, applying standard
delocalized resonance system. rules of valence to determine which atoms are bound
to which. The exception is with an atom label in
Triple bond. Automatic alignment on the left side of a compound.
This sort of atom label is displayed “backwards”
Quadruple Bond. (H3CO instead OCH3) and is therefore parsed from
right to left. Standard valences for each atom are
defined in the Isotopes Table.
A single bond near a closed circle is recognized as By definition, a “simple” atom label has all bonds
aromatic: attached to the first (or last) character. A multi-
attached atom label has bonds connected to more
than one character, or has all of its bonds attached to
a specific character in the middle of the atom label.
Multi-attached atom labels are always parsed from
beginning to end, but again the beginning might be
Atom Labels on the right if the atom label was in Automatic style
and on the left side of the original structure:
A simple atom label may contain any of the
following: A multi-attached label that
O is parsed from left to right.
Cl A single element.
CH2CCH3
O
A multi-attached label that

CH3 An element and some O is parsed from right to left.
H number of hydrogen
N atoms.
H3CCH2C
Me A nickname.
(C H2)4 OH A bond attached to the
open parenthesis of a
Ala CH2 (CH2 )3OH
repeating group is treated
as if bonded to the first of
those groups.
C(OCH3)3 Repeating units within
parentheses.
O(CH 2)4CH3 (CH2)4 A bond attached to the
close parenthesis or repeat
CH2 (CH2 )2CH 2
CH2 COOC (OPh)3 A series of any count of a repeating group
combination of the is treated as if bonded to
above. the last of those groups.

Chemical Conventions
Multiple fragments within a single label can be Chemically Significant Text
specified in the following ways:
Often it is simpler to write a chemical formula like
MeOH or H2O than it is to draw out an entire atoms-
COO-Na+ Implicitly, using standard
Administrator
and-bonds structure. ChemDraw correctly interprets

valence rules.
any unambiguous structural formula. For example,
CH3COCH2CH3 is recognized as methyl ethyl
Explicitly, using a space,
COO- Na+ ketone and MeOH is recognized as methanol. On the
period (unsuperscripted
other hand, C6H6 might mean benzene, or it might
or unsubscripted), bullet,
or combination. mean one of over 200 other isomers. C6H6 is not
COO-.Na+
recognized by ChemDraw, and generates an error
message if you try to analyze it. Generally, empirical
COO-•Na+ formulas (C2H6 and H2SO4) are not recognized, but
structural formulas (CH3CH3 and HOSO2OH) are.
COO- . Na+
Molecular weight and elemental analyses of
empirical structures is possible, but the Expand
(COO-)3 . 3Na+ An unsuperscripted, Label command does not work with them. Empirical
unsubscripted integer at structures are discarded when they are transferred to
(COO-)3 . Na+ Na+ Na+
the start of a fragment is other applications that require unambiguous
recognized as a structures.
stoichiometric multiplier
and is treated as if the Chemically-significant text must be entirely in
appropriate number of Formula or, for isotopes and charges, Superscript
fragments were drawn style. ChemDraw does not recognize a chemical
explicitly. formula embedded within a larger block of text.
NH4 + If you draw a bond, add an atom

label, and then delete the bond,
you have a chemically
meaningful text block whose
font, size, and style match other
atom labels.
If you create a caption with the

H 2O text tool and set it to Formula
style, you have a chemically
meaningful text block whose
font, size, and style match other
captions.

Charges
A “floating” charge placed
Charges may be created as part of a textual atom with the Chemical Symbols
NH3
label or with the appropriate symbol from the Tool is assigned to the nearest
Chemical Symbols Palette. Charges are always atom. If no atom is within the
assigned to a specific element in the atom label, (N+)H3 distance set as the Fixed
whose acceptable valences become those of the Length, the charge is ignored
similar isoelectronic neutral element. and not assigned to any atom.
O- A charge following an element A “floating” charge placed

is assigned to that element. within a delocalized system is
recognized by the Analyze
Structure function, but is
+NH3 A charge that does not follow
discarded when saved to
an element is assigned to the
formats that require all charges
next element.
(N+)H3 to be associated with specific
atoms.
NH3 + Charges that follow a
monovalent element with a Isotopes and Elements
repeat count are assigned to the
(N+)H3 element before that element. By default, ChemDraw correctly recognizes all
isotopes in the full Table of the Elements. This data
is provided by CRC Press, Inc. Isotopes are defined
CO2- Charges that follow other
in the Isotopes Table file. You can edit this file to add
repeating units are distributed
among those units. new isotopes in any text editor.
CO(O-)
35 A superscripted number
Cl
+ Charges may be superscripted. before the element
NH3
symbol indicates
isotope numbers.
Fe++ Multiple charges are
recognized appropriately.
Isotopes can be included
CH2 13COOH
anywhere that regular
2+ Charges may have repeat
Fe elements can.
counts as long as both the
Fe
+2 charge and the repeat count are
superscripted. O Deuterium and Tritium
can be indicated by their
T T
one-letter symbols.
D 3C OD

Radicals Complexes may also be represented with explicit
lone pairs and without any bonds.
Radicals are indicated with the appropriate symbol
from the Chemical Symbols Palette. As with If you use a plain bond to indicate a complex, you
may want to set Abnormal Valence to Allowed in the
Administrator
charges, they are assigned to the nearest atom.

Radicals always occupy one free valence, in Atom Properties dialog.
addition to any charge effects.
F3B NH3 Boron trifluoride-
ammonia complex.
Ph
Ph C C O O Boron trifluoride-
Ph acetic acid
complex.
H-Dot/H-Dash HO
H-Dot and H-Dash symbols from the Chemical B

Symbols Palette indicate the stereochemistry of a F F
single hydrogen atom. These symbols are most F
commonly used in fused systems.
Heme, a
H compound with
N two formal
N Fe N
covalent bonds and
two formal donor-
N
acceptor pairs.
H HO
O
Complexes Another
representation of
Compounds with electron pairs can act as Lewis heme.
bases, bonding with Lewis acids that are electron- N
deficient. Similar behavior can be seen between lone N Fe N
pairs and metals. N
The best representation of these types of interaction HO

O
is with a dative bond from the electron-pair donor to

the acceptor. With a plain bond instead of the dative
bond, ChemDraw would report a valence error. The
dative bond more accurately represents the electron
donation.

Multi-center Attachments
CO
Multi-center attachments are meaningful only when OC
created using Add Multi-Center Attachment from CO
the Structure Menu. This command creates a Mn
pseudo-atom that is disregarded during chemical
calculations, but still allows you to create diagrams
that look meaningful to an experienced chemist.
η-C5H5Mn(CO)3
Stereochemistry
Absolute stereochemistry is calculated for
M
tetrahedral atoms and double bonds according to the
η3 or π-Allyl complex Cahn-Ingold-Prelog (CIP) priority rules. The CIP
rules are designed to order ligands by their priority
and determine a descriptor based on the orientation
of the ordered ligands in space.
A ligand is an entity attached to a stereocenter. For
example, a tetrahedral carbon has four ligands
Fe
corresponding to its four substituents. When a
tetrahedral carbon is in a ring, it still has four
ligands: the two ligands outside the ring, a third
consisting of the ring “unpeeled” clockwise, and a
fourth consisting of the ring “unpeeled”
Ferrocene, a π-Aryl complex
counterclockwise.
Five rules are used to determine the priority of
Cl Cl
ligands are summarized below in simplified form.
Ti For more detailed information, see the references.
They are checked sequentially as follows:
• Rule 1—Higher atomic number precedes lower
• Rule 2—Higher atomic mass precedes lower
Cp2TiCl2, another π-Aryl complex
• Rule 3—cis precedes trans
• Rule 4—Like pairs of descriptors precede
unlike pairs
• Rule 5—R precedes S
ChemDraw checks differences up to 15 atoms
distant from the stereocenter.

Stereochemical Indicators considering the relationship between all
After the ligands are ranked, an indicator is assigned stereocenters. Stereochemical flags apply to the
nearest structure; if no structure is within the
as shown in the following table.1
distance specified by the Fixed Length value, the
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stereochemical flag is not assigned to any structure.

Stereocenter Indicator
The Absolute
Double bond Z if the highest ranking ligand Abs
flag indicates
COOH
of each pair are on the same side the exact
of the bond; otherwise E. NH2 stereoisomer as
drawn.
Tetrahedral atom When the lowest-ranking ligand
COOH
is located behind the central
atom: NH2
• R when remaining 3 The Relative

ligands are arranged Rel
flag indicates
COOH
clockwise in descending the exact
order NH2
stereoisomer as
drawn, or its
• S when remaining 3 ligands enantiomer.
COOH COOH
are arranged OR
counterclockwise in NH2 NH2
descending order
The Racemic
Rac
• r or s is used for COOH
flag indicates a
pseudoasymmetric atoms mixture of the
NH2
exact
stereoisomer as
Stereochemical Flags COOH
AND
COOH drawn and its
enantiomer.
While the chirality of a specific stereocenter can be NH2 NH2
indicated with the appropriate wedged, hashed, or

plain bond, sometimes it is useful to indicate the Polymer Representations
relative stereochemistry of a molecule as a whole,
Brackets are used to enclose repeated structures or
1. R.S. Cahn, C.K. Ingold, and V. Prelog, “Specifica-
tion of Molecular Chirality”, Angew. Chem., Int. Ed. structural fragments. ChemDraw provides bracket
Engl. 1966, 5, 385-414 (errata: 1966, 5, 511); Angew. properties to specify the orientation and context of
Chem. 1966, 78, 413-447. the repeating units. An explanation of the bracket
V. Prelog and G. Helmchen, “Basic Principals of the
CIP-System and Proposals for a Revision”, Angew.
properties is given in “Representing Polymers and
Chem. 1982, 94, 614-631; Angew. Chem. Int. Ed. Other Repeating Units” on page 143.
Engl. 1982, 21, 567-583.
P. Mata, A.M. Lobo, C. Marshall, and A.P. Johnson,
“The CIP Sequence Rules: Analysis and Proposal for
a Revision.” Tetrahedron:Asymmetry. 1993, 4, 657-
668.

References
“Graphic Representations (Chemical Formulae) of Message Description
Macromolecules (Recommendations 1994)” Pure
Appl. Chem., 66, 2469-2482 (1994). There are too Displayed for every unlabeled
many bonds to atom with more than 4 filled
“Source-Based Nomenclature for Copolymers this unlabeled valences. Filled valences
(Recommendations 1985) “Pure Appl. Chem., 57, Carbon. include sum of bond orders,
1427-1440 (1985). Also available at: charge, radicals, and free sites.
http://www.iupac.org/publications/books/pbook/ Aromatic bonds count 1.5 each,
PurpleBook-C7.pdf. rounded down unless it is the
only bond to the atom. Charge
“Basic Definitions of Terms Relating to Polymers
is signed and includes charge
(1974)” Pure Appl. Chem., 40, 479-491 (1974) Also implied by dative bonds. The
available at: Substituents query property
http://www.iupac.org/reports/1996/6812jenkins/ treats Free Sites, Up to and
index.html). Exactly the same way: an atom
with 2 explicit bonds and
Also see the Guide for the authors of papers and
“Substituents: Up To 3” or
reports in polymer science and technology from
“Substituents: Exactly 3” or
IUPAC. “Substituents: Free Sites 1” has
three filled valences.
Query Properties
By their nature, query properties do not represent An atom in this Displayed in a variety of cases
actual chemical features, but describe broad classes label has an where ChemDraw cannot find
or groups of features. For information on using invalid valence. a place to put a bond or cannot
query properties, see “Chapter 9: Drawing Query find a bond to put on an atom.
Structures.” Valid valences for each element
are listed in the Isotopes Table
Analysis Messages file.
When ChemDraw is unable to analyze your

ChemDraw can’t Displayed when ChemDraw
structure fully, two general types of messages are
interpret this finds text that it cannot identify
displayed: label. as an element, nickname,
• Status messages that report a problem that may generic nickname, or
not affect the final analysis alternative group name.
• Critical messages that may affect the final

Parentheses don’t Displayed when parentheses
analysis
match. cannot be matched into nested
open-close pairs.

Message Description Message Description
This label has Displayed when a plus and This named Displayed for any Alternative
Administrator
conflicting or minus charge have been alternative group Group Box whose contained
unassignable assigned to the same element, contains structures have varying
charges. charges have been assigned in fragments with numbers of attachment points.
more than one way, or a charge inconsistent Since all structures within an
has been assigned to a valences. Alternative Group Box are to
nickname, generic nickname, be used interchangeably, they
or Alternative Group name. must have the same number of
attachments. This is a status
Formula cannot Displayed for every label that message only.
be computed for contains a generic nickname,
queries. an element list or an alternative This named Displayed for any Alternative
group. This is a status message alternative group Group Box that is empty. This
only; analysis continues as if contains no is a status message only.
the problematic label were not fragment.
selected.
Part of a molecule Displayed for any Alternative
Text not in Displayed for the first caption is outside of the Group Box whose border
Formula style that is not an atom label or alternative group crosses part of a structure. This
won’t be Alternative Group name, and definition. is a status message only.
interpreted. which contains any text not in
Formula, Subscript, or This isolated Displayed for unlabeled single
Superscript style. This is a bond is probably bonds unattached to other
status message only, and not intended to bonds. All bonds are
appears only once regardless of have chemical interpreted chemically, usually
how many captions are in the significance. as C2H6, and may cause
selection. unexpected results if intended
as a graphical line only. This is
This named Displayed for any structure a status message only.
alternative group within an Alternative Group
contains no Box where the structure lacks The atom is very Displayed for any atom that is
attachment point. an attachment point. This is a close to another nearly touching another atom
status message only. atom or bond. or bond but not bound to it. If a
bond really was intended, the
analysis of the structure
produces incorrect results. This
is s status message only.

Message Description Message Description
The stereocenter Displayed for any asymmetric This label has an Displayed for every label that
has no center without attached unrecognized has a numeric superscript
stereobonds wedged, hashed, dashed, or isotopic mass. immediately preceding an
specified. bold bonds. This is a status atomic symbol, where the
message only, and appears only superscripted number does not
when Show Stereochemistry is correspond to a recognized
tuned on and there is at least isotope. For example, 24CH3.
one other wedged, hashed,
dashed, or bold bond in the
structure.
There is a valence Displayed for any

and charge error odd-membered ring drawn as a
somewhere in this delocalized system (with a
aromatic system. circle in the middle), where
there is no corresponding
associated charge. For
example, a delocalized
representation of
cyclopentadiene must include
either a negative charge or a
multicenter attachment.
The stereocenter Displayed for any stereocenter

has conflicting or (tetrahedral atom, asymmetric
ambiguous double bond, etc.) where the
stereobonds absolutely stereochemistry
specified. cannot be determined from the
structure as drawn. For
example, this message would
be shown for a carbon atom
attached by bold bonds to four
different ligands. This message
is displayed only when Show
Stereochemistry is also turned
on.

Administrator

Appendix B: Technical Support
Overview You can deliver your CS Software Problem Report
Form to Technical Support by the following
CambridgeSoft Corporation (CS) provides technical methods:
support to all registered users of this software WWW:
through the World Wide Web (WWW), and through http://www.cambridgesoft.com/support/mail
our Technical Support department.
Internet: support@cambridgesoft.com
Our Technical Support pages on the WWW contain Fax: 617 588-9360
answers to frequently asked questions (FAQs) and Mail: CambridgeSoft Corporation
general information about our software. You can
access our Technical Support page using the ATTN: Technical Support
following address: 100 CambridgePark Drive
http://www.cambridgesoft.com/support Cambridge, MA 02140 USA
If you don’t find the answers you need on the
WWW, please complete the following tasks before Serial Numbers
contacting the Technical Support. When contacting Technical Support, you must
1. Check the Readme file for known limitations or always provide your serial number. This serial
conflicts. number was on the outside of the original
ChemDraw box, and is the number that you entered
2. Check the system requirements for the software when you launched ChemDraw for the first time. If
at the beginning of this User’s Guide. you have thrown away your box and lost your
3. Read the Troubleshooting section of this installation instructions, you can find the serial
appendix and follow the possible resolution number in the following ways:
tactics outlined there.
4. If all your attempts to resolve a problem fail, fill
Macintosh
out a copy of the CS Software Problem Report With ChemDraw launched, choose About CS
Form at: ChemDraw from the Apple menu. The serial
http://www.cambridgesoft.com/support/mail. number appears at the bottom left of the about box.
• Try to reproduce the problem before
contacting us. If you can reproduce the
Windows
problem, please record the exact steps that With ChemDraw launched, choose About CS
you took to do so. ChemDraw from the Help menu. The serial number
• Record the exact wording of any error appears at the bottom left of the about box.
messages that appear. For more information on obtaining serial numbers
• Record anything that you have tried to correct and registration codes, see:
the problem. http//www.cambridgesoft.com/support/
codes.cfm
ChemDraw 7 Appendix B: Technical Support • 203

Troubleshooting Change the VM as follows:
• Macintosh OS 8/ 9: Memory control panel.
This section describes steps you can take that affect
the overall performance of ChemDraw, as well as • Windows 95/98 and Windows NT 4.0:
Administrator
System control panel, Performance tab.

steps to follow if your computer crashes when using
a CS software product.
System Crashes
Launching ChemDraw should never crash, but below are the
If ChemDraw can’t find the ChemDraw Items steps you should go through to try to resolve issues
folder, you are not able to launch the program. For that cause computer crashes while using a CS
additional information about the appropriate software product.
location, see “The ChemDraw Items Folder” on
1. Restart your computer (Macintosh) or restart
page 17.
Windows and try to reproduce the problem. If
Performance the problem recurs, continue with the following
steps.
Below are some ways you can optimize the
2. Take the steps appropriate for your system:
performance of ChemDraw:
• Macintosh OS 8/ 9: Use your Extensions
• (Macintosh): Increase the total amount of
Manager control panel to restart your
memory that the application can use:
computer with MacOS base extensions on.
• Select the ChemDraw application icon in the
If the problem no longer occurs, then you likely
Finder when ChemDraw is not running.
have an extension conflict. You should
• From the Edit menu, choose Get Info. determine which extension is causing the
Increase the memory allocation in the conflict, and then not have it load when using
Preferred size text box in the Memory ChemDraw. To isolate an extension, disable
Requirements section of the dialog box. half of your extensions using the Extensions
• (Windows) In the Performance tab in the Manager and test the problem again. Keep
System control panel (Windows NT 4.0), disabling half of your extensions until you find
allocate more processor time to ChemDraw. which extensions are causing the problem.
Please inform Technical support which
• Install more physical RAM. The more you
extensions are causing the problem.
have, the less ChemDraw will have to access
your hard disk to use Virtual Memory. • Windows: The most common conflicts for
Windows users concern Video Drivers,
• Increase the Virtual Memory (VM). Virtual
Printer Drivers, screen savers, and virus
memory extends RAM by allowing space on
protection. If you do need to contact us, be
your hard disk to be used as RAM. However,
sure to determine what type and version of
the time for swapping between the application
drivers you are using.
and the hard disk is slower than swapping with
physical RAM. Video Driver related problems: If you are
having problems with the display of
ChemDraw, try restarting your computer in
204 • Appendix B: Technical Support CambridgeSoft

Safe Mode (VGA mode for WinNT users).
See your Windows Help for restarting in Safe
Mode. If Safe (or VGA) mode helps, your
original video driver may need to be
updated—contact the maker of the driver and
obtain the most up-to-date driver. If you still
have trouble contact us with the relevant
details about the original driver and the
resulting problem.
Printer Driver related problems: Try using
a different printer driver. If using a different
driver helps, your original driver may need to
be updated–contact the maker of the driver
and obtain the most up-to-date driver. If you
still have trouble contact us with the relevant
resulting problem.
3. Try reinstalling the software. Before you
reinstall, uninstall the software and disable all
background applications, including screen
savers and virus protection. See the complete
uninstall instructions on the Technical Support
page on the WWW.
4. If the problem still occurs, use our contact form
at:
http://www.cambridgesoft.com/support/mail
and provide the details of the problem to
Technical Support.
ChemDraw 7 Appendix B: Technical Support • 205

Administrator
206 • Appendix B: Technical Support CambridgeSoft

Appendix C: Document Settings
Creating Style Sheets b. Type a name for the document.
c. Select the ChemDraw Items folder as the
and Stationery Pads location for saving the template.
5. Click OK or Save.
To create your own Style Sheet or Stationery Pad:
1. Create a new document. ChemDraw Style Sheets

2. Enter the settings in the Page Setup, Drawing,
Text Settings, and Color Palette dialog boxes.
and Stationery Pads
3. From the File menu, choose Save As. This following table contains drawing settings and
an example structure for each of the Style Sheets and
4. In the Save As dialog box:
Stationery Pads ChemDraw provides.
a. Select the CD Style Sheet (Windows) or CD
Stationery (Macintosh) file format.
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets/Stationery Pads
ACS 1996 • Fixed Length: 14.4 pt
ACS 1996 • Bold Width: 2 pt
• Line Width: 0.6 pt
• Margin Width: 1.6 pt
HO
• Hash Spacing: 2.5 pt
• Chain Angle (degrees): 120
O • Bond Spacing (% of length): 18
• Atom Label Font (Win/Mac): Arial/Helvetica
H N • Atom Label Size: 10 pt
H • Caption Font (Win/Mac): Arial/Helvetica
HO • Caption Size: 10 pt
• Drawing Area (Width x Height): 540 pt x 720 pt
Morphine
Morphine • Page Size: US Letter
• Reduction (%): 100
ChemDraw 7 Appendix C: Document Settings • 207

ChemDraw Style Sheets and Stationery Pads
Adv. Synth. Catal. • Fixed Length: 17 pt

Adv. Synth. Catal. • Bold Width: 2 pt
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HO • Line Width: 1 pt
O
• Bond Spacing (% of length): 18
H • Atom Label Size: 10 pt
N
H • Caption Font (Win/Mac): Times New Roman/Times
• Caption Size: 12 pt
HO • Drawing Area (Width x Height): 540 pt x 720 pt
Morphine
Helvetica Chimica Acta • Fixed Length: 17 pt

Helvetica Chimica Acta • Bold Width: 2.9 pt
HO
• Margin Width: 2 pt
• Hash Spacing: 2 pt
• Bond Spacing (% of length):14
O
N
• Caption Font (Win/Mac): Arial/Helvetica
H
HO • Drawing Area (Width x Height): 368 pt x 720 pt
Morphine
208 • Appendix C: Document Settings CambridgeSoft

J. Chin. Chem. Soc.
• Fixed Length: 18 pt
J. Chin. Chem. Soc. • Bold Width: 2.5 pt
HO • Line Width: 1 pt
O • Bond Spacing (% of length): 20
H
N • Atom Label Size: 12 pt
H • Caption Font (Win/Mac): Arial/Helvetica
HO
• Drawing Area (Width x Height): 693 pt x 918 pt
Morphine
• Fixed Length: 14.4 pt

J. Mol. Mod. • Bold Width: 2 pt
HO
O • Atom Label Font (Win/Mac): Times New Roman/Times
H N • Atom Label Size: 10 pt
HO • Caption Size: 10 pt
• Drawing Area (Width x Height): 8.5 cm x 25.4 cm (1
Morphine column); 17 cm x 25.4 cm (2 column)
• Page Size: US Letter

New Document
• Bold Width: 2 pt
Administrator
• Line Width: 1 pt
HO • Margin Width: 2 pt
O
• Atom Label Size: 10 pt
N
H
• Drawing Area (Width x Height): 7.5 in x 10 in
HO
Morphine
New Slide
HO • Line Width: 1.6 pt
O • Atom Label Font (Win/Mac): Arial/Helvetica

N • Caption Font (Win/Mac): Times New Roman/Times
H • Caption Size: 16 pt
HO • Drawing Area (Width x Height): 7.5 in x 10 in
Morphine • Reduction (%): 100

Phytomedicine • Bold Width: 1.33 pt
• Line Width: 1pt
HO • Hash Spacing: 3 pt
O • Caption Font (Win/Mac): Arial/Helvetica
H • Drawing Area (Width x Height): 540 pt x 720 pt
N • Page Size: US Letter
H • Reduction (%): 100
HO
Morphine
• Fixed Length: 0.43 cm

RSC 1 & 2 Column
• Bold Width: 0.056 cm
• Line Width: 0.016 cm
HO
• Margin Width: 0.044 cm
• Hash Spacing: 0.062 cm
O
H • Chain Angle (degrees): 120
N
H • Bond Spacing (% of length): 20
HO • Atom Label Font (Win/Mac): Arial/Helvetica
Morphine • Atom Label Size: 9 pt
• Drawing Area (Width x Height): 8.9 cm x 25.4 cm (1
column); 19 cm x 27.7 cm

SYNTHESIS, SYNLETT
Administrator

HO • Margin Width: 1.3 pt
O • Chain Angle (degrees): 120

H N
H • Atom Label Font (Win/Mac): Arial/Helvetica
HO
Morphine • Caption Size: 10 pt
• Drawing Area (Width x Height): 12 cm x 26.7 cm
• Page Size: A4

Appendix D: Automation
Macintosh For more information see the CambridgeSoft SDK
web pages at: http://sdk.cambridgesoft.com.
ChemDraw supports Apple Events™, a method by
which applications can send messages to each other.
Using Apple Events it is possible to develop scripts
for sequences of commands that can be executed
repeatedly.
ChemDraw supports the Required Suite, a basic set
of Apple Events that includes the Apple Events
required to open and print documents from the
Macintosh Finder.
ChemDraw supports the menu sharing Apple Events
used in conjunction with Frontier, by Userland, Inc.
Using Frontier, you can add items to the menu bar of
ChemDraw that execute Frontier scripts.
For a complete technical specification of the Apple
Events that ChemDraw supports, drag the
ChemDraw application icon onto the Script Editor
application icon or choose Open Dictionary from the
Script Editor’s File menu.
Windows
Through the ChemOffice Software Developer’s Kit
(SDK), you can use the ChemDraw Automation
interface to programmatically control ChemDraw
for Windows from any script or application written
in a language that supports Microsoft’s component
Object Model.
Using ChemDraw’s OLE embedding functionality,
you can embed ChemDraw structures in any OLE
container. The ChemDraw Menu Extensions
interface enables you to add custom menu
commands.
ChemDraw 7 Appendix D: Automation • 213

Administrator
214 • Appendix D: Automation CambridgeSoft

Appendix E: How ChemNMR Pro
Works
Overview 4000 parameters. It also implements models for
ethylenes (cis/trans) and cyclohexanes
ChemNMR Pro estimates chemical shifts for all (equitorial/axial).
hydrogen or carbon atoms for which additivity rules
are available. Following a hierarchical list, it first ChemNMR Limitations
identifies key substructures of a molecule. A
substructure provides the base value for the The program handles the following elements:
estimated shift. For example, benzene would be H, D, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si,
identified as the key substructure of trinitrotoluene. P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu,
When a substructure happens to be a ring system not Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc,
available in the data, ChemNMR approximates its Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La,
base shift using embedded rings and, if necessary, it Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb,
will even disassemble the ring into acyclic Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po,
substructures. At, Rn, Fr, Ra, Ac, Th, Pa, U, Nep, Pu, Am, Cm, Bk,
Cf, Es, Fm, Md, No, Lr. Functional groups are
ChemNMR views remaining parts of the molecule expanded automatically.
as substituents of a substructure. Each substituent
adds to or subtracts from the base shift of the In case of 1H NMR, it estimates shifts of about 90%
substructure to which it is attached. Additivity rules of all CHx-groups with a standard deviation of
determine the increment of each contribution. If an 0.2– 0.3 ppm. The use of polar solvents may
increment for a substituent cannot be determined, strongly increase these deviations. It does not
ChemNMR uses embedded substituents—smaller estimate shifts of hydrogen atoms bonded to
structural units with the same neighboring atoms. heteroatoms because they are significantly affected
Or, it will use increments of identical or embedded by solvents, concentration, impurities, and steric
substituents of a corresponding substructure by effects.
assuming that the effects of the substituents are of In case of 13C NMR, it estimates over 95% of the
the same magnitude. shifts with a mean deviation of -0.29 ppm and
ChemNMR provides a detailed protocol of the standard deviation of 5.5 ppm.
estimation process applied. It gives substructures as For more information see:
names, compound classes in most cases,
Fürst, A.; Pretsch, E. Anal. Chim. Acta 1990, 229,
substituents in form of a linear code, respectively.
17.
The data set for the 1H NMR Shift tool currently
contains 700 base values and about 2000
increments. The 13C NMR Shift tool is based on
ChemDraw 7 Appendix E: How ChemNMR Pro Works • 215

ChemNMR Limitations
Pretsch, E.; Fürst, A.; Badertscher M.; Bürgin, R.;
Munk, M. E. J. Chem. Inf. Comp. Sci. 1992, 32, 291-
295.
Bürgin Schaller, R.; Pretsch, E. Anal. Chim. Acta
Administrator
1994, 290, 295.

Bürgin Schaller, R.; Arnold, C.; Pretsch, E. Anal.
Chim. Acta 1995, 312, 95-105.
Bürgin Schaller, R.; Munk, M. E.; Pretsch, E.
J. Chem. Inf. Comput. Sci.1996, 36, 239-243.
216 • Appendix E: How ChemNMR Pro Works CambridgeSoft

ChemNMR Limitations
Appendix F: How ChemProp Works
ChemProp Values halogens and phosphorus atoms. If this method
is applied to molecules with internal hydrogen
ChemPropPro enables you to calculate predicted bonds, the standard deviation is 0.83 logP units.
values selected physical and thermodynamic
properties for structures of up to 100 atoms. The Henry’s Law
following topics describe how ChemProp obtains its
values. Henry’s Law Constant—The air to water partition
coefficient that is expressed as ratio of vapor
LogP pressure to water solubility or as a unitless
distribution coefficient that can be evaluated as a
LogP (partition coefficient for n-octanol/water)— ratio of the concentration in air to the concentration
three fragmentation methods are used to predict the in water.
logP values.
Two methods are used to predict Henry's Law
Method one is based on 94 atomic contributions constant.
evaluated from 830 molecules by least squares
1. The first is an approach based on the bond
analysis. This method works with a standard
contribution method. This method uses 59 bond
deviation of 0.47 logP units and can handle
molecules containing hydrogen, oxygen, nitrogen, contribution values and 15 correction factors.
The contributions were calculated by least
sulfur and halogens.
squares analysis using a data set of 345
1. Method two is an extension of method one that chemicals. This method estimates with a mean
is based on 120 atomic contributions evaluated error of 0.30 units and a standard deviation of
from 893 molecules by least squares analysis. 0.45 units and can handle molecules containing
In addition to the atoms introduced for method carbon, hydrogen, oxygen, nitrogen, sulfur,
one, it can handle molecules that contain phosphorus and halogens.
phosphorus and selenium atoms. This method 2. In the second method, Henry's Law constant is
works with a standard deviation of 0.50 logP estimated from an equation found using linear
units. regression. Multifunctional compounds were
2. Method three is based on 222 atomic omitted from this study. This method should not
contributions calculated from 1868 molecules be used for compounds where distant polar
by least squares analysis. This method allows a interaction is present.
calculation of logP with a standard deviation of
0.43 logP units and can handle molecules
containing hydrogen, oxygen, nitrogen, sulfur,
ChemDraw 7 Appendix F: How ChemProp Works • 217

LogP
Molar Refractivity Normal Boiling Point and Melting Point—
Estimated in K using two methods.
Molar refractivity—Two fragmentation methods 1. Joback's fragmentation method.
are used to estimate the molar refractivity value.
Administrator
2. The Joback method as modified by Stein. All

1. Method one includes 93 atomic contributions boiling points are estimated at a pressure of
evaluated from 504 molecules by using a 1 atm.
constrained least squares technique. This
method works with a standard deviation 1.27
cm3/mol and can handle molecules containing
hydrogen, oxygen, nitrogen, sulfur and
halogens.
2. The second method is an extension of method
one that includes 120 atomic contributions
evaluated from 538 molecules by using a
constrained least squares analysis technique. In
addition to the atoms introduced for method
one, this method can handle molecules with
phosphorus and selenium atoms. This method
works with a standard deviation of 0.77
cm3/mol.
ClogP and CMR

Specific algorithms for calculating LogP and molar
refractivity from fragment-based methods
developed by the Medicinal Chemistry Project and
BioByte.
For more information, see: www.biobyte.com
Other Properties
Heat of Formation, Gibbs Free Energy, Ideal Gas
Thermal Capacity, Freezing Point, Critical
Temperature, Critical Pressure, and Critical
Volume are estimated using Joback’s fragmentation
method.
218 • Appendix F: How ChemProp Works CambridgeSoft

Molar Refractivity
Appendix G: Chemistry File Formats
Overview The following is a sample Connection Table file
produced for cyclohexanol using ChemDraw. The
File formats other than ChemDraw may not preserve line numbers are added for purposes of discussion
all of your data. ChemDraw can create many types only.
of items—particularly graphical objects such as
Line 1 Cyclohexanol
boxes and curves—that cannot be saved into
chemical file formats. Line 2 7 7
Other file formats sometimes contain data that Line 3 0.0000 0.5000 0.0000 C
cannot be interpreted by ChemDraw. ChemDraw Line 4 -0.8667 0.0000 0.0000 C
always tries to interpret other file formats so that as
Line 5 -0.8667 -1.0000 0.0000 C
much chemically-relevant data is preserved, even if
that causes the actual appearance of the file to Line 6 0.0000 -1.5000 0.0000 C
change when it is saved and reopened.
Line 7 0.8667 -1.0000 0.0000 C
Most file formats supported by ChemDraw are Line 8 0.8667 0.0000 0.0000 C
proprietary or extremely complex and are
documented more thoroughly elsewhere. For Line 9 0.0000 1.5000 0.0000 O
example, you can find more information about Line 10 1 2 1 1
CambridgeSoft’s CDX file format at:
Line 11 2 3 1 1
sdk.cambridgesoft.com
Line 12 3 4 1 1
Connection Table File Line 13 4 5 1 1
Format Line 14 5 6 1 1
Line 15 1 6 1 1
The connection table format file described in this
section is generated for the cyclohexanol structure Line 16 6 7 1 1
shown below. All references to atom serial numbers Each line represents a data record containing one or
are based on the numbering shown. more fields of information about the structure.
Individual fields are delimited by space(s) or a tab.
7 OH The fields in the Connection Table format file used
by ChemDraw are discussed below. The field value
1 for Carbon 6 from the example file is included in
6 2
parentheses for reference.
5 3
4
ChemDraw 7 Appendix G: Chemistry File Formats • 219

Connection Table File Format
• Line 1 is the molecule name. The molecule 6. Bold
name is the file name when the file was created 7. Wedged with first atom at narrow end
using ChemDraw.
8. Wedged with second atom at narrow end
• Line 2 contains two fields: the first field is the
Administrator
9. Wavy
number of atom labels, and the second field is
the number of bonds. These fields must be 10. Hollow wedge with narrow end towards 1st
separated by at least one space. atom
• Lines 3–9 each contain 4 fields describing 11. Hollow wedge with narrow end towards 2nd
information about the individual atoms: the first atom
field is the X Cartesian coordinate (0.8667), the 12. Dative bond with arrow towards 2nd atom
second field is the Y Cartesian coordinate
13. Dative bond with arrow towards 1st atom
(0.0000), the third field is the Z Cartesian
coordinate (0.0000), and the fourth field is the
atom label (C).
The spacing of these fields is very important.
Any data outside the following columns
(especially data overlapping the ranges) may
render a file unreadable.
• Field 1: Columns 0–9
• Field 4: Columns 31–end
• Lines 10–16 each contain four fields describing
information about the individual bonds between
the atoms: the first two fields represent the
serial numbers of the atoms that are connected
by this bond (atom 1 and atom 6), the third field
is the bond order (1) and the fourth field is the
bond type (1).
The bond types for the Connection Table format are
as follows:
1. Single
2. Dashed
3. Hashed
4. Wedged hash with first atom at narrow end
5. Wedged hash with second atom at narrow end
220 • Appendix G: Chemistry File Formats CambridgeSoft

Connection Table File Format
Index
Numerics Analysis
information 124
C, 1H shifts, estimating 129
13 messages 199
35 mm Slide Boundary lines 159 Anion, drawing 85
3D models 128 Anonymous Alternative Groups 150
Apple Events, description 213
A Apply Settings command 11
Arc Tool
Abnormal Valence 136 description 8
Abnormally shaped arrows, creating 93 using 90
Absolute flag, drawing 140 Arcs
ACS Document 1996 207 drawing 90
Actual Size command 160 resizing 90
ACX information, finding 186 arcs 90
Acyclic Chain Tool, description 8 Arrow Tool
Acyclic chains description 7
adding 58 overview 86
length 58 palette 86
Add Arrows
chemical names 71 autoscaling 171
column to template 120 created with curves 93
row to template 120 resizing 87
to selection 97 Aspect Ratio, changing 102
Aligning objects Assigning
Align Submenu 163 atom mapping 150
overview 163 structures to spectra 128
rulers 161 Atom
with crosshair 162 moving 99
Alpha symbol, typing 78 numbering 75
Alternative Groups query properties 132
attachment point numbering 149 Atom Label text boxes, closing 78
attachment point symbol 148
Attachment Rank indicators 148
defining 147
description 147
multiple attachment points 148
Always Display and Print Atom Mapping 151
ChemDraw Index • 221

Atom Labels Automation 213
automatic justification 67 AutoNom 71
creating 72 Autosave 13
deleting 73 Autoscale
editing 72 bonds 171
hotkeys 73 empty document window 172
Index
justification 67 template color 117

layering 72 when transferring 170
margin width 72
multi-attached 111 B
overview 65
repeating 75 Background color, printing 18
specification 193 Baseline style, captions 66
text box 72 Benzene Ring
text boxes, creating new line 78
changing orientation 57
white space 72
drawing 57
Atom numbering
Benzene Ring Tool 56
editing 77
Beta symbol, typing 78
hiding 76
Bezier curves 91
position 77
BitMap file format 179
showing 76
Atom properties Bitmapped
abnormal valence 136 Fonts 79
description 133 printing quality 18
implicit hydrogens 134 bmp files 179
in query structures 131 Boiling Point
reaction changes 135 calculation 218
reaction stereo 135 definition 125
resetting defaults 132 Bold Bond Tool icon 52
ring bond count 134 Bold Wedge Bond Tool icon 52
substituents 133 Bold Width 50
unsaturation 134 Bond crossings
viewing 132 changing 61
Atom-To-Atom Mapping 150 white space 50
Attachment Point Bond Properties
defining 148 defining 136
multiple 148 descriptors 136
numbering 149 reaction center 139
symbol 148 removing 137
Attachment Point Tool 148 topology 138
Attachment Rank indicators, showing 149 types 137
Automatic viewing 137
drawing of structure 63 Bond query indicators 136
error checking 62 Bond Spacing, description 49
justification, atom labels 67
Mapping 151
222 • Index CambridgeSoft

Bond tool C
description 7
icons 52 Calculating
repeating a label 75 chemical properties 125
Bonds elemental analysis 125
adding 111 exact mass 125
autoscaling 171 formula 125
changing bond type 59 Molecular Weight 125
changing type 59 CambridgeSoft web site, accessing 187
double either 138 CambridgeSoft.com 187
drawing 53 Can. J. Chem. Document 207
drawing by clicking 54 Caption text boxes
editing 59 closing 78
Fixed Length 53 creating new line 78
layering 61 Captions
length and angle display 52 Analysis information 125
margin width 50 autoscaling 171
multi center attachment 109 coloring 69
orientation, changing 60 converting to structures 64
orientation, dative bond 53 creating 70
orientation, wedge bond 53 creating tables 167
quadruple 55 editing 70
selecting 96 formula 66
types 192 inserting from structure 71
Border of page 155 inserting rows in tables 168
Boxes justification 66
drawing 87 setting Font, Size and Styles 68
rotating 88 subscript 66
Braces 89 superscript 66
Bracket Table column spacing 168
usage 144 text overview 70
Brackets width 70
description 8 Carbon-13 shifts, see 13C, 1H shifts, estimating
drawing 89 Cation, drawing 85
properties, exporting 146 CCITT Group 3 and 4 184
setting properties 143 CD Template 179
tool 89 cds format 180
using to represent polymers 143 cdx
Bring to Front command 164 file format 179
Bruker JCAMP file format 181 saving as 15
Bullet, typing 78 cdxml format 179
Center on Page command 163
Centering objects 163
Chain Angle, description 49

Changing Chemical properties
aspect ratio 102 calculating 125
Bond orientation 60 ChemProp 125
bond type 59 Chemical Properties window 125
default settings 10 Chemical Symbols
perspective 159 palette 84
Index
settings when transferring 172 rotating 86

tolerance 96 tool 8, 84
Characters, special 78 Chemical syntax checking 62
Charges Chemical Warnings
specifications 195 overview 62
symbols, drawing 85 supressing 21, 62
Check Structure Chemically significant text 194
overview 123 Chemicals, purchasing online 186
when copying 124 Chemistry
Checking Chemistry 123 checking 123
Chem3D 128 of ChemDraw 191
ChemClub.com 189 ChemNews.Com 187
ChemDraw ChemNMR
2.x file format 179 limitations 215
3.5 file format 179 using 129
cdx format 179 ChemOffice SDK, accessing 189
closing 19 ChemProp
ctp, ctr file formats 179 calculations 217
customizing 9 description 217
HotKeys 17 using 125
HotKeys File 74 ChemStore.com 186
Nicknames 105 chm files 179
opening 5 CIP Rules 197
ChemDraw Items folder Clean Up Structure command 111
description 17 Clearing
HotKeys 73 mapping 152
isotope table 136 spectrum-structure assignments 129
moving 17 stereochemical markers 126
nicknames 105 Click to select objects 96
Open Special 17 Clipboard
overview 17 Check Structure 124
scripts 11 copy 99
style sheets and stationery pads 13 cutting 98
templates 117 Exporting 176
window menu 17 moving objects 98
ChemDraw Laser Prep 18 pasting 98
ChemDraw SDK 213 transferring objects 169
ChemFinder.com 185 viewing contents 169
Clipping file 170

CLogP 126 Creating
Closed Brackets, rotating 88 atom labels 72
Closed style, shapes 93 HotKeys 74
Closing mirror images 101
caption text box 78 new document 12
ChemDraw 19 SLN strings 178
documents 16 Stationery Pads 207
CMR 126 Style Sheets 207
CMYK, Planar and Contiguous 183 tables 167
Color templates 119
autoscaling 171 text 65
menu 114 Critical Pressure
overview 113 calculation 218
saving settings 117 definition 126
Color dialog box 115, 116 Critical Temperature
Color Palette 115 calculation 218
Coloring definition 125
captions 69 Critical Volume
objects 114 calculation 218
Column spacing 168 definition 126
Compression 184 Crosshair
Connection Table displaying 162
example file 219 moving 162
file format 180, 219 using to align objects 162
Context-sensitive Help 3 CT file format 180
Contract label 108 CTP file format 179
Conventions 2 CTR file format 179
Convert name to structure CTS file format 183
limitations 63 Curves
Convert structure to name, automatic captions 71 autoscaling 171
Converting for creating arrows 93
captions to structure 64 segment, deleting 93
name to structure 63 Custom templates 119
to 3D 128 Customized settings, saving 10
Copy Customizing
and Check Structure 124 ChemDraw 9
As SLN command 178 menu extension DLLs 213
As SMILES command 177 saving document settings 10
drag and drop 170 using Scripts 19
duplicating objects 99 Cut
objects 99 objects 98
transferring objects 169 using clipboard 169
Cycloalkane rings, converting to delocalized rings
57

Cyclohexane Chair Ring Tool Deleting
description 56 atom labels 73
orientation 57 Backspace key 97
Cyclohexane Ring Tool 56 curve segment 93
Cyclooctane Ring Tool 56 Delete key 97
Cyclopentadiene Ring Tool 56 Nicknames 108
Index
Cyclopentadiene Ring, changing orientation 57 objects 97

Cyclopentadiene rings, drawing 57 Pen tool shapes 93
Cyclopentane Ring Tool 56 Delocalized rings, drawing 57
Cyclopropane Ring Tool 56 Deselecting objects 97
Detecting errors
D Automatic error checking 62
Check Structure command 123
Daggers 89 Disable chemical warnings 21, 62
DARC-F1 Discarding changes 15
Format 180 Displaying
Query Format 180 atom mapping 151
Dashed Bond Tool icon 52 cross hairs 162
Databases entire page 160
support for query structures 131 Info window 52
supported 131 reaction mapping 151
Dative Bond rulers 161
drawing 53 Distorting objects 102
Tool icon 52 Distributing objects 163
Default DLL 213
atom properties, resetting 132 Docking
bond properties, resetting 137 palettes 8
changing 10 toolbars 9
document location 12 Document
file format 13 creating 12
save file format 15 location, default 12
Stationery pad 10 multi-paged 155
Style Sheet 10 posters 156
tool 8, 53 reverting to last saved 15
Defined Nickname 106 saving 15
Deflate compression 184 settings 207
Degree symbol, typing 78 style sheet and stationery pad settings 207
Delete Column, from template 120 Document Settings, overview 10
Delete Row, from template 120 Document Setup
multiple-paged documents 156
Posters 156

Document window Drawing Elements
drawing area 155 autoscaling 171
enlarging 155 color 87
orientation 158 distorting 88
reducing 155 fill patterns 87
Documentation web page 187 resizing 88
Double bond rotating 88
changing type 59 Drawing Elements Tool 7
drawing 55 Drawing settings
orientation 60 changing defaults 10
Double either bonds, drawing 55 Fixed Angles 53
Drag and drop 170 margin width, effect on atom labels 72
Drawing margin width, effect on bond crossing 50
acyclic chains 58 Duplicating
Arcs 90 labels 75
bonds by clicking 54 objects 99
boxes 87 dx file format 181
charge symbols 85 dz2- orbitals, drawing 83
cyclopentadiene rings 57
double bonds 55 E
double either bonds 55
dz2- orbitals 83 Editing
fixed length bonds 53 atom labels 72
free sites 140 atom numbers 77
H-Dash Symbol 84 bond orientation 60
H-Dot Symbol 84 bond type 59
mirror images 101 bonds 59
orbitals 81 captions 70
quadruple bonds 55 embedded objects 173
radicals 85 generic nickname file 141
resonance delocalized rings 57 query indicators 139
rings 56 Element
rings with fixed length 56 folder 17
sigma orbitals 82 list 142
single bonds 52 not-list 142
s-orbitals 82 recognized 195
stereochemical symbols 140 Elemental Analysis
structure automatically from name 63 caption 125
triple bonds 55 description 124
with templates 118 Embedding objects 173
Drawing area 155 Encapsulated PostScript, see EPS file format
Drawing daggers 89 Enclosing objects 89

Enlarge File format (continued)
document window 155 CTR 179
page size 159 cts 183
EPS file format DARC-F1 180
Macintosh 180 EPS (MAC) 180
overview 180 EPS (TEXT) 180
Index
Text 180 GIF 180

windows with preview 180 ISIS 181
Eraser Tool 7 ISIS/Reactions 181
Error checking 62 JDX 181
Error Messages 199 MDL MolFile 181, 182
Exact Mass MDL RGFile 182
caption 125 MSI MolFile 182
definition 124 native 15
Exiting 19 PICT 182
Expanding labels 109 PICT scaled 4x 182
Exporting 176 PNG 182
bracket properties 146 rxn 181
checking structure 124 SMD 183
compatibility 152 SPC 183
mapping 152 style sheet 180
PNG 182 Template 179
query properites 152 TGF 181
query structures 152 TIF 182
TIFF 183 TIFF 183
using Clipboard 176 TPL Style sheet 183
using file formats 178 WMF 183
Fill patterns, orbital tool 81
F Filled style, shapes 93
Fit to Window 160
f1q format 180 Fixed Angles
FAQs bonds 53
online, accessing 188 orbitals 81
Technical Support 203 toggling on/off 53
File format Fixed Lengths
Bitmap 179 bonds 53
cdx 15 description 50
cdxml 179 drawing with 53
ChemDraw 179 scaling 102
ChemDraw 3.5 179 toggling on/off 53
ChemDraw Stationery 180 Flags, stereochemical. See Indicators
Connection Table 180 Flip Horizontal command 101
connection table 219 Flip type 146
CT 180 Flip Vertical command 101
CTP 179 Flush Left justification 67

Flush Right justification 67 H
Font
imaging speed 79 Hard Coded HotKeys 74
new captions 68 Hash Spacing, description 50
substitution 65 Hashed Bond Tool icon 52
Footers, creating 157 Hashed Wedge Bond tool icon 52
Format H-Dash Symbol, drawing 84
atom labels 67 H-Dot and H-Dash, specification 196
text 65 H-Dot Symbol, drawing 84
Formula command Headers, creating 157
description 124 Heat of Formation
using 66
calculation 218
Free Energy
definition 126
calculation 218
Help
definition 126
context-sensitive 3
Free Sites
Macintosh 3
drawing 140
Windows 3
in queries 133
Henry’s Law, definition 126
Freezing Point, calculation 218
Hide Crosshair command 162
Front to Back ordering 164
Fusing templates 118 Hide Rulers command 161
Hiding
atom numbering 76
G palettes 8
High resolution
G Groups 147
non-PS printing 18
Galactic Industries file format 183
Gamma symbol, typing 78 printing 18
Generic Groups 147 Highlight box
Generic Nicknames selecting 96
description 141 size 54
editing file 141 Hollow Wedge Tool icon 52
where stored 17 Home page, CambridgeSoft 187
Getting Started Tutorial 21 HotKeys
Gibbs Free Energy HotKeys.txt 74
calculation 218 overview 73
definition 126 Hydrogens, implicit 134
GIF format 180 Hyphens, Font submenu 66
GRAMS software 183
Graphical User Interface 5
Graphics, inserting form other applications 174
Greek text 78
Grouping
objects 104
orbitals 81
using 104
GUI, see Graphical User Interface

I J
Ideal Gas Thermal Capacity, calculation 218 J. Mol. Mod.
Implicit Hydrogens 134 (1 Column) 207
Imported objects, selecting 96 (2 Column) 207
Imported Picture 179 JCAMP file format 181
Index
Importing JDX file format 181

overview 176 Joback’s Fragmentation Method 218
spectral data 181, 183 Joining, structures 103
using file formats 178 Justification
Include ChemDraw LaserPrep 176 atom labels 67
Indicators captions 66
atom numbering 76
query 139 K
query, editing 139
query, positioning 140 Kekule structures 57
stereochemical
stereochemistry 127, 198 L
stereochemistry, positioning 127
Indicators, stereochemical 140 Lab supplies, purchasing online 186
Info window, displaying 52 Labels
Insert Name as Structure 63 contracting 108
Inserting expanding 109
graphics 174 Landscape page orientation 158
name as structure 63 Lasso tool
objects 174 selecting objects 95
references in Word 174 toggling with Text Tool 75
rows in tables 168 Launching 5
Installation 4 Layering
Interface 5 atom labels 72
Internet, CambridgeSoft web site 187 objects 164
IR spectra, see spectra Layout, page 155
ISIS Lewis dot symbol, see Lone Pair Symbol
Reactions 181 Ligand, defined 197
SKC file format 181 Limitations, name-to-structure 63
TGF file format 181 Line Width 50
Isotopes Lines, drawing 88
file location 17 Link nodes 143
specifications 195 List Nicknames command 108
Isotopes Table 136 LogP
isotopes.txt 136 calculation 217
definition 126
Lone Pair Symbol 84

M mol file format 181
Molar refraction index
m/e, displaying 124 definition 126
Macintosh how calculated 218
Help 3 Molecular Design Limited, see MDL
system requirements 4 Molecular mass, definition 124
Magnifying Molecular Simulations MolFile 182
with Magnification control 160 Molecular Weight
with View menu 159 caption 125
Make Spectrum-Structure Assignment 128 definition 124
Manual Mapping display in status bar 9
clearing 152 how calculated 124
overview 151 Monochrome 183
Mapping Moving
atom 150 atoms, bond tool 60
automatic 151 atoms, Selection Tool 99
clearing 152 crosshair 162
exporting 152 in tables 168
manual 151 objects 98
reaction 150 MR, see Molar Refraction index
Margin Width MS, see spectra
adjusting 50 MSI MolFile format 182
description 50 Multi-attached atom labels command 111
effect on Bond crossings 50 Multi-Center Attachments
specifying 72 command 109
Margin width, specifying 72 overview 197
Marquee tool 95 Multiple Attachment Points 148
Mass spectra Multiple Bond tool 55
importing as JDX 181 Multiple Undo 14
importing as SPC 183 Multiple-paged documents, setup 156
mass/charge, displaying 124
Maximize objects 159 N
MDL MolFile 181, 182
MDL RGFile 182 Name
Melting Point, definition 125 as structure, inserting 63
Menu Extension DLLs 213 of structure, inserting 71
Message Area Name as Structure, Paste Special 64
bond info 52 Name to structure, converting 63
display of fixed angles 53 Name-to-structure
Messages limitations 63
analysis 199 Native file format 15
status 199 New Color Button 115
Mirror images, creating 101 New Command 12
mol 182 New document 12
New Slide 207

New Template, creating 119 Open command 13
Nicknames Open Special command 12
defining 106 Opening, ChemDraw 5
deleting 108 Orbital Tool
generic 141 description 7
overview 105 fill patterns 81
Index
troubleshooting 107 Fixed Angle 81

where stored 17 overview 81
nicknames.dat 105 Orbitals
NMR, see ChemNMR, Spectra drawing 81
Non-PostScript printing grouping 81
high resolution 18 type 81
Macintosh 176 Ordering objects 164
Non-Roman text 78 Orientation
Normal Boiling Point 218 Benzene Ring Tool 57
Normal view 160 Cyclohexane Chairs 57
Numbering atoms 75 Cyclopentadiene Ring Tool 57
double Bond 60
O of page 158
rings 56
Objects templates 118
aligning 162 user-defined templates 120
centering 163 Original view 160
deleting 97 Overlap, multipaged documents 156
distributing 163
joining 103 P
moving 98
ordering 164 Packbits, compression 184
reflecting 101 Page
selecting all 97 border 155
using crosshair with 161 layout 155
using rulers with 161 orientation 158
Objects, inserting form other applications 174 overlap 156
OLE 173 setup 157
OLE automation 213 Page Definition Language
Online Help, see Help PostScript 18
Online Menu QuickDraw 18
Browse ChemStore.com 186 Page Setup
CambridgeSoft Home Page 187 page layout 157
ChemOffice SDK 189 saving settings 159
CS Chem3D Technical Support 188 Paged documents 156
Lookup Suppliers on ChemStore.com 185 Paired brackets 89
overview 185
Register online 189

Palette Positioning
Arcs 90 atom number indicators 77
Brackets 89 crosshair 161
Chemical Symbols 84 grouping 104
color 115 objects 98
Multiple bonds 55 query indicators 140
orbital tools 81 rulers 161
Query tools 139 stereochemistry indicators 127
single bonds 52 using the Clipboard 98
Palettes Posters, setup 156
docking 8 PostScript
showing 8 commands 175
tearing off 8 EPS (MAC) 180
Paper Size 158 EPS (TEXT) 180
Parentheses 89 print quality 18
Partition coefficient, definition 126 printing 18
Paste Preferences
drag and drop 170 Check Structure 124
Duplicating objects 99 drawing, see Drawing Settings 10
objects 98 highlight box 54
using clipboard 169 Include ChemDraw LaserPrep 176
Paste Special Include PostScript 176
name as structure 64 Initialize PostScript Printer 176
SMILES 178 overview 9
Pen Tool 7 print 18
Pen tool shapes require CTRL+ENTER 78
deleting segments 93 require Option+Return 78
selecting 92 text, see Text Settings 10
Perspectives, changing 159 tolerance, joining structures 103
Use Bitmap Fonts When Available 79
Pi symbol, typing 78
Print Quality 18
PICT file format 182
Printing
PICT scaled 4x file format 182
atom mapping 151
Picture Layers
background color 18
atom labels 72 ChemDraw Laser Prep 18
Plain style, shapes 93 drawing elements fill 87
PNG file format 182 effect of PostScript commands 175
Polymers high-resolution non-PostScript 18
flip type 146 include PostScript 19
repeat pattern 146 orientation (of page) 158
source-based 144 overview 18
structure-based 144 page setup 157
Portrait page orientation 158 paper size 158
PostScript atom labels 18
preferences 18
reaction mapping 151

Properties R
atom in searching 131
atom, abnormal valence 136 R Groups 147
atom, description 133 Racemic flag, drawing 140
atom, implicit hydrogens 134 Radicals
atom, query 132 drawing 85
Index
atom, reaction changes 135 specification 196

atom, reaction stereo 135 RAM 4
atom, resetting defaults 132 Reaction Atom-Atom Map Tool 150
atom, ring bond count 134 Reaction Atom-To-Atom Mapping 150
atom, substituents 133 Reaction center 139
atom, unsaturation 134 Reaction Changes 135
atom, viewing values 132 Reaction mapping
bond 136 always display and print 151
bond descriptors 136 automatic 151
bond types 137 clearing 152
bond, reaction center 139 exporting 152
bond, removing 137 manual 151
bond, topology 138 overview 150
bond, viewing 137 Reaction Stereo 135
brackets 143 Red boxes on objects 62
calculating 125 Redo 14
Proton shifts, see 13C, 1H shifts, estimating Reduce
document window 155
Q object 160
page size 159
Quadruple bonds 55 Reference numbers in Microsoft Word 174
Queries Reflection 101
multiple rings 143 Registration marks 156
Queries, see searching Registration, online 189
Query indicators Relative flag, drawing 140
editing 139 Remove
overview 139 colors 117
Query properties rulers 161
exported 152 Remove Color button 115
overview 199 Repeat command, rotations 100
Query Structures Repeating a Label, bond tool 75
description 131 Repeating actions 14
exporting 152 Repositioning
Query Tools palette 139 atom number indicators 77
Quick Reference Card, descripiton 3 query indicators 140
QuickDraw stereochemistry indicators 127
bitmapped image 18
print quality 18
Quitting 19

Require S
Ctrl+Enter to Create New Line in Atom Labels
78 Sample code, SDK web site 189
Ctrl+Enter to Create New Line in Captions 78 Save As command 16
Requirements Save command
Macintosh 4 default file format 15
RAM 4 using 15
system 4 Saving
Windows 4 a copy of a document 16
Reset defaults changes automatically 13
atom properties 132 defaults 10
bond properties 137 document 15
Resize Handle 101 in different file formats 16
Resizing template documents 121
arcs 90 with different name or location 16
arrows 87 Scale
drawing elements 88 command 102
handle, double-clicking 101
dialog box 102
objects 101
Scaling
template panes 120
by a percentage 102
Resolution, TIFF 183
fixed length 102
Resonance Delocalized rings, drawing 57
objects 102
Reversing actions 14
when Transferring information 170
Revert command 15
Scripts menu 19
RGB Indexed color 183
SDK 213
RGFile format 182
SDK Online, accessing 189
Ring Bond Count 134
Searching
Ring pointer icon appearance 56
databases 131
Ring Tool 8
export compatibility 152
Rings
online for chemical information 185
drawing 56
query properties supported 131
drawing with fixed length 56
Select All command 97
orientation 56
Selecting
Rotate
all 97
chemical symbols 86
command 100 bonds 96
dialog box 100 Lasso 95
drawing elements 88 last object 96
objects 100 last tool 96
Rotation handle 100 Marquee 95
RSC Document 207 Pen tool shapes 92
Ruler Guides 161 several objects 97
Rulers structures 97
hiding 161 Selection Rectangle
showing 161 Resize handle 101
RXN file format 181 Rotation handle 100

Selection Tool SMILES
definition 7 creating 177
deleting with Delete key 97 overview 177
deselecting objects 97 paste 178
distorting objects 102 viewing clipboard 177
highlight box 96 SMIRKS, overview 177
Index
joining 103 Software Developer’s Kit 213

Lasso 7 s-orbitals, drawing 82
Marquee 7 SPC file format 183
selecting all 97 Special characters 78
selecting several objects 97 Spectra
using 95 assigning structures 128
Selection, adding to 97 exporting 181, 183
Send to Back command 164 importing 181, 183
Set Color Button 115 importing as JDX 181
Setting importing as SPC 183
default tool 8, 53 removing assignments 129
margin width 72 Spectrum-structure assignments
preferences 9 making 128
Settings removing 129
document 10 viewing 129
highlight box 54 Spiro linkage, templates 119
tolerance 54 Squiggly Bond tool see Wavy Bond tool 52
Shaded style, shapes 93 Standard Molecular Data, see SMD
Shapes Starting 5
closed 93 Stationery Pads
filled 93 creating 207
plain 93 default 10
shaded style 93 document settings 10
Sharing Information 169 Page Setup settings 159
Shift key, deselecting objects 97 provided 207
Show Crosshair 162 saving document settings 10
Show Page 160 Status bar 9
Show Rulers command 161 Status messages 199
Show Stereochemistry 126 Stereochemical Indicators 198
Showing Stereochemical symbols, drawing 140
atom numbering 76 Stereochemistry
palettes 8 drawing mirror images 101
sigma orbitals, drawing 82 how calculated 197
single bonds, drawing 52 indicators 127, 198
Single brackets 89 indicators, repositioning 127
skc format 181 removing markers 127
SLN strings 178 showing 126
SMD file format 183 terms supported 126

Structure Templates
automatic error checking 63 Autoscaling 118
automatically checking 62 coloring 117
checking 123 creating 119
checking automatically 63 drawing with 118
converting to name 71 file format 183
selecting 97 fusing 118
show stereochemistry 126 fusing with existing structure 118
Structure Diagram Generation 111 orientation 118, 120
Structures, 3D 128 overview 117
Style Sheets panel 120
color palette 117 resizing 120
creating 207 resizing template panes 120
default 10 reusing 119
document settings 10 saving template documents 121
file format 180 spiro linkage 119
Page Setup settings 159 Text
provided 207
atom label format 67
saving document settings 10
atom label text box 72
Style, caption 66
atom label, editing 72
Subscript command 66
atom labels, automatic justification 67
Substituents 133
caption editing 70
Superatom, ISIS 181
caption, creating tables 167
Superscript command 66
Supplier, finding online 185 coloring 69
Supress chemical warnings 21, 62 creating 65
Symbol font 78 formatting 65
Symbols, adding 78 types 65
Syntax Checking 123 Text Box
Synthesis/Synlett Document 207 atom labels 72
System requirements 4 closing 78
creating new line 78
T Text Settings
captions, font, size, and style 68
Table tool 164 changing defaults 10
Tables Text Tool
column spacing 168 atom labels 72
creating 167 labeling atoms 72
creating with Table tool 164 toggling with lasso tool 75
inserting rows 168 TGF file format 181
moving in 168 Thermal Capacity, calculation 218
Technical support 203 TIFF
Template Panels 120 description 183
Template Tool options 183
description 8 resolution 183
using 118

Toggling U
between tools 96
Undo 14
fixed length/fixed angle 53 command 14
text tool with lasso tool 79 lost on save 14
Tolerance Undocking
changing 103 palettes 8
toolbars 9
Index
effect on highlight box 96

joining 103 Ungroup command 104
Unsaturation 134
setting 54 Unspecified atom properties, in queries 133
Tool Up to, in queries 133
Acyclic Chain 58 Use Bitmap Fonts When Available 79
Alternative Group 147 Use Defaults
Arc 90 atom properties 132
bond properties 137
Arrow 86 Bracket properties 143
Attachment Point 148 Preferences 10
Bond 7, 52 User’s guide, online 187
Bracket 89 User-Defined Templates 119
Chemical Symbol 84 Using the clipboard 98
Drawing Elements 87
Lasso 95 V
Marquee 95 Variable attachment command 112
Orbital 81 Viewing
Pen 90 analysis information 124
atom properties 132
Query 139 bond properties 137
Reaction Atom-To-Atom Mapping 150 chemical properties 125
setting default 8, 53 Info window 52
Table 164 Spectrum-structure assignments 129
Templates 118
Text 65 W
Toolbars Warnings, chemical 62
docking 9 Web site, CambridgeSoft, accessing 187
overview 9 Wedge Bond, drawing 53
Tools Palette 7 What’s New 1
White space, adjusting in atom labels 72
ToolTips 3 Window
Topology 138 analysis 124
TPL style sheet 183 chemical properties 125
Transferring information Window menu
across platforms 172 overview 17
keeping in scale 170 stationery documents 12
Windows Help 3
overview 176 Windows Metafile 183
Triple bond, drawing 55 WMF format 183
Troubleshooting Word inserting references 174
online 188 WWW, technical support 203
Technical Support 204
Tutorial 21 Z
Types of bonds 192 Zooming, see Changing Perspectives

Contents
Introduction Tutorial 2: Reaction Queries ................................... 20
Opening A Specific Database ...........................20
How To Use This Guide............................................ 1 Searching for Reactants ....................................21
Conventions............................................................... 1 Tutorial 3: Using Forms .......................................... 23
Additional Help ......................................................... 1 Creating Data Boxes .........................................24
Quick Reference Card .........................................1 Editing Data Boxes ...........................................25
Online Help .........................................................1 Deleting Data Boxes .........................................26
ToolTips ..............................................................2 Creating and Saving a Form .............................26
Status Bar ............................................................2 Tutorial 4: Opening a Database............................... 27
Technical Support ...............................................2 Connecting a Database to a Form .....................27
Installation and System Requirements ...................... 2 Assigning Fields to Data Boxes ........................28
Tutorial 5: Creating Your Own Database ............... 29
Chapter 1: ChemFinder Basics Assigning Fields ................................................29
Adding Records ................................................31
ChemFinder Overview .............................................. 3 Tutorial 6: Working with Subforms ........................ 32
What’s New in ChemFinder 7?................................. 3 Creating a Subform ...........................................32
Using ChemFinder .................................................... 4 Linking the Subform .........................................33
Creating a Form ..................................................4
Creating or Opening a Database .........................4 Chapter 3: Creating and Editing
Using the Database Management Scheme ..........4 Forms
The Database Model ...........................................5
Understanding Forms and Databases ..................6 Overview ................................................................. 35
Browsing, Editing, Sorting .................................6 Opening an Existing Form ...................................... 35
Searching for Compounds ..................................6 Creating Forms Manually........................................ 35
Searching for Reactions ......................................6 Using the Form Tools .......................................35
The ChemFinder Window......................................... 7 Creating a New Form ........................................36
The Status Bar .....................................................9 Using the Grid ...................................................36
Opening ChemFinder ................................................ 9 Creating Boxes ..................................................36
Opening a Blank Form ............................................ 10 Creating Frames ................................................37
Creating a Database Connection ............................. 11 Creating Boxes with Frames .............................37
Using the Database Wizard ..................................... 11 Adding Plain Text .............................................38
Closing ChemFinder ............................................... 14 Adding a Button ................................................38
Adding Pictures .................................................38
Chapter 2: Tutorials Selecting a Database................................................ 39
Opening an Existing Chemical Database ..........40
Overview ................................................................. 15 Selecting the Data to Display ............................40
Tutorial 1: Searching a Database ............................ 15 Opening a Secured MS Access Database .........40
Opening the Demo Database ............................15 Creating a Database ..........................................41
Substructure Searching .....................................16 Saving a Form ......................................................... 41
Text Searching ..................................................19
Numerical Searching .........................................19
Combined Searching .........................................20
ChemFinder Contents • i
Setting Box Properties ............................................ 42 Sorting Data ............................................................ 66
Setting Data Box Styles ....................................42 Sorting Fields ....................................................66
Viewing Structures in Sorting from the Data Table .............................66
the ChemDraw Format .....................................43 Sorting in Reverse Order ..................................66
Setting Fixed and Live Labels ..........................43 Sorting Languages Other Than English ............67
Administrator
Adding a Data Box Menu .................................44 Resetting the Database ......................................67

Adding Scroll Bars ...........................................45 Deleting Data .......................................................... 67
Hiding Data Boxes ............................................45 Working with Structures Using ChemDraw ........... 67
Customizing Text .............................................45 Viewing Models using Chem3D............................. 69
Customizing Fonts ....................................... 45 Changing the Database Scheme .............................. 69
Customizing Numbers ................................. 46 Creating a Database................................................. 70
Setting Color .....................................................47 Creating Tables ....................................................... 70
Creating Forms Automatically................................ 48 Deleting Tables ....................................................... 71
Creating and Editing Tabs....................................... 50 Attaching Tables from Other Applications ............. 71
Editing Forms.......................................................... 50 Attaching Files from a
Selecting Objects on a Form .............................50 File-Based Database .........................................71
Moving Objects ................................................51 Attaching Files from a
Resizing Objects ...............................................51 Non File-Based Database .................................72
Deleting Objects ...............................................51 Creating a Portal Database ...................................... 73
Reversing and Restoring Changes ....................52 Adding Structures to
Ordering Objects ...............................................52 Non-Chemical Databases ..................................73
Aligning and Distributing Objects ....................52 Creating Fields ........................................................ 73
Changing the Layout of an Existing Form.............. 53 Adding Multiple Structures..................................... 75
Securing Forms ....................................................... 54 Deleting Fields ........................................................ 76
Setting Security Options ...................................55 Backing up Databases ............................................. 76
Disabling Security ............................................58 Moving Databases................................................... 76
Overriding Security ..........................................58
Chapter 5: Searching
Chapter 4: Working with Data
Overview ................................................................. 79
Overview ................................................................. 59 Beginning a Search ................................................. 79
Opening Databases.................................................. 59 Clearing the Form .............................................79
Read-Only Access ............................................59 Entering and Submitting a Query .....................79
Multi-user Access .............................................60 Stopping a Query ..............................................80
Secured Access .................................................60 Viewing Results ...................................................... 80
Browsing Databases ................................................ 61 Viewing Forms in Table View .........................80
The Data Table .................................................61 Viewing Continuous Forms ..............................80
Entering Data into a Database................................. 63 Switching Views ...............................................80
Clearing the Form .............................................63 Viewing Chemical Markers ..............................81
Adding New Data .............................................63 Refining a Search .................................................... 81
Committing the New Data ................................64 Restoring a Previous List ........................................ 81
Duplicating Records .........................................64 Resetting the Database ............................................ 82
Undoing Data Entry ..........................................64 Text Searching ........................................................ 82
Editing Data ............................................................ 64 Numerical Searching............................................... 82
Editing Data ......................................................64 Date Searching ........................................................ 83
Editing Structures .............................................65 Molecular Formula Searching................................. 83
Styled Text ........................................................65 Find List .................................................................. 84
Undoing Changes .............................................66
Redoing Changes ..............................................66
ii • Contents CambridgeSoft
Structure Searching ................................................. 84 Chapter 7: Importing and Exporting
Entering a Structural Query ..............................84 Data
Exact Full Structure Searching .................... 85
Substructure Searching ................................ 85 Overview ............................................................... 105
Fragment Searching ..................................... 86 Supported File Formats ......................................... 105
Similarity Searching..................................... 86 Saving Structures................................................... 105
Stereochemistry............................................ 87 Reading a Structure ............................................... 105
Using the Current Molecule as a Query ............87 Importing Structures.............................................. 106
Finding the Current Molecule ...........................87 Importing Individual Structure Files ...............106
Reaction Searching.................................................. 88 Importing Structure Data and
Entering a Reaction Query ................................88 Reaction Data Files .........................................106
Reaction Centers ...............................................88 Adding Data to an Existing Database .............108
Atom-to-Atom Mapping ...................................89 Merge Options............................................ 109
Searching for Reactants ....................................90 Changing the Data Field Definitions ..............110
Searching for Products ......................................90 Using Log Files ...............................................111
Searching for Intermediates ..............................90 Importing from a Specified Location ..............112
SQL Searching ........................................................ 91 Exporting Data Files.............................................. 113
Combined Searching ............................................... 91 Exporting an ASCII File .................................113
Managing Search Results ........................................ 91
Saving a Hit List ...............................................92 Chapter 8: Customizing ChemFinder
Restoring a Hit List ...........................................92
Search Examples ...............................................93 Overview ............................................................... 115
Working with Multiple Hit Lists.................. 93 Setting Preferences ................................................ 115
Using Atom Lists ......................................... 94 Display Preferences ........................................115
Atom Types and Bond Types....................... 94 Structure Display........................................ 115
Searching Fullerenes .................................... 94 Using Keyboard Shortcuts ......................... 116
Searching More Than One Substructure ...... 95 Scaling Structures ...................................... 116
Printing .................................................................... 95 Framing Pictures ........................................ 116
Page Setup .........................................................96 Grid Spacing .............................................. 116
Forms ........................................................... 96 Color Preferences ............................................117
Tables ........................................................... 96 Search Type Preferences .................................117
Print Preview .....................................................97 Search Details Preferences ..............................118
General Preferences ........................................120
Chapter 6: Relational Data and Structure Registration Options................... 120
Subforms ChemFinder Opening Options ................... 120
Setting the Recent File List Size ................ 121
Overview ................................................................. 99 Customizing Toolbars ........................................... 121
Accessing Relational Data Using Subforms ........... 99 Using the Periodic Table ....................................... 122
Creating a Subform ............................................... 100 ChemFinder Automation Language (CAL) .......... 123
Changing the Layout of an Existing Subform....... 102 Getting CAL Help ...........................................124
Working with Subforms ........................................ 102 Writing a Script ...............................................124
Searching a Subform ............................................. 103 Debugging a Script .........................................125
Viewing Subform Data in a Table......................... 103 Executing a Script on a Form ................................ 125
Using Scripts in Subforms..................................... 103 Communicating with Other Applications ............. 125
Using Scripts ...................................................126
Using Visual Basic ..........................................127
Using Microsoft Access with ChemFinder .....127
ChemFinder Contents • iii

Chapter 9: Accessing the Appendix B: Formula Input Rules
Overview ............................................................... 143
Online Menu Overview......................................... 129 Rules...................................................................... 143
Finding Chemical Suppliers on ChemStore.com .. 129
Administrator
Examples ............................................................... 143

Finding Information on ChemFinder.com ............ 129
Finding ACX Structures and Numbers ................. 130 Appendix C: Similarity Rules
ACX Structures ...............................................130
ACX Numbers ................................................130 Overview ............................................................... 145
Browsing ChemStore.com .................................... 130 Complete Structure Similarity............................... 145
Browsing CambridgeSoft.com ............................. 131 Substructure Similarity.......................................... 146
Accessing the Online
ChemFinder User’s Guide .................................... 131 Appendix D: Technical Support
Accessing CambridgeSoft Technical Support ...... 132
Registering Online ................................................ 132 Technical Support Overview................................. 147
Using the ChemOffice SDK ................................. 133 Serial Numbers...................................................... 147
Troubleshooting .................................................... 148
Appendix A: Structural Query Performance ....................................................148
Features System Crashes ...............................................148
Overview ............................................................... 135 Appendix E: ChemFinder

General Properties................................................. 135 Automation Language Commands
Atoms ..............................................................135
Bonds ..............................................................135 Overview ............................................................... 149
Substituents .....................................................136 CAL Help .............................................................. 149
Charges and Radicals ......................................136 Menu Commands .................................................. 149
Isotopes ...........................................................137 Box Creation Commands ...................................... 150
Stereochemistry ..............................................137 Box Manipulation Commands .............................. 151
Normalization .................................................138 Program Execution Commands............................. 152
Atom Properties .................................................... 138 General Commands............................................... 153
Special Atom Types ........................................138 File Commands ..................................................... 154
Atom Lists ......................................................139 Database Commands............................................. 154
Atom Not-Lists ...............................................139 Variable Commands.............................................. 155
Substituents: Exactly ......................................139 Environment Variables.......................................... 157
Substituents: Up To ........................................140 Script-Only Commands......................................... 157
Substituents: Free Sites ...................................140
Implicit Hydrogens .........................................140 Index
Unsaturation ....................................................141
Bond Properties..................................................... 141
Special Bond Types ........................................141
Topology .........................................................141
Reaction Center ..............................................142
iv • Contents CambridgeSoft
Introduction
How To Use This Guide Additional Help
This guide assumes that you are familiar with the You can refer to these additional resources for
basics of your operating system. If you are not, information:
please refer to your system manual before using
• The Quick Reference Card
ChemFinder.
• Online Help
The chapters in this guide are organized by task.
They are intended to help you familiarize yourself • ToolTips
with ChemFinder and start using it as quickly and • The Technical Support department at
efficiently as possible. The tutorials demonstrate
CambridgeSoft Corporation:
most of the ChemFinder features. Perform the
tutorials in the order they are presented. The http://www.cambridgesoft.com/support
subsequent chapters provide more detailed • The CambridgeSoft SDK web site:
information.
http://sdk.cambridgesoft.com
Conventions Quick Reference Card
The following conventions are used throughout this A Quick Reference card for ChemFinder is in the
user’s guide: back of this manual. This card provides summaries
of the commands and features of the program.
NOTE: Notes such as this are used to highlight Because many of the instructions require knowledge
information supplemental to the main text. of the interface elements, use the Quick Reference
card as you perform the tutorials in
“Chapter 2: Tutorials.”
ALTERNATIVE: Alternatives such as this
describe other ways to perform a task.
Online Help
You access the online Help from the Help menu. To
CAUTION display the online version of this user’s guide or go
Cautions such as this are used to point out actions that to the Tutorials:
may result in loss of data.
• From the Help menu, select Contents or
Tutorial.
The ChemFinder Help opens.
ChemFinder Introduction • 1
Conventions
ToolTips
ChemFinder provides ToolTips as an additional
form of online help. Rest your pointer on a tool to
Administrator
display a message box with a brief description of the

tools.
• Point to a tool icon and wait.
Status Bar
The bottom left corner of the ChemFinder Status Bar
displays a more detailed description of the tool
icons.
Technical Support
For information about Windows technical support,
see “Appendix D: Technical Support.”

Requirements
For installation instructions, see the Install.txt file on
your installation CD-ROM.
ChemFinder for Windows runs on IBM compatible
computers with the following:
• Windows 95/98/Me/NT/2000
• 32 MB RAM
• 70 MB disk space
Some databases require more space.
Chapter 1: ChemFinder Basics
ChemFinder Overview ChemFinder provides two associated directories:
• Samples—contains sample database files.
ChemFinder is a database management system for
anyone who works with chemical information. It • System—contains files required by
provides a place to store chemical structures, ChemFinder.
physical properties, notes, and tables of data. It takes
the place of that box of index cards you’ve been What’s New in
using to jot notes about interesting molecules and
reactions, but does it much better! With
ChemFinder 7?
ChemFinder, you can search through data efficiently ChemFinder 7.0 includes the following new
and quickly, and you can organize the data instantly. features:
ChemFinder is integrated with the following • Database Wizard—Takes you through the
CambridgeSoft products: steps of setting up a form and a database.
• ChemDraw • Form generator—Create new forms more
easily.
• Chem3D
• Tabs in forms and subforms—Separate long
• ChemDraw for Excel forms and subforms into smaller, more
• ChemDraw for Word manageable parts.
You can draw structures in ChemDraw to store in • Drop-down menus on forms—Save typing by
your ChemFinder database and view Chem3D choosing data from drop-down menus.
models from ChemFinder. • Additional Editing Options—Align and
distribute form objects, for example.
ChemFinder allows storage, retrieval, and searching
of molecular structures, text, and numerical data. • Continuous Forms—View all records
displayed simultaneously in a series of
Use it to keep track of what you find in your routine
miniforms.
literature scans. Make a database to keep the figures
that go in your thesis or your next paper. Use it as a • Importing Structures—Import a group of
reference, together with one of the CD-ROM structures into a new database or append them
databases provided. Use it as your corporate to an existing one.
database system, available to anyone on your • View structure properties—Choose structure
network. Use it as a registration system or front-end attributes to display with your structures. Find
search engine for your big mainframe database. Use specific atoms and bonds.
it as a custom viewer for your Oracle data, with or • View structures in ChemDraw Format—In
without chemical structures. addition to viewing structures in ChemFinder
format, you can now display them in
ChemDraw format.
ChemFinder Chapter 1: ChemFinder Basics • 3

What’s New in ChemFinder 7?
• Additional search preferences—Refine your Creating or Opening a
searches with the additional preferences offered
by the Search Details tab. Database
• Folders to organize your data—Arrange your When a form contains a single box, you can begin
Administrator
data in the Data Source Tree by folders. entering or browsing data. A data source, typically
the name of a field that stores data within a database,
• Find List—Find lists of values on any
may be associated with each data box.
non-structure field.
To attach a data source to a data box:
Using ChemFinder • Point to the box and press the right mouse
button.
The general steps for using ChemFinder are as
follows: A shortcut menu appears containing an option
to display the Data Source dialog box,
• Create a form
providing the following options: one tab allows
• Create or open a database you to create or select a database, and displays
• Add or manipulate data a tree diagram of the database layout; another
tab allows you to select, create, or modify fields
• Perform a search
within the database.
Creating a Form When opening an existing database, you open the
database, choose a field, return to the form, and the
You can open a new form and create data boxes on specified type of data of the first record pops into
the form to display your data. The adjustable grid your form box. You’re ready to browse, clicking
allows you to create a neatly-organized collection of buttons to move from record to record.
data boxes. You can customize boxes in the
following ways: ChemFinder allows you to work with multiple data
tables so that you can have a true relational database.
• Style or label in various ways Through subforms, you can interactively display
• Distinguish with your choice of font and color and search multiple data tables.
• Include pictures
ChemFinder provides complete set of form editing
Using the Database
capabilities, including the following: Management Scheme
• A tool palette to choose a box style while ChemFinder maintains a table of chemical
drawing information (structure, formula, molecular weight)
• Boxes may be selected, moved, resized, or and relies on Microsoft’s Data Access Objects
restyled either singly or in groups (DAO) and Open Database Connectivity (ODBC) to
• Ability to cut and paste connect to an external database system for managing
the rest of the data. Systems with DAO or ODBC
• Multiple-level undo
drivers include Access, FoxPro, dBASE, Btrieve,
• Creating tabs
Paradox, SQL Server, Oracle, and others. If you
have any of these systems, you can trust your data to
it, and manage it either from within ChemFinder or
from within the external database system itself.
4 • Chapter 1: ChemFinder Basics CambridgeSoft

Using ChemFinder
If you don’t have a database system, ChemFinder
comes with the Microsoft Jet database engine, the
same Microsoft-developed engine used by Access
and Visual Basic. The sample databases provided
with the program are in Jet format, so if you happen
to have Access or Visual Basic, you can use those
programs to view (or edit) all the data in these
databases except for the structural information.
A collection of records is a table. A table is defined
The Database Model by a set of fields, generally set up once and rarely
modified, and a set of records which grows as entries
A database is a collection of information. In are added.
ChemFinder the information is organized into
In spreadsheet terminology:
increasing levels of complexity.
• A data item is found in a cell.
NOTE: At the simplest level is the data item • A field corresponds to a column.
itself, for example the word “pyrrole.”
• A record corresponds to a row.
• A table corresponds to a worksheet.
The data item is stored within a field, such as

A database is a storehouse for tables–possibly one,
“Mol Name.” A field contains information of a
possibly more than one. A database containing only
specific type. For example, a field can contain
one table is known as a simple (or flat or flat-file)
numeric, text, or structure information.
database.
Databases containing multiple tables are called
relational. Relational databases are discussed further
in “Chapter 6: Relational Data and Subforms” on
page 99.
A form displays data from a single table, but may
contain subforms that display data from other tables.
If the tables have a field in common, then any record
retrieved in the form calls up the related records in
A record is a set of related data items, one per field,
the subform.
representing a single entry in the database. On a
form, you see a single record at a time.

Using ChemFinder
Understanding Forms and searched by exact match, substring, or range, with
Boolean operators. Queries are flexible and entered
Databases directly on the form.
There is an important distinction between forms and
Substructure queries are drawn in ChemDraw, and
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databases. Databases are where data is actually

can include the following query features:
stored. A form is used only to display the
information stored in the database. No data is stored • Variable bond types
in a form. The form acts like a window, letting you • Query atom types
select which fields and tables you want to view.
• Atom type lists
You may want to have more than one form accessing
If the query contains stereochemistry, you can
the same database. For example, you may want to
choose whether it must be matched in the search.
create one sample form for working with structural
Hits are displayed with the query substructure
data and a more complicated one to include
highlighted in red.
literature or lab data. By switching between forms,
you can look at just those fields you want to see. For Formula queries can include ranges of elements,
more information, see “Chapter 6: Relational Data element counts of zero, and other variability. An
and Subforms” on page 99. intelligent query processor allows formulas to be
entered in free format, with repeated elements,
Browsing, Editing, Sorting subgroup counts, and without case sensitivity.
Molecular weight queries can be ranges, with target
You can create, modify, or delete boxes on the
ChemFinder form while browsing. For example, precision automatically determined based on the
number of significant digits in the query. Data
you can create a simple form showing structure and
queries can include wild card characters, arithmetic
basic data, and when you come to a compound of
interest, create a couple of temporary boxes to see and Boolean operators, or raw SQL.
additional data.
Searching for Reactions
To edit data, you modify the data directly on the
You can search and store molecular transformations,
form. You can also add new records. You access
find the products of a reaction, or find the reactants
ChemDraw from within ChemFinder to create or
that combine to create a product. Search reactions by
edit chemical structures.Changes are automatically
substructure to find bond-forming transformations,
validated and stored in the database when you move
bond-order changes, or cyclization reactions. Find
to a different record.
information on your planned synthesis routes.
To sort data, you right-click a data box and choose
Automatic atom-to-atom mapping speeds the
sort, or double-click a header in the data table view.
creation of accurate reactions and queries. The fate
of individual atoms is tracked from reactants to
Searching for Compounds
products, and reaction centers are automatically
Molecules can be searched by full structure, perceived. You can create or adjust atom-to-atom
substructure, Tanimoto similarity, formula, or mapping and reaction center information manually
molecular weight. Text and numeric data can be for complicated transformations.

Using ChemFinder
The ChemFinder space where you create and view structures and data.
The toolbars contain icons that change the way the
Window pointer behaves or that perform actions
corresponding to menu commands.
The ChemFinder window consists of menus,
commands, and toolbars and the form window. The The components of the ChemFinder window are
central part of the form window contains the work shown below.
.
Title bar Main toolbar Text toolbar Search toolbar
Main
menu
Main
Form form
toolbar
Framed
data box
Structure
box
Shortcut Subform
menu
Record
toolbar
Table
header
Data
table
Status
bar
Read-only Add Query Current Current Total

indicator indicator indicator record list size database size

The ChemFinder Window
Screen Description Screen Description
Element Element
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Current list size Displays the number of records Menu bar Contains all the commands
through which you are specific to the ChemFinder
browsing. Might be less than the application for manipulating
total database size if you have forms, tables, databases, and
recently performed a search. their contents.
Current record Displays the position within the New record Displays “ADD” if you are in
current hit list of the record you indicator the process of adding a new
are viewing. record that had not yet been
committed to the database.
Data box Displays data corresponding to a
specific field of the current Query indicator Displays “QRY” if you are in the
record. process of entering a search
query.
Data table Displays many records at once
in a rows-and-columns view. Read-only Displays “READ” if the
indicator database is read-only and cannot
be modified.
Form toolbar Contains icons representing the
form-creation tools available in
ChemFinder. Click a tool icon to Record toolbar Contains icons for commands in
select it. The selected tool the Record menu. Click an icon
determines what action is to perform the command.
carried out when you drag in a
form window. Search toolbar Contains icons for commands in
the Search menu. Click an icon
Framed data box Displays data in a Data Box to perform the command.
surrounded by a labeled frame.
Shortcut menu Provides options related to the
Main form Displays data contained in one item on which you have
record of the database. right-clicked.
Main toolbar Contains icons representing Status bar Displays information about the
general-purpose menu current state of the ChemFinder
commands such as copying, application.
saving, and printing. Click an
icon to perform the command.

The ChemFinder Window
To the left of these counters are three other
Screen Description indicators that show the general status of the
Element database. The first displays the word “READ” when
you are using a read-only database, such as one that
Subform Displays records in a table is on a CD-ROM.
related to the record shown in
the Main Form.
Table header Displays the name of a field. The second indicator displays the word “ADD”
Double-clicking on a table when you are entering a new record.
header sorts on that field.
Title bar Contains the name of the The third displays “QRY” when you are entering a
application or document as a query.
window title. Also, the title bar
can be dragged to move a
window.
To hide or show the Status Bar:
Total database Displays the total number of • From the View menu, deselect or choose Status
size records in the current table. Bar.
The Status Bar Opening ChemFinder

While you move among records, counters in the To open the ChemFinder application, do one of the
lower right corner of the ChemFinder window following:
change to indicate the current record, the current list
• Double-click the ChemFinder application icon.
size, and the total size of the database. The lower left
corner of the window displays help for menu items • Click Start, point to Programs, point to
and other information. ChemOffice 2002, and then choose
ChemFinder.
When you first open a form, the current list size
equals the total database size. The total database size
changes only when you add or delete records. If you
search to find a subset of the entries in the database,
then the current list size changes to indicate the
number of hits in the search.

Opening ChemFinder
ChemFinder opens and the ChemFinder 7 3. Deselect Show opening dialog.
dialog box appears. Subsequent openings of ChemFinder will not
display the ChemFinder 7 dialog box.
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To open the ChemFinder 7 dialog box if it is not

displayed:
• From the File menu, choose New.
Opening a Blank Form

You can open a blank form, and then create the form
through which you view data from a database. A
form contains form objects, such as data boxes and
buttons. For more information about form objects,
see “Creating Forms Automatically” on page 48.
To open a blank form:
The ChemFinder 7 dialog box enables you to • In the ChemFinder 7 dialog box, click Blank
perform the following tasks. Form, and then click Open.
• Blank Form—Open a blank form to create A blank form, Form1, appears in the
your own form. For more information, see ChemFinder window.
“Opening a Blank Form” on page 10.
• Database Connection—Allows you to open a
blank form and connect it to a database. You can
create the form manually or choose to create it
automatically. For more information, see
“Creating a Database Connection” on page 11.
• The Database Wizard—Guides you through
the process of setting up a form with a database
connection. For more information, see “Using
the Database Wizard” on page 11.
• Existing tab—Allows you to open an existing
form in your file system.
• Recent tab—Allows you to open a form on the
recently-used file list.
You can choose whether the ChemFinder 7 dialog
box is displayed when Chemfinder opens by doing
the following:
1. From the File menu, choose Preferences. For more information about creating a form and
2. In the Preferences dialog box, click the using the Form tools to customize it, see “Chapter 3:
General tab. Creating and Editing Forms.”

Opening a Blank Form
Creating a Database Using the Database
Connection Wizard
To open a blank form and connect it to a database: You can use the Database Wizard open or create a
database in which to store information and then
1. In the ChemFinder 7 dialog box, click create a form in which to display the data.
Database Connection, and then click Open.
To use the Database Wizard:
The Form Properties dialog box appears,
displaying the Database tab, and a form is 1. In the Open dialog box, click Database Wizard
created. and then click Open.
The Welcome dialog box appears.
2. Click Next.
If you want to Then click
The Relational database dialog box appears.
open an existing Open Database and
database to associate choose a database from the
with the form Open dialog box.
create a new, empty Create Database, name

database to associate the database, select a
with the form location, and then click
Save.
use the Database Database Setup Wizard.

Wizard to open a
database connection For more information, see
and design a form “Using the Database
Wizard” as follows.

Creating a Database Connection

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open an existing Open Database.

database to associate
with the form Choose a database from
the Open dialog box. For
more information, see
“Selecting a Database” on
page 39.
open an existing Open ODBC Data

ODBC data source to Source. 5. Select the table to connect to the form and click
associate with the Next.
form For more information, see
“Attaching Files from a The Structure Source dialog box appears.
Non File-Based Database”
on page 72.
create a database to Create New Database.

associate with the
form A database source tree
appears in the Form
Properties dialog box. For
more information, see
“Creating a Database” on
page 70.
4. Click Next.
If you opened a database containing more than
one table, the Table dialog box appears.
For structures from Click
the same location as the Default location.

database
a source outside of the MolServer, and in

database the MolServer
window, type a path.

Using the Database Wizard
7. Click Next. 12. Choose the size and spacing of the boxes and
The Form dialog box appears. grid:
For boxes that are Choose
larger and spaced further Large.

apart
medium, relative to the Medium.

Large and Small settings
smaller and spaced closer Small.

together
13. If your database contains at least two tables,

8. To have a Structure box to be created first in the you can create subforms by clicking Add
upper left corner of the form, click Structure in subforms.
upper left of form. 14. Click Next.
9. In Choose Fields to be included section, click The Subform dialog box appears.
the field names to include.
If you do not select this, the boxes are generated
in the order they appear in the list.
10.Select the form style:
For boxes In the Form style

section, click
surrounded by a Framed.
frame
labeled above Titled.
15. Select the sources to link from and to and then

labelled to the left Labelled. click Add.
16. Click Next.
not labeled Plain.
11. Choose the number of columns, between one

and four.

Using the Database Wizard
The final Database Wizard dialog box appears.
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17. To make changes, click Back until you find the

information to change.
18. Click Finish.
The form you created appears with data (unless
the database is new).
Closing ChemFinder
Closing an application frees up the memory that it
uses so that other applications can have more
memory available to them.
To close the ChemFinder application:
• From the File menu, choose Exit.
If you have forms open that have not been saved, a
message appears asking whether you want to save
them before you close the application.

Closing ChemFinder
Overview ChemFinder performs the following types of
searches:
The tutorials introduce you to ChemFinder basic
• Text and structure searches, demonstrated in
functions. “Tutorial 1: Searching a Database” and
Tutorial 1.
“Tutorial 2: Reaction Queries” illustrate the basics
of searching databases. “Tutorial 3: Using Forms” • Reaction searches, demonstrated in Tutorial 2.
through “Tutorial 6: Working with Subforms” In this tutorial, you will learn how to search
illustrate how to use forms to interact with databases substructures and text in the CS_Demo Database.
and how to work with data within a database. This database is included with ChemFinder as a
You may want to use the Quick Reference card sample database of approximately 300 organic and
inorganic compounds.
while you perform the tutorials.
Perform the tutorials in the sequence they are Opening the Demo Database
presented because each tutorial develops on and
refers to the previous ones. To open the CS_Demo database:
1. Open ChemFinder and in the Open dialog box,
Tutorial 1: Searching a click the Existing tab.
Database 2. From the File menu, choose Open.

The Open dialog box appears.
ChemFinder helps you organize and find
information. One way to find information is to
browse through the database one record at a time,
like turning the pages in a book. This is a good way
to see some of the information available. However,
because databases can be very big, browsing is often
inefficient.
Searching a database is like using the index of a
book. With an index, you can quickly focus on the
few pages you are interested in. When you search a
database, you find only those few records that have
the information you look for. After you have this
smaller collection (a hit list), you can then browse it
much more efficiently than you could the whole
database.
ChemFinder Chapter 2: Tutorials • 15

Tutorial 1: Searching a Database
3. In the Samples directory, select CS_demo.cfw. 2. Right-click the Structure box and choose Edit
Structure.
ChemDraw opens and you can enter your
structure search query.
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3. In ChemDraw, draw benzene.
4. Click Open.
The CS_Demo database opens in ChemFinder.
4. Click the ChemFinder window.

The benzene molecule from ChemDraw
appears.
To set the correct options for a substructure search:
1. From the Search menu, select Substructure if

it is not already selected.
2. From the Search menu, deselect Similarity if it
Substructure Searching
is already selected.
To enter a query and search for a substructure:
NOTE: You can also set search preferences on
1. From the Search menu, choose Enter Query, or the Search tab of the Preferences dialog box.
from the Search toolbar, click Enter Query For more information, see “Chapter 8:
. Customizing ChemFinder”
The form is cleared to allow you to enter your
search terms. The status indicator in the status
bar is changed to remind you that you are in
query mode and the color of the form may
change.

The Search menu should appear as follows: There are three methods for browsing the hits:
• The Record commands and toolbar—navigate
through records using the Record menu or tools.
• Data Table—view records in a table.
• Continuous Forms—view multiple records in
their own forms.
To use the Record menu or tools, do one of the
following:
• From the Record menu, choose First Record,
Previous Record, Next Record, Last Record,
or Go to Record.
• Click the corresponding buttons in the Record
toolbar.
First Go To Last
3. From the Search menu, choose Find or click Record Record Record
the Find button .
ChemFinder begins searching. The progress of
the search is indicated by counters in the status
bar at the bottom of the window.
When the search is complete, the number of hits Previous Next
is displayed in the Current List Size window of Record Record
the Status Bar, and the form displays the first
NOTE: As you change records, counters in the
hit.
Status bar indicate the current record, the current
list size, and the total size of the database.
In this search you get 123 hits of structures that To view the database in a table that shows the
contain an aromatic six-membered ring. The list records in a list:
you can browse is limited to the hits found in
• From the View menu, point to Data Table, and
the search.
then choose In Current Window.
In a substructure search, the matched portion of
each molecule is highlighted in red.
NOTE: If a search gets no hits, an alert appears

and you are returned to the query mode with the
query on display.

The Table view appears and displays all the • Position the pointer over a table header divider
records of the current list (in this case, the 123 and drag to the width you want.
records that were hit by the search) in a table.
Pointer
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To retrieve all the records in your database:

You can sort the records for a specific field in Table
View. • From the Search menu, choose Retrieve All, or
click Retrieve All .
To sort records in Table view by the MolWeight
field: NOTE: After searching, you do not need to retrieve
all your records before performing another search.
1. From the View menu, point to Data Table, and
You can perform another search directly.
then choose In Current Window.
2. Double-click on the MolWeight table header. To use continuous forms to browse your records:
1. On the View menu, point to Continuous

Forms, and then choose In Current Window.
The Continuous Forms view appears.
The molecular weight field is sorted in

increasing order.
To change the column widths of your table:

Text Searching You get 12 hits with names starting with
“benz”.
In this exercise, you perform a molecular formula
search and then a text search.
To find compounds in the CS_demo database with 5. From the View menu, point to Data Table, and
six carbons and one or two nitrogen atoms: then choose In Current Window.
1. In the CS_demo database, from the Search The Table view appears. Browse to verify that
menu, choose Enter Query. the molecular names are correct.
The form is cleared so that you can enter a new
query. NOTE: Notice that this search gave you “benzene”
but not “bromobenzene.” The query you entered
2. Click the Formula box and type C6N1-2. above is an “anchored substring” and only give you
any string starting with the indicated substring. For
NOTE: This entry specifies a molecular more information on how to specify text searches,
formula having six carbon atoms and one or see “Chapter 5: Searching” on page 79.
two nitrogen atoms.
3. Click Find or press Enter. Numerical Searching

The Status Bar indicates that 12 hits were
To search in the CS_Demo Database for compounds
retrieved from the 285 records in the database.
with molecular weights between 90 and 100:
1. Click Switch Views .

2. From the Search menu, choose Retrieve All.
4. From the View menu, point to Data Table, and
then choose In Current Window. 3. From the Search menu, choose Enter Query.
The Table view appears. Browse to verify that The form is cleared so that you can enter a new
the molecular formulas are correct. query.
4. Click the Molecular Weight box and type
To find all compounds in the CS_Demo Database
90-100.
with molecular names starting with “benz:”
1. Click Switch Views .

The Form view appears.
2. From the Search menu, choose Enter Query.
query.
3. Click the Molecule Name box, and type benz.
4. Click Find or press Enter.

You get 11 hits with molecular weights between You get 8 hits from the 285 records in the
90 and 100. database.
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6. From the View menu, point to Data Table, and 7. From the View menu, point to Data Table, and
then choose In Current Window. then choose In Current Window.
The Table view appears. Browse to verify that The Table view appears. Browse to verify that
the molecular weights are correct. the molecular names are correct.
Congratulations! You have completed the tutorial on
NOTE: A molecular weight query is a decimal
searching a database using ChemFinder.
value or range. The precision of the search depends
on the number of significant digits entered. For
more information on molecular weight searching, Tutorial 2: Reaction
see “Chapter 5: Searching” on page 79.
Queries
Combined Searching In addition to helping you organize information
about individual substances, ChemFinder also
In some cases, you may want to combine structure allows you to store and search chemical reactions.
searching with text searching to find a specific class
of compounds. For example, you may want to find There are many ways to search reactions, depending
all compounds in the database that have a benzene on what sort of information you are interested in. In
substructure and that have a molecular weight this set of exercises, you learn some general
greater than 400. methods to search for different parts of reactions
using a sample from the ISICCR database. This
To perform a combined search: database is included with ChemFinder as a sample
database of approximately 250 reactions extracted
from the ISI’s ChemPrep database of Current
The form is cleared so that you can enter a new Chemical Reactions.
query.
2. Right-click the Structure box and choose Edit Opening A Specific Database
Structure. To open the ISICCR database:
ChemDraw appears.
1. From the File menu, choose Open.
The benzene molecule appears in the form.
5. Click the Molecular Weight box and type >400.

Tutorial 2: Reaction Queries
2. In the Samples directory, select Isiccr.cfw, and 2. Right-click in Structure box and choose Edit
then click Open. Structure.
ChemDraw opens.
3. In ChemDraw, draw the following:
Mg
X
This structure represents a carbon atom bonded
to a magnesium atom, which is bonded to any
type of halogen. The arrow at the right indicates
that you are looking for this substructure as a
reactant.
The ISICCR database opens in ChemFinder. The ChemDraw substructure appears.
5. From the Search menu, select Substructure if
it is not already selected.
6. From the Search menu, deselect Similarity if it
is already selected.
The Search menu should appear as follows:
NOTE: The ISICCR.cfw form is formatted for a

large screen (1024 X 768). If you have a smaller
screen, open ISICCRsm.cfw for an improved view.
Searching for Reactants

Searching for reactants is useful if you have a known
starting material and you are interested in learning
more about what substances it can produce.
For example, to search for Grignard reactions, or

reactants:
1. From the Search menu, choose Enter Query, or 7. From the Search menu, choose Find or click
from the Search toolbar, click Enter Query the Find button.
.
The form clears.

ChemFinder searches. The progress of the search is Center property of “Make/Break.” The arrow at
indicated by counters in the status bar at the bottom the left indicates that you are looking for this
of the window. substructure as a product.
When the search is complete, the number of hits is
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NOTE: For more information about assigning

displayed in the Current List Size window of the bond properties, see the ChemDraw User’s
Status Bar, and the form displays the first hit. In a Guide.
substructure search, the matched portion of each
molecule is highlighted in red. 4. Click the ChemFinder window.
You get 3 hits—reactions in which an alkyl The ChemDraw structure is inserted in the
magnesium halide is consumed. Browse the list of form.
three hits as in previous tutorials. 5. Click Find or press Enter.
In the next exercise, you search for information on a You get 3 hits containing a product with a
particular reaction product. Searching for products carbonyl ring that was formed during the course
of reactions is very common in syntheses, where you of the reaction.
know what you are aiming for but you do not know
how to produce it. In this example, we look for
reactions that close a ring alpha to a carbonyl.
Before you start the search, restore the entire
database:
• From the Search menu, choose Retrieve All.
To perform a reaction product search:

query.
2. Right-click on the Structure data box and
choose Edit Structure. In many cases, you have some idea of both your
ChemDraw appears. starting materials and your products, but are looking
3. In ChemDraw, draw the following: for some information on how to get from one to the
other.
RngRxn
O
Rng To search for reactions that reduce a carbonyl to an
alcohol:
In this structure, both single bonds have been
1. Click Enter Query.
marked as having a “Ring” topology. The left
bond has also been marked as having a Reaction The form is cleared.
2. Right-click the Structure box and choose Edit
Structure.

3. In ChemDraw, draw the following, and set the You added the restriction that the atoms
Reaction Center Bond Properties to Change adjacent to the carbon must not be oxygen
for both reaction centers: atoms or hydrogen atoms. You specified that the
oxygen in the product must be bonded to a
O OH
hydrogen and not, for example, a second
Rxn Rxn
carbon.
NOTE: For more information about assigning 4. Click the ChemFinder window.
bond properties, see the ChemDraw User’s
The ChemDraw substructure appears.
Guide.
You get 12 hits. Each reaction shows the
The ChemDraw structure appears. reduction of a ketone to an alcohol.
5. Click Find or press Enter. Congratulations! You have completed the tutorial on
Browse through the 23 hits. Each of the searching for reactions using ChemFinder.
reactions found shows the transformation of a
carbon-oxygen double bond to a carbon-oxygen Tutorial 3: Using Forms
single bond.
Forms allow you to display your data in a
This hit list includes reductions of aldehydes, customized format, to browse and search through
acids, esters, ethers, and the desired ketone your database, and to interact with other
reduction. applications, such as ChemDraw and Chem3D.
In this example, you refine the list to get a smaller hit In this tutorial, you learn to create, edit, and save the
list. To get a ketone reduction reaction, you can following form:
refine the previous query.
To enter a more specific query:

The form is cleared.
2. Right-click the Structure box and choose Edit
Structure.
ChemDraw appears.
3. In ChemDraw, draw the following with
Reaction Center Bond Properties set to
Change for both reaction centers:
H
O O
Rxn Rxn
[NOT H,O] [NOT O,H] [NOT H,O] [NOT O,H]

Tutorial 3: Using Forms
You create forms using the Form toolbar shown 5. Draw two more boxes in the same way. You edit
below: them in later steps
.
Selection Frame Text Button Subform

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Data box Framed box Picture Grid

For detailed information about each tool, see
“Chapter 3: Creating and Editing Forms.”
A Frame, a Framed Box, and a Text Box are
Creating Data Boxes different types of boxes and require a label.
Data and structures from a database are displayed in To draw a Framed Box:
boxes. You create boxes using the tools in the Form
1. Click the Framed Box tool and drag
toolbar. The Form toolbar only appears when you
diagonally to create a framed box.
select Layout mode.
The Enter the Label dialog box appears.
To create a data box:
1. From the Main toolbar, click New .

A new, blank form appears in the ChemFinder
window.
2. Click the Layout mode tool .
2. In the Enter a Label dialog box, type Frame
The Form toolbar appears. box and click OK.
3. Click the Data Box tool . The label appears above the Framed Box.
4. In the form window, drag diagonally to create a
box.
3. Click the Frame tool .

4. Place the pointer at the corner of one of the data The picture appears in the area you dragged in
boxes and click and drag to create a border the form.
around the data box.
Editing Data Boxes

Edit the data boxes using the Selection tool:
5. In the Enter a Label dialog box, type Frame 1. Click the Selection tool .
and click OK.
2. Select the upper left box by clicking anywhere
The label appears above the box. in it.
A selected data box is designated by four black
squares at its corners.
To place a picture in your form:
1. Click the Picture tool and drag in the 3. Click an empty space in the form with the
form. Selection tool to deselect the box.
The Open dialog box appears. To select multiple boxes:
2. In the ChemFinder System directory, click • Shift+click each box.

Atomengy.wmf, and then click Open.
NOTE: You can select all the boxes on the form

by choosing Select All from the Edit menu.

The frame and the box work as one object when you Deleting Data Boxes
select, move, resize, or delete. To separate them into
To delete a data box:, do one of the following:
two objects:
• From the Edit menu, choose Bring to Front. • Select a box and press Delete or Backspace.
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• From the Edit menu, choose Clear or Cut.

To resize a box:
To clear the entire form:
• Select a single box, and resize it by dragging a
side or corner. • From the Edit menu, choose Select All, and
press Delete to remove the contents of the form.
Creating and Saving a Form

To create and save a new form:
To reposition a box: 1. Draw the form shown below.
• Select a box, point within the selection, and

drag the box.
If you select multiple boxes, dragging the center of

a selected boxes moves all of them at once.
To edit with the Clipboard: 3. In the Save As dialog box, save the form as
1. Select a box. tut3.cfw in the directory you want.
2. Try each of the following: 4. From the File menu, chose Close.
• From the Edit menu, choose Cut. Congratulations! You have completed the third
tutorial.
• From the Edit menu, choose Paste.
• From the Edit menu, choose Undo (Paste).
• From the Edit menu, choose Redo (Paste).
NOTE: Undo and Redo work over multiple levels.

You can use Undo and Redo repeatedly to reverse
multi-step operations.

Tutorial 4: Opening a The Box Properties dialog box appears with the
Database tab displayed.
Database
After you create a form, you can use it to connect to
a database that actually stores information. In this
tutorial, you use the form you saved as “tut3.cfw” in
the previous tutorial to access and retrieve
information from an existing database.
Connecting a Database to a
Form
To connect a database to your form:
1. From the File menu, choose Open. 4. Click Open Database.
NOTE: The Open and Create Database
2. Select tut3.cfw and click Open. buttons work with ChemFinder databases only.
To access data in other types of databases, use
the Attach Table button. For more information
about data sources, see “Attaching Tables from
Other Applications” on page 71.
The form you created in the previous tutorial

appears, but all of its fields are blank You can
use this form to display the demonstration
database.
3. Right-click the Structure box and choose Data
Source. 5. Select CS_demo.mdb and click Open.
The database opens, and the Box Properties
dialog box appears displaying the Database tab.
6. Select a table.

Tutorial 4: Opening a Database
A list of the tables in the database and the fields To assign fields to the other data boxes:
in each table are shown. The field you select
1. Right-click in the Name box and choose
determines what type of data appears in the box.
Molname.
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NOTE: Because you opened a database and

table, the shortcut menu displays the fields in
the database.
Assigning Fields to Data Boxes

To display structures from the CS_Demo database in
a Structure box on your form: The Molname field in the database is linked to
the Name box, and the data item for the first
• From the list of fields in the Box Properties
record appears in the Name box.
dialog box, click Structure, and then click OK.
2. Right-click in the Formula box and choose
The Structure field is linked to the Structure Formula.
box. In the Structure data box, you can see the
3. Right-click in the Mol ID box and choose
contents of the Structure field for the first
MOL_ID.
record in the CS_Demo database.

5. In the Save As dialog box, save the form as
tut4.cfw in the directory of your choice.
Congratulations! You have created your own
customized form for viewing the CS_Demo
database.

Tutorial 4: Opening a Database
Tutorial 5: Creating Your The name of the database appears in the Name
box in the Box Properties dialog box.
Own Database
In this tutorial you create a new database using the
techniques you learned in Tutorial 3.
1. Create the following new form. Select the
Layout tool if the Form toolbar is not visible.
ChemFinder creates one data table (MolTable)

containing four fields: Structure, Formula,
2. From the File menu, choose Save As, and save MolWeight, and MOL_ID.
your form as mydb.cfw. 6. Click OK.
3. Right-click in the Structure box and choose The form appears.
Data Source.
The Box Properties dialog box appears with the Assigning Fields
Database tab displayed.
To assign fields to the Structure, ID, and Formula
boxes:
1. Right-click in the Structure box and choose

Structure.
2. Right-click in the ID box and choose MOL_ID.
3. Right-click in the Formula box and choose
Formula.
Two data boxes, Name and Boiling Point, do not
have fields assigned to them.
4. Click Create Database.

5. Type mydb.mdb and click Save.

Tutorial 5: Creating Your Own Database
Create a field for the Name data box: To create a field for the Boiling Point box:
1. Right-click in the Name data box, and choose 1. Right-click in the Boiling Point data box, and
Field. choose Field.
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The Box Properties dialog box appears with the 2. Click Create Field.
Field tab displayed. The Create Field dialog box appears.
3. Type Boiling Point in the Name box.
4. Select Real from the Type drop-down menu.
NOTE: You use the field type “Real” to create

a field containing real numbers (such as -123.7
and 43.242) as data.
2. Click Create Field.

The Create Field dialog box appears.
5. Click OK.
You created two fields in the database. Assign the
fields to data boxes.
1. In the Box Properties dialog box, click

Compound Name.
3. Type Compound Name in the Name box and

click OK.
NOTE: The maximum number of characters

you can enter in any text field is 254 characters.
If you want a text field to contain more than 254
characters, choose Memo from the Type
drop-down list.
The field name appears in the data source tree.

4. Click OK.
2. Click OK.

The Name field is linked to the Name data box. The benzene molecule appears in the Structure
3. Right-click in the Boiling Point data box and Data box on the form. ChemFinder calculates
choose Boiling Point. the molecular formula.
The Boiling Point field is linked to the Boiling

Point data box.
Adding Records
Now that you created new fields and assigned them
to data boxes, you can add data to your database.
1. Deselect the Layout tool to hide the Form

toolbar. 5. Click the Name box and type Benzene.
2. Right-click the Structure box and choose Edit 6. Click the Boiling Point box and type 80.1.
Structure.
ChemDraw opens. NOTE: You do not need to enter a Molecule ID.
This field is automatically generated by
ChemFinder and cannot be edited.
To commit your new record, do one of the

following:
• From the Record menu, choose Commit
Changes.
• Click the Commit Changes button .
You entered the first record in your database. The
size of your database is indicated in the Status Bar.
Enter two more records:
1. From the Record menu, choose Add New

Record, or click Add Record .
2. Add a record for n-Pentane (shown below),
with a bp = 36.1.
4. Click the ChemFinder form.

3. Repeat step 1 and then add a record for
Cyclohexane (shown below), with a bp = 80.7.
Tutorial 6: Working with
Subforms
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Subforms allow you to display relational data. If you

have a database containing two or more data tables,
and these data tables share a common, linking field,
NOTE: After you have two or more records in
then you can display data from both tables.
your database, you can commit changes by
Whenever the value of the linking field changes in
moving to a different record using the Record
tools. the main form, the subform only displays those
records from its table which have the same value in
4. From the File menu, choose Save. the linking field. You can also use subforms to
display data from different databases.
NOTE: Choosing Save saves any changes
made to your form. Clicking Commit Changes In this tutorial, you open the CS_Demo database and
saves the data into your database. display the MolTable in the main form. Then you
display the Synonyms table of the CS_Demo
database in a subform. By defining the MOL_ID
field as the linking field, you display the two sets of
data relationally. To select a subform, you click the
title bar.
Creating a Subform
1. Open your ChemFinder form tut4.cfw.
Opening this form connects you to the
CS_Demo.mdb database.
2. Maximize the size of the tut4.cfw window by
dragging one of the bottom corners of the
window or by clicking the Maximize button.
3. Click the Subform tool .

Tutorial 6: Working with Subforms
4. In the form, click and drag to create a large To open a database using the subform:
subform.
1. Right-click on the Synonym data box in the
subform and choose Data Source.
The Box Properties dialog box appears.
NOTE: If there is not room on the right side of

your form, you can put the subform on the
bottom of the form.
You design a subform exactly like you design a main

form.
• Click the Framed Box button, and create a box
labeled Synonym within the subform.
2. Click the + symbol next to the Synonyms table
Your form should appear similar to the one
to display the fields contained in that table.
shown below:
3. Select Synonym and click OK.
You are displaying data from the MolTable of the
CS_Demo.mdb in the main form and data from the
Synonyms table of the CS_Demo.mdb in the
subform. However, the two forms are not related.
To demonstrate this:
• Navigate the form using the Record tools, and
NOTE: You may display the subform with or
note that only one form is changing its records.
without a title by right-clicking on the title bar and
selecting Properties, and then selecting the Subform
tab. A check box “With title” toggles title off and on. NOTE: When the title bar of the subform is
highlighted, the subform is active. The Record tools
and menu commands apply only to the subform. To
deactivate the subform, click any empty space on the
main form.
Linking the Subform

You must define the linking field for each table:
• MOL_ID field for MolTable.
• SYN_ID field for Synonyms.

To define the links: The MOL_ID field links the main form and
subform.
1. Right-click the title bar of the subform and
choose Properties. 5. Click anywhere outside the subform box, and
browse your database using the Record tools.
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NOTE: Clicking the title bar of a subform box As each molecule record of the MolTable is
is equivalent to clicking anywhere inside any displayed, the subform shows the first matching
other type of box. You can set the box properties ID from the Synonyms table.
and manipulate the box. Clicking inside a
subform activates the subform and allows you
to work within it.
The Subform Properties dialog box appears

with the Subform tab displayed.
6. Click inside the subform box.
Now when you browse, you are browsing only the

entries in the subform.
1. Browse the current Synonyms subset by

clicking a Record tool.
2. With the subform still active, click Switch
Views , or double-click in the subform.
2. In the Data Source Tree, choose MOL_ID.

The field appears in the Parent field section.
3. Choose SYN_ID from the Relate to list.
3. Click outside the subform and browse.

The table window shows you the complete list
of synonyms for each molecule.
To save and close the file:

Congratulations! You have completed the
ChemFinder Tutorials.
4. Click OK.

Chapter 3: Creating and Editing Forms
Overview Opening an Existing
You use forms to interact with information in a Form
database. A ChemFinder form is composed of data
boxes for viewing or modifying data items, such as To open a ChemFinder form, do one of the
structures, numbers, text, or pictures. A form can following:
also contain subforms for relational access to • In the ChemFinder 7 dialog box, click the
different data tables and different databases. Existing tab and choose the form from the
You can create a form in the following ways: directory.
• In the ChemFinder 7 dialog box, click the
• Manually, using the Form tools.
Recent tab and choose the form from the list of
• Automatically, using the Form Generator dialog recently-used files.
box.
• From the File menu, choose Open, or click
The example below shows a form displaying a . In the Open dialog box, choose the file,
single record of information from a database. and then click Open.
The file is opened, and if the form is connected to a
database, the database is opened with the first record
displayed in the form.
Creating Forms
Manually
You create a form and define it by using the Form
tools to create objects and the Box Properties dialog
box to set the form properties.
Using the Form Tools

You must use the Form Tools toolbar to design a
form. Box creation commands are not available
from the menu.
To display the Form tools, do one of the following:
• Click Layout on the Main toolbar.
• From the View menu, point to Toolbars, and
then click Form Edit.
ChemFinder Chapter 3: Creating and Editing Forms • 35

Opening an Existing Form
The Form toolbar appears providing tools for Creating Boxes
you to create and edit a form.
A ChemFinder form is composed of a collection of
Selection Form Text Button Subform boxes that display data. Each box displays one data
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item of the current record. To create a data box, use

one of the tools on the Form toolbar.
NOTE: The Form toolbar is not visible unless the

Layout button is selected.
Data box Framed box Picture Grid
The Data Box displays a data item or structure. You
Creating a New Form can use it to display any data from a database,
To create a new form: including text, numbers, dates, molecules, reactions,
or pictures. It is the only box that allows you to edit
• Click . data in the database. Data boxes do not have labels,
A blank form, Form1, appears. but you can label them by adding a Frame or Plain
Text. You can also use the Data Box to display static
data not from a database.
To draw a Data Box:

1. Click the Data Box tool .
2. On the form, press and drag diagonally to create
a box.
Using the Grid

In a new form, the snap grid is turned on by default.
This grid helps you align boxes on the form. Turning To specify what type of data is displayed in the box,
on the grid forces objects to snap to the grid as they see “Setting Box Properties” on page 42. If the form
are drawn. already has a database open, you can right-click on
the data box to choose from a list of the available
To toggle the grid on or off, do one of the following:
fields.
• Click the Grid tool on the Form toolbar.
• From the View menu, choose Grid.
NOTE: You can change the grid spacing using the

Preferences dialog box. See “Setting Preferences”
on page 115.
36 • Chapter 3: Creating and Editing Forms CambridgeSoft

Creating Forms Manually
Creating Frames Creating Boxes with Frames
The Frame tool allows you to create a label The Framed Box tool allows you to create a data box
surrounding a data box or group of boxes. When you and a frame simultaneously. You name the frame in
draw a new frame, you are automatically prompted the Enter the Label dialog box.
for a text label to be attached to it.
When you create a data box and frame with the
To create a frame: Framed Box tool, these two items are connected. To
manipulate them separately:
1. Click the Frame tool .
• Select the Framed box and from the Edit menu,
2. On the form, press and drag diagonally to create
choose Bring to Front.
a frame.
The Enter the Label dialog box appears: To create a framed data box:
1. Click the Framed Box tool .

2. On the form, click and drag to create a box.
3. In the Enter the Label dialog box, type the label
you want to attach to the frame, and click OK.
The framed data box is labeled.
3. Type the label you want to attach to the frame.
4. Click OK.
A fixed label appears on the frame.
To change a label:
1. Right-click on the edge of a frame and choose

Label.
2. Enter the new label as above.
To edit the label of a framed data box:
Another way to change a frame’s label is in the Box
Properties dialog. For more information, see 1. Select the frame by carefully right-clicking near
“Setting Box Properties” on page 44. the edge of the framed box and select Label.
2. In the Enter Box Label dialog box, type the new
You can use a frame to show “live” data from the
label.
database. If a frame is connected to a database field,
it is updated automatically as you browse or search. 3. Click OK.
For example, you might place a frame around a
structure field, where the label on the frame
represents the name of the current structure. The
label changes every time the structure does. You
must use Box Properties to set up a live data
connection for a frame.

Adding Plain Text Adding a Button
The Plain Text tool allows you to display text To place a button on a form:
without a box or a frame. You can use it to place a
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static label on the form. But, like a frame, you can 1. Write a script using the ChemFinder
use it to display live data if desired. Automation Language (CAL).
2. Click the Button tool on the Form toolbar.
To use the Plain Text tool:
3. On the form, click and drag to draw a button.
1. Click the Plain Text tool .
2. On the form, click and drag to create an area to
specify where the text will appear.
The Enter the Text dialog box appears.
4. Enter a label that corresponds to the name of the

script and click OK.
For more information about using a button to run a
3. Type the text you want to display.
script, see “Executing a Script on a Form” on page
4. Click OK. 125.
Adding Pictures
The Picture tool allows you to create a Picture Box
to display a Windows metafile. It can display a static
metafile stored in a .WMF file, or a live one stored
in a picture column of a database.
To create a Picture Box:
1. Click the Picture tool .

2. On the form, click and drag to create an area for
the picture to occupy.
The Open dialog appears.
3. In the Open dialog box, select the Windows
NOTE: To change the font or color of the text in
metafile (.wmf) you want to display, and then
any type of box, see “Customizing Fonts” on page
click Open.
45.

The picture appears in your form.
Selecting a Database
A ChemFinder form does not store data directly, but
is simply the window through which you look at
data. When creating a form, you need to specify the
source of the data to display. A form displays data
from a single table in a database. To specify the data
source for a form, you must open or create a
NOTE: The metafile is not actually embedded in database, and then select a table.
the form. Only its filename is saved with the form. If
you move or rename the metafile, the form will not If you want to view data from more than one table,
display the corresponding picture. However, if you you must create a form for each table. Typically, you
make changes to the picture and keep its filename create a main form for one main table and a subform
the same, the picture in the form will be updated. for each other table. For more information, see
“Chapter 6: Relational Data and Subforms” on page
To read in a picture file or to replace a picture in a 99.
Picture Data Box: You can connect a database to the form before
creating boxes, or any time after. If the form is
1. Right-click a picture and choose Read File.
already connected to a database, you can change the
The Open dialog box appears. database or the data source. If the form has boxes
2. In the Open dialog box, select the metafile you with fields connected to them, then the boxes
want to display in the Picture Data Box, and automatically connect to fields of the same name in
click the Open button. the newly-opened database.
The new metafile replaces the picture in the
Picture Data Box.
Opening an Existing Chemical
Database
To save a metafile from a Picture Data Box:
To open a database to associate with a form:
1. Right-click on the Picture Box and choose
Save File. 1. From the Box Properties Database tab, click
Open Database.
2. In the Save As dialog box, type a file name and
then click Save. The Open dialog box appears.
The picture is saved to a file in Windows
metafile (.wmf) format.

To choose the data box to display:
1. In a box or frame, right-click choose Field.

The Field properties appears. The sample
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database is shown below.
2. In the Open dialog box, choose a database with

an .mdb file extension, and then click Open.
The Open Box Properties dialog box appears.
The Agrobase database is shown below.
2. From the data source tree, select the field to

display.
3. Click OK.
The field data is displayed in the box.
Opening a Secured MS Access

Database
To open a secured Microsoft Access database in
ChemFinder, you need to set the appropriate
permissions in Access.
A data source tree appears in the left side of the
Box Properties Database dialog box, displaying To set the permissions:
the fields and their tables.
1. Open the desired database in MS Access.
3. Click OK.
2. On the Tools menu, point to Security, and then
The database is associated with the form. choose User and Group Permissions.
Selecting the Data to Display 3. Select all of the available Permissions options
for the tables you want to open in ChemFinder.
You indicated the source of the data to display on the
form, but the form is still blank. To see the data, you 4. Click OK.
need to indicate what data to show in each box. You 5. Open the database in ChemFinder.
can use the Box Properties dialog box, as described
in “Setting Box Properties” on page 44.

Creating a Database Saving a Form
You can create a new, empty database and associate
In most non-database applications—including
it with a form.
ChemDraw and Chem3D—you edit data on the
To create a database: screen, but your changes are not made permanent
until you choose Save from the File menu.
1. On the Box Properties Database tab, click
In database programs such as ChemFinder, your
Create Database.
changes are automatically and permanently saved to
The Save As dialog box appears. the database when you switch records. This is
“committing” the changes. You then have the
opportunity to revert to the original data by choosing
Undo Changes from the Record menu.
The Save command in the File menu refers only to
changes made on the form itself, such as the position
of boxes. Choosing the Save command from the File
menu has no effect on changes you make to data
stored in the database. Saving a form also saves
subforms and changes that you make to subforms.
2. In the File Name box, type a name for your

After you create a form, you can save it. When you
database, and then click Open. retrieve the saved form, it automatically opens a
connection to the database defined in the forms.
The Box Properties dialog box appears. The
Box Properties Database tab for the sample To save a form:
database, Sample, is shown below. 1. From the File menu, choose Save, or to save the
form under a new File name, choose Save As.
The Save dialog box appears.
A data source tree appears, containing the

database and its tables and fields. 2. Choose the directory in which you want to save
3. Click OK. the form, type a filename, and click Save.
The Box Properties dialog box closes. ChemFinder saves the form with a .cfw
extension.

Saving a Form
Setting Box Properties • Picture—displays Windows metafile data.
Pictures are scaled to fit within picture boxes,
You can use the Box Properties dialog box to set with fixed height to width ratios.
ChemFinder form attributes, including: data source, • Structure—displays chemical structures or
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display type, font, and box style. reactions. Reactions are laid out for best fit with
To open the Box Properties dialog box: the box and the layout may change if the box is
reshaped. You can set preferences for molecule
• Right-click on a data box and choose
display. For more information, see “Setting
Properties.
Preferences” on page 115.
• Memo—displays styled data. If the data in a
field contains rich text, markup characters are
displayed.
• Formula—displays any kind of text but
numbers are subscripted. Formulas are
presented in modified Hill order, as follows: If
a substance contains both carbon and hydrogen,
the carbons are listed first, followed by the
hydrogen atoms, followed by other elements
alphabetically by element symbol. If a
substance contains carbon, the carbons are
listed first, followed by other elements
alphabetically by element symbol. Otherwise,
Setting Data Box Styles all elements are listed alphabetically by element
You can use the Box Properties dialog box to change symbol.
the style of a data box on a form. For example, you • Button—displays alphanumeric data. Can
can change a data box to a frame or picture. display single line of data.
The Box Style menu only shows applicable styles • Subform—used with subforms. For more
for each field. For example, you cannot show a real information, see “Chapter 6: Relational Data
number in a Picture. and Subforms” on page 99.
For information about field types, see “Creating • Rich Text—used in Memo fields. You can
Fields” on page 73. format text with the Text Format toolbar.
You can choose from the following styles: To set the box style:
• Data Box—displays alphanumeric data. Can 1. Right-click in the data box to change and
display multiple lines of data. choose Properties.
• Frame—displays alphanumeric data. Can The Box Properties dialog box appears.
display single line of data.
• Plain Text—displays alphanumeric data. Can
display single line of data.

Setting Box Properties
2. On the Box tab, in the Box Style section, select
the structure format to view from the menu:
If you want the Then choose
ChemDraw format Structure

(ChemDraw style).
ChemFinder format Structure

(ChemFinder style).
2. From the Box Style menu, choose the box style. Setting Fixed and Live Labels
3. Click OK. In the Box Properties dialog box, you can designate
whether the data source is fixed or from a field.
Viewing Structures in the Fixed data is attached to the form and does not
ChemDraw Format change as you browse. Data from a field is stored in
You can display structures in a structure box in the database and is different for each record. As you
ChemFinder or ChemDraw format. The ChemDraw browse, the label updates according to the contents
format displays more graphically-rich drawings of the field.
than the ChemFinder format. However, ChemFinder For example, a data box with a live label in a frame
does not use all of the Chemdraw drawing features can display molecular name, formula, or other data
when searching. from fields. As you browse through the database, the
For example, textual annotations are ignored, label changes with the corresponding structure.
R-group tables are not recognized. Certain graphics,
such as rectangles and orbitals, are not transferred.
and ChemFinder does not consider their chemical
implications.
To choose how to view structures:
1. Right-click in a structure data box and choose

Properties.
To specify live labels for a data box:
1. In the Box tab, select the field to associate, and

then click Field.
2. Click OK.

The box label updates as you change records. 3. Take the appropriate action:
To specify fixed labels for a data box:

1. In the Box tab, select the field to associate, and
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then click Fixed. use a list from a From table and

2. Type a label. If you choose a structure or picture database table as the follow the
field, click to browse to the file to display. data box menu instructions at the
bottom of the dialog
3. Click OK. box.
The box label is fixed.
create your own list Fixed list of choices
Adding a Data Box Menu for the data box menu and follow the
instructions at the
You can add a menu containing a list of choices to a
bottom of the dialog
data box so you can choose an item from it to appear
box.
in the data box.
To add a menu: use a list from a a. From table. A

database table and list appears.
1. Right-click on a data box and choose add your own items to
Properties. the data box menu b. Click Fixed list
of choices, and
edit the list.
2. Click the Choices tab.
4. Click OK.
The Choices tab appears.
A button appears in the lower right corner of the
box.
5. Click the button to display the menu.

Adding Scroll Bars 3. Click OK.
You can add scroll bars to a data box so you can 4. Deselect the Layout Mode button to view the
scroll through any additional data that is not visible results.
within a data box.
Customizing Text
To add a scroll bar:
You can customize text fonts, sizes, styles, colors,
1. Right-click a data box and choose Properties. and alignment in Rich Text boxes and Memo fields
The box properties dialog box appears. using the Text Format toolbar. All of the standard
text formatting options are available.
Font Bold Underline Subscript Color Bullets
Font Italic Superscript Center

size Align Align
left right
To display the Text Format toolbar:
1. From the View menu, choose Toolbars.

2. In the Box style section, select With scroll
2. In the Toolbars dialog box, select Text Format
bars.
Tools.
3. Click OK. 3. Click OK.
The scroll bar appears on the bottom right in the The Text Format toolbar appears.
data box.
NOTE: Text copied from a word processor such as
Hiding Data Boxes Microsoft Word retains its styles when pasted into a
Rich Text box.
You can show or hide boxes when switching
between query and browse mode. For example, hide
data boxes when you want hide non-searchable Customizing Fonts
boxes during query entry. Show data boxes to All the labels on ChemFinder objects including all
display information useful for query entry. the text on a form can be edited to your
When you are in form layout mode, all boxes are specifications. You can edit any box’s font, font
visible, regardless of the setting. style, size, and color.
To set when boxes are hidden:
1. Right-click on the box and choose Properties.

2. In the Box Style area, select Hidden in Browse
Mode or Hidden in Query Mode.

To set the font for a box: To specify the numeric format:
1. Click Font. 1. Right-click on a data box containing numeric

The Font dialog box appears. data and choose Properties.
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The Box properties dialog box appears.
2. Click Format.
2. Set the text font, style, size, and color. The Numeric Format dialog box appears.
The sample area previews the font.
3. Click OK to commit the changes.
NOTE: To change the color of the atom labels in

the structure box, you must use the Periodic Table.
See “Using the Periodic Table” on page 122.
Customizing Numbers
Using the Box Properties dialog box, you can 3. Select the appropriate option:
specify how numeric data is displayed in forms you
can customize the following properties:
• Currency symbol display
• Decimal position
a varying number of Unformatted.
• Scientific notation decimal places
a currency symbol Currency and select

the symbol from the
drop-down menu.

display
the currency symbol Symbol on right

to the right of the when a currency
number symbol is selected.
a standard Fixed point and

floating-point value select the number of
with a selected decimal places.
number of decimal 3. Take the appropriate action:
places
To set the Click

the numbers Scientific and select
background color
displayed in scientific the number of
of the
notation decimal places.
An example of the format you select is shown in form Form Background.

the Sample area of the dialog box.
4. Click OK. form in query mode Query Background.
The format is applied to the current data box.

Setting Color
You can set the following color options:
• The form background color
• The color of the form in query mode
• The default background for all forms
To set the form background and form query colors:
1. Right-click on a data box and choose

Properties.
2. Click the Form tab. 4. Select a color.
The Form properties appear. 5. Click OK.
The Form or Query Background button changes
to reflect the color you choose.

To set the default background color: The Open dialog box appears.

2. In the Preferences dialog box, click Color.
Administrator
3. On the Color tab, click Form Background.

4. In the Color dialog box, select a color and click
OK.
The color you chose becomes the default form
background color.
Creating Forms
Automatically 3. Choose a database and click OK. This example
uses the Cs_demo database in the samples
ChemFinder provides a Form Generation dialog box folder.
from which you can automatically create a form.
You choose the form style and properties from
pre-defined options.
1. Right-click and choose Data Source.

The Form Properties dialog box appears.
4. In the Form Properties dialog box, click the

Form tab.
2. Click Open Database.
5. Click Generate new form and then click Style.

Creating Forms Automatically
The Form Generation dialog box appears. 10. Choose the size and spacing of the boxes and
grid:
If you want the boxes Then, for Grid

to be Size, choose
larger and spaced further Large.

apart
medium, relative to the Medium.

Large and Small settings
6. In Choose Fields to be included section, click smaller and spaced closer Small.
the field names to include. together
7. To have a Structure box to be created first in the
11. Click OK.
upper left corner of the form, click Structure in
upper left of form. Your form settings are saved.
If you do not select this, the boxes are generated 12. Click OK.
in the order they appear in the list. In the following dialog box, click No to create a
8. Select the form style: new form.
If you want the Then, in the Form

boxes to style section, click
be surrounded by a Framed.
frame
The generated form appears in the window.
be labeled above Titled.
be labeled to the left Labeled.
not be labeled Plain.
9. Choose the number of columns, between one

and four.

Creating Forms Automatically
Creating and Editing Editing Forms
Tabs You can move or resize boxes and other objects on
your form with the Selection tool and the items in
Administrator
You can use tabs on a form to access information the Edit menu.
more easily by dividing a long form into smaller
parts contained on separate tabs. Selecting Objects on a Form
To create tabs on a form: You can use the Selection tool to choose data boxes
and other objects on a form so you can move, resize,
1. Right-click an empty part of a form and choose
or delete them.
Add Tab.
When the selection tool is active, the Edit menu
Two tabs appear in the lower left corner of the
commands apply to the boxes themselves. When the
form. The Cs_demo form with tabs is shown
selection tool is not active, the Edit Menu
below.
commands apply to the contents of the active data
box.
To select an object on a form:
• On the Form toolbar, click the Selection
tool , and then click an object on the form
to select it.
A highlight appears around the object
indicating that it is selected.
To rename a tab: Selection Marks
1. Right-click the tab and choose Rename Tab.

The Tab Name dialog box appears. To select multiple objects on a form:
1. On the Form toolbar, click the Selection

tool .
• Shift+click multiple objects.
2. Type a name for the tab and click OK. • Drag the Selection tool around the boxes
you want to select.
The new name appears on the tab.
To select all the objects in the form:
To remove a tab:
• Right-click the tab and choose Delete Tab.
The tab is removed.

Creating and Editing Tabs
Moving Objects To resize objects on a form:
You can move data boxes or any other object to a 1. On the Form toolbar, click the Selection
different place on a form with the Selection tool. tool .
To move objects on a form: 2. Position the pointer over an edge or corner of

the object until the pointer is a double-headed
1. On the Form toolbar, click the Selection arrow.
tool .
2. Select the objects to move.
3. Drag the objects to a different place.
NOTE: To move a subform, you must click- drag 3. Drag in the direction you want to resize.
the title bar of the subform, not its contents.
To resize objects one pixel at a time:
To move objects one pixel at a time: 1. Select the object you want to resize.
1. Select the objects you want to move. 2. Place the mouse pointer over an edge or corner
of the object until it is a double-headed arrow.
2. Press an arrow key in the direction you want to
move the objects. 3. Press an arrow key in the direction you want to
resize the object.
The objects move one pixel in the direction of
the arrow key. The edge of the object moves one pixel in the
direction of the arrow key.
Resizing Objects
Deleting Objects
You can resize a data box or any other object by
stretching it with the Selection tool. You can remove data boxes and other objects from a
form with the Selection tool or items on the Edit
menu.
NOTE: You cannot resize more than one object at a
time or simultaneously resize a box and its frame, To remove objects from a form completely:
unless you create a framed box using the Framed
Box tool. For more information, see “Creating 1. On the Form toolbar, click the Selection
Boxes with Frames” on page 37. tool .
2. Select the objects you want to delete.
3. From the Edit menu, choose Clear.
The object is removed from the form.

Editing Forms
Reversing and Restoring The order in which data boxes are created is the
order in which the cursor moves as you press Tab.
Changes You can set to which data box the cursor moves first
You can use the items on the Edit menu to reverse or or last.
Administrator
restore changes you made to a form.

To set the cursor to move to a data box first:
To reverse or restore changes:
1. Select a data box.
• From the Edit menu, take the appropriate
action: 2. From the Edit menu, click Send to Back.
3. Press the Tab key.
If you want to Then choose The cursor moves to the box you set.
To set the cursor to move to a data box last:

reverse the effect of Undo.
the last change you 1. Select a data box.
made to the form or
object 2. From the Edit menu, click Bring to Front.
The box you set is the last box the cursor moves
reverse the effect of Redo. to when you press Tab repeatedly.
Undo
Aligning and Distributing
Objects
NOTE: Undo and Redo work over multiple
changes. Either command can be used repeatedly to You can line up objects relative to each other by
reverse multi-step operations. aligning them and space objects at an equal distance
apart by distributing them.
Ordering Objects
NOTE: In framed dialog boxes, the inner data box
You can use the Bring to Front and Send to Back is aligned, not the frame.
commands to place data boxes in a specific
sequence as follows: To line up objects on a form:
• Select which overlapping data box is on top.
1. Shift+click the objects to align.
• Set the order in which the cursor moves when
you press the Tab key.
To put a box on top or bottom:
1. Select the box.

2. From the Edit menu, choose Bring to Front to
put it on top, or choose Send to Back to put it
on the bottom.

Editing Forms
2. From the Edit menu, point to Align, and then
take the appropriate action:
Changing the Layout of
an Existing Form
If you want to line Then choose
up along the You can use the Form Generation dialog box to
automatically change the overall layout of an
top edge of the first Top. existing form.
object you place on
the form To change the layout of an existing form:
1. In a form, right-click the background, and then

middle of an object in Vertical Center.
choose Properties.
a vertical line
2. In the Form Properties dialog box, click the
bottom edge of an Bottom. Form tab.
object
left edge of an object Left.
middle of an object in Horizontal Center.

a horizontal line
right edge of an object Right.
The form objects line up according to your

choice.
To evenly space objects on a form:
1. Shift+click the objects to distribute. 3. Click Generate new form, and then click Style.
2. From the Edit menu, point to Distribute, and
The Form Generation dialog box appears.
then take the appropriate action:
If you want to Then choose

space objects
evenly between the
outer boxes of the form Vertically.
left and right of the Horizontally.

form
The form objects are spaced according to your

choice.

Changing the Layout of an Existing Form
4. In Choose Fields to be included section, click A message box appears.
the field names to include.
5. To have a Structure box in the upper left corner
of the form, click Structure in upper left of
Administrator
form.
6. In the Form style section, select the form style:
If you want the Then, in the Form
boxes to style section, click If you want to Then click
be surrounded by a Framed. change the overall layout for Yes.

frame the current form
be labeled above Titled. create a new form based on the No.

existing form
be labeled to the left Labeled.
not be labeled Plain.

Securing Forms
You can control the options available to users of
7. In the Columns list, choose the number of your forms by setting the security options.
columns, between one and four.
You can also provide the database connection
8. In the Grid size list, choose the size and spacing
information used to log on to an MS Access
of the boxes and grid:
database. MS Access provides a security system that
allows the creation and management of usernames
If you want the boxes to Then choose and passwords, and the assignment of permissions
be to those usernames. MS username password account
information is stored in the Workgroup Information
larger and spaced further Large. file (.mdw, .mda). For more information about
apart securing an MS Access database, see the Access
user’s guide.
medium, relative to the Large Medium.
and Small settings
smaller and spaced closer Small.

together
9. Click OK.

Securing Forms
Setting Security Options 3. Type the user name to use for logon in the
Username box.
To set what ChemFinder form options are available
to users: The Enable button becomes available.
4. Type the password to use for logon in the
1. Right-click in the form you want to secure, and
Password box.
choose Properties.
Use of a password is optional.
The Form tab of the Box Properties Dialog box
appears. To enforce workgroup security in an MS Access
Workgroup Administrator database:
If you want to Then
enter a workgroup Type the name of the MS

file name Access Workgroup
database in the
Workgroup Information
file box.
browse for the Click File and select the

2. Click Security.
workgroup file file.
NOTE: The Security button does not appear if
the security on your form has been set to not To select the database security options you want
allow access to the Security options. enabled:
The Form Security dialog box appears.
If you want users to Then click
use a username password Logon to MS

to log on to the MS Access
Access database (.mdb Database.
files)
use a username password Protect

to open the molecule Molecule
database (.mst files) Database.
The lower left corner of the dialog box indicates

whether security is defined.

Securing Forms
If you want users to Then click If you want users to Then click
be able to
be prompted to log on to a Prompt for
Administrator
database with a username Database Logon. access OLE Allow OLE

password when the form automation writing Automation Access.
is open and programming
be prompted to log on Validate Form use all of the above Create/Open/Save/

with a username Access. options Change Forms.
password to open a form
To select the edit options you want enabled:
be able to access the Form Security Dialog • Take the appropriate action:
Security dialog box Available.
If you want users to be able to Then click

encounter all of the above Database
options Security.
clear forms Clear.
To select the form creation and form access options
you want enabled: delete relational and structural Cut.
data
copy relational and structural data Copy.

If you want users to Then click and multiple table rows to the
be able to clipboard
create forms Create New Forms. paste relational and structural Paste.
data from the clipboard
open forms Open Other Forms.
edit forms Save Changed Forms.

Perform all of the above functions Cut/Copy/
Paste.
change the layout of Change Form Layout.
a form
open forms when Open Form in CFW

using NET version NET.
of ChemFinder

Securing Forms
To select the searching options you want enabled:
If you want users to be Then click
• Take the appropriate action: able to
If you want users to be Then click save and manipulate hit Enable Hit List
able to search for lists Tools.
exact structure only Exact Structure. search the entire Search Over Full
database Database.
substructures only Substructure.
update database records Update Records.
similar structures only Similarity.
use ChemDraw to edit Edit Structure.
structures
any type of structures Structure
searching.
add database records Add New Records.
To select the record options you want enabled:
delete database records Delete Records.
perform all of the above Browse/Query/

If you want users to be Then click functions Update Records.
able to
To allow users to import data SDFiles or RDFiles:
browse databases Browse Database
Records. • Click Import Data.
To allow users to export data, including delimited
view data in forms in a View Form as Table. text files:
table
• Click Export Data.
edit and view structures Edit/View To select the print options:

in ChemDraw Structures in
ChemDraw. • Take the appropriate action:
view structures in View Structures in If you want users to be Then click

Chem3D Chem3D. able to print
submit queries Query Database a single record only Single record.

Records.
all records Multiple

use current hit list for Search Over records.
searching Current List.

Securing Forms
To finish selecting options: Overriding Security
1. Click Enable. You can temporarily remove security so you can edit
2. Click OK. the security options.
Administrator
The options you choose are applied to the form. To override security to temporarily disable it:
Disabling Security 1. In the Form Security dialog box, click Override

Security.
You can disable security and reset the defaults.
The Validate Security dialog box appears.
To disable security and reset defaults:
1. In the Form Security dialog box, click Disable.

The Validate Security dialog box appears.
2. Type the Username and Password and click

OK.
3. Click OK.
2. Type the User name and Password, and then You are allowed to edit the security options.
click OK. To turn the security back on:
3. Click OK. • In the Form Security dialog box, click Override
Security is disabled and the defaults are reset. Security.
“No Security Defined” appears in the lower left
corner of the Form Security dialog box.

Securing Forms
Chapter 4: Working with Data
Overview Read-Only Access
Any of the following conditions determine whether
You work with data within ChemFinder by entering
a database opens in read-only mode:
it into a database, editing it, and interfacing with
ChemDraw and Chem3D. • If any component files (extensions .cfw, .mdb,
.ldb, .mst, .msi) have read-only attributes.
You can perform all of these functions on data using
the commands in the menus, or you can use the • If the files are on read-only media, such as
buttons in the Record toolbar for most of these CD-ROM.
functions. • If you select Read-only in the File Open dialog
Add Commit Omit box when you open a form or database.
Record Changes Record When you open a read-only database, the following
conditions apply:
• READ appears in the status line.
• You can not modify data in text or structure
boxes.
Undo Delete
Changes Record
Opening Databases
When you open a database in ChemFinder, you can
access the data in any of three ways:
• Normal access—you can read and write data.
• Read-Only access—you can read but not write
data. The database is write-protected.
• Secured access—you must open the database
with a user name and password. You are subject
to the security restrictions applied to the
database.
NOTE: Earlier versions of ChemFinder cannot

read ChemFinder 7.0 .cfw files.
ChemFinder Chapter 4: Working with Data • 59

Opening Databases
Multi-user Access Secured Access
If a database resides on a network, more than one ChemFinder supports the following types of
ChemFinder user may access it at the same time. security:
Administrator
Each user can view, print, or modify records

• Form access—ChemFinder enforces form
independently of the others.
access security by requiring a user name and
The following table shows how the type of user password, which are stored in the form (.cfw)
affects the other users in the group. file.
• Molecule file access—ChemFinder enforces
User type Affect on other users molecule file access security by requiring a user
name and password, which are stored in the
Multiple readers in User actions do not affect each database’s .mst file.
read-only access other.
• Microsoft Jet Relational Database Engine—
the database engine that underlies Microsoft
Multiple writers in All users can read and write. A Access enforces security. The user names and
normal access user may see another user’s edits. passwords are stored in an MS Access
If two users try to edit the same
Workgroup Administrator database.
area at the same time, one is
alerted that the database is When you open a form or database that has security
temporarily locked. options applied to it, you are prompted to enter a
username and password to log on.
One writer, The writer, in normal access, is When you open a secured MS Access database from
multiple readers not affected by the readers. The within ChemFinder, a username, password, and
readers, in read-only access, may
workgroup information file is required. Contact
see the writer’s edits.
your Access Database Administrator for this
information.
If two people are viewing the same record within a
database, and one person changes the data in that To open a secured form:
record, the second person will not see the changes 1. In the Validate Form Security dialog box, type
immediately. The changes will be visible when the your username and password, and then click
second user switches to another record, and then OK.
back to it.
60 • Chapter 4: Working with Data CambridgeSoft

Opening Databases
If the form you access includes a secured You can go directly to a specific record as follows:
molecule database, the Database Logon dialog 1. From the Record menu, choose Go To Record,
box appears: or click the Go To Record tool .
The Record Number dialog box appears.
NOTE: The current record number is

displayed in the Status Bar.
2. Type your username, password, and 2. Type the number of the record (within the
Workgroup Information File name, and then current list) to display, and click OK.
click OK. The specified record is displayed.
The form opens.
NOTE: Record numbers are temporary, referring
Browsing Databases only to positions within the current list in its current
sort order. For example, if you have done a search
You can browse a database using the buttons on the that found ten hits, then the only valid record
Record toolbar. numbers are 1–10. If you want to move to a specific
absolute location in a database, you must run a
First Record Go to Record Last Record search for a value in a field that identifies that
location.
The Data Table

Previous Record Next Record Sometimes browsing through a data record set is
To Browse: more convenient if the data is presented in tabular
format.
• Click First Record to display the first record in
the database.
NOTE: You cannot add or modify records while
• Click Previous Record to display the record viewing data in a table.
before the currently shown record.
• Click Next Record to display the record after To display data in a table:
the currently shown record. • On the View menu, point Data Table, and then
• Click Last Record to display the last record in choose In Separate Window.
the database. A list window containing the fields and records
in the form appears.

Browsing Databases
Administrator
2. Click-drag to adjust the column width.
NOTE: To hide the column, continue dragging

To display a particular record in the form: until the border overlaps with the border of the
• Click that record’s entry in the list window. adjoining column.
By default, the fields in the Data Table are displayed
To resize the row heights in the Data Table:
in the order in which they were created.
To reorder the columns in the Data Table: 1. Place the cursor on the dividers in the left
header.
NOTE: The column order is not stored in the form. The cursor changes to the icon shown below.
3. Click one of the column headers to select the

column.
2. Click-drag to adjust the row height.
4. Drag that header to a new position.

The cursor changes to the icon shown below.
The new position is indicated with a dashed
vertical line.
To resize the column widths in the Data Table:
1. Place the cursor on the dividers in the top

header.
The cursor changes to the icon shown below.

Browsing Databases
Entering Data into a To add a structure:
1. Right-click in a box with a structure field.

Database
You enter data into a database by adding a new
record. Adding a new record consists of three steps:
If you want to Then right-click and choose
• Clearing the form
draw a structure a. Edit Structure.
• Adding new data
ChemDraw opens.
• Committing the new entries
b. Draw the new structure in
Clearing the Form the From ChemFinder
window.
To begin adding a new record:
1. Create a form and link it to a database. For more c. Click the ChemFinder
information, see “Creating Forms Manually” on window or close the
page 35. ChemDraw window to
insert the structure into the
The form should contain all the data boxes you form.
want to view and edit. The boxes should be
assigned to their appropriate fields. import a a. Read Structure.
2. From the Record menu, choose Add New structure b. Select the file to insert and
Record, or click the Add Record tool . click Open.
All of the boxes in the form are cleared to The file is inserted into
prepare for entering new data. The Status Bar is ChemFinder.
updated to show that you are in record addition
mode:
NOTE: See the ChemDraw User’s Guide for
information about using ChemDraw.
Adding New Data

To add alphanumeric data:
• Click in a box with an alphanumeric field and
type the data.

Entering Data into a Database
Committing the New Data Undoing Data Entry
When you finish entering all of the data items, do Before committing a new data entry, you can revert
one of the following: the contents of the form to its previous unmodified
state.
Administrator
• Perform another action such as moving to

another record or printing. To undo your changes:
The record is automatically committed. • From the Record menu, choose Undo
Changes, or click the Undo Changes button
• From the Record menu, choose Commit .
Changes or click the Commit Changes tool
After you commit the changes, they cannot be
.
undone.
The new record is added to the database.
Editing Data
NOTE: Selecting Commit Changes (or moving to
another record if you have two or more records) Modifying the data in a database is performed by
saves the data to the database. You do not need to directly changing the data items on the form and
select Save from the File menu; choosing Save saves committing those changes.
any changes to the form layout, not changes to data
in a database. NOTE: The Formula and MolWeight fields are
automatically calculated by ChemFinder from the
Duplicating Records Structure field and cannot be edited by the user. The
MOL_ID field is also set automatically by
You can create a new record by modifying an ChemFinder and cannot be edited.
existing one. To duplicate a record:
• From the Record menu, choose Duplicate Editing Data
Record.
To edit data:
You are in Add Mode and the form fills with
data from the previously displayed record. • Click the data box whose data item you want to
When you select Commit Changes, you create a edit.
new record whose fields contain the data on If you click on a Structure data or a picture box it is
displayed. Before committing the duplicate, highlighted. If you click on a data box containing
you can modify fields or structure and commit alphanumeric data, a cursor appears in the data box.
changes just as you would with any other new
record. To edit alphanumeric data:
1. Replace it with the text or number you want.
NOTE: When duplicating records, only those fields 2. From the Record menu, choose Commit
that are visible on the form are duplicated. Data in Changes, or move to a different record.
fields present in the database but not visible on the
form are not copied into the new record. The new
NOTE: Moving to a different record always
record has a new Molecule ID.
commits changes first.

Editing Data
Editing Structures Styled Text
You can edit structures by using the ChemDraw Memo\Rich Text fields are the only fields that allow
drawing tools. You can also neaten the appearance you to store and display styled text, and only when
of a structure by cleaning it up. For details about displayed in a Data Box with a Rich Text Box Style.
how clean up works, see the ChemDraw User’s For more information on creating this type of box,
Guide. see “The Data Box Tool” on page 42 and “Changing
the Box Style” on page 46.
Before committing a data entry, you can revert to the
You make changes to text fonts, sizes, styles, colors,
previous unmodified record by choosing Undo and alignment in Rich Text boxes with the tools on
Changes from the Record menu or clicking the the Text menu or the Text Format toolbar shown
Undo tool. below.
To edit structural data: Text copied from a word processor such as
Microsoft Word retains its styles when pasted into a
1. Do one of the following: Rich Text box.
• Right-click in the structure box and choose
To display the Text Format toolbar if it is not visible:
Edit Structure.
• Double-click the structure box. 1. On the View menu, point to Toolbars, and then
choose Text Format.
ChemDraw opens and the structure appears in
the From ChemFinder window. The Text Format Tools appear.
2. Edit the structure using ChemDraw. Subscript
3. Click in the ChemFinder window or close the Font Bold Underline Color Align Bullets
ChemDraw window when you are finished. Left
4. From the Record menu, choose Commit
Changes, or move to a different record.
The changes are stored. Font Size Italic Superscript Center Align
Right
To clean up a structure:
1. Right-click in the box containing the structure

to neaten.
2. Choose Clean Structure.
3. To save the cleaned up structure, choose
Commit Changes from the Record menu.

Editing Data
Undoing Changes NOTE: You cannot edit records sorted by formula
Before committing your changes, you can revert to or molecular weight. However, if you attempt to sort
the previous unmodified state. one of these fields, ChemFinder offers to set up a
database (a portal database) which allows the
Administrator
To undo your changes: operation. For details, see “Attaching Tables from
• From the Edit menu, choose Undo or click Other Applications” on page 71.
.
After you commit the changes, they cannot be Sorting Fields
undone.
To sort a field:
Redoing Changes • Right-click in the field you want to sort, point to
Sort, and then choose Ascending or
When you undo an action, the Redo command
Descending.
becomes active. You can reverse the effect of the
Undo command by choosing the Redo command.
Sorting from the Data Table
To redo the last action performed:
To sort directly from the Data Table:
• From the Edit menu, choose Redo or click
1. From the View menu, choose Data Table.
.
2. In the Data Table, double-click on the table
The last action undone is reinstated.
header of the field you want to sort.
Sorting Data
You can sort most types of data in a form. Sorting the
Mol_ID field, the molecular weight field, or any
other numeric field arranges the current list in
increasing or decreasing order. Sorting the structure
field arranges that field by increasing number of Sorting in Reverse Order
atoms contained in the structure. Sorting by formula To sort a column in reverse order:
orders the records by increasing C-H-N count
followed alphabetically by any other elements. • Double-click on the table header again.
Sorting text fields such as molecular name sorts the
records alphabetically.
After sorting, the database must be reset to its
original state before you can update it.

Sorting Data
Sorting Languages Other Than Deleting Data
English You can delete the contents of individual fields by
Text that you sort must be in the same language as using the Delete or Backspace keys.
default language of the system on which the
database was created, or an incorrect sort order can To delete an entire record:
occur. 1. Move to the record that you want to delete using
the Record commands or tools.
The ChemFinder sample databases, created in
English, can be sorted correctly using the following 2. From the Record menu, choose Delete Record,
languages: or click the Delete Record tool .
• English The record is permanently removed.

• German
NOTE: You can delete multiple records if you use
• French the Table view.
• Portuguese
• Italian
• Modern Spanish
Working with Structures
If you want to sort text in a different language than Using ChemDraw
the one in which the database was created, perform
You can enter or edit ChemDraw structures within
the following procedure:
Data Boxes that are of the Structure field type.
1. On a computer using the same language as the
To edit a structure:
text you want to sort, open MS Access.
• In the structure data box, do one of the
2. Open the .mdb file you want to sort.
following:
3. Compact the database: on the Tools menu,
• Right-click and choose Edit Structure.
point to Database Utilities, and then click
Compact Database. • Double-click in the structure data box.
4. After the database is compacted, close MS ChemDraw opens.

Access.
The correct sort information is written into the
database. When you perform a sort in
ChemFinder, the sort order will be correct.
Resetting the Database

To reset the database to its original state:
• From the Search menu, choose Retrieve All.

Deleting Data
If you already have a structure in a data box, that Structures and reactions drawn with query
structure appears in the From ChemFinder window properties are generally meaningful only in the
in ChemDraw. You can modify and manipulate the context of a query. Query structures can be stored in
structure just like any other ChemDraw structure. a ChemFinder database, but they are not treated as
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Markush structures and are not guaranteed to be hit

If there is no structure in the ChemFinder data box,
by all valid search queries. For more information,
the From ChemFinder window is blank. You can see “Appendix A: Structural Query Features” on
draw a structure to store in the ChemFinder
page 135.
database.
ChemDraw allows you to draw many objects that
1. In the From ChemFinder window, edit the have no chemical meaning. These include boxes,
existing structure or draw a new structure. circles, arrows, orbitals, and others. It also allows
2. Click in the ChemFinder window or close you to assign non-chemical styles (color) to objects
ChemDraw to insert the ChemDraw structure. that have chemical meaning. ChemFinder ignores
these properties, and stores only objects with
3. From the Record menu, choose Commit
chemical meaning in structure fields.
Changes, or move to a different record.
The changes are stored. To store a ChemDraw drawing exactly as drawn,
store it as a picture. You can copy and paste a
With a few exceptions, ChemFinder can store any
ChemDraw drawing into a Picture field.
chemically meaningful structure or reaction that can
be drawn in ChemDraw. Within ChemDraw, you
can confirm that a structure is chemically
meaningful by selecting it and choosing Check
Structure from the Structure menu. For more
information, see the ChemDraw User’s Guide.
The principal exception is with “bare” heteroatoms.
If you draw the following structure:
N
ChemDraw reports an illegal valence when you NOTE: Objects stored in a Picture field have no
choose the Check Structure command. ChemFinder chemical significance and cannot be searched.
automatically infers hydrogen atoms to main-group
elements as necessary to fill their lowest acceptable
valence. The structure above is registered in
ChemFinder as methylamine, CH3NH2.

Working with Structures Using ChemDraw
Viewing Models using Changing the Database
Chem3D Scheme
ChemFinder also provides access to Chem3D. From
You can create or remove tables or fields in an
a Structure data box, you can view the
three-dimensional model of the structure. existing or new database as long as the database is
not read-only and you have permission to modify it.
To view the molecular model for a structure: You may also attach, or link, tables from external
1. In a Structure data box containing a structure,
data sources.
right-click, and then choose View Model. You use the Box Properties dialog box to perform
the following procedures.
To access the Box Properties dialog box:

1. Create or open a form and link it to a database.
For detailed instructions, see “Creating a
Database” on page 70.
• From the File menu, choose Database.
• Right-click any empty space in the form
window and choose Data Source.
The Box Properties:Database dialog box
appears.
Chem3D opens an untitled window and converts the
two-dimensional structure into a three-dimensional If the database contains more than one table, only
model. You can manipulate the model like any other one is selected at any given time. The contents of the
Chem3D model. Field tab of the dialog box, and of the form, reflect
the selected table.
NOTE: See the Chem3D User’s Guide for more
information about using Chem3D. To select a table:
• Click the table name.
2. Click on the ChemFinder window to return to
the form.
NOTE: Unlike interaction with ChemDraw,

changes you make to a model within Chem3D are
not transmitted back to ChemFinder. You can put a
picture of the Chem3D model into a database by
saving the Chem3D model as a metafile and
inserting it into a Picture field. The picture does not
retain a connection table and cannot be edited.

Viewing Models using Chem3D
Creating a Database Creating Tables
Instead of opening an existing database, you may There is no limit to the number of tables a database
want to create a new, empty one. This procedure can contain. You may want multiple tables in a
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results in a simple database with one table for database in order to manage relational data, or
storing structures. simply to organize different collections of
information in the same place.
To create a database:
A table must contain at least one column. When you
1. Right-click and choose Properties.
create a new table, ChemFinder creates a numeric
2. Click Create Database. column called ID. You can use this column to store
The Save As dialog box appears. integer data, or delete it and replace it with your own
columns.
3. Choose the directory to which you want to save
the database. Table names must:
4. Specify a name for the database, and click • Begin with a letter
Save.
• Not contain punctuation characters
ChemFinder creates the database containing one • Not be the same as a table already on display
table (called MolTable) with four fields:
To create a new, empty table:
• Structure
• Formula 1. Right-click and choose Properties.
• Molecular weight The Box Properties dialog box appears.

• Mol_ID 2. Click the Table tab.
The Mol_ID field corresponds to a column in the The Table tab appears:
table where a numeric ID is automatically entered as
each structure is registered. The other fields
represent information stored in the structural portion
of the database, linked to the assigned ID.
Molecular formulas and molecular weights are
automatically calculated from a structure. These
internal fields cannot be edited or deleted.
After creating a database, you can create fields for
storing other types of data. It is not necessary to
create the entire set of fields before working with the
database. You may add more fields later. 3. Click Create Table.
The Create Table dialog box appears.

Creating a Database
Attaching Tables from
Other Applications
You can use ChemFinder to add chemical structures
to a database you have already developed. If your
database was developed in Microsoft Access, you
4. Type a name for the new table, and then click can open it directly in ChemFinder.
OK.
If you are using another database system such as
The table appears in the Data Source tree. FoxPro, dBASE, Btrieve, Paradox, SQL Server, or
Oracle, you cannot open the database directly. You
must open or create a ChemFinder database, and use
Attach Table to link to tables in the data source.
After you attach a table, it appears and functions as
if it were part of your local ChemFinder database.
The procedure you use depends on whether the
tables you want to attach are from a file-based
(Access, FoxPro, dBASE) or non file-based (Oracle
or SQL Server) database system.
Attaching Files from a

File-Based Database
Deleting Tables To attach a file-based database table:
To delete a table from the database:
2. Click the Table tab, and then click Attach
1. In the data source tree, select the table to delete.
Table.
2. Click the Delete Table button.
The Attach Table dialog box appears.
3. Click Yes.
The table and all data it contains are
immediately deleted from the database.
CAUTION
You cannot undo a deleted table. Before you delete a
table, create a backup copy of the database to prevent
accidental loss of data. For more information, see
“Backing up Databases” on page 76.

Deleting Tables
3. Click Open MS Access Database. The Select Data Source dialog box appears.
4. From the Files of Type drop-down menu,
choose the type of database you want to access.
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NOTE: The list of file types available in the

Attach Table Open dialog varies from one
computer to another. The files for which you
have drivers installed shown. For example, if
the Paradox is not installed, you may not have
Paradox drivers on your system or in the
drop-down list.
NOTE: If the database type you wish to access

is not on the list, it may not be a file-based
system, and you need to connect using ODBC.
For detailed instructions, see “Attaching Files 4. From the Machine Data Source tab, select the
from a Non File-Based Database” on page 72. ODBC data source to access, and then click OK.
5. Choose the database to access, and then click NOTE: The ODBC data source dialog box
OK. shows all data sources known to ODBC,
including ChemFinder, Access, and other
6. In the tree diagram, click the name of the table file-based data sources. If you attempt to open
you want to attach, then click OK. one of these through the ODBC dialog, you get
an error message. File-based data sources must
The Database dialog box appears, showing the
be opened using Open Database, as described
newly-attached table along with the original above.
MolTable. The database is ready to use.
NOTE: If the ODBC data source dialog does
Attaching Files from a Non not show the database you seek, you may need
File-Based Database to create a new data source. You can do this
using the New button. For details, click the
If the database you want to attach is not file-based, Help button in the ODBC dialog box.
such as Oracle or SQL Server, you can attach it
using Microsoft’s Open Database Connectivity 5. If you are prompted for a user name and
(ODBC). password, enter it. If you don’t know what name
and password to use, see your System
To attach a non-file-based database table: Administrator.
1. Right-click and choose Properties. 6. Click on the name of the table you want to
2. Click the Table tab, and then click Attach attach, then click OK.
Table. The source of the data to display on the form is
The Attach Table dialog box appears. indicated, but the form is still blank. To access the
data, you need to draw some data boxes, and
3. In the Attach Table dialog box, click Open
indicate what data to show in each of those boxes.
Oracle/ODBC Data Source.

Attaching Tables from Other Applications
Creating a Portal 5. Click Create Field.
Database The Create Field dialog box appears.
To carry out certain operations, such as sorting

structural data, ChemFinder needs to create
temporary tables in a database.
Instead of accessing the read-only source directly,
you can create a portal database–a local, writable
database with attachments to the external tables of
interest. The portal looks and behaves just like the
target database, but without the limitations.
ChemFinder creates a portal database when needed.
For example, if you use a database CD, search, and 6. From the Type drop-down list, choose
attempt to sort by formula, a message appears that Structure, and then click OK.
offers to create a local database, attach the current
table, save the form, and proceed with the sort. If You do not provide a name or other details when you
you create the local database, you can use the new create Structure columns. ChemFinder
form to get the data with full functionality and automatically creates four columns and names them.
performance. These columns contain no data until you enter
When you are using a read-only database, structures into the database.
ChemFinder offers to create a portal database.
ChemFinder does not automatically create a portal
database during searching because it would destroy
Creating Fields
the hit list. When this happens, ChemFinder displays Whether you created a new database or are working
a message. You can manually create a portal in an existing one, you can add or remove fields in
database or sort to automatically create one, and
then repeat the search. the selected table.
You can choose from the following types of fields:
Adding Structures to
Text field—Allows you to enter text such as
Non-Chemical Databases
names, comments, and references. A text field is
If you opened a database that you created using a fixed in length, and requires that you choose a
program other than ChemFinder and you want to maximum length (“width”) for any data item to be
add structures to it, you can create structure fields in stored in the field. If you enter a width of 50, then
any modifiable (non-attached) table. you can’t store any item with more than 50
characters in that field.
To create a structure field:
1. Open a database. You can specify widths of text fields as large as 254
characters. If this is insufficient, you need to create
2. Right click, choose Properties.
a Memo/Rich Text field instead.
3. Click the table to which you want to add
structures.
4. Click the Field tab.

Creating a Portal Database
Because the text field width cannot be modified You can create more than one set of structure fields
after a field is created, it is often wise to err on the in a table. Each is assigned a unique set of names,
side of caution and make it longer than you need and each refers to its own ID column in the table,
initially. On the other hand, larger field widths also although all structural data is taken from the same
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create larger files and slower search times. structure database files.
To create a field:
Integer field—Used for whole numbers such as
ID's. All integers in ChemFinder are long, so can 1. Right-click on a data box and choose
Properties.
accommodate billions of values (232 of them).
Real field—Used for real numbers such as
physical constants and unit prices. Real numbers in
ChemFinder are double-precision. The Field properties appear.
Picture field—Allows you to store a Windows

metafile, such as a spectrum or experimental setup,
as a data item in a database.
NOTE: A Picture box on a form may be used to

display a static, decorative picture attached to the
form, or it may be used to show pictures stored in the
database which change as you move from record to
record.
Memo/Rich Text field—Used to display text.

Memo fields can be of any length. Because memo
fields are less structured, searching them can be The Create Field dialog box appears.
slower than searching a text field. Additionally,
memo fields cannot be sorted.
Memo fields are the only fields that can store Styled
Text. For more information, see “Styled Text” on
page 65.
Date field—Allows you to store dates. The dates
are displayed according to the settings in the
Windows Regional Settings control panel.
4. In the Name box, type a name.
Structure field—Consists of four fields: a 5. In the Type box, choose a data type.
numeric ID stored in the relational database, plus
6. For text fields only, in the Width box, choose a
three fields (Structure, Formula, MolWeight) that
width.
take data from the ChemFinder structure database
files. 7. Click OK.
The name of the new field appears in the data
source tree.

Creating Fields
Adding Multiple
Structures
You can include more than one structure on the same
form by creating multiple structure columns in a
table. Each structure column you create represents
four types of data:
• The structure displayed as a diagram.
6. Select Structure from the Type drop-down list.
• The Molecule ID, which connects the structure
An uneditable name is assigned to the field.
to a record in a relational table.
• The formula derived from the structure.
• The molecular weight derived from the
structure.
To create multiple structure columns in a table:

1. From the File menu, choose Database.
The Form Properties dialog box appears.
7. Click OK.
Four new fields appear in the list and are named
to belong to the same set of structure columns.
8. Connect the new fields to boxes by
right-clicking on the appropriate data box and
choosing the field.
2. Create or open a database.

4. Select the Table in which you want to create
new structure columns.
The Create Field dialog box appears.

Adding Multiple Structures
Deleting Fields 3. Make backup copies of files with extensions:
.mdb, .mst, and .msi. Select the files and drag
Just as you can create any field and assign it to a data them to another directory or use the Edit menu
box at any time, you can modify the database by to Copy and Paste.
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deleting fields from the selected table.

NOTE: Your database may not contain files with
To delete a field: all the indicated extensions. Not all of these files are
1. In the field list, select the field to be deleted. present in all databases.
2. Click Delete Field.
You do not need to back up the ChemFinder form
3. When prompted whether you want to delete the file (.cfw extension) or the Jet lock file (.ldb).
selected field, click OK to delete it or click
Cancel to leave it unmodified. To use the saved data, you may directly open the
backed-up .mdb file as you would open any
CAUTION database. Alternatively, you may replace a database
with its backup copy by restoring the backup file
When you delete a field, all data contained in the field
is also deleted. You are not warned explicitly about copies to their former locations.
this.
Moving Databases
Backing up Databases ChemFinder saves only the definition of the form
and information for connecting to the database. The
ChemFinder does not back up databases. To back up actual data are stored in files with .msi and .mst
a ChemFinder database, use Windows Explorer to extensions for structure data and in files with an
make backup copies. .mdb extension for non-structural data. If you want
to move a database to another computer, you must
To back up the current database:
move (for a default ChemFinder database) at least
1. If necessary, obtain the database name and four separate files. This number might be greater if
location by viewing the Box Properties: you have several forms that access the same
Database dialog box. database.
The Name box shows the full pathname of the
main database (.mdb) file. NOTE: The .msi, .mst, and .mdb files all have the
2. In Windows Explorer, navigate to the folder same file name, but the name of the .cfw files might
containing the database files. be different depending on how you saved them.
Accompanying the .mdb file are several After you move the database to its new location,
associated files with the same name but open your forms to make sure the data source links
different extensions. have been retained. If ChemFinder cannot locate the
data source and displays an empty form, you need to
use the Database command on the File menu to
reconnect to the data source.

Deleting Fields
If the form is connected to a remote data source on a
network, you have fewer files to move. The data
source can remain on the remote machine, and you
only move the .cfw file that contains your form for
accessing the data. You may need to reconnect it to
the data source if it is not done automatically. This
situation is common in large organizations where
several people access the same central data source.

Moving Databases
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Moving Databases
Chapter 5: Searching
Overview In Query mode:
• The form background color changes.
ChemFinder performs chemical structure searches
and text searches. When searching text, you can • QRY appears in the status bar.
search in fields such as molecular weight, formula • Form boxes are displayed according to their
and references. When structure searching, you can visibility properties. For more information, see
search by substructure, full structure, or structural “Hiding Data Boxes” on page 45.
similarity. You can also combine structure searching
with text searching. Entering and Submitting a
To search, use the Search menu or the corresponding Query
tools in the Search toolbar.
To enter the query:
Enter Retrieve Previous Restore Over
Query All List Current 1. Position the cursor over the field you want to
Query
List search and click to select it.
2. Enter the query in the data boxes.
To submit the search, do one of the following:
• From the Search menu, choose Find.
Find Find Current Save Restore Find
Molecule List Previous List • Click Find .
List
• Press Enter.
Beginning a Search ChemFinder searches. The number of hits is

shown in the Status Bar at the lower right corner
Searching includes the following steps: of the window.
• Clearing the form.
• Entering the query in the form. NOTE: If a search gets no hits or an error occurs,
an alert appears and you are returned to Query
• Submitting the query to the search engine. mode to enter a different query.
Clearing the Form Because the hit list is a subset of the complete
To clear the form: database, you can browse it as you would any
• From the Search menu, choose Enter Query, database using the Record commands in the Record
or click Enter Query . menu.
You are in Query mode. For example, to view the hits in tabular form:
• From the View menu, choose Data Table.
ChemFinder Chapter 5: Searching • 79

Beginning a Search
Stopping a Query Viewing Continuous Forms
To stop a structure query in progress, press Esc. The You can view multiple records at one time with the
query stops and you return to browse mode. Continuous Form View. Multiple records appear in
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a miniform.
NOTE: Only queries that involve structural data To see records in the continuous forms:
(structure, molecular formula, and molecular
weight searches) can be stopped in this manner. SQL • From the View menu, point to Continuous
searches and searches that involved non-structural Forms, and then choose the appropriate option:
data cannot be aborted.
Viewing Results replace the current In Current Window.

You can view search results in: form Continuous forms are
• A single form shown in the current
window.
• In a table containing multiple forms
• Continuous forms
create a new window In Separate Window.
You can also view chemical markers on structures to display the forms An additional window
and search for a particular atom or bond number.
opens and displays the
continuous forms.
Viewing Forms in Table View
To view forms in table view:
Switching Views
• From the View menu, point to Data Table, and
take the appropriate action: When you switch views they follow the order: Form
to Table to Continuous Form.
If you want a table to Then choose To switch views:
In Current Window. 1. From the View menu, choose Switch Views or

replace the current
form click .
The view changes sequentially.
appear in a different In Separate Window.
window
A table appears with all the information from

the form.
80 • Chapter 5: Searching CambridgeSoft

Viewing Results
Viewing Chemical Markers 2. Type A and the atom number or B and the bond
number to find.
ChemFinder enables you to display the following
chemical markers in structure boxes: A circle appears on the structure temporarily to
show where the number is located.
• Atom numbers
• Bond numbers Refining a Search
• Stereochemistry You can refine a hit list of one or more records by
• Reaction info entering a query that searches only the hit list, not
• Atom-to-Atom map the entire database.
For detailed information about the markers, see the To refine a search:
ChemDraw User’s Guide. 1. On the Search menu, verify that Over Current
You can also find specific atom or bond numbers. List is selected.
To view chemical markers: 2. From the Search menu, choose Enter Query,
or click Enter Query .
• On the View menu, point to Structure, and then
ChemFinder searches over the previously
choose the marker to view.
retrieved hit list. If no hits are found, a message
The Atom number markers are shown on the appears asking whether to search over the entire
following structure: database.
Restoring a Previous
List
After you refine a hit list, you have a smaller list. To
return to the previous, less-refined list:
• From the Search menu, choose Restore
Previous List, or click on the Search
To locate a particular atom or bond: toolbar.
1. On the View menu, point to Structure, and then The previous hit list is restored.
choose Locate atom/bond.
The Locate atom or bond dialog box appears.

Refining a Search
Resetting the Database Examples of queries:
After you perform a search, you can return to the Entry Possible hits
complete database. If you want to refine your search
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by searching the hit list from your first search, do not benz benzene, benzoic acid, not
reset the database. When you reset the database, the bromobenzene
hit list from your first search is discarded.
benz or strings starting with benz or
To reset the database:
*bromo* containing bromo
• From the Search menu, choose Retrieve All or
click the Retrieve All tool on the Search =benzene Benzene, not benzoic acid, not
toolbar. benzene-d6, not bromobenzene
The hit list is discarded, and the complete
database is reset, with the current record on Numerical Searching
display.
Searching numerical data allows you to find
Text Searching information such as boiling points and molecular
weights.
Text searching allows you to search for strings of
Ranges are specified using a hyphen between the
text. You could use text searching to find chemical
values at either end of the range.
names, comments, etc.
For numerical searching, the query is a decimal
For text searches, ChemFinder interprets the query,
value or range. If a single value is given, the number
then passes it as Structured Query Language (SQL)
of significant digits determines the precision of the
to the relational database. The following rules apply
search. A hit is any value that rounds off to the
to these queries:
query.
• A text string is taken as an “anchored
Examples of queries:
substring,” which hits any string starting with
the indicated substring.
Entry Possible hits
• Text strings may contain wild cards or Boolean
operators. Wild cards are “%” and “*”; these 90 values from 89.5 to 90.5
characters are equivalent and hit any string.
• Boolean operators are “OR” and “AND.” They 90.1 values from 90.05 to 90.15
may be used to combine search terms within
90–100 values from 90 through 100,
one field.
inclusive
• If the text query has a “=” in front (=toluene),
then the search requires an exact text match. >=90 and <=100 values from 90 through 100,
inclusive
>90 and <100 values from 90 through 100,

exclusive

Resetting the Database
Date Searching Molecular Formula
Dates might be used to track individual reaction Searching
runs, purchasing histories, and so on. Searching
dates is very similar to searching numerical data. Formula searching allows you to search molecular
compositions, exact or in the range that you specify.
Ranges are specified using a hyphen between the
values at either end of the range. Ranges may also be The following table shows query examples.
indicated using inequality operators (<, >) together
with the AND operator. Entry Possible hits
Dates are always displayed according to the

C6H6 compounds with 6 carbons and
preferences set in the operating system’s
6 hydrogen atoms, plus any
International control panel.
number of other elements.
The following table shows query examples.
=C6H6 compounds with 6 carbons and
Entry Possible hits 6 hydrogen atoms and no other
elements.
Apr 11, 1971 the exact date April 11, 1971
C6N0 compounds with 6 carbons, no
nitrogens, plus any number of
March 31, 1971– any date in the second quarter
other elements.
July 1, 1971 of the year 1971
C6 N1-3 compounds with 6 carbons and

>April 11, 1971 any date after April 11, 1971
one to three nitrogen atoms, plus
any number of other elements.
Formula queries consist of element symbols and

element counts or ranges. The following rules apply:
• Symbols may be one or two letters. Symbols
may be in upper or lower case; if there are
ambiguities, the program resolves them
according to rules described in Appendix B.
• Capitalize the symbols properly.
• Insert spaces between symbols.
• Use the Periodic Table to enter formulas. For
more information, see “Using the Periodic
Table” on page 122 and “Appendix B: Formula
Input Rules.”

Date Searching
• Element counts are single integers or ranges To find a list:
(two integers separated by a hyphen). If a count 1. From the Search menu, choose Find List.
is omitted, it is assumed to be 1.
The Find List dialog box appears.
• If the formula query is precede by “=” (=C6H6
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for example), then the search requires an exact

formula match, containing no elements other
than those indicated. If there is no “=”, then the
search is a partial match: other elements may be
present in the hits.
• Symbols may be repeated. For example,
“CH3CH3” is interpreted as “C2H6.”
NOTE: Formula searches are completely non-

structural: CH3CH2OH matches both dimethyl
ether and ethyl alcohol because both
compounds have the same condensed formula:
C2H6O. 2. From the Column menu, choose an ID.
• Parentheses may be used to group elements and 3. Paste or type a list of ID parameters into the
apply a count to the entire group. For example, Find List box.
“(CH2)3” is interpreted as “C3H6.” 4. Click OK.
• Spaces or non-alphanumeric characters other
The list of matching records is retrieved.
than parentheses are ignored.
Find List Structure Searching

ChemFinder allows you to search structures in four
You can search for a list of records using any text or
ways: by full structure or substructure, with an exact
number field. You use the Find List command to
match or by similarity. In addition, ChemFinder also
search for lists of values on any non-structure field. supports most of the query functions in ChemDraw
Type parameters into the Find List box as follows: so you can define the search more precisely.
• If the column you search is an integer type, you Entering a Structural Query
can use hyphens to indicate ranges.
To begin a structural query:
• If the column you search is an number or text
type, you cannot use hyphens to indicate • From the Search menu, choose Enter Query, or
ranges. click Enter Query, to clear the form.
• If the column you search is a text type, you must
use quotes around any item that contains
comments. For example, you must type
1,2-Pyran as ‘1,2-Pyran.’

Find List
To place a structure into a data box use any of the matched. For more information, see “Search Type
following methods: Preferences” on page 117 and “Stereochemistry” on
page 87.
• Double-click in the structure box and open
ChemDraw.
Substructure Searching
• Right-click and use Edit Structure to open
Substructure searching, the default searching type,
ChemDraw.
finds structures that contain the query and any
• Right-click and use Read Structure File to additional attachments at the open positions. Results
open an existing molecule file.
have the substructure highlighted in red. Using
• Use Paste from the Edit menu to insert a ChemDraw Pro, you can attach different features,
structure from the clipboard. such as atom lists and variable bond types, to a query
Enter the query: to perform a narrower or broader search.
1. From the File menu, choose Preferences and For more information about what query features you
click the Search Type tab. may use and how these features affect a search, see
2. On the Search Type tab, select the appropriate “Appendix A: Structural Query Features” on page
options. 135.
3. From the Search menu, choose Find. An example of substructure searching of
If Substructure is deselected, ChemFinder does a Cyclopentane:
Full Structure search. If Similarity is deselected,
ChemDraw performs an Exact Match search. These This substructure query will hit
options can be combined in any of four
combinations:
• Exact Full Structure
• Exact Substructure
• Similar Full Structure O
• Similar Substructure
The status bar counters indicate search progress. O
When the search is complete, the form displays the
first hit. The list you can browse is limited to the
hits. In a complete structure or substructure search,
the hit portion of each molecule is highlighted in
HO
red. If a search doesn’t find any hits, you are
returned to query mode.
Exact Full Structure Searching

Deselecting both Substructure and Similarity finds O
structures that completely match the query. You may and other molecules
get more than one hit if there are duplicates in the
database or if there are stereoisomers in the database
and you did not specify a particular one to be

Structure Searching
Cl
NOTE: In searching substructures, ChemFinder
finds the substructure query regardless of its
orientation or drawing presentation in the targeted
molecules. Bonds shown in bold above are actually
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highlighted in red in ChemFinder.
For more examples of substructure searching, see The hit list will include the reaction that produces
“More Search Examples” on page 97. these products:
Cl
Fragment Searching
You can draw more than one structure or structure
+
fragment in your substructure search query. You can Cl
choose whether to permit fragments to overlap in the
target structure Search Preferences dialog box. For
more information, see “Chapter 8: Customizing Match Extraneous Fragment
ChemFinder”.
The hit list will not include this reaction if “Permit
For example, if you perform the following extraneous fragments in full structure searches” is
substructure query with “Query fragments can deselected.
overlap in target” selected:
Similarity Searching
OH
The similarity option finds structures that have
The hit list will include the following: structural features that generally correspond to those
in the query. Similarity searches are by their nature
“fuzzy”. In a full structure similarity search, the
OH
results are guaranteed to include all those you would
The dot indicates an atom shared between the two
obtain from a substructure search with the same
fragments. The hit list will not include this molecule
query. Usually, they include additional hits. For this
if “Query fragments can overlap in target” is
reason, similarity searches are useful if you have a
deselected.
general idea of the types of compounds you are
When you perform a full structure search in a looking for, but don’t have a precise conception of
database that contains mixtures or reaction data, you the target compound.
may get hits containing more than one structure. You
Unlike exact searches, similarity searches do not
can choose whether to include hits with extraneous
highlight matched portions of the target compounds.
fragments in the Search Preferences dialog box. For
Similarity searching matches general structural
more information, see “Chapter 8: Customizing
features and not specific atoms and bonds, so
ChemFinder” on page 115.
highlighting specific areas would not be appropriate.
For example, if you perform the following full
You can adjust the degree of similarity using the
structure query with “Permit extraneous fragments
Search Preferences dialog box.
in full structure searches” selected:

Structure Searching
To search by similarity instead of exact structure: Using the Current Molecule as
• From the Search menu, check Similarity. a Query
For a detailed description of the similarity searching As you browse through a database, you may submit
algorithms, see “Appendix C: Similarity Rules” on any structure on the screen as the structural query.
page 145. Often, you use similarity or substructure searches
(see above) with this type of query to find related
Stereochemistry compounds.
You can specify whether or not you want a structure
To use the current molecule for a query:
search to consider stereochemistry. The two types of
stereochemistry recognized are tetrahedral chirality 1. Using the Record commands, go to the record
and cis/trans double-bond geometry. If these options containing the structure that you want to use as
are checked in the Search tab of the Preferences a query.
dialog, then any stereochemistry indicated on the
2. From the Search menu, choose Current Mol As
query must be matched by the target. For more
Query.
information on changing searching preferences, see
“Search Details Preferences” on page 118. All boxes of the form are cleared except the
structure so that the molecule on display can be
NOTE: Stereochemistry is perceived in the query used as part of the query. You can then continue
from (a) hashed or wedged bonds at a tetrahedral with the query as if you had drawn the structure
center, and (b) unsymmetrical substitution at a C=C from scratch.
double bond.
Finding the Current Molecule
4. From the Search menu, choose Find Current The Find Current Molecule command, located in the
Mol, or click Search tool . Search menu and on the Search toolbar, is similar to
ChemFinder begins the search and displays the the Current Mol as Query command discussed
search status on the lower right corner of the status above. As you browse through the database you may
bar. When the search is complete, the form displays find a molecule that interests you, and want to find
the first hit, and the list you can browse is restricted other related records.
to the records hit by the query. The Find Current Molecule feature lets you perform
a quick structural search of the structure currently
being displayed on the form. However, this feature
does not allow you to enter other search terms. The
type of structure search (complete structure,
substructure, and/or similarity) is determined by
what you have selected in the Search menu.

Structure Searching
To find the current molecule: Clear the form:
1. Browse to the record containing the structure of • From the Search menu, choose Enter Query, or
interest. click the Enter Query tool.
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The form clears.

2. From the Search menu, choose the type of
structure search you want to perform. Enter the query:
3. From the Search menu, choose Find Current 1. Right-click in the Structure box and choose Edit
Mol, or click Search tool . Structure.
ChemFinder begins the search and displays the 2. Draw the structure or substructure or reaction in
search status on the lower right corner of the status the From ChemFinder window.
bar. When the search is complete, the form displays 3. Click the ChemFinder application window to
the first hit, and the list you can browse is restricted
bring the structure back from ChemDraw.
to the records hit by the query.
Now you can enter more query terms in the other
Reaction Searching data boxes for a combined search.
You can search and store reactions. In a reaction, one 1. From the Search menu, select or deselect the
or several compounds (reactants) are transformed Substructure option.
into other compounds (products). Individual
reactants (or products) are separated from each other NOTE: The Similarity option is not available
with plus signs. The reactants are separated from the for reaction queries.
products with an arrow.
2. From the Search menu, choose Find.
Reactions may have multiple steps, for example
The search proceeds as with simple structure
(A)—>(B)—>(C)—>(D). Here, (A) is the reactant
searching.
and (D) is the product. (B) and (C) are intermediates
for the complete reaction. Reaction Centers
A multi-step reaction is actually a shorthand The most important part of a reaction is the part that
notation for many related reactions. In the example actually changes from the reactants to the products.
above, (B) is an intermediate for the complete This part, which probably includes a number of
reaction, but it is also a reactant relative to (C) or atoms and bonds, is called the reaction center. For
(D). It is also a product relative to (A). The complete example, only the bold bond below (and the two
reaction implies many subreactions, such as: atoms on either side) is part of the reaction center.
(B)—>(D) and (A)—>(B). The rest of the structure is unchanged from the
reactant to the product:
Entering a Reaction Query
O OH
The general procedure for creating a reaction query
is very similar to creating a structural query.
F Cl F Cl

Reaction Searching
By default, ChemFinder considers reaction centers Since the corresponding n-octanal—>n-octanol
whenever you search for reactions. For information reaction would probably occur under very similar
on changing searching preferences, see“Setting conditions, it is a reasonable thing to look at.
Preferences” on page 115. ChemFinder assumes that Generally, you want to use substructure queries that
any atoms and bonds that change in the query must include little beyond the reaction center in question
be part of the reaction center of the target. when you are searching for reactions.
For example:
NOTE: ChemFinder supports several query
F Cl properties to allow you to specify exactly how a
bond participates in a reaction center. For more
does not hit
information about these properties, see “Search
O OH Details Preferences” on page 118.
F Cl F Cl
The second most important part of reaction
when the “Reaction query must hit reaction center”
searching is the atom-to-atom map. You can specify
preference is selected. Even though there is a C-F
maps in ChemDraw, where they are stored as part of
bond in the target reactant and a C-Cl bond in the
the data about a reaction. Maps are used during
target product, these bonds do not participate in the
searching to resolve certain types of structure search
reaction, which really affects another part of the
hits.
compound. If you deselect the “Reaction query must
hit reaction center” preference, this query hits the Consider a simple esterification reaction:
target above.
O O
+ OH + H2O
When creating reaction queries, it is important to
OH O
consider what sort of information you are really
Does the ester oxygen come from the acid or the
looking for. Suppose you want to convert n-decanal
alcohol? You specify the fate of individual atoms
to n-decanol:
through an atom-to-atom map. In reality, the ester
oxygen in this reaction originates in the alcohol, so
O
the atom-to-atom map looks like this:
O 3 O 3
6
OH 4
+ OH + H2 O
1 1
5
2 OH 5 2 O
Are you really interested only in these two 4 6
compounds? You might be interested in any reaction By matching numbers across the arrow, you can see
that converts a straight-chain aldehyde to the where atoms move during the course of the reaction.
alcohol: The other reaction (not observed experimentally),
where the ester oxygen comes from the acid, would
H H H H
be mapped like this:
O OH
H H H

Reaction Searching
O 3
6
OH
O 3
6
Searching for Products
+ + H2 O
1
2 OH 5
1
2 O
5 If you know the desired end product but not how to
4 4
get there, you can do a products query. A products
ChemFinder uses atom-to-atom map information to
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query is similar to a reaction search, except that

determine reacting centers for reactions. If only
there is nothing to the left of the arrow. For example,
some atoms are mapped, ChemFinder uses that
consider the query:
information and does not worry about the specific
fates of the other atoms. For example, if you don’t
know (or don’t care) about the mapping of some
atoms, you can leave them unspecified in the atom-
to-atom map. If you are doing a substructure search, this finds any
reactions in which bicyclo[2.2.1]heptane or a
By default, atom-to-atom mapping is not displayed
compound containing this substructure is produced.
within ChemFinder. You can turn on this display by
checking the “Show atom-to-atom maps” check box
Searching for Intermediates
in the Display tab of the Preferences dialog. For
more information, see “Setting Preferences” on page Rarely, you may be looking for reactions for which
115. you only know something about an intermediate. An
Intermediate Search is very similar to a normal
NOTE: For information about specifying reaction search, except that there are arrows on both
atom-to-atom maps with ChemDraw, see the sides of the target structure. For example, consider
ChemDraw User’s Guide. the query:
R C C O
Searching for Reactants
This finds any reactions containing the Ketene
If you know what starting materials you are structure shown as an intermediate.
interested in but don’t know their products, you
might perform a reactants query. A reactants query
NOTE: ChemFinder cannot predict products or
is very similar to a reaction search, except that there
intermediates of reactions. It finds this information
is nothing to the right of the arrow. For example, only if it is already present in the database.
consider the query:
O
If you are doing a substructure search, this finds any

reactions in which maleic anhydride or a compound
containing a maleic anhydride substructure is
consumed or transformed.

Reaction Searching
SQL Searching An example of combined searching:
Suppose you want to find all molecules in the
SQL (Structured Query Language) can be used to
CS_Demo database that contain a benzene ring and
create powerful searches. The details of the
which have names related to “penicillin.”
language are not discussed here.
1. From the Search menu, choose Enter Query, or
Queries beginning with a backslash (\) are taken as
straight SQL, and passed directly to the database as click Enter Query, to clear the form.
the WHERE clause of the SQL query. These must 2. Draw a benzene ring in ChemDraw and import
contain column names and punctuation as dictated the structure into ChemFinder.
by SQL. For example, a valid query might be 3. Enter *penicillin in the Molname field.
“\[molname] like 'benz*' and [bpoint] > 200”.
4. From the Search menu, choose Find, with the
A straight SQL query may be entered in any box of Substructure option selected.
the form which contains non-structural data. The You get 2 hits of molecules whose names contain
SQL query is not associated with the box in which it
“penicillin” and whose structures have an aromatic
is entered.
ring of six carbon atoms.
Combined Searching NOTE: In a combined search, progress reports are

You can combine structure searching with text given only during the structure search part. When
searching to find a specific class of compounds. For the counters at the bottom of the screen are
example, you may want to find all compounds in the advancing, structures are being searched. You can
press Esc to end a search during the structure
database whose names end in “mycin” and whose
searching. You cannot end a search during the SQL
structures contain a phenyl ring. Because you are
searching by pressing Esc.
entering multiple queries in different data boxes,
there is an “AND” condition between data items in
different fields. Managing Search
To perform a combined search: Results
1. From the Search menu, choose Enter Query, or
After you have created a query, performed the
click Enter Query to clear the form.
search and retrieved the results, you can save the hit
2. Enter the structural query, if any. list. This hit list can serve as a record of your search
3. Enter the text and/or numeric queries. results. You can also combine hit lists in various
ways.
4. From the Search menu, choose Find, or press
Enter.

SQL Searching
Saving a Hit List Restoring a Hit List
Create a query and perform the search. Once you have saved a hit list, you can perform
another search and then integrate the results from
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1. When you have received the hit list, from the the second search with the results from the first.
Search menu, choose Save List or click Save Thus, you can perform Boolean operations on
List . different searches.
The Save As dialog appears for you to save the
To integrate the results of two searches:
hit list as a text file.
1. Perform a search and save the hit list.
2. Perform another search.
3. From the Search menu, choose Restore List or
click the Restore List button .
The Open dialog appears for you to choose the
file that you want to integrate with the current
hit list.
4. From the Open dialog box, open the text file
that you want to integrate with the current hit
list.
2. In the Save As dialog, type a filename for the The Restore List dialog box appears.
hit list, and click Save.
The file consists of a list of values of the primary key
of each record in the hit list. If there is no primary
key, the molecule ID is used.
To edit a saved hit list, open the text file with a text
editor such as Notepad and edit the values you want
changed.
5. Select the integration option and click OK.

• Replace current list—discards the current
hit list and display the records from the hit
list you chose to open.
• Intersect with current list—displays only
those records that appear in both the current
hit list and in the saved hit list. This is a
Boolean AND operation.

Managing Search Results
• Subtract from current list—displays only search, you want to find which of these compounds
those records that are in the current hit list do not contain a carbon-nitrogen bond. By
but that are not in the saved hit list. For integrating hitlists, you can perform this search.
example, if the current list contains records,
To create the hitlist for the first part of this search:
1, 2, 3, 4, and 5, and the restored list contains
records 4, 5, 6, and 7, then only records 1, 2, 1. Open the CS_Demo database.
and 3 will be displayed. This is a Boolean
2. Create the first query by drawing benzene in the
NOT operation; it shows the records in the
Structure data box and entering 50-200 in the
current list that are not also in the restored
Molecular Weight Data Box.
list.
3. Search the query.
• Union with current list—displays all
records in either the current list or the saved You get 75 hits.
hit list. This is a Boolean OR operation. 4. From the Search menu, choose Save List.
The hit lists are integrated. You can browse and 5. Save the hitlist as benz.txt.
save this new hit list just as any other hit list.
To create another hitlist for the second part of the
NOTE: If you merge two lists and get an empty search:
result, an alert appears and the list is reset to
the full database. 1. Draw the query shown below in the Structure
Data Box.
Search Examples C N
2. Search the query.
The following are examples of searching options.
By specifying atom and bond properties, you see You get 103 hits.
how to use the query functions in ChemDraw to 3. From the Search menu, choose Save List.
search the database more effectively. All
4. Save the hit list as c-n.txt.
substructure search query properties recognized by
ChemFinder are listed and described in Integrate the two hitlists:
“Appendix A: Structural Query Features” on page
135. 1. From the Search menu, choose Restore List.
2. In the Open dialog box, open the benz.txt file.
Working with Multiple Hit Lists
3. In the Restore List dialog box, click Replace
A detailed example of how you can use hitlist current list, and then click OK.
management to perform specific, sophisticated
You return to your first list of 75 hits
searches follows.
4. From the Search menu, choose Restore List.
Suppose you want to search for all compounds in the
CS_Demo database that contain a benzene 5. In the Open dialog box, open the c-n.txt file.
substructure and have molecular weights between 6. In the Restore List dialog, click Subtract from
50 and 200. After you perform this combined current list, and then click OK.

The hit list is reduced to the 60 records with
This atom can be any non-hydrogen atom
compounds containing a benzene substructure,
not containing a C-N substructure, and having A
molecular weights between 50 and 200. This may be a single or double bond
S/D
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If you had chosen the “Replace current list” option [S,Se,Te]

This atom must be S, Se, or Te
in the last step, then only the “C-N” records would
be displayed. Choosing “Intersect with current list” The “A” label denotes that the atom may match any
would display those records in either list. Finally, atom except hydrogen. The indicator near the bond
choosing “Union with current list” would display all indicates that the bond has been defined; in this case,
records from both lists. in the Bond Properties dialog of ChemDraw, you
specified that the bond type may be single or double,
Using Atom Lists S/D. Finally, by entering “S,Se,Te” enclosed in
brackets, you specified that one of these elements
Using the text tool in ChemDraw, you can enter in a must match in the target molecules.
structural query a list of possible atom types, one of
which must match in the target compound. Searching Fullerenes
If you want to search for molecules containing a A search of fullerenes can illustrate the restrictions
benzene ring with an ether, amine or phosphane you can place on a formula search. Suppose you
group, a query might look like the following: want to find all fullerenes containing 20 to 80 carbon
atoms, but you also do not want to include large
organic molecules.
[O,N,P]
The formula query could be:
C20-80 H0
Atom Types and Bond Types By designating zero hydrogen atoms, you exclude
hydrocarbons from the hit list. By clearly
To broaden or narrow a search query, you can define
capitalizing the elements and spacing the query, you
the properties of the atoms and bonds in a structural
query. These properties are definable in ChemDraw avoid searching ambiguities, although there were no
Pro using the Atom Properties and Bond Properties ambiguities in this example.
dialogs accessible from the Structure menu.
Suppose you want to find all molecules that contain
a non-oxygen chalcogenide bonded to another atom,
not necessarily carbon. You also want the bond type
between the chalcogen and the other atom to be a
single or double bond. The query, drawn in
ChemDraw Pro, may look like this:

Searching More Than One Printing
Substructure
ChemFinder can print high-quality hard copies of
A substructure search may contain more than one
your forms and tables. You can customize the format
substructure unit. Suppose you want to find all
of the printout by specifying the number of forms
compounds in the CS_Demo database which
per page and the layout of the forms.
contain a benzene substructure and another
substructure unit containing chlorine bonded to any
atom. A structure query, as drawn in ChemDraw NOTE: When you print a table, the columns are
would look like this: printed in the order they appear in the Data Table
A Cl window. To prevent a particular column from
printing, adjust it to zero width in the window.
ChemFinder uses the standard system commands to

print ChemFinder forms. The available options
depend on the printer you are using. Refer to your
You should get five hits. Browse the hits. By printer’s documentation for more detailed
specifying the query as above, you obtain hits such information.
as benzyl chloride, shown below, where the
To print a ChemFinder document:
substructure units are not connected.
Cl
1. Specify the page layout:
H H
• From the File menu, choose Page Setup.
2. Decide the layout of your forms or tables on the
printed page.
3. Specify the printer options:
The substructure units can overlap; they can share a • From the File menu, choose Print Setup.
common atom. Examples of this overlap are shown • Make the appropriate selections for the
below. printer you are using and click OK.
O Cl
O
OH 4. Optionally, from the File menu, choose Print
Cl
OH Preview and confirm the layout of the pages.
O
5. Print:
O Cl • From the File menu, choose Print.
• Make your selections in the Print dialog box
and click Print.

Printing
Page Setup Tables
The Page Setup dialog box allows you to format and To display the Page Setup for tables:
layout the printed document. You can customize the
1. Make sure a table is the active window.
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number of forms printed per page, the size of the

margins, and the layout of the forms. There are 2. From the File menu, choose Page Setup.
separate Page Setup dialogs for printing forms and
for printing tables.
Forms
To display the Page Setup for forms:
1. Make sure a form is the active window.

2. From the File menu, choose Page Setup.
The Page Setup dialog box appears.
3. In the Margin section, enter the size of the
margins.
4. In the Titles and Grid Lines section, set the
preferences for which parts of the table get
printed.
NOTE: Changes made in the Titles and Grid

Lines section are reflected in the Preview.
For tables that are too tall and too wide to fit on one
printed page, you can choose the order in which the
pieces are printed.
3. In the top drop-down menu, choose the unit of
measurement (inches or centimeters) for the • In the Page Order section, indicate the order
margins. you want the pages printed.
4. In the margin boxes, enter the size of the For tables smaller than one page, you can choose
margins. how to position the printout on the paper:
5. In the Layout section, choose the tile or the
1. In the Center on Page section, select either (or
stacked format by clicking the appropriate radio
button. both) of horizontal and vertical centering.
6. Select the number of forms (up to eight) you
want printed per page.
7. To size the forms proportionately to fit flush
within the chosen margins, select Scale to Fit.

Printing
Print Preview 3. Use the Zoom In or Zoom Out tool to magnify
or reduce the preview on screen.
The Print Preview dialog box displays the document
on screen as it looks when printed. This preview
allows you to see the output so you can make any
changes before printing. You can print the document
from the Print Preview dialog box.
To access the Print Preview dialog box:
1. From the File menu, choose Print Preview.
Click Close to exit Print Preview.
2. Select one of the following:

• Print to print the document.
• Next Page or Previous Page to scroll to the
next or previous page.
• Two Page or One Page to toggle the
preview to one or two pages at a time.

Printing
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Printing
Chapter 6: Relational Data and
Subforms
Overview • If you are running a stockroom and you want to
store package sizes and prices in the same place
Subforms allow you to work with multiple data because they are related. Each chemical may be
tables in a relational database. You should be available in lots of package sizes, and you
familiar with working with ChemFinder forms and wouldn’t want to re-draw the structure every
databases before proceeding to subforms. time you added a new package. You can use a
subform so the physical property information is
Accessing Relational entered once in the main form and the package
sizes and prices are entered many times in the
Data Using Subforms subform.
A subform is a special box within a form that By linking these two data tables with a linking
behaves like a separate form file. A subform is used field you can make these tables relational; one
to display information stored within a database, but table can interact with the other. The contents of
it usually displays data from a different database (or a linking field are not important, as long as they
different table within the same database) than the are different for each record in the main form.
main form. A subform is usually linked to the main Various forms of ID numbers are often used as
form, so that retrieval of data in the main form also linking fields. As you browse through the main
retrieves related records in the subform. form, corresponding records in the subform
appear.
Like other types of boxes, you can move select and
resize a subform on the main form. However, you In ChemFinder 6, when you view the subform data
cannot select it by clicking inside it. You must click source, the data source tree shows the subform table
the title bar. When you click inside a subform, you and the field by which it is linked to the main form.
you activate the miniature form inside the box and In ChemFinder 7, the main form table and the field
can work within it. by which it is linked to the subform is shown. When
you upgrade a database from ChemFinder 6 to
Below are examples of subform use: ChemFinder 7, you link by the subform data source
• If you have data that is associated in a and not the main form data source. The subforms are
“one-to-many” relationship. For example, if linked as they were in ChemFinder 6.
you want to view a chemical structure together
with its physical properties, stored in a separate
table.
ChemFinder Chapter 6: Relational Data and Subforms • 99

Accessing Relational Data Using Subforms
Creating a Subform
You create a subform, place form objects on it, and
connect the subform to a database just as you do a
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regular form. For detailed information, see

“Chapter 3: Creating and Editing Forms.”
.
To create a subform:
1. Click the Subform button .
2. Draw a large box on a form.
A subform appears with a border and scroll 2. Click the Database tab, and then click Open
bars. Database.
Within the subform, you can use the form tools to

create data boxes just as you would with a regular
form. You can also add tabs to your subforms. For
more information, see “Chapter 3: Creating and
Editing Forms.”
By default, newly created subforms are associated
with the same database as the main form.
To use a different database from the form as the data

source for the subform:
1. Right-click on the title bar of the subform and

choose Properties.
The Subform Properties dialog box appears.
3. Choose a database and then click Open.

The Database properties appear. The following
illustration shows the CS_Demo database.
100 • Chapter 6: Relational Data and Subforms CambridgeSoft

Creating a Subform
4. Select a table.
NOTE: The subform tab is only available if
you right-click the subform’s title bar.
2. In the Data Source tree, click the main form

field to link to the subform. For example, the
illustration above shows the Molname field
selected.
The field name appears in the Parent Field
section.
3. From the Relate to list, choose the appropriate
field from the subtable. For example, the
illustration above shows Synonym selected.
To use the subform relationally to the main form, 4. OK.
they must have one field in common. This Linking
Field must share the same data type (text, integer, The Subform is connected to the database you
real) as a field in the main form. The fields do not chose.
need the same name. In this example, when a record is retrieved in
To link the field to the subform: the main form, its “Molname” is used to search
the “Synonym” field of the Synonyms table.
1. On the Subform Properties dialog box, click the The subform displays the hits from this search.
Subform tab.
Changing the Layout of
an Existing Subform
You can use the Form Generator to automatically
change the overall layout of an existing subform.

Changing the Layout of an Existing Subform
To change the layout of an existing subform:
Working with Subforms
You must select a subform to work with it. The
2. Click the Form tab. subform title bar is highlighted when the subform is
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3. Click Generate New Form, and then click selected. After a subform is selected, the toolbars
Style. affect the subform. You can use the Record tools to
browse the subform and add records.
4. In the Form Generation dialog box, click the
fields to include. To select a subform:
5. In the Form style section, select the form • Click anywhere in the subform.
options you want. For a detailed description of
To return to the main form:
the options, see “Changing the Layout of an
Existing Form” on page 53. • Click the main form.
6. Click OK. To select a subform box:
7. In the Properties dialog box, click OK. • With the selection tool, click in the title bar.
An alert box appears.
change the overall Yes.

layout for the current
subform
create a new subform No.
The subform is automatically changed.

By default, the table name of the subform is
displayed in bold, 8 point Arial font.

Working with Subforms
Searching a Subform Using Scripts in
You search a subform the same way you search the Subforms
main form. You can search a subform and the main
form simultaneously. You can specify a CAL script to be executed when
you click an item in a subform in table view. The
To search: subform can then be used as a list selection box. The
1. From the Search menu, choose Enter Query to script can use CAL commands to retrieve the
clear the subform and main form. clicked item, and perform an action on it. For more
information about CAL, see “Appendix E:
2. Enter a query in the data boxes you want.
ChemFinder Automation Language Commands” on
3. From the Search menu, choose Find. page 149.
If the subform is linked to the main form, a
To specify a CAL script:
cleared form appears. The search is executed,
and ChemFinder returns you to the main form 1. Right-click on the subform header and choose
where it displays a hit list containing records Properties.
related to those that match in the subform The Subform Properties dialog box appears.
search. You can browse and save this hit list just
as you would a hit list from a main form search.
If the subform is not linked to the main form, it
behaves independently of the main form and is
searched separately.
Viewing Subform Data

in a Table
If you have more than one record in the subform
associated with a single record in the main form, it
may be more convenient to view the subform as a
table while you browse through the main form. The 2. In the Table script box, type the name of a CAL
table view shows you the complete list of related script or click and select a script.
records for each entry in the main form. 3. Click OK.
To display a subform in Table view: In Table view, the entries are blue and
• Select the subform and do one of the following: underlined indicating that they are hot linked to
a script.
• Double-click on a record in the table.
4. Click any of the hot links to run the script.
• From the View menu, point to Data Table,
and then choose In Current Window.
A table view of the records in the subform
appears.
To return to the Form view, repeat the above action.

Searching a Subform
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Using Scripts in Subforms
Chapter 7: Importing and Exporting
Data
Overview Saving Structures
You can move data into and out of a database if the To save the structure on display:
data is in ChemFinder supported file formats. You
can import or single files, import or export 1. In its structure data box, right-click and choose
databases, or add data to and existing database. Save Structure.
Supported File Formats 2. Choose the destination directory.
ChemFinder allows you work with individual 3. Type the file name and choose a file format.
chemical structures and reactions in various file 4. Click Save.
formats. The supported formats are:
The structure is saved to the indicated file. You can
• ChemDraw (cdx) read these files with any application that supports
• ChemDraw XML (cdxml) the specified file format.
• Chem3D (c3d)
• Connection Table (ct) NOTE: You must have ChemDraw Pro installed to
save most file types.
• MDL Molfile (mol)
• MDL RXNfile (rxn) Reading a Structure
• MDL RDFile (rdf)
• MDL SDFile (sdf) ChemFinder can read files of any of the supported
structural formats. For example, if you have
• MDL Sketch (skc) structures stored in ChemDraw format, you can
• MDL Graphic (tgf) open them directly from ChemFinder without
• Questel F1D (f1d) having to redraw them.
• Questel F1Q (f1q) To read a structure from a file into a structure box:
• SMD 4.2 (smd)
1. In the structure box, right-click and choose
Supported formats for output files only:
Read Structure.
• Bitmap (bmp)
• Encapsulated Postscript (eps)
2. Choose the file to read.
• GIF (gif)
• TIFF (tif)
• Windows metafile (wmf)
For detailed descriptions of the file formats, see the
ChemDraw Users Guide.
ChemFinder Chapter 7: Importing and Exporting Data • 105

Supported File Formats
3. Click Open. 2. From the Files of type menu, choose one of the
The structure is read into the structure box. The following:
database is not affected by this operation, until
you choose Commit Changes or move off of the To import files from Choose
Administrator
record.
a single directory the file type to import
Importing Structures and click Open.
ChemFinder enables you to import a collection of
multiple directories a. Files in folders.
structures into a new database or append or merge
them with an existing database. You can import b. In the Choose
single files or individual structure-data files. Structure Files
dialog box, select the
Importing Individual Structure directories to import.
Files c. Select or type the file

types to import.
To import structures:
d. Click OK.
1. From the File menu, choose Import Structures.
The Open Chemical Structures dialog box The Data Import dialog box appears.
appears. 3. Set the options as described in “Importing
Structure Data and Reaction Data Files” on
page 106.
4. Click Import.
The structures are imported to the specified
database.
Importing Structure Data and

Reaction Data Files
ChemFinder allows you to import and export
Structure Data files (SDFiles) and Reaction Data
files (RDFiles) directly into and out of a database.
Because these files contain both structures and data,
ChemFinder creates fields in the database to
accommodate the incoming data.
In RDFiles, incoming data may be hierarchical and
complex. When loading RDFiles, ChemFinder
converts the data to a relational form, creating new
tables as necessary and generating linking data.
106 • Chapter 7: Importing and Exporting Data CambridgeSoft

Importing Structures
NOTE: When importing RDFiles, boxes are
automatically created on the form only for fields in
the root table of the RDFile. Subforms must be
created and positioned manually.
If you have a blank form when you import,

ChemFinder creates boxes. If you have a form with
boxes when you import, no new boxes are created.
However, new fields are always created in the
database as necessary. You can add more data boxes
later if you want to display these fields. For
example, if the database has a MOLNAME field but
no MOLREGNO field, and you import an SDFile
that contains both, ChemFinder uses the existing
MOLNAME field, but creates a new MOLREGNO The Import dialog box scans the file to determine
field. what data fields are present and how much space to
You can import with a form linked to a database, a allow for them in the database. The number of
blank form, or no form. If you import with no form, records scanned is shown in the status bar. If the
ChemFinder creates a new form. input file is large, the scan may take a while.
To interrupt the scan:
To import structure and reaction data files:
• Press Esc.
1. From the File menu, point to Import, and then
take the appropriate action: A message box appears to confirm that you
really want to stop. The scan continues until
you click Yes.
If you want to import a file Then choose
with To abort the scan:
• Click Stop scanning.
an .sdf extension SDFile.
NOTE: It is not recommended to let the scan go to
an .rdf extension RDFile. completion, so that all needed fields are created in
the database before loading.
2. Choose the file to import and click Open. When the scan is finished, the progress bar is
replaced by the output database name. The dialog
The Data Import dialog box appears.
box for the Sample.sdf file is shown below.

target database. If the structure is not found, a new
record is created and appended to the database. If the
structure is found, a new record is not created.
You must specify what to do with the associated
Administrator
non-structural data by choosing one of following

options on the Merge tab:
Replace existing data—If there is new, incoming
data of type A, and the existing structure already has
data of type A, then the old data is erased and
replaced with the new. Existing data of type B is
untouched if there is no type B in the incoming file.
The default output database name and location is the

same as the input file.
Append to existing data—If there is new, incoming
To import to a different database: text data of type A, and the existing structure
• Type a pathname or click , browse to already has data of type A, then the resulting data on
file becomes a multi-line concatenation of the old
another location, and then click OK.
and the new. Append is not available for numeric
data; incoming numeric data always replaces
Adding Data to an Existing existing.
Database
When you import new data into an existing
database, incoming records may coincide with those
already in the database. You may choose one of
three options for adding data to an existing database:
Overwrite—Deletes the existing database, creates a
new database in the same location, and imports the
data into the new database. Skip entry—If there is new, incoming data of type
Append—Adds new data to the end of the existing A, and the existing structure already has data of type
database. Data existing before the import is A, then the incoming data is ignored and the existing
unchanged. Appending may lead to duplicate entries data is left untouched.
in the database, but it is fast and no data is lost.
Merge—Combines the new data with the existing
data. As each record is read from the SDFile or
RDFile, its structure is looked up in the (growing)

Merge Options The following table describes the Match by options
on the Merge tab:
The Merge tab of the Data Import dialog box allows
you to choose how your data is merged.
Option Description
Structure Search for exact match on

molecule or reaction in input file.
Other field Search for match on text or

numeric data.
Both structure Requires match in structure and

and other specified text or numeric data.
Custom SQL General mechanism for more

complex matching.
If no hits are found in the search, a new record is

added to the database. If hits are found, the first
record hit is modified as specified in the If match is
already on file options.
To choose how data is added to an existing database:

1. Click Overwrite, Append, or Merge.
2. If you chose Merge, click the Merge tab and

specify how to match the files and what to do
with matches that are already on file.

enough to hold any text you might add later. For
more information on text field widths, see “Creating
Fields” on page 73.
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To change the definition of a field before it is created

in the database:
1. In the Import tab dialog box, click the field to

change.
3. Click OK when you have entered all of the

options you want.
The file is imported into the database.
Changing the Data Field

Definitions
The Data Field Import dialog box appears.
ChemFinder can determine what sort of fields to
create in the database, based on the characteristics of
incoming data. For example, if all items of type
“Melting Point” in an SDFile are numeric, then a
numeric field is created for them. The field scan
shows the results of this determination.
You can override this automatic determination. For
example, if you are loading another SDFile into the
same database later, and it contains Melting Point
entries with non-numeric text, then you may want to
establish this as a text field instead of numeric.
If you want to Then
If you select a Text field type, you can specify the
width of the text field by entering a new value in the change the name of in the Output
Width box. Text fields are limited to 254 characters. the column being Column Name box,
Longer strings of text must be stored in Memo loaded type a new name.
fields. Because the width of a text field cannot be
changed after it is created, make fields that are long

You can choose whether to create the log file or not.
If you want to Then If you choose to create the log file, you can save it
with a different name or append to an existing log
change the data type from the Output file.
of the column Column Type menu,
To set logging options:
choose a different
data type. 1. From the Data Import dialog box, click the
Logging tab.
change the width of type the width.
The Logging tab appears.
the output column
import this field into click Import this

the database field. If deselected,
data in this field is
disregarded.
3. Click OK.
The Input Field information changes.
Using Log Files
During the import, ChemFinder creates a log file of
the actions taken. The log file (.log) is a text file that
is created alongside the input file and overwrites any
previous log file. The log records data of your choice
form the following options during the import.
• Errors—errors and warnings 2. In the Log File section, click the appropriate
• General data—information about the input file options:
and import process
If you Click
• Records processed—logs an entry for each
record of the input file
do not want a Do not generate log file.
• Structures registered—logs an entry for each log file
structure stored in the database
want a log file a. Log to file.
• Data registered—shows each data item stored
in the database b. If desired, type or
browse to a new name
• Database schema—shows input fields found
and path.
and columns generated
The log file for an RDFile import additionally c. If desired, click Append
presents an overview of the data table hierarchy to existing file.
within the RDFile.
3. In the Log Data section, click the data types to
include in the log.

4. If you want the import to pause when errors are
encountered, click Show alerts and warnings
during import.
5. If you want to view the log automatically when
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the import finishes, click Display log file after

import.
6. If you selected to merge the incoming data,
click the Merge tab and in the Log section,
select whether to log hits, misses or both.
Importing from a Specified

Location
You can start an import from an arbitrary location in
an SDFile or RDFile, such as a byte or line number.
To set the location from which to import: 3. Select the appropriate options.
1. Click the Advanced tab. To start from Click

The Start Position dialog box appears. the beginning of the • beginning.
SDFile or RDFile
a specified line • line and type the
number line number.
a specified byte • byte and type the

number byte number.
a specified record • record and type

the record number.
2. Select the position and click OK.

The Advanced tab appears.

Exporting Data Files Exporting an ASCII File
Delimited text files may be the most universal file
You can create a new SDFile, RDFile, or delimited
format used by non-chemical applications. In a
text file by exporting records from an existing
delimited text file, each line represents a record, and
database. When you export a file, all records in the all fields in the record are listed in order from left to
current hit list are saved. For each record, all fields right, separated by some character such as a tab or a
present on the form are written to the file. You can comma. Individual records are separated by carriage
prevent fields from being output by hiding their returns. ChemFinder allows you to include a header
columns in Table view. line at the start of the file that lists the names of all
of the fields.
To export a file:
When exporting a delimited text file, all records in
1. From the File menu, point to Export, and then the current hit list are saved. For each record, all
take the appropriate action: fields present on the form are written to the file.
You can import a delimited text file saved by
To export a file Then choose ChemFinder into many other applications, including
spreadsheets and external database systems.
with the .sdf extension SDFile.
To choose options for exporting an ASCII file:
with the .rdf extension RDFile.
1. From the Preferences dialog box, click the
with the .txt extension Delimited Text. General tab.
The General Preferences tab appears.
in the ChemFinder 5 format ChemFinder 5.
in the ChemFinder 7 format ChemFinder 7.

2. Type a name for the file you export, and click
Save.
The file is exported.
NOTE: In ChemFinder 7.0 you can save data in

SDFiles, RDFiles. Use Export Subform Data in the
Preferences dialog box.

Exporting Data Files
To export an ASCII Click

file with
Administrator
a delimited list of Include header.

field names as the first
line
tabs as the type of Tab delimited.

delimiter
commas as the type of Comma delimited.

delimiter
a different, specific Other, and type the

type of delimiter symbol you want to
use as a delimiter.
structures in the Export SMILES.

database as SMILES
strings
subform data included Export subform

data.
NOTE: Subform data

is saved as one string
of text, rather than as
multiple records.
3. Click OK.

Exporting Data Files
Chapter 8: Customizing ChemFinder
Overview Structure Display
To display hydrogen atoms on heteroatoms or on
ChemFinder allows you to customize the terminal carbons:
application in the following ways:
• Check the Show hydrogens on heteroatoms
• Customize display of your molecules, fonts,
or Show hydrogens on terminal carbons
pictures and forms.
check boxes, respectively.
• Design the toolbars to your specifications.
Not checking the boxes means these types are
• Perform automated tasks, such as interfacing
with Microsoft Excel, or by using displayed without implicit hydrogens.
ChemFinder’s automated scripting language,
CAL.
Setting Preferences
The Preferences dialog box allows you to customize
the display of molecules, pictures, and forms, and
set options for searching and exporting.
Show hydrogen Show hydrogen
1. Click the tab containing the preferences to set. atoms on heteroatoms atoms on heteroatoms
2. Select the preferences, and click OK. Show hydrogen Show hydrogen
atoms on terminal atoms on terminal
Display Preferences carbons carbons
To set the Display preferences:
To display reaction centers:
• From the File menu, choose Preferences.
• Select Show reaction centers.
The Display tab appears.
With reaction centers shown, any bond that
changes in the course of a reaction is colored.
Additionally, any atoms that participate in
reaction centers are circled if none of their
adjacent bonds participate in the reaction
center.
ChemFinder Chapter 8: Customizing ChemFinder • 115

Setting Preferences
Using Keyboard Shortcuts
When using a form, you can use keyboard shortcuts
to show or hide atom-to-atom maps, reaction
centers, atom numbers, and bond numbers.
Administrator
To use keyboard shortcuts:

• Select Enable keyboard shortcuts.
To toggle these properties use the following keys:
Show reaction Show reaction centers
• A: show/hide atom numbers
centers
• B: show/hide bond numbers
To display atom-to-atom maps: • M: show/hide atom-to-atom maps
• Select Show atom-atom maps. • R: show/hide reaction centers
With atom-to-atom maps shown, equivalent Scaling Structures
atoms in reactants and products are colored the
To scale each structure so that it is as large as
same.
possible within its structure box:
• Click Fit to box.
To display all structures with a constant bond length:
1. Select Uniform bond length.

2. Select the bond length percentage.
With “Uniform bond length” selected,
Show atom-to- Show atom-to-atom structures may be reduced in size if they are too
atom maps maps large to fit within the structure box, but they
will never be enlarged.
These two preferences affect only the display of
reactions. Not checking the boxes means these Framing Pictures
types are displayed as all other atoms and
To select whether the pictures in a form are
bonds.
surrounded by a border:
• Select Framed.
Grid Spacing
To set the grid spacing (in pixels) on a form:
• Type in a number, or press the up and down
arrows to change the current value by one unit.
Choosing a small grid spacing allows you to place
objects more precisely by snapping to a tighter
matrix.
116 • Chapter 8: Customizing ChemFinder CambridgeSoft

Setting Preferences
Color Preferences 5. Click OK.
To set the color preferences: Search Type Preferences

• In the Preferences dialog box, click the Color You can set preferences for the type of structure for
tab. which you want to search.
To set Search Type preferences:

The color tab allows you to specify the color of

various interface elements.
To set a color:
3. Click the button corresponding to the interface
element you want to change. 2. Click the Search Type tab.
The color dialog box appears. The Search Type tab appears.
4. Select the new color.

Setting Preferences
3. Take the appropriate action: Search Details Preferences
You can set preferences for the details of each
search.
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search for a substructure of Substructure. To set Search Details preferences:

the molecule
search for the whole Full Structure. The Preferences dialog box appears.
molecule
search for an exact match of Identity.

the molecule
search for compounds with Similar and set

characteristics similar to the the degree of
query similarity.
NOTE: The
higher the
value, the fewer
hits found.
search for compounds with Similar 2. Click the Search Details tab.
characteristics similar to the Substructure
The Search Details tab appears.
query and set the
degree of
similarity.
NOTE: The
higher the
value, the fewer
hits found.
limit the next search to the Search over

current hit list. current list.
When Search over current
list is deselected, queries
run over the entire database.
4. Click OK.

Setting Preferences

prohibit generic Generics hit only
structures from hitting generics.
allow uncharged atoms Hit any charge on
any other structures in a
in the query to match heteroatom.
query.
charged atoms in the
target.
require that the Match
NOTE: Charged atoms
stereochemistry of the stereochemistry
in the query must always
target structure match and click How to set
match charged atoms in
that of the query how the
the target, regardless of
structure. stereochemistry is
this setting.
matched.
allow uncharged carbon Hit any charge on The Stereochemical Search Preferences dialog
atoms in the query to carbon. box appears.
match charged carbon
atoms in the target.
NOTE: Charged atoms
in the query must always
match charged atoms in
the target, regardless of
this setting.
allow hits to contain Permit extraneous

molecular fragments in fragments in full
addition to that which structure searches.
was hit by the query.
allow fragments in the Query fragments

query to overlap (share can overlap in
4. Set the Tetrahedral stereo center hits:
one or more atoms) in target.
the target.
If you want a Then, in
tetrahedral
require that any reaction Reaction query stereocenter in the
center present in the must hit reaction query to
query overlap with center.
reaction centers in the
match the target Tetrahedral stereo
target. This preference
exactly. center hits, click
applies only to reaction
Same.
searching.

Setting Preferences
To set the general preferences:
If you want a Then, in
tetrahedral 1. From the File menu, click Preferences.
stereocenter in the
query to
Administrator
2. Click the General tab.

match same or opposite Tetrahedral stereo The General tab appears.
configuration at the center hits, click
center of the target. Either.
match any target. Tetrahedral stereo

center hits, click
Any.
5. Set the Double bond hits:
If you want the Then in

stereocenters of a
database in the
query to
match the target Double bond hits, Structure Registration Options

structure exactly. click Same.
To have ChemFinder present an alert when
attempting to enter a structure with an atom in a
match any Double bond hits, non-standard valence state:
configuration in the click Any.
target. • In the Registration section, click Check
valences.
6. Click OK. To have ChemFinder confirm when you are about to
modify data in the database:
General Preferences
• In the Registration section, select Ask to
The general preferences are as follows:
commit changes.
• ASCII file export (see “Exporting an ASCII
File” on page 113) ChemFinder Opening Options
• Alerts You can set ChemFinder to open with the
ChemFinder 7 Opening dialog box or to open the
• ChemFinder opening window
last form you were using.
• List of the last files used

Setting Preferences
To set the options for what ChemFinder displays
when it starts up:
1. On the General preferences tab, select one of

the following:
If you want to set Then click

ChemFinder to
start with the opening Show opening

dialog box dialog.
open the last form you Open last form on

used startup. To add an option to a toolbar that is already in the
ChemFinder window:
2. Click OK.
1. In the Customize dialog box, click the
Commands tab.
Setting the Recent File List Size
You can set the number of files you opened recently
that ChemFinder shows.
To set the list size for the most recent files opened:
1. From the General preferences tab, choose the

number of file names to display.
2. Click OK.
Customizing Toolbars
ChemFinder lets you format your toolbars. You can
Customize the toolbars by dragging buttons on or
off.
2. Locate the command and click+drag an option
To open the Customize dialog box: from the Commands window to a toolbar in the
ChemFinder window.
• From the View menu, point to Toolbars, and
then choose Customize. The option appears where you drop it on a
toolbar.
The Customize dialog box appears.
You can delete a button by dragging it off the
toolbar.

Customizing Toolbars
To return a toolbar to the default settings:

Toolbars tab.
Administrator
The Toolbars tab appears and shows all of the

toolbars that currently appear in the
ChemFinder window.
2. Click Reset All.
Using the Periodic Table

ChemFinder features a periodic table for data
display and formula entry. Selecting an element
displays physical and historical data.
2. Click the toolbar you want to return to default To display the Periodic Table window:
settings, and then click Reset. 1. From the View menu, choose Periodic Table.
The toolbar in the ChemFinder window
changes to the default settings.
To return all the toolbars to the default settings:

Toolbars tab.
The Toolbars tab appears and shows all of the
toolbars that currently appear in the
ChemFinder window.
2. Click on an element to display its name, mass,

and other properties in the top box, and to
display its symbol in the bottom edit box.

Using the Periodic Table
By clicking on different elements and numbers To edit the element’s physical data:
sequentially, you can create a molecular formula in 4. Click in the desired editable text box and enter
the bottom editable text box. You can then paste this the changes.
formula into the form for a formula query.
5. Click OK.
To copy a formula from the Periodic Table to the The color of the element is shown in the periodic
form: table for that element and in any structure data boxes
1. Click+drag the text to copy, and then press in which that element is present.
Ctrl+C. To change the color of an element:
2. Click OK in the Periodic Table window to close • Click Color.
it.
To reset an element’s physical data to the default:
3. In the form, click the formula box into which
you want to paste the text and press Ctrl+V. • In the Element Editor, click Revert to Default.
To display data about the selected element in the

NOTE: The data of the Periodic Table is stored in
Element Editor, do one of the following:
a tab-delimited ASCII file, so it can be easily edited
• Display the desired element and click the with a text editor or spreadsheet program. There are
display box at the top of the Periodic Table two files, called PTCUST.TXT (customer-modified
window. version) and PTDFLT.TXT (factory default version),
located in your ChemFinder system directory. Do
• Double-click the desired element button. not change PTDFLT.TXT.
ChemFinder
Automation Language
(CAL)
ChemFinder is equipped with its own scripting
language, the ChemFinder Automation Language
(CAL). CAL is used to operate the program from the
keyboard, or to create custom scripts for automating
simple operations such as switching between forms
or sending data to Microsoft Excel.
The Element Editor displays properties of the For more information, see The CambridgeSoft SDK
selected element. The top three items of the standard site on the World Wide Web at:
elements are not editable, but you can modify the http://sdk.cambridgesoft.com/
others to create a customized version of the table.
To perform a CAL command:
• From the Scripts menu, choose Command
Line.

ChemFinder Automation Language (CAL)
Writing a Script
To create a script:
Administrator
1. Open Notepad or another text editor.

2. Type CAL commands, and save the file with
The Enter CAL Command dialog box appears. You extension .cfs in the System subdirectory.
can type CAL commands and execute them one at a The name of the script appears on the Scripts
time. menu.
The Command drop-down list contains previously Alternatively:
entered commands.
1. Create a button on a form.
To rerun a previously entered command: 2. Label the button.
1. Select the command from the list. 3. Right-click and choose Edit Script.
2. Click Execute. The following dialog box appears.
For detailed information about the command
language, see “Appendix E: ChemFinder
Automation Language Commands” on page 149.
Getting CAL Help

To display information about the CAL scripting
language: 4. Click Yes to create a new file.
To execute a script:
• In the Enter CAL Command dialog box, click
Help. • Choose the script from the Scripts menu.
The CAL Scripting Help window appears
NOTE: To execute a script that does not appear on
containing commands, variables, and syntax
the menu, use the Command line and enter “Call
notes. <script filename>”.
Debugging a Script
You can step through a script line-by-line when
debugging it.
To view a script line-by-line:
1. From the Scripts menu, choose Command

Line.
The Enter CAL Command dialog box appears.

ChemFinder Automation Language (CAL)
• The directory containing the ChemFinder
application.
The corresponding name that ChemFinder looks for
is one with the first 8 characters of the button label,
with all spaces replaced by underscores, and the .cfs
extension.
2. Type step on and click Execute. this turns on
the step mode, where each step is displayed. For example, you have a script that displays a
molecule’s NMR spectrum named
3. Run a CAL script by doing one of the
Show spectrum.cfs. You can run this script by
following:
clicking a button you create instead of choosing it
from the Scripts menu. If the button label is “Show
If your script Then
Spectrum” ChemFinder looks for the script
“SHOW_SPE.CFS” and executes it to display the
appears in the Scripts choose the appropriate spectrum.
menu. script.
To run the script:
does not appear in the in the Enter Script • Click the button on the form.
Scripts menu. Command dialog box,
For more information, see “Adding a Button” on
type call and the name
of your script, and page 38.
then click Execute.
Communicating with
4. Press any key except Escape to execute the
command and go to the next command.
Other Applications
As each step is encountered, it is displayed in There are two general methods of communicating
the status line. with other Windows applications such as Microsoft
Excel: by using a script within ChemFinder, or by
5. Press Esc to stop debugging the script.
using a Visual Basic procedure within the other
6. In the Enter Script Command dialog box, type application. The following is an overview of each
step off to exit the debugging mode. method.
Executing a Script on a Using Scripts

Form A ChemFinder (CAL) script can communicate with
other Windows applications using either of two
After you write a script, you can place a button on a commands:
form to execute that script. When you click the
EXEC—to start an application and possibly pass
button, ChemFinder looks for a script with the
information on the command line.
corresponding name in one of three places:
DDE—to communicate using Dynamic Data
• The same directory that contains the form.
Exchange with a DDE-ready application.
• The ChemFinder System directory.

Executing a Script on a Form
Using EXEC is straightforward, but limited. You This procedure takes data one way, from
can start all Windows applications by this command. ChemFinder to Excel. Returning modified data from
Most can be passed a filename on the command line, Excel to ChemFinder can be done using other
such that the specified file is opened (or printed) on techniques described in this chapter.
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startup. A few applications can accept more detailed

instructions. Consult the application’s manual for Here is a script to start up Excel:
information about how it can be operated using the
*RUNEXCEL.CFS – script to start
command line.
Excel
If you have Visual Basic or similar programming
language, you can extend the power of EXEC. You *
can write an application using the advanced features EXEC “c:\msoffice\excel\excel.exe”
of Visual Basic, and then call the application from
within ChemFinder using the EXEC command. If the Excel program is on your search path, you can
eliminate the complete pathname and just give the
Using DDE is more complicated. You can operate executable name (“exec excel.exe”); if not, you may
most Microsoft Office components and many other
need to modify this script to indicate where
programs to varying extents with DDE. For
EXCEL.EXE is located on your system.
example, practically every command on the Excel
menu can be executed by DDE. The syntax is rather Here is a script to transfer the current hit list from
difficult, but can usually be worked out by ChemFinder to Excel:
experimenting and consulting online help. An
example is given below. *TOEXCEL.CFS – script to send data
DDE is the most direct way of using Excel to view *to Excel
data from ChemFinder. *
To use MS Excel to view ChemFinder data: WRITETEXT C:\DATA.TMP

1. Start MS Excel. You can start it manually using DDE Excel System
a CAL script or by starting the application in [OPEN(“C:\DATA.TMP”)]
Windows. DDE Excel
2. In ChemFinder, obtain the hit list you want to System
transmit to Excel. If you want to work with the [COLUMN.WIDTH(1,”C1:C4”,,3,1)]
entire database, from the Search menu, choose
Retrieve All. The first line writes out the current ChemFinder hit
list as a temporary delimited ASCII file. By default,
3. Execute a short CAL script (below) which
all fields that appear in boxes on the current form—
exports the hit list as comma-delimited text to a
except structure, but including formula and
temporary file, then instructs Excel with DDE
molecular weight—are written. The second line
to load that file into a spreadsheet.
instructs Excel to open the file. Excel can
4. Activate Excel to work with the data in the automatically recognize the file format as tab-
spreadsheet. delimited. The third line instructs Excel to auto-size
column widths 1–4 to fit their contents.

Communicating with Other Applications
Field objects, used to query the data in the
NOTE: This example requires that the text export database, and Molecule objects, for accessing
delimiter be set to TAB in the General tab of the details of molecular structures.
Preferences dialog, otherwise Excel may not read
the file correctly. For more information, see the CambridgeSoft SDK
web site:
You can include either or both of these scripts on the http://sdk.cambridgesoft.com/
Scripts menu, and you can activate them with
buttons on the form. To include a script on the Using Microsoft Access with
Scripts menu, give it a filename with extension
“.cfs”, and place it in the ChemFinder System
ChemFinder
directory, or in the directory containing the The methods described above for communicating
ChemFinder application. To activate a script from a between ChemFinder and Excel apply also to
button, label the button with a script filename or Access. You can start Access using the EXEC
string which can be converted into a filename. For command. You can send it DDE commands
example, if TOEXCEL.CFS exists in the contained in a CAL script, although Access provides
ChemFinder System directory, label a button fewer capabilities with DDE than does Excel. Or
“ToExcel” to start the script. For more information, you can write programs using Access Basic that rely
see “Adding a Button” on page 38. on ChemFinder’s OLE Automation methods. In
addition, you can use Access directly to operate on a
Using Visual Basic ChemFinder database.
The second method of communicating between A ChemFinder molecule database consists of three
ChemFinder and other applications such as Excel is components: the structure storage files (with file
using OLE Automation. ChemFinder is an OLE extensions .mst and .msi), the data storage files,
Automation server, meaning that it offers a which include a Microsoft Access database (file
collection of data management capabilities to extensions .mdb and .ldb), and the forms (with file
outside programs capable of communicating with extension .cfw) used to view the structures and the
OLE objects. While this collection is currently fairly data.
small, it is adequate for a variety of data retrieval
If you have Access on your system, double-clicking
and search tasks. This feature allows you to write a
an .mdb file in Explorer starts up Access and opens
custom Visual Basic procedure that directly
the specified database.
retrieves and manipulates data from ChemFinder.
When you open a ChemFinder database in Access,
The general procedure for accessing ChemFinder you will see the same tables as displayed in the
data from within a Visual Basic script is as follows. ChemFinder Database dialog box, including the
1. Create a ChemFinder Document object, main structure table (usually named “MolTable”),
typically passing a filename so that you open a but you will not see columns for structure, formula,
form complete with its database connection. or molecular weight. These fields cannot be
manipulated directly using Access.
2. Use methods of the Document object to move
through the database, search, and access data.
Document methods include some that access

The following are some of the operations you can
perform on a ChemFinder database using Access.
Most of these capabilities are not available through
the current version of ChemFinder:
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• Compress or repair the database

• Change column (field) or names or formats
• Change table names
• Add or delete columns or tables
• Import or export tables
• Load non-structural data from various file
types, including delimited ASCII, Excel, Word
• Move quantities of data from one column or
row to another
• Carry out complex queries on non-structural
data
• Permanently change the sort order of a table
For more information about these actions, please
consult the Microsoft Access User’s Guide.
Do not add or delete records to the MolTable within
Access, because the data component of the database
will become out of synchrony with the structure
component.

Chapter 9: Accessing the
Online Menu Overview
You can access different areas of the CambridgeSoft
web site from within ChemFinder with the Online
menu. To use the Online menu, you must have
internet access.
Finding Chemical
Suppliers on
ChemStore.com
Exchange) of the CambridgeSoft web site.
You can search ChemACX.Com for chemicals by
To access Lookup Suppliers on ChemStore.Com: supplier or by chemical name.
• From the Online menu, choose Find Suppliers
on ChemStore.com. Finding Information on
The ChemACX.Com page opens in your
browser.
ChemFinder.com
Find Information on ChemFinder.com opens
ChemFinder.com, where you can search the
ChemFinder database for chemical information.
To access ChemFinder.Com:
• From the Online menu, choose Find
ChemFinder Chapter 9: Accessing the CambridgeSoft Web Site • 129

Finding Chemical Suppliers on ChemStore.com
ChemFinder.com opens in your browser.
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2. Type the ACX registry number.

3. Click OK.
The Structure appears in your document.
ACX Numbers
To Find an ACX number for a structure:
1. In a ChemFinder document, select the structure
for which you want to find an ACX number.
Finding ACX Structures Number from Structure.
The ACX number appears in the Find ACX
and Numbers Number from Structure dialog box.
ChemFinder searches ACX and returns information
about related structures and numbers. You can place
the returned information in your document.
ACX Structures
To find an structure that corresponds to an ACX
number:

Structure from Number.
Browsing
The Find Structure from ACX number dialog ChemStore.com
box appears.
ChemStore.com.

Finding ACX Structures and Numbers
The ChemStore.Com page opens in your The CambridgeSoft web site in your browser.
browser.
Check the CambridgeSoft web site for new product

You can search ChemStore.Com for chemicals, lab information. You can also get to ChemStore.Com,
supplies, chemistry-related software, and other ChemNews.Com, and other pages through
items you want to buy. You can access CambridgeSoft.Com.
ChemACX.Com, LabEqwip.Com, and other pages
from ChemStore.Com. Accessing the Online
Browsing ChemFinder User’s
CambridgeSoft.com Guide
Browse CS ChemFinder Documentation opens the
Browse CambridgeSoft.com opens the Home page
Technical Support Manuals page where you can
access current and previous versions of the
To access the CambridgeSoft Home Page: ChemFinder User’s Guide.
CambridgeSoft.com.

Browsing CambridgeSoft.com
To access the CambridgeSoft Manuals page: The Technical Support page opens in your
browser.
1. From the Online menu, choose Browse
CS ChemFinder Documentation.
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2. Click version of the manual to view.

A PDF version of the ChemFinder User’s Guide
appears.
Accessing Use the Tech Support page to find answers to

CambridgeSoft Frequently Asked Questions (FAQs), the technical
support newsletter, documentation, downloads, and
Technical Support contact a Technical Support Representative.
Browse CS ChemFinder Technical Support opens

the Tech Support page of the CambridgeSoft web
Registering Online
site. Register Online opens the ChemClub page of the
CambridgeSoft web site, where you can register
To access CS ChemFinder Technical Support:
your copy of ChemOffice.
CS ChemFinder Technical Support.

Accessing CambridgeSoft Technical Support
To register online:
1. From the Online menu, choose Register

Online.
The CambridgeSoft home page opens in your
browser.
The ChemOffice SDK page contains

for the Application Programming Interfaces (APIs).
2. Click the Register tab.

3. Click Register Your Software.
4. Register ChemFinder.
Using the ChemOffice

SDK
The ChemOffice Software Developer’s Kit (SDK)
enables you to customize your applications.
To browse the ChemOffice SDK:
ChemOffice SDK.
The CS ChemOffice SDK page opens in your
browser.

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Appendix A: Structural Query Features
Overview Atoms
Atom types specified in the query must match atoms
To perform a substructure search in ChemFinder,
at corresponding positions in the target. Hydrogen is
you must first draw the query structure itself. Query
structures can be drawn in many different programs, an exception—see “Substituents” on page 136.
but we recommend using ChemDraw, and this
Appendix is focused on using ChemDraw to draw
Bonds
query structures. For more information about the All bonds explicitly drawn in the query must match
structure drawing and query capabilities of in the target. For certain caveats, see
ChemDraw, please consult the ChemDraw User’s “Stereochemistry” on page 137 and
Guide. “Normalization” on page 138. ChemFinder
recognizes the following standard bond types:
ChemFinder does its best to follow your instructions
even if those instructions are contradictory. For
example, you can create a query such as the Bond Type Description
following:
Single target must have single bond
This bond is marked so here
that it must not be in a ring
Chn
Dashed same as Single

That bond is already in a ring, so ChemFinder
returns no hits for this query. Hashed same as Single
General Properties Wedged Hashed specifies stereochemistry down

from the point end to the wide
ChemFinder allows the following general properties end
to be assigned to a query:
• Atom Wedged specifies stereochemistry up
• Bond from the point end to the wide
end
• Substituents
• Charges and radicals Wavy specifies stereochemistry
• Isotopes “either” at both ends
• Stereochemistry
Hollow Wedged same as Wedged
• Normalization
ChemFinder Appendix A: Structural Query Features • 135

General Properties
Hydrogen atoms in the query must match hydrogens
Bond Type Description in the target when the query hydrogen is at the end
of an explicit bond. The matched hydrogen in the
Dative same as Single target may be implicit in an unlabeled carbon atom.
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Double target must have double bond;

H O
stereo dictated by geometry
H N
Double Either target must have double bond;
any stereochemistry ok finds any of: does NOT find any of:
OH
Double Bold same as Double
Cl
O
Triple target must have triple bond NH2

HN O
here
O
Substituents Br
NH2
OH
In ChemFinder, a substituent is defined as a non- H OH
H OH
hydrogen atom connected by a bond of any order.

For example, a carbonyl oxygen is a substituent of H N
H NH2
the carbonyl carbon. Br
All unfilled valences in the query may be filled by

hydrogen atoms or by non-hydrogen substituents. Charges and Radicals
The normal valence of an atom is determined from Charges or radicals specified on atoms in the query
data in the Periodic Table window. For example, must match those in the target. Uncharged atoms in
carbon has a valence of 4, while sulfur has valences the query may or may not match charged atoms in
of 2, 4, and 6. Any explicit charges, radicals, or the target, depending on the state of the appropriate
query properties modify the normal valence. For check box in the Search tab of the Preferences
example, a carbocation has a valence of 3. dialog.
Hydrogen atoms in the query may match non-
hydrogen substituents in the target if the hydrogen in
the query is implicit on an unlabeled carbon atom or
heteroatom.
136 • Appendix A: Structural Query Features CambridgeSoft

General Properties
The valence of a charged atom is taken to be the
With a Substructure Search, the query:
valence of the isoelectronic neutral atom.
With a substructure search, the query:
N+ finds any of: does NOT find any of:
13
HO CH3
13 T
finds any of: does NOT find any of: C
O 13
CH3
O
HO
2
NH3+ H
13
D
NH2 O CH3
D D
H2 + D
N 13
O CH3
N-
Stereochemistry
N+
Stereochemistry specified on the query must match
HO-
N the target if the relevant Match Stereo item is
selected in the Search tab of the Preferences.
Stereochemistry is specified at a tetrahedral site by
using stereo bonds (up, down, either).
Isotopes Stereochemistry about a double bond is specified by
the geometry of the drawing. ChemFinder cannot
Isotopic labels specified in the query must match the currently interpret other stereochemistry types
target. Unlabeled atoms in the query match (allenic, square planar, octahedral, etc.) and ignores
unlabeled or isotopically labeled atoms in the target. them during a search.
Additionally, D is treated interchangeably with 2H,
and T is treated the same as 3H. When evaluating a possible match, the following
rules are applied:
• Unspecified stereochemistry (a plain bond)
may match any stereochemistry (either a
wedged, hashed, or a plain bond).
• Specific bond types need not match as long as
the overall stereochemistry at a given atom does
match.
• Implicit hydrogens are taken into consideration
in both the query and the target if doing so helps
to determine the chirality of a stereocenter.

General Properties
Normalization
With a full structure search and the Match Closed rings of alternating single and double bonds
Tetrahedral stereo option selected, the query:
match their alternative resonance forms if aromatic
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HO
by the Hückel 4n+2 rule.
O
With a full structure search and the Match Double

N OH
H Bond stereo option selected, the query:
finds any of: does NOT find any of:
HO HO
O O
OH
N OH N OH
H H
H H
N OH N OH
O O
HO HO
H
O H
O
HO HO
O O
N H OH N OH
H H
H
O H
O
O O
H H
Atom Properties
ChemFinder allows special atom properties to be
assigned to an atom in a query. These properties are
usually only meaningful during a search. They
generally serve to broaden or narrow the scope of
the search.
Special Atom Types

ChemFinder recognizes five special atom types that
can match any one of a predefined set of elements:
Amatches any non-hydrogen atom
Qmatches any heteroatom (non-hydrogen, non-
carbon)

Atom Properties
Rmatches any atom, including hydrogen Substituents: Exactly
Xmatches any halogen (F, Cl, Br, I, At) This property specifies a precise value for the
Mmatches any metal atom, shaded gray in the number of substituents on an atom, including those
periodic table below: explicitly drawn. This property is only meaningful
in a substructure search.
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar X3
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr This atom is marked

with the atom property
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Substituents:Exactly 3
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac finds any of: does NOT find any of:

Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr Cl
Atom Lists
As with the predefined special atom types, an atom
list is a list of atoms, one of which must match the
target atom.
HO O
For example:
[Cl,Ag,N] atom must be Cl or Ag or N O O
Atom lists may contain only elements. Special atom

types, nicknames (Ph), and structural fragments
(NH2, OCH2CH3) may not be included in an atom
list. ChemFinder recognizes a maximum of five
atoms in an atom list.
Atom Not-Lists
The opposite of an atom list is a list of atoms, none
of which must match the target atom. For example:
[NOT O,S,Se] atom must not be O or S or Se (but
may be any of the 100 other elements)
Atom not-lists have the same restrictions as atom
lists.

Atom Properties
Substituents: Up To Substituents: Free Sites
This property specifies a maximum value for the The Substituents: Free Sites property specifies the
number of substituents on an atom, including those maximum number of additional substituents that
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explicitly drawn. This property is only meaningful may be present on an atom. This property is only
in a substructure search. meaningful in a substructure search.

NOTE: Specifying Free Sites: 0 is a quick way to
U2
indicate that you want no further substitution at a
site. Target structures will match the query structure
This atom is marked
with the atom property as drawn, with no additional ligands.
Substituents:Up to 2
finds any of: does NOT find any of: With a substructure search, the query:
*2
This atom is marked

Substituents:Free Sites 2

H
Cl
HO
O
CH3
HO O
O O
Implicit Hydrogens
This atom property may have either of two values:
Allowed (default) or Not Allowed. If implicit
hydrogens are Not Allowed, the atom must be fully
substituted in the target.

Atom Properties
This property is only meaningful in a substructure
search.
Bond Properties
ChemFinder allows special properties to be assigned
NOTE: This atom property does not affect the to bonds in a query. These properties usually will
display of implicit hydrogens, only their presence in only be meaningful during a search. They generally
a search. For more information about displaying serve to broaden or narrow the scope of the query.
implicit hydrogens, see “Setting Preferences” on
page 115. Special Bond Types
The table below describes the special bond types
Unsaturation that ChemFinder allows.
Sometimes it is useful to specify that an atom must
or must not be attached to unsaturated (aromatic, Bond Type Description
double, or triple) bonds. ChemFinder allows
searches for atoms whose unsaturation Must Be Aromatic target bond must be aromatic as
Absent (all bonds to the atom are single). It also defined by the Hückel 4n+2 rule
allows searches for atoms with at least one multiple
(double, triple, or aromatic) bond. The default value, Any target can have any bond type here
Undefined, finds targets without regard to the
hybridization of the atom. S/D target must have a single bond or a
double bond here
This property is only meaningful in a substructure
search.
Tautomeric same as S/D
With a substructure search, the query: D/A target must have a double bond or
an aromatic bond here
O
This atom is marked
Unsaturation: Must Be Present
S
OH S/A target must have a single bond or
an aromatic bond here
O O Topology
OH OH If Ring or Chain is chosen, the target bond must or
O HO must not be in a ring, respectively.
HO O
OH
OH
O
OH

Bond Properties
Reaction Center
The reaction center refers to those bonds that are
directly affected by a reaction. This property allows Not Modified target must have a bond here,
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you to specify just how a given bond is affected. and regardless of whether it is
part of the reaction center or
Property Description not, its order must not change
over the course of the
reaction
Unspecified target must have a bond here,
but the bond can participate
This property is only meaningful when searching a
in the reaction in any fashion,
or not at all reaction database.
Center target must have a bond here

that directly participates in
the reaction in some way
Make/Break target must have a bond here

that is either made (if in a
product) or broken (if in a
reactant)
Change target must have a bond here

whose bond order changes
over the course of the
reaction, but is not made or
broken
Make&Change target must have a bond here

that is either made (if in a
product) or broken (if in a
reactant) or whose bond
order changes over the course
of the reaction
Not Center target must have a bond here,

and that bond must not
participate in the reaction

Bond Properties
Appendix B: Formula Input Rules
Overview Because of this rule, if you properly capitalize all
symbols, no ambiguities will arise.
When you type a formula in ChemFinder, you are If symbols are not properly capitalized (such as all
not required to enter symbols in any particular case. lower-case), then, with the exception noted below,
This can give rise to ambiguities. This appendix the shortest symbol which matches is preferred.
describes how ChemFinder interprets formulas and Thus “co” is taken as carbon-oxygen instead of
resolves these ambiguities. cobalt.
Consider an example. In entering a formula query, The exception is: if two characters represent a valid
you type: two-letter symbol and also a valid one-letter symbol
followed by an invalid one, then the two-letter
cooh symbol is favored. Thus “cl” is not taken as carbon
Most chemists recognize this as a carboxyl group: followed by the (invalid symbol) L, but instead is
carbon, two oxygens, hydrogen. However, it might taken as chlorine.
be interpreted as cobalt (Co), oxygen, hydrogen.
Similarly, “CLI” might be carbon-lithium or it might Examples
be chlorine-iodine. “PHE” might be phosphorus-
There is an easy way to experiment with formula
helium or, since ChemFinder allows 3-character
amino-acid symbols as special atom types, it might interpretation: use the Periodic Table. Type a
be phenylalanine (Phe). formula into the text box at the bottom, then click
anywhere outside that box. ChemFinder interprets
One way to avoid ambiguity is to separate letters the formula and redisplays it with correct
with spaces. For example, the string “c o” cannot
capitalization.
possibly be interpreted as cobalt. Another way to
avoid ambiguity is to enter formulas using the ChemFinder interprets some ambiguous formulas as
Periodic Table instead of typing them. ChemFinder follows:
allows free-format input, and attempts to make the
most reasonable interpretations of them by using the Formula Chemfinder Interpretation
rules described below.
cooh COOH
Rules Cooh CoOH
If a symbol is properly capitalized (first letter upper
case, followed by zero, one, or two lower-case cnosi CNOSI
letters), then the longest valid symbol which
cNoSi CNoSi
matches is preferred. Thus “Phe” matches
phenylalanine rather than phosphorus; “Co” bru BrU
matches cobalt.
b ru BRu
ChemFinder Appendix B: Formula Input Rules • 143

Rules
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144 • Appendix B: Formula Input Rules CambridgeSoft

Examples
Appendix C: Similarity Rules
Overview Present, they are often stored as bits, and another
name for a compound’s set of descriptors is its
Often you might not be looking for a specific bitscreen.
compound, but any compound that is “close
Consider the query and target compounds shown
enough” will do. ChemFinder uses the Tanimoto
graphically below. Both have similar numbers of
equation to determine if compounds are similar. You
descriptors present - the query has 23, while the
can specify “how similar” in the Searching tab of the
target has 24. But are they “close enough”?
Preferences dialog.
Exact searching relies on the notion of an atom-and- Bitscreen Desc. # Name
bond table: a specific set of atoms joined to each
other in a certain order by a given set of bonds. If Query 23 Q
some atoms or bonds are missing, added, or
different, the query structure and the target structure Target 24 T
do not match.
Most similarity searching, on the other hand, relies Q and T 17 Q ∩ T
instead on the notion of molecular descriptors. Each
compound can be represented by a collection of Q or T 30 Q ∪ T
qualitative terms that describe general aspects of the
structure.
For example, benzoic acid might be described as:
Complete Structure
• organic acid Similarity
• contains 6-membered ring One of the hallmarks of a good similarity algorithm
• contains delocalized ring is whether it is commutative. That is, two
compounds should have the same similarity value
• contains C-double-bond-O no matter which you compare to which. The full
As you can see, the descriptors can be very broad, structure Tanimoto similarity test is commutative. It
compares the number of descriptors they have in
and they can overlap. The set of descriptors used by
common (in the intersection of the query and the
ChemFinder is very large. target) to the number of descriptors they have in
When you draw a compound, ChemFinder total (in the union of the query or the target). The
compares it against all of the descriptors it knows ratio of these two values is known as a Tanimoto
coefficient, and is always a value between 0% and
about. Some descriptors will be present in your
100%.
compound and some will not. Since each descriptor
for a given compound is either Present or Not Q∩T
Tanimoto Coefficient
Q∪T
ChemFinder Appendix C: Similarity Rules • 145

Complete Structure Similarity
For the two compounds above, the Tanimoto
coefficient is 17/30, or about 57%. This is not very
similar. Although ChemFinder will allow you to
specify any Tanimoto value down to 0%, for most
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cases you will likely be looking for compounds that

have Tanimoto coefficients of 90% or higher.
Substructure Similarity
Unlike full structure similarity, substructure
similarity is not commutative: you are comparing a
portion of one structure against the entire other
structure, and so it does matter which you compare
to which. In considering substructure similarity,
ChemFinder finds what percentage of descriptors in
the query are also present in the target.
This value will always be at least as large as the
complete-structure Tanimoto coefficient for the
same two compounds, and usually it will be larger.
The two compounds above are 17/23, or about 74%
similar by substructure similarity. For a given
coefficient value, a substructure similarity search
will always return all of the hits in a full structure
similarity search, and will often return additional
ones as well.
146 • Appendix C: Similarity Rules CambridgeSoft

Substructure Similarity
Appendix D: Technical Support
Technical Support • Please record anything that you have tried to
correct the problem.
CambridgeSoft Corporation (CS) provides technical
methods:
support to all registered users of this software
through the World Wide Web (WWW), and through E-mail:
our Technical Support department. Http://www.cambridgesoft.com/support/mail
answers to frequently asked questions (FAQs), in
Mail:
addition to some general information about our
CambridgeSoft Corporation
software. You can access our Technical Support
ATTN: Technical Support
page using the following address:
100 CambridgePark Drive
WWW, please complete the following tasks before
Serial Numbers
contacting the Technical Support Department. When contacting Technical Support, you must
1. Check the ReadMe file for known limitations or always provide your serial number. This serial
conflicts. number was on the outside of the original product
box and is the number that you entered when you
2. Check the system requirements for the software
installed ChemFinder for the first time. If you have
at the beginning of this User’s Guide.
thrown away your box and lost your installation
3. Read the Troubleshooting section of this instructions, you can find the serial number as
appendix and follow the possible resolution follows:
• With ChemFinder launched, choose About CS
4. If all your attempts to resolve a problem fail, fill
ChemFinder from the Help menu. The serial
out a CS Software Problem Report Form at:
number will appear at the middle left of the
www.cambridgesoft.com/support/mail About box.
• Try to reproduce the problem before contacting
us. If you can reproduce the problem, please
record the exact steps that you took to do so.
• Record the exact wording of any error messages
that appear.
ChemFinder Appendix D: Technical Support • 147

Serial Numbers
Troubleshooting Setup) and retest the problems. If using a
different driver helps, your original driver may
This section describes steps you can take that affect need to be updated. Contact the maker of the
the overall performance of ChemFinder, as well as driver and obtain the most up-to-date driver. If
Administrator
steps to follow if your computer crashes when using you still have trouble, contact us with the
a CS software product. relevant details about the original driver and the
resulting problem.
Performance Printer Driver-related problems: Try using a
Below are some ways you can optimize the different printer driver. If using a different
performance of ChemFinder: driver helps, your original driver may need to
be updated-contact the maker of the driver and
1. Install more physical RAM. The more you
have, the less ChemFinder will have to access
have trouble, contact us with the relevant details
your hard disk to use Virtual Memory. about the original driver and the resulting
2. Increase the Virtual Memory (VM). Virtual problem.
memory extends RAM by allowing space on 5. Try reinstalling the software. Before you
and the hard disk is slower than swapping with savers and virus protection. Use the
physical RAM. You can change VM for
Add/Remove Control Panel.
Windows 95/98/NT 4.0 on the System control
panel, Performance tab. 6. If the problem still occurs, fax, e-mail, or use the
WWW at:
System Crashes http://www.cambridgesoft.com/support/mail
to submit the details of the problem to Technical
ChemFinder should never crash, but below are the Support.
steps you should go through to try to resolve issues
that cause computer crashes while using a CS
software product.
3. Restart Windows, then try to reproduce the
problem. If the problem does reoccur, keep
reading.
4. The most common conflicts for Windows users
concern Video Drivers, Printer Drivers, screen
savers, and virus protection. If you do end up
needing to contact us, be sure to determine what
type and version of drivers you are using.
Video Driver-related problems: If you are
ChemFinder, try switching to the VGA video
driver in the display Control Panel (or System
148 • Appendix D: Technical Support CambridgeSoft

Troubleshooting
Appendix E: ChemFinder Automation
Language Commands
Overview The CAL Scripting Help window appears:
ChemFinder Automation Language (CAL) is a set

of commands that control many of ChemFinder’s
operations.
You invoke CAL commands in either of two ways:
• Interactively—You type commands and
execute them one at a time on a command line.
• Scripts—You use ASCII files containing a
series of CAL commands to be executed
automatically in sequence.
Arguments to commands consist of numbers and Menu Commands
text strings. You can enter a text string without Menu commands consist of a two-word command
punctuation unless the argument is not the last one from the main menu and in some cases an optional
on the command line and contains multiple words or argument.
spaces. In this case, you must enclose the argument
in quotation marks. Following are examples of commands:
file new
CAL Help edit paste
Information about the CAL command and variables
search find
is available in the CAL Scripting Help window. To
access CAL Help: record next
• In the Enter Cal Command dialog box, click You do not need to spell out menu commands. You
Help. can enter just enough letters to uniquely identify the
menu option. For example, to execute the Record
Next command, type:
rec n
ChemFinder Appendix E: ChemFinder Automation Language Commands • 149

CAL Help
Some menu commands open a dialog box and wait
for user feedback. To avoid this, a limited number of Box Type String
menu commands can take explicit arguments:
Text static text
FILE OPEN [filename]
Administrator
FILE SAVE [filename] Picture pathname of a Windows

RECORD GO TO RECORD [recno] metafile
Box Creation Button pathname of a script file, or

name as it appears on Scripts
Commands menu
DBOX coords [fieldname]

Subform <nothing>
FRAME coords [text]
TEXT coords [text] Arrowbox <nothing>
PICT coords [filename] Framedbox name of database field to be

BUTTON coords [scriptname] displayed in the box, and static
label for upper left
SUBFM coords
If the text string is omitted, you can supply it later
ARROWBOX coords
using SETFIELD or SETTEXT. For a button, you
FRAMEDBOX coords [fieldname] [text] must use SETTEXT if you want its visible label to
be different from the name of its script.
To create a new box on the form:
1. Specify the box type with the appropriate Box coordinates are specified in this order: left, top,
keyword. right, bottom. Units are in pixels; the origin is at the
upper left, with coordinates increasing from left to
2. Type four integers giving the rectangular
right and top to bottom, so that coordinates will
coordinates of the box after the keyword.
range from left = 0 to right = 640 or 1024 or
3. If desired, type a text string giving further whatever fits your screen, and from top = 0 to
information appropriate to the box type, as bottom = 480 or 768 or similar.
shown below:
When a new box is created, it adopts the current
font. To specify a particular font for a box, use the
Box Type String FONT command prior to creating the box.
Data box name of database field to be

displayed in the box
Frame static label for upper left
150 • Appendix E: ChemFinder Automation Language Commands CambridgeSoft

Box Creation Commands
When specifying a script name, give one of the SETTEXT box text
following:
ACTIVATE subform
• The complete pathname of the script file.
DEACTIVATE
• A simple name without extension, if the script
SCALE
is stored in the standard scripts subdirectory
with the standard file extension. If the script SCALE TO FIT
name appears on the Scripts menu, you can use
To work with a box or subform on the form, you
the name from the menu.
specify a keyword followed by a box identifier. A
The table below shows examples of Box Creation box is identified in one of two ways:
Commands:
• By point—Give the coordinates of a point
anywhere within the box. When coordinates fall
Command Action in more than one box, the most recently created
box is used.
FRAME 10 10 300 60 create frame with label
• By text—Give a string that matches the text
Molecular Formula at upper left
associated with the box (fieldname, static text,
filename, or scriptname). The identifier string
DBOX 20 20 290 50 create data box for does not need to match the entire box text, but
formula formula in above frame must match at least the first part of it.
FORMEDIT controls the behavior of the SELECT
TEXT 100 100 300 create a static text command. With FORMEDIT ON, SELECT affects
150 "A Label” string boxes. With FORMEDIT OFF, SELECT affects the
contents of those boxes.
PICT 500 300 600 400 put specified picture at
C:\LOGO.WMF lower right SELECT and UNSELECT choose boxes to be
modified by editing operations. DELBOX is a
shortcut for FORMEDIT ON, followed by
BUTTON 500 10 550 create button at upper
SELECT, followed by Edit Clear. SETFIELD
40 DEMO right to run script
connects a database field to an existing box; for a
DEMO.CFS
button, it attaches a script name (see above
regarding script names). SETTEXT attaches a text
Box Manipulation string to a box or replaces the one currently attached;
see box creation commands (above) for a list of what
Commands the text strings mean for various box types.
FORMEDIT ON|OFF ACTIVATE and DEACTIVATE are the same as

SELECT and UNSELECT, but work on subforms.
SELECT box Following an ACTIVATE command, all subsequent
UNSELECT box commands apply to the active subform and any
boxes it contains. The DEACTIVATE command is
DELBOX box required to once again refer to the main form and its
SETFIELD box fieldname contents.

Box Manipulation Commands
SCALE scales all items in the current form by the CALL executes a specified CAL script. If the call is
percentage factor you specify. Use this to fit your made from within another script, when the called
forms to different size screens. See script finishes executing it returns control to the
SCALE_TO_FIT below. caller. CALL must be followed by a scriptname, as
Administrator
described above.
SCALE_TO_FIT scales all elements in the form
such that the string you specify will fit in the form at DOS executes a DOS command line. Follow the
the currently selected font size. See FONT below. DOS keyword with any string you might type at a
DOS command prompt. If you do not type any
The table below shows examples of Box
arguments after the DOS command, you get an
Manipulation Commands:
interactive command prompt window. You can use
this feature to manipulate files, execute programs or
Command Action batch files, get directory listings, format disks, etc.
During execution of the command, a command
SELECT 11 11 select formula frame created prompt window appears on the screen; when
above finished, the window goes away and control returns
to the calling script.
SELECT formu select formula data box created
EXEC starts a Windows program and optionally
above
passes it command-line arguments. Follow the
EXEC keyword with any string you might use in the
SETFIELD 21 21 change field for formula data
Program Manager’s File Run command. This
molweight box to molweight
command starts a program, but does not return from
it. To return to ChemFinder, you need to use Task
Program Execution Manager or click in the ChemFinder frame window.
DDE sends a Dynamic Data Exchange message to a
Commands specified application. Follow the DDE keyword
CALL scriptname with three arguments:
DOS doscommand • The service name—usually the name of the

recipient application.
EXEC wincommand
• The topic name—a string recognized by the
DDE ddecommand recipient, identifying the nature of the message.
LAUNCH filename It is typically SYSTEM.
Program execution commands call up external • The command—an instruction to the service
processes and pass data to them. All require an indicating what you want it to do.
argument, which may need multiple components. Details of these components depend on the service
you’re addressing.

Program Execution Commands
The table below shows examples of Program TIMEDMSG displays a message box similar to the
Execution Commands: MSG command, but the message disappears
automatically after a specified number of seconds.
Command Action For example: TIMEDMSG 10 “This message will
disappear automatically after 10 seconds.”
CALL execute script file located in FONT changes the current font. Any boxes created
myscript scripts directory subsequently adopt this font. Follow the keyword
with a name from your Windows font list, followed
DOS erase execute DOS command to optionally by (a) font size in points (default is 8); (b)
junkfile.dat delete a file style from the list below (default is 0, or plain text);
(c) color, as three values for red, green, blue, each
EXEC notepad execute Windows program ranging from 0 to 255 (default is 0,0,0, or black).
myfile.txt
Font styles are sums of bold (1), italic (2), and
underline (4). Thus a style value of 1 means bold, 3
DDE CHEM3D send DDE message to means bold+italic, 6 means italic+underline, and so
CFWIN "open qualified service
on.
benz.mol"
SEEPTAB briefly displays the periodic table
window, then closes it. The window will be
General Commands displayed for the amount of time specified (1
decisecond = 0.1 second). If the duration is omitted,
MSG message
it will be displayed for four seconds.
TIMEDMSG [n] <msg>W
QUITECLOSE closes the active form. This
FONT fontname [size [style r g b]] command is similar to FILE CLOSE, but
automatically discards any changes instead of
SEEPTAB [decisecs]
prompting the user what to do.
QUIETCLOSE
HIDETABLE closes the Table View window for the
HIDETABLE current form. If a subform is active, it returns the
SET subform to form view.
CLEAN SET allows you to modify ChemFinder’s basic

settings, including most of those found in the
HELP Preferences dialog and several that cannot be
GET [v] section number, itemnumber accessed in any other way. See the online help for a
complete listing of parameters that can be SET.
SOUND filename.wav
CLEAN will attempt to standardize the bond lengths
SYSMETRIC [v] index and angles of the current molecule. It is the same as
MSG displays a message box with the specified text, opening the molecule in ChemDraw, and selecting
and waits for the user to click OK. the Clean Up Structure command.

General Commands
HELP displays a list of all valid CAL commands. you are positioned to a valid entry in the database.
The valid parameter types are listed for each READMOL reads a specified structure file and
command, as is a brief description. replaces the current molecule in the form.
WRITEMOL saves the current molecule to a
GET retrieves a value from the ChemFinder.ini file.
Administrator
specified structure file; if the file doesn’t exist, it is

Follow the keyword with a variable name and the
created, otherwise it is overwritten. For both
section and item number of the value you want to
READMOL and WRITEMOL, the format of the file
retrieve.
is determined by its extension; for example,
SOUND plays a .wav file you specify. benzene.cdx is a ChemDraw file.
SYSMETRIC retrieves the specified system metric WRITETEXT exports the current list as delimited
into a variable. text with whatever delimiter is specified in the
Preferences dialog.
The table below shows examples of General
Commands: The table below shows examples of File
Commands:
Command Action
Command Action
MSG “Click OK to display message, wait for
continue” click READMOL read specified file to become
benz.mol current molecule
FONT Times 12 1 255 change font to red 12-
00 point Times bold WRITEMOL write current molecule to
saved.mol specified file
GET V1,4,5 place the value of item
number 5 in section 4 into WRITETEXT export current list to a text file
the variable V1 hits.txt
SOUND beep.wav play the sound in the files

beep.wav Database Commands
OPENDB [R / R / RE] dbname
File Commands CRETABLE tablename
READMOL filename DELTABLE tablename
WRITEMOL filename SELTABLE tablename
WRITETEXT filename CREFIELD fieldname
READMOL and WRITEMOL operate on the DELFIELD fieldname
current molecule. These commands will work only
SORT [D] fieldname
if there is at least one structure-related box
(structure, formula, or molweight) on the form, and

File Commands
OPENDB opens a standard molecule database. PASSWORD [v] [default]
Specify a pathname to the .mdb file, or a name from
the ODBC Data sources list. You can specify the GETDATA [v] box
mode of database opening: PUTDATA box text
• R—read-only APPEND ON|OFF
• E—exclusive
APPENDVAL [v] [text]
• RE—read-only and exclusive
INCREMENT [v]
CRETABLE creates tables in the current database.
DECREMENT [v]
DELTABLE deletes tables in the current database.
LET v v op v
SELTABLE selects a table form the current database
and makes it the current working table for CAL has nine variables called V1, V2, ..., V9. These
subsequent field actions. are temporary storage locations you can use to move
CREFIELD creates fields in the current table in the information between form boxes and other data
current database. You can specify the field type and sources.
width in the CREFIELD command. The default text
field is 50 characters wide. Variable names can be substituted in any CAL
command. Any item shown in italics in a command
DELFIELD deletes fields in the current table in the description may be replaced by the name of a
current database. variable, prefixed with a dollar sign.
SORT sorts the database contents on the specified For example:
field. The default sorts the database in ascending
order. You can specify descending order with D. MSG message may be either of:
The table below shows examples of Database MSG "An explicit message"
Commands: message explicitly coded into the script
MSG $V2
Command Action message taken from variable 2 at run time
CRETABLE MyTable creates a new table You may concatenate variables and variables and
literals together in CAL commands. You must add
both a leading and trailing dollar sign to the variable
DELTABLE MyTable deletes a new table
name.
For example:
Variable Commands MSG$V2$$V1$
SETVAL [v] text
Displays a message box with the value of V2
READVAL [v] filename immediately followed by the value of V1.
WRITEVAL [v] filename Most commands for manipulating variables take an
optional variable number as the first argument. If the
INPUT [v] [prompt]
number is omitted, it is assumed to be 1.

Variable Commands
SETVAL puts the specified text into a variable. The table below shows examples of Variable
READVAL reads the contents of a text file into a Commands:
variable. WRITEVAL copies the contents of a
variable to a file.
Command Action
Administrator
INPUT displays a text input dialog, accepts data

from the user and stores it in a variable. An optional
prompt string is displayed in the box when it SETVAL "some store text in V1
appears. text"
PASSWORD is the same as INPUT, but displays all

SETVAL V2 store text in V2
characters as asterisks.
"other text"
GETDATA retrieves the contents of a form box (as
long as it is not a structure) into a variable; see above
READVAL V9 read text from file into V9
for how to identify a box. PUTDATA copies
tmpdata.txt
specified text into a form box. Form names are case-
sensitive. Be sure to use the same case as the form
box name into which you want to store data. APPEND ON turn on append mode
APPEND determines whether data in a storage
location is kept if other data is being moved there. WRITEVAL append contents of V1 to
APPEND ON causes any subsequent data output.txt file
movements to append new data to old; APPEND
OFF causes old data to be overwritten. This applies SETVAL V2 append text to contents of
to all variable commands except PUTDATA. The "append me" V2
default at program startup is APPEND OFF.
APPENDVAL is a shortcut designed to make it APPEND OFF turn off append mode
easier to build string values. It is the same as setting
APPEND ON, doing a SETVAL, and then restoring
APPEND to its original state. INPUT V2 "enter prompt and get user input
new data" to V2
INCREMENT adds 1 to the value of a variable. Use
INCREMENT in loops.
GETDATA V3 copy data from molname
DECREMENT subtracts 1 from the value of a molname box to V3
variable. Use DECREMENT in loops.
LET allows you to perform mathematical operations PUTDATA molname store given string in
on variables that contain integer or real-number “benzene” molname box
values. Only one operator per line is supported. It
recognizes the following operators: LET V3$V1+ $V4 sets V3 equal to the value
• + for addition stored in V1 plus the value
• - for subtraction stored in V4
• * for multiplication
• / for division

Variable Commands
Environment Variables Command Action
$INDEX
SETVAL V1 V1 now equals total
$RECNO
$NUM_RECS number of records in the
$NUM_RECS current list
$DTBA_NAME_LONG
SETVAL V1 V1 now equals, for
$DTBA_NAME_SHORT $DTBA_NAME_ example
LONG “c:\chemfinder\mydb.mdb
$FORM_NAME_LONG
”
$FORM_NAME_SHORT
$CFW_DIR SETVAL V1 V1 now equals, for
$FORM_NAME_ example “mydb”
$FORM_DIR SHORT
$SYSTEM_DIR
SETVAL V1 V1 now equals, for
$SYSTEM_DIR example,
NOTE: To view a complete list of variables, click
“c:\chemfndr\system”
Help on the Enter Cal Command dialog box.
ChemFinder provides several variables to allow you Script-Only Commands

to retrieve information about the current
ChemFinder environment. They cannot be set *text
directly, but are modified as a consequence of other :label
commands.
label:
For example, the menu command:
GOTO label
Record Next
IF v1 op v2 stmt
increments the current RECNO by 1.
LOOP [count]
The table below shows examples of Environment
ENDLOOP
Variables:
PAUSE [dseconds]
Command Action EXIT
INTERACTIVE ON / OFF
SETVAL 1 V1 now equals the number
$RECNO of the current record STEP ON / OFF
Script-only commands are useful only in script files,
not interactive CAL.

Environment Variables
An asterisk (*) is used to mark a line as a comment The table below shows examples of Script-Only
and not a command that should be executed. Commands:
Labels and GOTO give a mechanism for jumping
backwards in a script. A label may be any text string Command Action
Administrator
starting or ending with a colon; it must appear prior

to any GOTO that references it. start: a label
IF is a standard conditional statement. It compares

IF $V1 = "" provide an error message if the
two values according to an operator, and then
MSG Empty variable V1 is empty
executes its final statement if the result is true. Valid
value!
operators are:
= <> < > PAUSE 100 pause 10 seconds
LOOP begins a section of code that will execute GOTO start go to specified label
repeatedly, until ENDLOOP is reached. By default,
the number of times the code executes is equal to the LOOP 10 begin loop to repeat ten times
number of records in the current list, but you can
provide a specific count in the LOOP statement.
PAUSE pause the default time: 2
PAUSE temporarily stops the script from executing seconds
for a specified number of tenths of a second. If no
number is given, the duration of the pause is 2 ENDLOOP return to LOOP statement until
seconds. done
EXIT ends the script immediately.
INTERACTIVE turns interactive mode on or off. NOTE: Script commands are subject to change.
See the Readme for up-to-date information.
STEP toggles single-step (debugging) mode on and
off.

Script-Only Commands
Index
Symbols Additional help 1
Aligning objects 52
- operator (in queries) 83 Anchored substring text queries 82
% wildcard character 82 AND operator
( operator in formula queries 84 hit lists 92
* wildcard character 82 queries 82, 83, 91
< operator in queries 83 Anti-aromaticity 138
= operator in queries 82, 84 Append data 108
> operator in queries 83 Append to existing data 108
\ operator in queries 91 Appending data on import 108
Aromaticity 138
A ASCII file, exporting 113
Atom labels, colors 45
A (any atom type) 138 Atom lists 94, 139
Access Atom not-lists 139
attaching tables from 71 Atom numbers, finding 81
DAO 4 Atom properties 138
manipulating .mdbfiles 127 Atom types
multi-user 60 A (any) 138
Read-only 59 in queries 135
secured 60 M (metal) 138
using with ChemFinder 127 overview 94
ACX information, finding 130 Q (heteroatom) 138
ADD indicator special 138
description 8 X (halogen) 138
when displayed 9, 63 Atom-atom mapping
Add New Record command 63 display preferences 116
Adding reaction queries 89
data 63 Attaching
data to database 108 non file-based databases 72
fields 73, 128 tables from file-based database 71
menu to data box 44 tables from other applications 71
multiple structures to forms 75
records 9, 63
scroll bars 45
structures 63
tables 69, 103, 128
ChemFinder Index • 159

B C
Backing up 76 CAL
Bitscreen 145 execute with button 38
Administrator
Bond numbers, finding 81 executing command with button 125

Bond properties Help 124
in queries 141 overview 123
ring/chain 141 CambridgeSoft web site, accessing 131
Bond types Camsoft.com 131
double either 136 Cells 5
in queries 135 cfs file extension 124, 127
overview 94 cfw file extension 42, 127
special 141 Chain bonds 141
Boolean operations Change views 80
in queries 82 Changing box style 43
on hit lists 92 Charges in queries 136
Box creation commands, CAL 150 Check valences 120
Box Manipulation commands, CAL 151 Chem3D, viewing models 69
Boxes ChemClub.com 132
changing styles 43 ChemDraw
creating 36 editing structures 65, 67
deleting 51 format, viewing in 43
font 45 ChemFinder
hiding or showing 45 closing 14
moving 51 overview 3
properties 42 provided directories 3
resizing 51 starting 9
selecting 50 window components 7
style 42 ChemFinder Automation Language, see CAL 149
Bring to Front 52 ChemFinder.com 129
Browsing Chemical markers, displaying 81
overview 6 Chemicals, purchasing online 130
with record tools 61 ChemNews.Com 131
Btrieve 4, 71 ChemOffice SDK, accessing 133
Button ChemStore.com 130
attaching to scripts 125 Cleaning structures 65
creating 38 Clearing forms 79
Closing ChemFinder 14
Color Preferences 117
Columns
adding in 128
changing formats 128
definition 5
Combined searching 91
160 • Index ChemFinder

Commit Changes command 64, 65, 68 D
Committing changes vs. saving 41
Communicating with other applications Data
using DDE 126 adding 63
using OLE Automation 127 committing 64, 66
using scripts 126
deleting 67
Concurrent access 60
displaying 36
Connection Table files 105
editing 64
Continuous forms 80
Conventions, document 1 entering 63, 69
Counterions 68 exporting 113
Create Database button 70 sorting 66
Create Table dialog box 71 Data Box tool 36
Creating Data boxes
boxes 36 creating 36
button 38 description 8
data box menu 44 hiding or showing 45
data boxes 36 Data items 5
database, overview 4 Data Source
databases 70 command 40, 71
form, overview 4 ODBC 71
forms, automatically 48 selecting 40, 71
forms, manually 35 Data Table
forms, overview 35 columns 95
multiple tables 69, 103 description 8
new form 36 displaying 61
picture boxes 38 moving columns 62
scripts 124 Page Setup 96
subforms 100
printing 95
tables 70
resizing columns 62
tabs 50
resizing rows 62
text 38
Creating frames 37 sorting 66
Current hit list, exporting 113 subforms 103
Current list Database commands, CAL 154
counter 9 Database logon 61
description 8 Database size 9
exporting 113 Databases
retrieving all records 82 adding structures119 73
size 9 backing up 76
Current Mol as a Query command 87 cells 5
Current record 8, 9 columns 5
Customizing compressing 128
fonts 45 creating 70
numbers 46 data items 5
text 45 fields 5
toolbars 121

Databases (continued) E
flat-file 5, 70
management scheme 4 Editing
model 5 data 64
Administrator
moving 76 fields 64
multiple tables 72 forms 50
non-chemical 71, 73 forms, overview 35
opening 40, 59 labels 37
overview 4 overview 6
read-only 9 redo 52
records 5 structures 65
resetting 67 structures with ChemDraw 67
rows 5 undo 52
selecting 39 Editing form layout 53
tables 5 Editing tabs 50
vs. forms 6 Element Editor 123
Date fields 74 Element ranges in queries 84
Dates Elements
display preferences 83 colors 123
queries 83 physical data 123
dBASE 4, 71 selecting 122
DDE, to communicate with other applications 126 Enter Query command 79, 81
Debugging scripts 125 Enter Script Command dialog box 124
Delete Record command 67 Enter the Label dialog box 37, 38
Deleting Entering
boxes 51 data 63, 69
contents of fields 67 queries 9, 79
data 67 reaction queries 88
fields 76 structures 63
objects 51 Entering query 79
records 67 Environment Variables, CAL 157
tables 71 Exact structure searching 85
Delimited text files Exact text match queries 82
exporting 113 Excel
headers 113 communicating with using CAL 123
directories provided 3 communicating with using DDE 126
Disabling security 58 Exiting 14
Display preferences 115 Exporting
Distributing objects 53 ASCII file 113
Documentation web page 131 current hit list 92, 113
Double either bond type 136 current list 113
Duplicating records 64 data 113
delimited text files 113
tables 128

F Forms
adding multiple structures 75
FAQ clearing 79
online, accessing 132 creating automatically 48
Technical support 147 creating manually 35
Fields editing 50
adding 128 layout, changing 53
changing formats 128 moving 76
date 74 multiple, for one database 6
deleting 76 opening 35
deleting contents 67 overview 4
editing 64 Page Setup commandn 96
formula 70 printing 95
illustration 5 saving 41
integer 74 setting security 54
memo 74, 110 style 48
Mol_ID 70 vs. databases 6
molecular weight 70 window 7
picture 74 Formula field 70
picture, description 74 Formula queries 83
real 74 Formulas
structure 70 element ranges, in queries 84
text 73, 110 input rules 143
width 110 parentheses in queries 84
File Commands, CAL 154 query rules 83
File extensions 76 sorting 66
File formats, supported 105 FoxPro 4, 71
File-based databases, attaching tables 71 Frame tool 37
Files, log 111 Framed Box tool 37
Find command 79 Framed Boxes
Find Current Molecule command 87 creating 37
Find List 84 description 8
Find list 84 Frames 37
Finding atom and bond numbers 81 Frames, creating 37
First Record command 61 Framing pictures 116
Fit to box 116 Free sites, in queries 140
Fixed labels 37, 43 Frequently asked questions 147
Flat-file databases 5, 70
Fonts, customizing 45
Form toolbar 8, 36
Form tools 35

G I
General CAL commands 153 ID queries 84
Generics hit only generics 119 Implicit hydrogens
Administrator
Go To Record command 61 added to structures 68

Grid Tool 36 in queries 140
Grids Importing
setting spacing 48 append to existing data 108
spacing 116 appending 108
changing field definition 110
H hit lists 92
log files 111
Headers, delimited text files 113 merging 108
Help overwriting 108
CAL 124 RDFiles 106
online 1 replace existing data 108
Quick Reference card 1 SDFiles 106
Status Bar 2 skip entry 109
Tooltips 2 specifying location 112
Hiding annotations 116 tables 128
Hiding data boxes 45 Importing structures 106
Hit any charge on carbon 119 Installation 2
Hit any charge on heteroatom 119 Integer fields 74
Hit lists Integrated products 3
Boolean operations 92 Intermediates
current 9 queries 90
intersecting 92 searching 88
joining 93 Internet, CambridgeSoft web site 131
replacing 92 Intersect with current list 92
restoring 92 ISIS/Graphic files 105
saved as text files 92 ISIS/Sketch files 105
saving 92 Isotopes 137
Home page, CambridgeSoft 131
How to use this guide 1 J
Hydrogens
added to structures 68 Jet database engine 5
in queries 136

L Molecular formula queries 83
Molecular weight field 70
Lab supplies, purchasing online 130 Moving
Labels boxes 51
buttons 125 forms and databases 76
editing 37 MS Access Workgroup information 54
fixed 37, 43 msi file extension 76, 127
fonts 45 MSI Molfiles 105
live 43 mst file extension 76, 127
Last Record command 61 Multiple structures, adding to forms 75
Launching ChemFinder 9 Multi-step reactions 88
Layout Tool 35 Multi-user access 60
layout, form, changing 53
ldb file extension 127 N
Linking subforms to main forms 99
Live labels 43 New features in ChemFinder 7 3
Locating atom and bond numbers 81 New form, creating 36
Log files 111 New Record indicator 8
Logon, database 61 Next Record command 61
No implicit H on metals 120
M Non file-based databases, attaching 72
Normalization, in queries 138
M (metal) 138 Numbers, customizing 46
Magnification level 97 Numeric format 46
Main Form 8 Numerical queries 82
Main toolbar 8, 35
Management scheme, databases 4 O
Mapping atoms in reaction queries 89
Margins 96 Objects
Match stereochemistry 119 aligning 52
Mathematical operators, in CAL command 156 distributing 53
mdb file extension 76, 127 spacing 53
MDL Molfiles 105 Objects, deleting 51
MDL RXNFiles 105 ODBC
Memo fields 74, 110 adding structures to existing sources 73
Menu Bar 8 overview 4
Menu commands, CAL 149 selecting data sources 71
Menu, adding to data box 44 OLE Automation
Merge data 108 communicating with other applications 127
Merging data on import 108 overview 127
Microsoft Jet database engine 5 Online Help 1
Models, viewing using Chem3D 69
Modifying data 64
Mol_ID field 70

Online Menu Picture fields, description 74
Browse ChemStore.com 130 Picture tool 38
CambridgeSoft Home Page 131 Pictures
ChemOffice SDK 133 cannot be edited 69
Administrator
CS Chem3D Technical Support 132 cannot be searched 68

Lookup Suppliers on ChemStore.com 129 framing 116
overview 129 not chemically significant 69
Register online 132 preferences 116
Open Database button 40 reading 39
Open last form on startup 121 saving 39
Opening storing ChemDraw drawing as 68
ChemFinder 9 structures 68
databases 40, 59 updating 39
forms 35 Plain Text tool 38
hit lists 92 Portal database 73
pictures 39 Precision, numerical queries 82
Opening options 120 Preferences
Operators, in CAL commands 156 color 117
OR operator date display 83
hit lists 93 display 115
queries 82 grid spacing 116
Oracle open 120
attaching tables 71 picture display 116
driver 4 Recent File List Size 121
Other applications, attaching tables from 71 registration 120
Other applications, communicating with registration of structures 120
using DDE 126 search details 118
using OLE Automation 127 search type 117
using scripts 126 setting 115
Overriding security 58 stereochemistry 119
Overwrite data 108 structure display 115
Overwriting data on import 108 Previous Record command 61
Print command 95
P Print Preview command 97
Print Setup command 95
Page Setup Printing
forms 96 layout 96
tables 96 margins 96
Page Setup command 96 overivew 95
Paradox 4, 71 scale to Fit 96
Password 55, 60 Products
Periodic Table 122, 136 queries 90
Permit extraneous fragments in full structure searching 88
searches 119 Program Execution commands, CAL 152
Picture boxes, creating 38

Q Queries (continued)
special bond types 141
Q (heteroatom) 138 SQL 82, 91
QRY indicator 8, 9 stereochemistry 87, 137
Queries stopping 80
anchored substring 82 structural similarity 86
atom lists 94, 139 structures 84
atom not-lists 139 subforms 103
atom properties 135 submitting 79
atom properties in 138 substituents 136, 139
atom types 94, 135 substructure 85
bond properties 141 text 82
bond types 94, 135 unsaturation 141
Booleans 82 using current structure 87
charges 136 wildcards 82
dates 83 Query fragments can overlap in target 119
entering 9, 79 Query properties
exact structure 85 conflicting 135
exact text match 82 overview 135
finding current structure 87 Questel F1D files 105
formulas 83 Questel F1Q files 105
free sites 140 Quick Reference card 1
hydrogens 136 Quitting 14
ID 84
implicit AND between fields 82, 91 R
implicit hydrogens 140
inequalities 83 Radicals, in queries 136
intermediates 90 Ranges, in queries 82
isotopes 137 RDFiles
multiple fields 91 exporting 113
multiple substructures 95 importing 106
Reactants
normalization 138
queries 90
numbers 82
searching 88
overview 79
Reaction centers
precision 82 bond type 145
products 90 bond types 142, 143
progress display 85 display preferences 116
radicals 136 overview 88
ranges 82, 83 Reaction queries 88
reactants 90 atom-atom mapping 89
reactions 88 creating 88
refining 81 intermediates 90
similarity rules 145 overview 6
special atom types in 138 products 90
reactants 90

Reaction query must hit reaction center 89, 119 S
Reactions
centers 88 Sample code, SDK web site 133
multiple-step 88
Sample directory 3
Read File command 39
Administrator
READ indicator 8, 9 Save command

Read Structure command 105 effect on changes 41
Read-only access 59 not needed when editing data 64
Real fields 74 Save dialog box 41
Recent file list size, setting 121 Save List command 92
Record Save Structure command 105
toolbar, browsing with 61 Saving
toolbar, description 8 changes to forms 14
toolbar, illustration 59 forms 41
Record Number dialog box 61
hit lists 92
Record tool 61
Records pictures 39
adding 9, 63 subform 41
current 8, 9 vs. committing119 41
deleting 67 Scale to Fit, when printing 96
duplicating 64 Scaling structures 116
illustration 5 Script-Only Commands, CAL 157
moving between 61 Scripts
retrieving all 82 attaching to buttons 125
Redo 52 communicating with other applications 126
Redo command 66 debugging 125
Refining queries 81
executing 124
Registration of structures, preferences 120
Registration preferences 120 using in subforms 103
Registration, online 132 writing 124
Relational databases 5, 72, 99 Scroll bars, adding 45
Renaming tabs 50 SDFiles
Replace current list 92 exporting 113
Replace existing data 108 importing 106
Requirements SDK Online, accessing 133
RAM 2 SDK, www address 123
system 2 Search details preferences 118
Resetting database 67 Search toolbar 8, 79
Resetting the database 82
Search Type preferences 117
Resizing boxes 51
Resonance, forms 138 Searching
Restore List command 92 see also Queries
Restore Previous List command 81 for numbers 82
Restoring changes 52 online for chemical information 129
Results, viewing 80 overview 79
Reversing changes 52 Secured access 60
Ring bonds 141 Securing forms 54
Rows 5

Security Stereochemistry
disabling 58 allenic, not supported 137
MS Access Workgroup information 54, 55 cis/trans double bonds 87, 137
options 55 octahedral, not supported 137
overriding 58 overview 87
setting options 55 queries 137
Selecting search preferences 119
a database 39 square planar, not supported 137
boxes 50 tetrahedral 87, 137
Selection tool 50 trigonal bipyrimidal, not supported 137
Send to Back 52 Stopping a query 80
Serial number 147 Structure display preferences 115
Setting Structure field 70
box properties 42 Structures
numeric format 46 adding 63
Setting alerts 120 adding to non-chemical database 73
Setting preferences 115 checking chemistry 68
Shortcut menu 8 chemically-significant text 68
Show hydrogens on heteroatoms 115 cleaning 65
Show hydrogens on terminal carbons 115 editing 65, 67
Show opening dialog 121 entering 67, 120
Show reaction centers 115 file formats 105
Showing importing 106
annotations 116 pictures 68
data boxes 45 queries 84
Similarity searching query properties 135
overview 86 red highlighting in queries 85
rules 145 registration 120
Skip entry 109 scaling 116
SMD files 105 sorting 66
Sorting Style, box, changing 43
data table 66 Styled text 65
fields 66 Subforms
formulas 66 creating 100
in languages 67 data table 103
permanently 128 description 9
structures 66 linking 99
text 66 linking fields 99
Sorting data 66 overview 99
SQL 91 searching 103
SQL Server 4, 71 switching between forms and data tables 103
Sructure columns 75 using scripts 103
Starting ChemFinder 9 Submitting query 79
Status Bar 2, 8, 9 Substituents, in queries 136, 139
Substructure searching, overview 85

Supplemental information 1 Tools
Supplier, finding online 129 Data Box 36
Support, technical 147 Frame 37
Supported file formats 105 Framed box 37
Administrator
Switch views 80 Grid 36

System directory 3 Layout 35
System requirements 2 Picture 38
Plain Text 38
T record 61
Tooltips 2
Table header 9 Transferring information to other computers 76
Table view 80 Troubleshooting
Tables guidelines 148
adding 69, 103, 128 online 132
changing names 128
creating 70 U
definition 5
deleting 71 Undo 52
exporting 128 Undo Changes command 64, 65, 66
importing 128 Uniform bond length 116
Tabs Union with current list 93
creating and editing 50 Unsaturation, in queries 141
renaming 50 User’s guide, online 131
Tanimoto similarity 145 Username 55, 60
Technical support 147
Temporary database 73 V
Tetrahedral stereo center hits 119
Text Valence
as structures 68 charged atoms 137
creating 38 non-standard state 120
customizing 45 unfilled 136
queries 82 Valences, check 120
sorting 66 Variable Commands, CAL 155
Text fields 73, 110 View format for structures, selecting 43
Text Format toolbar 45, 65 Viewing
Text, styled 65 chemical markers 81
Title Bar 9 continuous forms 80
Toolbars switching views 80
customizing 121 table 80
description 8 Viewing models using Chem3D 69
text 65 Viewing results 80
Visual Basic 5, 127

W
Web site, CambridgeSoft, accessing 131
What’s New 3
Width of fields 110
wildcard
% 82
* 82
Windows metafiles 36, 38, 39
wmf 39
X
X (halogen) 138
Z
Zooming 97

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User’s Guide
CS Chem3D 6.0
for Windows and Macintosh (5.0)
CS Chem3D is a stand alone application within

CS ChemOffice, an integrated suite including
CS ChemDraw for chemical structure drawing,
CS ChemFinder for searching and information integration, and
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I N
o, it’s not okay to copy your colleague’s software. Software is
protected by federal copyright law, which says that you can’t
s it
make such additional copies without the permission
of the copyright holder. By protecting the investment of
computer software companies in software development, the
copyright law serves the cause of promoting broad public
availability of new, creative, and innovative products. These compa-
okay to
nies devote large portions of their earnings to the creation of new
software products and they deserve a fair return on their investment.
The creative teams who develop the software — programmers, writers,
graphic artists and others — also deserve fair compensation for their
efforts. Without the protection given by our copyright laws, they would
copy my
be unable to produce the valuable programs that have become so
important in our daily lives: educational software that teaches us much
needed skills; business software that allows us to save time, effort and
money; and entertainment and personal productivity software that
enhances leisure time.
colleague’s Q
That makes sense, but what do I get out of
software? A
purchasing my own software?
When you purchase authorized copies of software

programs, you receive user guides and tutorials, quick
reference cards, the opportunity to purchase upgrades,
and technical support from the software publishers.
For most software programs, you can read about user
benefits in the registration brochure or upgrade
Q
flyer in the product box.
A
What exactly does the law say about copying
software?
The law says that anyone who purchases a copy of

software has the right to load that copy onto a single
computer and to make another copy “for archival
purposes only.” It is illegal to use that software on
more than one computer or to make or distribute
copies of that software for any other purpose unless
specific permission has been obtained from the copyright owner. If you
pirate software, you may face not only a civil suit for damages and
other relief, but criminal liability as well, including fines and jail terms
Q
of up to one year.
A
So I’m never allowed to copy software for any
other reason?
That’s correct. Other than copying the software you

purchase onto a single computer and making another
copy “for archival purposes only,” the copyright law
prohibits you from making additional copies of the
software for any other reason unless you obtain the
permission of the software company.
Q
The SPA also offers a number of
At my company, we pass disks around all the
A
other materials designed to help
time. We all assume that this must be okay you comply with the Federal
since it was the company that purchased the Copyright Law. These materials
software in the first place. include:
Many employees don’t realize that corporations • SPA Software Management

are bound by the copyright laws, just like every- Guide. This guide, available for $80,
one else. Such conduct exposes the company (and contains SPA’s 8 point program for
possibly the persons involved) to liability for copyright maintaining copyright compliance, an
infringement. Consequently, more and more corporations concerned internal controls analysis and questionnaire,
about their liability have written policies against such “softlifting”. Em- a software audit guide, SPAudit, “It’s Just
ployees may face disciplinary action if they make extra copies of the Not Worth the Risk” video and other
company’s software for use at home or on additional computers within educational materials.
the office. A good rule to remember is that there must be one autho-
• SPAudit (DOS and Macintosh). This Kit,
Q
rized copy of a software product for every computer upon which it is
run. available free of charge, will audit hard disks
to inventory programs and summarize the
number and location of each application.
A
Do the same rules apply to bulletin boards and
• “It’s Just Not Worth the Risk” video. This 12-
user groups? I always thought that the reason they minute video, available for $10, has helped
got together was to share software. over 20,000 organizations dramatize to their
employees the implications and conse-
Yes. Bulletin boards and user groups are bound by the quences of software piracy.
copyright law just as individuals and corporations.
However, to the extent they offer shareware or public • “Don’t Copy that Floppy” video. This 9
domain software, this is a perfectly acceptable practice. minute rap video, available for $10, is
Similarly, some software companies offer bulletin boards and user designed to educate students on the ethical
groups special demonstration versions of their products, which in use of software.
some instances may be copied. In any event, it is the responsibility of
the bulletin board operator or user group to respect copyright law and • Other educational materials including,
Q
to ensure that it is not used as a vehicle for unauthorized copying or “Software Use and the Law,” a brochure
distribution. detailing the copyright law and how software
should be used by educational institutions,
corporations and individuals; and several
A
posters to help emphasize the message that
What about schools and professional unauthorized copying of software is illegal.
training organizations?
The same copyright responsibilities that apply to To order any of these materials, please send
Q
individuals and corporations apply to schools your request to:
and professional training organizations. No one
is exempt from the copyright law. “SPA Anti-Piracy Materials”
A
Software Publishers Association
1730 M Street, NW, Suite 700, Washington,
D.C. 20036
(202) 452-1600
I’ll bet most of the people who copy software
don’t even know that they’re breaking the law.
Special thanks to Aldus Corporation for their
contribution to this brochure. We urge you to
Because the software industry is relatively new, and be-
make as many copies as you would like in
cause copying software is so easy, many people are either order to help us spread the word that unautho-
unaware of the laws governing software use or choose to rized copying of software is illegal.
ignore them. It is the responsibility of each and every software user to
understand and adhere to copyright law. Ignorance of the law is no
Reprinted by CambridgeSoft Corporation with
excuse. If you are part of an organization, see what you can do to ini-
permission from the Software Publishers
tiate a policy statement that everyone respects. Also, suggest that your Association.
management consider conducting a software audit. Finally, as an indi-
vidual, help spread the word that the users should be “software legal.”
Contents
Introduction The Measurements Table ............................. 14
Deleting Measurement Table Data .............. 14
About Chem3D ......................................................... 1 Using Model Tables to Manipulate Models ......14
About CS MOPAC.................................................... 1 Model Coordinates ............................................14
About Gaussian ......................................................... 1 Internal Coordinates ..................................... 14
About This User’s Guide........................................... 1 Cartesian Coordinates .................................. 15
Additional Information.............................................. 1 Customizing the User Interface............................... 15
Quick Reference Card .........................................1 Changing the Font and Font Size ......................15
Online Information .............................................2 OLE Automation ...............................................16
Online Help .................................................... 2 The Window Menu (Windows)............................... 16
ToolTips ......................................................... 2 Closing Chem3D ..................................................... 16
Context-Sensitive Help .................................. 2
CambridgeSoft Web Pages .................................2 Chapter 2: Tutorials
Conventions............................................................... 2
Terminology .............................................................. 2 Tutorial 1: Building Models with the Bond Tools .. 17
Installation/System Requirements............................. 3 Tutorial 2: Building Models with the Text Building Tool
21
Chapter 1: Chem3D Basics Replacing Atoms ...............................................22
Using Labels to Create Models .........................22
Starting Chem3D....................................................... 5 Using Substructures ..........................................23
Graphical User Interface ........................................... 5 Tutorial 3: Examining Conformations .................... 24
Model Window ...................................................6 Tutorial 4: Searching For Conformations ............... 28
The Messages Window .......................................6 Tutorial 5: Transferring Information from ChemDraw
The Movie Controller .........................................7 30
Magnification Buttons ........................................7 Tutorial 6: Viewing Molecular Surfaces ................. 30
The Tools Palette ................................................7 Tutorial 7: Mapping Properties onto Surfaces ....... 31
The Model Table Area ........................................7 Tutorial 8: Computing Partial Charges ................... 33
Model Building Basics .............................................. 8
The Settings Dialog Box .....................................8 Chapter 3: Creating, Opening, and
Default Settings.............................................. 9 Importing Models
Stationery and Templates............................... 9
Model Display .....................................................9 Overview ................................................................. 37
Atom Labels................................................... 9 Creating a Model ..................................................... 37
Model Data .......................................................10 Opening an Existing File......................................... 37
Atom Types.................................................. 10 Switching Between Open Models................ 37
Rectification ................................................. 11 Creating a Model Using Templates......................... 38
Bond Lengths and Bond Angles .................. 11 Importing a Model................................................... 38
Internal and External Tables ................................... 11 Supported Formats for Importing .....................38
The Table Editor ...............................................11 File Format Options ..........................................39
Standard Measurements ............................... 13 Cambridge Crystal Data Bank ..................... 39
Bond Length................................................. 13 Cartesian Coordinates .................................. 40
Bond Angles................................................. 13 Connection Table ......................................... 40
Showing and Hiding Model Tables ..................13 Protein Data Bank ........................................ 41
Chem3D Contents • i
Saving Models......................................................... 41 Setting Charges ....................................................... 59
Saving Changes ................................................42 Setting Serial Numbers ........................................... 59
Saving a Model with a Different Name or Loca- Changing Stereochemistry ...................................... 60
tion ............................................................... 42 Inversion ...........................................................60
Saving a Model in a Different File Format .......42 Reflection ..........................................................60
Saving Models as Templates ............................43 Refining a Model..................................................... 61
Contents
Discarding Recent Changes to a Model .................. 43 Rectifying Atoms ..............................................61

Closing Models ....................................................... 43 Cleaning Up a Model ........................................61
Using the Measurements Table ........................62
Chapter 4: Building and Editing
Models Chapter 5: Manipulating Models
Overview ................................................................. 45 Overview ................................................................. 63
Setting the Model Building Controls ...................... 45 Selecting.................................................................. 63
Building Modes ................................................46 Selecting Single Atoms and Bonds ...................63
Building with Tools ................................................ 46 Selecting Multiple Atoms and Bonds ...............63
Creating a Bond ................................................47 Deselecting Atoms and Bonds ..........................63
Adding Bonds ...................................................47 Selecting Atoms in a Group ..............................64
Creating Uncoordinated Bonds ........................48 Using the Selection Rectangle ..........................64
Removing Bonds and Atoms ............................48 Selecting a Subset of Atoms ................................... 64
Selecting Bonds and Atoms ..............................48 Select Reverse ...................................................64
Building Models With The Text Building Tool...... 49 Select Element ..................................................64
Labels ................................................................49 Select Adjacent .................................................65
The Table Editor .......................................... 50 Select Fragment ................................................65
Specifying Order of Attachment.................. 50 Showing and Hiding Atoms .................................... 65
Specifying Ring Closure .............................. 50 Show H’s and Lp’s ...........................................65
Using Substructures ..........................................51 Hiding Selected Atoms .....................................65
Building with Substructures .............................51 Hiding Unselected Atoms .................................65
Example 1. Building Ethane with Substructures Showing All Atoms ..........................................65
51 Showing Unselected Atoms ..............................66
Example 2. Building a Model with a Substructure Reversing Atoms Shown ..................................66
and Several Other Elements......................... 52 Defining Groups...................................................... 66
Example 3. Polypeptides.............................. 52 Moving Atoms or Models ....................................... 66
Example 4. Other Polymers ......................... 53 Rotating Models ...................................................... 67
Building Models Using ChemDraw or ISIS/Draw . 53 X- or Y-Axis Rotations .....................................67
Replacing an Atom with a Substructure ...........53 Rotating Fragments ...........................................67
Changing an Atom to Another Element.................. 54 Internal Rotations ..............................................67
Changing an Atom to Another Atom Type............. 55 Rotating Around a Specific Axis ......................68
Changing Bonds ...................................................... 55 Using the Rotate Dialog Box ............................68
Using Bond Tools .............................................55 Trackball Tool ..................................................68
Creating Bonds by Bond Proximate Addition ..56 Changing Orientation .............................................. 69
Adding Fragments................................................... 57 Aligning to an Axis ...........................................69
Setting Measurements ............................................. 57 Aligning to a Plane ...........................................69
Setting Bond Lengths .......................................57 Resizing Models...................................................... 70
Setting Bond Angles .........................................58 Resizing Windows ............................................70
Setting Dihedral Angles ....................................58 Scaling a Model ................................................70
Setting Non-Bonded Distances (Atom Pairs) ...58 Using Magnification Controls ..........................71
Atom Movement When Setting Measurements 58 Centering a Selection ........................................71
Setting Constraints .................................................. 59 Changing the Z-matrix ............................................ 71
ii • Contents Chem3D
The First Three Atoms in a Z-matrix ................72 Chapter 7: Inspecting Models
Atoms Positioned by Three Other Atoms .........72
Positioning of H(14)..................................... 73 Model Data .............................................................. 93
Positioning by Bond Angles ........................ 74 Pop-up Information ................................................. 93
Positioning by Dihedral Angle..................... 74 Non-Bonded Distances ................................ 95
Setting Origin Atoms ................................... 74 Measurement Tables .........................................95
Removing Measurements from a Table ....... 95
Chapter 6: Displaying Models Editing Measurements.................................. 96
Optimal Measurements ................................ 96
Overview ................................................................. 75 Non-Bonded Distances in Tables................. 96
Structure Displays ................................................... 75 Showing Bond Lengths ................................ 96
Model Types .....................................................76 Showing Bond Angles ................................. 97
Displaying Dot Surfaces ...................................77 Showing Dihedral Angles ............................ 98
Coloring Displays .............................................78 Showing Close Contacts .............................. 98
Coloring by Element .................................... 78 Showing Ring Closures................................ 99
Coloring by Group ....................................... 78 Showing the Deviation from Plane ............ 100
Coloring by Partial Charge .......................... 78 Displaying the Coordinates Tables .................101
Coloring Black ............................................. 79 Internal Coordinates ................................... 101
Coloring by Depth........................................ 79 Cartesian Coordinates ................................ 101
Coloring the Background Window .............. 79 Displaying the Groups Table ..........................101
Colorizing Individual Atoms ............................79 Coloring Groups......................................... 102
Atom Fill Patterns .............................................80 The Message Window ........................................... 102
Depth Ratio .......................................................81 Docking Models .................................................... 102
Solid Spheres ....................................................81 Comparing Models by Overlay ............................. 105
Solid Spheres Size By .................................. 82 Animations ............................................................ 107
Solid Spheres Size % ................................... 82 Creating and Playing Movies ..........................108
Solid Spheres Vary Size by Depth ............... 82 Editing a Movie ...............................................108
Bond Display ....................................................82 Movie Control Panel .......................................108
Bond Width .................................................. 82 Spinning Models .............................................109
Cylindrical Bond Pattern.............................. 82 Spin About Selected Axis .......................... 109
Taper Cylindrical Bonds .............................. 82 Spin Torsional Angles................................ 109
Atom Labels ......................................................83
Default Display Options............................... 83 Chapter 8: Printing and Exporting
Displaying Labels Atom by Atom .............. 83 Models
Stereo Views .....................................................83
Molecular Surface Displays .................................... 84 Printing Models ..................................................... 111
Extended Hückel ...............................................84 Specifying Print Options .................................111
Displaying Molecular Surfaces ............................... 84 Printing ............................................................112
Molecular Surface Types ..................................86 Exporting Models Using Different File Formats .. 112
Molecular Surface Colors .................................86 Formats for Publishing Applications ..............113
Molecular Surface Isovalues .............................87 WMF (Windows only) ............................... 113
Setting the Surface Grid ....................................87 EMF (Windows only) ................................ 113
Solvent Accessible Surface ...............................88 Bitmap (Windows only)............................. 113
Connolly Molecular Surface .............................90 PICT (Macintosh only) .............................. 113
Total Charge Density ........................................91 EPS............................................................ 113
Total Spin Density ............................................91 TIFF ........................................................... 114
Molecular Electrostatic Potential ......................92 3DMF ........................................................ 115
Molecular Orbitals ............................................92 Chem3D Templates and Stationery ........... 115
Visualizing Surfaces from Other Sources ............... 92 Movie (Macintosh only)............................. 115
Chem3D Contents • iii

PICS (Macintosh only) ............................. 115 Torsion Energy........................................... 132
Graphics Interchange Format (GIF) .......... 115 Non-Bonded Energy .................................. 133
Portable Network Graphics Format (PNG) 115 van der Waals Energy ................................ 133
Formats for Chemistry Modeling Applications 115 Cutoff Parameters for van der Waals Interactions
Alchemy.................................................... 115 133
Cartesian Coordinates ................................ 115 Electrostatic Energy ................................... 133
Contents
Connection Table ....................................... 116 charge/charge contribution......................... 134

Gaussian Input .......................................... 116 dipole/dipole contribution.......................... 134
Gaussian Checkpoint ................................. 117 dipole/charge contribution ......................... 134
Gaussian Cube ........................................... 117 Cutoff Parameters for Electrostatic Interactions
Internal Coordinates.................................. 117 134
MacroModel Files..................................... 118 OOP Bending ............................................. 135
Molecular Design Limited MolFile (MDL MolF- Pi Bonds and Atoms with Pi Bonds........... 135
ile) .............................................................. 118 Stretch-Bend Cross Terms ......................... 136
MSI ChemNote ......................................... 118 User-Imposed Constraints.......................... 136
MOPAC Files ........................................... 118 Molecular Dynamics Simulation ....................136
MOPAC Graph Files ................................. 119 Molecular Dynamics Formulas.................. 137
Protein Data Bank Files ............................. 119 Quantum Mechanics Theory in Brief.................... 137
ROSDAL Files (RDL) .............................. 119 Approximations to the Hamiltonian........... 138
Standard Molecular Data (SMD).............. 120 Restrictions on the Wave Function ............ 139
SYBYL Files............................................. 120 Spin functions ............................................ 139
Job Description File Formats ................................ 120 LCAO and Basis Sets................................. 139
JDF Files .................................................... 120 The Roothaan-Hall Matrix Equation ......... 140
JDT Files.................................................... 120 Ab Initio vs. Semiempirical ....................... 140
Exporting With the Clipboard............................... 120 The Semiempirical Methods ...........................140
Transferring to ChemDraw .............................120 Extended Hückel Method .......................... 140
Transferring to Other Applications .................120 Methods Available in CS MOPAC .................141
Copying Postscript (Macintosh Only) ...........121 RHF............................................................ 141
Edit Graphic Object (Macintosh Only) ................. 121 UHF............................................................ 141
Configuration Interaction........................... 141
Chapter 9: Computation Concepts Approximate Hamiltonians in MOPAC................ 142
Choosing a Hamiltonian .................................142
Computational Chemistry Overview .................... 123 MINDO/3 Applicability and Limitations... 142
Computational Methods Overview ....................... 123 MNDO Applicability and Limitations ....... 143
Uses of Computational Methods ....................124 AM1 Applicability and Limitations........... 143
Choosing the Best Method .............................124 PM3 Applicability and Limitations ........... 144
Molecular Mechanics Methods Applications MNDO-d Applicability and Limitations.... 144
Summary.................................................... 125
Quantum Mechanical Methods Applications Chapter 10: MM2 Computations
Summary.................................................... 125
Potential Energy Surfaces ...............................126 MM2 Overview..................................................... 145
Potential Energy Surfaces (PES) ............... 126 Minimize Energy................................................... 145
Single Point Energy Calculations ...................127 Tracking Specific Measurements ...................146
Geometry Optimization ..................................128 Running a Minimization .................................147
Molecular Mechanics Theory in Brief .................. 129 Queuing Minimizations ..................................147
The Force-Field ..............................................130 Minimizing Ethane .........................................147
MM2 .......................................................... 130 Comparing Two Stable Conformations of Cyclohex-
Bond Stretching Energy............................. 131 ane ...................................................................149
Angle Bending Energy............................... 131 Locating the Global Minimum................... 150
iv • Contents Chem3D
Molecular Dynamics ............................................. 151 Charges From an Electrostatic Potential .........175
Performing a Molecular Dynamics Computation . Wang-Ford Charges ................................... 175
151 Electrostatic Potential ................................ 175
Dynamics Settings ..........................................152 Molecular Surfaces .................................... 176
Job Type Settings ............................................153 Polarizability .............................................. 176
Computing the Molecular Dynamics Trajectory Calculating the Dipole Moment of meta-Nitrotol-
for a Short Segment of Polytetrafluoroethylene uene ............................................................ 176
(PTFE)........................................................ 154 COSMO Solvation in Water ...................... 177
Compute Properties ............................................... 155 Comparing the Stability of Glycine Zwitterion in
Showing Used Parameters..................................... 157 Water and Gas Phase ......................................177
MM2 Dihedral Driver (Macintosh Only).............. 157 Hyperfine Coupling Constants ........................178
Analyzing Conformations of n-Butane ...... 158 Hyperfine Coupling Constants for the Ethyl Radical
Repeating an MM2 Computation.......................... 159 179
Using .jdf Files ...................................................... 159 Spin Density .......................................................... 180
UHF Spin Density ...........................................180
Chapter 11: MOPAC Computations UHF Spin Density for the Ethyl Radical ........180
RHF Spin Density ...........................................182
MOPAC Overview................................................ 161 RHF Spin Density for the Ethyl Radical .........182
Minimize Energy................................................... 161 Using the *.out file ................................................ 182
The Job Type Tab ...........................................161 Using Keywords .................................................... 183
The Theory Tab ..............................................162 Creating an Input File............................................ 184
Specifying the Electronic Configuration ........163 Running Input Files ............................................... 185
Even-Electron Systems ...................................164 Repeating MOPAC Jobs ....................................... 185
Ground State, RHF..................................... 164 Running MOPAC Jobs.......................................... 185
Ground State, UHF .................................... 165 Creating Structures From .arc Files....................... 186
Excited State, RHF..................................... 165
Excited State, UHF .................................... 165 Chapter 12: Gaussian Computations
Odd-Electron Systems ....................................165
Ground State, RHF..................................... 165 Gaussian Overview ............................................... 187
Ground State, UHF .................................... 165 Gaussian 98 ........................................................... 187
Excited State, RHF..................................... 165 Minimize Energy................................................... 187
Excited State, UHF .................................... 166 The Job Type Tab ...........................................187
The General Tab .............................................166 The Theory Tab ...............................................188
Minimizing Energy .........................................167 The Properties Tab ..........................................189
The Default Minimizer............................... 167 The General Tab .............................................189
Keywords ........................................................167 Job Description File Formats ................................ 190
Optimize to Transition State ................................ 168 .jdt Format .................................................. 190
Locating the Eclipsed Transition State of Ethane . .jdf Format.................................................. 190
169 Computing Properties............................................ 191
Compute Properties .............................................. 170 Creating a Gaussian Input File .............................. 191
MOPAC Properties ........................................171 Running a Gaussian Input File .............................. 191
Heat of Formation, DHf ............................. 171 Repeating a Gaussian Job...................................... 192
Gradient Norm ........................................... 171 Running a Gaussian Job ........................................ 192
Dipole Moment .......................................... 171
The Dipole Moment of Formaldehyde ...........172 Chapter 13: GAMESS Computations
Charges....................................................... 172
Comparing Cation Stabilities in a Homologous Se- GAMESS Overview .............................................. 193
ries of Molecules .............................................172 Installing GAMESS............................................... 193
Mulliken Charges ....................................... 173 Minimize Energy................................................... 193
Chem3D Contents • v
The Theory Tab ..............................................193 Browse ChemStore.com........................................ 211
The Job Type Tab ...........................................194 Browse CambridgeSoft.com ................................ 212
Specifying Properties to Compute ..................194 Browse CS Chem3D Documentation.................... 212
Specifying the General Settings .....................195 Browse CS Chem3D Technical Support............... 213
Saving Customized Job Descriptions.................... 195 Register Online...................................................... 213
Running a GAMESS Job ...................................... 195 Browse ChemOffice SDK..................................... 214
Contents
Repeating a GAMESS Job.................................... 196

Appendix A: Substructures .....215
Chapter 14: SAR Descriptors
Overview ............................................................... 215
SAR Descriptor Overview .................................... 197 Defining Substructures ...................................215
Chem3D Property Broker ..................................... 197
ChemProp Std Server........................................... 197 Appendix B: Atom Types .........219
ChemProp Pro Server............................................ 198
Limitations ......................................................199 Overview ............................................................... 219
Error Messages ...............................................199 Assigning Atom Types.......................................... 219
MM2 Server .......................................................... 200 Atom Type Characteristics .............................219
MOPAC Server ..................................................... 201 Defining Atom Types............................................ 220
GAMESS Server ................................................... 201
Appendix C: Technical Support 221
Chapter 15: SAR Descriptor
Computations Overview ............................................................... 221
Serial Numbers...................................................... 221
Overview ............................................................... 203 Macintosh.............................................................. 221
Selecting Properties To Compute ......................... 203 Windows ............................................................... 222
Sorting Properties ...........................................203 Troubleshooting .................................................... 222
Removing Selected Properties ........................203 Performance ....................................................222
Property Filters...................................................... 203 System Crashes ...............................................222
Setting Parameters................................................. 204
Results ................................................................... 204 Appendix D: 2D to 3D Conversion
225
Chapter 16: ChemSAR for Excel
ChemSAR for Excel Overview............................. 205 Overview ............................................................... 225
Configuring ChemSAR for Excel ......................... 205 Stereochemical Relationships ............................... 225
The ChemSAR Wizard ......................................... 205 Example 1 .......................................................225
Selecting ChemSAR Descriptors .......................... 208 Example 2 .......................................................225
Adding Calculations to an Existing Worksheet .... 208 Example 3 .......................................................226
Customizing Calculations ..................................... 208 Example 4 .......................................................226
Calculating Statistical Properties .......................... 209 Labels .................................................................... 226
Descriptive Statistics ......................................209
Correlation Matrix ..........................................210
Appendix E: MM2 ......................227
Rune Plots .......................................................210
Overview ............................................................... 227
Chapter 17: Accessing the MM2 Parameters................................................... 227
Other Parameters................................................... 227
Viewing Parameters .............................................. 227
Online Menu Overview......................................... 211 Editing Parameters ................................................ 227
Find Suppliers on ChemStore.com ....................... 211 The MM2 Force Field in Chem3D........................ 228
Find Information on ChemFinder.com ................. 211 Chem3D Changes to Allinger’s Force Field......... 228
vi • Contents Chem3D
Charge-Dipole Interaction Term .....................228 Bond Stretching Parameters .................................. 241
Quartic Stretching Term .................................229 Bond Type .......................................................241
Electrostatic and van der Waals Cutoff Terms 229 KS ...................................................................241
Pi Orbital SCF Computation ...........................229 Length .............................................................241
Bond Dipole ....................................................241
Appendix F: MOPAC ................ 231 Record Order ...................................................242
Angle Bending, 4-Membered Ring Angle Bending,
Overview ............................................................... 231 3-Membered Ring Angle Bending ........................ 242
MOPAC Background ............................................ 231 Angle Type ......................................................242
Potential Functions Parameters ............................. 231 KB ...................................................................242
Adding Parameters to MOPAC............................. 232 –XR2– .............................................................242
–XRH– ............................................................243
Appendix G: Automation ......... 233 –XH2– .............................................................243
Record Order ...................................................243
Macintosh .............................................................. 233 Pi Atoms ................................................................ 243
Windows................................................................ 234 Atom Type ......................................................243
Electron ...........................................................244
Appendix H: Parameter Tables 235 Ionization ........................................................244
Repulsion ........................................................244
Parameter Table Overview.................................... 235 Pi Bonds ................................................................ 244
Parameter Table Use ............................................. 235 Bond Type .......................................................244
Parameter Table Fields.......................................... 236 dForce .............................................................244
Atom Type Numbers ......................................236 dLength ...........................................................244
Quality ............................................................236 Record Order ...................................................245
Reference ........................................................237 Electronegativity Adjustments .............................. 245
Estimating Parameters........................................... 237 MM2 Constants ..................................................... 245
Creating Parameters .............................................. 237 Cubic and Quartic Stretch Constants ..............245
The Elements Table............................................... 238 Type 2 (-CHR-) Bending Force Parameters for C-C-
Symbol ............................................................238 C Angles ..........................................................245
Covalent Radius ..............................................238 Stretch-Bend Parameters .................................246
Pattern .............................................................238 Sextic Bending Constant .................................246
Color ...............................................................238 Dielectric Constants ........................................246
Atom Types ........................................................... 238 Electrostatic and van der Waals Cutoff Parameters
Name ...............................................................238 246
Symbol ............................................................238 MM2 Atom Types ................................................. 246
van der Waals Radius .....................................239 Atom type number ..........................................247
Atom Type Number ........................................239 R* ....................................................................247
Charge .............................................................239 Eps ...................................................................247
Maximum Ring Size .......................................239 Reduct .............................................................247
Rectification Type ...........................................239 Atomic Weight ................................................247
Geometry ........................................................239 Lone Pairs .......................................................247
Number of Double Bonds, Triple Bonds, and Delo- Torsional Parameters............................................. 248
calized Bonds ..................................................240 Dihedral Type .................................................248
Bound-to Order ...............................................240 V1 ....................................................................248
Bound-to Type ................................................240 V2 ....................................................................248
Substructures ......................................................... 240 V3 ....................................................................249
References ............................................................. 240 Record Order ...................................................249
Reference Number ..........................................241 Out-of-Plane Bending ........................................... 250
Reference Description .....................................241 Bond Type .......................................................250
Chem3D Contents • vii

Force Constant ................................................250
Record Order ..................................................250
VDW Interactions ................................................. 250
Record Order ..................................................251
Appendix I: File Formats ..........253

Contents
Editing File Format Atom Types .......................... 253

Name ...............................................................253
Description ......................................................253
File Format Examples ........................................... 254
Alchemy File ..................................................254
FORTRAN Formats................................... 255
Cartesian Coordinate Files ..............................255
Atom Types in Cartesian Coordinate Files 255
The Cartesian Coordinate File Format....... 255
FORTRAN Formats................................... 259
Cambridge Crystal Data Bank Files ...............259
Internal Coordinates File ................................260
Bonds ......................................................... 262
FORTRAN Formats................................... 262
MacroModel ...................................................263
FORTRAN Formats................................... 264
MDL MolFile .................................................264
Limitations ................................................. 266
FORTRAN Formats................................... 266
MSI MolFile.......................................................... 266
FORTRAN Formats................................... 270
MOPAC ..........................................................270
FORTRAN Formats................................... 272
Protein Data Bank Files ........................................ 272
FORTRAN Formats................................... 273
ROSDAL ........................................................275
SMD ................................................................275
SYBYL MOL File ..........................................278
FORTRAN Formats................................... 280
SYBYL MOL2 File ........................................280
FORTRAN Formats................................... 283
Index
viii • Contents Chem3D

Introduction
About Chem3D When Gaussian is correctly installed, Chem3D
communicates with it and serves as a graphical front
Chem3D is an application designed to enable end for Gaussian’s traditionally text-based input and
scientists to model chemicals. It combines powerful output.
building, analysis, and computational tools with a Chem3D is compatible with Gaussian 98 for
easy-to-use graphical user interface, and a powerful Windows and Macintosh. Windows requires the
scripting interface. 32-bit version of Gaussian.
Chem3D provides computational tools based on
molecular mechanics for optimizing models, About This User’s Guide
conformational searching, molecular dynamics, and
This manual describes Chem3D for Windows and
calculating single point energies for molecules.
Macintosh operating systems. Illustrations are taken
from both platforms, so may differ from what you
About CS MOPAC see on your screen.
CS MOPAC is an implementation of MOPAC, the This guide assumes you are familiar with your
well known, semi-empirical modeling application, computer’s operating system. For details about
that takes advantage of the easy-to-use interface of using your operation system, refer to the user
Chem3D. CS MOPAC includes MOPAC 2000, the documentation provided with it.
latest version supported by Fujitsu Corporation and
MOPAC’s author, Dr. James Stewart. Additional Information
There are two versions of CS MOPAC:
Additional Chem3D information is available as
• The standard version (Std) follows:
• The professional version (Pro) • The original MOPAC manual, in PDF format,
MOPAC Std allows you to perform simple energy on your CD-ROM.
minimizations. MOPAC Pro adds advanced • A Quick Reference card at the back of this
functionality, such as computing properties and manual.
more advanced energy minimizations.
• Online Help.
About Gaussian • CambridgeSoft Web Pages.
Gaussian is—according to its own manual— “a
connected system of programs for performing a
Quick Reference Card
variety of semi-empirical and ab initio molecular The Chem3D Quick Reference Card is in the back of
orbital (MO) calculations.” Gaussian is not included the manual. The card provides a summary of the
with CS Chem3D, but is available separately from commands and features for each application. Use
Gaussian, Inc., Suite 230, Carnegie, PA 15106 USA. the Quick Reference cards when you perform the
Phone: 412-279-6700, Fax: 412-279-2118, tutorials in “Chapter 2: Tutorials.” because the card
E-mail: info@gaussian.com, contains information about the parts of the interface.
Worldwide Web: www.gaussian.com
Chem3D Introduction • 1
Online Information CambridgeSoft Web Pages
Chem3D provides the following types of online The following table contains the URLs of web pages
information: related to Chem3D.
Administrator
• Online Help—An online version of this guide.

For information
• Context-sensitive Help—Displays Help topics about … Access …
related to user interface objects.
• ToolTips—Displays a short description of user Technical Support http://www.camsoft.com/
interface objects. support/
Online Help Software http://sdk.camsoft.com/

Developer’s kit
To access the online Help:
• From the Help Menu, choose Help Contents or Active X control http://sdk.camsoft.com/
click .
A web browser is required to view the Help. Purchasing http://store.camsoft.com/
You can use Internet Explorer version 4.0 or CambridgeSoft
greater or Netscape Navigator version 4.0 or products and
greater. chemicals
ToolTips Conventions
To access ToolTips:
This guide uses the following conventions:
• Point at an item in the Toolbar or Tool palette.
indicates a feature is available only in the
A description of the item appears. Ultra version of Chem3D.
Context-Sensitive Help indicates a feature is available only in the

Pro and Ultra versions of Chem3D.
To access context-sensitive Help:
• Do one of the following: NOTE: Notes are used throughout this User’s
Guide to highlight information that may be out of
context to the current discussion.
For Help Do this …
on …
Terminology
interface a.Press Shift-F1 or click . The following terminology is used in this guide:
objects
b.Click any menu item or tool. • Point—Move the mouse until the pointer is
over the item you want.
dialog boxes a.Click . • Press—Push down on a keyboard key.
• Click—Press and release the mouse button.
b.Click in the dialog box.
• Double-click—Click the mouse button twice in
Information about the selected item appears. rapid succession.
2 • Introduction Chem3D
• Drag—Hold down the mouse button, move the
mouse, and release the mouse button.
• Select—Highlight an object or choose an
option. Selecting an item does not start an
action, it marks the item upon which you want
to act or provide information.
• Deselect—Removing the highlight from,
canceling, or clearing a selection.
• Choose—Select a command from a menu,
click a Toolbar button, or click a button.
Choosing an item performs a command.
• Key-click—Hold the specified Key and click
the mouse button. For example, Shift+click
means hold down the Shift key and click the
mouse button.
• Key-drag—Hold down the specific Key and
drag a selection. For example, Shift+drag
means hold down the Shift key and drag the
pointer.
Installation/System
Requirements
To install Chem3D with CS MOPAC, see the Read
Me document that came with your software.
Late-breaking news about installation is contained
in the Read Me file on your installation CD-ROM.
TheWindows system requirements are as follows:

• Windows 95, 98 or NT 4.0
• Pentium processor
• 32 MB RAM
Chem3D Introduction • 3
Administrator
4 • Introduction Chem3D
Chapter 1: Chem3D Basics
Starting Chem3D Graphical User Interface
Start Chem3D in one of the following ways: The Graphical User Interface (GUI) is the part of
Chem3D that you interact with in order to perform
• From the desktop, double-click the Chem3D
tasks. The GUI consists of a model window, a
icon. messages window, a table window, the movie
• From the Start menu, point to Programs, controller, a tools palette, menus and commands,
and then choose CSChem3D. and dialog boxes. The Chem3D GUI is shown
below.
Chem3D opens and a new (empty) model
window appears.
Model window Model Tables area

Title bar
Menu bar
Toolbar
Status bar
Tools Palette
Movie Controller
Magnification
controls
Height bar
Expansion
button
Messages window Rotation bars
Chem3D Chapter 1: Chem3D Basics • 5

Model Window The Messages Window
The Model window is the work space where you do Contains messages associated with a model. The
your modeling. The model window contains the following table describes the Messages window
workspace, the status bar, and the rotation bars. If controls.
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there is textual information about the model, it

appears in the Messages window. Object Description
The following table describes the objects in the
Model window. Expansion button Shows or hides the
Messages window.
Object Description First button Displays the first
message associated with
Model area The workspace where a the model.
molecular model is viewed,
built, edited, or analyzed. The Previous button Displays the message
origin of the Cartesian axes before the current
(0,0,0) is always located at the message.
center of this window, regardless
Next button Displays the message
of how the model is moved or
after the current
scaled. The Cartesian axes do not
message.
move relative to the window.
Last button Displays the last
Status bar Displays information about the message associated with
active frame of your model and the model.
about hidden atoms in your
model. Height bar Drag this bar to change
the height of the
Rotation bars Rotates a model around different Messages window.
axes, depending on which atoms
are selected.
Title bar Displays the model file name.
Menu bar Contains menus of tasks you can

perform on a model.
6 • Chapter 1: Chem3D Basics Chem3D

The Movie Controller The Tools Palette
The Movie Controller contains buttons for The Tools palette contains tools that allow you to
recording and replaying frames and for starting and create and manipulate models. The tools are shown
stopping analyses. The following table describes below.
the movie controller
Select tool
Object Description
Trackball tool
Start button Plays a recorded movie.
Single Bond tool
Stop button Stops a movie, recording
or computation. Double Bond tool
Record button Creates a movie of Triple Bond tool

subsequent rotations.
Uncoordinated Bond tool
Slider Displays the position of
Text Building tool
the current frame of a
movie. Drag the slider to
Eraser tool
move to a specific frame.
For detailed descriptions of the tools see “Building
Magnification Buttons with Tools” on page 46.
When the movie controller is displayed, the
magnification buttons are available. The The Model Table Area
magnification buttons allow you to magnify or
The Model Table area displays information about a
reduce the model.
specific model. You can display one of the following
The following table describes the magnification measurements tables in the area:
buttons.
• Measurements
Button Description • Groups

• Cartesian Coordinates
Reduce button Reduces model size.
• Internal Coordinates
Click once to reduce by
10%. Click and hold to Model tables contain information that describes
reduce continuously. information in a model. For example, the bond
lengths, bond angles, dihedral angles and other
Magnify button Enlarges model size. data. This information is unique to the model and
Click to magnify by controlled by Chem3D.
10%. Click and hold to For more information, see “Showing and Hiding
reduce continuously. Model Tables” on page 13.

The Measurements table displayed in the Model
Table area is shown below: Table Element Description
Field Name Identifies the type of
Column Divider Field Name Cell information in the cells with
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which it is associated.
Row Count
Column Divider Used to change the width of
Column the column by dragging.
Heading
Cell Contains one value of one
Record field in a record. All records
Selector in a given table contain the
same number of cells.
Model Building Basics

Chem3D applies the settings you select and the
parameters from external tables as you create
The following table describes the elements of the models.
Measurement table.
The Settings Dialog Box
Table Element Description
The Settings dialog box allows you to configure
Row Count Displays the number of rows settings for your model. You can open the Settings
and the type of data in the dialog box and leave it open so you can change
table. settings while you work.
Column Heading Contains field names To open the Settings dialog box:
describing the information in • From the View menu, choose Settings.
the table.
The Settings dialog box appears:
Record Selector Used to select an entire
record. Clicking a record
selector highlights the
corresponding atoms in the
model window.

The settings are organized into control panels. To To specify the rendering type, atom fill pattern, and
select a control panel, choose it from the drop-down color:
menu at the top of the Settings dialog box. • In the Settings dialog box, choose Model
Display, and then select the desired settings.
Default Settings
To specify the display of serial numbers and
If you make changes to settings when a model is
element symbols, do one of the following:
open, and then save the model in Chem3D format,
all the settings are saved with the model. To use the • In the Settings dialog box, choose Atom
same settings when you create new models: Labels, and then select Element Symbols and
• From the File menu, choose Set Default Serial Numbers.
Settings. • With an atom selected, from the Object menu,
The default settings are stored in the point to Show Element Symbols or Show
Preferences file. Atom Labels, and then choose Show.
Stationery and Templates Atom Labels

Chem3D provides Stationery (Macintosh) or An atom label describes the display of element
Templates (Windows) with pre-configured symbols and serial numbers.
settings.You can save settings to create your own The serial number for each atom is assigned in the
Stationery (Macintosh) or Templates (Windows). same order that you build. However, you can
For more information see “Saving Models as reserialize the atoms. For more information see
Templates” on page 43. “Setting Serial Numbers” on page 59.
The element symbol comes from the Elements
Model Display table. The default color and pattern used for an
The model of ethane shown below displays the element are defined in the Elements table. For more
cylindrical bonds display type (rendering type) with information, see “Coloring by Element” on page
the element symbols and serial numbers for all 78.
atoms.

Model Data The model data changes to reflect the atoms that are
selected in the model. For example, the illustration
If you point to an atom, information about the atom below shows the information displayed when three
appears. contiguous atoms H(3)-C(1)-C(2) are selected. This
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The following illustration shows the information information includes the atom you point to, its atom
that appears when you point at C(1). By default, type, the atoms in the selection, and the angle.
this information includes the element symbol, serial
number, atom type, and formal charge.
If you select four contiguous atoms the dihedral

The model data changes when you point to a bond angle appears in the model data. If you select two
instead of an atom. For example, in the illustration bonded or non-bonded atoms, the distance between
below, the information about the bond between those atoms appears.
C(1) and C(2) is displayed. To specify the information that appears:
• In the Settings dialog box, choose Pop-up
Information, and then select the information to
appear.
Atom Types
Atom types contain much of the Chem3D chemical
intelligence for building models with reasonable 3D
geometries. If an atom type is assigned to an atom,
you can see it in the model data when you point to
it. In the previous illustration of pointing
information, the selected atom has an atom type of
“C Alkane”.

An atom that has an atom type assigned has a Bond Lengths and Bond Angles
defined geometry, bond orders, type of atom used to
You can apply standard measurements
fill open valences (rectification), and standard bond
automatically (bond lengths and bond angles) as
length and bond angle measurements (depending on
you build or later. Standard measurements are
the other atoms making up the bond).
determined using the atom types for pairs of bonded
The easiest way to build models uses a dynamic atoms or sets of three adjacent atoms.
assignment of atom types that occurs as you build.
For example, when you change a single bond in a
model of ethane to a double bond, the atom type is
Internal and External
automatically changed from C Alkane to C Alkene. Tables
In the process, the geometry of the carbon and the Chem3D provides two types of tables:
number of hydrogens filling open valences changes.
• Internal model tables—Contain information
You can also build models without assigning atom
about a specific model. Model tables are
types. This is often quicker, but certain tasks, such
displayed in the Chem3D window as described
as rectification or MM2 Energy Minimization, will
also correct atom types because atom types are in “The Model Table Area” on page 7.
required to complete these tasks. • External tables—Contain information used by
all models. The external tables appear in a
To assign atom types as you build:
separate window, called the CS Table Editor,
• In the Settings dialog box, choose Building, described in “The Table Editor” on page 11.
and then select Automatically Correct Atom
Types. The Table Editor
Atom type information is stored in the Atom Types External tables, managed by the Table Editor, store
table. To view the Atom Types table: information that Chem3D uses to construct models,
• From the View menu, choose Atom Types. perform computations and display results.
Information used to build and perform
Rectification computations are called parameters. Parameter data
are not unique to any particular model window, but
Rectification is the process of filling open valences
are global data called upon by Chem3D as needed
of the atoms in your model, typically by adding
to build and work with models. For more
hydrogen atoms.
information about parameter tables, see
To rectify automatically as you build, do one of the “.”
following:
Examples of external tables are:
• In the Settings dialog box, choose Building,
• Elements, Atom Types, and Substructures
and then select Automatically Rectify.
tables that you use to build models.
• In the Tools menu, choose Rectify.
• Torsional Parameters tables that are used by
Chem3D when you perform an MM2
computation.
• Tables that store data gathered during Dihedral
Driver conformational searches.

To view an external table:
Element Description
• From the View menu, choose the table to view.
The Table Editor window opens, displaying the VDW radius (van Used to specify the size of
der Waals radius) atom balls and dot surfaces.
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selected table.
The Atom Types table where the C Alkane atom NOTE: The space filling
type is highlighted is shown below. model display is set in the
Model Display control panel.
The appearance of VDW dot
surfaces is specified for the
entire model in the Atoms
Display control panel, or for
individual atoms using the
Show Dot Surfaces command
in the Object menu.
Atom type number Used for cross-referencing

data in other parameter tables.
The following table describes the elements of the These parameter tables may
Atom types table. have measurements
specifying standard (optimal)
Element Description bond lengths and angles used
for building your models, and
Symbol fields Contains the element symbol parameters, such as force
associated with the atom type. constants, used for
This symbol links the Atom performing MM2
Type table and the Elements computations.
table. The element symbol is
used in atom labels and when For example, C Alkane has an
you save files in file formats atom type number of “1” and
that do not support atom Hydrogen has an atom type
types, such as MDL MolFile. number of “5”. In the Bond
Stretching parameters table
shown below, the
carbon-hydrogen bond in
ethane is specified as a “1-5
bond”. The ± field specifies
the formal charge of the atom
type.
Rectification type Specifies the type of atom

that is used to fill the open
valences of an atom during
rectification.

Bond Length
Element Description
The Bond Stretching parameters table shows the
Geometry Indicates the number of bond distance information used for a model of
bonds that the atom type must ethane with C Alkane and H atom types is shown
have and the geometry of the below. Bond Type 1-1 refers to the bond between
bonds around the atom type. two C Alkane atoms (atom type number 1) and
Bond Type 1-5 refers to the bond between C Alkane
Bound-to type Specifies the atom type that (atom type number 1) and Hydrogen (atom type
this atom must be bound to. If number 5).
there is no restriction, this
field is empty.
Bound-to order Specifies the order of the

bond acceptable between this
atom type and the atom type
specified in the bound-to
type.
For example, for

“C Carbonyl”, only double
Bond Angles
bonds can be formed to
bound-to type “O Bond angle information displayed for a selection of
Carboxylate”. If there is no three contiguous atoms using the standard
bound-to type specified, this measurement taken from the Angle Bending
field is not used. parameters table, including the 3 and 4-membered
Ring Angle Bending parameters tables.
Standard Measurements Showing and Hiding Model
Whenever there is more than one atom in the model
window, the bond lengths and angles between atom
Tables
types in the model are found by referencing the You can display or close the tables that display
bond stretching and angle bending parameters. information about the model.
Standard measurements are the optimal (or To show a Model Table, do one of the following:
equilibrium) bond lengths and angles between
atoms based on their atom type. The values for each • From the Analyze menu, point to Show
particular atom type combination are actually an Measurements, and then choose a table to
average for many compounds each of which have view.
that atom type (for example, a family of alkanes). • From the Tools menu, point to Show Model
Standard measurements allow you to build models Table, and then choose the table to view.
whose 3D representation is a fair approximation of
the actual geometry when other forces and
interactions between atoms are not considered.

To close a Model Table, do one of the following: Using Model Tables to
• From the Tools menu, point to Show Model Manipulate Models
Table, and then deselect the table.
You can use the records in the Measurements table
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• Drag the left edge of the Model Table to the to manipulate the corresponding atoms in the
right edge of the Model Window. model. For example, if you click any of the bond
records the corresponding atoms in the model are
The Measurements Table selected.
The Measurements table displays all of the different If you edit the Actual field, you change the value in
types of measurements: bond lengths, interatomic the model, and see atoms in the model move.
distances, bond angles, and dihedral angles.
If you edit the Optimal value, you change the
An example of a Bond Length measurement table is measurement or apply a constraint. These values
shown below: are used only in Clean Up Structure and MM2
computations.
Model Coordinates
Each of the atoms in your model occupies a
position in space. In most modeling applications,
there are two ways of representing the position of
each atom: internal coordinates and Cartesian
coordinates. Chem3D establishes internal and
Cartesian coordinates as you build a model.
Internal Coordinates
Internal coordinates for a model are often referred
to as a Z-matrix (although not strictly equivalent),
and are the most commonly used coordinates for
The Actual field contains model-specific preparing a model for further computation.
information. The Optimal field contains standard Changing a Z-matrix allows you to enter relations
measurement values from the bond stretching and between atoms according to angles and lengths.
angle bending parameter tables.
You can edit the values within the table, or move
Deleting Measurement Table Data atoms within the model and use the Set Z-matrix
commands in the Object menu.
You can isolate information in the Measurements
table by deleting the records that you do not want to Dialog boxes control some of the fields in the
view. Internal Coordinates table. For example, if you
click the Angle Type field for an atom, a dialog box
To delete records: containing three options appears, in which you
• Select the records and from the Edit menu, select the angle type.
choose Clear.
Deleting records in a Measurements table does
not delete the corresponding atoms.

Below is an example of the internal coordinates An example of the Cartesian coordinates for ethane
(Z-matrix) for ethane: is shown below.
Cartesian Coordinates
Cartesian coordinates are also commonly accepted
as input to other computation packages. They Customizing the User
describe atomic position in terms of X-, Y-, and
Z-coordinates relative to an arbitrary origin. Often, Interface
the origin corresponds to the first atom drawn. Chem3D allows you to customize the GUI using
However, you can set the origin using commands in the Settings dialog box, with scripts, or with OLE
the Object menu. automation.
Instead of editing the coordinates directly in this
table, save the model using the Cartesian Changing the Font and Font
Coordinates file format, and then edit that file with
a text editor. If you do edit coordinates in the table,
Size
turn off Automatic Rectification and Apply To set the font that appears in a model window:
Standard Measurements in the Building control
panel while you edit so that other atoms are not 1. From the View menu, choose Settings.
affected. The Settings dialog box appears.
2. Select Text from the drop-down menu.
3. In the Text control panel, choose the font and

font size.
The script is executed.

OLE Automation If you want to … Then choose …
OLE automation allows you to control certain
aspects of Chem3D from other applications, such as Organize all icons for Arrange Icons.
minimized windows as a
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Visual Basic and Microsoft Excel, using macros.

The library of functions available for use in a macro row at the bottom of the
are listed in “Appendix G: Automation.” application window
In order for another application to have access to
Chem3D, you must link the Chem3D library to the Closing Chem3D
application initiating the macro. The Chem3D
library is stored in the file “Chem3D.tlb”. In Quitting an application frees up the memory the
addition, we also provide a header file, application uses so that other applications can have
“Chem3D.h”, for use by C/C++ programmers. Both more available to them.
of these files are installed with the Chem3D To close Chem3D:
software. For information about creating macros, • Macintosh: From the File menu, Choose Quit
see the documentation for the application where Chem3D.
you are writing the macro.
• Windows: From the File menu, choose Exit
The Window Menu Chem3D.
(Windows) A message appears asking whether you want to

save the model before closing the window.
The Window menu lists all open Chem3D
documents. The document you choose from the
Windows menu becomes the active window.
The Window menu contains standard Windows
commands that enable you to organize your
document windows and icons within the
Application window as follows:
If you want to … Then choose …
Arrange open windows in an Cascade.

overlapping sequence with
their title bars visible. Click a title bar to
switch to that
window.
Resize all open windows Tile.

and display them in a
horizontal row.

Tutorial 1: Building 2. Point in the model window, click-drag to the
right and release the mouse button.
Models with the Bond A model of ethane appears. When you rotate the
model in a later step, you will see the other
Tools hydrogens.
The following tutorial introduces model building
with Chem3D.
To build a model:
1. Start Chem3D.
An untitled model window appears as the active
window.
2. From the View menu, choose Settings.

The Settings dialog box appears. NOTE: By default, the hydrogens are
automatically added using the Automatic
Rectification setting.
3. Drag the lower right corner of the window

diagonally to the left to reduce its size.
To see the three-dimensionality of your model you
can perform free-hand rotations using the Trackball
Tool. The Trackball Tool mimics a sphere in which
your model is centered. You can rotate your model
by rotating the sphere.
To rotate the model with the Trackball tool:
1. Click the Trackball tool .
Depth Ratio Slider 2. Point near the center of the model window and
hold down the mouse button.
3. Drag the Depth Ratio slider to the left until the
3. Drag the cursor in any direction to rotate the
value is zero. model.
Draw ethane using a bond tool.
1. Click the Single Bond tool .
Chem3D Chapter 2: Tutorials • 17

A circle appears while you are dragging. An information box appears next to the atom
Dragging within the circle allows you to rotate you are pointing at. The first line contains the
around the X-and Y-axes. atom label. In this case, you are pointing to
C(1). The second line contains the name of the
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atom type, C Alkane.
You can also use the trackball to rotate your

model around the Z-axis by dragging the
pointer around the outside of the trackball
circle. To avoid XY-rotation, position the
pointer near the edge of the model window
3. Move the pointer over the C-C bond to display
before dragging to ensure that dragging begins
its bond length and bond order.
at a position outside the circle.
4. Release the mouse button at an orientation close

to the following illustration.
Display information about angles by selecting

several atoms.
Examine the atoms and bonds in the model using the 1. Shift-click C(2), C(1) and H(7).
Select tool.
2. Point at any of the selected atoms or bonds.
1. Click the Select tool .
The angle for the selection appears.
2. Move the pointer over the far left carbon.
NOTE: Depending on how much you rotated

the model, the far left carbon might be C(2).
18 • Chapter 2: Tutorials Chem3D

To display information about contiguous atoms: 3. From Object menu, point to Set Bond Order,
and then choose Single.
1. Hold the Shift key and select four contiguous
atoms. The bond order is reduced by one.
Hide the hydrogens to make it easier to build.
2. Point at any portion of the selection.
• From the Tools menu, deselect Show H’s and
The dihedral angle formed by those four atoms
Lp’s.
is displayed.
The hydrogens are hidden. The number of
hidden atoms appears in the Status bar.
Change the ethane model to an ethylene model.

Add more atoms to the model:
1. Click the Double Bond tool .
1. Click the Single Bond tool .
2. Hold down the mouse button over C(1) and drag
2. Drag upward from the left carbon.
to C(2).
3. Another C-C bond appears.
3. Point to the bond.
The bond length decreased and the bond order
increased.
4. Continue adding bonds until you have 6

carbons as shown below.
Continue to build on this model to build

cyclohexane.
2. Click the double bond.

Create a ring: All the atoms and bonds in view are selected.
1. Drag from one carbon onto another.

The pointing information appears when you
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drag properly.
3. From the Object menu, point to Show Serial

Numbers, and then choose Show.
4. From the Object menu, point to Show Element

2. Release the mouse button to close the ring. Symbols, and then choose Show.
NOTE: These commands apply only to the

selected atoms. Any new atoms you draw are
not labeled.
The serial numbers that appear do not reflect a

normal ordering because you started with a
smaller model and built up from it.
5. Click in white space within the model window

Add serial numbers and atom labels.
to deselect all the atoms and bonds.
2. Drag diagonally across all the atoms and bonds

and release the mouse button.
You can reserialize the atoms as follows:
1. Select the Text Building tool .
2. Click the first atom.

A text box appears on the atom. To find the energy minimum:
1. From the MM2 menu, choose Minimize Energy.
2. Leave the values in the dialog box as they are

and click Run.
After the minimization is complete:
2. Select a directory in which to save the file.

3. Type the number you want to start at (1 for this
example). 3. Type “tut1” in the text box at the bottom of the
dialog box.
4. Press Enter or Return.
The first atom is renumbered as (1). 4. Click Save.
5. Double-click each of the atoms in the order you 5. Click the model window to activate it.
want them to be numbered. 6. From the File menu, choose Close Window.
Each time you double-click an atom to serialize
it, the new serial number is one greater than the Tutorial 2: Building
serial number of the previously serialized atom.
Models with the Text
6. From the Tools menu, choose Show H’s and Building Tool
Lp’s and examine the model using the
Trackball Tool.
This tutorial illustrates alternative methods to build
models using the Text Building Tool.
The hydrogens appear as far apart as possible.
Double-clicking with any other tool selected has the
Because you built the structure by using bond tools, same effect as single-clicking with the Text Building
you may have distorted bond angles and bond tool. Triple-clicking has the same effect as
lengths. double-clicking with the Text Building tool.
To correct for distorted angles and lengths:
NOTE: Element symbols and substructure names
1. From the Edit menu, choose Select All. are case sensitive.
All of the atoms in the model are selected.
Open a file:
2. From the Tools menu, choose Clean Up
Structure. 1. From the File menu, choose Open.
To locate an energy minimum for your structure 2. Locate and select the file, tut1, that you created
which represents a stable conformation of your in the previous tutorial.
model, you can use the Minimize Energy command
in the MM2 menu. 3. Click Open.
For more information about energy minimization
see “Chapter 9: Computation Concepts.”

Replacing Atoms Using Labels to Create Models
To change one element into another: You can also create models by typing atom labels
(element symbols and numbers) into a text box.
1. Click the Text Building tool .
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NOTE: You can use all elements in the

2. Click a hydrogen atom attached to C(1). periodic table building. View the elements by
A text box appears. choosing Elements from the View menu. View the
Atom Types by choosing Atom Types from the View
3. Type C. menu.
Build the model of 4-methyl-2-pentanol shown
The hydrogen attached to C(1) is changed to a
below:
carbon. The valence is filled with hydrogens to
form a methyl group because Automatic CH 3
Rectification is turned on. CH 3 CH CH 2 CH CH 3
OH
Replace two more hydrogens using an alternative
method:
1. From the File menu, choose New Model.
• Double-click two more hydrogens to change
them to methyl groups. 2. Click the Text Building tool .
To refine the structure to an energy minimum to take 3. Click in the empty space in the model window.
into account the additional interactions imposed by A text box appears where you clicked.
the methyl groups:
• From the MM2 menu, choose Minimize Energy 4. In the text box, type the labels as if you were
and click Run. naming the structure: pick the longest chain of
carbons as the backbone, and specify other
When the minimization is complete:
groups as substituents. Enclose substituents in
1. From the File menu, choose Save As. parentheses after the atom to which they are
attached.
2. Type tut2a.
Type CH3CH(CH3)CH2CH(OH)CH3.
4. Click Save. Refine the model as follows.
Save a copy of the model using a different name: • From the Tools menu, choose Clean Up
Structure.
If you want a more accurate representation of a low
2. Type tut2b. energy conformer, optimize the geometry of the
model as follows:
• From the MM2 menu, choose Minimize Energy
4. Click Save. and click Run.

To specify text equivalent to the structure of Over 200 substructures are pre-defined in Chem3D.
1,2-dimethyl cyclopentane shown below: These substructures include the most commonly
used organic structures.
H2
C
H2C CH 2
NOTE: You can view the available
substructures by choosing Substructures from the
CH CH
View menu. Text typed in the text box is case
CH 3CH 3 sensitive. You must type it exactly as it appears in the
Substructures table.
2. Click the Text Building tool . Build a model of nitrobenzene:
3. Click in the empty space in the model window. 1. From the File menu, choose New Model.
4. Type CH(CH3)CH(CH3)CH2CH2CH2. 2. Click the Text Building tool .
5. Press Enter or Return. 3. Click the empty space in the model window.
The trans-isomer appears. 4. Type Ph(NO2) in the text box.
6. From the Tools menu, choose Clean Up 5. Press Enter or Return.

Structure.
A model of nitrobenzene appears. The
You cannot specify stereochemistry when you build substructure in this example is the phenyl
models with labels. The structure of 1,2-dimethyl group. Substructures are defined with specific
cyclopentane appears in the trans conformation. attachment points for other substituents. For
To obtain the cis-isomer: phenyl, the attachment point is C(1).
1. Click the Select tool . Build another protein model:
2. Click C(1). 1. From the File menu, choose New Model.
3. From the Object menu, choose Invert. 2. Click the Text Building tool .
The cis-isomer appears. You can rotate the 3. Click an empty space in the Model window.
molecule to see the differences between the
A text box appears.
isomers after you invert the molecule.
4. Type H(Ala)12OH.
Using Substructures
Using labels are useful for simple structures.
However, if you make larger, more complex 6. Rotate this structure to see the alpha helix that
structures, use a combination of labels and forms.
pre-defined substructures.

Change the model display type: 4. Type tut3.
1. From the View menu, choose Settings. 5. Click Save.

The Settings dialog box appears. 6. From the View menu, choose Settings.
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2. Select Model Display and choose Wire Frame The Settings dialog box appears.
as the Model Type.
7. Slide the Depth Ratio slider to the left until the
3. Rotate the model so you are viewing it down the value is zero.
center of the helix as shown below:
9. Click an empty space in the model window.
10.Type CH3CH3.

A model of ethane appears.
View the Measurements table:
1. From the Analyze menu, point to Show

Measurements, and then choose Show Bond
4. In the Settings dialog box, choose Ribbons as Lengths.
the Model Type to see an alternative display
commonly used for proteins.
Angles.
The Measurements table appears with the
information you chose. The measurements in
the Actual and Optimal columns are nearly
Tutorial 3: Examining identical. The Actual column represents the
Conformations measurements for the model in the active
window. The Optimal measurements (for bond
This tutorial uses steric energy values to compare
lengths and bond angles only) represent the
two conformations of ethane. The conformer with
standard measurements in the Bond Stretching
the lower steric energy value represents the more
likely conformation. and Angle Bending parameter tables.
Build ethane:
1. From the File Menu, choose New Model.
2. From the File Menu, choose Save As.

Only the X- and Y-rotation bars are active.
These Rotations bars are always active because
they are not dependent on any atoms being
selected.
3. Click the Y-Axis rotation bar and drag to the

left.
The pointer appears as a hand, and the Rotation
bar is highlighted.
As you drag, the status bar shows details about
the rotation.
4. Stop dragging when you have an end-on view

of ethane.
This staggered conformation, where the
hydrogens on adjoining carbons are a maximum
distance from one another (which represents the
All atoms and bonds are initially selected. To global minimum on a potential energy plot)
deselect them: represents the most stable conformer of ethane.
1. Click the Select tool . .
2. Click in the white space in the Model window.

Chem3D shows the most common conformation of
a molecule. you can rotate parts of a molecule, such
as a methyl group, to see other conformations.
Rotate the orientation of the model to obtain a
Newman projection (viewing the model along a
bond.) This orientation helps clarify the
conformations of ethane.
To rotate a methyl group on a ethane model: To examine this result numerically, calculate the
steric energy of this conformation and then compare
1. Ensure that Show Status Bar is selected on the
it to a higher energy (eclipsed) conformation.
Tools menu.
The Status Bar appears above the model. 1. From the MM2 menu, choose Compute
Properties.
2. Ensure that Show Rotation Bars is selected on
The Compute Properties dialog box appears.
the Tools menu.
The Rotation Bars appear around the edges of 2. Click Run.
the model window. The Messages contoller appears beneath the
model window. The Steric Energy results
appear. The last line displays the total energy.

To display several messages at once, click the 2. From the Object menu, point to Show Element
expansion triangle . Symbols, and then choose Show.
You will also save the frames you create during the
rotation as individual frames that you can later
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replay as a movie.
To begin recording:
1. Make sure that Show Movie Controller is

selected on the Tools menu.
The Movie Controller appears below the model
window.
2. Click Record in the Movie Controller.
NOTE: The values of the energy terms shown are To rotate the dihedral angle, rotate C(1) and all its
approximate and may vary slightly based on the type bonded atoms, while C(2) remains stationary:
of processor used to calculate them.
1. Click C(1).
To obtain the eclipsed conformer of ethane, rotate a

NOTE: If C(2) is on top instead od C(1), click C(2)
dihedral angle (torsional angle). Rotating a dihedral
in this step instead of C(1).
angle is a common way of analyzing the
conformational space for a model.
To view dihedral angles:
• While looking at the status bar, drag the
1. From the Analyze menu, point to Show Internal rotation bar (left, vertical rotation
Measurements, and then choose Show bar) until you have completed a rotation of
Dihedral Angles. -60°.
All of the model’s dihedral angles are added to • Double-click the rotation bar and type the
the bottom of the Measurements table. number of degrees you want to rotate the
model.
2. Click the H(3)-C(1)-C(2)-H(8) dihedral record to
select the corresponding atoms in the model. • Type the value for the dihedral in the
Measurements table.
Although the serial numbers and element symbols
are shown in the Measurements table, they do not
appear in your model.
To help keep visual track of the atoms as you change

the dihedral angle you can display the serial
numbers and element symbols for the selected
atoms.


3. Drag the movie Controller knob to the last
frame to show the eclipsed view.
To see the animation from a different perspective:

1. Drag the Y-rotation bar to the right about 40
degrees.
To stop recording:
• Click Stop in the Movie Controller.
The status bar indicates that you are at a frame
other than Frame #1.
In the Measurements table, notice that the dihedral
for H(3)-C(1)-C(2)-H(8) is now minus 120 degrees,
2. Click Start in the Movie Controller to
as shown in the model.
play the animation again.
3. Click Stop to stop the animation.
4. Drag the Movie Controller knob to the left to

move to the last frame.
To compute steric energy:

1. From the MM2 menu, choose Compute
Properties
2. Click Run.
The final line in the Messages window appears as
follows:
To animate the dihedral rotation:
1. Click Start in the Movie Controller.

The model rotates from the staggered to NOTE: The values of the energy terms can vary
slightly based on the type of processor used to
eclipsed conformation.
calculate them.
2. Click Stop to stop the animation.

The steric energy for the eclipsed conformation (3.9 To create the model:
kcal/mole) is greater in energy than that of the
staggered conformation (~3 kcal/mole), indicating 1. Click the Single Bond tool .
that the staggered configuration is the conformer
2. Drag in the model window to create a bond.
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that is more likely to exist.
NOTE: As a rule, steric energy values should only

be used for comparing different conformations of
the same model.
3. Point to a carbon and drag upwards to create a
second bond.
To conclude the tutorial:
1. From the File menu, choose Close Window.
2. When the Do you want to save changes?

dialog box appears, click No or Don’t Save.
Tutorial 4: Searching
For Conformations
Tutorial 3 demonstrated how you can rationalize the
most likely conformer by comparing steric energy 4. Drag from the far right carbon to add another
values of different conformations. In Tutorial 4, you bond.
build on this idea and use a few more tools to see this
visually and numerically.
3. Type tut4 in the text box.
5. Click Save.
Next, you will reorient the model to get an end-on
In this tutorial, you use the Chem3D bond tools to view to vary one dihedral angle using the Object
build your model. When you use the bond tools menu.
instead of the Text Building tool, you can control the
placement of each atom. If you type
CH3CH2CH2CH3 into a text box you would get the
same model, however it would appear in the
staggered form.

To reorient the model: To generate numerical data:
1. Click the Select tool . 1. From the View menu, choose Settings.
2. Shift-click C(1) and then C(2). The Settings dialog box appears.
2. Select Movies.
3. Drag the Smoothness slider to 30 degrees per

frame.
4. Click the Model window.
5. With the C(1)-C(2) atoms selected, rotate the

C(1)-C(2) dihedral angle.
6. Click Record in the Movie Controller.

3. From the Object menu, point to Move To, and
7. Double-click the Internal rotation bar and type
then choose Move to X-Axis.
360.
The two selected atoms are reoriented parallel
The status bar indicates 12 new frames
to the X-axis.
captured, for a total of 13.
8. Click Stop .
To compute the steric energy for each frame:

Properties
2. Click Run.
3. After the calculation is complete, move to the

4. From the Object menu, point to Move To, and next frame by dragging the Movie Controller
then choose Move to Z-Axis. knob to the left.
The two selected atoms are reoriented parallel
4. Repeat step 1 and step 2 for all 13 frames.
to the Z-axis.
In the next series of steps, you rotate the dihedral 5. Click the expansion triangle in the
angle formed by the C-backbone and calculate the Message controller.
Steric Energy of each conformation. The Messages table appears, displaying several
The goal for this part of the tutorial is to demonstrate messages.
how to generate numerical data. You can plot the
In the Messages table you can see the total energy
data to determine local and global minimums that
for each frame. If you have a graphing program, you
are relevant for the rotation of a particular dihedral.
can plot the total energy versus the dihedral angle
However, the single dihedral of interest may or may
rotation.
not be known.

Tutorial 5: Transferring 3. Click the ChemDraw document window.
Information from 4. From the Edit menu, choose Paste.
ChemDraw You can also import a Chem3D model back into

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ChemDraw as a two-dimensional structure.

This tutorial demonstrates working with ChemDraw
(or ISIS/Draw) and Chem3D. The tutorial assumes 1. Click the Chem3D model window.
you are familiar with ChemDraw.
2. Rotate the benzene model to a nearly-edge-on
1. Launch ChemDraw. view using the X-axis Rotation bar.
An untitled document window appears.
2. In ChemDraw, select the Benzene Ring tool.
3. Click in the model window to place a benzene

ring.
4. Click the Select tool to select the last drawn 3. From the Edit menu point to Copy As, and then
structure. choose Copy As ChemDraw Structure.
5. From the Edit menu, choose Copy. 4. Click the ChemDraw document window.
6. Open Chem3D. 5. From the Edit menu, choose Paste.
7. From the Edit menu, choose Paste. You can now work with the pasted structure as
if it were any other ChemDraw structure.
The ChemDraw structure is converted into a 3D
representation.
Tutorial 6: Viewing
Molecular Surfaces
Frontier molecular orbital theory says that the
highest occupied (HOMO) and lowest unoccupied
(LUMO) molecular orbitals are the most important
in terms of a molecule’s reactivity. This tutorial
examines the reactivity of double bonds by looking
at the simplest molecule containing a double bond,
ethene.
To create an ethene model:

You can work with the model in Chem3D. You can 1. From the File menu, choose New Model.
also paste the model back into ChemDraw.
1. In Chem3D, from the Edit menu, choose Select
All. 3. Click in the model window.
2. From the Edit menu, choose Copy. A text box appears.

4. Type CH2CH2. These are only two of twelve different orbitals
available. The other ten orbitals represent various
5. Press Enter or Return. interactions of sigma orbitals. Only the pi orbitals
A molecule of ethene appears. are involved in the HOMO and the LUMO. Because
the HOMO and LUMO control the reactivity of a
To view the Highest Occupied Molecular Orbital
molecule, you can conclude that it is the pi bonding
(HOMO):
interactions of ethene that control its reactivity. This
1. From the Analyze menu, choose Extended is a specific case of a more general rule: pi bonds are
Huckel Surfaces. more reactive than sigma bonds.
2. From the View menu, choose Molecular

Orbitals.
Tutorial 7:
3. In the Orbital list box, select HOMO (N=6).
Mapping Properties
4. Click Show Surface.
onto Surfaces
The pi bonding orbital surface appears. NOTE: This example requires Gaussian 98. You
can also map properties onto surfaces using CS
MOPAC or Extended Hückel calculations.
The allyl radical, CH2=CHCH2·, is a textbook

example of resonance-enhanced stabilization:
H H
C C
2C CH2 H2C CH2
To examine Radicals with Spin Density surfaces:
To view the Lowest Unoccupied Molecular Orbital 1. From the File menu, choose New Model.
(LUMO):
1. In the Orbital list box, select LUMO (N=7).
3. Click in the model window.
A text box appears.
The pi antibonding orbital surface appears.
4. Type CH3CHCH2.

A molecule of 1-propene appears.
Create a radical:
1. Select one of the H6, probably one of the left

atoms in the molecule.
2. Press Delete.

A dialog box appears asking if you want to turn
off rectification. Chem3D is chemically
intelligent, and knows that in most cases carbon
atoms have four substituents. Radicals are one
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of the rare exceptions.
3. Click Turn Off Automatic Rectification.
4. From the Gaussian menu, choose Minimize

Energy.
Most of the surface is grey, indicating that there is no
5. In the Theory tab, set the Wave Function to contribution to it from unpaired electrons. The two
Open Shell (Unrestricted). areas of red centered over each of the terminal
carbons is a visual representation of the expected
6. In the Theory tab, set the Spin Multiplicity to 2. delocalization of the radical—there is some radical
character simultaneously on each of the terminal
This molecule is intended to be a radical, and setting
carbons.
the Spin Multiplicity ensures that it is.
Hide this surface:
One of the best ways to view spin density is by
mapping it onto the Total Charge Density surface. • Press Hide Surface.
This allows you to see what portions of the total
charge are contributed by unpaired electrons, or Determine the raw spin density alone, not mapped
radicals. onto the charge density surface.
To view Spin Density mapped onto Total Charge 1. From the View menu, choose Total Spin
Density Surface: Density.
1. In the Properties tab, select Molecular 2. If you are running under Windows, In the
Surfaces. Surface Type drop-down menu, choose
Translucent.
2. Press Run, and wait for the computation to
finish. When the computation is finished, the 3. Click Show Surface.
status bar will be blank. The surface appears.
3. From the View menu, choose Total Charge
Density.
4. In the Map Property drop-down menu, choose

Spin Density.
5. Click Set Isocharge and set to 0.0050.

The surface appears.

There is a large concentration of unpaired spin over partial charge on an atom, the more likely it is to
each of the terminal carbons and a small form bonds with other atoms whose partial charge is
concentration over the central hydrogen. This extra the opposite sign.
little bit of spin density is not very significant—you
could not even see it when looking at the mapped Using the theories in Extended Hückel, MOPAC, or
display earlier, but the calculations show that it is, in Gaussian, you can compute the partial charges for
fact, there. each atom. In the following example, the partial
charges for phenol are computed by Extended
Hückel.
Tutorial 8: Computing
Partial Charges 1. From the File menu, choose New Model.
To compute the charge of a molecule, the number of 2. Click the Text Building tool .
electrons contributed by each of its atoms can be
subtracted from the number of protons in the 3. Click in the model window.
nucleus of each of its atoms. Each atom of a A text box appears.
molecule contributes an integral charge to the
molecule as a whole. This integral contribution is 4. Type PhOH.
known as the formal charge of each atom.
Certain types of atoms in Chem3D deal with this
A molecule of phenol is created.
explicitly by having non-integral formal charges.
For example, the two oxygen atoms in nitro-benzene To compute Extended Hückel charges:
each have charges of -0.500 because there is one • From the Analyze menu, choose Extended
electron that is understood to be shared across the Hückel Charges.
two N-O bonds.
Messages are added to the message table listing
However, as shown above, electrons in molecules
the partial charge of each atom.
actually occupy areas of the molecule that are not
associated with individual atoms and can also be You can graphically display partial charges in the
attracted to different atomic nucleii as they move following ways:
across different atomic orbitals. In fact, bonds are a • By coloring atoms.
representation of the movement of these electrons
between different atomic nucleii. • By varying the size of atom spheres.
Because electrons do not occupy the orbitals of a • By varying the size of the dot surfaces.
single atom in a molecule, the actual charge of each
To display partial charges:
atom is not integral, but is based on the average
number of electrons in the model that are occupying 1. From the View menu, choose Settings.
the valence shells of that atom at any given instant.
By subtracting this average from the number of 2. From the pop-up menu at the top of the
protons in the molecule, the partial charge of each Settings dialog box, choose the Model Display
atom is determined. control panel.
Visualizing the partial charge of the atoms in a
3. Make sure the Color by Depth check box is
molecule is another way to understand the model's
deselected.
reactivity. Typically the greater the magnitude of the

4. From the Color pop-up menu, choose Color By 3. From the Size By pop-up menu in the Solid
Partial Charge. Spheres section, choose Size By Partial
All of the atoms are colored according to a scale Charge.
from blue to white to red. Atoms with a large
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negative partial charge are deep blue. Atoms

with a large positive partial charge are deep red.
As the magnitude of the charges approaches 0,
the color of the atom becomes paler.
In this representation of phenol, the oxygen atom

and its two adjacent atoms are large because they
have relatively large partial charges of opposite
signs. The rest of the atoms are relatively small.
You can display dot surfaces whose size is specified

by partial charge.
1. From the Size By pop-up menu in the Solid

For phenol, the greatest negative charge is on the Spheres section, choose Size By VDW Radius.
oxygen atom. The greatest positive charge is on the
adjacent carbon atom (with the adjacent hydrogen 2. Select the Show By Default check box in the
atom a close second). The rest of the molecule has Dot Surfaces section.
relatively pale atoms; their partial charges are much
closer to zero. 3. From the Size By pop-up menu in the Dot
Surfaces section, choose Size By Partial
In addition to color, you can vary the size of atom Charge.
spheres or dot surfaces by partial charge.
4. From the pop-up menu at the top of the
1. Make sure that Color By Element is selected in Settings dialog box, choose the Model Display
the Color pop-up menu. control panel.
2. From the pop-up menu at the top of the 5. From the Color pop-up menu, choose Color By
Settings dialog box, choose the Atom Display Element.
control panel.

In this representation of phenol, the oxygen atom
and its two adjacent atoms have large dot surface
clouds around them because they have relatively
large partial charges of opposite signs. The rest of
the atoms are relatively small. Their dot surfaces are
obscured by the solid spheres. If another molecule
were to react with this molecule, it would tend to
react where the large clouds are, near the oxygen
atom.

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Chapter 3: Creating, Opening, and
Importing Models
Overview
Chem3D provides the following starting points for
modeling:
• Creating a model using the Chem3D tools
• Opening an existing 3D model
• Creating a model from stationery or templates
• Importing files in other chemistry file formats
Creating a Model
To create a model: 2. Select the file to open.
• From the File menu, choose New Model. 3. Click Open.

A new model window is created with the title, The file opens as the active window.
Untitled-n.
You create the model in the window using the Switching Between Open Models
Chem3D tools. For detailed information on creating Each time you open a model, a model window
models, see “Chapter 4: Building and Editing appears. If you have opened more than one model,
Models.” the model windows are stacked. The window in
front is the active window where you can actually do
Opening an Existing File work. All open models are listed in the Window
menu.
You can open existing Chem3D files and Chem3D
To make another window active, do one of the
files created in an earlier version.
following:
To open a Chem3D model: • Click an exposed area of the window you want
to be active.
• Press Ctrl+Tab to switch between windows.
Chem3D Chapter 3: Creating, Opening, and Importing Models • 37

Creating a Model Using You can edit some of the Atom Types. Editable file
formats are indicated in the table below by an
Templates asterisk (*) after their name. For more information
about editing file formats see “Appendix B: Atom
Chem3D provides pre-configured documents as
Types.”
templates or stationery pads. To create a model
using a template:
File Format Name Extension
• From the File menu, point to Template, and
then choose a model. Alchemy* Alchemy .alc,.mol
An untitled window appears. The settings and
or models stored in the template or stationery Cartesian Cart Coords 1 .cc1
document are part of the new window. Coordinate
Cart Coords 2 .cc2
Importing a Model Cambridge CCDB, Bank, .dat,.ccd
You can open a file stored in a different file format Crystal Data
in Chem3D the same way as you open native FDAT format
Chem3D files.
ChemDraw ChemDraw .cdx,.chm
The Open dialog box appears. Connection Conn Table .ct,.con
Table
2. Select the file format to open.
Gaussian Input Gaussian Input .gjc,.gjf
Some file formats activate an Options button
when selected. You can open the file using the
Gaussian Gaussian .fchk,.fch
default options or you can click the Options Formatted Formatted
button to change the default options. See“File Checkpoint Checkpoint
Format Options” on page 39.
Gaussian Cube Gaussian Cube .cub
3. Locate the directory where the file is located
and choose the file to open. Internal Int Coords .int
4. Click Open. Coordinates*
Supported Formats for Job Description .jdf

File
Importing
The following table lists the file formats and Job Description .jdt
Windows extensions supported by Chem3D for Template
importing. For additional information about file
formats see “Exporting Models Using Different File MacroModel MacroModel .mcm,.dat,
Formats” on page 112 and Appendix I: File Formats
in online Help. MDL MolFile MDL MolFile .mol

As described in the specifications of the Cambridge
File Format Name Extension Crystal Data Bank format, bonds are automatically
added between pairs of atoms whose distance is less
MSI ChemNote* MSI .msm than that of the sum of the covalent radii of the two
ChemNote atoms. The bond orders are guessed based on the
ratio of the actual distance to the sum of the
MOPAC data file MOPAC .mop,.dat,.m. covalent radii. The bond orders, bond angles, and
p.g., .zmt the atom symbols are used to determine the atom
types of the atoms in the model.
MOPAC graph MOPAC Graph .gpt
file
Actual Distance /
Bond order Sum of Covalent Radii
Protein Data PDB .pdb,.ent
Bank
Triple 0.81
Standard SMD File .smd
Double 0.87
Molecular Data
Delocalized 0.93
SYBYL MOL* SYBYL .sml
Single 1.00
SYBYL MOL2 * SYBYL2 .sm2,.ml2
Windows Regular .wmf To select CCDB file open options:

MetaFile MetaFile 1. In the Open dialog box, click Options.
Enhanced Enhanced .emf The CCDB Options dialog box appears.

MetaFile MetaFile
File Format Options

Some file formats provide options that allow you to
include information you specify when you open the
model.
Cambridge Crystal Data Bank

The specific format of Cambridge Crystal Data
Bank (CCDB) used by CS Chem3D is the FDAT
format, described on pages 26 through 42 of the data
file specifications of the Cambridge Structural
Database, Version 1 File Specifications from the
Cambridge Crystallographic Data Centre. For
further details about the FDAT format, please refer
to the above publication or contact the Cambridge
Crystallographic Data Centre.

2. Select the appropriate option: The Cartesian Coordinates Options dialog box
appears.
If you want to … Then click …
create a model containing A Single

a single molecule without Molecule.
using the symmetry
positions in line 4 of the
CDDB file
open a model with all All Symmetries.

symmetries so that the
original molecule is 2. Select the appropriate option:
duplicated once for each
symmetry and not
If the file contains … Then click …
translated
a connection table for each By Serial Number.
open a unit cell model A Unit Cell.
atom containing serial
that contains several
numbers
packed molecules
oriented in the correct
a connection table for each By Position.
symmetries and repeated
atom that describes
and translated so that
adjacent atoms by their
every atom in each
position in the file
symmetry appears in the
unit cell
no connection table Missing.
3. Click OK. serial numbers Expect Serial

Numbers.
atom type numbers Expect Atom
To select the Cartesian Coordinate open options:
Type Numbers.
1. In the Open dialog box, click Options.
Connection Table
To select the Connection Table open options:

The Cartesian Coordinates Options dialog box 2. Select the appropriate option
appears.
open files with no Bond Proximate

explicit bonding Atoms.
information
compute atom and Compute Atom Types

bond types as the file and Bond Orders.
opens
2. Select the appropriate options: add hydrogens and Rectify Atoms.

lone pairs to fill open
To ignore the … Click … valences as the file
opens
top line in the file. Line.
3. Click OK.
first two lines of the file 2 Lines.
three lines of the file 3 Lines.

Saving Models
To save a Chem3D model:
Protein Data Bank 1. From the File menu, choose Save.
You can choose different options to open The Save As dialog box appears. The dialog
Brookhaven Protein Data Bank files (PDB). box that appears depends on the platform you
To select PDB file open options: are using.

The Protein Data Bank Options dialog box
appears.

To save a copy of a Chem3D model under a different
NOTE: Chem3D (or Chem3D molecular model, name or in a different location:
depending on your operating system) is the native
file format that Chem3D recognizes as its own. It 1. From the File menu, choose Save As.
stores all information about the model. Other file The Save As dialog box appears.
formats may drop information because of their
internal structure. For example, under Windows, 2. Type a different name or choose a new location.
saving a file as EPS will remove the chemical
significance of the connection between atoms and 3. Click Save.
bonds, and store only a picture of the model. EPS
files in Windows do not store a preview. For more Saving a Model in a Different
information about file formats, see File Format
“Chapter 8: Printing and Exporting Models.”
Save a file as a different type to export information
to other applications. For more information about
2. Type a file name.
other file formats, see “Chapter 8: Printing and
3. Select a directory in which to save the file. Exporting Models.”
To save a Chem3D model in another file format:

4. Click Save.
When you save a model in the native Chem3D 1. From the File menu, choose Save As.
file format the name of the window changes to The Save As dialog box appears.
the name that you typed.
2. Select a file format.
Saving Changes 3. Type a file name for the model.
Any new information that you add to the window is
stored in your computer’s memory (RAM) until you 4. Select a directory in which to save the model.
save it.
5. Click Save.
To save changes to a model: If you type a name that already exists for a
• From the File menu, choose Save. model that is in the same directory, the existing
The contents of the file is updated. file is replaced with the new file.
The original model in the Chem3D format
Saving a Model with a Different Name remains in the active window. The file in the
or Location new format is saved with the name and in the
Use the Save As command to save a copy of your location you specified.
model under a different name, save a copy to a
different location, or save a copy using a different
file format. Save a copy under a different name or
location to keep earlier revisions of your model.

Saving Models as Templates
You can save a model with its specific settings to
reapply the settings when you create new models.
To save a model as a template:

2. Choose Chem 3D Templ.
3. Click Save.
Discarding Recent
Changes to a Model
To retrieve the last saved version of a model:
• From the File menu, choose Revert to Saved.
The last model you saved appears. Any changes
made since the last save are lost.
To remove the last action performed:

• From the Edit menu, choose Undo.
Closing Models
When you are finished with a model you can close
the model window and file it.
To close the active window:
• From the File menu, choose Close Window.
The model in the active window closes. If you
have made any changes to this model since last
opening or saving, a message appears asking
whether you want to save the file.

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44 • Chapter 3: Creating, Opening, and Importing Models Chem3D

Chapter 4: Building and Editing Models
Overview
Chem3D enables you to build or change a model
using any of the following methods:
• Bond tools that build using carbon exclusively.
• Text Building tool that allows you to build
models using atom labels and substructures.
• ChemDraw or ISIS/Draw structures imported
from the Clipboard.
Usually, a combination of methods yields the best
results. For example, you might build a carbon
skeleton of a model with the bond tools, and then
change some of the carbons into other elements. Or 2. Select Building from the drop-down list.
you can build a model exclusively using the Text The following tables describes the Building
Building Tool. controls.
NOTE: For information on drawing phosphate

groups, see the CambridgeSoft Chem3D Technical Control Description
Support page at: http://www.camsoft.com/support/
Correct Atom Determines whether atom types
Types are assigned to each atom as
Setting the Model you build. Atom types, such as
“C Alkane” specify the valence,
Building Controls bond lengths, bond angles, and
You can control how you draw by changing options geometry for the atom.
in the Building control panel in the Settings dialog
box. The intelligent mode (the default mode) in Rectify Determines whether the open
Chem3D is active when you select all the options. valences for an atom are filled,
You can also build in a faster, less intelligent mode usually with hydrogen atoms.
by turning off one or more of the options.
Apply Standard Determines whether the
To display the Building control panel: Measurements standard measurements
associated with an atom type
are applied as you build.
The Settings dialog box appears.
Chem3D Chapter 4: Building and Editing Models • 45

Control Description
Building with Tools
The Chem3D tools palette is shown below:
Fit Model to Determines whether the entire
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Window model is resized and centered in Select Tool

the model window after a
change to the model is made. Trackball Tool
Bond Proximate Determines whether a bond is Single Bond Tool

Addition (%) created between a selection of
atoms. For more information Double Bond Tool
see “Creating Bonds by Bond
Proximate Addition” on page Triple Bond Tool
56.
Uncoordinated Bond Tool
NOTE: For more information about atom types,
Text Building Tool
standard measurements, and rectification, see
“Model Building Basics” on page 8. Eraser Tool
Building Modes The following table describes the tools.
The Building control options determine the Building Tool Name Description
Mode and the speed with which you build. The two
building modes are as follows: Select Select individual atoms and
• Intelligent Mode—Chem3D’s default building bonds by clicking. Select
mode. All building controls are selected. This multiple atoms and bonds by
mode yields a chemically reasonable 3D model Shift+clicking. Drag or
as you build. Shift+drag to select rectangular
areas containing atoms and
• Fast Mode—One or more building control are
bonds. Option+drag (Macintosh)
deselected. This mode is similar to freehand
or Alt+drag (Windows) to drag
drawing in a 2D drawing package. It provides a
along the Z- axis only.
quick way to generate a backbone structure.
When you finish building your model, you can Trackball Rotate an entire model around
create a chemically reasonable 3D model by the X and Y axes by dragging.
choosing Rectify from the Tools menu and Option+drag (Macintosh) or
Clean Up Structure from the Tools menu. Alt+drag (Windows) to rotate
along the Z-axis only.
Single Bond Draw single bonds by dragging

in the model window.
46 • Chapter 4: Building and Editing Models Chem3D

A model of ethane appears.
Tool Name Description
Double Bond Draw double bonds by dragging

in the model window.
Triple Bond Draw triple bonds by dragging in

the model window.
Uncoordinated Draw uncoordinated bonds by

When Correct Atom Types and Rectify settings
Bond dragging in the model window.
are set in the Building control panel, the atom
Text Building Type in a new element, atom type is set as C Alkane and rectification results
type, formal charge or serial in adding the appropriate number of hydrogens.
number for a selected atom. Type
a substructure name to replace Adding Bonds
selected atoms. Click in empty
To add a bond to a model:
space to add a new fragment.
When a text box is visible, 1. Select a bond tool.
shift-click an atom to add or
2. Point to an atom and drag in the direction you
remove it from the set of replaced
atoms. Shift-drag across atoms to want to create another atom.
add or remove them from the set
of replaced atoms.
Eraser Erase bonds and atoms by

clicking.
Creating a Bond 1.Press and hold down the 2.Drag in any direction
mouse button over an and release the mouse
When you use a bond tool to create atoms, carbon atom. button.
atoms are always created. You can change the atoms
When the Rectify option is set in the Building
to other elements after you create the generic model.
control panel, the hydrogen is replaced by a
To create a model using a Bond tool: carbon.
• Click a bond tool.The Single Bond tool
is used in this example.
To draw a bond:
1. Point in the model window.
2. Drag in the direction you want the bond to be

oriented.
3. Release the mouse button to complete the bond.

To create a backbone of carbons and hydrogens: Dummy atom
• Repeat step 1 and step 2 until you have the
model you want.
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After you have the backbone, you can change

the carbons to different heteroatoms.
Creating Uncoordinated Bonds

You can create an uncoordinated bond with a
dummy atom using the Uncoordinated Bond tool.
An uncoordinated bond allows you to specify a Removing Bonds and Atoms
connection between two atoms without a strict
definition of the type of bond. This bond is often When you remove bonds and atoms:
used in coordination complexes for inorganic
• Click a bond to remove only that bond.
compounds, and later changes to another element.
• Click an atom to remove the atom and all
Dummy atoms are also useful for positioning atoms
in a Z-matrix, perhaps for export to another attached bonds.
application for further analysis. This is a common To remove an atom or bond, do one of the following:
use when models become large and connectivities
are difficult to specify. Dummy atoms are ignored in • Click the Eraser tool and click the atom
any computations. or bond.
• Select the atom or bond, and from the Edit
To add an uncoordinated bond and dummy atom:
menu, choose Clear.
1. Click the Uncoordinated Bond tool . • Select the atom or bond and press Delete.
2. Point to an atom and click-drag from the atom.
Selecting Bonds and Atoms
Use the Select tool to select atoms and bonds for
building and manipulation. Click a bond to select the
bond and all attached atoms. Click an atom to select
only that atom.
To use the Select tool:

1. Press and hold down 2. Drag in any direction
the mouse button over an and release the mouse
button. 2. Click the bond or atom to select.
atom.
An uncoordinated bond and a dummy atom are

added to the model. The atom created is labeled
Du, the Chem3D element symbol for Dummy
atoms.

Building Models With tool selected. Triple-clicking in the model
window is equivalent to double-clicking with
The Text Building Tool the Text Building tool selected.
The Text Building tool allows you to enter text that
The interpretation of the text in a text box depends
represents elements, atom types (elements with
on whether atoms are selected as follows:
specific hybridization), substructures, formal
charges, and serial numbers. • If the model window is empty, a model is built
using the text.
NOTE: For all discussions below, all the Building • If you have one or more atoms selected, the text
control panel options in the Settings dialog box are is added to the model at that selection if
assumed to be turned on. possible. If the specifications for a selected
atom are violated, the connection cannot be
The information you type must exactly match, made.
including correct capitalization, something in either
the Elements, Atom Types, or Substructures table. • If you have a model in the window, but do not
have anything selected, a second fragment is
To view the tables, choose one from the
View menu. An auxiliary application, the Table added, but is not connected to the model.
Editor, opens for viewing and editing the tables. • When a text box is visible, you can modify the
selection by Shift-clicking or Shift-dragging
Some general rules about using the Text Building
across atoms.
Tool are as follows:
• Text is case sensitive. For example, the correct Labels
way to specify a chlorine atom is “Cl”. The
correct way to specify the phenyl group To use an element symbol in a text box:
substructure is to type “Ph”. Typing “ph” or
1. Select the Text Building tool.
“PH” will not be recognized correctly.
• Pressing Enter or Return applies the text to the 2. Click in the model window.
model by creating new atoms, replacing atoms, A text box appears.
setting charges, and so on.
3. Type C.
• Typing a formal charge directly after an element
symbol will set the formal charge for that atom. 4. Press Enter or Return.
For example “PhO-” will create a model of a A model of methane appears.
phenoxide ion instead of phenol. The atom type is automatically assigned as a
• If you double click an atom, the contents of the C Alkane, and the appropriate number of
previous text box are applied to that atom. If the hydrogens are automatically added.
atom is one of several selected atoms, then the To use the same text to add another methyl group:
contents of the previous text box are applied to
• Point to the atom you want to replace, in this
all of the selected atoms. example a hydrogen, and double-click.
• If a tool other than the Text Building tool is The model is changed to ethane. Notice that
selected, double-clicking in the model window additional hydrogens are automatically
is equivalent to clicking with the Text Building removed.

To add a different element: The Table Editor
1. Click a hydrogen atom. To use the Table Editor to enter text in a text box:
A text box appears over the atom.
1. From the View menu, choose Atom Types.TBL.
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2. Type N.
2. Select the element or atom type in the table.
3. In the Table Editor, from the Edit menu, choose
A nitrogen is added to form ethylamine. Copy.
To build ethylamine in one step: 4. Click in the Chem3D Model Window.
1. Click in the model window. 5. In Chem3D, from the Edit menu, choose Paste.
A text box appears. The copied text appears in the text box.
2. Type CH3CH2NH.
Specifying Order of Attachment
3. Press Enteror Return. In both the simple and complex forms for using the
A model of ethylamine appears. Text Building tool, you can specify the order of
You can use a text box to change the atom type and attachment and repeating units by numbers and
bonding characteristics. parentheses.
To change the atom type of some atoms: For example:

• Type (CH3)3CNH2 into a text box with no
1. Click a carbon atom. atoms selected and press Enter or Return.
A text box appears. A model of tert-butylamine appears.
2. Shift-click the other carbon atom.
Specifying Ring Closure
Both atoms are selected.
To generate a ring, your label must leave at least 2
3. Type C Alkene. open valences for Chem3D to fill.
To build cyclohexane using labels (rather than a
substructure):
The atom type and the bond order are changed
• Type CH((CH2)4)CH into a text box with no
to reflect the new model of ethyleneamine. You
atoms selected and press Enteror Return.
can point at the atoms and bonds to display this
new information. A model of cyclohexane appears.
To get a reasonable structure:
1. Select the entire model:
2. From the Tools menu, choose Clean Up

Structure.

Using Substructures Building with Substructures
You can use pre-defined functional groups called You must know where the attachment points are for
substructures to build models. Some advantages for each substructure to get meaningful structures using
using substructures in your model building process this method. Pre-defined substructures have
are as follows: attachment points as defined by standard chemistry
• Substructures are energy minimized. conventions. For more information see “Appendix
A: Substructures.”
• Substructures have more than one attachment
To use a substructure as an independent fragment,
atoms (bonding atoms) pre-configured.
make sure there are no atoms selected.
For example, the substructure Ph for the phenyl
To insert a substructure into a model, select the
group has a single attachment point. The atoms which are bonded to the attachment points of
substructure COO for the carboxyl group has the substructure.
attachment points at both the Carboxyl carbon
and the Alcohol Oxygen. These provide for To build a model using a substructure:
insertion of this group within a model. Similar
multi-bonding sites are defined for all amino 1. Type the name of the substructure into a text
acid and other polymer units. box.
• Amino Acid substructures come in both alpha 2. Press the Enter or Return.
(indicated by the amino acid name alone) and
The substructure appears in the model window.
beta (indicated by a beta preceding the name of
the amino acid) forms. The dihedral angles have When you replace an atom or atoms with a
been preset for building alpha helix and beta substructure, the atoms which were bonded to the
sheet forms. replaced atoms are bonded to the attachment points
of the substructure. The attachment points left by the
• You can use substructures alone or in replaced atoms are also ordered by serial number.
combination with single elements or atom
types. Example 1. Building Ethane with
• Using a substructure automatically creates a Substructures
record in the Groups table that you can use for
To build a model of ethane using a substructure:
easy selection of groups, or coloring by group.
1. Type Et or EtH into a text box with no atoms
• Substructures are particularly useful for
building polymers. selected.
• You can define your own substructures 2. Press Enter or Return.

and add them to the substructures table, or
create additional tables. For more information,
see “Appendix A: Substructures.”
To view the available substructures:

• From the View menu, choose
Substructures.TBL.

A model of ethane appears. Example 3. Polypeptides
use substructures for building polymers, such as
proteins:
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1. Type HAlaGlyPheOH into a text box with no

atoms selected.
The additional H and OH cap the ends of the

polypeptide. If you don’t cap the ends and
automatic rectification is on, Chem3D tries to
fill the open valences, possibly by closing a
NOTE: When automatic rectification is on, the free ring.
valence in the ethyl group is filled with a hydrogen.
If automatic rectification is off, you need to type 2. Press Enter or Return.
“EtH” to get the same result. For substructures with Ring closing bonds appear whenever the text in
more than one atom with an open valence, explicitly a text box contains two or more open valences.
specify terminal atoms for each open valence.
The alpha form of the neutral polypeptide chain
composed of Alanine, Glycine, and
Example 2. Building a Model with a Phenylalanine appears.
Substructure and Several Other
NOTE: You can use the amino acid names
Elements
preceded with a “b–” to obtain the beta
To build a model with substructures and other conformation, for example “Hb–Alab–Glyb–
elements: PheOH”.
1. Type PrNH2 into a text box with no atoms The appropriate bonding and dihedral angles
selected. for each amino acid are pre-configured in the
substructure.
A model of propylamine appears.
The appropriate bonding site for the Pr
substructure is used for bonding to the
additional elements NH2.
H(8)
H(13)
H(9)
H(5)
H(11)
C(2)
N(4) C(3)
C(1)
H(12)
H(7)
NOTE: To better view the alpha helix formation,
H(10) use the Trackball Tool to reorient the model to an
H(6)
end-on view. For more information see “.”

To change the polypeptide to a zwitterion:
Building Models Using
1. Select the Text Building tool. ChemDraw or ISIS/Draw
2. Click the terminal nitrogen. You can use other 2D drawing packages to create
chemical structures and then copy them into
A text box appears over the nitrogen atom.
Chem3D for automatic conversion to a 3D model.
3. Type + and press Enter or Return. The Chem3D clipboard handles ChemDraw and
ISIS/Draw structures copied into model windows.
The charge is applied to the nitrogen atom. Its
atom type changes and a hydrogen atom is To build a model with 2D drawings:
added.
1. In the source program, such as ChemDraw,
4. Click the terminal oxygen. copy the structure to the clipboard.
A text box appears over the oxygen atom.
2. In Chem3D, from the Edit menu, choose Paste.
5. Type - in the text box and press Enteror Return. The 2D structure is converted to a 3D model.
The charge is applied to the oxygen atom. Its The standard measurements are applied to the
atom type changes and a hydrogen atom is
structure. For more information see “Appendix
removed.
D: 2D to 3D Conversion.”
For amino acids that repeat, put parentheses around
the repeating unit plus a number rather than type the Non-bond or atom objects copied to the clipboard
amino acid repeatedly. For example, type (arrows, orbitals, curves) are ignored by Chem3D.
“HAla(Pro)10GlyOH”. Nicknames in ChemDraw and Superatoms in
ISIS/Draw are expanded if Chem3D finds a
Example 4. Other Polymers corresponding substructure and a group for the
nickname is added to the Groups table. If a
The formation of a PET (polyethylene terephthalate) corresponding structure is not found, you must
polymer with 4 units (a.k.a.: Dacron, Terylene, define a substructure. For information on defining
Mylar) ia shown below: substructures see “Appendix A: Substructures.”
• Type OH(PET)4H into a text box with no atoms
selected and press Enter or Return. Replacing an Atom with a
The H and OH are added to cap the ends of the Substructure
polymer. The substructure you use must have the same
number of attachment points as the atom you are
replacing. For example, if you try to replace a
carbon in the middle of a chain with an Ethyl
substructure, an error occurs because the ethyl group
has only one open valence and the selected carbon
has two.

To replace an individual atom with a substructure:
Changing an Atom to
1. Click the Text Building tool. Another Element
2. Click the atom to replace. To change an atom from one element to another:
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A text box appears.

1. Click the Text Building tool.
3. Type the name of the substructure to add
2. Click the atom to change.
(case-sensitive).
A text box appears.
3. Type the symbol for the element you want
The substructure replaces the selected atom.
(case-sensitive).
For example, to change benzene to biphenyl:
1. Click the atom to replace. As long as the Text Building tool is selected, you can
A text box appears. double-click other atoms to make the same change.
For example, to change benzene to pyridine:
1. Click the atom to replace and type N.
2. Type Ph.

Changing an Atom to To change the bond order of a bond between two
atoms:
Another Atom Type 1. Select the bond tool.
To change a single atom:
2. Drag over the bond to change.
To change the bond order of one or more bonds
2. Click the atom to change. using a command:
A text box appears. 1. Click the Select tool.
3. Type the name of the atom type (case sensitive).
2. Shift-click all the bonds to change.
3. From the Object menu, point to Set Bond
To change more than one atom: Order, and then choose a bond order.
All the bonds in the selection change to the
1. Shift-click the atoms to change.
bond order you chose.
2. Type the name of the atom type (case sensitive).
To change the bond order by changing the atom type
3. Press Enter or Return. of the atoms on either end of the bond:
For many atom types that change bond order, you 1. Click the Text Building tool.
must select all atoms attached to the bond so that the
correct bond forms. 2. Shift-click all the atoms that are attached to
bonds whose order you want to change.
For example, to change ethane to ethene:
3. Type the atom type to which you want to change
1. Select both carbons. the selected atoms.
2. Type C Alkene. 4. Press Enter or Return.
3. Press Enter or Return. The bond orders of the bonds change to reflect
the new atom types.
Changing Bonds To change a model to have alternating double bonds
To change the bond order of a bond you can use the (this example uses Ball & Stick model display with
bond tools, commands, or the Text Building tool. Pattern by Element atom fill):
Using Bond Tools 1. With the Select tool, shift-click the bonds to
change.
The bond tool enables you to change the bond order
in the following ways: 2. From the Object menu, point to Set Bond
Order, and then choose Double.
• One bond at a time.
• Several bonds at once.
• By changing the atoms types on the bond.

The alternating bonds change to double bonds. Pairs of atoms whose distance from each other is
If Correct Atom Types and Rectify are on, the less than the standard bond length, plus a certain
atom types are corrected and the rectification of percentage are considered proximate. The lower the
the atoms changes. percentage value, the closer the atoms have to be to
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the standard bond length to be considered

proximate. Standard bond lengths are stored in the
Bond Stretching Parameters table.
To set the percentage value:

The Settings dialog box appears.
2. Select Building from the drop-down list.

To break several bonds in a model:
1. Shift-click the bonds to break. 3. Use the Bond Proximate Addition% arrows
to adjust the percentage added to the standard
2. From the Object menu, choose Break Bond. bond length when Chem3D assesses the
The bonds and the atom types are corrected and proximity of atom pairs.
rectified. The process broke three bonds and
You can adjust the value from 0 to 100%. If the
created four fragments: two methane fragments
value is zero, then two atoms are considered
and two ethane fragments. The separation is
proximate only if the distance between them is
visually skewed by the overlapping hydrogens.
no greater than the standard bond length of a
bond connecting them. If the value is 50, then
two atoms are considered proximate if the
distance between them is no greater than 50%
more than the standard length of a bond
connecting them.
To create bonds between proximate atoms:
1. Select the atoms that you want tested for bond

Creating Bonds by Bond proximity.
Proximate Addition 2. From the Object menu, choose Bond
Atoms that are within a certain distance (the bond Proximate.
proximate distance) from one another can be If they are proximate, a bond is created.
automatically bonded.
Chem3D determines whether two atoms are
proximate based on their Cartesian coordinates and
the standard bond length measurement.

Adding Fragments Setting Measurements
A model can be composed of several fragments. You can set the following measurements using the
If you are using bond tools, begin building in a Object menu:
corner of the window. • Bond lengths
If you are using the Text Building tool: • Bond angles
• Dihedral angles
1. Click in an empty area of the window.
• Distance between non-bonded atoms
A text box appears.
When you use the Clean Up Structure command, the
2. Type in the name of an element, atom type, or bond length and bond angle values are overridden
substructure. by the standard measurements from the Optimal
column of the Measurement table. These optimal
3. Press Enter or Return. values are the standard measurements in the Bond
The fragment appears. Stretching and Angle Bending parameter tables. For
all other measurements, performing a Clean Up
For example, to add water molecules to a window Structure or MM2 computation alters these values.
containing a model of formaldehyde: To use values you set in these computations, you
1. Click the Text Building tool. must apply a constraint.
2. Click in the approximate location you want a Setting Bond Lengths

water molecule to appear.
A text box appears. To set the length of a bond between two bonded
atoms:
3. Type H2O.
1. Select two adjacent atoms.
4. Press Enter or Return
2. From the Object menu, choose Set Bond
The fragment appears.
Length.
5. Double-click in a different location to add The Measurements table appears, displaying
another H2O molecule. distance between the two atoms. The Actual
value is highlighted.
3. Edit the highlighted text.

Setting Bond Angles Atom Movement When Setting
To set a bond angle:
Measurements
When you change the value of a measurement, the
1. Select three contiguous atoms for a bond angle.
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last atom selected moves. Chem3D determines

2. From the Object menu, choose Set Bond which other atoms in the same fragment also move
Angle. by repositioning the atoms that are attached to the
moving atom and excluding the atoms that are
The Measurements table appears, displaying
attached to the other selected atoms.
the angle value. The Actual value is
highlighted. If all of the atoms in a measurement are within a
ring, the set of moving atoms is generated as
follows:
4. Press Enter or Return. • Only one selected end atom that describes the
measurement moves while other atoms
Setting Dihedral Angles describing the measurement remain in the same
position.
To set a dihedral angle:
• If you are setting a bond length or the distance
1. Select four contiguous atoms. between two atoms, all atoms bonded to the
2. From the Object menu, choose Set Dihedral non-moving selected atom do not move. This
Angle. set of non-moving atoms is extended through
all bonds. From among the remaining atoms,
The Measurements table appears, displaying
the angle value. The Actual value is any atoms which are bonded to the moving
highlighted. atom move; this set of moving atoms is also
extended through all bonds.
• If the Automatically Rectify check box in the
4. Press Enter or Return. Building control panel is selected, rectification
atoms that are positioned relative to an atom
Setting Non-Bonded Distances that moves may also be repositioned.
(Atom Pairs) For example, consider the following structure:
To set the distance between two non-bonded atoms

(an atom pair): 8 18
1. Select two unbonded atoms. 10

1 6
15 19
2 7
9
2. From the Object menu, choose Set Distance. 5
17
16
The Measurements table appears, displaying 14
4 3
the distance. The Actual value is highlighted. 11
12
13

If you set the bond angle C(1)-C(2)-C(3) to 108 2. Select the atom or atoms to change.
degrees, C(3) becomes the end moving atom. C(1)
and C(2) remain stationary. H(11) and H(12) move 3. Type + or - followed by the number of the
because they are not part of the ring but are bonded formal charge.
to the moving atom. If the Automatically Rectify
check box is selected, H(10) may move because it is
a rectification atom and is positioned relative to To set the formal charge of an atom in a molecular
C(3). fragment as you build you can add the charge after
the element in the text as you build.
Setting Constraints To add the charge:
You use constraints to set a bond length, bond angle,
dihedral angle, or non-bonded distance that is 1. Type “PhO-” into a text box with no atoms
applied when you use Clean Up Structure or perform selected.
a Docking, Overlay, or MM2 computation.
NOTE: Constraints are not recognized by The phenoxide ion molecule appears.
MOPAC 98.
To remove the formal charge from an atom:
To set constraints: 1. Click the Text Building tool.

• When you set angles and distances, enter the 2. Select the atom or atoms whose formal charge
value of the constraint in the Optimal field. you want to remove.
You must leave the Measurements table visible
during any of the operations. 3. Type +0.
When you use Apply Standard Measurements, 4. Press Enter or Return.

which is only valid for bond lengths and bond
angles, replacing the optimal value is actually a
replacement to the values in the bond stretching and
Setting Serial Numbers
angle bending parameter tables. In the case of Atoms are assigned serial numbers when created.
dihedral angles and non-bonded distances your You can view the serial numbers in the following
constraint will have the effect of keeping that ways:
measurement constant (or nearly so) while the
• Point to the atom to display the pop-up
remainder of your model undergoes computation.
information.
The constraint doesn’t remove the atoms from a
computation. • With an atom selected, from the Object menu,
point to Show Serial Numbers, and then
Setting Charges choose Show.
Atoms are assigned a formal charge based on the • In the Settings dialog box, choose the Atom
atom type parameter for that atom and its bonding. Labels control panel, and then click Show
You can display the charge by pointing to the atom. Serial Numbers.
To set the formal charge of an atom: Serial numbers are initially assigned based on the
order in which you add atoms to your model.

To change the serial number of an atom: 2. From the Object menu, choose Invert.
1. Click the Text Building tool. The Invert command only repositions side
chains extending from an atom.
2. Click the atom to reserialize.
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For example, if you choose Invert for the structure

A text box appears. below when C(1) is selected:
3. Type the serial number.

If the serial numbers of any unselected atoms
conflict with the new serial numbers, then those
unselected atoms are renumbered also.
The following structure appears.
To reserialize another atom with the next sequential
number:
• Double-click the next atom you want to
reserialize.
To reserialize several atoms at once:
2. Hold down Shift and select several atoms.
3. Type the starting serial number. To invert several dihedral angles (such as all of the
dihedral angles in a ring) simultaneously:
Normally, the selected atoms are reserialized in the 1. Select the dihedral angles to invert.
order of their current serial numbers. However, the
2. From the Object menu, choose Invert.
first four atoms selected are reserialized in the order
you selected them. All of the dihedral angles that make up the ring
are negated. Atoms positioned axial to the ring
Changing are positioned equatorial. Atoms positioned
equatorial to the ring are positioned axial.
Stereochemistry
You can alter the stereochemistry of your model by Reflection
inversion or reflection.
use the Reflect command to perform reflections on
your model through any of the specified planes.
Inversion
When you choose the Reflect commands certain
The Invert command performs a symmetry Cartesian coordinates of each of the atoms are
operation about a selected chiral atom. negated. When you choose Reflect Through Y-Z
To perform an inversion: Plane, all of the X coordinates are negated. You can
choose Reflect Through X-Z Plane to negate all of
1. Select the atom. the Y coordinates. Likewise, you can choose Reflect

Through X-Y Plane to negate all of the Z
coordinates. You can choose Invert through Origin
Refining a Model
to negate all of the Cartesian coordinates of the After building a 3D structure, you may need to clean
model. it up. For example, if your model was built without
automatic rectification, atom type assignment, or
If the model contains any chiral centers, each of
standard measurements, you can apply these as a
these commands change the model into its
refinement.
enantiomer. If this is done, all of the Pro-R
positioned atoms become Pro-S and all of the Pro-S
positioned atoms become Pro-R. All dihedral angles
Rectifying Atoms
used to position atoms are negated. To rectify the selected atoms in your model:
• From the Tools menu, choose Rectify.
NOTE: Pro-R and Pro-S within Chem3D are not
equivalent to with the specifications R and S used in Atoms are added and deleted so that each
standard chemistry terminology. selected atom is bonded to the correct number
of atoms as specified by the geometry for its
For example, if you choose Reflect through Y-Z atom type. This command also assigns atom
Plane from the Tools menu for the structure below types before rectification.
when any atom is selected: The atom types of the selected atoms are
changed so that they are consistent with the
bound-to orders and bound-to types of adjacent
atoms.
Cleaning Up a Model
Normally, Chem3D creates approximations of
chemically correct structures. However, it is
possible to create unrealistic structures, especially
when you build strained ring systems. To correct
unrealistic bond lengths and bond angles use the
Clean Up Structure command.
Chem3D produces the following structure (an
To clean up the selected atoms in a model:
enantiomer):
• From the Tools menu, choose Clean Up
Structure.
The selected atoms are repositioned to reduce
errors in bond lengths and bond angles. Planar
atoms are flattened and dihedral angles around
double bonds are rotated to 0 or 180 degrees.

Using the Measurements Table
You can override the standard measurements which
Chem3D uses to position atoms by using the
Measurements table. If you specify an optimal value
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for a particular measurement and that measurement

is to be standardized, Chem3D uses the optimal
value for the measurement instead of the standard
measurement.
NOTE: Other commands that you can use to

position atoms include the Minimize Energy
commands in the MM2 and MOPAC menus and the
Optimize to Transition State command in the
MOPAC menu in CS MOPAC Pro. These commands
are discussed in “Chapter 10: MM2 Computations”
and “.”

Chapter 5: Manipulating Models
Overview Selecting Multiple Atoms and
Chem3D provides tools that enable you to
Bonds
manipulate the models you create. You can show or To select multiple atoms and bonds:
hide atoms and select groups to make them easier to
manipulate. Molecules can be rotated, aligned, and • Shift-click the atoms or bonds.
resized. When you hold down the Shift key and click an
unselected atom and the atoms at the other ends
Selecting of the bonds are selected you also select
adjacent bonds.
Most operations require that the atoms and bonds
that are operated on are selected. The appearance of To quickly select all atoms and bonds in a model:
selection varies by model display type:
• Stick bonds are drawn thicker.
• Cylindrical bonds are drawn with thick edges. NOTE: If the last action performed was typing in a
text box, all of its text is selected instead of the atoms
• Atoms are drawn as round dots in wire frame or
in the model.
stick models.
• Atoms in ball & stick, cylindrical bond, and
space filling models have thick outlines. Deselecting Atoms and Bonds
• Ribbon models do not indicate which atoms are When you deselect an atom, you deselect all
selected. adjacent bonds. When you deselect a bond, you
deselect the atoms on either end if they are not on
Selecting Single Atoms and another selected bond.
Bonds To deselect a selected atom or bond:

• Shift-click the atom or bond.
To select an atom or bond:
If Automatically Rectify is on when you deselect an
1. Click the Select tool . atom, adjacent rectification atoms and lone pairs are
also deselected.
2. Click the atom or bond.
Any previously selected atoms and bonds are NOTE: A rectification atom is an atom bonded to
deselected. When you click a bond, both atoms only one other atom and whose atom type is the
on the bond are selected. rectification type for that atom.
To deselect all atoms and bonds:

• Click in an empty area of the Model window.
Chem3D Chapter 5: Manipulating Models • 63

Selecting Atoms in a Group If you hold down the Shift key and all of the
atoms within the Selection Rectangle are
To select atoms that are defined in a group: already selected, then these atoms are
deselected.
1. From the Tools menu, point to Show Model
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Tables, and then choose Groups. Selecting a Subset of

The Groups table appears along the right side of
the model.
Atoms
To view, edit, or otherwise manipulate a subset of
2. Click the icon next to the group to select, or atoms in your model, use commands in the Edit
Shift-click several icons. menu.
NOTE: If your Groups table contains a group Select Reverse

named “backbone”(created automatically if you
To deselect all selected atoms and select all
import most PDB files), you can select this group to
deselected atoms:
select the backbone of the polypeptide chain.
• From the Edit menu, point to Select Atoms,
and then choose Select Reverse.
Using the Selection Rectangle
The bonds which connect two newly selected
To select several atoms and bonds using the atoms are selected.
Selection Rectangle:
• Click-drag diagonally across the atoms you Select Element
want to select. Previously selected atoms are not deselected when
you choose Select Element.
To select all atoms of the same element:
and then choose Select Element.
The word Element in this command is replaced by
the element symbol of the last atom that you selected
by clicking in the model window.
For example, if you last clicked a carbon atom in the
model window, then the Select Element command
Any atoms that fall at least partially within the changes to Select C.
Selection Rectangle are selected. A bond is selected You can specify the element in Select Element by
only if both atoms on the bond are also selected. selecting a record in the Internal or Cartesian
To keep previously selected atoms selected: Coordinates tables.
• Hold down the Shift key while you make For example, if you click the record selector for H(8)
another selection. in the Internal Coordinates table, the Select Element
command changes to Select H.
64 • Chapter 5: Manipulating Models Chem3D

Select Adjacent For example, in the following model of
methoxybenzene, all the hydrogens have been
Previously selected atoms are not deselected when hidden, as indicated in the status bar.
you choose Select Adjacent.
To select all atoms and bonds adjacent to each
selected atom:
and then choose Select Adjacent.
Select Fragment
To select all atoms and bonds in the same fragment
as any selected atom:
and then choose Select Fragment. Hiding Selected Atoms
Showing and Hiding To hide an atom or group of atoms:
Atoms 1. Click the atom with the Select tool.
You may want to view your models with different 2. From the Object menu, choose Hide Selected.
atoms visible or not visible. You can temporarily Any bond to a selected atom is also hidden. If
hide atoms using the Object menu. Rectify is on, then rectification atoms bonded to
The Status bar displays the number of atoms hidden selected atoms are also hidden. Selected atoms
along its right edge. Hiding atoms does not remove are deselected before they are hidden.
them from computations or analyses.
Hiding Unselected Atoms
To hide all unselected atoms:
• From the Object menu, choose Hide
Unselected.
Show H’s and Lp’s Any bond to an unselected atom is also hidden.
If Rectify is on, then rectification atoms bonded
To show all hydrogen atoms and lone pairs in the to unselected atoms are also hidden.
model:
• From the Tools menu, choose Show H’s and Showing All Atoms
Lp’s. To show atoms that are hidden:
A check mark appears beside the command, • From the Object menu, choose Show All
indicating that it has been selected. Atoms.
Any atom or bond previously hidden with the Hide
When Show H’s and Lp’s is not selected, hydrogen
Selected or Hide Unselected commands appears.
atoms and lone pairs are automatically hidden.
When you choose Show All Atoms, Chem3D
automatically selects Show H’s and Lp’s from the
Tools menu.

Showing Unselected Atoms The color of a group is used to color the atoms in the
group if the Color popup in the Model Display
To show hidden atoms that are adjacent to any control panel is set to Color By Group.
selected atom:
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• From the Object menu, choose Show Adjacent

Atoms.
Reversing Atoms Shown

To show atoms that are hidden and to hide atoms that
are visible:
• From the Object menu, choose Show Reverse.
Defining Groups
You can define a portion of your model as a group. To enter a reference number for the group:
This provides a way to easily select and to highlight
part of a model (such as the active site of a protein) 1. Click the Ref# cell to open it.
for visual effect.
2. Type a reference number.
After the group is defined you can close the Groups
table. However, with the Groups table open, you can
select all the atoms in a group by clicking the icon to Moving Atoms or
the left of the name. Models
When you use the Define Group command, the You can use the Select Tool to move atoms to
Atoms field, which lists all the atoms in the group, is different locations. If the atom, group of atoms,
filled in. bond, or group of bonds that you want to move are
To define a group: already selected, then all of the selected atoms
move.
1. Select the atoms and bonds in the model you
want in the group. To move an atom to a different location on the X-Y
plane:
2. From the Object menu, choose Define Group.
1. Point to the atom using the Select Tool.
The Groups table appears with the name cell
already open. 2. Drag the atom to the desired location.
3. Type a name for the group and press Enter or Dragging moves the atoms parallel to the X-Y
Return to close the cell. plane, changing only their X- and
To define a color for the group: Y-coordinates. If Automatically Rectify is on,
then the unselected rectification atoms that are
1. Double-click the Color cell. adjacent to selected atoms move with the
2. Set the color using the Color dialog box that selected atoms.
appears.
3. Click OK.

To move a model or a fragment: X- or Y-Axis Rotations
1. With the Select Tool, select the model or
To perform a rotation about the X- or Y-axis:
fragment.
1. Point to the X-axis Rotation bar or Y-axis
2. Drag the model to the new location. Rotation bar.
Rotating Models 2. Drag the pointer along the Rotation bar.
Chem3D allows you to freely rotate the model Rotating Fragments

around axes. Four rotation bars are located on the
periphery of the model window. You can use these If more than one model (fragment) is in the model
rotation bars to view your model from different window, you can rotate a single fragment or rotate
angles, by rotating around different axes. You can all fragments in the model window.
also double-click a Rotation bar to open the Rotate
To rotate only one fragment:
dialog box where you can type the number of
degrees to rotate. 1. Select an atom in the fragment you want to
If you want to save the rotation frames to later replay rotate.
as a movie, click the Record button in the Movie
Controller. 2. Drag a rotation bar.
To display the Rotation bars: To rotate all fragments:

• From the Tools menu, choose Show Rotation • Shift-drag a Rotation bar.
Bars.
Internal Rotations
The Rotation bars appear on the corners of the
Model window. Internal rotations alter a dihedral angle and create
another conformer of your model. You can rotate an
Internal Rotation Bar Selected Axis internal angle using the Internal Rotation bar.
Rotation Bar
To perform internal rotations in a model, you must
select either one atom, one bond, or a fragment that
contains exactly one atom that is attached to one
unselected atom.
The internal rotation is specified by a bond. The
fragment at one end of the bond is stationary while
the fragment attached to the other end rotates. If only
one atom is selected, then the stationary fragment is
defined by whichever atom bonded to the selected
atom has the lowest serial number. If a fragment is
selected, then that fragment rotates and the
unselected atoms remain stationary.
Y-Axis Rotation Bar X-Axis Rotation Bar

For example, consider ethoxybenzene (phenetole) Using the Rotate Dialog Box
as follows:
To rotate a model a specific amount of degrees:
To perform a rotation about C-O bond where the
phenyl group moves: 1. Double-click a Rotation bar.
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1. Select O(3) or select the phenyl group. The Rotate dialog box appears.
2. Drag the pointer along the Internal Rotation

bar.
To perform a rotation about the C-O bond where the

ethyl group moves:
2. Type the number of degrees to rotate.
1. Shift-click C(4) and O(3).
3. Click Rotate.
2. Drag the pointer along the Internal Rotation
bar. Trackball Tool
Use the Trackball tool to freely rotate a model.
Rotating Around a When you select the Trackball tool, the pointer
Specific Axis becomes a hand and a circle, representing the
trackball.
You can rotate your model around an axis you
specify by selecting any two atoms in your model. To rotate your model around the Y-axis:
You can add dummy atoms as fragments to specify
an axis around which to rotate. 1. Click the Trackball tool .
2. Point to an atom.
3. Drag to the left or right, parallel to the X-axis.

Axis of
Axis of rotation The hand closes as if grabbing the model, and
Rotationot Trackball Rotation appears in the Status bar.

To rotate your model around the X-axis: The model rotates so that the two atoms you
select are parallel to the appropriate axis.
1. Position the pointer near the top of the model.
If Fit Model To Window is turned on, the center
2. Drag the pointer up and down, parallel to the of the model is still defined in terms of two
Y-axis. atoms you select. Automatic centering prevents
a majority of your model from being drawn
To rotate around the Z-axis:
outside of the model window.
1. Position the pointer outside the Trackball circle.
For example, to see an end-on view of ethanol:
2. Drag the pointer around the outside of the
1. Click the Select tool.
trackball.
2. Shift-click C(1) and C(2).
You can also rotate around the Z-axis by holding
down a modifier key and dragging within the
Trackball circle.
1. Position the pointer within Trackball circle.
2. Press Option (Macintosh) or Alt (Windows)

while dragging the pointer clockwise.
The cursor changes to a double-headed arrow.
then choose Z Axis.
Changing Orientation Aligning to a Plane

Chem3D allows you to change the orientation of
your model along a specific axis. However your You can align a model to a plane when you select
model moves, the origin (0, 0, 0) is always located three or more atoms. When you select three atoms,
in the center of the model window. those atoms define a unique plane. If you select
more than three atoms, a plane is computed that
Aligning to an Axis minimizes the average distance between the selected
atoms and the plane.
To position your model parallel to either the X-, Y-,
To position a plane in your model parallel to a plane
or Z-axis:
of the Cartesian Coordinate system:
1. Select two atoms only.
1. Select three or more atoms.
then choose X Axis, Y Axis, or Z Axis.

2. From the Object menu, point to Move To, and 3. Select the third carbon atom such that no two
then choose X-Y Plane, Y-Z Plane, or X-Z selected atoms in the ring are adjacent.
Plane.
The entire model rotates so that the computed
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plane is parallel to the X-Y, Y-Z, or X-Z plane.

The center of the model remains in the center of
the window.
To move three atoms to a plane and two of the atoms

onto an axis:
1. Select the two atoms. then choose X-Y Plane.
2. From the Object menu, point to Move To, and The model moves to the position shown below.
then choose a Move to Axis command.
3. Shift-click the third atom.

then choose a Move to Plane command.
For example, to move a cyclohexane chair so that

three alternating atoms are on the X-Y Plane:
1. Select two non-adjacent carbon atoms in the Resizing Models

ring. Chem3D provides the following ways to resize your
model:
• Resizing the model window
• Scaling
• Using magnification controls
Resizing Windows
2. From the Object menu, point to Move To, and Dragging a resize handle (Macintosh) or a window
then choose X Axis. corner or window border (Windows) changes the
size of the window. If Fit Model is on, the model
The model moves to the position shown below. resizes so that it is centered and in full view within
the window.
Scaling a Model
To scale a model to the window size:
• From the Tools menu, choose Fit Model To
Window.

To scale all frames including the active frame: • Click the Magnify button .
• From the Tools menu, choose Fit All Frames The model is reduced by 10%. Click and hold
To Window. the Magnify button to continuously increase the
size.
To fit only a selection within the active window:
• From the Tools menu, choose Fit Selection To Centering a Selection
Window.
To center your model based on a particular selection:
NOTE: These Fit commands only affect the scale of 1. Select one or more atoms.
the model. Atomic radii and interatomic distances
do not change. 2. From the Object menu, point to Move To, and
then choose Move To Center.
Using Magnification Controls This command places the centroid of the selected
atoms at the origin. Chem3D calculates the centroid
You can reduce or enlarge a model using the of the selected atoms by averaging their X, Y, and Z
magnification menu commands or buttons. coordinates.
The Magnify and Reduce buttons are available when
the Movie Controller is visible. To display the NOTE: This command affects all frames of your
Movie controller: model, not just the active frame.
• From the Tools menu, choose Show Movie
Controller. If you choose Move to Center, select different
atoms, and then choose one of the Move to Axis or
Move to Plane commands, the model is centered on
the same set of atoms as were selected when you last
chose Move to Center.
Reduce Magnify
button button Changing the Z-matrix
To reduce the size of a model, do one of the The relative position of each atom in your model is
following: determined by a set of measurements called internal
coordinates or a Z-matrix. The internal coordinates
• From the Tools menu, choose Reduce.
for any particular atom consist of measurements
The model is reduced by 10%. (bond lengths, bond angles, and dihedral angles)
• Click the Reduce button . between it and other atoms. All but three of the
atoms in your structure (the first three atoms in the
The model is reduced by 10%. Click and hold Z-matrix which describes your model) are
the Reduce button to continuously reduce the positioned in terms of three previously positioned
size. atoms.
To increase the size of a model, do one of the To view the current Z-matrix of a model:
following: • From the Tools menu, point to Show Model
• From the Tools menu, choose Magnify. Tables, and then choose Internal Coordinates.
The model is enlarged by 10%.

The First Three Atoms in a Atoms Positioned by Three
Z-matrix Other Atoms
The first three atoms in a Z-matrix are defined as In the following set of illustrations, each atom D is
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follows: positioned relative to three previously positioned

atoms C, B, and A. Three measurements are needed
• Origin atom —The first atom in a Z-matrix. to position D: a distance, and two angles.
All other atoms in the model are positioned
Atom C is the Distance-Defining atom; D is placed
(either directly or indirectly) in terms of this
a specified distance from C. Atom B is the First
atom. Angle-Defining atom; D, C, and B describe an
• First Positioned atom—Positioned only in angle.
terms of the Origin atom. Its position is
Atom A is the Second Angle-Defining atom. It is
specified by a distance from the Origin atom.
used to position D in one of two ways:
Usually, the First Positioned atom is bonded to
the Origin atom. • By a dihedral angle A-B-C-D
• Second Positioned atom—Positioned in terms • By a second angle A-C-D.

of the Origin atom and the First Positioned In the left example, atom D is positioned in terms of
atom. There are two possible ways to position a dihedral angle, thus the second angle is the
the Second Positioned atom, as described in the dihedral angle described by A-B-C-D. This dihedral
following example. angle is the angle between the two planes defined by
D-C-B and A-B-C.
In the left example, the Second Positioned atom is a
specified distance from the First Positioned atom. In In the right example, if you view down the C-B
addition, the placement of the Second Positioned bond, then the dihedral angle appears as the angle
atom is specified by the angle between the Origin formed by D-C-A. A clockwise rotation from atom
atom, the First Positioned atom, and the Second D to atom A when C is in front of B indicates a
Positioned atom. positive dihedral angle.
In the right example, the Second Positioned atom is

a specified distance from the Origin atom. In
addition, the placement of the Second Positioned
atom is specified by the angle between the First
Positioned atom, the Origin atom, and the Second
Positioned atom.
When D is positioned using two angles, there are

two possible positions in space about C for D to
occupy: a Pro-R position and a Pro-S position.

In this orientation, D is somewhere in front of the
NOTE: The terms Pro-R and Pro-S used in plane defined by A, B and C if positioned Pro-R, and
Chem3D to position atoms bear no relation to the somewhere behind the plane defined by A, B and C
Cahn-Ingold-Prelog R/S specification of the if positioned Pro-S.
absolute stereochemical configuration of a chiral When you point to or click an atom, the information
atom. Pro-R and Pro-S refer only to the positioning box which appears can contain information about
of D and do not imply any stereochemistry for C. C how the atom is positioned.
may be chiral, or achiral.
Positioning of H(14)
The most convenient way to visualize how the If H(14) is positioned by C(5)-C(1), C(13) Pro-R,
Pro-R/Pro-S terms are used in Chem3D to position then the position of H(14) is a specified distance
D is described in the following examples: from C(5) as described by the H(14)-C(5) bond
To position Atom D in Pro-S Orientation (left) and length. Two bond angles, H(14)-C(5)-C(1), and
Pro-R Orientation (right): H(14)-C(5)-C(13), are also used to position the
atom.
1. Orient the Distance-Defining atom, C, the First
Because H(14) is positioned by two bond angles,
Angle-Defining atom, B, and the Second there are two possible positions in space about C(5)
Angle-Defining atom, A, such that the plane for H(14) to occupy; the Pro-R designation
which they define is parallel to the X-Y plane. determines which of the two positions is used.
2. Orient the First Angle-Defining atom, B, to be
directly above the Distance-Defining atom, C,
such that the bond joining B and C is parallel to
the Y-axis, and the Second Angle-Defining
atom, A, is somewhere to the left of C.
If an atom is positioned by a dihedral angle, the three

atoms listed in the information about an atom would
all be connected by dashes, such as C(6)-C(3)-C(1),
and there would be no Pro-R or Pro-S designation.

The commands in the Set Z-Matrix submenu allow Positioning by Dihedral Angle
you to change the Z-matrix for your model using the
concepts described previously. To position an atom relative to three previously
positioned atoms using a bond distance, a bond
Because current measurements are retained when
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angle, and a dihedral angle:

you choose any of the commands in the Set Z-
Matrix submenu, no visible changes in the model 1. With the Select tool, click the dihedral-angle
window occur. defining atom.
Positioning by Bond Angles 2. Shift-click the first angle-defining atom.
To position an atom relative to three previously 3. Shift-click the distance-defining atom.

positioned atoms using a bond distance and two
bond angles: 4. Shift-click the atom to position.
1. With the Select tool, click the second

You should now have four atoms selected, with
the atom to be positioned selected last.
angle-defining atom.
5. From the Object menu, point to Set Z-Matrix,
2. Shift-click the first angle-defining atom.
and then choose Position by Dihedral.
3. Shift-click the distance-defining atom. For example, using the previous illustration, choose
atoms in the following order: C(7), C(6), C(1),
4. Shift-click the atom to position.
C(10) to position C(10) by a dihedral angle in a ring.
You should now have four atoms selected, with Then choose Position by Dihedral.
the atom to be positioned selected last.
Setting Origin Atoms
5. From the Object menu, point to Set Z-Matrix,
and then choose Position by Bond Angles. To specify the origin atoms of the Z-matrix for a
model:
For example, consider the following structure:
1. With the Select tool, click the first one, two, or
2 10
three atoms to start the Z-matrix.
3 1 9
2. From the Tools menu, point to Set Z-Matrix,
4 6 8 and then choose Set Origin Atom or Set Origin
5 7 Atoms.
The selected atoms become the origin atoms for
To position atom C(7) by two bond angles, select the Z-matrix and all other atoms are positioned
atoms in the following order: C(5), C(1), C(6), C(7),
relative to the new origin atoms. Because
then choose Position by Bond Angles.
current measurements are retained, no visible
changes to the model occur.

Chapter 6: Displaying Models
Overview The Settings dialog box appears.
2. Choose Model Display.

You can display molecular models in several ways,
depending on what information you want to learn The Model Display control panel of the Settings
from them. The atoms and bonds of a model can take dialog box appears.
on different appearances. These appearances are
generically termed rendering types, and the term,
model display, is used in Chem3D. Depending on
the type of molecule, certain model displays may
offer advantages by highlighting structural features
of interest. For example, the Ribbons model display
might be the option of choice to show the
conformational folding of a protein without the
distracting structural detail of individual atoms.
Model display options are divided into two general

types:
• Structure displays
• Molecular surface displays 3. Set the new options.
Structure Displays NOTE: You can specify the bond fill pattern and
Structures are graphical representations based on the thickness of the bonds in the Bond Display control
traditional physical three-dimensional molecular panel. The pattern or color of an atom can be
model types. The following structure display types specified in the Model Display control panel. You
are available from Model Display view of the can specify whether or not the solid spheres appear
Settings dialog box: by default, and how their sizes are calculated using
the Atom Display control panel.
• Wire Frame
• Sticks
• Ball and Stick
• Cylindrical Bonds
• Space Filling
• Ribbons
To change the structural display type of a model:
Chem3D Chapter 6: Displaying Models • 75

Model Types Model Type Description
The following table describes the Chem3D model
types: Cylindrical Bonds Cylindrical Bond
models are similar to
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Model Type Description Ball and Stick models

except that all bond
Wire Frame Wire Frame models are types are drawn as
the most simple model cylinders. The bonds
type. Bonds are can be shaded with
displayed as pixel-wide different patterns to
lines. Atoms are not identify bond order.
displayed explicitly, but
each half of a bond is
Space Filling Space Filling models are
colored to represent the
more complex to draw
element color for the
and slowest to display.
atom at that end. Wire
Atoms are scaled to
Frame models are well
100% of the van der
suited for extremely
Waals (VDW) radii
large models such as
specified in the Atom
proteins.
Types table.
Sticks Stick models are similar NOTE: The VDW radii
to Wire Frame, are typically set so that
however, the bonds are overlap between
slightly thicker. As this non-bonded atoms in
model type is also fairly space filling models
fast, it is another good indicates a significant
choice for visualizing (approximately 0.5
very large models such kcal/mole) repulsive
as proteins. interaction.
Ball and Stick Ball and Stick models

show bonds drawn as
thick lines and atoms are
drawn as filled spheres.
The atom spheres are
filled with a pattern or
color that corresponds to
the element or position
of the atom.
76 • Chapter 6: Displaying Models Chem3D

Model Type Description
Ribbons Ribbons models show

large protein molecules
in a form that highlights
secondary and tertiary
structure. Ribbon
models can be Colored
by Group to help
identify the amino acid The dot surface is based on the VDW radius set in
constituents. Your the Atom Types table.
model must have a Dot surfaces can be displayed on an atom-by-atom
protein backbone in basis or on all atoms.
order to display ribbons.
To change the display of dot surfaces on an
The following caveats atom-by-atom basis:
apply to the Ribbon
model display type: 1. Select the atoms whose display you want to
change.
• Do not provide pop-up
information. 2. From the Object menu, point to Show Dot
Surfaces and then choose Show.
• Print as bitmaps.
To display dot surfaces by default on all atoms:
• Copy to the Macintosh
clipboard as bitmaps 1. In the Settings dialog box, choose Atom
only—no PostScript Display.
information copies.
2. In the Dot Surfaces area, click Show By
• Set your monitor to Default.
display 256 colors or All atoms currently in the model window display the
more. selected option.
You can vary the number of dots displayed in a
Displaying Dot Surfaces surface. This is useful when dot surfaces are applied
You can add dot surfaces to any of the model display to a very small or very large models.
types like the wire frame model as shown below: To change the dot density used for VDW dot
surfaces:
1. In the Settings dialog box, choose Atom

Display.
2. Drag the density slider to the right to make the

surface more dense or to the left to make it less
dense.

Coloring Displays Coloring by Group
You can change the colors used to display your To change the color of atoms to colors associated
model in the Model Display control panel. with groups in the Groups table for that model:
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• In the Model Display control panel, select by

Group from the Color menu.
To view the groups for the active model:

• From the Tools menu, point to Show Model
Tables, and then choose Groups.
Atoms that are not part of a group are colored
gray. An atom which is part of more than one
group is colored according to the first group in
the Groups table that contains the atom.
To change a color associated with a group in the

active model:
Coloring by Element 1. From the Tools menu, point to Show Model

To change the color of atoms to match the colors for Tables, and then choose Groups.
each element specified in the Elements table:
2. Double-click the Color field for the group.
The Color or Color Picker dialog box appears.
Element from the Color menu.
3. Select the color to use and click OK.
To change the colors of the elements in
the Elements table, so that Color by Element uses 4. From the File menu, choose Close Window.
these new colors for display in all models:
5. Click Save.
1. From the View menu, choose Elements.
The Table Editor opens. Coloring by Partial Charge
When coloring by partial charge, atoms with a
2. Double-click the Color field for an element.
highly negative partial charge are deep blue. Atoms
The Color or Color Picker dialog box appears. with a highly positive partial charge are deep red. As
the partial charge gets closer to 0, the atom is paler.
3. Select the color to use and click OK. Atoms with a 0 partial charge are white.
4. From the File menu, choose Close Window. To change the color of atoms to colors based on the
partial charges of the atoms:
5. Click Save.
Partial Charge from the Color menu.
The Partial Charge is the result of a
calculation—Extended Huckel, MOPAC, or
Gaussian. If you have not performed a

calculation, the partial charge for each atom is To change the background color of the model
0. If you have performed more than one window:
calculation, you can specify the calculation to
use by choosing the Partial Charges dialog box 1. In the Model Display control panel, click
from the View menu. Background Color.
The Color or Color Picker dialog box appears.
Coloring Black
2. Select a color and click OK.
Coloring models black is useful when models need
to appear in black-and-white printed material. When
you use black-and-white, you can fill the atoms with NOTE: The background colors are not saved in
patterns to show different elements. PostScript files or used when printing, except when
you use the Ribbons display.
To change the color of atoms to black or shades of
gray:
• In the Model Display control panel, from the
Colorizing Individual Atoms
Color menu, choose Black. You can mark atoms individually using the Colorize
command in the Object menu.
Coloring by Depth
To change an atom to a new solid color:
To indicate depth within a model, you can shade the
model so that the closer the atoms are, the brighter 1. Select the atoms to change.
they are.
2. From the Object menu, choose Colorize.
To color atoms based on their depth or Z coordinate: The Set Atom Color dialog box appears.
• In the Model Display control panel, click Color
by Depth.
Atoms with negative Z coordinate (behind the
X-Y plane) are darker than atoms of the same
element with positive Z coordinates (in front of
the X-Y plane).
Coloring the Background Window

Chem3D allows you to select a color for the
background of your models. A black background
can be particularly striking for ribbon displays as
shown below.
3. Select any color set to 100%.
4. Click Set.
The color of the atoms changes to the new color.

To remove a custom atom color from the model Atom Fill Patterns
display:
You can change the fill pattern of atoms using the
1. Select the atoms whose colors you want to Model Display control panel. This Setting applies
change. only to Ball and Stick, Cylindrical Bonds, or Space
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Filling models.
2. From the Object menu, choose Colorize.
The Set Atom Color dialog box appears. NOTE: You can change the default color
and pattern for an element by editing the Color and
3. Click Set 0%. Pattern fields in the Elements table.
The custom colors are removed from the
selected atoms. To change the fill pattern:
You can tint atoms with a color instead of changing 1. In the Model Display control panel, choose one
the color entirely. Next to each color in the Set Atom
of the following from the Atom Fill menu:
Color dialog box is a color weight percentage that
specifies how much of the mix-in color you want to
include when displaying the selected atom. If you want to fill
atoms with patterns
For example, if you want all of the atoms in a based on their … Then select …
fragment to be tinted blue, but still have different
colors depending on their element: element Pattern By Element
• Select a blue color and specify its color weight
as a number less than 100%. A value around Z coordinates Pattern By Depth.
50% is often a good choice.
The atoms in front of
To change one of the colors in the color mix: the X-Y plane
(positive
1. In the Set Atom Color dialog box, select the
Z-coordinates) fill
color to change.
with lighter patterns.
2. Do one of the following: Atoms receding from
• Click Edit Color. the X-Y plane
(negative
• Double-click the color.
Z-coordinates) fill
3. Specify a color weight less than 100%. with increasingly
darker patterns.
4. Click Set.

For example, if the depth ratio is 0, all atoms of the
If you want to fill same radius are the same size. As the depth ratio
atoms with patterns increases, the atoms with positive Z coordinates
based on their … Then select … appear larger than the atoms with negative
Z coordinates.
element using solid Solid Colors.
The width of bonds in Cylindrical Bonds models are
colors
Select Color By affected in proportion to the sizes of the atoms to
Element or Color By which the bonds are attached. A bond between two
Group from the Color atoms with different Z coordinates becomes more
menu. Select Color By wedge-like as the depth ratio increases.
Depth to specify the
coloration of the Solid Spheres
atoms, or the atoms In Ball and Stick, Cylindrical Bond, and Space
appear black. Filling models, you can display the solid spheres
representing atoms in individual atoms or all atoms.
NOTE: If your model
is displayed on a black To change the display of solid spheres on individual
and white monitor, atoms:
then Solid Colors
appears the same as 1. Select the atoms to change.
Pattern By Element.
2. From the Object menu, point to Show Solid
Spheres, and then choose Show, Hide, or
element by mixing the Shadowed Colors. Default.
shadow color you
specify. Specify the shadow To display solid spheres by default on all atoms:
color to mix with the
• In the Atom Display control panel, click Show
element color by
clicking the Shadow By Default in the Solid Spheres.
Color button. The
color dialog box
appears where you can
specify a shadow
color.
Depth Ratio
The Depth Ratio slider controls the size and color of
nearer atoms and bonds relative to atoms and bonds
farther away.

In several model types, atoms can be represented If this check box is not selected, only bonds in
using solid spheres. You can base the size of the Cylindrical Bonds models are affected by the Depth
spheres on different properties of the atoms. Ratio slider.
Solid Spheres Size By Bond Display

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The maximum radius of the sphere that represents

You can customize the following bond display
an atom can be based on the VDW Radius or Partial
characteristics:
Charge. To specify which property to use, choose it
from the Size By pop-up menu in the Atom Display • Bond width
control panel. • Cylindrical bond pattern
The VDW Radius is specified using the atom type of • Taper bond pattern
the atom.
The Partial Charge is the result of a calculation: Bond Width
Extended Huckel, MOPAC, or Gaussian. If you The Bond Width slider in the Bond Display control
have not performed a calculation, the partial charge panel controls the width of bonds relative to the size
for each atom is 0. If you have performed more than of the atoms.
one calculation, you can specify the calculation to
use by choosing the Partial Charges dialog box from A scale of 1 produces very thin bonds. A scale of
the View menu. 100 produces very thick bonds. Increasing the value
of the Bond Width slider by 1 increases the thickness
When sizing by partial charge, the magnitude of the
of Cylindrical bonds by 0.0001Å times the value of
charge is used. An atom with a partial charge of
the Atom Size slider.
0.500 will have the same radius as an atom with a
partial charge of -0.500. For example, if the Atom Size is 20 and the Bond
Width is 30, cylindrical bonds are 0.06Å in diameter.
Solid Spheres Size % You can also change the width of bonds in Wire
The value of the Size % slider in the Atom Display Frame and Ball and Stick models by changing the
control panel represents a percentage of the value of the Bond Width slider. As the value of the
maximum radius specified for each atom. The Bond Width slider increases and the scale of the
maximum radius is set in the Size By pop-up menu. model increases, bonds become thicker.
This percentage ranges from 0 (small) to 100 (large).
Thus, when the Atom Size is 100, the atoms are Cylindrical Bond Pattern
scaled to their maximum radii. The value of this The Bond Display control panel contains menus that
setting affects Ball and Stick and Cylindrical Bond control the pattern used to fill cylindrical bonds
models. when that model display type is chosen. You can
choose a bond pattern for each bond.
Solid Spheres Vary Size by Depth

If you select Vary Size By Depth in the Atom Taper Cylindrical Bonds
Display control panel, the Depth Ratio slider applies If you select Taper Cylindrical Bonds, then
to atoms in Ball and Stick and Cylindrical Bonds cylindrical bonds are tapered more sharply
models. according to the Z coordinates of the corresponding

atoms. Accentuated tapering is an easy way to get The Stereo Views control panel appears.
more visual information about the
three-dimensionality of your model.
Atom Labels
You can control the appearance of element symbols
and serial numbers using the Atom Labels control
panel, and the corresponding commands in the
Object menu.
Default Display Options

To display Element Symbols and Serial Numbers as
you build:
• In the Atom Labels control panel, select
Element Symbols and Serial Numbers. 2. Select Display Stereo Views to display two
views of the model next to each other.
The right view is the same as the left view,
rotated about the Y-axis.
3. Specify the number of degrees of rotation by

All atoms currently in the model window
clicking the Stereo Offset arrows.
display the selected options.
Five degrees is a typical stereo offset for stereo
Displaying Labels Atom by Atom viewing. You can set the value of the Stereo
Offset control to 90 degrees to create
To display of element symbols or serial numbers in
orthogonal (simultaneous front and side) views.
individual atoms:
Stereo views can be shown either direct or
1. Select the atoms to change. cross-eyed. Some people can cross their eyes and
From the Object menu, point to the label to focus on two images, creating an enhanced three
display, and then choose Show. dimensional effect. This effect may be easier to
achieve on a printed stereo view of your model than
Stereo Views on the screen.
The Stereo Views control panel allows you to To select whether the views are cross-eyed or direct,
display and manipulate your model with two do one of the following:
different orientations at the same time. • Select Cross-Eyed to rotate the right frame to
the left. If your left eye focuses on the
To use the Stereo Views control panel:
right-hand model and your right eye focuses on
1. From the Settings dialog box, choose Stereo the left-hand model, the two stereo views can
Views. overlap.
• Select Direct to rotate the right view further to
the right.

Molecular Surface To display the resulting surfaces:
• From the View menu, choose one of the
Displays molecular surface types.
Molecular Surface displays provide information
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The currently selected calculation is named

about entire molecules, instead of the atom and bond
Extended Huckel.
information provided by the Structure displays.
Surfaces are good ways to show information about a • Click Show Surface.
molecule’s physical and chemical properties. They
To compute partial charges using the Extended
display aspects of the external surface interface or
Hückel method:
electron distribution of a molecule.
• From the Analyze menu, choose Extended
Unlike atom and bond data, Molecular Surface
Huckel Charges.
information applies to the entire molecule. Before
any molecular surface can be displayed, the data For each atom in the model, a message is created
necessary to describe the surface must be calculated listing the atom and its partial charge. If you have
using Extended Hückel or one of the methods selected Partial Charge in the Pop-up Information
available in CS MOPAC or Gaussian 2000. This control panel, then the partial charges will appear as
requires that under MOPAC you must choose the part of the pop-up information when you point to an
property Molecular Surfaces as one of the properties atom.
to be calculated.
Displaying Molecular
NOTE: Solvent Accessible Surface is an exception
and is automatically calculated from parameters Surfaces
stored in the Chem3D parameters tables. It is not To display a surface:
necessary to perform any additional calculations to
view a Solvent Accessible Surface, and the Show 1. Decide what surface type to display.
Surface button is always active.
2. Perform the necessary calculation using
Extended Hückel, CS MOPAC, or Gaussian
Extended Hückel 2000. Include the Molecular Surfaces property
Extended Hückel is a semi-empirical method that calculation whenever it is available.
can be used to rapidly generate molecular surfaces
for most molecular models. NOTE: CS MOPAC or Gaussian
2000 surfaces calculations are only available in
The Extended Hückel method is used in two
Chem3D Ultra.
commands in the Analyze menu: Extended Hückel
Surfaces and Extended Hückel Charges.
To compute molecular surfaces using the Extended

Hückel method:
• From the Analyze menu, choose Extended
Huckel Surfaces.
At this point, a calculation has been performed and
the results of the calculation are stored with the
model.

3. From the View menu, choose one of the surface
types.
Extended Gaussi
Surface Type Hückel MOPAC an
Solvent Yes Yes Yes

Accessible
Connolly Yes Yes Yes

Molecular
Surface
Types Total Charge Yes Yes Yes
Density
with Molecular Yes Yes Yes

Orbital map
A dialog box appears where you can set the with Spin Yes Yes
parameters for the display of the chosen Density map
molecular surface.
with Partial Yes Yes Yes
4. In the dialog box, select the Calculation type. Charges
Different calculation types can provide
with Molecular Yes Yes
different results. If you have performed more
Electrostatic
than one calculation on a model, for example,
Potential map
both an Extended Hückel and an AM1
calculation, you must choose which calculation Total Spin Yes Yes
to use when generating the surface. Density
5. Select a surface type from the menu.
Molecular Yes Yes
Not all surfaces can be displayed from all Electrostatic
calculations. For example, a Molecular Electrostatic Potential
Potential surface may be displayed only following a
Gaussian or MOPAC calculation. If a surface is Molecular Yes Yes Yes
unavailable, the Show Surface button is inactive. Orbitals
To generate surfaces from MOPAC or Gaussian, you
must choose Molecular Surfaces as one of the
properties calculated by these programs summarized
in the following table.
NOTE: Spin Density map requires that MOPAC or

Gaussian computations be performed with an open
shell wavefunction.

Molecular Surface Types Surface Type Description
Chem3D offers four different types of surface
displays, each with their own properties. These Translucent The surface is
types are shown in the following table: displayed in solid
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form, but is partially

Surface Type Description transparent so you can
also see the atoms and
Solid The surface is bonds within it.
displayed as an opaque Translucent is a good
form. Solid is a good compromise between
choice when you are surface display styles.
interested in the details NOTE: Translucent
of the surface itself, surfaces are not
and not particularly available on
interested in the Macintosh.
underlying atoms and
bonds. Molecular Surface Colors
To set the color of a surface:
Wire Mesh The surface is
• In the molecular surface dialog box, set the
displayed as a
connected net of lines. color of the surface.
Wire Mesh is a good To change the color of a surface:
choice when you want
to focus on surface 1. In the molecular surface dialog box, click Solid
features, but still have Color.
some idea of the atoms The Color or Color Picker dialog box appears.
and bonds in the
structure. 2. Select the new color.
Dots The surface is 3. Click OK.

displayed as a series of
unconnected dots. Dots The new color appears in the molecular surface
are a good choice if dialog box.
you are primarily
interested in the NOTE: The Molecular Electrostatic Potential
underlying structure Surface and Molecular Orbital Surface dialogs each
and just want to give an allow you to specify two colors. These colors may be
idea of the surface changed independently, following the procedure
shape. above.

Molecular Surface Isovalues However, high Grid values can also take a long time
to calculate. The default settings of 30x30x30 are a
The isovalue is, by definition, the constant value good compromise between speed and smoothness.
used to generate the surface (iso = same). For each
surface property, values can be calculated To set the Grid value:
throughout space. For example, the electrostatic • In the Molecular Surface dialog box, set the
potential is very high near each atom of a molecule, Grid for the surface.
and vanishingly small far away from it. Chem3D
To change the Grid value:
generates a surface by connecting all the points in
space that have the same value, the isovalue. • Click Set Grid.
Weather maps are a common example of the same The Grid Settings dialog box appears.
procedure in two dimensions, connecting locations
of equal temperature (isotherms) or equal pressure
(isobars).
To set the isovalue:
1. In the molecular surface dialog box, click Set

Isovalue.
NOTE: The exact name of this button reflects

the type of isovalue in each window. For
example, in the Total Charge Density Surface
You can set the grid density for the X, Y, and Z
dialog box, it is Set Isocharge.
axes independently. If Synchronize is selected,
The IsoCharge dialog appears. the settings for the other axes are the same as
the axis being adjusted.
To adjust the number of points used to create the

grid:
1. Deselect Synchronize before moving the

sliders.
2. Type the new isovalue. 2. Click Points.
3. Click Set. 3. Modify the X, Y, and Z axis sliders.
The new isovalue appears in the Molecular
Surface dialog box. To adjust the origin point of the grid (Å), which
controls the offset of the grid used to display the
surface relative to the underlying structure:
Setting the Surface Grid
The Surface Grid is a measure of how smooth the 1. Click Origin.
surface appears. The higher the grid density, the
2. Modify the X, Y, and Z axis sliders.
more points are used to calculate the surface. With a
higher grid density, the surface appears smoother.

To adjust the length (Å) of each axis of the grid: Solvent Accessible Surface
1. Click Points. The solvent accessible surface represents the portion
of the molecule that solvent molecules can access.
2. Modify the X, Y, and Z axis sliders.
When viewed in the ball and stick representation, a
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Reducing the length of a single axis by 50% or more molecule may appear to have many nooks and
is a good way to generate clipping planes. crannies, but often these features are too small to
3. Click OK.
affect the overall behavior of the molecule. For
example, in a ball-and-stick representation, it might
The new Grid Settings appear in the Molecular appear that a water molecule could fit through the
Surface dialog box. big space in the center of a benzene molecule. The
solvent accessible surface, which has no central
NOTE: You cannot set Grid Settings for each axis hole, shows that it cannot. The size and shape of the
independently when displaying Solvent Accessible solvent accessible surface depends on the particular
surfaces. Instead of a Set Grid button, the Solvent solvent, since a larger solvent molecule will
Accessible Surface dialog box has a single slider predictably enjoy less access to the crevices and
labeled Resolution, which changes the grid for all interstices of a solute molecule than a smaller one.
three axes simultaneously.
To determine the solvent-accessible surface, a small
probe sphere simulating the solvent molecule is
• In the Molecular Surface dialog box, change
rolled over the surface of the molecule (van der
any other settings that are unique to the surface
Waals surface). The solvent-accessible surface is
type.
defined as the locus described by the center of the
Some of the Molecular Surface dialog boxes provide probe sphere, as shown in the diagram below.
options not present in others. This is particularly true
for the Molecular Orbital Surface dialog box, which Solvent accessible surface
van der Waals surface
lets you choose which orbital to display. These
surface-specific options are discussed below.
To display the surface:
• Click Show Surface.
The desired surface appears.
Solvent probe
To clear all surfaces and discard the data used to
generate them:
1. From the Edit menu, choose Clear Molecular
Surfaces.
2. From the dialog box that appears, select the

surface data to discard.
3. Click Clear.
The selected surfaces are hidden and the data
used to create them are discarded. Because
surfaces take a lot of memory, clearing
unneeded surfaces ensures the smallest possible
files.

To access the Solvent Accessible Surface dialog The Map Property provides color-coded
box: visualization of Atom Colors, Group Colors,
• From the View menu, choose Solvent Hydrophobicity, Partial Charges, or Electrostatic
Potential (derived from partial charges)
Accessible Surface.
superimposed upon the solvent-accessible surface.
Hydrophobicity is displayed according to a
widely-used color convention derived from amino
acid hydrophobicities1, where the most hydrophobic
(lipophilic) is red and the least hydrophobic
(lipophobic) is blue. The following table shows
molecule hydophobicity.
Molecule Hydrophobicity
Phe 3.7 Most hydrophobic (Red)
Met 3.4
Ile 3.1
The Solvent Radius can be set from 0.1 to 10 Å Leu 2.8

using the slider. The default solvent radius is 1.4 Å,
Val 2.6
which is the value for water. Radii for some
common solvents are shown in the following table: Cys 2.0
Trp 1.9
Solvent Radius (Å)
Water 1.4 Ala 1.6
Methanol 1.9 Thr 1.2

Ethanol 2.2
Gly 1.0
Acetonitrile 2.3
Ser 0.6 Middle (White)
Acetone 2.4
Pro –0.2
Ether 2.4
Pyridine 2.4 Tyr –0.7
DMSO 2.5 His –3.0

Benzene 2.6
1. Engelman, D.M.; Steitz, T.A.; Goldman,
Chloroform 2.7 A., “Identifying nonpolar transbilayer
helices in amino acid sequences of
membrane proteins”, Annu. Rev. Biophys.
Biophys. Chem. 15, 321-353, 1986.

To display a Connolly Surface:
Molecule Hydrophobicity
1. From the View menu, select Connolly
Gln –4.1 Molecular.
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Asn –4.8 The Connolly Surface dialog box appears.
Glu –8.2
Lys –8.8
Asp –9.2
Arg –12.3 Least hydrophobic (Blue)

The Partial Charges and Electrostatic Potential
(derived from the partial charges) properties are
taken from the currently selected calculation. If you
have performed more than one calculation on the
model, you can specify which calculation to use by
choosing the Partial Charges or Molecular
Electrostatic Potential dialog boxes from the View 2. Select the appropriate options.
menu and choosing a Calculation from the
Calculation pop-up menu in that dialog box. 3. Click Show Surface.
The Connolly Surface of Crambin is shown
Connolly Molecular Surface below:
The Connolly surface, also called the molecular
surface, is similar to the solvent-accessible surface.
Using a small spherical probe to simulate a solvent,
it is defined as the surface made by the contact of the
solvent sphere with the van der Waals surface. The
volume enclosed by the Connolly surface is called
the solvent-excluded volume. These surfaces are
shown in the following illustration.

Total Charge Density
The total charge density is the electron density in the
space surrounding the nuclei of a molecule, or the
probability of finding electrons in the space around
a molecule. The default isocharge value of 0.002
atomic units (a.u.) approximates the molecule’s van
der Waals radius and represents about 95% of the
entire three-dimensional space occupied by the
molecule.
The total charge density surface is the best visible
representation of a molecule’s shape, as determined
by its electronic distribution. The Total Charge
Density surface is calculated from scratch for each Total Spin Density
molecule. The Total charge density is generally The total spin density surface describes the
more accurate than the Space Filling display. difference in densities between spin-up and
spin-down electrons in any given region of a
molecule’s space. The larger the difference in a
given region, the more that region approximates an
unpaired electron. The relative predominance of
spin-up or spin-down electrons in regions of the
total spin density surface can be visualized by color
when total spin density is mapped onto another
surface (total charge density). Entirely spin-up
(positive value) electrons are red, entirely
spin-down (negative) blue, and paired electrons
(neutral) are white.
The total spin density surface is used to examine the
unpaired electrons of a compound. The surface
exists only where unpaired electrons are present.
Map Property maps a color-coded visualization of a Viewing the total spin density surface requires that
selected property onto the charge density surface. spin density is calculated by MOPAC or Gaussian
The available properties are Molecular Orbital, Spin using an Open Shell Wavefunction.
Density, Electrostatic Potential, and Partial Charges.
The color scale uses red for the highest magnitude
and blue for the lowest magnitude of the property.
Neutral is white. The scale is shown below.
The Set Orbital button applies to Molecular Orbital
Map Property; clicking it opens a dialog box, shown
below, with a menu of orbitals which may be
mapped onto the surface. The orbital number
appears in parentheses in the Map Property menu.

Molecular Electrostatic
Potential
The molecular electrostatic potential (MEP)
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represents the attraction or repulsion between a

molecule and a proton. Attraction is represented by
negative values and repulsion is indicated by
positive values. Experimental MEP values can be
obtained by X-ray diffraction or electron diffraction
techniques, and provide insight into which regions
of a molecule are more susceptible to electrophilic
or nucleophilic attack. You can visualize the relative
MEP values by color when MEP is mapped onto
another surface (total charge density). The most
positive MEP value is red, the most negative blue,
and neutral is white. You can specify the isocontour value for any
computed MO surface using the Set Isocontour
button in the Molecular Orbital Surface dialog box.
The default isocontour value for a newly computed
surface is the value you last specified for a
previously computed surface. If you have not
specified an isocontour value, the default value is
0.01.
NOTE: The default isocontour value for an MO

surface imported from a cube file is 0.01 regardless
of any previously set isocontour value.
Molecular Orbitals
Molecular orbital (MO) surfaces visually represent
Visualizing Surfaces
the various stable electron distributions of a from Other Sources
molecule. According to frontier orbital theory, the You can use files from sources other than Chem3D
shapes and symmetries of the highest-occupied and to visualize surfaces. From Windows sources, you
lowest-unoccupied molecular orbitals (HOMO and can open a Gaussian Formatted Checkpoint (.fchk)
LUMO) are crucial in predicting the reactivity of a or Cube (.cub) file.
species and the stereochemical and regiochemical
From sources other than Windows, create a
outcome of a chemical reaction.
Gaussian Cube file, which you can open in
Chem3D.

Chapter 7: Inspecting Models
Model Data You can display the following information about a
bond:
You can view information about an active model as • Labels of the two atoms which make up the
a pop-up or in measurement windows. bond
• Bond length
Pop-up Information
• Bond order
You can display information about atoms and bonds
by pointing to them so that pop-up information • Information relative to other selected atoms,
appears. You can specify what information appears such as the angle formed by three atoms and the
by using the Pop-up Information control panel in the dihedral angle formed by four atoms.
Settings dialog box.
You can display the following information about an

atom:
• Atom label (element and serial number)
• Cartesian coordinates
• Atom type
• Internal coordinates (Z-matrix)
• Information relative to other selected atoms,
such as: the distance between two atoms, the
angle formed by three atoms, the dihedral angle NOTE: Precise bond orders for delocalized pi
formed by four atoms systems are computed whenever the MM2
Force Field is computed.
• Formal Charge
• Partial Charge The Pop-up Information control panel allows you to
Atom pop-up information is shown below: select what information appears when you point at
atoms and bonds.
To display the Pop-up Information control panel:
2. Select Pop-up Information from the

drop-down menu.
Chem3D Chapter 7: Inspecting Models • 93

The Pop-up Information control panel appears.
If you want to Then Select…
display …
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the atom type Atom Type.

corresponding to the
first column of a record
in the Atom Types table
a list of the atoms used Z-matrix.

to position the atom
The Z-matrix definition
includes whether the
second angle used to
3. Take the appropriate action: position the selected
atom is a dihedral angle
or a second bond angle.
If you want to … Then …
If atoms other than the
display pop-up Leave Show one at which you are
information Information While pointing are selected,
Pointing selected. the measurement
formed by all the
hide pop-up Deselect Show selected atoms appears.
information Information While
Pointing.
the distance between Bond Length.
the atoms attached by a
The information about an atom or bond always
bond in angstroms
begins with the name of that object, such as
C(12) for an atom or O(5)-P(3) for a bond.
the bond orders Bond Order.
To set what pop-up information appears: calculated by Minimize
Energy, Steric Energy, Bond orders are usually
or Molecular Dynamics 1.000, 1.500, 2.000, or
If you want to Then Select… 3.000 depending on
display … whether the bond is a
single, delocalized,
the three numerical Cartesian double, or triple bond.
values indicating the Coordinates. The computed bond
atom’s position along orders can be fractional.
the X, Y, and Z axes
94 • Chapter 7: Inspecting Models Chem3D

Measurement Tables
If you want to Then Select…
display … The Measurements tables contain internal
measurements between various atoms in your
model.
the partial charge Partial Charge.
according to the To display internal measurements:
currently selected If more than one
calculation was • From the Analyze menu, point to Show
calculation
performed, you can Measurements, and then choose the table to
specify the calculation display.
to use as follows:
a.From the View menu,

choose Partial
Charges.
b.In the Partial Charges

dialog box, choose the
appropriate
calculation.
Non-Bonded Distances
To display non-bonded atoms measurements: The measurements are listed in the following order:
• Select two non-bonded atoms and point to one • Bond lengths
of them. • Interatomic distances
The interatomic non-bonded distance appears in the • Bond angles
last line of the pop-up window.
• Dihedral angles
For example, in the cyclohexane model below, when
you select two non-bonded atoms and point to one of Measurements of the same type are organized by
them, the interatomic non-bonded distance appears serial number.
in the last line of the pop-up window.
Removing Measurements from a Table
You can remove information from the
Measurements table without affecting the model.
For example, when tracking a measurement during
an analysis and Copy Measurements to Messages is
turned on, you may only want to see a subset of
measurements.

To remove measurements form a table: Chem3D reconciles the actual distance between
atoms in two fragments to their optimal distances by
1. Drag diagonally across the measurements you rigidly moving one fragment relative to the other.
want to remove.
Non-Bonded Distances in Tables
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The record select icons are highlighted.
2. Do one of the following: To display non-bonded atom measurements:
• From the Edit menu, choose Clear. 1. Select the atoms.

• Press Delete or Backspace. 2. From the Object menu, choose Set Distance.
Editing Measurements The Measurements table appears with the

measurement between the selected atoms.
If you select a measurement in the Measurements
table, the corresponding atoms are selected in the Showing Bond Lengths
model window. If you select atoms in your model,
any corresponding measurements are selected. To display all of the bond lengths for a model in the
Measurements table:
To change the value of a measurement: • From the Analyze menu, point to Show
1. Select the text in the Actual column. Measurements, and then choose Show Bond
Lengths.
2. Type a new measurement value in the selected
cell. For example, to display the bond lengths in a
penicillin molecule1:
When atoms are deleted or hidden, any
measurements that refer to them are removed from 2. Click in an empty model window.
the Measurements table. A text box appears.
Optimal Measurements 3. Type Penicillinyl and press Enter or Return.
Optimal measurements are used only when the
4. Select the N(1)-C(5) bond.
Measurements table is visible. When the
Measurements table is not visible, the standard 5. From the Analyze menu, point to Show
measurements are taken from the parameter tables.
To specify optimal values for particular Lengths.
measurements, use the Optimal column. The
Optimal column value is used instead of the
corresponding standard measurement when that
measurement is required in an operation such as
Clean Up Structure.
Chem3D uses the optimal distance between atoms 1. The unsubstituted penicillin ring system is used in
in different fragments with the Dock command. the following examples. Typically, the carbonyl
When you choose Dock from the Tools menu, carbon of the acetamido moiety attached to C6 of the
penicillin ring is substituted by groups other than
hydrogen.

The Measurements table appears with the bond For example, to display the bond angles in a
lengths for the penicillin molecule. That the penicillin molecule:
N(1)-C(5) bond length is 1.468Å.
2. Click in an empty model window.

A text box appears.
3. Type Penicillinyl and press Enter or Return.

6. Click the N(1)–C(5) bond record to select the
corresponding atoms in the model.
Angles.
The Measurements table appears with the bond
angles for the penicillin molecule. The N(1)-
C(5)-C(6) bond angle is about 87°.
6. Click the N(1)-C(5)-C(6) angle record to select

the corresponding atoms in the model.
When you select any of the bond angle records
in the Measurements table, the corresponding
atoms and bonds in the model are selected.
When you select one or more of the bond length

records in the Measurements table the 7. Click the N(1)-C(5)-C(6) angle record.
corresponding atoms and bonds in the model
are selected.
Showing Bond Angles

To display all of the bond angles for a model in the
Measurements table:
• From the Analyze menu, point to Show
Angles.

The corresponding atoms in the model are 5. Select the C(7)-N(1)-C(2)-C(8) dihedral angle.
selected.
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Measurements, and then choose Show
Dihedral Angles.
Showing Dihedral Angles The Measurements table appears with the
To display the dihedral angles for a model in the dihedral angles for the penicillin molecule. The
Measurements table: C(7)-N(1)-C(2)-C(8) dihedral angle is
approximately 107°.
Measurements, and then choose Show
Dihedral Angles.
For example, to display the dihedral angles in a

penicillin molecule:

Showing Close Contacts
A text box appears.
To display the close contacts for a model in the
3. Type Penicillinyl and press Enter or Return. Measurements table:
Measurements, and then choose Show Close
Contacts.
Two atoms are considered to be in close contact if
the distance between them is less than or equal to the
sum of their van der Waals radii. The van der Waals
radii used to determine close contacts are located in

the Atom Types table. In general, the van der Waals In the following illustration, C(8) and H(17) are in
radii in the parameter set supplied with close contact because the distance between them,
Chem3D were computed on the assumption that a 2.442Å, is less than the sum of their van der Waals
hydrogen atom is in close contact with another atom radii, 2.597Å.
when the energy of interaction is greater than or
equal to 0.5 kcal/mol.
For example, to display the Close Contacts in a


A text box appears.


Measurements, and then choose Show Close
Contacts. Showing Ring Closures
The Measurements table appears with the close
To display the ring closure bonds and ring closure
contacts records shown between the bond
angles in the Measurements table:
length records and the bond angle records.
• From Analyze menu, point to Show
Measurements, and then choose Show Ring
Closures.
For example, to display the Ring Closures in a

Atoms C(7) and H(17) are in close contact; their 1. Click the Text Building tool.
distance apart is approximately 2.4Å.
6. Click in a blank area of the Measurements A text box appears.
table to deselect all measurements.
7. Click the C(7), H(17) close contact record.
When you select any of the close contact
Measurements, and then choose Show Ring
records in the Measurements table, the
Closures.
corresponding atoms in the model are selected.

The Measurements table appears with the ring A text box appears.
closure bonds and ring closure angles in the
penicillin molecule.
A penicillin model appears in the model
The C(2)-C(3) and C(6)-C(7) bonds are ring
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window.
closure bonds.
Numbers and then choose Show.
7. Select the sulfur atom.
8. Shift-click the other atoms in the

5. Select the C(2)-C(3) and C(6)-C(7) ring closure
five-membered penicillin ring.
records.
The molecule should appear as follows:
The corresponding bonds in the model are
selected, as shown in the following illustration.
9. From the Analyze menu, choose Deviation

from Plane.
Showing the Deviation from Plane
When the deviation from plane calculation is
The Deviation from Plane command allows you to complete, the value appears in the Message
compute the RMS Deviation from the least squares
window.
plane fitted to the selected atoms in the model.
For example, to examine the Deviation from Plane NOTE: The five atoms in the five-membered ring of
for five atoms in a penicillin molecule: penicillin are not totally coplanar; there is a slight
pucker to the ring.
3. Click the model window.

Displaying the Coordinates To change which atoms Chem3D uses to position
each atom:
Tables
use the commands in the Set Z-matrix submenu in
You can view the internal coordinates or the the Tools menu.
Cartesian coordinates of your model by choosing
Show Model Table from the Tools menu. Cartesian Coordinates
The fields in the Cartesian Coordinates table contain
Internal Coordinates
the atom name and the X-, Y- and Z- coordinates for
The Internal Coordinates table contains one entry each atom. The order of atoms is determined by their
for each atom. The fields contain a description of serial numbers. All of the atoms in a fragment are
how each atom in the model is positioned relative to listed in consecutive records. Hydrogen, lone pair
the other atoms in the model. and dummy atoms are listed after heavy atoms.
The order of atoms in the Internal Coordinates table
To display the Cartesian Coordinates table:
is determined by the Z-matrix. The origin atom is
listed first, and the rest of the atoms are listed in the 1. From the Tools menu, point to Show Model
order that they are positioned. For more information Table, and then choose Cartesian
see “Changing the Z-matrix” on page 71. Coordinates.
To display the Internal Coordinates table: The Cartesian Coordinates table appears.
1. From the Tools menu, point to Show Model
Table, and then choose Internal Coordinates.
The Internal Coordinates table appears.
When you select a record in the Cartesian

Coordinates table, the corresponding atom is
selected in the model. When you select an atom in
the model, the corresponding record is selected in
the Cartesian Coordinates table.
When you select a record in the Internal Coordinates Displaying the Groups Table
table, the corresponding atom is selected in the
Chem3D creates a group when you use a
model. When you select atoms in the model, the
substructure name in text when building a model or
corresponding records are selected in the Internal
when you import PDB files containing residue
Coordinates table.
information. You can create groups manually using
To edit measurements in the Z-matrix: the Define Group command in the Object menu.
1. Type a new measurement in the selected cell. To select atoms in a group:

• Click the Record selector for the group to
select.

Coloring Groups The Message Window
To color all the atoms in a group: Calculations on models and other operations,
produce messages. The messages are displayed in
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the Messages window. For information about the

2. Select the Model Display control panel. Message Controller, see “Model Window” in
"Chapter 1, Introduction."
3. Select by Group from the Color menu.
Each atom in your model appears in the color
specified for its group.
To change the color of a group:
1. Double-click the Color field in the Groups

table.
When you select a message in the Messages table
The Color dialog box or Color Picker opens. that includes information about atoms, the atoms are
2. Select a new color for the group. selected in the model window.
When you save your model, the messages in the
3. Click OK. Messages table are stored with the model.
The color of the atoms in your model for that You can remove information from the Messages
group will change to the new color. The change table without affecting the model.
you made only applies to the selected group.
To remove messages:
If a group was created by a substructure instead of
by using the Define Group command, you can 1. In the Messages table, drag diagonally across
change the substructure color globally so the color is the messages you want to remove.
applied to any new group created.
The record select icons are highlighted.
To change substructure colors:
1. From the View menu, choose the
• From the Edit menu, choose Clear.
• Press Delete or Backspace.
The Table Editor opens.
2. Double-click the Color field to change. Docking Models

The Color dialog box or Color Picker opens. The Dock command enables you to position a
fragment into a desired orientation and proximity
3. Select a new color for the group.
relative to a second fragment. Each fragment
4. Click OK. remains rigid during the docking computation.
The Dock command is available when two or more
The new color is applied to any created by
distances between atoms in one fragment and atoms
substructure.
in a second fragment are specified. These distances
The color of the atoms in your model for that group are entered into the Optimal field in the
change the color as discussed above. Measurements table.

An atom pair is an atom in one fragment which has 4. Drag the Y-axis rotation bar until both polymer
a distance specified to an atom in a second fragment. molecules are –55° about the Y-axis.
For example, to see docking simulate the association The resulting model appears as shown in the
of regions of similar lipophilicity and hydrophilicity following illustration (the second model may appear
on two proximate polymer chains: in a different position on your computer):
Build a polymer chain:

A text box appears.
4. Type (AA-mon)3(C2F4)4(AA-mon)3H

A polyacrylic acid/polytetrafluoroethylene
block copolymer appears in the model window.
To set optimal distances between atoms in one
The text, (AA-mon)3, is converted to a polymer
fragment and atoms in the second fragment:
segment with three repeat units of acrylic acid.
The text, C2F4)4, is converted to a polymer 1. In the Settings dialog box, choose the Atom
segment with four repeat units of Labels control panel.
tetrafluoroethylene.
2. Click Serial Numbers.
Build a copy of the chain: The serial numbers appear for the visible atoms
• Double-click in the model window well above in the model window. Setting distances between
atoms pairs is easier when the serial numbers
the first polyacrylic
are displayed.
acid/polytetrafluoroethylene block copolymer
molecule. 3. Select C(6) in the bottom molecule.
A second polymer molecule appears above the 4. Shift-click C(98) in the top molecule.
first polyacrylic acid/polytetrafluoroethylene
block copolymer molecule. 5. From the Object menu, choose Set Distance.
The Measurements table appears with the
Orient the chains: Actual field highlighted. The Actual field
1. Click in the empty space in the model window contains the current distance between the two
to deselect any atoms in the model window. atoms listed in the Atoms field.
2. From the Tools menu, choose Rotation Bars. 6. Click the Optimal cell.
The Rotation Bars appear around the model. 7. Type 5 and press Enter or Return.
3. From the Tools menu, choose Status Bar. The optimal distance between C(6) and C(98) is
The Status Bar appears. specified as 5.000Å.

To have a reasonable dock, you must specify at least
four atom pairs. In the following example, fourteen
atoms pairs are specified. The following the
Measurements table illustration contains the
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fourteen atom pairs and their optimal distances.
To reproduce this example:

• Set the measurements between your two
polymer molecules to match the measurements
in the following illustration.
Ignore the distances in the Actual cell because they
depend on how the second polymer was positioned 3. Type 0.100 for the Minimum RMS Error value
relative to the first polymer when the second
and 0.010 for the Minimum RMS Gradient.
polymer was created.
The docking computation stops when the RMS
Error or the RMS Gradient becomes less than
the Minimum RMS Error and Minimum RMS
Gradient value.
4. Click Display Every Iteration.

How the fragments are moved after each
iteration of the docking computation are
displayed.
To save the iterations as a movie, do one of the

following:
• Click Record Each Iteration.
Click the Movie Controller Record button
before you start the Dock computation.
When the docking computation begins, the
Message Controller and the Movie Controller
appear.
To begin the docking computation:
To stop the docking computation:
• Click the Movie Controller Stop button.
Labels control panel and deselect Show Serial
Numbers. Docking and recording are also stopped.
While the docking computation proceeds, one
2. From the Tools menu, choose Dock.
molecule remains stationary and the second
The Dock dialog box appears. molecule moves.
The Messages window displays messages
describing each iteration of the docking
computation.

The following illustration shows the docked
polymer molecules.
Comparing Models by
Overlay
Choose the Overlay command from the Tools menu
to lay one fragment in a model window over a
second fragment (superimpose). Each fragment
remains rigid during the overlay computation.
Common uses of Overlay include:

• Comparing structural similarities between
The following illustration shows the distances models with different composition.
between atom pairs at the completion of the docking • Comparing conformations of the same model.
computation. The distances in the Actual cell are
close to the distances in the Optimal cell. For example, to superimpose a molecule of
Methamphetamine on a molecule of Epinephrine
(Adrenalin) to demonstrate their structural
similarities:

A text box appears.
4. Type Epinephrine and press Enter or Return.

A molecule of Epinephrine appears.
5. Click in the model window, below the

Epinephine molecule.
A text box appears.
6. Type Methamphetamin and press Enter or

Your results may not exactly match those described Return.
here. The relative position of the two fragments or A molecule of Methamphetamine appears
molecules at the start of the docking computation beneath the Epinephrine molecule.
can affect your results. For more accurate results,
lower the minimum RMS gradient. 7. From the Tools menu, deselect Show H’s and
Lp’s.
The hydrogen atoms and lone pairs in the
molecule are hidden.

The two molecules should appear as shown in For an acceptable overlay, you must specify at least
the following illustration. You may need to three atom pairs, although it can be done with only
move or rotate the models to display them as two pairs. In this example, five atoms pairs are
shown. specified. The following illustration contains these
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atom pairs.
9
10
1
11
2
3
4
8 43
34 44
5
12
7 35
6 37
42
36
13 38
41
40 39

Labels.
To perform the overlay computation:
9. Click Show Serial Numbers. 1. Create atom pairs between the Epinephrine and
The serial numbers appear for all the visible Methamphetamine molecules as shown in the
atoms. Measurements table above.
To perform an overlay, you must first identify atom

NOTE: To help see the two overlaid fragments,
pairs by selecting an atom in each fragment, and
you can color a fragment. For more
then display the atom pairs in the Measurements
information see “Coloring Groups” on page
table.
102
1. Select C(11) in the top molecule.
2. Shift-click C(44) in the bottom molecule.
Labels, and then deselect Show Serial
3. From the Object menu, choose Set Distance. Numbers.
The Measurements table appears with the 3. From the Tools menu, choose Overlay.
Actual cell highlighted. The Actual cell
The Overlay dialog box appears.
contains the current distance between the two
atoms listed in the Atom cell.
The optimal distances for overlaying two fragments
are assumed to be zero for any atom pair that appears
in the Measurements table. Ignore the distances in
the Actual cell because they depend on the position
of the Methamphetamine molecule relative to the
Epinephrine molecule.

4. Type 0.100 for the Minimum RMS Error and
0.010 for the Minimum RMS Gradient.
The overlay computation stops when either the
RMS Error or the RMS Gradient becomes less
than the Minimum RMS Error and Minimum
RMS Gradient value.
5. Click Display Every Iteration.
6. Click Start.
How the fragments are moved at each iteration
of the overlay computation is displayed. The following illustration shows the distances
between atom pairs at the completion of the overlay
To save the iterations as a movie, do one of the computation. The distances in the Actual cells are
following: quite close to zero.
• Click the Record Each Iteration check box.
• Click the Movie Controller Record button
before performing the Overlay computation.
The Message Controller and the Movie
Controller appear.
As the overlay proceeds, one molecule remains
stationary and the second molecule moves.
Your results may not exactly match those described.
To stop the overlay computation:
The relative position of the two fragments or
• Click the Movie Controller Stop button. molecules at the start of the computation can affect
The Overlay operation stops. Recording is also the final results.
stopped.
The Messages window displays messages
Animations
describing each iteration of the overlay You can animate any of the visualization operations
computation. such as rotation and spinning, and iterations from
computations by saving frames in a movie. The
The following illustration shows the Epinephrine Movie Controller controls the creation and playback
and Methamphetamine molecules after the overlay of movies.
computation finishes.
The Movie Controller is shown below:
Start button Record button Movie Controller Slider
Stop button Movie Controller Slider Knob

Creating and Playing Movies Movie Control Panel
To display the Movie Controller: You can control how a movie is created by changing
settings in the Movies control panel in the Settings
• From the Tools menu, choose Movie dialog box. You can specify the number of frames
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Controller. and at what increment they are captured.

The Movie Controller appears automatically during
To display the Movies control panel:
a computation.
To create a movie:
2. In the Settings dialog box, choose Movies.
1. Click Record.
3. Take the appropriate actions:
2. Begin the rotation or analysis you want to save
as a movie.
To stop recording:
• Click Stop.
show the model Click Track Rotations
To manually view different frames of your movie: monochrome when in Monochrome.
• Drag the Slider knob to the frame to view. using the Rotation bars
or the Trackball tool
To play back a movie you created:
• Click Start. specify the speed at Drag the Speed slider
To stop playback of a movie: which the movie is knob to the left to play
replayed your movie at a slower
• Click Stop.
speed (a smaller number
of degrees per second).
Editing a Movie Drag the Speed slider
You can change the frames in a movie by removing knob to the right to play
them. your movie at a faster
speed (a larger number
To remove all frames before the frame that you are of degrees per second).
viewing:
• From the Edit menu, point to Clear Frames,
and then choose Clear Previous Frames.
To remove all frames after the frame you are

viewing:
and then choose Clear Subsequent Frames.
To remove all frames except for the one that you are
viewing:
and then choose Clear All Other Frames.

Spin Torsional Angles
To spin the torsional angles specified by selecting
specify the number of Drag the Smoothness two, three, or four atoms:
degrees of rotation that slider knob to the left to • From the Analyze menu, choose Spin
is captured as a frame capture more frames (a Torsional Angles.
while recording. smaller number of
The internal rotation is specified by a bond. The
degrees of rotation
fragment at one end of the bond is stationary
capture a frame). Drag
the Smoothness slider while the fragment attached to the other end
knob to the right to rotates. If only one atom is selected, then the
capture fewer frames (a stationary fragment is defined by whichever
larger number of atom bonded to the selected atom has the lowest
degrees of rotation serial number. If a fragment is selected, then
capture a frame). that fragment rotates and the unselected atoms
remain stationary.
Spinning Models To stop spinning:
You can spin models about a selected axis or by • Click Stop.
torsional angles. The number of frames created
Spins are automatically recorded.
when you choose a Spin command is set using the
Smoothness Slider in the Movies control panel. To replay the spin:
Click Start.
Spin About Selected Axis
To spin the model around an axis specified by a
selection:
1. Select only two atoms or one bond.
2. From the Analyze menu, choose Spin about

Selected Axis.
To stop spinning:
• In the Movie Controller, click Stop.
Spins are automatically recorded.
To replay the spins:
• Click Start.

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Chapter 8: Printing and Exporting Models
Printing Models 2. Select the appropriate options:
You can print Chem3D models to PostScript and If you want to … Then click …
non-PostScript printers. Before printing you can
specify options about the print job.
choose a vertical Portrait or
Specifying Print Options (Portrait) or Landscape.
horizontal
To prepare your model for printing: (Landscape)
orientation for your
1. From the File menu, choose Print Setup (Page model
Setup).
The Print Setup dialog box appears. The resize your model Scale To and type a
available options depend on the printer you use. according to a scaling scaling value.
factor
Scaling factors are
measured in pixels
per angstrom. A pixel
is 1/72 of an inch, or
approximately 1/28
of a centimeter. With
a value of 28
pixels/Ångstrom your
model is scaled so
that a distance of one
Ångstrom in the
model is 1 centimeter
in the printed image.
If you specify a value
of 72
pixels/angstrom, a
distance of one
angstrom in the
model is scaled to 1
inch on the printed
image.
Chem3D Chapter 8: Printing and Exporting Models • 111

Exporting Models Using
Different File Formats
scale your model so Scale To Full Page. The following table shows most of the chemistry file
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the printed image fills formats supported by Chem3D for export. For more
the printed page information about file formats, see Appendix I: File
Formats in the online Help.
print a footer at the Include Footer.
bottom left of the
printed page File Format Name Extension
containing the name
of the model and the Alchemy Alchemy .alc
date and time changes
were last made Cartesian Cart Coords 1 .cc1
Coordinate
Printing Cart Coords 2 .cc2

To print the contents of the active window:
ChemDraw ChemDraw .cdx
• From the File menu, choose Print.
The Print dialog box appears. The contents of Connection Conn Table .ct
the dialog box depend upon the type of printer Table
you are using.
GAMESS Input GAMESS .inp
If a model window is active, then a picture of
Input
the model is printed. The picture of the model is
scaled according to the settings in the Page
Gaussian Input Gaussian Input .gjc
Setup dialog box.
If a table is active, then the contents of the table Internal Int Coords .int
prints. The table is printed using the font and Coordinates
size specified in the Text control panel of the
Settings dialog box. MacroModel MacroModel .mcm
Molecular MDL MolFile .mol

Design Limited
MolFile
MSI ChemNote MSI .msm

ChemNote
MOPAC input MOPAC .mop

file
112 • Chapter 8: Printing and Exporting Models Chem3D

WMF (Windows only)
File Format Name Extension
The Windows Metafile file format saves the 16-bit
MOPAC graph .gpt GDI representation of a Chem3D picture. The WMF
file file format enables you to transfer Chem3D pictures
to other applications, such as Microsoft Word for
Protein Data Protein DB .pdb Windows, that support that WMF file format. The
Bank Windows Metafile format can be used by Windows
3.x, 95, 98, and NT.
ROSDAL Rosdal .rdl
EMF (Windows only)
Standard SMD File .smd The Enhanced Metafile format is a 32-bit superset of
Molecular Data the 16-bit metafile. It contains a more elaborate set
of commands for displaying a picture, but is less
SYBYL MOL SYBYL .sm1 widely supported than the WMF format. It is
compatible with Windows 95, 98, and Windows NT,
SYBYL MOL2 SYBYL2 .sm2 but not with Windows 3.x.
To save a model with a different format, name or Bitmap (Windows only)

location: The Bitmap file format saves the bitmapped
1. From the File menu, choose Save As. representation of a Chem3D picture. The Bitmap
file format enables you toy transfer
The Save File dialog box appears. Chem3D pictures to other applications, such as
Microsoft Word for Windows, that support bitmaps.
2. Specify the name of the file, the folder, and disk
where you want to save the file. PICT (Macintosh only)
3. Select the file format in which you want to save The PICT file format saves the bitmap
the model. representation of a Chem3D picture. The PICT file
format enables you to transfer Chem3D pictures to
4. Type a file name. other applications, such as Microsoft Word, that
support the PICT file. The PICT format is also used
5. Click Save.
for transferring information to and from the
When you save a file in another file format, only Clipboard.
information relevant to the file format is saved. For
example, you will lose dot surfaces, color, and atom EPS
labels when saving a file as an MDL MolFile.
The PostScript file format saves models as
Formats for Publishing encapsulated postscript file (EPS). EPS files are
ASCII text files containing the scaleable PostScript
Applications representation of a Chem3D picture. You can open
The following file formats that are used to export EPS files using other applications such as
models as pictures for desktop publishing and word PageMaker. You can transfer EPS files among
processing software. platforms, including Macintosh, Windows, and
UNIX.

TIFF If you want to … Then choose …
The Tagged Image File Format (.tifF) contains
binary data describing a bitmap image of the model. use printing press style CMYK Contiguous.
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TIFF format is a high resolution format commonly of color encoding.

used for saving graphics for importing into desktop Stores colors non-
publishing applications on the same or on different sequentially. For
computer platforms. TIFF images can be saved example:
using a variety of resolution, color, and compression CMYKCMYK. The
options. As TIFF images can get large, choosing PackBits
appropriate options is important. compression type
When you save a file as TIFF, an option button provides no
appears in the Save As dialog box. compression for this
type of file.
To specify the save options:
1. Click Options: NOTE: If objects in your document are black and

The TIFF Options dialog box appears. white they are saved as black and white regardless
of which Color options you set. If you import
drawings from other applications and want them to
print Black and White you must set the Color option
to Monochrome.
4. Choose a compression option:
2. Choose a resolution. The size of the file If you want to … Then choose …
increases as the square of the resolution.
reduce file size by PackBits.
3. Choose a color option:
encoding repeating
bytes of information as
If you want to … Then choose … output. For example,
for a line of color
force objects to black Monochrome. information such as:
and white. CCCCCMMMMMYY
YYYKKKKK, the
compression yields a
store colors using RGB Indexed.
smaller file by
computer monitor style
representing the
of color encoding.
information as
C46M5Y5K.
fax transmissions of CCITT Group 3 or

images CCITT Group 4.

3DMF Format (PNG)
Use the Portable Network Graphics (PNG) file
The 3D MetaFile (3DMF) file format contains a
format to publish models on the world wide web.
3-dimensional object data describing the model.
Applications that can import PNG files include
YOu can import 3DMF files into many 3D modeling
Netscape Communicator and Microsoft Internet
applications and the latest versions of the Macintosh
Explorer.
Scrapbook. You can transfer 3DMF files between
Macintosh and Windows platforms.
Formats for Chemistry
Chem3D Templates and Stationery Modeling Applications
The Chem3D Template (Windows) or Chem3D The following file formats are used to export models
Stationery (Macintosh) file format is used to open to chemistry modeling application other than
and save pre-configured documents. Pre-configured Chem3D.
documents store Settings and models that Chem3D
uses when you create a new Model.
Alchemy
Movie (Macintosh only) Use the Alchemy (.alc) file format for saving models
for importing into TRIPOS applications such as
Use this file format to save a movie you have created
Alchemy.
for the active model. You can import the resulting
movie file into any application that supports the
QuickTime file format, such as MacroMind Director
and Microsoft Word. Use Cartesian Coordinates 1 (.cc1) or 2 (.cc2) to
export the X, Y, and Z Cartesian coordinates for
your model.
PICS (Macintosh only)
When you save a file as Cartesian Coordinates, an
Use this file format to save each frame of a movie
option button appears in the Save As dialog box.
for the active model. You can import he resulting file
into any application that supports the PICS file To specify the save options:
format, such MacroMind Director.
1. Click Options:
Graphics Interchange Format (GIF) The Cartesian Coordinates Options dialog box
Use the Graphics Interchange Format (GIF) to appears.
publish a Chem3D model on the on the world wide
web. The GIF format allows Web Browsers to view
the picture on the web, instead of in Chem3D.
The model window background color is used as the
transparent color in the GIF format graphic.
Portable Network Graphics

2. Select the appropriate options: The Connection Table Options dialog box
appears.
If you want the file Then click …
to …
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contain a connection By Serial Number.

table for each atom with
serial numbers
contain a connection By Position.

table for each atom that
describes adjacent atoms Select the appropriate options:
by their positions in the
file If you want to add … Then click …
not contain a connection Missing. a blank line to the top of 1 Blank Line.
table the file
contain serial numbers Include Serial

two blank lines to the top 2 Blank Lines.
Numbers.
of the file
contain atom type Include Atom Type

three blank lines to the 3 Blank Lines.
numbers Text Numbers.
top of the file
contain internal Save All Frames.

coordinates for each Gaussian Input
view of the model
Use the Gaussian Input (.gjc, .gjf) file format to save
models to submit for Gaussian calculations. Only
Connection Table the Molecule Specification section of the input file
is saved. For atoms not otherwise specified in
Chem3D uses the atom symbols and bond orders of
Chem3D, the charge by default is written as 0, and
connection table files to guess the atom symbols and
the spin multiplicity is written as 1. You can edit
bond orders of the atom types.
Gaussian Input files using a text editor with the
When you save a file as a Connection Table, an addition of keywords and changing optimization
Options button appears in the Save As dialog box. flags for running the file using the Run Gaussian
Input file within Chem3D, or using Gaussian
To specify the save options:
directly.
1. Click Options.

When you click Options in the Save As dialog box,
Gaussian Checkpoint the following dialog box appears:
A Gaussian Checkpoint (.fchk, .fch) file stores the
results of Gaussian Calculations. It contains the final
geometry, electronic structure (including energy
levels) and other properties of the molecule.
Chem3D displays atomic orbitals and energy levels
stored in Checkpoint files. If Cubegen is installed,
molecular surfaces are calculated from the
Checkpoint file.
Gaussian Cube Select the appropriate options:

A Gaussian Cube (.cub) file results from running
Cubegen on a Gaussian Checkpoint file. It contains If you want to … Then click …
information related to grid data and model
coordinates.
save your model using Use Current
Chem3D displays the surface the file describes. If the Z-matrix described in Z-matrix.
more than one surface is stored in the file, only the the Internal Coordinates
first is displayed. You can display additional table of the model
surfaces using the View menu.
build a Z-matrix in which Only Serial
Internal Coordinates the current serial number Numbers; Bond and
Internal Coordinates (.int) files are text files that ordering of the atoms in Dihedral Angles.
describe a single molecule by the internal the model is preserved in
the Z-matrix Pro-R/Pro-S and
coordinates used to position each atom. The serial
Dihedral angles are
numbers are determined by the order of the atoms in
used to position
the file. The first atom has a serial number of 1, the
atoms.
second is number 2, and so on.
You cannot use a Z-matrix to position an atom in
build a Z-matrix in which Only Serial
terms of a later-positioned or higher serialized atom. Numbers; Dihedral
the current serial number
If you choose the second or third options in the Angles Only.
ordering of the atoms in
Internal Coordinates Options dialog box, the nature
the model is preserved in
of the serialization of your model determines The Pro-R and Pro-S
the Z-matrix
whether a consistent Z-matrix can be constructed. If stereochemical
the serial numbers in the Z-matrix which is about to designations are not
be created are not consecutive, a message appears. used in constructing
You are warned if the atoms in the model must be the Z-matrix from a
reserialized to create a consistent Z-matrix. model. All atoms are
positioned by
dihedral angles only.

When you click Options in the Save As dialog box,
MacroModel Files the MOPAC options dialog box appears:
The MacroModel1 (.mcm, .dat) file format is
defined in the MacroModel Structure Files version
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2.0 documentation.
Molecular Design Limited

MolFile (MDL MolFile)
The MDL Molfile format saves files by MDL
applications such as ISIS/Draw, ISIS/Base, MAACS
and REACCS. The file format is defined in the
article, “Description of Several Chemical Structure Click the Save All Frames check box to create a
File Formats Used by Computer Programs MOPAC Data file in which the internal coordinates
Developed at Molecular Design Limited” in the for each view of the model are included. The initial
Journal of Chemical Information and Computer frame of the model contains the first 3 lines of the
Science, Volume 32, Number 3, 1992, pages usual MOPAC output file (see the example file
244–255. below). Each subsequent frame contains only lines
Use this format to export files to MDL’s ISIS describing the Z-matrix for the atoms in that frame.
applications and other chemistry-related
applications. NOTE: For data file specifications, see page 13 of
the online MOPAC manual.
MSI ChemNote
To edit a file to run using the Run MOPAC Input File
Use the MSI ChemNote (.msm) file format to export command:
files to Molecular Simulations applications such as
ChemNote. The file format is defined in the 1. Open the MOPAC output file in a text editor.
ChemNote documentation. The output file below shows only the first four
atom record lines. The first line and column of
MOPAC Files the example output file shown below are for
The MOPAC (.mop) file format is used to save purposes of description only and are not part of
models in MOPAC data file format. You can edit the output file.
MOPAC files using a text editor with the addition of
keywords and changing optimization flags for C1 C2 C3 C4 C5 C6 C7 C8
running the file using the Run MOPAC Input file
within Chem3D, or using MOPAC directly. L1
L2: Cyclohexanol
L3:
L4: C 0 0 0 0 0 0 0 0 0
1. MacroModel is produced within the Department
L5: C 1.54152 1 0 0 0 0 1 0 0
of Chemistry at Columbia University, New York,
N.Y.

5. To specify particular coordinates to optimize,
L6: C 1.53523 1 111.7747 1 0 0 2 1 0
change the optimization flags in C3, C5 and C7
L7..Ln C 1.53973 1 109.7114 1 -55.6959 1 1 2 3 for the respective internal coordinate. The
available flags in MOPAC are:
Ln+1
1 Optimize this internal coordinate

2. In L1, type the keywords for the computations
you want MOPAC to perform (blank in the 0 Do not optimize this internal
example above). -1 Reaction coordinate or grid index
L2 is where enter the name that you want to T Monitor turning points in DRC
assign to the window for the resulting model.
However, Chem3D ignores this line. 6. Add additional information in line Ln+1. For
example, symmetry information used in a
3. Leave L3 blank.
SADDLE computation.
4. L4 through Ln (were n is the last atom record)
7. Leave the last line in the data file blank to
include the internal coordinates, optimization
indicate file termination.
flags, and connectivity information for the
model. 8. Save the file in a text only format.
• C1 is the atom specification.
• C2 is the bond distance (for the connectivity MOPAC Graph Files
specified in C8). A MOPAC Graph (.gpt) file stores the results of
• C3 is the optimization flag for the bond MOPAC calculations that include the GRAPH
distance specified in C2. keyword. It contains the final geometry, electronic
structure, and other properties of the molecule.
• C4 is the bond angle (for the connectivity
specified in C8). Protein Data Bank Files
• C5 is the optimization flag for the bond angle Brookhaven Protein Data Bank files (.pdb) are used
specified in C4. to store protein data and are typically large in size.
• C6 is the dihedral angle (for the connectivity the file format is taken from the Protein Data Bank
Atomic Coordinate and Bibliographic Entry Format
specified in C8).
Description, 1985.
• C7 is the optimization flag for the dihedral
angle specified in C6. ROSDAL Files (RDL)
The ROSDAL Structure Language1 (.rdl) file format
is defined in Appendix C: ROSDAL Syntax, pages
91-108, of the MOLKICK User’s Manual. The
ROSDAL format is primarily used for query
searching in the Beilstein Online Database.
ROSDAL format files are for export only.
1. ROSDAL is a product of Softron, Inc.

for several models are the same size, and Fit Model
Standard Molecular Data to Window is on, then the models should copy as the
(SMD) same size.
Use the Standard Molecular Data (.smd) file format
Transferring to ChemDraw
Administrator
for exporting information in a format for use in

online chemical database searching with the STN You can transfer information to ChemDraw as a 3D
Express application. model or as a 2D model.
SYBYL Files To transfer a model as a 3D structure:
Use the SYBYL (.sml, .sm2) file formats to export 1. Select the model.
models for use in Tripos’s SYBYL applications.
2. From the Edit menu, and choose Copy.
Job Description File To transfer a model as a 2D structure:

Formats 1. Select the model.
You can use Job description files to save customized
default settings for calculations. You can save
customized calculations as a Job Description file choose Copy as ChemDraw Structure.
(.jdf) or Job Description Stationery (.jdt). Saving
3. Open Chem3D.
either format in a Chem3D job folder adds it to the
appropriate Chem3D menu. 4. From the Edit menu, choose Paste.
JDF Files The model is pasted into Chem3D.
The .jdf file format is a file format for saving job Transferring to Other
descriptions. When you open a .jdf file, you can edit
and save the settings. Applications
JDT Files To copy and paste a space-filling model into a word
processing, desktop publishing, presentation or
The .jdt file format is a template format for saving drawing application, such as Microsoft Word or
settings that can be applied to future calculations. PowerPoint:
You can the edit the settings of a template file,
however you cannot save your changes. 1. Select the model.
Exporting With the 2. From the Edit menu, point to Copy As, and then
choose Copy as Bitmap.
Clipboard
3. Paste the model into the target application
The size of the file that you copy to the clipboard
document.
from Chem3D is determined by the size of the
Chem3D model window. If you want the size of a Alternatively, you could use Save As Bitmap from
copied molecule to be smaller or larger, resize the the Save As menu item under the File menu to create
model window accordingly. If the model windows a file to insert into or link to the target application
document.

The Clipboard on the Macintosh stores pictures as When you finish making changes:
PICTs. The PICT format is supported by most • Close the Chem3D Model window.
applications for easy transport of information.
The Chem3D Model window closes and the
Copying Postscript picture in the ChemDraw document is updated.
(Macintosh Only) To display the location of the document that the
picture being edited:
If you want to publish Chem3D pictures, include
• Command-click while pointing at From
PostScript information of the Chem3D models when
“Application Name” in the title bar.
the model is transferred using the Clipboard. The
quality of the output is greatly enhanced.
To include PostScript with pictures:
• In the Settings dialog box, choose the Pictures
control panel, and then click Include
PostScript Commands in Pictures.
Edit Graphic Object

(Macintosh Only)
Chem3D supports the Edit Graphic Object (EGO)
protocol for making changes to Chem3D pictures
that are pasted in other types of documents. When a
picture is transferred from Chem3D into another
type of document that supports the EGO protocol,
you can open the picture and it appears in a Chem3D
model window. Any changes you make to the model
are reflected in the other document when you close
the Chem3D model window.
NOTE: All colors, except for the Background

Color, are transferred with a Chem3D picture
pasted into another document type. The Background
Color is always removed.
For example, to edit a Chem3D picture pasted into

CS ChemDraw:
• With the Select tool, double-click the Chem3D
picture.
Chem3D opens with a Model window titled
From CS ChemDraw. You can use all of the
Chem3D tools available to edit the picture.

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Chapter 9: Computation Concepts
Computational Chem3D supports a number of powerful
computational chemistry methods and extensive
Chemistry Overview visualization options.
Computational chemistry extends beyond the Computational Methods

traditional boundaries separating chemistry from
physics, biology, and computer science. It allows the Overview
exploration of molecules by using a computer when Computational chemistry encompasses a variety of
an actual laboratory investigation may be mathematical methods which fall into two broad
inappropriate, impractical, or impossible. As an categories:
adjunct to experimental chemistry, its significance
continues to be enhanced by increases in computer • Molecular mechanics—applies the laws of
speed and power. classical physics to molecular nuclei without
explicit consideration of electrons.
Aspects of computational chemistry include:
• Quantum mechanics—relies on the
• Molecular modeling. Schrödinger equation to describe a molecule
• Computational methods. with explicit treatment of electronic structure.
• Computer-Aided Molecular Design (CAMD). Quantum mechanical methods can be
• Chemical databases. subdivided into two classes: ab initio and
semiempirical.
• Organic synthesis design.
The generally accepted method classes are shown in
While a number of different definitions have been the following chart.
proposed, the definition offered by Lipkowitz and
Boyd of computational chemistry as “those aspects
of chemical research that are expedited or rendered Computational Chemistry Methods
practical by computers” is perhaps the most
inclusive.
Molecular modeling, while often taken to include Molecular Quantum
computational methods, can be thought of as the Mechanical Methods Mechanical Methods
rendering of a 2D or 3D model of a molecule’s
structure and properties. Computational methods,
on the other hand, calculate the structure and
property data necessary to render the model. Within Semiempirical Ab Initio
a modeling program, such as Chem3D, Methods Methods
computational methods are referred to as
computation engines, while geometry engines and
graphics engines render the model.
Chem3D Chapter 9: Computation Concepts • 123

Chem3D provides the following methods: Choosing the Best Method
• Molecular mechanical MM2 method.
Not all types of calculations are possible for all
• Semiempirical Extended Hückel, MINDO/3, methods and no one method is best for all purposes.
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MNDO, MNDO-d, AM1 and PM3 methods For any given application, each method poses
through Chem3D and CS MOPAC. advantages and disadvantages. The choice of
• Ab initio methods through Chem3D’s Gaussian method depend on a number of factors, including:
interface. • The nature of the molecule
• The type of information sought
Uses of Computational
• The availability of applicable experimentally
Methods determined parameters (as required by some
Computational methods calculate the potential methods)
energy surfaces (PES) of molecules. The potential
• Computer resources
energy surface is the embodiment of the forces of
interaction among atoms in a molecule. From the The three most important of the these criteria are:
PES, structural and chemical information about a
• Model size—The size of a model can be a
molecule can be derived. The methods differ in the
way the surface is calculated and in the molecular limiting factor for a particular method. The
properties derived from the energy surface. limiting number of atoms in a molecule
increases by approximately one order of
The methods perform the following basic types of
magnitude between method classes from ab
calculations:
initio to molecular mechanics. Ab initio is
• Single point energy calculation—The energy limited to tens of atoms, semiempirical to
of a given spacial arrangement of the atoms in a hundreds, and molecular mechanics to
model or the value of the PES for a given set of thousands.
atomic coordinates.
• Parameter Availability—Some methods
• Geometry optimization—A systematic depend on experimentally determined
modification of the atomic coordinates of a parameters to perform computations. If the
model resulting in a geometry where the net model contains atoms for which the parameters
forces on the structure sum to zero. A of a particular method have not been derived,
3-dimensional arrangement of atoms in the that method may produce invalid predictions.
model representing a local energy minimum (a Molecular mechanics, for example, relies on
stable molecular geometry to be found without parameters to define a force-field. Any
crossing a conformational energy barrier). particular force-field is only applicable to the
• Property calculation—Predicts certain limited class of molecules for which it is
physical and chemical properties, such as parametrized.
charge, dipole moment, and heat of formation. • Computer resources—Requirements increase
Computational methods can perform more in relative to the size of the model for each of
specialized functions, such as conformational the methods.
searches and molecular dynamics simulations.
124 • Chapter 9: Computation Concepts Chem3D

Ab initio: The time required for performing Quantum Mechanical Methods
computations increases on the order of N4, Applications Summary
where N is the number of atoms in the model.
Semiempirical: The time required for Useful information determined by quantum
computation increases as N3 or N2, where N is mechanical methods includes:
the number of atoms in the model. • Molecular orbital energies and coefficients.
MM2: The time required for performing • Heat of Formation for evaluating
computations increases as N2, where N is the conformational energies.
number of atoms.
• Partial atomic charges calculated from the
In general, molecular mechanical methods are molecular orbital coefficients.
computationally less expensive than quantum
mechanical methods. The suitability of each • Electrostatic potential.
general method for particular applications can • Dipole moment.
be summarized as follows.
• Transition-state geometries and energies.
Molecular Mechanics Methods • Bond dissociation energies.
Applications Summary
The semiempirical methods available in Chem3D
Molecular mechanics in Chem3D apply to: and CS MOPAC apply to:
• Systems containing thousands of atoms. • Systems containing up to 120 heavy atoms and
300 total atoms (in CS MOPAC for Windows)
• Organic, oligonucleotides, peptides, and
saccharides. or 60 heavy atoms and 120 total atoms (in CS
MOPAC for Macintosh).
• Gas phase only (for MM2).
• Organic, organometallics, and small oligomers
Useful techniques available using MM2 methods (peptide, nucleotide, saccharide).
include:
• Gas phase or implicit solvent environment.
• Energy Minimization for locating stable
• Ground, transition, and excited states.
conformations.
Ab initio methods, available through the Gaussian
• Single point energy calculations for comparing
interface, apply to:
conformations of the same molecule.
• Systems containing up to 30 atoms.
• Searching conformational space by varying a
• Organic, organometallics, and molecular
single dihedral angle.
fragments (catalytic components of an
• Studying molecular motion using Molecular enzyme).
Dynamics.
• Gas or implicit solvent environment.
• Study ground, transition, and excited states
(certain methods).

The following table summarizes the method types Potential Energy Surfaces
Method Type Advantages Disadvantages Best For A potential energy surface (PES) can describe:
• A molecule or ensemble of molecules having
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Molecular Least intensive Particular force Large

Mechanics computationally— field applicable systems constant atom composition (ethane, for
(MM2) fast and useful with only for a limited (thousands of
limited computer class of molecules atoms) example) or a system where a chemical reaction
Uses classical resources occurs.
physics Does not calculate Systems or
Can be used for electronic processes
Relies on force- molecules as large properties with no
• Relative energies for conformers (eclipsed and
field with as enzymes breaking or staggered forms of ethane).
embedded Requires forming of
empirical experimental data bonds
parameters (or data from ab Different potential energy surfaces are generated
initio) for for:
parameters
• Molecules having different atomic composition
Semiempirical Less demanding Requires Medium- (ethane and chloroethane).
(MOPAC) computationally experimental data sized systems
than ab initio (or data from ab (hundreds of
Uses quantum methods initio) for atoms)
• Molecules in excited states instead of for the
physics parameters same molecules in their ground states.
Capable of Systems
Uses calculating Less rigorous than involving
experimentally transition states and ab initio methods electronic
• Molecules with identical atomic composition
derived empirical excited states transitions but with different bonding patterns, such as
parameters
propylene and cyclopropane.
Uses
approximation
extensively Potential Energy Surfaces (PES)
The true representation of a model’s potential
Ab Initio Useful for a broad Computationally Small
(Gaussian) range of systems intensive systems (tens energy surface is a multi-dimensional surface whose
of atoms) dimensionality increases with the number of
Uses quantum Does not depend on
physics experimental data Systems independent variables. Since each atom has three
involving
Mathematically Capable of electronic
independent variables (x, y, z coordinates),
rigorous—no calculating transitions visualizing a surface for a many-atom model is
empirical transition states and
parameters excited states Molecules or impossible. However, we can generalize this
systems problem by examining any 2 independent variables,
without
available such as the x and y coordinates of an atom, as shown
experimental below.
data (“new”
chemistry)
Systems
requiring
rigorous
accuracy

All the minima on a potential energy surface of a
molecule represent stable stationery points where
the forces on atoms sum to zero. The global
minimum represents the most stable conformation;
the local minima, less stable conformations; and the
saddle points represent transition conformations
between minima.
Saddle Point
Single Point Energy
Potential Energy
Calculations
Local Minimum
Global Minimum Single point energy calculations can be used to
calculate properties of the current geometry of a
model. The values of these properties depend on
where the model currently lies on the potential
The main areas of interest on a potential energy surface as follows:
surface are the extrema as indicated by the arrows,
• A single point energy calculation at a global
are as follows:
minimum provides information about the
• Global minimum—The most stable model in its most stable conformation.
conformation appears at the extremum where
the energy is lowest. A molecule has only one • A single point calculation at a local minimum
global minimum. provides information about the model in one of
many stable conformations.
• Local minima—Additional low energy
extrema. Minima are regions of the PES where • A single point calculation at a saddle point
a change in geometry in any direction yields a provides information about the transition state
higher energy geometry. of the model.
• Saddle point—The point between two low • A single point energy calculation at any other
energy extrema. The saddle point is defined as point on the potential energy surface provides
a point on the potential energy surface at which information about that particular geometry, not
there is an increase in energy in all directions a stable conformation or transition state.
except one, and for which the slope (first Single point energy calculations can be performed
derivative) of the surface is zero. before or after performing an optimization.
NOTE: At the energy minimum, the energy is not NOTE: Do not compare values from different
zero; the first derivative (gradient) of the energy methods. Different methods rely on different
with respect to geometry is zero. assumptions about a given molecule.

Geometry Optimization The following illustration shows some concepts of
minimization. For simplicity, this plot shows a
Geometry optimization is used to locate a stable single independent variable plotted in two
conformation of a model. This should be performed dimensions.
before performing additional computations or
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analyses of a model.
Locating global and local energy minima is often
accomplished through energy minimization.
Locating a saddle point is optimizing to a transition
state.
The ability of a geometry optimization to converge
to a minimum depends on the starting geometry, the
potential energy function used, and the settings for a
minimum acceptable gradient between steps
(convergence criteria).
Geometry optimizations are iterative and begin at

some starting geometry as follows:
The starting geometry of the model determines
1. The single point energy calculation is which minimum is reached. For example, starting at
performed on the starting geometry. (b), minimization results in geometry (a), which is
the global minimum. Starting at (d) leads to
2. The coordinates for some subset of atoms are geometry (f), which is a local minimum.The
changed and another single point energy proximity to a minimum, but not a particular
calculation is performed to determine the minimum, can be controlled by specifying a
energy of that new conformation. minimum gradient that should be reached.
Geometry (f), rather than geometry (e), can be
3. The first or second derivative of the energy reached by decreasing the value of the gradient
(depending on the method) with respect to the where the calculation ends.
atomic coordinates determines how large and in Often, if a convergence criterion (energy gradient) is
what direction the next increment of geometry too lax, a first-derivative minimization can result in
change should be. a geometry that is near a saddle point. This occurs
because the value of the energy gradient near a
4. The change is made. saddle point, as near a minimum, is very small. For
example, at point (c), the derivative of the energy is
5. Following the incremental change, the energy
0, and as far as the minimizer is concerned, point (c)
and energy derivatives are again determined
is a minimum. First derivative minimizers cannot, as
and the process continues until convergence is a rule, surmount saddle points to reach another
achieved, at which point the minimization minimum.
process terminates.
NOTE: If the saddle point is the extremum of
interest, it is best to use a procedure that specifically
locates a transition state, such as the CS MOPAC
Pro Optimize To Transition State command.

You can take the following steps to ensure that a
minimization has not resulted in a saddle point.
Molecular Mechanics
• The geometry can be altered slightly and Theory in Brief
another minimization performed. The new Molecular mechanics describes the energy of a
starting geometry might result in either (a), or molecule in terms of a set of classically derived
(f) in a case where the original one led to (c). potential energy functions. The potential energy
functions and the parameters used for their
• The Dihedral Driver (Macintosh only) can be
evaluation are known as a “force-field”.
employed to search the conformational space of
the model. For more information see “Chapter Molecular mechanical methods are based on the
10: MM2 Computations.” following principles:
• A molecular dynamics simulation can be run, • Nuclei and electrons are lumped together and
which will allow small potential energy barriers treated as unified atom-like particles.
to be crossed. After completing the molecular • Atom-like particles are typically treated as
dynamics simulation, individual geometries can spheres.
then be minimized and analyzed. For more • Bonds between particles are viewed as
information see “Chapter 10: MM2
harmonic oscillators.
Computations.”
• Non-bonded interactions between these
You can calculate the following properties with the particles are treated using potential functions
computational methods available through Chem3D derived using classical mechanics.
using the PES:
• Individual potential functions are used to
• Steric energy describe the different interactions: bond
• Heat of formation stretching, angle bending, and torsional (bond
• Dipole moment twisting) energies, and through-space
(non-bonded) interactions.
• Charge density
• Potential energy functions rely on empirically
• COSMO solvation in water
derived parameters (force constants,
• Electrostatic potential equilibrium values) that describe the
• Electron spin density interactions between sets of atoms.
• Hyperfine coupling constants • The sum of interactions determine the spatial
distribution (conformation) of atom-like
• Atomic charges
particles.
• Polarizability
• Molecular mechanical energies have no
• Others, such as IR vibrational frequencies meaning as absolute quantities. They can only
be used to compare relative steric energy
(strain) between two or more conformations of
the same molecule.

The Force-Field The following illustration shows the major
interactions.
Molecular mechanics typically treats atoms as
spheres, and bonds as springs. The mathematics of
spring deformation (Hooke’s Law) is used to
Administrator
describe the ability of bonds to stretch, bend, and

twist. Non-bonded atoms (greater than two bonds
apart) interact through van der Waals attraction,
steric repulsion, and electrostatic attraction and
repulsion. These properties are easiest to describe
mathematically when atoms are considered as
spheres of characteristic radii.
The total potential energy, E, of a molecule can be
described by the following summation of
interactions:
Different kinds of force-fields have been developed.
Energy = Stretching Energy + Bending Energy +
Some include additional energy terms that describe
Torsion Energy + Non-Bonded Interaction
other kinds of deformations, such as the coupling
Energy
between bending and stretching in adjacent bonds,
The first three terms, given as a, b, and c below, are in order to improve the accuracy of the mechanical
the so-called bonded interactions. In general, these model.
bonding interactions can be viewed as a strain The reliability of a molecular mechanical force-field
energy imposed by a model moving from some ideal depends on the parameters and the potential energy
zero strain conformation. The last term, which functions used to describe the total energy of a
represents the non-bonded interactions, includes the model. Parameters must be optimized for a
two interactions shown below as d and e. particular set of potential energy functions, and thus
The total potential energy can be described by the are not easily transferable to other force fields.
following relationships between atoms. The
numbers indicate the relative positions of the atoms. MM2
a. Bond Stretching: (1-2) bond stretching between Chem3D uses a modified version of Allinger’s
directly bonded atoms MM2 force field. For additional MM2 references
see “.”
b. Angle Bending: (1-3) angle bending between The principal additions to Allinger’s MM2 force
atoms that are geminal to each other. field are:
c. Torsion Energy: (1-4) torsional angle rotation • A charge-dipole interaction term
between atoms that are vicinal to each other. • A quartic stretching term
d. Repulsion for atoms that are too close and • Cutoffs for electrostatic and van der Waals
attraction at long range from dispersion forces terms with 5th order polynomial switching
(van der Waals interaction). function
• Automatic pi system calculations when
e. Interactions from charges, dipoles, quadrupoles
necessary
(electrostatic interactions).
• Torsional and non-bonded constraints

Chem3D stores the parameters used for each of the problem. However, the Morse Function leads to a
terms in the potential energy function in tables. large increase in computation time. As an
These tables are controlled by the Table Editor alternative, cubic stretch and quartic stretch
application, which allows viewing and editing of the constants are added to provide a result approaching
parameters. a Morse-function correction.
Each parameter is classified by a Quality number. The cubic stretch term allows for an asymmetric
This number indicates the reliability of the data. The shape of the potential well, allowing these long
quality ranges from 4, where the data are derived bonds to be handled. However, the cubic stretch
completely from experimental data (or ab initio term is not sufficient to handle abnormally long
data), to 1, where the data are guessed by Chem3D. bonds. A quartic stretch term is used to correct
The parameter table, MM2 Constants, contains problems caused by these very long bonds. With the
adjustable parameters that correct for failings of the addition of the cubic and quartic stretch term, the
potential functions in outlying situations. equation for bond stretching becomes:
E Stretch = 71.94 ∑ K s [(r − ro ) 2 + CS(r − ro )3 + QS(r − ro ) 4 ]

NOTE: Editing of MM2 parameters in the Table Bonds
Editor should only be done with the greatest of
caution by expert users. Within a force-field
equation, parameters operate interdependently; Both the cubic and quartic stretch constants are
changing one normally requires that others be defined in the MM2 Constants table.
changed to compensate for its effects. To precisely reproduce the energies obtained with
Allinger’s force field: set the cubic and quartic
stretching constant to “0” in the MM2 Constants
Bond Stretching Energy
tables.
E Stretch = 71.94 ∑ K s (r − r )
Bonds
o
2
Angle Bending Energy
The bond stretching energy equation is based on E Bend = 0.02191418 ∑ K b (θ − θ o )2

Hooke’s law. The Ks parameter controls the stiffness Angles
of the spring’s stretching (bond stretching force The bending energy equation is also based on
constant), while ro defines its equilibrium length Hooke’s law. The Kb parameter controls the stiffness
(the standard measurement used in building of the spring’s bending (angular force constant),
models). Unique Ks and ro parameters are assigned while θ0 defines the equilibrium angle. This
to each pair of bonded atoms based on their atom equation estimates the energy associated with
types (C-C, C-H, O-C). The parameters are stored in deformation about the equilibrium bond angle. The
the Bond Stretching parameter table. The constant, constant, 0.02191418, is a conversion factor to
71.94, is a conversion factor to obtain the final units obtain the final units as kcal/mole.
as kcal/mole.
Unique parameters for angle bending are assigned to
The result of this equation is the energy contribution each bonded triplet of atoms based on their atom
associated with the deformation of a bond from its types (C-C-C, C-O-C, C-C-H). For each triplet of
equilibrium bond length. atoms, the equilibrium angle differs depending on
This simple parabolic model fails when bonds are what other atoms the central atom is bonded to. For
stretched toward the point of dissociation. The each angle there are three possibilities: XR2, XRH
Morse function would be the best correction for this or XH2. For example, the XH2 parameter would be

used for a C-C-C angle in propane, because the other The numbers refer to atom types, which can be
atoms the central atom is bonded to are both found in the Atom Types Table in Chem3D.
hydrogens. For isobutane, the XRH parameter • -CHR- Bending K for 1-1-1 angles
would be used, and for 2,2-dimethylpropane, the
• -CHR- Bending K for 1-1-1 angles in
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XR2 parameter would be used.

4-membered rings.
The effect of the Kb and θ0 parameters is to broaden
or steepen the slope of the parabola. The larger the • -CHR- Bending K for 22-22-22 angles in
value of Kb, the more energy is required to deform 3-membered rings.
an angle from its equilibrium value. Shallow The -CHR- Bending Kb for 1-1-1 angles allows
potentials are achieved with Kb values less than 1.0. more accurate force constants to be specified for
A sextic term is added to increase the energy of Type 1 (-CHR-) and Type 2 (-CHR-) interactions.
angles with large deformations from their ideal The -CHR-Bending Kb for 1-1-1 angles in
value. The sextic bending constant, SF, is defined in 4-membered rings and the -CHR- Bending Kb for
the MM2 Constants table. With the addition of the 22-22-22 angles (22 is the atom type number for C
sextic term, the equation for angle bending Cyclopropane) in 3-membered rings differ from the
becomes: -CHR- Bending Kb for 1-1-1 angles and require
separate constants for accurate specification.
E Bend = 0.02191418 ∑ K b [(θ − θ o ) + SF(θ − θ o ) ]
2 6
Angles
Torsion Energy
∑ [1 + cos(nφ − φ )]
Vn
Ε Twist =
NOTE: The default value of the sextic force Torsions 2
constant is 0.00000007. To precisely reproduce This term accounts for the tendency for dihedral
the energies obtained with Allinger’s force angles (torsionals) to have an energy minimum
field: set the sextic bending constant to “0” in occurring at specific intervals of 360/n. In Chem3D,
the MM2 Constants tables. n can equal 1, 2, or 3.
There are three parameter tables for the angle V1 V V

bending parameters:
Ε Twist = ∑
Torsions 2
(1 + cos φ ) + 2 (1 + cos2φ ) + 3 (1+ cos3φ )
2 2
• Angle Bending parameters
The Vn/2 parameter is the torsional force constant. It
• 3-Membered Ring Angle Bending parameters determines the amplitude of the curve. The n
• 4-Membered Ring Angle Bending parameters signifies its periodicity. nφ shifts the entire curve
about the rotation angle axis. The parameters are
There are three additional angle bending force
determined through curve-fitting techniques.
constants available in the MM2 Constants window.
Unique parameters for torsional rotation are
These force constants are specifically for carbons
assigned to each bonded quartet of atoms based on
with one or two attached hydrogens. The following
their atom types (C-C-C-C, C-O-C-N, H-C-C-H).
force constants are available.
Chem3D provides three torsional parameters tables:
• Torsional parameters
• 4-Membered ring torsions
• 3-Membered ring torsions.

Non-Bonded Energy The R* and Epsilon parameters are stored in the
MM2 Atom Types table.
The non-bonded energy represents the pairwise sum
of the energies of all possible interacting For certain interactions, values in the VDW
non-bonded atoms, i and j, within a predetermined interactions parameter table are used instead of
“cut-off” distance. those in the MM2 atom types table. These situations
include interactions where one of the atoms is very
The non-bonded energy accounts for repulsive
electronegative relative to the other, such as in the
forces experienced between atoms at close
case of a water molecule.
distances, and for the attractive forces felt at longer
distances. It also accounts for their rapid falloff as
Cutoff Parameters for van der Waals
the interacting atoms move farther apart by a few
Ångstroms. Interactions
The use of cutoff distances for van der Waals terms
van der Waals Energy greatly improves the computational speed for large
Repulsive forces dominate when the distance molecules by eliminating long range, and relatively
between interacting atoms becomes less than the insignificant, interactions from the computation.
sum of their contact radii. In Chem3D repulsion is Chem3D uses a fifth-order polynomial switching
modeled by an equation which combines an function so that the resulting force field maintains
exponential repulsion with an attractive dispersion second-order continuity. The cutoff is implemented
interaction (1/R6): gradually, beginning at 90% of the specified cutoff
distance. This distance is set in the MM2 Constants
table.
E van der Waals = ∑ ∑ ε (290000e −12.5/R - 2.25R -6 )
i j The van der Waals interactions fall off as 1/r6, and
where can be cut off at much shorter distances, for example
10Å. This cut off speeds the computations
rij
R= significantly, even for relatively small molecules.
R + Rj
* *
i
The parameters include: NOTE: To precisely reproduce the energies

obtained with Allinger’s force field: set the van der
• Ri* and Rj*—the van der Waals radii for the Waals cutoff constants to large values in the MM2
atoms Constants table.
• Epsilon (ε)—determines the depth of the
attractive potential energy well and how easy it
Electrostatic Energy
is to push atoms together
qiqj
• rij—which is the actual distance between the
atoms
E Electrostatic = ∑ ∑ Dr
i j ij
At short distances the above equation favors The electrostatic energy is a function of the charge
repulsive over dispersive interactions. To on the non-bonded atoms, q, their interatomic
compensate for this at short distances (R=3.311) this distance, rij, and a molecular dielectric expression,
term is replaced with: D, that accounts for the attenuation of electrostatic
interaction by the environment (solvent or the
E van der Waals = 336.176 ∑ ∑ εR
-2
molecule itself).
i j

In Chem3D, the electrostatic energy is modeled Bond dipole parameters, µ, for each atom pair are
using atomic charges for charged molecules and stored in the bond stretching parameter table. The
bond dipoles for neutral molecules. charge, q, is stored in the atom types table. The
molecular dielectric is set to a constant value
There are three possible interactions accounted for
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between 1.0 and 5.0 in the MM2 Atom types table.

by Chem3D:
• charge/charge NOTE: Chem3D does not use a distance-
• dipole/dipole dependent dielectric.
• dipole/charge.
Each type of interaction uses a different form of the
Cutoff Parameters for Electrostatic
electrostatic equation as shown below: Interactions
The use of cutoff distances for electrostatic terms, as
charge/charge contribution for van der Waals terms, greatly improves the
computational speed for large molecules by
qi q j eliminating long-range interactions from the
E = 332.05382∑ ∑ computation.
i j Dq rij
As in the van der Waals calculations, Chem3D
where the value 332.05382 converts the result to invokes a fifth-order polynomial switching function
units of kcal/mole. in order to maintain second-order continuity in the
force-field. The switching function is invoked as
dipole/dipole contribution minimum values for charge/charge, charge/dipole,
or dipole/dipole interactions are reached. These
µi µ j
E = 14.388∑ ∑
Dµ rij3
(cos χ − 3cos α i cos α j ) cutoff values are located in the MM2 Constants
parameter table.
i j
where the value 14.388 converts the result from Since the charge-charge interaction energy between
ergs/mole to kcal/mole, χ is the angle between the two point charges separated by a distance r is
two dipoles µi and µj, αi and αj are the angles the proportional to 1/r, the charge-charge cutoff must be
dipoles form with the vector, rij, connecting the two rather large, typically 30 to 40Å, depending on the
at their midpoints, and Dµ is the (effective) dielectric size of the molecule. The charge-dipole, dipole-
constant. dipole interactions fall off as 1/r2, 1/r3 and can be
cutoff at much shorter distances, for example 25 and
dipole/charge contribution 18Å respectively. To precisely reproduce the
energies obtained with Allinger’s force field: set the
qi µ j cutoff constants to large values (99) in the MM2
E = 69.120 ∑ ∑
rij 2
D µ Dq
(cos α )
j Constants table.
i j
where the value 69.120 converts the result to units of

kcal/mole.

OOP Bending
NOTE: The method used is that of D.H. Lo and
Atoms that are arranged in a trigonal planar fashion, M.A. Whitehead, Can. J. Chem., 46, 2027(1968),
as in sp2 hybridization, require an additional term to with heterocycle parameter according to G.D. Zeiss
account for out-of-plane (OOP) bending. MM2 uses and M.A. Whitehead, J. Chem. Soc. (A), 1727
the following equation to describe OOP bending: (1971). The SCF computation yields bond orders
which are used to scale the bond stretching force
∑ K [(θ − θ ) constants, standard bond lengths and twofold
2
Ε= b o + SF(θ − θ o ) 6 ]
Out of Plane torsional barriers.
The form of the equation is the same as for angle

bending, however, the θ value used is angle of The following is a step-wise overview of the
deviation from coplanarity for an atom pair and θ ο process:
is set to zero. The illustration below shows the θ 1. A Fock matrix is generated based on the
determined for atom pairs DB. favorability of electron sharing between pairs of
D atoms in a pi system.
x
2. The pi molecular orbitals are computed from
A C the Fock matrix.
θ
y
3. The pi molecular orbitals are used to compute a
B
new Fock matrix, then this new Fock matrix is
The special force constants for each atom pair are
located in the Out of Plane bending parameters used to compute better pi molecular orbitals.
table. The sextic correction is used as previously Step 2 and 3 are repeated until the computation
described for Angle Bending. The sextic constant, of the Fock matrix and the pi molecular orbitals
SF, is located in the MM2 Constants table. converge. This method is called the self-
consistent field technique or a pi-SCF
Pi Bonds and Atoms with Pi Bonds calculation.
For models containing pi systems, MM2 performs a
Pariser-Parr-Pople pi orbital SCF computation for 4. A pi bond order is computed from the pi
each system. A pi system is defined as a sequence of molecular orbitals.
three or more atoms of types which appear in the
Conjugate Pi system Atoms table. Because of this 5. The pi bond order is used to modify the bond
computation, MM2 may calculate bond orders other length(BLres) and force constant (Ksres) for
than 1, 1.5, 2, and so on. each bond in the pi system.
6. The modified values of Ksres and BLres are used

in the molecular mechanics portion of the MM2
computation to further refine the molecule.

Stretch-Bend Cross Terms For non-bonded distance constraints the additional
term and force constant is:
Stretch-bend cross terms are used when a coupling
∑ 10
occurs between bond stretching and angle bending.
Ε= (r − ro )
6 2
For example, when an angle is compressed, the
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Distance
MM2 force field uses the stretch-bend force
constants to lengthen the bonds from the central
atom in the angle to the other two atoms in the angle. Molecular Dynamics
Simulation
∑ K sb (r − ro )(θ − θ o )
1
Ε=
Stretch / Bend 2 In its broadest sense, molecular dynamics is
concerned with simulating molecular motion.
The force constant (Ksb) differs for different atom Motion is inherent to all chemical processes. Simple
combinations. vibrations, like bond stretching and angle bending,
The seven different atom combinations where force give rise to IR spectra. Chemical reactions,
constants are available for describing the situation hormone-receptor binding, and other complex
follow: processes are associated with many kinds of
intramolecular and intermolecular motions. The
• X-B, C, N, O-Y MM2 method of molecular dynamics simulation
• B-B, C, N, O-H uses Newton’s equations of motion to simulate the
movement of atoms.
• X-Al, S-Y
Conformational transitions and local vibrations are
• X-Al, S-H
the usual subjects of molecular dynamics studies.
• X-Si, P-Y Molecular dynamics alters the values of the
• X-Si, P-H intramolecular degrees of freedom in a stepwise
fashion. The steps in a molecular dynamics
• X-Ga, Ge, As, Se-Y, P-Y simulation represent the changes in atom position
where X and Y are any non-hydrogen atom. over time, for a given amount of kinetic energy.
The driving force for chemical processes is
User-Imposed Constraints described by thermodynamics. The mechanism by
Additional terms are included in the force field which chemical processes occur is described by
when constraints are applied to torsional angles and kinetics. Thermodynamics describes the energetic
non-bonded distances by the Optimal field in the relationships between different chemical states,
Measurements table. These terms use a harmonic whereas the sequence or rate of events that occur as
potential function, where the force constant has been molecules transform between their various possible
set to a large value (4 for torsional constraints and states is described by kinetics.
106 for non-bonded distances) in order to enforce The Molecular Dynamics command in the MM2
the constraint. menu can be used to compute a molecular dynamics
For torsional constraints the additional term and trajectory for a molecule or fragment in Chem3D. A
force constant is described by: common use of molecular dynamics is to explore the
conformational space accessible to a molecule, and
Ε= ∑ 4(θ − θ o )2 to prepare sequences of frames representing a
molecule in motion. For more information on
Torsions
Molecular Dynamics see “Chapter 10: MM2
Computations.”

Molecular Dynamics Formulas Quantum mechanical methods describe molecules
in terms of explicit interactions between electrons
The molecular dynamics computation consists of a
and nuclei. Both ab initio and semiempirical
series of steps that occur at a fixed interval, typically
methods are based on the following principles:
about 2.0 fs (femtoseconds, 1.0 x 10-15 seconds). The
Beeman algorithm for integrating the equations of • Nuclei and electrons are distinguished from
motion, with improved coefficients (B. R. Brooks) is each other.
used to compute new positions and velocities of • Electron-electron (usually averaged) and
each atom at each step.
electron-nuclear interactions are explicit.
Each atom (i) is moved according to the following
• Interactions are governed by nuclear and
formula:
electron charges (i.e. potential energy) and
xi = xi + vi∆t + (5ai – ai old) (∆t)2/8 electron motions.
Similarly, each atom is moved for y and z, where xi, • Interactions determine the spatial distribution
yi, and zi are the Cartesian coordinates of the atom,
of nuclei and electrons and their energies.
vi is the velocity, ai is the acceleration, aiold is the
acceleration in the previous step, and ∆t is the time • Quantum mechanical methods are concerned
between the current step and the previous step. The with approximate solutions to Schrödinger’s
potential energy and derivatives of potential energy wave equation.
(gi) are then computed with respect to the new
Cartesian coordinates. ΗΨ = ΕΨ
New accelerations and velocities are computed at • The Hamiltonian operator, H, contains
each step according to the following formulas (mi is information describing the electrons and nuclei
the mass of the atom): in a system. The electronic wave function, Ψ,
aiveryold = aiold describes the state of the electrons in terms of
aiold = ai their motion and position. E is the energy
associated with the particular state of the
ai = –gi / mi
electron.
vi = vi + (3ai + 6aiold – aiveryold) ∆t / 8
Quantum Mechanics NOTE: The Schrödinger equation is an

eigenequation, where the “H” operator, the
Theory in Brief Hamiltonian, operates on the wave function to
The following information is intended to familiarize return the same wave function and a constant.
you with the terminology of quantum mechanics and The wave function is called an eigenfunction,
to point out the areas where approximations are and the constant, an eigenvalue.
made in semiempirical and ab initio methods. For
complete derivations of equations used in quantum • Exact solutions to the Schrödinger equation are
mechanics, you can refer to any quantum chemistry
possible only for the simplest 1 electron-1
text book.
nucleus system. These solutions, however,
yield the basis for all of quantum mechanics.

• The solutions describe a set of allowable states created by all other electrons and nuclei. Each
for an electron. The observable quantity for electron in its own orbital is unimpeded by its
these states is described as a probability neighbors.
function. This function is the square of the wave The electronic Hamiltonian is thus simplified by
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function, and when properly normalized, representing it as a sum of 1-electron Hamiltonians,

describes the probability of finding an electron and the wave equation becomes solvable for
in that state. individual electrons in a molecule once a functional
form of the wave function can be derived.
∫Ψ 2
(r)dr = 1
Helec = ∑ H ieff
i
where r = radius (x, y and z)
H eff ψ = εψ
• There are many solutions to this probability
For a molecular system, a matrix of these 1-electron
function. These solutions are called atomic
Hamiltonians is constructed to describe the
orbitals, and their energies, orbital energies.
1-electron interactions between a single electron and
• For a molecule with many electrons and nuclei the core nucleus. The following represents the
the aim is to be able to describe molecular matrix for two atomic orbitals, φµ and φν.
orbitals and energies in as analogous a fashion
to the original Schrödinger equation as H uv = ∫ φ µ H eff φv dτ
possible.
However, in molecular systems, this Hamiltonian
Approximations to the Hamiltonian does not account for the interaction between
electrons with 2 or more different interaction centers
The first approximation made is known as the Born-
or the interaction of two electrons. Thus, the
Oppenheimer approximation, which allows separate
Hamiltonian is further modified. This modification
treatment of the electronic and nuclear energies. Due
renames the Hamiltonian operator to the Fock
to the large mass difference between an electron and
operator.
a nucleus, a nucleus moves so much more slowly
than an electron that it can be regarded as motionless
relative to the electron. In effect, this approximation Fψ = Eψ
considers electrons to be moving with respect to a The Fock operator is composed of a set of 1-electron
fixed nucleus. This allows the electronic energy to Hamiltonians that describe the 1-electron, 1 center
be described separately from nuclear energy by an interactions and is supplemented by terms that
electronic Hamiltonian, which can be solved at any describe the interaction between 2-electrons. These
set of nuclear coordinates. The electronic version of terms include a density matrix, P, and the Coulomb
the Schrödinger equation is: and exchange integrals. The final equation for the
Fock operator is represented by the Fock matrix.
H elec Ψelec = E elec Ψelec
F uv = H uv + ∑ Pλσ [Coulomb + Exchange Integrals]
Another approximation assumes that electrons act
independently of one another, or, more accurately,
that each electron is influenced by an average field

The Fock matrix has two forms: must be used to compute MOs. This uses the sum of
Restricted (RHF)— Requires that spin up and spin 1-electron atomic orbitals whose individual
down electrons have the same energy and occupy contributions to the MO is each weighted by a
the same orbital. U molecular orbital expansion coefficient, Cνi.
Unrestricted (UHF)—Allows the alpha and beta ψ i = ∑ Cviφv

spin electrons to occupy different orbitals and have v
different energies. The set of atomic orbitals, {φν}, being used to
generate the sum is called the basis set. Choice of an
Restrictions on the Wave Function appropriate basis set {φν} is an important
For a molecular orbital (MO) with many electrons, consideration in ab initio methods.
the electronic wave function (Ψ) is restricted to There are a number of functions and approaches
meeting these requirements: used to derive basis sets. Basis sets are generally
• Ψ must be normalized so that composed of linear combinations of Gaussian
functions designed to approximate the AOs.
+∞
Minimal basis sets, such as STO-3G, contain one
∫ cψ dv = n
2
contracted Gaussian function (single zeta) for each
−∞ occupied AO, while multiple-zeta basis sets (also
where n is the number of electrons. c is a called split valence basis sets) contain two or more
normalization coefficient and Ψ2 is interpreted contracted Gaussian functions. For example, a
as the probability density. This ensures that double-zeta basis set, such as the Dunning-Huzinaga
each electron exists somewhere in infinite basis set (D95), contains twice as many basis
space. functions as the minimal one, and a triple-zeta basis
• Ψ must be antisymmetric, meaning that it must set, such as 6-311G, contains three times as many
change sign if the positions of the electrons in a basis functions.
doubly-occupied MO are switched. This Polarized basis sets allow AOs to change shape for
requirement accommodates the Pauli exclusion angular momentum values higher than ground-state
principle. configurations by using polarization functions. The
6-31G* basis set, for example, adds d functions to
Spin functions heavy atoms.
Spin functions, α and β, represent the allowed A variety of other basis sets, such as diffuse function
angular momentum states for each electron, spin up basis sets and high angular momentum basis sets,
(↑) and spin down (↓) respectively. The product of are tailored to the properties of particular of models
the spatial function (φI), which represents the MO, under investigation.
and the spin function is the spin orbital (αφi or βφI The coefficients (Cνi) used for a given AO basis set
are the only two possible for any single MO). Spin (φν) are derived from the solution of the Roothaan-
orbitals are orthogonal. Hall matrix equation with a diagonalized matrix of
orbital energies, E.
LCAO and Basis Sets
Rigorous solution of the Hartree-Fock equations,
while possible for atoms, is not possible for
molecules. Generally an approximation known as
Linear Combination of Atomic Orbitals (LCAO)

The Roothaan-Hall Matrix Equation the classification of methods with one-electron
Hamiltonians; some prefer to classify these as
This equation, shown below, includes the Fock
empirical.
matrix (F), the matrix of molecular orbital
coefficients (C) from the LCAO approximation, the The method descriptions that follow represent a very
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overlap matrix (S), and the diagonalized molecular simplified view of the semiempirical methods
orbital energies matrix (E). available in Chem3D and CS MOPAC. For more
information see the online MOPAC manual.S
FC = SCE Extended Hückel Method
Since the Fock equations are a function of the Developed from the qualitative Hückel MO method,
molecular orbitals, they are not linearly the Extended Hückel Method (EH) represents the
independent. As such the equations must be solved earliest one-electron semiempirical method to
using iterative, self-consistent field (SCF) methods. incorporate both σ and p valence systems. It is still
The initial elements in the Fock matrix are guessed. widely used, owing to its versatility and success in
The molecular coefficients are calculated and the analyzing and interpreting ground-state properties
energy determined. Each subsequent iteration uses of organic, organometallic, and inorganic
the results of the previous iteration until no further compounds of biological interest. Built into
variation in the energy occurs (a self-consistent field Chem3D, EH is the default semiempirical method
is reached). used to calculate data required for displaying
molecular surfaces.
Ab Initio vs. Semiempirical
The EH method uses a one-electron Hamiltonian
Ab initio (meaning literally “from first principles”) with matrix elements defined as follows:
methods use the complete form of the Fock operator
to construct the wave equation. The semiempirical H µµ = − I µ
methods use simplified Fock operators, in which
H µν = 0.5K( H µµ + Hνν ) S µν µ ≠ν
1-electron matrix elements and some of the two
electron integral terms are replaced by empirically where Iµ is the valence state ionization energy
determined parameters. (VSIE) of orbital µ as deduced from spectroscopic
Both the SCF RHF and UHF methods underestimate data, and K is the Wolfsberg-Helmholtz constant
the electron-electron repulsion and lead to electron (usually taken as 1.75). The Hamiltonian neglects
correlation errors, which tend to overestimate the electron repulsion matrix elements but retains the
energy of a model. The use of configuration overlap integrals calculated using Slater-type basis
interaction (CI) is one method available to correct orbitals. Because the approximated Hamiltonian (H)
for this overestimation. For more information see does not depend on the MO expansion coefficient
“Configuration Interaction” on page 141. Cνi, the matrix form of the EH equations:
The Semiempirical Methods HC = SCE
Semiempirical methods can be divided into two can be solved without the iterative SCF procedure.
categories: one-electron types and two-electron
types. One-electron semiempirical methods use only
a one-electron Hamiltonian, while two-electron
methods use a Hamiltonian which includes a two-
electron repulsion term. Authors differ concerning

Methods Available in CS better estimates of the energy in systems where
energy levels are closely spaced, and where bond
MOPAC breaking is occurring.
The approximations that MOPAC uses in solving UHF can be run on both open and closed shell
the matrix equations for a molecular system follow. systems. The major caveat to this method is the time
Some areas requiring user choices are: involved. Since alpha and beta electrons are treated
separately, twice as many integrals need to be
• RHF or UHF methods
solved. As your models get large, the time for the
• Configuration Interaction (CI) computation may make it a less satisfactory method.
• Choice of Hamiltonian approximation
(potential energy function)
Configuration Interaction
The effects of electron-electron repulsion are
RHF underestimated by SCF-RHF methods, which
results in the overestimation of energies.
The default Hartree-Fock method assumes that the
molecule is a closed shell and imposes spin SCF-RHF calculations use a single determinant that
restrictions. The spin restrictions allow the Fock includes only the electron configuration that
matrix to be simplified. Since alpha (spin up) and describes the occupied orbitals for most molecules
beta (spin down) electrons are always paired, the in their ground state. Further, each electron is
basic RHF method is restricted to even electron assumed to exist in the average field created by all
closed shell systems. other electrons in the system, which tends to
overestimate the repulsion between electrons.
Further approximations are made to the RHF
Repulsive interactions can be minimized by
method when an open shell system is presented.
allowing the electrons to exist in more places (i.e.
This approximation has been termed the 1/2 electron
more orbitals, specifically termed virtual orbitals).
approximation by Dewar. In this method, unpaired
The multi-electron configuration interaction
electrons are treated as two 1/2 electrons of equal
(MECI) method in MOPAC addresses this problem
charge and opposite spin. This allows the
by allowing multiple sets of electron assignments
computation to be performed as a closed shell. A CI
(i.e., configurations) to be used in constructing the
calculation is automatically invoked to correct
molecular wave functions. Molecular wave
errors in energy values inherent to the 1/2 electron
functions representing different configurations are
approximation. For more information see
combined in a manner analogous to the LCAO
“Configuration Interaction” on page 141.
approach.
With the addition of the 1/2 electron approximation,
For a particular molecule, configuration interaction
RHF methods can be run on any starting
uses these occupied orbitals as a reference electron
configuration.
configuration and then promotes the electrons to
unoccupied (virtual) orbitals. These new states,
UHF
Slater determinants or microstates in MOPAC, are
The UHF method treats alpha (spin up) and beta then linearly combined with the ground state
(spin down) electrons separately, allowing them to configuration. The linear combination of
occupy different molecular orbitals and thus have microstates yields an improved electronic
different orbital energies. For many open and closed configuration and hence a better representation of
shell systems, this treatment of electrons results in the molecule.

Approximate The two major questions to consider when choosing
a potential function are:
Hamiltonians in MOPAC • Is the method parameterized for the elements in
There are five approximation methods available in the model?
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MOPAC: • Does the approximation have limitations which

• MINDO/3 render it inappropriate for the model being
studied?
• MNDO
For more detailed information see the MOPAC
• AM1
online manual.
• PM3
• MNDO-d MINDO/3 Applicability and Limitations
The potential energy functions modify the HF MINDO/3 (Modified Intermediate Neglect of
equations by approximating and parameterizing Diatomic Overlap revision 3) is the oldest method.
aspects of the Fock matrix. Using diatomic pairs, it is an INDO (Intermediate
Neglect of Diatomic Orbitals) method, where the
The approximations in semiempirical MOPAC degree of approximation is more severe than the
methods play a role in the following areas of the NDDO methods MNDO, PM3 and AM1. This
Fock operator: method is generally regarded to be of historical
• The basis set used in constructing the 1-electron interest only, although some sulfur compounds are
atom orbitals is a minimum basis set of only the still more accurately analyzed using this method.
s and p Slater Type Orbitals (STOs) for valence The following table shows the diatomic pairs that
electrons. are parameterized in MINDO/3. An x indicates
parameter availability for the pair indicated by the
• The core electrons are not explicitly treated. row and column. Parameters of dubious quality are
Instead they are added to the nucleus. The indicated by (x).
nuclear charge is termed Neffective.
For example, Carbon as a nuclear charge of +6-
2 core electrons for a effective nuclear charge of
+4.
• Many of the 2-electron Coulomb and Exchange
integrals are parameterized based on element.
Choosing a Hamiltonian
Overall, these potential energy functions may be
viewed as a chronological progression of
improvements from the oldest method, MINDO/3 to
the newest method, PM3. However, although the
improvements in each method were designed to
make global improvements, they have been found to
be limited in certain situations.

MNDO Applicability and Limitations AM1 Applicability and Limitations
MNDO (Modified Neglect of Differential Overlap) AM1 (Austin Model 1) may be applied to the
may be applied to the elements shaded in the table elements shaded in the table below:
below.
The following limitations apply to MNDO: Important factors relevant to AM1 are:
• Sterically crowded molecules are too unstable, • AM1 is similar to MNDO; however, there are
for example, neopentane. changes in the core-core repulsion terms and
reparameterization.
• Four-membered rings are too stable, for
example, cubane. • AM1 is a distinct improvement over MNDO, in
that the overall accuracy is considerably
• Hydrogen bonds are virtually non-existent, for
improved. Specific improvements are:
example, water dimer. Overly repulsive
nonbonding interactions between hydrogens • The strength of the hydrogen bond in the
and other atoms are predicted. In particular, water dimer is 5.5 kcal/mol, in accordance
simple H-bonds are generally not predicted to with experiment.
exist using MNDO. • Activation barriers for reaction are markedly
• Hypervalent compounds are too unstable, for better than those of MNDO.
example, sulfuric acid. • Hypervalent phosphorus compounds are
• Activation barriers are generally too high. considerably improved relative to MNDO.
• Non-classical structures are predicted to be • In general, errors in ∆Hf obtained using AM1
unstable relative to the classical structure, for are about 40% less than those given by
example, ethyl radical. MNDO.
• Oxygenated substituents on aromatic rings are • AM1 phosphorus has a spurious and very
out-of-plane, for example, nitrobenzene. sharp potential barrier at 3.0Å. The effect of
this is to distort otherwise symmetric
• The peroxide bond is systematically too short geometries and to introduce spurious
by about 0.17 Å. activation barriers. A vivid example is given
• The C-O-C angle in ethers is too large. by P4O6, in which the nominally equivalent

P-P bonds are predicted by AM1 to differ by • The barrier to rotation in formamide is
0.4Å. This is by far the most severe practically non-existent. In part, this can be
limitation of AM1. corrected by the use of the MMOK option. The
• Alkyl groups have a systematic error due to MMOK option is used by default in CS
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the heat of formation of the CH2 fragment MOPAC. For more information about MMOK
being too negative by about 2 kcal/mol. see the online MOPAC Manual.
• Nitro compounds, although considerably MNDO-d Applicability and Limitations

improved, are still systematically too
MNDO-d (Modified Neglect of Differential Overlap
positive in energy.
with d-Orbitals) may be applied to the elements
• The peroxide bond is still systematically too shaded in the table below:
short by about 0.17Å.
PM3 Applicability and Limitations

PM3 (Parameterized Model revision 3) may be
applied to the elements shaded in the following
table:
MNDO-d is a reformulation of MNDO with an

extended basis set to include d-orbitals. This method
may be applied to the elements shaded in the table
below. Results obtained from MNDO-d are
generally superior to those obtained from MNDO.
The MNDO method should be used where it is
necessary to compare or repeat calculations
The following apply to PM3: previously performed using MNDO.
• PM3 is a reparameterization of AM1.
The following types of calculations, as indicated by
• PM3 is a distinct improvement over AM1. MOPAC keywords, are incompatible with
• Hypervalent compounds are predicted with MNDO-d:
considerably improved accuracy. • COSMO (Conductor-like Screening Model)
solvation
• Overall errors in ∆Hf are reduced by about 40%
relative to AM1. • POLAR (polarizability calculation)
• Little information exists regarding the • GREENF (Green’s Function)
limitations of PM3. This should be corrected • TOM (Miertus-Scirocco-Tomasi self-consistent
naturally as results of PM3 calculations are reaction field model for solvation)
reported.

Chapter 10: MM2 Computations
MM2 Overview
The Chem3D MM2 menu provides computations
using the MM2 force field.
The MM2 procedures described assume that you
understand how the potential energy surface relates
to conformations of your model. If you are not
familiar with these concepts, see “Chapter 9:
Computation Concepts.”
As discussed in “Chapter 9: Computation
Concepts”, the energy minimization routine
performs a local minimization only. Therefore, the
results of minimization may vary depending on the
starting conformation in a model.
Minimize Energy
4. Set the convergence criteria using the following
To minimize the energy of the molecule based on options.
MM2 Force Field:
NOTE: If you are planning to make changes to any
NOTE: You cannot minimize models containing
of the MM2 constants, such as cutoff values or other
phosphate groups drawn with double bonds. For
parameters used in the MM2 force field, please
information on how to create a model with
make a backup copy of the parameter tables before
phosphate groups you can minimize, see the
making any changes. This will assure that you can
CambridgeSoft Chem3D Technical Support page at:
get back the values that we ship with Chem3D, in
http://www.camsoft.com/support/
case you need them.
1. Build the model for which you want to

minimize the energy.
2. To impose constraints on model measurements,

set the optimal column measurement to
constrain the Measurements table.
3. From the MM2 menu, choose Minimize Energy.

The Minimize Energy dialog box appears.
Chem3D Chapter 10: MM2 Computations • 145

store each iteration Select Record Every
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specify the Type a Minimum RMS as a frame in a Iteration.

convergence criteria Gradient. movie for replay
for the gradient of later
the potential energy If the slope of the potential
surface energy surface becomes too view the value of Select Copy Measurements
small, then the minimization each measurement to Messages.
has probably reached a local in the messages
minimum on the potential window
energy surface, and the
minimization terminates. restrict movement Select Move Only Selected
of a selected part of Atoms.
The default value of 0.100 is
a model during the
a reasonable compromise Constraint is not imposed on
minimization
between accuracy and speed. any term in the calculation
Reducing the value means and the values of any results
that the calculation continues are not affected.
longer as it tries to get even
closer to a minimum. Tracking Specific
Increasing the value shortens
the calculation, but leaves
Measurements
you farther from a minimum. You can show the value of each measurement in the
Increase the value if you Message window if the Measurements table is
want a better optimization of visible. You can use this to track a particular
a conformation that you measurement during minimization.
know is not a minimum, but
you want to isolate for To isolate a measurement of interest:
computing comparative data. 1. From the Tools menu, point to Show Model
Table, and then choose Measurements.
watch the Select Display Every
minimization Iteration. 2. Select the measurements you do not want to
process “live” at track.
each iteration in the NOTE: Displaying or
calculation recording each iteration 3. From the Edit menu, choose Clear.
adds significantly to the time
The remaining measurements are copied to the
required to minimize the
structure. Messages window during the minimization.
146 • Chapter 10: MM2 Computations Chem3D

NOTE: Chem3D guesses parameters if
Queuing Minimizations
you try to minimize a structure containing atom You can start to minimize several models without
types not supported by MM2. Examples include waiting for each model to finish minimizing. If a
inorganic complexes where known parameters are computation is in progress when you begin
limited. You can view all parameters used in the minimizing a second model, the minimization of the
analysis using the Show Used Parameters second model is delayed until the first minimization
command. See “Showing Used Parameters” on stops.
page 157. If you are using other applications, you can run
minimization with Chem3D in the background. You
Running a Minimization can perform any action in Chem3D that does not
change the position of an atom or add or delete any
To begin the minimization of a model: part of the model. For example, you can move
• Click Run. windows around during minimization, change
settings, or scale your model.
The Message Controller appears when the
minimization begins. The Status Bar appears is Minimizing Ethane
updated for every iteration of the computation,
showing the iteration number, the steric energy Ethane is a particularly straightforward example of
value at that iteration, and the RMS gradient. minimization, because it has only one
After the RMS gradient is reduced below the minimum-energy (staggered) and one
requested value, the minimization ends, and the maximum-energy (eclipsed) conformation.
final steric energy components and total appear To minimize energy in ethane:
in the Messages table.
1. From the File menu, choose New Model
Intermediate status messages may appear in the
Messages window. A message appears if the An empty model window appears.
minimization terminates abnormally, usually
due to a poor starting conformation.
To interrupt a minimization that is in progress:
A text box appears.
• Click Stop in the Movie Controller.
The minimization and recording stops. 4. Type CH3CH3 and press Enter or Return.
A model of Ethane appears.

6. From the MM2 menu, choose Minimize Energy

and click Run.
The calculation is performed. Messages appear
and the last one appears in the Message
controller.

To view all the messages: If the Rotation Bars are not visible, display them as
• Click the expansion button in the Message follows:
window. 1. From the Tools menu, choose Show Rotation
Bars.
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The values of the energy terms shown below are

approximate and can vary slightly based on the
type of processor used to calculate them. 2. Reorient the model by dragging the Y-axis
rotation bar until you have an end-on view.
The Total Steric Energy for the conformation is

0.8180 kcal/mol. The 1,4 VDW term of 0.6768
dominates the steric energy. This term is due to the
H-H repulsion contribution. To force a minimization to converge on the
transition conformation to determine the barrier to
To view the value of one of the dihedral angles that rotation:
contributes to the 1,4 VDW contribution:
1. In the Measurements table, type 0 in the
1. Select the atoms making up the dihedral angle Optimal column for the selected dihedral angle.
as shown below by Shift-clicking H(7), C(2),
C(1), and H(4) in that order. 2. From the MM2 menu, choose Minimize.
3. Click Run.
2. From the Object menu, choose Set Dihedral

Angle.
The following measurement appears. Entering a value in the Optimal column imposes a
constraint on the minimization routine. You are
increasing the force constant for the torsional term
in the steric energy calculation so that you can
optimize to the transition state.
The 60 degree dihedral represents the lowest
energy conformation for the ethane model.

When the minimization is complete, the reported Comparing Two Stable
energy values are as follows. The energy for this
eclipsed conformation is higher relative to the
Conformations of Cyclohexane
staggered form. The majority of the energy In the following example you compare the
contribution is from the torsional energy and the 1,4 cyclohexane twist-boat conformation and the chair
VDW interactions. global minimum.
To build a model of cyclohexane:
NOTE: The values of the energy terms shown here
are approximate and can vary slightly based on the 1. From the File menu, choose New Model.
type of processor used to calculate them. An empty model window appears.

A text box appears.
4. Type CH2(CH2)5 and press Enter or Return.
Before minimizing, it is wise to use the Clean Up
Structure command to refine the model. This
generally improves the ability of the Minimize
The dihedral angle in the Actual column becomes 0,
Energy command to reach a minimum point.
corresponding to the imposed constraint.
• From the Tools menu, choose Clean Up
The difference in energy between the global
Structure.
minimum and the transition state is 2.73 kcal/mole,
which is in agreement with literature values.
NOTE: The Clean Up Structure command is very
To further illustrate points about minimization: similar to the minimize energy command in that it is
a preset, short minimization of the structure.
• Remove the value from the Optimal column for
the dihedral angle and choose Minimize from
To perform the minimization:
the MM2 menu.
• From the MM2 menu, choose Minimize Energy,
After the minimization is complete, you are still at 0 and click Run.
degrees. This is an important consideration for When the minimization is complete, reorient
working with the MM2 minimizer. It uses first the model, using the Trackball Tool and/or the
derivatives of energy to determine the next logical X and Y Rotation bars so it appears as follows.
move to lower the energy. However, for saddle
points (transition states), the region is fairly flat and
the minimizer is satisfied that a minimum is reached.
If you suspect your starting point is not a minimum,
try setting the dihedral angle off by about 2 degrees
and minimize again.

The conformation you converged to is not the conformations. To obtain the new starting
well-known chair conformation, which is the global conformation, change the dihedrals of the twist
minimum. Instead, the model has converged on a conformation so that they represent the potential
local minimum, the twist-boat conformation. This is energy valley of the chair conformation.
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the closest low-energy conformation to your starting To locate the global minimum:
conformation.
• To see the twist conformation better, from the
Had you built this structure using substructures that Tools menu, deselect Show H’s and Lp’s.
are already energy minimized, you would be close to
the chair conformation. The hydrogens are hidden.
The minimizer does not surmount the saddle point to
locate the global minimum and the closest minimum
is sought.
The energy values in the Messages table are as
follows:
The most precise way to alter a dihedral angle is to
change its Actual value in the Measurements table
when dihedral angles are displayed. An easier way
to alter an angle, especially when dealing with a
ring, is to move the atoms by dragging and then
cleaning up the resulting conformation.
To change a dihedral angle:
• Drag C1 below the plane of the ring, then drag
C4 above the plane of the ring.
are approximate and can vary slightly based on the
type of processor used to calculate them.
The major contributions are from the 1,4 VDW and

Torsional aspects of the model.
For cyclohexane, there are six equivalent local
minima (twist-boat), two equivalent global minima
(chair), and many transition states (one of which is
the boat conformer).
Locating the Global Minimum

Finding the global minimum is extremely
challenging for all but the most simple molecules. It
requires a starting conformation which is already in During dragging, the bond lengths and angles
the valley of the global minimum, not in a local were deformed.
minimum valley. The case of cyclohexane is
straightforward because we already know that the
global minimum is either of the two possible chair

To return them to the optimal values before
minimizing:
Molecular
1. From the MM2 menu, choose Minimize Energy
Dynamics
and click Run. Molecular Dynamics uses Newtonian mechanics to
simulate motion of atoms, adding or subtracting
2. When the minimization is complete, reorient kinetic energy as the model’s temperature increases
the model using the Rotation bars to see the or decreases.
final chair conformation. Molecular Dynamics allows you to access the
conformational space available to a model by
NOTE: The values of the energy terms shown here storing iterations of the molecular dynamics run and
are approximate and can vary slightly based on the later examining each frame.
type of processor used to calculate them.
Performing a Molecular
Dynamics Computation
4
To perform a molecular dynamics simulation:
1. Build the model (or fragments) that you want to

1 include in the computation.
This conformation is about 5.5 kcal/mole more NOTE: The model display type you use affects
stable than the twist-boat conformation. the speed of the molecular dynamics
For molecules more complicated than cyclohexane, computation. Model display will decrease the
where you don’t already know what the global speed in the following order: Wire Frame<
minimum is, some other method is necessary for Sticks < Ball and Sticks< Cylindrical Bonds <
locating likely starting geometries for minimization. Ribbons< Space Fill and VDW dot surfaces <
One way of accessing this conformational space of a Molecular Surfaces.
molecule with large energy barriers is to perform
molecular dynamics simulations. This, in effect, 2. Minimize the energy of the model (or
heats the molecule, thereby increasing the kinetic fragments), using MM2 or MOPAC.
energy enough to surmount the energetically
disfavored transition states. Another way to search 3. To track a particular measurement during the
conformational space is through use of the MM2 simulation, choose one of the following:
Dihedral driver (available for Macintosh only). • Select the appropriate atoms and from the
Object menu, choose Set Bond Angle or Set
Bond Length.
• From the Analyze menu, choose one of the
Show commands and remove the
measurements you are not interested in.
4. From the MM2 menu, choose Molecular

Dynamics.

The Molecular Dynamics dialog box appears interval of 100 fs or more can be used to obtain
with the default values. samples of conformational space over a longer
.
computation.
• Terminate After—causes the molecular
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dynamics run to stop after the specified number

of steps. The total time of the run is the Step
Interval times the number of steps.
• Heating/Cooling Rate—dictates whether
temperature adjustments are made. If the
Heating/Cooling Rate check box is checked, the
Heating/Cooling Rate slider determines the rate
at which energy is added to or removed from the
model when it is far from the target
temperature.
A heating/cooling rate of approximately 1.0
kcal/atom/picosecond results in small
corrections which minimally disturb the
5. Enter the appropriate values. trajectory. A much higher rate quickly heats up
the model, but an equilibration or stabilization
6. Click Run. period is required to yield statistically
meaningful results.
Dynamics Settings
To compute an isoenthalpic trajectory (constant
Use the Dynamics tab to enter parameter values for total energy), deselect Heating/Cooling Rate.
the parameters that define the molecular dynamics
Target Temperature—the final temperature to
calculations:
which the calculation will run. Energy is added
• Step Interval—determines the time between to or removed from the model when the
molecular dynamics steps. The step interval computed temperature varies more than 3%
must be less than ~5% of the vibration period from the target temperature.
for the highest frequency normal mode, (10 fs
The computed temperature used for this
for a 3336 cm–1 H–X stretching vibration).
purpose is an exponentially weighted average
Normally a step interval of 1 or 2 fs yields
temperature with a memory half-life of about
reasonable results. Larger step intervals may 20 steps.
cause the integration method to break down,
because higher order moments of the position
are neglected in the Beeman algorithm.
• Frame Interval—determines the interval at
which frames and statistics are collected. A
frame interval of 10 or 20 fs gives a fairly
smooth sequence of frames, and a frame

Job Type Settings
If you want to … Then Click …
Use the Job Type tab to set options for the
computation. save a file Click Save Step Data In
containing the and browse to choose a
Time (in location for storing this
picoseconds), Total file.
Energy, Potential
Energy, and The word “heating” or
Temperature data “cooling” appears for
for each step. each step in which
heating or cooling was
performed. A summary of
this data appears in the
Message window each
time a new frame is
created.
To begin the computation:

• Click Run.
Select the appropriate options:
The computation begins. The Start button in the
Movie Controller is highlighted. If you have
If you want to … Then Click … chosen to Record each iteration, the Record
button is highlighted. Messages for each
record each Record Every Iteration. iteration and any measurements you are
iteration as a frame tracking appear in the Message window.
in a movie for later
The following Molecular Dynamics dialog box
replay
appears, allowing you to change the settings of
the Dynamics tab as the simulation proceeds.
track a particular Copy Measurements to
measurement Messages.
restrict movement Move Only Selected

of a selected part of Atoms.
a model during the
minimization Constraint is not imposed
on any term in the
calculation and the values
of any results are not
affected.
The simulation ends when the number of steps

specified is taken.

To stop the computation prematurely: To view the last several messages:
• Click Stop in the Movie Controller. 1. Click the expansion button in the Message
window.
Computing the Molecular Dynamics
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Trajectory for a Short Segment of

Polytetrafluoroethylene (PTFE)
To build the model:

2. Click the Stop button in the Move Controller
3. Click in the model window. after 20 frames have been computed.
A text box appears. The Molecular Dynamics computations and
recording stops.
4. Type F(C2F4)6F and press Enter or Return.
A polymer segment consisting of six repeat To replay the movie:
units of tetrafluoroethylene appears in the • Click Start in the Movie Controller.
model window. The frames computed during the molecular
To perform the computation: dynamics calculation are played as a movie.
1. Select C(2), the leftmost terminal carbon, then To review the results:
shift-click C(33), the rightmost terminal carbon. 1. View the Messages window to examine the
2. From the Object menu, choose Set Distance. measurement data included in the molecular
dynamics step data.
A measurement for the overall length of the
molecule appears in the Measurements table. 2. Drag the Movie slider knob to the left until the
first step appears.
3. From the MM2 menu, choose Molecular
Dynamics.
4. Click the Job Type tab and check Copy

Measurements to Messages.
5. Click Run.
When the calculation begins, the Message Window
appears. As the molecular dynamics calculation The C(2)-C(33) distance for the molecule
proceeds, the frame associated with each step is before the molecular dynamics calculation
retained and the number in the frame scroll box began is approximately 9.4Å.
increases incrementally.

3. Scroll down to the bottom of the Messages Compare the steric energies of cis- and trans-2-
window and examine the C(2)-C(33) distance butene.
for the molecule at 0.190 picoseconds (which
To build trans-2-butene and compute properties:
corresponds to frame 20 in the Movie slider of
the model window). 1. From the File menu, choose New Model.

A text box appears.
4. Type trans-2-butene and press Enter or

Return.
The C(2)-C(33) distance is approximately
13.7Å, 42% greater than the initial C(2)-C(33) A molecule of trans-2-butene appears in the
distance. model window.

Compute Properties Properties.
Compute Properties represents a single point energy The Compute Properties dialog box appears.
computation that reports the total steric energy for
the current conformation of a model (the active
frame, if more than one exists).
NOTE: The Steric Energy is computed at the end of

an MM2 Energy minimization.
A comparison of the steric energy of various

conformations of a molecule gives you information
on the relative stability of those conformations.
NOTE: In cases where parameters are

not available because the atom types in your model
are not among the MM2 atom types supported,
Chem3D will attempt an educated guess. You can
view the guessed parameters by using the Show
Used Parameters command after the analysis is
completed.
6. Click Run.
The Message window appears. When the steric
energy calculation is complete, the individual
steric energy terms and the total steric energy
appear.

To view the last several messages: • The Non-1,4 van der Waals term represents the
• Click the expansion button in the Message energy for the through-space interaction
window. between pairs of atoms that are separated by
more than three atoms.
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For example, in trans-2-butene, the Non-1,4 van der

Waals energy term includes the energy for the
interaction of a hydrogen atom bonded to C(1) with
a hydrogen atom bonded to C(4).
The 1,4 van der Waals term represents the energy for
the through-space interaction of atoms separated by
two atoms.
For example, in trans-2-butene, the 1,4 van der
The units are kcal/mole for all terms. At the Waals energy term includes the energy for the
beginning of the computation the first message interaction of a hydrogen atom bonded to C(1) with
indicates that the parameters are of Quality=4 a hydrogen atom bonded to C(2).
meaning that they are experimentally The dipole/dipole steric energy represents the
determined/verified parameters. energy associated with the interaction of bond
dipoles.
are approximate and can vary slightly based on the For example, in trans-2-butene, the Dipole/Dipole
type of processor used to calculate them. term includes the energy for the interaction of the
two C Alkane/C Alkene bond dipoles.
The following values are displayed: To build a cis-2-butene and compute properties:
• The Stretch term represents the energy 1. Do one of the following:
associated with distorting bonds from their • Click the Select tool and select all the atoms
optimal length. in the model window.
• The second steric energy term is the Bend term. • From the Edit menu, choose Select All.
This term represents the energy associated with 2. From the Edit menu, choose Clear to delete the
deforming bond angles from their optimal model.
values.
3. Double-click in the model window.
• The Stretch-Bend term represents the energy
A text box appears.
required to stretch the two bonds involved in a
bond angle when that bond angle is severely 4. Type cis-2-butene and press Enter or Return.
compressed. A molecule of cis-2-butene appears in the
model window.
• The Torsion term represents the energy
associated with deforming torsional angles in 5. From the MM2 menu, choose Compute
the molecule from their ideal values. Properties.
The steric energy terms for cis-2-butene
appears in the Messages window.

Below is a comparison of the steric energy
components for cis-2-butene and trans-2-butene.
Showing Used
Parameters
NOTE: The values of the energy terms shown here You can display all parameters used in an MM2
are approximate and can vary slightly based on the calculation in the Messages window. The list
type of processor used to calculate them. includes a quality assessment of each parameter.
Highest quality empirically-derived parameters are
rated as 4 while a lowest quality rating of 1 indicates
that a parameter is a “best guess” value.
trans-2-
Energy Term butene cis-2-butene To show the used Parameters:
• From the MM2 menu, choose Show Used
Stretch: 0.0627 0.0839 Parameters.
Bend: 0.2638 1.3235 The parameters appear in the Messages

window.
Stretch-Bend: 0.0163 0.0435
Torsion: -1.4369 -1.5366
Non-1,4 van der -0.0193 0.3794

Waals:
1,4 van der 1.1742 1.1621

Waals:
Dipole/Dipole: 0.0767 0.1032
Total: 0.137 1.5512
The significant differences between the steric

energy terms for cis and trans-2-butene are in the
Bend and Non-1,4 van der Waals steric energy MM2 Dihedral Driver
terms. The Bend term is much higher in cis-2-butene
because the C(1)-C(2)-C(3) and the C(2)-C(3)-C(4)
(Macintosh Only)
bond angles had to be deformed from their optimal The dihedral driver allows you to access the
value of 122.0° to 127.4° to relieve some of the conformational space of a model by varying a single
steric crowding from the interaction of hydrogens on dihedral angle. At each dihedral angle value, the
C(1) and C(4). The interaction of hydrogens on C(1) model is energy minimized using the MM2 force
and C(4) of trans-2-butene is much less intense, thus field and the steric energy of the model is computed.
the C(1)-C(2)-C(3) and the C(2)-C(3)-C(4) bond The conformation, steric energy, and dihedral angle
angles have values of 123.9°, much closer to the are added as a record in a Table Editor table). After
optimal value of 122.0°. The Bend and Non-1,4 van the computation is complete you can view the data
der Waals terms for trans-2-butene are smaller,
therefore trans-2-butene has a lower steric energy
than cis-2-butene.

to locate the models with the lowest steric energy • Click the cell of a small or large version of the
values and use these as starting points for further model to select it, choose Copy from the Edit
refinement in locating a stationery point. menu in the table to copy the model to the
Clipboard, then return to Chem3D, open a new
To use the dihedral driver:
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model window (or use the model window used

1. Select four contiguous atoms in your model that to initiate the dihedral driver) and choose paste
define the dihedral angle of interest. from the Edit menu to paste the model in
Chem3D.
2. From the MM2 menu, choose Dihedral Driver.
The computation begins. The computation first Analyzing Conformations of n-Butane
performs a minimization on the current
Build a model of n-butane:
conformation. Next, it rotates the dihedral in 10
degree increments through 360 degrees for a 1. Click the Text Building tool.
total of 37 conformations.
NOTE: This command clears all the messages in 3. Type CH3CH2CH2CH3 into the text box.
the Messages table prior to staring the computation.
If you have messages that you want to keep, copy 4. Press Enter or Return.
them to another application that accepts tab-
delimited text. To analyze the model:

The Table Editor opens and a new table is created
containing the model, rotational constant and steric 2. Click in empty space to deselect all the atoms.
energy for each iteration of the computation.
3. Shift-click the carbons in sequence, for
The models appear very tiny in the table because
during the computation, the records in the table are example from C1 to C4.
closed.
After the computation is complete, you can view the
Steric energy values and determine the
conformations of interest.
To view the full model do any of the following:

• Open the record by clicking the record selector.
• Open several records by shift-clicking the
record selectors for the individual records to
open, and then press Command-Right Arrow. NOTE: If you do not click the carbons in a
• To open all records in the table, from the Edit rational sequence, your computation fails,
menu in the Table Editor, choose Select All and because the dihedral is ambiguously defined.
press Command-Right Arrow.

4. From the MM2 menu, choose Dihedral Driver.
Using .jdf Files
The computation begins. The dihedral is rotated
You can run MM2 computations on previously
10 degrees at a time followed by a
created job description files (.jdf). The job type and
minimization. settings are saved in the .jdf file.
NOTE: The minimization is possible because To run an MM2 job:
the dihedral is constrained during the
minimization. This constraint is an additional 1. From the MM2 menu, choose Run MM2 Job.
term added to the potential function equations.
2. Choose the file and click Open.
The time for the computation may be quite long The dialog box for the appropriate computation
because you are performing a series of appears.
minimizations. The time for analysis increases in
proportion to the number of atoms in the model. 3. Change parameters if desired and click Run.
The data appears in a table after each iteration. You

can view this data or graph the energy versus
dihedral in a graphing application.
To graph the data:
If you have Microsoft Excel version 4.0 or later, you
can select these two columns of information (by
dragging diagonally over all the cells in the rows
that you want to graph) and choose the Script
“Graph”. The data is graphed using Microsoft Excel.
For more information about this script choose About
Scripts in the Help menu within the Table Editor
application.
Repeating an MM2
Computation
After you perform an MM2 computation, you can
repeat the job as follows:
1. From the MM2 menu, choose Repeat [name of

computation].
The appropriate dialog box appears.
2. Change parameters if desired and click Run.

The computation proceeds.

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Chapter 11: MOPAC Computations
MOPAC Overview
MOPAC is a molecular computation application that
features a number of widely-used, semi-empirical
methods. Chem3D includes MOPAC and provides a
graphical user interface (GUI) that allows you to
perform MOPAC computations directly on the
model in the Chem3D model window. As a
computation progresses, you can view the model
change appearance to reflect the computed result.
Computations are limited in CS MOPAC to 250
heavy atoms.
The following procedure assume you have a basic
understanding of the computational concepts and
terminology of semi-empirical methods, and the
concepts involved in geometry optimization
(minimization) and single-point computations. For The Job Type Tab
more information see “Chapter 9: Computation
Concepts.” Use the Job Type tab to set options for display and
recording results of calculations, and to enter the
The Chem3D CD-ROM contains the complete
Minimum RMS Gradient value.
MOPAC manual in Adobe Acrobat .pdf format. The
manual, along with the Adobe Acrobat Reader
application, is in the folder named Documentation.
Minimize Energy
Minimizing energy is generally the first molecular
computation performed on a model.
To minimize energy of a model:
1. From the MOPAC menu, choose Minimize

Energy.
Chem3D Chapter 11: MOPAC Computations • 161

Choose the appropriate options:
If you want to … Then Click…
If you want to … Then Click…
watch the Display Every Iteration.
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Type a Minimum RMS minimization

specify the NOTE: Displaying or
Gradient. process “live” at
convergence recording each iteration
each iteration in the
criteria for the adds significantly to the
If you want to use a value calculation.
gradient of the time required to minimize
potential energy <0.01, you must specify
LET in the additional the structure.
surface. See also
“Gradient Norm” keywords section.
on page 171. record each Record Every Iteration.
If the slope of the iteration as a frame
potential energy surface in a movie for later
becomes too small, then replay
the minimization has
probably reached a local
view the value of Copy Measurements to
minimum on the potential
each measurement Messages.
energy surface, and the
in the Message
minimization terminates.
window
The default value of
0.100 is a reasonable The Theory Tab
compromise between
accuracy and speed. Use the Theory tab to specify the Method and Wave
Function.
Reducing the value
means that the calculation
continues longer as it tries
to get even closer to a
minimum.
Increasing the value

shortens the calculation,
but leaves you farther
from a minimum.
Increase the value if you
want a better
optimization of a
conformation that you
know is not a minimum,
but you want to isolate for
computing comparative
data.
162 • Chapter 11: MOPAC Computations Chem3D

1. Select the appropriate method. You can assign a charge using the Text Building tool
or by specifying it in MOPAC:
NOTE: For more information about the To use the Text Building tool:
available MOPAC methods, see “Chapter 9:
Computation Concepts.” 1. Click the Text Building tool.
2. Click an atom in your model.
2. Select the appropriate Wave Function. 3. Type a + or -.

Selecting a wave function from the Wave Function For example, clicking a carbon and typing “+”
menu involves deciding whether to use RHF or UHF in a text box to make it a carbocation.The
computations. charge is automatically sent to MOPAC.
RHF is the default Hartree-Fock method used for
To specify the charge in MOPAC:
both open and closed shell systems. When an open
shell system is computed, the RHF calculation uses 1. From the MOPAC menu, choose Minimize
the 1/2 electron approximation and a configuration Energy.
interaction calculation for a single microstate.
UHF is an alternative form of the HF method that 2. On the General tab, in the Additional Keywords
can be used for both open and closed shell systems. box, type the keyword CHARGE=n, where n is
UHF computations take at least twice as long as a positive or negative integer (-2, -1, +1, +2).
RHF. This may be the deciding consideration of Different combinations of spin-up (alpha electrons)
method when large molecules are being studied. and spin-down (beta electrons) lead to various
To use RHF: electronic energies. These combinations are
• Select the Closed Shell (Restricted) wave specified as the Spin Multiplicity of the molecule.
function. The following table shows the relation between total
spin S, spin multiplicity, and the number of unpaired
To use UHF: electrons.
• Select the Open Shell (Unrestricted) wave
function.
Spin Keyword (# unpaired electrons)
NOTE: MOPAC requires that UHF be selected in 0 SINGLET 0 unpaired

order to calculate Hyperfine Coupling Constants.
1/2 DOUBLET 1 unpaired
Specifying the Electronic 1 TRIPLET 2 unpaired
Configuration 1 1/2 QUARTET 3 unpaired
MOPAC must have the net charge of the molecule in 2 QUINTET 4 unpaired
order to determine whether the molecule is open or
closed shell. 2 1/2 SEXTET 5 unpaired
If a molecule has a net charge, be sure you have

either specified a charged atom type or added the
charge.

To determine the appropriate spin multiplicity, Even-Electron Systems
consider whether:
If a molecule has an even number of electrons, the
• The molecule has an even or an odd number of ground state and excited state configurations can be
electrons. Singlet, Triplet, or Quintet (not likely). Normally the
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• The molecule is in its ground state or an excited ground state is Singlet, but for some molecules,
state. symmetry considerations indicate a Triplet is the
most stable ground state.
• To use RHF or UHF methods.
The following table shows some common Ground State, RHF
permutations of these three factors: The Ground State, RHF configuration is as follows:
RHF (Closed Shell) • Singlet ground state—the most common
Electronic configuration for a neutral, even electron stable
State Keywords to Use
organic compound. No additional keywords are
Spin State OPEN(n1,n2) a ROOT = n C.I.= n necessary.
Ground SINGLET
• Triplet ground state—Use the following
DOUBLET 1,2
TRIPLET 2,2
keyword combination: TRIPLET OPEN(2,2)
QUARTET 3,3 • Quintet ground state—Use the following
QUINTET 4,4
keyword combination: QUINTET OPEN(4,4)
SEXTET 5,5
1st Excited SINGLET 2
DOUBLET 2 2
NOTE: The OPEN keyword is normally necessary
TRIPLET 2 3 only when the molecule has a high degree of
QUARTET 2 4 symmetry, such as molecular oxygen. The OPEN
QUINTET 2 5 keyword increases the active space available to the
SEXTET 2 6 SCF calculation by including virtual orbitals. This
2nd Excited SINGLET 3 is necessary for attaining the higher multiplicity
DOUBLET 3 3 configurations for even shell system. The OPEN
TRIPLET 3 3 keyword also invokes the RHF computation using
QUARTET 3 4 the 1/2 electron approximation method and a C.I.
QUINTET 3 5
calculation to correct the final RHF energies. To see
SEXTET 3 6
the states used in a C.I. calculation, type MECI as
a. The OPEN keyword is necessary only when the
molecule has high symmetry, such as molecular an additional keyword. The information is printed at
oxygen. the bottom of the *.out file.
UHF (Opwn Shell)
Electronic State Spin State
Ground SINGLET
DOUBLET
TRIPLET
QUARTET
QUINTET
SEXTET

Ground State, UHF Second excited quintet: OPEN(4,4) ROOT=3
QUINTET C.I.=n, where n=5 is the simplest case.
For UHF computations, all unpaired electrons are
forced to be spin up (alpha).
Excited State, UHF
• Singlet ground state—the most common
Only the ground state of a given multiplicity can be
configuration for a neutral, even electron, stable
calculated using UHF.
organic compound. No additional keywords are
necessary. Odd-Electron Systems
• UHF will likely converge to the RHF solution Often, anions, cations, or radicals are odd-electron
for Singlet ground states. systems. Normally, the ground states and excited
• Triplet or Quintet ground state: Use the state configuration can be doublet, quartet or sextet.
keyword TRIPLET or QUINTET.
Ground State, RHF
NOTE: When a higher multiplicity is used, the Doublet ground state: This is the most common
UHF solution yields different energies due to configuration. No additional keywords are
separate treatment of alpha electrons. necessary.
Quartet: Use the following keyword combination:
QUARTET OPEN(3,3)
Excited State, RHF
Sextet ground state: Use the following keyword
First Excited State: The first excited state is actually
combination: SEXTET OPEN(5,5)
the second lowest state (the root=2) for a given spin
system (Singlet, Triplet, Quintet).
Ground State, UHF
To request the first excited state, use the following
For UHF computations all unpaired electrons are
sets of keywords:
forced to be spin up (alpha).
Doublet ground state: This is the most common
First excited Singlet: ROOT=2 OPEN(2,2) configuration for a odd electron molecule. No
SINGLET (or specify the single keyword additional keywords are necessary.
EXCITED)
UHF will yield energies different from those
First excited triplet: ROOT=2 OPEN (2,2) obtained by the RHF method.
TRIPLET C.I.=n, where n=3 is the simplest case.
Quartet and Sextet ground state: Use the keyword
First excited quintet: ROOT=2 OPEN (4,4) QUARTET or SEXTET.
QUINTET C.I.=n, where n=5 is the simplest case.
Second Excited State: The second excited state is Excited State, RHF
actually the third lowest state (the root=3) for a First Excited State: The first excited state is actually
given system (Singlet, Triplet, Quintet). To request the second lowest state (the root=2) for a given spin
the second excited state use the following set of system (Doublet, Quartet, Sextet). To request the
keywords: first excited state use the following sets of
Second excited Singlet: OPEN(2,2) ROOT=3 keywords.
SINGLET First excited doublet: ROOT=2 DOUBLET C.I.=n,
Second excited triplet: OPEN(2,2) ROOT=3 where n=2 is the simplest case.
TRIPLET C.I.=n, where n=3 is the simplest case.

First excited quartet: ROOT=2 QUARTET C.I.=n,
where n=4 is the simplest case.
First excited sextet: ROOT=2 SEXTET C.I.=n,
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Second Excited State: The second excited state is

actually the third lowest state (the root=3) for a
given system (Singlet, Triplet, Quintet). To request
the second excited state use the following set of
keywords:
Second excited doublet: ROOT=3 DOUBLET
C.I.=n, where n=3 is the simplest case.
Second excited quartet: ROOT=3 QUARTET
C.I.=n, where n=4 is the simplest case.
Second excited sextet: ROOT=3 SEXTET C.I.=n,
2. Select properties to calculate. For a detailed
NOTE: If you get an error indicating the active description of the properties, see “Compute
space is not spanned, use C.I.> n for the simplest Properties” on page 170.
case to increase the number of orbitals available in
the active space. To see the states used in a C.I. The General Tab
calculation, type MECI as an additional keyword.
The general tab allows you to specify additional
The information is printed at the bottom of the *.out
MOPAC keywords to tailor a calculation to more
file.
exacting requirements. For example, you might use
additional keywords to control convergence criteria,
Excited State, UHF to optimize to an excited state instead of the ground
state, or to calculate additional properties.
Only the ground state of a given multiplicity can be
calculated using UHF. • Click the General tab to type any additional
keywords that you want to use to modify the
The Properties Tab optimization.
The Properties tab allows you to select the
properties and charges to calculate from the NOTE: Other properties that you might specify
minimized structure. through the additional keywords section of the
dialog box may affect the outcome. For more
1. Click the Properties tab. information see “Using Keywords” on page 183.

MOPAC uses its default BFGS minimizer.
s
NOTE: Because the BFGS keyword is not sent to

MOPAC, it does not appear in the output file. For
more information about the EF routine, see page
160 in the MOPAC manual.
NOTE: Occasionally, intermediate messages

regarding the status of the minimization appear in
the Messages window. A message appears if the
minimization terminates abnormally, usually due to
a poor starting conformation.
For descriptions of error messages reported by

MOPAC, see Chapter 11, pages 325–331, in the
MOPAC manual.
Minimizing Energy To interrupt a minimization that is in progress:
To begin the minimization of a model: • Click Stop in the Movie Controller.
• On the General tab, click Run.
Keywords
The information about the model, and the
keywords are sent to the MOPAC program. The following table contains keywords
automatically sent to MOPAC and those you can use
The Default Minimizer to affect convergence.
Chem3D uses the Eigenvector Following (EF)

routine as the default geometry optimization routine Keyword Description
(minimizer) by automatically inserting the EF
keyword. This is because EF is generally superior to EF Automatically sent to MOPAC
the modified Broyden-Fletcher-Goldfarb-Shanno to specify the use of the
(BFGS) routine used as the default by MOPAC. Eigenvector Following (EF)
To use the BFGS routine: minimizer.
• On the General tab, specify BFGS in the
BFGS Prevents the automatic insertion
Additional Keywords section.
of EF and restores the BFGS
minimizer.
GEO-OK Automatically sent to MOPAC

to override checking of the Z-
matrix.

Keyword Description
MMOK Automatically sent to MOPAC

to specify Molecular Mechanics
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correction for amide bonds. Use

the additional keyword NOMM
to turn this keyword off.
RMAX=n.nn The calculated/predicted energy

change must be less than n.nn.
The default is 4.0.
RMIN=n.nn The calculated/predicted energy

change must be more than n.n.
The default value is 0.000.
PRECISE Runs the SCF calculations using

a higher precision so that values 2. On the Theory tab select Method, and Wave
do not fluctuate from run to run. Function.
3. On the Properties tab, select the properties you

LET Overrides safety checks to make
wish to calculate from the final optimized
the job run faster (or faster).
conformation.
RECALC=5 Use this keyword if the 4. On the General tab, type any additional
optimization has trouble
keywords that you want to use to modify the
converging to a transition state.
optimization.
Optimize to 5. Click Run.
Transition State The information about the model and the

keywords are sent to MOPAC. As the
To optimize your model to a transition state, use a optimization proceeds, the Messages window
conformation that is as close to the transition state as appears.
possible. Do not use a local or global minimum,
because the algorithm cannot effectively move the The Messages window displays intermediate
geometry from that starting point. messages about the status of the minimization. IA
message appears if the minimization terminates
To optimize a transition state: abnormally, usually due to a poor starting
conformation.
1. Choose Optimize to Transition State.
The Optimize to Transition State dialog box
appears.

The following contains keywords automatically sent
to MOPAC and some additional keywords you can NOTE: For descriptions of error messages
use to affect convergence. reported by MOPAC see Chapter 11, pages 325–
331, in the MOPAC manual.
Keyword Description
To interrupt a minimization that is in progress:
EF Automatically sent to MOPAC • Click Stop in the Movie Controller.
to specify the use of the
Eigenvector Following Locating the Eclipsed
minimizer.
Transition State of Ethane
GEO-OK Automatically sent to MOPAC Build a model of ethane:
to override checking of the
Z-matrix. 1. From the File menu, choose New Model
MMOK Automatically sent to MOPAC 2. Click the Text Building tool.

to specify Molecular
Mechanics correction for
amide bonds. Use the A text box appears.
additional keyword NOMM to
4. Type CH3CH3 and press Enter or Return.
turn this keyword off.
A model of ethane appears with all atoms
RMAX=n.nn The calculated/predicted selected.
energy change must be less
than n.nn. The default is 4.0. 5. Click the Select tool.
6. Click in an empty area of the window to

RMIN=n.nn the calculated/predicted energy
deselect the atoms in ethane.
change must be more than n.n.
The default value is 0.000. 7. In the Tools menu, make sure that Show
Rotation Bars is selected.
PRECISE Runs the SCF calculations
using a higher precision so that 8. Click C(1).
values do not fluctuate from run
to run. 9. Double-click the Internal Rotation Bar and
type 57 in the text box that appears.
LET Overrides safety checks to A nearly eclipsed conformation of ethane with
make the job run faster (or
C(1) selected is displayed.
further).
RECALC=5 Use this keyword if the

optimization has trouble
converging to a transition state.

Use Mopac to create the precise eclipsed transition
state: NOTE: If you perform an Energy
Minimization from the same starting dihedral,
1. Shift-click C(2) and any two nearly eclipsed
your model would optimize to the staggered
hydrogen atoms, such as H(4) and H(7), to
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conformation of ethane where the dihedral is 60

identify the dihedral to track. degrees, instead of optimizing to the transition
You should have a nearly coplanar four-atom state.
chain, such as H(4)-C(1)-C(2)-H(7), selected.

Measurements, and then choose Show Compute
Dihedral Angle. Properties
The Measurements table appears and displays To perform a single point calculation on the current
an actual value for the selected dihedral angle of conformation of a model:
-3.149 degrees.
1. From the MOPAC menu, choose Compute
Properties.
The Compute Properties dialog box appears.
2. On the Theory tab, choose a potential energy

function to use for performing the calculation.
NOTE: For more information about the potential

energy functions available in MOPAC see
“Chapter 9: Computation Concepts.”
3. From the MOPAC menu, choose Optimize to
Transition State. 3. On the Properties tab, select the properties to
calculate.
4. Click the Copy Measurements to Messages.
5. Click Run.
The ethane model minimizes so that the
dihedral is 0 degrees, corresponding to the
eclipsed conformation of ethane, a known
transition state between the staggered minima
conformations.
To see the Newman projection of the eclipsed ethane

model:
1. Select both carbon atoms.
2. From Object menu, point to Move To, and then

choose Move to Z-Axis.

4. On the Properties tab, set the charges.
NOTE: You can use the keyword ENPART and open
5. On the General tab, type any additional the *.out file at the end of a run to view the energy
keywords, if necessary. components making up the heat of formation and
SCF calculations. See the MOPAC online manual
6. Click Run. reference page 137, for more information.
MOPAC Properties
Gradient Norm
The following section describes the properties that
you can calculate for a given conformation of your This is the value of the scalar of the vector of
model, either as a single point energy computation derivatives with respect to the geometric variables
using the Compute Properties command, or after a flagged for optimization. This property (called
minimization using either the Minimize Energy or GNORM in the MOPAC manual) is automatically
Optimize to Transition State commands. selected for a minimization, which calculates the
GNORM and compares it to the selected minimum
Heat of Formation, ∆Hf gradient. When the selected minimum is reached,
the minimization terminates.
This energy value represents the heat of formation
Selecting this property for a Compute Properties
for a model’s current conformation. It is useful for
operation (where a minimization is not being
comparing the stability of conformers of the same
performed) will give you an idea of how close to
model.
optimum geometry the model is for the particular
calculation.
NOTE: The heat of formation values include the
zero point energies. To obtain the zero point energy
NOTE: The GNORM property is not the same as
for a conformation run a force operation using the
the MOPAC keyword GNORM. For more
keyword FORCE. The zero-point energy is found at
information see the MOPAC manual, pages 31 and
the bottom of the *.out file.
180.
The heat of formation in MOPAC is the gas-phase

heat of formation at 298K of one mole of a Dipole Moment
compound from its elements in their standard state.
The dipole moment is the first derivative of the
The heat of formation is composed of the following energy with respect to an applied electric field. It
terms: measures the asymmetry in the molecular charge
∆Η f = Ε elec + Ε nucl + Ε isol + Ε atom distribution and is reported as a vector in three
dimensions.
Where: The dipole value will differ when you choose
• Eelec is calculated from the SCF calculation. Mulliken Charges, Wang-Ford Charges or
• Enucl is the core-core repulsion based on the Electrostatic Potential, as a different density matrix
is used in each computation.
nuclei in the molecule.
• Eisol and Eatoms are parameters supplied by the NOTE: For more information see the MOPAC
potential function for the elements within your manual, page 119.
molecule.

The following table contains the keywords 6. On the Theory tab, choose AM1.
automatically sent to MOPAC.
7. On the Properties tab, select Dipole.
Keyword Description 8. Click Run.
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GEO-OK Automatically sent to MOPAC The results shown in the Messages window indicate
to override checking of the the electron distribution is skewed in the direction of
Z-matrix. the oxygen atom.
X Y Z Total
MMOK Automatically sent to MOPAC Dipole -2.317 0.000 -0.000 2.317
to specify Molecular Mechanics (vector
correction for amide bonds. Use Debye)
to turn this keyword off. If you rotate your model, the X,Y, and Z components
of the dipole differ. However, the total dipole does
not. In this example, the model is oriented so that the
The Dipole Moment of significant component of the dipole lies along the
Formaldehyde X-axis.
To calculate the dipole moment of formaldehyde: Charges

The property, Charges, determines the atomic
charges using a variety of techniques discussed in
2. Click the Text Building tool. the following sections. In this example the charges
are the electrostatic potential derived charges from
3. Click in the model window. Wang-Ford, because Wang-Ford charges give useful
A text box appears. information about chemical stability (reactivity).
4. Type H2CO and press Enter or Return. Comparing Cation Stabilities in

A model of formaldehyde appears. a Homologous Series of
Molecules
To build the model:

A text box appears.
4. For tri-chloro, type CCl3 and press Enter or

Return
Energy.

5. Repeat step 1 through step 4 for the other From these simple computations, you can reason
cations: type CHCl2 for di-chloro; type CH2Cl that the charge of the cation is not localized to the
for mono-chloro and CH3 for methyl cation. central carbon, but is rather distributed to different
extents by the other atoms attached to the charged
carbon. The general trend for this group of cations is
NOTE: The cations in this example are even that the more chlorine atoms attached to the charged
electron closed shell systems and are assumed carbon, the more stable the cation (the decreasing
to have Singlet ground state. No modifications order of stability is tri-chloro >di-chloro > mono-
through additional keywords are necessary. The chloro > methyl).
default RHF computation is used.
Mulliken Charges
This property provides a set of charges on an atom
6. For each model, click the central carbon, type +
basis derived by reworking the density matrix from
and press Enter or Return.
the SCF calculation. Unlike the Wang-Ford charges
The model changes to a cation and insures that utilized in the previous example, Mulliken charges
the charge is sent to MOPAC. give a quick survey of charge distribution in a
molecule.
To perform the computation:
1. From the MOPAC menu, choose Minimize NOTE: For more information, see the MOPAC
Energy. online manual, page 41 and 121.
2. On the Theory tab, choose AM1. The following table contains the keywords
automatically sent to MOPAC.
3. On the Properties tab, select Charges in the
Properties list.
Keyword Description
4. Select Wang-Ford from the Charges list.
MULLIK Automatically sent to MOPAC
5. Click Run. to generate the Mulliken
The results for the model appear in the Message Population Analysis.
window when the computation is complete.
The molecules are now planar, reflecting sp2 to override checking of the Z-
hybridization of the central carbon. matrix.
The following table shows the results:
tri-chloro di-chloro mono-chloro methyl
cation cation cation cation to specify Molecular Mechanics
C(1) C(1) 0.11255 C(1) 0.32463 C(1) 0.72465
0.03660 the additional keyword NOMM
Cl(2) 0.31828 Cl(2) Cl(2) H(2) 0.08722 to turn this keyword off.
0.33189 0.35852
Cl(3) 0.32260 Cl(3) 0.33171 H(3) 0.15844 H(3) 0.09406
Cl(4) 0.32253 H(4) 0.22384 H(4) 0.15841 H(4) 0.09406

Example, using Mulliken charges to analyze charge 2. Click H10, type NO2, and then press Enter or
distribution in a series of mono-substituted phenoxy Return.
ions.
Para nitrophenoxide ion is formed.
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Perform minimization as in the last step.

2. Click the Text Building tool. • For the last two monosubstituted nitro phenols,
first, select the nitro group using the Select
Tool and press the delete key. Add the nitro
A text box appears. group at the meta (H9) or ortho (H8) position
4. Type PhO-and press Enter or Return.

and repeat the analysis.
A phenoxide ion model appears. The data from this series of analyses are shown
below. The substitution of a nitro group at para, meta
and ortho positions shows a decrease in negative
charge at the phenoxy oxygen in the order
meta>para>ortho, where ortho substitution shows
the greatest reduction of negative charge on the
phenoxy oxygen. You can reason from this data that
the phenoxy ion is stabilized by nitro substitution at
the ortho position.
Phenoxide p-Nitro m- Nitro o-Nitro

NOTE: All the monosubstituted phenols under
C1 0.39572 C1 0.41546 C1 0.38077 C1 0.45789
examination are even electron closed shell systems
and are assumed to have Singlet ground state. No C2 -0.46113 C2 -0.44929 C2 -0.36594 C2 -0.75764
modifications by additional keywords are necessary.
C3 -0.09388 C3 -0.00519 C3 -0.33658 C3 0.00316
The default RHF computation is used.
C4 -0.44560 C4 -0.71261 C4 -0.35950 C4 -0.41505
5. From the MOPAC menu, choose Minimize C5 -0.09385 C5 -0.00521 C5 -0.10939 C5 -0.09544
Energy. C6 -0.46109 C6 -0.44926 C6 -0.41451 C6 -0.38967
6. On the Theory tab, choose PM3. This O7 -0.57746 O7 -0.49291 O7 -0.54186 O7 -0.48265
automatically selects Mulliken from the
H8 0.16946 H8 0.18718 H8 0.21051 N8 1.38805
Charges list.
H9 0.12069 H9 0.17553 N9 1.31296 H9 0.16911
7. On the Property tab, select Charges.
H10 0.15700 N10 1.38043 H10 0.19979 H10 0.17281
8. Click Run. H11 0.12067 H11 0.17561 H11 0.14096 H11 0.13932
To build para-nitrophenoxide ion: H12 0.16946 H12 0.18715 H12 0.17948 H12 0.18090
1. Click the Text Building tool. O13 -0.70347 O13 -0.65265 O13 -0.71656
O14 -0.70345 O14 -0.64406 O14 -0.65424

Charges From an Electrostatic Below are the keywords automatically sent to
MOPAC.
Potential
The charges derived from an electrostatic potential
computation give useful information about chemical Keyword Description
reactivity.
PMEP Automatically sent to MOPAC to
The electrostatic potential is computed by creating
specify the generation of Point
an electrostatic potential grid. Chem3D reports the
Charges from PMEP.
point charges derived from such a grid.
In general, these atomic point charges give a better QPMEP Automatically sent to MOPAC to
indication of likely sites of attack when compared to specify the Wang/Ford
atomic charges derived from the Coulson density electrostatic Potential routine.
matrix (Charges) or Mulliken population analysis
(Mulliken Charges). The uses for electrostatic GEO-OK Automatically sent to MOPAC to
potential derived charges are generally the same as override checking of the
for atomic charges. For examples, see “Charges” on Z-matrix.
page 172.
There are two properties available for calculating MMOK Automatically sent to MOPAC to
atomic point charges: Wang-Ford Charges and specify Molecular Mechanics
Electrostatic Potential. correction for amide bonds. Use
Wang-Ford Charges to turn this keyword off.
This computation of point charges can be used with
the AM1 potential function only. Electrostatic Potential
For information about the elements covered using Use the electrostatic potential property when the
the AM1 potential function see ‘Chapter 9: element coverage of the AM1 potential function
Computation Concepts” and the MOPAC online does not apply to the molecule of interest. For more
manual, page 223. information see the MOPAC online manual, page
223.
NOTE: For elements not covered by the AM1 The following table contains the keywords
potential function, use the Electrostatic Potential automatically sent to MOPAC and those you can use
property to get similar information on elements to affect this property.
outside this properties range.
Keyword Description
ESP Automatically sent to MOPAC to

specify the Electrostatic
Potential routine.
POTWRT Add this keyword if you want to

print out the ESP map values.

Calculating the Dipole Moment of
Keyword Description
meta-Nitrotoluene
GEO-OK Automatically sent to MOPAC to Create a model of m-nitrotoluene:
override checking of the
Administrator
Z-matrix. 1. From the File menu, choose New Model.
MMOK Automatically sent to MOPAC to 2. Click the Text Building tool.

specify Molecular Mechanics
the additional keyword NOMM A text box appears.
4. Type PhCH3 and press Enter or Return.
A model of toluene appears. Reorient the model
Molecular Surfaces
using the Trackball tool until it is oriented like
Molecular surfaces calculate the data necessary to the model shown in step 8.
render the Total Charge Density, Molecular
Electrostatic Potential, Spin Density, and Molecular 5. From the Edit menu, choose Select All.
Orbitals surfaces.
Polarizability Numbers, and then click Show.
The polarizability (and hyperpolarizability) 7. With the Text Building tool, click H(9), and
property provides information about the distribution then type NO2 in the text box that appears.
of electrons based on presence of an applied electric
field. In general, molecules with more delocalized 8. Press Enter or Return.
electrons have higher values for this property. A model of m-nitrotoluene appears.
Polarizability data is often used in other equations
for evaluation of optical properties of molecules. 13
For more information see the MOPAC online 15

7
14
manual, page 214.

The polarizability and hyperpolarizability values 1 8
12
reported are the first order (alpha) tensors (xx, yy, 6
2
zz, xz, yz, xy), second order (beta) tensors and third
order (gamma) tensors. 3
17
5
9
11 4
NOTE: Polarizabilities cannot be calculated using
the MINDO/3 potential function. 10 16
Use MOPAC to find the dipole moment:

Energy.
2. On the Theory tab, choose AM1.

3. On the Property tab, select Polarizabilities. COSMO Solvation in Water
4. Click Run. The COSMO method is useful for determining the
stability of various species in a solvent. The default
The following table is a subset of the results solvent is water. For more information, see the
showing the effect of an applied electric field on the MOPAC online manual, page 216.
first order polarizablity for m-nitrotoluene.
NOTE: You can also use the
alpha xx alpha yy alpha zz Miertus-Scirocco-Tomasi solvation model, which is
Applied
available using the MST keyword. This method is
field (eV)
recommended only for water as the solvent. A
discussion of this method can be found in the
0.000000 108.23400 97.70127 18.82380
MOPAC online documentation.
0.250000 108.40480 97.82726 18.83561
The following contains the keywords automatically
0.500000 108.91847 98.20891 18.86943 sent to MOPAC and those you can use to affect this
property.
The following table contains the keywords Comparing the Stability of

to affect this property.
Glycine Zwitterion in Water and
Gas Phase
Keyword Description To compare stabilities:

POLAR (E=(n1, Automatically sent to MOPAC
n2, n2)) to specify the polarizablity 2. Click the Text Building tool.
routine. n is the starting voltage
in eV. The default value is 3. Click in the model window.
E = 1.0.
A text box appears.
You can reenter the keyword 4. Type HGlyOH and press Enter or Return.
and another value for n to
A model of glycine appears.
change the starting voltage.
H
GEO-OK Automatically sent to MOPAC H
to override checking of the
C
Z-matrix.
O
H C
MMOK Automatically sent to MOPAC H N
Mechanics correction for O
amide bonds. Use the H
additional keyword NOMM to

5. From the MOPAC menu, choose Minimize 4. Perform a minimization with and without the
Energy. COSMO solvation property selected as
performed for the glycine model.
6. On the Theory tab, choose PM3.
The following table summarizes the results of the
Administrator
7. On the Property tab, Ctrl-click or four analyses.

Command-click Heat of Formation and
COSMO Solvation. Solvent
Form of ∆H Accessible
8. Click Run. glycine (kcal/mole) Surface Å2
The results appear in the Messages window.
neutral (H2O) -108.32861 52.36067
Energy. zwitterion -126.93974 52.37133
10. On the Property tab, deselect COSMO (H2O)
Solvation.
neutral (gas) -92.75386
11. Click Run.
The results appear in the Messages window. zwitterion (gas) -57.83940
To create the zwitterionic form: From this data you can reason that the glycine
zwitterion is the more favored conformation in
1. Click the Text Building tool. water and the neutral form is more favored in gas
phase.
2. Click the nitrogen, type +, and then press Enter
or Return. Hyperfine Coupling Constants
3. Click the oxygen, type -, and then press Enter Hyperfine Coupling Constants are useful for
or Return. simulating Electron Spin Resonance (ESR) spectra.
The glycine zwitterion is formed. Hyperfine interaction of the unpaired electron with
the central proton and other equivalent protons
cause complex splitting patterns in ESR spectra.
H H ESR spectroscopy measures the absorption of
microwave radiation by an unpaired electron when it
C is placed under a strong magnetic field.
O Hyperfine Coupling Constants (HFCs) are related to
C the line spacing within the hyperfine pattern of an
N ESR spectra and the distance between peaks.
Species that contain unpaired electrons are as

O follows:
• Free radicals
• Odd electron molecules
• Transitionmetal complexes

• Rare-earth ions 4. Type EtH and press Enter or Return.
• Triplet-state molecules 5. Click the Select tool.
For more information see the MOPAC online
manual, page 34. 6. Select H(8).
The following table contains the keywords 7. Press Delete or Backspace.

to affect this property. If you have automatic rectification on, a message
appears asking to turn it off to perform this
operation.
Keyword Description
• Click Turn Off Automatic Rectification.
UHF Automatically sent to MOPAC
if you choose “Open Shell
4
(Unrestricted)” wave functions
Unrestricted Hartree-Fock 1 5 7
methods. 3
2
Hyperfine Automatically sent to MOPAC
to specify the hyperfine
computation.
6
to override checking of the To perform the HFC computation:
Z-matrix.
MMOK Automatically sent to MOPAC Energy.
2. On the Theory tab, choose the PM3 potential
Mechanics correction for
amide bonds. Use the function and the Open Shell (Unrestricted)
additional keyword NOMM to wave function.
3. On the Properties tab, choose Hyperfine
Coupling Constants.
Hyperfine Coupling Constants
4. Click Run.
for the Ethyl Radical
To build the model:

A text box appears.

The unpaired electron in the ethyl radical is The following table contains the keywords
delocalized. Otherwise, there would be no coupling automatically sent to MOPAC and those you can use
constants. to affect this property.
Administrator
Hyperfine Coupling Constants Keyword Description
C1 0.02376 UHF Automatically sent to MOPAC if

you choose “Open Shell
C2 -0.00504 (Unrestricted)” wave functions
H3 -0.02632 Unrestricted Hartree-Fock
methods.
H4 -0.02605
H5 0.00350 to override checking of the
Z-matrix.
H6 0.05672
H7 0.05479 to specify Molecular Mechanics
Spin Density to turn this keyword off.
Spin density arises in molecules where there is an
unpaired electron. Spin density data provides SPIN You can add this keyword to
relative amounts of alpha spin electrons for a print the spin density matrix in
particular state. the *.out file.
Spin density is a useful property for accessing sites
of reactivity and for simulating ESR spectra. UHF Spin Density for the Ethyl
Two methods of calculating spin density of Radical
molecules with unpaired electrons are available:
RHF Spin Density and UHF Spin Density. To calculate the UHF spin density:
1. Create the ethyl radical as described “Hyperfine

UHF Spin Density
Coupling Constants for the Ethyl Radical” on
The UHF Spin Density removes the closed shell page 179.
restriction. In doing so, separate wave functions for
alpha and beta spin electrons are computed. For
more information see the MOPAC online manual,
page 152.

Atomic Orbital Spin Density A.O.
4
-0.07896 H3 s
1 5 7
3 0.07815 H4 s
2
0.01046 H5 s
0.05488 H6 s
6
0.05329 H7 s
Energy. You can reason from the result shown below that the
unpaired electron in the ethyl radical is more
3. On the Theory tab, select PM3. localized at pz orbital on C1. Generally, this is a
good indication of the reactive site
4. On the Properties tab, select Open Shell
(Unrestricted) and Spin Density.
The Message window displays a list of atomic
orbital spin densities.
The atomic orbitals are not labeled for each
value, however, the general rule is shown in the
table below (MOPAC only uses s, px, py and pz
orbitals).
Atomic Orbital Spin Density A.O.
0.07127 C1 s
0.06739 C1 px
0.08375 C1 py
0.94768 C1 pz
-0.01511 C2 S
-0.06345 C2 px
-0.01844 C2 py
-0.03463 C2 pz

RHF Spin Density 4. On the Properties tab, choose Spin Density.
RHF Spin Density uses the 1/2 electron correction The Message window displays the total spin
and a single configuration interaction calculation to densities for each atom (spin densities for all
isolate the alpha spin density in a molecule. This orbitals are totaled for each atom).
Administrator
method is particularly useful when the UHF Spin

Density computation becomes too resource NOTE: You can look in the *.out file for a
intensive for large molecules. For more information breakdown of the spin densities for each atomic
see the MOPAC online manual, page 28. orbital.
The following table contains the keywords
to affect this property. Total Spin Density
0.90744 C1
Keyword Description
0.00644 C2
ESR Automatically sent to MOPAC
to specify RHF spin density
0.00000 H3
calculation.
0.00000 H4
to override checking of the Z-
0.00001 H5
matrix.
0.04395 H6
to specify Molecular Mechanics
0.04216 H7
You can reason from this result that the unpaired
electron in the ethyl radical is more localized on C1.
Generally, this is a good indication of the reactive
RHF Spin Density for the Ethyl site.
Radical
Using the *.out file
To calculate the RHF spin density: In addition to the Messages window, information
1. Create the ethyl radical as described in
about the Mopac computations are located in the
*.out and *.aax files.
“Hyperfine Coupling Constants for the Ethyl
Radical” on page 179. Each computation performed using MOPAC creates
a *.out file containing all information concerning
2. From the MOPAC menu, choose Minimize the computation. A summary *.aax file is also
Energy. created, (where x increments from a to z after each
run). The *.out file is overwritten for each run, but a
3. On the Theory tab, choose PM3 and Closed new summary *.aax file, *.aax, file is created after
Shell (Restricted). each computation (*.aaa, *.aab, and so on.)

the .out and .aax files are located in the MOPAC
Data folder (Macintosh) or in the Temp directory
Using Keywords
(Windows). The Temp directory is the directory to You can use additional keywords to perform other
which your TMP or TEMP environment variable calculations or save information to the *.out file.
points (often C:\TEMP). If you don’t specify a path You can type any of the available in MOPAC
the file is in one of the following locations: keywords into the Additional Keyword section of
any MOPAC dialog box. The information generated
• Windows NT 4.0:
by these keywords does not appear in the Messages
C:\ Temp\CSMOPACOutput
window. To see the information generated by
• Windows 95 and 98: additional keywords, you must view the *.out file
C:\Windows\Temp\CSMOPACOutput generated by MOPAC.
The following information is found in the summary For a complete list of keywords see the MOPAC
file for each run: online manual.
Keywords that output the details of a particular
• Electronic Energy (Eelectronic)
computation are shown in the following table.
• Core-Core Repulsion Energy (Enuclear) Terms marked with an asterisk (*) appear in the
• Symmetry *.out file.
• Ionization Potential
Data Keyword
• HOMO/LUMO energies
All Energy Components* ENPART
The *.out file contains the following information by
default.
Zero Point Energy DFORCE
• Starting atomic coordinates
• Starting Z-matrix Vibrational Energies* DFORCE
• Molecular orbital energies (eigenvalues) Microstates used in MECI MECI

• Ending atomic coordinates calculation*
The workings of many of the calculations can also
HOMO/LUMO Energies* none
be printed in the *.out file by specifying the
appropriate keywords before running the
Ionization Potential* none
calculation. For example, specifying MECI as an
additional keyword will show the derivation of
Symmetry* none
microstates used in an RHF 1/2 electron
approximation calculation. For more information
Print localized orbitals LOCALIZE
see “Using Keywords” on page 183.
Print final eigenvectors VECTORS
NOTE: Close the *.out file while performing (molecular orbital
MOPAC computations or the MOPAC application coefficients)
stops functioning.
Bond Order Matrix* BONDS

The following table contains the keywords that
invoke additional computations. Terms marked with Description Keyword
an asterisk (*) appear in the *.out file.
Increase SCF criteria PRECISE
Administrator
Description Keyword NOTE: Increases

criteria by 100 times.
UV absorption energies* CIS This is useful for
increasing the
NOTE: Performs
precision of energies
C.I. using only the
reported.
first excited Singlet
states and does not
Increase the total CPU T = n [M,H,D]
include the ground
time allowed for the job.
state. Use MECI to NOTE: The default
print out energy is 1h (1 hour) or 3600
information in the seconds.
*.out file.
Vibrational Analysis* FORCE Creating an Input File

NOTE: Useful for A MOPAC (.MOP) input file is associated with a
determining zero model and its dialog box settings.
point energies and To create a MOPAC input file:
normal vibrational
modes. Use DFORCE 1. From the MOPAC menu, choose Create Input
to print out vibration File.
information in *.out
file.
No MM correction NOMM
NOTE: By default,
MOPAC performs a
molecular mechanics
(MM) correction for
CONH bonds.
Resolve density matrix* PI
NOTE: Resolve
density matrix into
sigma and pi bonds.
2. Select the appropriate settings and click Create.

Running Input Files NOTE: If you are opening a MOPAC file where a
Chem3D allows you to run previously created model has an open valence, such as a radical, you
MOPAC input files. For more information about the can avoid having the coordinates readjusted by
MOPAC file format see “Chapter 8: Printing and Chem3D by turning off Automatically Rectify in the
Exporting Models.” Building control panel.
To run an input file:

NOTE: MOPAC input files that containing multiple
1. From the MOPAC menu, choose Run Input
instances of the Z-matrix under examination will not
File. be correctly displayed in Chem3D. This type of
The Run MOPAC Input File dialog box MOPAC input files includes calculations that use the
appears. SADDLE keyword, or model reaction coordinate
geometries.
Repeating MOPAC Jobs

After you perform a MOPAC calculation, you can
1. From the MM2 menu, choose Repeat [name of

computation].

2. Type the full path of the MOPAC file or Browse
to the file location.
Running MOPAC Jobs
3. Select the appropriate options. For more
Chem3D enables you to select a previously created
information about the options see “Minimize MOPAC job description file (.jdf). The .jdf file can
Energy” on page 161. be thought of as a set of Settings that apply to a
particular dialog box. For more information about
4. Click Run.
.jdf files see “Chapter 8: Printing and Exporting
A new model window appears displaying the Models.”
initial model. The MOPAC job runs and the
results appear. To create a .jdf file:
All properties requested for the job appear in 1. From the MOPAC menu, choose a calculation.
the *.out file. Only iteration messages appear
2. After all settings for the calculation are
for these jobs.
specified, click Save As.

To run a MOPAC job from a .jdf file:
Creating Structures
1. From the MOPAC menu, choose Run MOPAC From .arc Files
Job.
When you perform a MOPAC calculation, the
Administrator
The Open dialog box appears. results are stored in an .arc file in the following
directory: C:/Temp/CSMOPACOutput.
2. Select the .jdf file to run.
The dialog box corresponding to the type of job You can create a structure from the .arc file as
saved within the file appears. follows:
1. Open the .arc file in a text editor.

3. Click Run.
2. Delete the text above the keywords section of
the file as shown in the following illustration.
Delete text through

this line
Keywords
section
3. Save the file with a .mop extension.
4. Open the .mop file.

Chapter 12: Gaussian Computations
Gaussian Overview
The following procedures describe the graphical
user interface (GUI) Chem3D provides for users of
Gaussian 98. For information about how to use
Gaussian 98, see the documentation supplied by
Gaussian, Inc., makers of the application.
Gaussian 98
Gaussian 98 is a powerful computational chemistry
application including both ab initio and
semiempirical methods. Gaussian is a
command-line application that requires a user to
type text-based commands and data instead of
selecting graphical objects and menu items.
Chem3D serves as a front-end GUI for Gaussian 98,
enabling you to create and run Gaussian jobs in
Chem3D. The model in the Chem3D window
transparently provides the data for Gaussian
The Job Type Tab
computations. Menus and dialog boxes replace the The Job Type tab of the dialog box defaults to
many Gaussian commands, although Chem3D Minimize Energy when you select Minimize Energy
preserves the option to use them for less common from the menu. Job Type can be changed to
and advanced computations. Compute Properties from within this tab.
Minimize Energy Select the appropriate options:
To perform a minimize energy computation on a

molecule:
From the Gaussian menu, choose Minimize Energy.
The Minimize Energy dialog box appears. minimization process
“live” at each NOTE: Displaying or
iteration in the recording each iteration
calculation adds significantly to the
time required to minimize
the structure.
Chem3D Chapter 12: Gaussian Computations • 187

The Theory Tab
Use the Theory tab to specify the combination of
basis set and particular electronic structure theory
record each iteration Record Every Iteration. referred to in Gaussian documentation as the model
Administrator
as a frame in a movie chemistry. By default, this tab is optimized for

for later replay setting up ab initio computations.
view the value of Copy Measurements to

each measurement in Messages.
the Measurement
table
calculate the second Do Not Calculate Force

derivative matrix Constants.
determined from
atomic radii and a
simple valence force
field. This is the
Gaussian default
initial guess.
calculate the initial Calculate Initial Force To set the Theory specifications:
force constant at the Constants.
current level of 1. Select the appropriate Method.
theory. Corresponds
to the Gaussian NOTE: To use a Method or Basis Set that is not
on the list, type it in the Additional Keywords
keyword Opt =
section on the General page. For more
CalcFC information, see “The General Tab” on page
189.
calculate a new force Calculate Force
constant at every Constants At Each Point. 2. Select the wave function to use: Closed Shell
point in the (Restricted), Open Shell (Unrestricted), or
minimization. Restricted Open Shell.
Corresponds to the 3. Select the Basis Set.
Gaussian keyword
Opt=CalcAll. 4. Select the Diffuse function to add to the basis
set.
calculate using the Use Tight Convergence 5. Select the Polarization Heavy Atom.
equivalent to the Criteria. If you select a Heavy Atom function, also
Gaussian keyword choose an H option.
Opt=Tight
6. Select a Spin Multiplicity value between one
and 10.
188 • Chapter 12: Gaussian Computations Chem3D

The Properties Tab The General Tab
The Properties tab allows you to select the The General tab allows you to customize the
properties and charges to calculate from the calculation for the model.
minimized structure.
To set the properties and charges: To specify the general settings:
1. From the Properties list, select the properties to 1. From the Solvation Model list, choose a
calculate. solvation model:
• Gas Phase
2. From the Population Analysis list, select the
method to compute atomic charges: • Onsager Model (Dipole & Sphere)
• Mulliken population analysis • Tomasi’s PCM Model (PCM)
• Electrostatic potential-derived charges • Isodensity Model (I-PCM)
according to the CHelp, CHelpG, and Merz- • Self-consistent Isodensity Model (SCI-
Singh-Kollman schemes PCM)
• Natural Bond Order analysis (NBO)
2. Type the dielectric constant, ε, for the solvent.
• Analysis according to the Theory of atoms in
The box does not appear for gas-phase
molecules by Bader et al. (Atoms In
computations.
Molecules).
3. Type Gaussian keywords in the Additional
Keywords text box for access to less common
or more advanced functionality.

In the Results In text box, specify the path to the The custom job description appears in the
directory where results are stored by typing or menu.
browsing.
Administrator
Job Description File

Formats
Job description files are like Preferences files; they
store the settings of the dialog box. You may save
the file as either a .jdf or a .jdt type. You modify and
Save a customized job to appear as a Gaussian menu save .jdf files more easily than .jdt files.
item as follows:
.jdt Format
1. In the Menu Item Name text box, type the name
The .jdt format is a template format intended to
of the job description. serve as a foundation from which other job types
2. Click Save As.
may be derived. The Minimize Energy and Compute
Properties job types supplied with Chem3D are
The Save dialog box appears. examples of these. To discourage modification of
these files, the Save button is deactivated in the
3. Browse to the Gaussian Job folder within the
dialog box of a template file.
CS Gaussian folder within the Chem3D folder.
.jdf Format
NOTE: The file must be saved in the Gaussian
Job folder in order for it to appear in the menu. The .jdf format is a file format for saving job
descriptions. Clicking Save within the dialog box
saves modifications without the appearance of a
4. Select the file type to save. For more
warning or confirmation dialog box.
information, see “Job Description File
Formats” on page 190. Saving either format within the Gaussian Job folder
adds it to the Gaussian menu for convenient access.
5. Click Save.

Computing Properties The Create Input File dialog box appears.
To specify the parameters for computations to

predict properties of a model:
• From the Gaussian menu, choose Compute
Properties.
The Compute Properties dialog box appears and
displays the Properties tab with the top four
properties of the menu preselected.
2. Click Create.
An input file saves in Gaussian’s native .GJF
format.
NOTE: The .GJF Gaussian Input File is not the

same as the .GJC Gaussian Input File. The .GJC file
stores only the model coordinates and not the
Gaussian keywords specifying computational
Creating a Gaussian parameters.
Input File
A Gaussian Input file contains the coordinates and Running a Gaussian
geometry of the model and the Gaussian keywords Input File
taken from the settings of the dialog box.
If you have a previously created .GJF Gaussian
To create a Gaussian Input file: input file, you can run the file from within Chem3D.
1. From the Gaussian menu, choose Create Input To run a Gaussian input file:
File.
1. From the Gaussian menu, choose Run Input
File.

The Run Gaussian Input file dialog box
appears.
Repeating a Gaussian
Job
After you perform a MOPAC calculation, you can
Administrator
1. From the Gaussian menu, choose Repeat

[name of computation].

2. Type the full path of the Gaussian file or
Browse to location. Running a Gaussian
3. Select the appropriate options. Job
Chem3D enables you to select a previously created
If you want to … Then click … Gaussian job description file (.jdf). The .jdf file can
be thought of as a set of Settings that apply to a
watch the Display Every Iteration. particular dialog box.
minimization You can create a .jdf file from the dialog box of any
process “live” at NOTE: Displaying or of the MOPAC calculations (Minimize Energy,
each iteration in the recording each iteration Optimize to Transition State) by clicking Save As
calculation adds significantly to the after all Settings for the calculation have been set.
time required to minimize For more information about .jdf files see
the structure. “Chapter 8: Printing and Exporting Models.”
To run a Gaussian job:

record each iteration Record Every Iteration.
as a frame in a movie 1. From the Gaussian menu, choose Run
for later replay Gaussian Job.
track a particular Copy Measurements to
measurement Messages. 2. Select the file to run.
The dialog box corresponding to the type of job
4. Click Run. (Minimize Energy, Compute Properties, and so
A new model window is created and the initial on.) saved within the file appears.
model appears. The Gaussian job runs and the
3. Click Run.
results will appear.
All properties requested for the job appear in
the *.out file. Only iteration messages appear
for Gaussian Input File jobs.

Chapter 13: GAMESS Computations
GAMESS Overview
GAMESS is available in Chem3D for Windows
only. The General Atomic and Molecular Electronic
Structure System (GAMESS) is a general ab initio
quantum chemistry package maintained by the
Gordon research group at Iowa State University. It
computes wavefunctions using RHF, ROHF, UHF,
GVB, and MCSCF. CI and MP2 energy corrections
are available for some of these.
GAMESS is a command-line application, which
requires a user to type text-based commands and
data. Chem3D serves as a front-end graphical user
interface (GUI), allowing you create and run
GAMESS jobs from within Chem3D.
Installing GAMESS
You must download and install the GAMESS 2. Use the tabs to customize your computation.
application separately. See the following sections for details.
You cand download the GAMESS application and 3. Click Run.

documentation from the following web site:
http://www.msg.ameslab.gov/GAMESS/ The Theory Tab
GAMESS.html Use the Theory tab to specify the combination of
basis set and particular electronic structure theory.
Minimize Energy By default, this tab is optimized for setting up
ab initio computations.
To perform a GAMESS Minimize Energy
computation on a model: For more detailed information, see the $BASIS
section of the GAMESS documentation.
1. Form the GAMESS menu, choose Minimize
To specify the calculation settings:
Energy.
The Minimize Energy dialog box appears with 1. From the Method list, choose a method.
the Theory tab displayed.
2. From the Wave Function list, choose a
function.
Chem3D Chapter 13: GAMESS Computations • 193

3. From the Basis Set list, choose the basis set.
NOTE: To use a Method or Basis Set that is not
on the list, type it in the Additional Keywords view the value of Copy Measurements to
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section on the General tab. For more each measurement in Messages.

information, see “Specifying the General the Measurement
Settings” on page 195. table
4. From the Diffuse list, select the diffuse function

calculate using the Use Tight Convergence
to add to the basis set. equivalent to the Criteria.
Gaussian keyword
5. Set the Polarization functions.
Opt=Tight
If you select a function for Heavy Atom, also
select an H option.
Specifying Properties to
6. Select a Spin Multiplicity value between 1 and Compute
10.
Use the Properties tab to specify which properties
The Job Type Tab are computed. The default Population Analysis type
is Mulliken.
Use the Job Type tab to set options for display and
recording results of calculations. To specify properties:
To set the job type options: 1. In the Minimize Energy dialog box, click
Properties.
1. In the Minimize Energy dialog box, click the
Job Type tab.
2. Select the appropriate options:

minimization process
live at each iteration NOTE: Displaying or
in the calculation recording each iteration
adds significantly to the
time required to minimize
the structure.
record each iteration Record Every Iteration.

as a frame in a movie
for later replay
194 • Chapter 13: GAMESS Computations Chem3D

2. On the Properties tab, set the following
options:
Saving Customized Job
• Select the properties to calculate
Descriptions
After you customize a job description, you can save
• Select the Population Analysis type
it as a Job Description file to use for future
calculations.
Specifying the General
For more information, see “Job Description File
Settings Formats” on page 120.
Use the General tab to customize the calculation to
To save a GAMESS job:
the model.
1. On the General tab, type the name of the file in
To set the General settings:
the Menu Item Name text box.
1. In the Minimize Energy dialog box, click The name you choose will appear in the
General. GAMESS menu.
2. Click Save As.

The Save dialog box appears.
3. Select the GAMESS Job folder in the CS

GAMESS folder in the Chem3D folder.
NOTE: You must save the file in the GAMESS

Job folder for it to appear in the menu.
4. Select the .jdf or .jdt file type.
5. Click Save.
Your custom job description appears in the
GAMESS menu.
2. On the General tab, set the following options:

Running a GAMESS Job
If you have a previously created .inp GAMESS job
• Select the Solvation model.
file, you can run the file in Chem3D.
• Type the dielectric constant for the solvent.
The box does not appear for gas-phase To run the job file:
computations. 1. From the GAMESS menu, choose Run
• In the Results In box, type or browse to the GAMESS Job.
path to the directory where results are stored. The Open dialog box appears.
• If desired, add GAMESS keywords to the
2. Type the full path of the GAMESS file or
Additional Keywords dialog box.
Browse to location.
Chem3D Chapter 13: GAMESS Computations • 195

3. Click Open.
4. Change settings on the tabs if desired.

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5. Click Run.
A new model window is created and the initial
model will appear. The GAMESS job runs and
the results appear.
Properties requested for the job appear in the
*.out file. Only iteration messages will appear.
Repeating a GAMESS
Job
After a GAMESS computation has been performed,
you can repeat it using the GAMESS menu.
To repeat a GAMESS job:
1. From the GAMESS menu, choose Repeat

[name of computation].

196 • Chapter 13: GAMESS Computations Chem3D

Chapter 14: SAR Descriptors
SAR Descriptor ChemProp Std
Overview Server
The ChemProp Std Server enables you to calculate
Chem3D for Windows provides a set of physical and
the following structural properties:
chemical property predictors. These predictors,
which help predict the structure-activity relationship
(SAR) of molecules, are referred to as SAR Property Description
descriptors in this user’s guide. These descriptors
are also available in ChemSAR for Excel. Connolly Solvent The locus of the center
Accessible Surface of a spherical probe
Area (Angstroms2) (representing the
Chem3D Property solvent) as it is rolled
Broker over the molecular
model.
In Windows, the Chem3D Property Broker provides
an interface in Chem3D and ChemSAR for Excel
Connolly Molecular The contact surface
that allows you to calculate properties using many
Surface Area created when a spherical
calculation methods provided by various Property
(Angstroms2) probe sphere
Server components.
(representing the
The components of the Property Broker-Server solvent) is rolled over
architecture are illustrated below: the molecular model.
Chem3D ChemSAR for Excel Connolly The volume contained

Solvent-Excluded within the contact
Volume (Angstroms3) molecular surface.
Property Broker Interface
Exact Mass (g/mole) The exact molecular
mass of the molecule,
where atomic masses of
each atom are based on
ChemProp Std the most common
isotope for the element.
ChemProp Pro
Property Formal Charge The net charge on the
Servers MM2 (electrons) molecule.
MOPAC
GAMESS
Chem3D Chapter 14: SAR Descriptors • 197

For the latest information about the Connolly
Property Description programs and definitions of the area and volume
properties, see the following web site:
Molecular Formula The molecular formula http://www.best.com/~connolly/
showing the exact
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number of atoms of each NOTE: The default Probe Radius used in the
element in the molecule. calculation is 1.4 angstroms. You can change the
Probe Radius value in the Parameters dialog box.
Molecular Weight The average molecular
(atomic mass units) mass of the structure,
The Principal Moments of Inertia are the diagonal
where atomic masses are
elements of the inertia tensor matrix when the
based on the weighted
Cartesian coordinate axes are the principal axes of
average of all isotope
the molecule, with the origin located at the center of
masses for the element.
mass of the molecule. In this case, the off-diagonal
elements of the inertia tensor matrix are zero and the
Ovality The ratio of the
three diagonal elements, Ixx, Iyy, and Izz correspond
Molecular Surface Area
to the Moments of Inertia about the X, Y, and Z axes
to the Minimum Surface
of the molecule.
Area. The Minimum
Surface Area is the
surface area of a sphere ChemProp Pro
having a volume equal Server
to the Solvent-Excluded
Volume of the molecule. CS ChemProp Pro server allows you to predict the
Computed from the following physical and thermodynamic properties
Connolly Molecular of molecules.
Surface Area and
Solvent-Excluded NOTE: Fragmentation methods and literature
Volume properties. values are used for these calculations. Use the Full
Report property to view references for the methods.
Principal Moments of The Moments of Inertia
Inertia (X, Y, Z) when the Cartesian
(grams/mole coordinate axes are the Property Description
Angstroms2) principal axes of the
molecule. Boiling Point The boiling point for the
(Kelvin) structure at 1 atm.
The surface area and volume calculations are
performed with Michael Connolly’s program for Critical Temperature The temperature (Tc)
computing molecular surface areas and volume (M. (Kelvin) above which the gas form
L. Connolly. The Molecular Surface Package. J. of the structure cannot be
Mol. Graphics 1993, 11). liquefied, no matter the
applied pressure.
198 • Chapter 14: SAR Descriptors Chem3D

Property Description Property Description
Critical Pressure (bar) The minimum pressure Standard Gibbs Free The Gibbs free energy
(Pc) that must be applied to Energy (kJ/mole) (∆G) for the structure at
liquefy the structure at the 298.15 K and 1 atm.
critical temperature.
Vapor Pressure (Pa) The vapor pressure for the
Critical Volume The volume occupied (Vc) structure at 25° C.
(cm3/mole) at the compound’s critical
temperature and pressure. Water Solubility at Prediction of the water
25° C (mg/L) solubility of the structure.
Full Report A detailed list of
information used for Limitations
performing the
calculations, including Property prediction using CS ChemProp Pro has
additional properties and following limitations:
literature references used.
• Single molecules with no more than 100 atoms.
Results for other
fragmentation methods are • Literature values for Partition Coefficients
included. (LogP) and Henry’s Law Constant are not
available for all molecules.
Heat of Formation The heat of formation
• Some atom arrangements are not parameterized
(kcals/mole) (∆Hf) for the structure at
298.15 K and 1 atm. for the fragmentation methods used to calculate
the properties.
Henry’s Law The logarithm of Henry’s Because of these limitations, the property prediction
Constant (unitless) law constant. fails for some molecules.
Ideal Gas Thermal The constant pressure Error Messages

Capacity (J/[mole K]) (1 atm) molar heat
capacity at 298.15 K for an If ChemProp Pro fails, one of the following error
ideal gas compound. messages appears:
LogP The logarithm of the Error Message Cause

partition coefficient for
n-octanol/water. Unparametrized A fragment in the molecule
fragment is unrecognized so no
Melting Point The melting point for the parameters exist for the
(Kelvin) structure at 1 atm. property calculation.
Molar Refractivity The molar refraction Out of memory There is insufficient memory
(cm3/mole) index. failure for the calculation.

Error Message Cause Property Description
Data not in database The literature values for this Charge-Charge Energy The sum of the
property are not in the (kcal/mol) electrostatic energy
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database. representing the

pairwise interaction of
Bad MDL Molfile The molecule is too large or charged atoms.
format complex, causing bad input
data to be generated. Charge-Dipole Energy The sum of the
(kcal/mol) electrostatic energy
Invalid aggregate A fragment in the molecule terms resulting from
is unrecognized or there is interaction of a dipole
more than one disjointed and charged species.
molecule or fragment.
Dipole Moment Molecular dipole
Too many There is more than one (Debye) moment.
molecules molecule.
Dipole-Dipole Energy The sum of the
Too many atoms There are more than 100 (kcal/mol) electrostatic energy
atoms. terms resulting from
interaction of two
exceeded MDL The input data generated for dipoles.
Molfile size limit this molecule exceeds the
maximum size limit. Non-1,4 van der Waals The sum of pairwise van
Energy (kcal/mol) der Waals interaction
energy terms for atoms
MM2 Server separated by more than 3
The MM2 server computes property predictions chemical bonds.
using the methods of molecular mechanics. For
more information on MM2, see “Chapter 9: Stretch-Bend Energy The sum of the stretch-
Computation Concepts” and “Chapter 10: MM2 (kcal/mol) bend coupling terms of
Computations.” the force-field equation.
The MM2 server provides the following property
calculations: Torsion Energy The sum of the dihedral
(kcal/mol) bond rotational energy
term of the force-field
Property Description equation.
Bending Energy The sum of the Total Energy (kcal/mol) The sum of all terms the
(kcal/mol) angle-bending terms of the force-field equation.
the force-field equation.

van der Waals Energy The sum of pairwise van Symmetry Point group symmetry.
(kcal/mol) der Waals interaction
energy terms for atoms Total Energy (eV) The sum of the MOPAC
separated by exactly 3 Electronic Energy and the
chemical bonds. MOPAC Repulsion Energy.
MOPAC Server GAMESS Server

The MOPAC server calculates property predictions GAMESS uses ab initio computational methods to
based on semi-empirical computational methods. compute property predictions. For more
For more information, see “Chapter 9: Computation information, see “Chapter 9: Computation
Concepts” and “Chapter 11: MOPAC Concepts” and “Chapter 13: GAMESS
Computations.” Computations.”
The MOPAC server provides the following property The GAMESS server provides the following
calculations: property calculations:
Alpha Coefficients First order polarizability Dipole Moment Molecular dipole moment.
coefficients. (Debye)
Beta Coefficients Second order polarizability HOMO Energy (eV) Energy of the highest
coefficients. occupied molecular orbital.
Dipole (Debye) Molecular dipole moment. LUMO Energy (eV) Energy of the lowest
unoccupied molecular
Electronic Energy The total electronic energy. orbital.
(298 K) (eV at 0o
Celsius) Repulsion Energy Total core-core internuclear
Energy (eV) repulsion between atoms.
Gamma Third order polarizability
Coefficients coefficients. Total Energy (eV) The total energy of the
molecule.
HOMO Energy Energy of the highest
(eV) occupied molecular orbital.
LUMO Energy Energy in of the lowest

(eV) unoccupied molecular orbital.
Repulsion Energy Total core-core internuclear

(eV) repulsion between atoms.

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Chapter 15: SAR Descriptor
Computations
Overview 3. From the list of Available Properties, select the
properties to calculate.
Chem3D for Windows performs property prediction
calculations. These computed properties are the 4. Click Add.
descriptors that may be used to estimate the The properties you select appear in the Selected
structure-activity relationship (SAR) of molecules. Properties list.
Selecting Properties To NOTE: Some properties may not be computed for a

particular model because of the limitations of
Compute standard computational methods.
To select properties for computation:
1. From the Analyze menu, choose Compute Sorting Properties

Properties.
To sort the properties in the Property and Method
The Compute Properties dialog box appears. columns:
• Click the column heading.
The items in the columns are sorted.
Removing Selected Properties

To remove properties from the Selected Properties
list:
1. Select the properties to delete or click Select All

to select all the properties.
2. Click Remove.
The properties are removed from the list.
Property Filters
Property filters allow you to select what properties
appear in the Available Property list.
2. Set appropriate values for the Class, Server,
Cost, and Quality filters. The property filters are:
For more information, see “Property Filters” on • Class—limits the list of available properties to
page 203. types calculations that you specify.
Chem3D Chapter 15: SAR Descriptor Computations • 203

• Server—limits the list of available properties to
those properties computed by the servers you
specify.
• Cost—represents the maximum acceptable
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computational cost. It limits the list of available

properties to those which are less than or equal
to the computational cost specified.
• Quality—represents the minimum acceptable
data quality. It limits the list of available
properties to those with quality greater than or
equal to the quality specified.
3. Edit the value or select the method.
Setting Parameters 4. Click OK.
If a property has one or more parameters that affect
The new value is set.
the result of the calculation, you can specify the
values or calculation method of those parameters. If
several properties have the same parameters, you Results
can change the parameters simultaneously.
To perform the calculation:
To change a parameter: • Click OK.
1. Select the property or properties in the Selected Chem3D performs the calculation and displays
Properties list. the results in the Messages window.
2. Click Parameters.
One of the following dialog boxes appears,
depending on the selected parameters.
204 • Chapter 15: SAR Descriptor Computations Chem3D

ChemSAR for Excel 3. Click ChemFinder for Excel and ChemSAR
for Excel.
Overview 4. Click OK.
ChemSAR for Excel is Chem3D Ultra for Windows
5. Click New ChemFinder Worksheet .
add-in for Microsoft Excel 97 and higher.
ChemSAR for Excel enables you to calculate the The ChemSAR toolbar appears.
physiochemical properties (descriptors) for a set of
structures in an Excel worksheet. Select Mark Dependent Rune Options
Descriptors Columns Plots
ChemSAR for Excel provides statistical tools to
help identify trends in the calculated properties and
correlate the data.
To run ChemSAR for Excel, you must have the

following installed on your computer:
• Chem3D Calculate Mark Independent Descriptive
Now Columns Statistics
• ChemFinder
• MS Excel The ChemSAR Wizard
The ChemSAR wizard leads you through the steps
Configuring ChemSAR required to perform property calculations on a set of
for Excel molecules.
To make the ChemSAR for Excel menu appear in To perform property calculations using the
the Excel menu bar: ChemSAR Wizard:
1. Open MS Excel. 1. From the ChemSAR menu, choose Wizard.
2. From the Tools menu, choose Add-Ins.

The Add-Ins dialog box appears.
Chem3D Chapter 16: ChemSAR for Excel • 205

The Step 1 of 4 dialog box appears. 4. Type the cell to be the heading cell for the
structure column.
5. Click Next.
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The Step 3 of 4 dialog box appears.
2. Select the appropriate option:
The buttons on the right are active when you use

create a new New ChemFinder
a range of cells in your worksheet. To make the
ChemFinder worksheet Worksheet.
buttons available, type a cell range.
convert the current Convert The buttons are active as shown below.
Excel worksheet to a Worksheet.
ChemFinder worksheet
3. Click Next.
6. To display graphics of your structures in the

worksheet, choose Show Structures As 2D
Pictures.
206 • Chapter 16: ChemSAR for Excel Chem3D

use structures entered a. Select the text to
as text. include.
use data from a a. Click Import
ChemFinder ChemFinder b. Click Convert From
database Database. Chemical Name.
b. In the Import Table

dialog box choose use specific a. Type the range of
the database and structures in cells containing the
click Open. worksheet structures to use.
b. Click Use Selected

use an active a. Click Get Current Range.
ChemFinder hit list List from
ChemFinder.
8. Click Next.
b. Click Yes. The Step 4 of 4 dialog box appears.
import a structure a. Click Import SD

data file into the File.
ChemFinder
worksheet b. In the Importable
dialog box choose
the database and
click Open.
import a file of one of a. Click Load from

the following format File.
types: .CDX, .MOL,
.SKC, .f1d, .f1q, or b. In the Choose
.RXN. Molecule to Load
dialog box, choose 9. Click Select Descriptors.
the file.
10. In the Select Descriptors dialog box, select the
appropriate descriptors.
use structures entered a. Select the strings to
as SMILES strings. include. For more information on using the Select
Descriptors dialog box, see “Selecting
b. Click Convert From ChemSAR Descriptors” on page 208.
SMILES. 11. Click Finish.
The calculations are performed and the results
appear in the worksheet.

Selecting ChemSAR 6. To delete a property from the list, click
Remove.
Descriptors
7. To view the calculation method of a property,
The Select Descriptors dialog box allows you to
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select it and click Parameters.

specify which physical properties to calculate for
your worksheet. Properties are calculated for entire 8. Click OK.
molecules. If you want to calculate the properties of
a molecule fragment, you must add that fragment to The calculations are performed.
your worksheet.
To select descriptors:
Adding Calculations to
an Existing Worksheet
1. From the ChemSAR menu, choose Select
When you add structures to a worksheet that already
Descriptors.
has calculated properties, you can calculate the
The Select Descriptors dialog box appears: properties for only the added structures without
recalculating the entire worksheet.
To calculate properties for added structures:
1. In a worksheet with calculated properties, add

the structures for which you want to calculate
properties.
2. Click Calculate Now .

The properties are calculated and added to the
worksheet.
2. Select the calculation type from the Class Customizing

drop-down list. Calculations
3. Select the computational model from the Server You can use the ChemSAR Options dialog box to
drop-down list. customize a calculation by changing the default
settings.
4. Use the Cost and Accuracy sliders to set the
appropriate ratio. To change the defaults:
The greater the cost number, the greater the 1. From the ChemSAR menu, choose Options.
time it takes for the calculation.
The greater the accuracy number, the greater the
accuracy of method used to perform the
calculations.
5. Select the properties to calculate and click Add.

The ChemSAR Options dialog box appears. 5. Do one of the following:
To perform the calculation Click …

on …
a selected molecule Now.
the entire worksheet OK.
2. To populate any unfilled valences with

hydrogen atoms, select Hydrogen Fill All Calculating Statistical
Atoms. Properties
3. To customize the partial charge calculation, ChemSAR for Excel allows you to calculate the
click Calculate Partial Charges using. following statistical properties:
a. Select a type of method from the drop-down • Descriptive Statistics
list. • Correlation matrix
b. To further customize the calculation, click • Rune Plot
Options and then select a Charge Method
and Theory to use. Descriptive Statistics
c. Click Use Custom Settings.
ChemSAR calculates the following statistics for
4. To customize the how the 3D geometry is every column in the data set:
optimized, select Optimize 3D Geometry • Mean
using.
• Minimum
a. Select a type of method from the drop-down
• Maximum
list.
• Range
b. To further customize the calculation, click
Options and then select a Optimization • Count
Method, Theory, and RMS Gradient to use. • Sum
c. Click Use Custom Settings. • Standard deviation
• Median
To perform the statistical calculations:

• From the ChemSAR menu, choose Descriptive
Statistics.
The results are added as a separate worksheet.

Correlation Matrix
ChemSAR calculates scatter plots for each property
to every other property.
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To calculate the correlation matrix:

• From the ChemSAR menu, choose Correlation
Matrix.
The results are displayed on a separate
worksheet. correlating cells are colored.
Rune Plots
Rune plots are used to compare data and visualize
how normally the data is distributed. The data is
transformed on a scale of zero to one. Each data set
is then plotted next to each other. You can then
identify data sets that are not normally distributed
and exclude them from any further calculation.
To create Rune plots:
• From the ChemSAR menu, choose Rune Plots.
The plot is added as a separate worksheet.

Chapter 17: Accessing the CambridgeSoft
Web Site
Online Menu Overview Find Information on
The Chem3D for Windows Online menu allows you ChemFinder.com
to access different parts of the CambridgeSoft web Find Suppliers on ChemFinder.com opens
site from within Chem3D. To use the Online menu, ChemFinder.com, where you can search the
you must have internet access. ChemFinder database for chemical information.
Find Suppliers on To access Lookup Suppliers on ChemStore.Com:
ChemStore.com • From the Online menu, choose Find

ChemFinder.com opens.
Exchange) of the CambridgeSoft web site.
To access Lookup Suppliers on ChemStore.Com:

• From the Online menu, choose Find Suppliers
on ChemStore.com.
The ChemACX.Com page opens.

Browse ChemStore.com

ChemStore.com.
You can search ChemACX.Com for chemicals by The ChemStore.Com page opens.
supplier or by chemical name.
Chem3D Chapter 17: Accessing the CambridgeSoft Web Site • 211

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You can search ChemStore.Com for chemicals, lab

supplies, chemistry-related software, and other Check the CambridgeSoft web site for new product
items you want to buy. You can access information. You can also get to ChemStore.Com,
ChemACX.Com, LabEqwip.Com, and other pages ChemNews.Com, and other pages through
from ChemStore.Com. CambridgeSoft.Com.
Browse Browse CS Chem3D

CambridgeSoft.com Documentation
Browse CambridgeSoft.com opens the Home page Browse CS Chem3D Documentation opens the
of the CambridgeSoft web site. Chem3D documentation page where you can access
current and previous version of the Chem3D User’s
To access the CambridgeSoft Home Page: Guide.
CambridgeSoft.com. To access the CambridgeSoft Home Page:
The CambridgeSoft web site appears. 1. From the Online menu, choose Browse CS
Chem3D Documentation.
The Chem3D Documentation page appears.
212 • Chapter 17: Accessing the CambridgeSoft Web Site Chem3D

2. Select a version of the manual to view and click
Get Manual.
Browse CS Chem3D
Technical Support Use the Tech Support page to find answers to
Browse CS Chem3D Technical Support opens the Frequently Asked Questions (FAQs), the technical
Tech Support page of the CambridgeSoft web site. support newsletter, more documentation, and other
items.
To access CS Chem3D Technical Support:
• From the Online menu, choose Browse CS Register Online
Chem3D Technical Support.
Register Online opens the ChemClub page of the
The Tech Support page appears. CambridgeSoft web site. Register your copy of
ChemOffice here.
To get to Register Online:

• From the Online menu, choose Register
Online.
Chem3D Chapter 17: Accessing the CambridgeSoft Web Site • 213

The ChemClub.Com page opens. To get to ChemOffice SDK:
• From the Online menu, choose ChemOffice
SDK.
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The CS ChemOffice SDK page opens.
The ChemOffice SDK page offers more

for the Application Programming Interfaces (APIs).
To access the ChemOffice SDK page, you must be a
member of CS ChemClub.
Register your CambridgeSoft software or join the

CS ChemClub on the ChemClub.Com page.
CS ChemClub members get news, access to
chemical searching, free downloads, and chemical
software on the web. The membership is free of
charge.
To access the ChemOffice SDK page, you must be a
member of CS ChemClub.
Browse ChemOffice
SDK
ChemOffice SDK brings you to the CS ChemOffice
SDK (Software Developer’s Kit) page of the
CambridgeSoft web site.
214 • Chapter 17: Accessing the CambridgeSoft Web Site Chem3D

Appendix A: Substructures
Overview For example, Chem3D stores with the substructure a
dihedral angle formed by two atoms in the
You can define substructures that you can add to a substructure and two unselected atoms. If more than
substructures table. one dihedral angle can be composed from selected
(substructure) and unselected (non-substructure)
When you define a substructure, the attachment
atoms, the dihedral angle that is saved with the
points (where unselected atoms are bonded to
substructure consists of the atoms with the lowest
selected atoms) are stored with the substructure.
serial numbers.
If a substructure contains more than one attachment
Consider the following model to define a
point (such as Ala), the atom with the lowest serial
substructure for alanine:
number normally becomes the first attachment
point. The atom with the second lowest serial
number becomes the second attachment point, and
so on. However, there are situations where this
general rule is not valid. The following rules cover
all possible situations for multiple attachment points
in substructures; Rule 3 is the normal situation
described above:
Rule 1: If an atom has an open valence and is not
attached to an atom that is unselected, it goes after
any atom that is attached to an unselected atom. Since polypeptides are specified beginning with the
N-terminal amino acid, N(4) should have a lower
Rule 2: If an atom is attached only to rectification serial number than the Carboxyl C(6). To ensure that
atoms, it goes after any atom that is attached to a chain of alanine substructures is formed correctly,
non-rectification atoms. C(1) should have a lower serial number than O(3) so
Rule 3: If two atoms are the same according to the that the C-C-N-C dihedral angle is used to position
above criteria, the atom with the lowest serial adjacent substructures within a label.
number goes first.
Rule 4: If two atoms are the same according to the Defining Substructures
above criteria, then the one which is attached to the
To define a substructure:
atom with the lowest serial number goes first.
In addition to the attachment points, the 1. Build a model of the substructure using the
measurements between the selected atoms and Bond tools and the Text Building tool.
nearby unselected atoms are saved with the
substructure to position the substructure relative to 2. Select the atoms to define.
other atoms when the substructure is used to convert 3. From the Edit menu, choose Copy.
labels into atoms and bonds.
Chem3D Appendix A: Substructures • 215

To save the substructure definition: 5. Select the hyphen to the right of the name, in the
Model column.
Substructures table. 6. From the Edit menu, choose Paste.
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The Table Editor opens and the Substructures

7. Select the cell in the Name column.
table becomes the active window.
8. Type “RCOOR” for the name of the
2. From the Edit menu, choose New Compound.
substructure.
3. Select the hyphen to the right of the name, in the
To save the substructure:
Model column.
1. Close the Substructures table.
4. From the Edit menu, choose Paste.
2. Click Save.
5. Select the cell in the Name column.
Suppose you want to insert an ester elsewhere in the
6. Type the name of the substructure. chain.
7. Close the Substructures table. To insert the ester between C(6) and C(7):
8. Click Save. 1. Select the Text Building Tool.
For example, consider an ester substructure, 2. Click the C(6)-C(7) bond.

R1COOR2. You can build this substructure as part of
the following model: 3. Type RCOOR in the text box and press Enter or
Return.
The C(6) - C(7) bond is deleted. Additional
hydrogens are added to both C(6) and C(7) if
the Automatically Rectify check box in the
Building control panel (Settings dialog box) is
selected.
To insert the ester substructure:

To define the substructure: 1. Shift-click one of the hydrogens bonded to C(6)
1. Select C(3), O(4) and O(5). and one of the hydrogens bonded to C(7).
2. From the Edit menu, choose Copy. 2. Press Enter or Return.

The Table Editor opens and the Substructures
4. From the Edit menu, choose New Compound.
216 • Appendix A: Substructures Chem3D

C(6) and C(7) are separated and the ester with Chem3D. Templates and Stationery are
substructure is inserted. pre-configured to create tables with the same fields
as the table after which it is named.
To create a substructure table:

• In the Table Editor, from the File menu, point to
Templates, and then choose Substructures.TBT
(Windows) or Substructures (Macintosh).
A new substructures table appears as the active
window.
After you add substructures to the table, make sure
If you want to append an ester onto the end of the you save it in the C3DTABLE directory (Windows)
chain as a carboxylic acid, you can simply or the Chem3D Parameters folder (Macintosh).
double-click a hydrogen to replace it with the ester Storing the tables in these locations make them
(as long as the name of the substructure is in the text available in the View menu.
box). Replacing H(8) would produce the following
structure:
Notice that the carbon atom in the ester has replaced

the hydrogen. This is because, when the ester was
defined, the carbon atom had a lower serial number
(3) than the oxygen atom that formed the other
attachment point in the substructure (5).
NOTE: When defining substructures with multiple

attachment points, it is critical to note the serial
numbers of the atoms in the substructure so that you
can correctly orient the substructure when it is
inserted in the model. See the rules for multiple
attachment points discussed at the beginning of this
section.
You can use templates (Windows) or Stationery

(Macintosh) to create new substructures tables in
addition to the standard substructure table provided
Chem3D Appendix A: Substructures • 217

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218 • Appendix A: Substructures Chem3D

Appendix B: Atom Types
Overview NOTE: For comparing bond orders, an atom type
Chem3D assigns atom types when you build with that contains one double bond may be assigned to an
Automatically Correct Atom Types turned on. You atom that contains two delocalized bonds. For
can also create your own atom types. example, all six carbons in benzene are C Alkene.
Assigning Atom Types If the maximum ring size field of an atom type is
specified, then the atom must be in a ring of that size
When you replace atoms, Chem3D attempts to or smaller to be assigned the corresponding atom
assign the best atom type to each atom by comparing type.
the information about the atom (such as its symbol
If an atom is bound to fewer ligands than are
and the number of bonds to the atom) to each atom
specified by an atom type geometry but the
type record in the Atom Type table.
rectification type is specified, then the atom can be
When you have selected the Automatically Correct assigned to that atom type. Chem3D fills the open
Atom Types check box in the Building control valences with rectification atoms.
panel, atom types are corrected when you delete
For example, consider the atom types for the
atoms or bonds, or when you add atoms or bonds. In
following structure:
addition, if this check box is selected, then the atom
types of pre-existing atoms may change when you
replace other atoms with other atoms of a different
type.
If the wrong atom type is assigned to an atom, you
can specify the correct atom type by selecting the
Text Building Tool, clicking the atom, typing the
name of the atom type into the text box, and pressing
the Return key.
Atom Type Characteristics

The characteristics of an atom must match the
following atom type characteristics for Chem3D to
O(3) matches the criteria specified for the atom type
assign the atom type to the atom.
O Carbonyl. Specifically, it is labeled ‘O’, it is
• The symbol. bound to a C Carbonyl by a double bond and it is
• The bound-to type (if specified for the atom attached to exactly one double bond and no triple
type). bonds.
• The bound-to order (if the bound-to type is
specified).
• The number of double, triple and delocalized
bonds.
Chem3D Appendix B: Atom Types • 219

If an atom can be assigned to more than one atom 4. Enter the appropriate data in each field of the
type, atom types are assigned to atoms in the table. Be sure that the name for the parameter is
following order: not duplicated elsewhere in the table.
1. Atom types whose bound-to types are specified
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5. From the File menu, choose Save, then choose

and are not the same as their rectification types. Close Window.
2. Atom types whose bound-to types are specified You now can use the newly defined atom type.
and are the same as their rectification types.
To define or edit an atom type in a file interpreter:
3. Atom types whose bound-to types are not
1. In the Table Editor, choose the file interpreter
specified.
that you want to modify from the Chem3D File
For example, in the model depicted above, O(4) Interpreters folder (Macintosh), or C3DFILTR
could be one of several atom types. First, it could be directory (Windows).
an O Ether atom for which the bound-to type is
unspecified (priority number 3, above). 2. Follow the directions above for defining or
Alternatively, it could be an O Alcohol for which the editing atom types in the Atom Types table.
bound-to type is the same as the rectification type, H
Alcohol (priority number 2, above). A third
possibility is O Carboxyl, for which the bound-to
type is C Carbonyl and the rectification type is H
Carboxyl (priority number 1). Because the
characteristic of a specified bound-to type which is
not the same as the rectification type (number 1 in
the priority list above) is given precedence over the
other two possibilities, the O Carboxyl atom type is
assigned to the oxygen atom.
Defining Atom Types

If you need to define atom types, whether to add to
the atom types table for building or to add to a file
format interpreter for importing, here is the general
procedure:
To add or edit an atom type to the Atom Types table:
1. From the View menu, choose Atom Types or

Atom Types.TBL.
The Table Editor opens and the Atom Types
2. From the Edit menu, choose New Atom Type.
3. To edit an atom type, click in the cell that you

want to change and type new information.
220 • Appendix B: Atom Types Chem3D

Appendix C: Technical Support
support to all registered users of this software WWW: http//www.camsoft.com/support
through the World Wide Web (WWW), and through
Internet: support@camsoft.com
ATTN: Technical Support
access our Technical Support page using the
http://www.camsoft.com/support Cambridge, MA 02140 USA
WWW, please complete the following tasks before
contacting the Technical Support.
Serial Numbers
1. Check the Readme file for known limitations or When contacting Technical Support, you must
conflicts. always provide your serial number. This serial
number was on the outside of the original Chem3D
2. Check the system requirements for the software box, and is the number that you entered when you
at the beginning of this User’s Guide. launched Chem3D for the first time. If you have
3. Read the Troubleshooting section of this thrown away your box and lost your installation
appendix and follow the possible resolution instructions, you can find the serial number in the
tactics outlined there. following ways:
4. If all your attempts to resolve a problem fail, fill Macintosh

out a copy of the CS Software Problem Report
• With Chem3D launched, choose About CS
Form at the back of this User’s Guide. This
Chem3D from the Apple menu. The serial
form is also available on-line through our number appears at the bottom left of the about
WWW Technical Support page.
box.
• Try to reproduce the problem before • In the Finder, single-click on the Chem3D
contacting us. If you can reproduce the
application icon and choose Get Info from the
problem, please record the exact steps that
File menu. The serial number is listed
you took to do so.
immediately after the version.
• Record the exact wording of any error
messages that appear.
• Record anything that you have tried to correct
the problem.
Chem3D Appendix C: Technical Support • 221

Windows • Increase the Virtual Memory (VM). Virtual
memory extends RAM by allowing space on
• With Chem3D launched, choose About CS
Chem3D from the Help menu. The serial
number appears at the bottom left of the about
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box.
physical RAM.
• Open the Chem3D.ini file (in your Windows
Change the VM as follows:
directory) using any text editor. The serial
number appears in the line starting • Macintosh: Memory control panel.
“SERIAL_NO=”. • Windows 95/98, NT 4.0: System control
For more information on obtaining serial numbers panel, Performance tab.
and registration codes, see:
http//www.camsoft.com/support/codes.cfm System Crashes
Chem3D should never crash, but below are the steps
Troubleshooting you should go through to try to resolve issues that
cause computer crashes while using a CS software
This section describes steps you can take that affect
product.
the overall performance of Chem3D, as well as steps
to follow if your computer crashes when using a CS 1. Restart your computer (Macintosh) or restart
software product. Windows and try to reproduce the problem. If
the problem recur, continue with the following
Performance steps.
Below are some ways you can optimize the 2. Take the steps appropriate for your system:
performance of Chem3D:
• (Macintosh): Restart your computer while
• (Macintosh): Increase the total amount of holding Shift down to turn off all system
memory that the application can use: extensions. Try to reproduce the problem.
• Select the Chem3D application icon in the If the problem no longer occurs, then you likely
Finder when Chem3D is not running. have an extension conflict. You should
• From the Edit menu, choose Get Info. determine which extension is causing the
Increase the memory allocation in the conflict, and then not have it load when using
Preferred size text box in the Memory Chem3D. To isolate an extension, disable half
Requirements section of the dialog box. of your extensions using the Extensions
Manager and test the problem again. Keep
• (Windows) In the Performance tab in the
disabling half of your extensions until you find
System control panel (Windows NT 4.0),
which extensions are causing the problem.
allocate more processor time to Chem3D.
• Install more physical RAM. The more you extensions are causing the problem.
have, the less Chem3D will have to access your
• (Windows): The most common conflicts for
hard disk to use Virtual Memory.
222 • Appendix C: Technical Support Chem3D

sure to determine what type and version of
drivers you are using.
Video Driver related problems: If you are
Chem3D, try switching to the VGA video
driver in the display Control Panel (or
System Setup, and then retest the problems.
If using a different driver helps, your original
driver may need to be updated–contact the
maker of the driver and obtain the most up-
to-date driver. If you still have trouble
contact us with the relevant details about the
original driver and the resulting problem.
resulting problem.
page on the WWW.
4. If the problem still occurs, Fax or E-mail the
details of the problem to Technical Support.
Chem3D Appendix C: Technical Support • 223

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224 • Appendix C: Technical Support Chem3D

Appendix D: 2D to 3D Conversion
Overview Example 1
This section discusses how Chem3D performs the
conversion from two to three dimensions when
opening a ChemDraw or ISIS/Draw document,
when pasting a ChemDraw or ISIS/Draw structure
from the Clipboard, or when opening a ChemDraw
connection table file. While Chem3D can read in
and assimilate any ChemDraw structure, you can In Example 1, the two phenyl rings are trans about
assist Chem3D in the two- to three-dimensional the cyclopentane ring. The phenyl ring on the left is
conversion of your models by following the attached by a wedged hashed bond; the phenyl ring
suggestions in this Appendix. on the right is attached by a wedged bond.
Chem3D uses the atom labels and bonds drawn in You can also use dashed, hashed, and bold bonds.
CS ChemDraw to form the structure of your model. However, you should be aware of potential
For every bond drawn in CS ChemDraw, a ambiguity where these non-directional bonds are
corresponding bond is created in Chem3D. Every used. A dashed, hashed, or bold bond must be
atom label is converted into at least one atom. between one atom that has at least three attachments
Dative bonds are converted to single bonds with a and one atom that has no more than two
positive formal charge added to one atom (the atom attachments, including the dashed, hashed, or bold
at the tail of the dative bond) and a negative formal bond.
charge added to the other (the head of the dative
bond). Example 2
+ -
S O
Stereochemical
Relationships H
N
Chem3D uses the stereobonds and H-Dot and
H-Dash atom labels in a ChemDraw structure to
In Example 2, the nitrogen atom is placed behind the
define the stereochemical relationships in the
ring system and the two methyl groups are placed in
corresponding model. Wedged bonds in
front of the ring system. Each of these three atoms is
CS ChemDraw indicate a bond where the atom at
bonded to only one other atom, so they are presumed
the wide end of the bond is in front of the atom at the
to be at the wide ends of the stereobonds.
narrow end of the bond. Wedged hashed bonds
indicate the opposite: the atom at the wide end of a
wedged hashed bond is behind the atom at the other
end of the bond.
Chem3D Appendix D: 2D to 3D Conversion • 225

Example 3 Labels
Chem3D uses the atom labels in a two-dimensional
structure to determine the atom types of the atoms.
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Unlabeled atoms are assumed to be carbon. Labels

are converted into atoms and bonds using the same
H method as that used to convert the text in a text box
into atoms and bonds. Therefore, labels can contain
several atoms or even substructures.
In Example 3, however, the hashed bond is
ambiguous because both atoms on the hashed bond
are attached to more than two bonds. In this case the
hashed bond is treated like a solid bond. Wavy bonds
are always treated like solid bonds.
H-Dots and H-Dashes are also used to indicate
stereochemistry. H-Dots become hydrogen atoms
attached to carbon atoms by a wedged bond.
H-Dashes become hydrogen atoms attached by a
wedged hashed bond.
Example 4
Example 4 shows cis-decalin on the left and

trans-decalin on the right as they would be drawn in
CS ChemDraw to be read in by Chem3D. Of course,
you can specify a cis fusion with two H-Dashes
instead of two H-Dots.
As a general rule, the more stereobonds you include
in your model, the greater is the probability that
Chem3D will make correct choices for chirality and
dihedral angles.
When converting two-dimensional structures,
Chem3D uses standard bond lengths and angles as
specified in the current set of parameters. If
Chem3D tries to translate strained ring systems, the
ring closures will not be of the correct length or
angle.
226 • Appendix D: 2D to 3D Conversion Chem3D

Appendix E: MM2
Overview Other Parameters
This appendix contains miscellaneous information The rest of the parameters consist of atom types and
about the MM2 parameters and force field. elements in the periodic table which were not
included in the original MM2 force field, such as
MM2 Parameters metals. The rectification type of all the non-MM2
atom types in the Chem3D Parameter tables is
The original MM2 parameters include the elements Hydrogen (H). The atom type numbers for these
commonly used in organic compounds: carbon, atom types range from 111 to 851. The atom type
hydrogen, nitrogen, oxygen, sulfur and halogens. number for each of the non-MM2 atom types in the
The atom type numbers for these atom types range MM2 Atom Type Parameters table is based on the
from 1 to 50. atomic number of the element and the number of
ligands in the geometry for that atom type. To
The MM2 parameters were derived from three determine an atom type number, the atomic number
sources: is multiplied by ten, and the number of ligands is
1. Most of the parameters were provided by Dr. N. added.
L. Allinger. For example, Co Octahedral has an atomic number
of 27 and six ligands. Therefore the atom type
2. Several additional parameters were provided by number is 276.
Dr. Jay Ponder, author of the TINKER program.
In a case where different atom types of the same
3. Some commonly used parameters that were not element have the same number of ligands (Iridium
provided by Dr. Allinger or Dr. Ponder are Tetrahedral, Atom Type # 774 and Iridium Square
Planar, Atom Type # 779), the number nine is used
provided by CambridgeSoft Corporation.
for the second geometry.
However, most of these parameters are
estimates which are extrapolated from other
parameters.
Viewing Parameters
The best source of information on the MM2 To view the parameters used by Chem3D to perform
parameter set is Molecular Mechanics, Burkert, MM2 computations:
Ulrich and Allinger, Norman L., ACS Monograph • From the View menu, choose a parameter table.
177, American Chemical Society, Washington, DC,
1982. The Table Editor application opens and the
table you chose becomes the active window.
A method for developing reasonable guesses for
parameters for non-MM2 atom types can be found
in “Development of an Internal Searching
Editing Parameters
Algorithm for Parameterization of the MM2/MM3 You can edit the parameters that come with
Force Fields”, Journal of Computational Chemistry, Chem3D. Parameters that you add or change can be
Vol 12, No. 7, 844-849 (1991). guesses or approximations that you make, or values
obtained from current literature.
Chem3D Appendix E: MM2 • 227

In addition, there are several adjustable parameters MM2 program (QCPE 395), and Ponder’s TINKER
available in the MM2 Constants table. For system (M.J. Dudek and J.W. Ponder, J. Comput.
information on parameters and MM2 constants, see Chem., 16, 791-816 (1995)).
“The Force-Field” on page 130. For a review of MM2 and applications of molecular
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mechanics methods in general, see Molecular

NOTE: Before performing any editing we strongly Mechanics, by U. Burkert and N. L. Allinger, ACS,
recommend that you create back-up copies of all the Washington, D.C., USA, 1982. Computational
parameter files located in the Chem3D Parameters Chemistry, by T. Clark, Wiley, N.Y., USA, 1985,
folder (Macintosh) or the C3DTable directory also contains an excellent description of molecular
(Windows). mechanics.
For a description of the TINKER system and the
To add a new parameter to the Torsional parameters detailed rationale for Ponder’s additions to the MM2
table: force field, visit the TINKER home page at
http://dasher.wustl.edu/tinker.
1. From the View menu, choose Torsional
Parameters or Torsional Parameters.TBL. For a description and review of molecular dynamics,
see Dynamics of Proteins and Nucleic Acids, J.
The Table Editor is opens and the Torsional Andrew McCammon and Stephen Harvey,
Parameters table becomes the active window. Cambridge University Press, Cambridge, UK, 1987.
2. From the Edit menu, choose New Torsional Despite its focus on biopolymers, this book contains
a cogent description of molecular dynamics and
Parameter.
related methods, as well as information applicable to
3. Enter the appropriate data in each field of the other molecules.
parameter table. Be sure that the name for the
parameter is not duplicated elsewhere in the Chem3D Changes to
table. Allinger’s Force Field
4. From the File menu, choose Save. The Chem3D implementation of the Allinger Force
The new parameter table is saved. Field differs in these areas:
5. From the File menu, choose Close Window. 1. A charge-dipole interaction term
2. A quartic stretching term

The MM2 Force Field in
3. Cutoffs for electrostatic and van der Waals
Chem3D terms with a fifth-order polynomial switching
Chem3D includes a new implementation of Norman function
L. Allinger’s MM2 force field based in large
measure on work done by Jay W. Ponder of 4. Automatic pi system calculation when
Washington University. This appendix does not necessary
attempt to completely describe the MM2 force field,
but discusses the way in which the MM2 force field Charge-Dipole Interaction Term
is implemented and used in Chem3D and the
Allinger’s potential function includes one of two
differences between this implementation, Allinger’s
possible electrostatic terms: one based on bond
dipoles, or one based on partial atomic charges. The
228 • Appendix E: MM2 Chem3D

addition of a charge-dipole interaction term allows Because the charge-charge interaction energy
for a combined approach, where partial charges are between two point charges separated by a distance r
represented as bond dipoles, and charged groups, is proportional to 1/r, the charge-charge cutoff must
such as ammonium or phosphate, are treated as point be rather large, typically 30 or 40Å. The charge-
charges. dipole, dipole-dipole, and van der Waals energies,
which fall off as 1/r2, 1/r3, and 1/r6, respectively, can
Quartic Stretching Term be cut off at much shorter distances, for example,
25Å, 18Å, and 10Å, respectively. Fortunately, since
With the addition of a quartic bond stretching term,
the van der Waals interactions are by far the most
troublesome negative bond stretching energies
numerous, this cutoff speeds the computation
which appear when long bonds are treated by
significantly, even for relatively small molecules.
Allinger’s force field are eliminated.
The quartic bond stretching term is required Pi Orbital SCF Computation
primarily for molecular dynamics; it has little or no
effect on low energy conformations. Chem3D determines whether the model contains
any pi systems, and performs a Pariser-Parr-Pople pi
To precisely reproduce energies obtained with orbital SCF computation for each system. A pi
Allinger’s force field: system is defined as a sequence of three or more
• Set the quartic stretching constant in the MM2 atoms of types which appear in the Pi Atoms table
Constants table window to zero. window (PIATOMS.TBL) .
The method used is that of D.H. Lo and M.A.
The quartic term is eliminated.
Whitehead, Can. J. Chem., 46, 2027 (1968), with
heterocycle parameters according to G.D. Zeiss and
Electrostatic and van der Waals M.A. Whitehead, J. Chem. Soc. (A), 1727 (1971).
Cutoff Terms The SCF computation yields bond orders which are
used to scale the bond stretching force constants,
The cutoffs for electrostatic and van der Waals terms
standard bond lengths, and twofold torsional
greatly improve the computation speed for large
barriers.
molecules by eliminating long range interactions
from the computation. A step-wise overview of the process used to do pi
system calculations is as follows:
To precisely reproduce energies obtained with
Allinger’s force field: 1. A matrix called the Fock matrix is initialized to
• Set the cutoff distances to large values (greater represent the favorability of sharing electrons
than the diameter of the model). between pairs of atoms in a pi system.
Every interaction is then computed. 2. The pi molecular orbitals are computed from
The cutoff is implemented gradually, beginning at the Fock matrix.
50% of the specified cutoff distance for charge and
3. The pi molecular orbitals are used to compute a
charge-dipole interactions, 75% for dipole-dipole
new Fock matrix, then this new Fock matrix is
interactions, and 90% for van der Waals
interactions. Chem3D uses a fifth-order polynomial used to compute better pi molecular orbitals.
switching function so that the resulting force field is
second-order continuous.
Chem3D Appendix E: MM2 • 229

4. Step 2 and Step 3 are repeated until the
computation of Fock matrix and the pi
molecular orbitals converge. This method is
called the self-consistent field technique or a
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pi-SCF calculation.
5. A pi bond order is computed from the pi

molecular orbitals.
6. The pi bond order is used to modify the bond

length (BLres) and force constant (KSres) for
each sigma bond in the pi system.
7. The values of KSres and BLres are used in the

molecular mechanics portion of the MM2
computation to further refine the molecule.
To examine the computed bond orders after an MM2

computation:
1. In the Pop-up Information control panel, select

Bond Order.
2. Position the pointer over a bond.

The information box contains the newly computed
bond orders for any bonds that are in a pi system.
230 • Appendix E: MM2 Chem3D

Appendix F: MOPAC
Overview Historically, these approximations were made to
allow ab initio calculations to be in the reach of the
The appendix contains miscellaneous information computer du jour. Currently, ab initio methods are
about MOPAC. within the reach of the desktop computer for small
molecules, however, larger molecules are still more
You can also find additional information about
efficiently modeled on the desktop using semi-
MOPAC by visiting the MOPAC home page on the
empirical or molecular mechanics methodologies.
World Wide Web:
To understand the place that the potential energy
http://home.att.net/~mrmopac
functions in MOPAC take in the semi-empirical
arena, here is a brief chronology of the
MOPAC Background approximations that that comprise the semi-
MOPAC was created by Dr. James Stewart. The empirical methods. The first approximation was
weakness in MOPAC was its lack of user interface termed CNDO for Complete Neglect of Differential
and complexity of use. MOPAC 2000 is a revised Overlap. The next approximation was termed INDO
version of MOPAC 97, and is newly available. for Intermediate Neglect of Differential Overlap,
Next followed MINDO/3, which stands for
MOPAC 2000 is copyrighted software. Fujitsu, Ltd.
“Modified Intermediate Neglect of Differential
is the copyright owner. Now, in cooperation with
Overlap”. Next was MNDO, which is short for
Fujitsu, MOPAC 2000 is coupled with Chem3D, in
“Modified Neglect of Differential Overlap” which
the form of CS MOPAC, to provide greater usability
corrected MINDO/3 for various organic molecules
to this powerful program, for to both the veteran and
made up from elements in rows 1 and 2 of the
novice molecular modeller.
periodic table. AM1 improved upon MNDO
MOPAC implements semi-empirical methodology markedly. Finally the most recent, PM3 is a
for analyzing molecular models. reparameterization of AM1. The approximations in
Semi-empirical methods for molecular modeling PM3 are the same as AM1.
were originally created to allow solutions of the The potential energy functions represent a series of
electronic Schrödinger equation improvements to account for the initial assumption
that complete neglect of diatomic orbitals would
Potential Functions yield useful data for molecules to resource intensive
for using ab initio. This initial assumption was not
Parameters the case, and so a series of improvements ending
MOPAC provides five potential functions with AM1 and PM3 have arisen.
MINDO/3, MNDO, PM3, AM1, and MNDO-d. All
are SCF (Self Consistent Field) methods. Each
potential function represents an approximation in
the mathematics for solving the Electronic
Schrödinger equation for a molecule.
Chem3D Appendix F: MOPAC • 231

Adding Parameters to
MOPAC
Parameters are in constant development for use with
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PM3 and AM1 potential functions. If you find that

the standard set of parameters that comes with
CS MOPAC does not cover an element that you
need, for example Cu, you can search the literature
for the necessary parameter and add it at run time
when performing a MOPAC job. This flexibility
greatly enhances the usefulness of MOPAC.
You can add parameters at run time using the
keyword EXTERNAL=name, where name is the
name of the file (and its full path) containing the
additional parameters.
A description for the required format of this file can
be found in Figure 3.4, page 29 of the online
MOPAC manual.
232 • Appendix F: MOPAC Chem3D

Appendix G: Automation
Macintosh To learn more about Apple Scripting (or scripting in
general) you can refer to any of the following
Chem3D and the Table Editor support Apple® references:
Events, a method by which applications can send AppleScript Language Guide, English Dialect by
messages to each other. Using Apple Events it is Apple Computer (part of the AppleScript
possible to develop scripts for sequences of Developers Toolkit, available through APDA).
commands that can be executed repeatedly. Addison-Wesley, 1994. ISBN: 0-201-40910-0.
Support includes: AppleScript Finder Guide, English Dialect by Apple
• A basic set of Apple Events that includes the Computer (part of the AppleScript Developers
Apple Events required to open and print Toolkit, available through APDA). Addison-
documents from the Macintosh Finder. Wesley, 1994.
• Apple Events for manipulating the basic tools AppleScript Scripting Additions Guide, English
Dialect by Apple Computer (part of the AppleScript
in Chem3D documents, windows and files.
Developers Toolkit, available through APDA).
• Menu sharing Apple Events used in conjunction Addison-Wesley, 1994. ISBN: 0-201-40736-1.
with Frontier, by Userland, Inc. Inside Macintosh: Interapplication Communication
by Apple Computer, Addison-Wesley, 1993. ISBN:
To view the supported Apple Events:
0-201-62200-9.
1. Launch the Script Editor application. This Danny Goodman’s AppleScript Handbook by
application comes with System 7.1 and later. Danny Goodman, Random House, 1994. ISBN: 0-
679-75806-2.
2. From the File menu, choose Open Dictionary.
The Tao of AppleScript, by Derrick Schneider,
3. In the dialog box that appears, select the Hayden Books, 1994. ISBN: 1-56830-115-4.
CS Chem3D or the Table Editor application. Applied Mac Scripting by Tom Trinko, M&T
Books, 1995. ISBN 1-55828-330-7.
4. Choose OK.
Scripting the Scriptable Finder by Steve Michel,
The Dictionary is displayed in a scrollable Heizer Software, 1995.
window.
Ultimate Mac Programming by Dave Mark, IDG
For more detailed information about the Books, 1994. ISBN: 1-56884-195-7.
AppleScript interface of Chem3D, see the
CambridgeSoft SDK web pages at:
http://sdk.camsoft.com/
Chem3D Appendix G: Automation • 233

Windows
Chem3D is implemented as an OLE Automation
Server that allows outside applications, such as
Administrator
Microsoft Excel, to externally control some aspects

of Chem3D.
You can write scripts in any Visual Basic
environment, including that provided by Microsoft
Excel, and in C/C++. For Visual Basic, use the type
library, Chem3D.tlb, installed with your software.
For C/C++, use the header file Chem3D.h installed
with your software.
For more detailed information about the Automation
interface of Chem3D, see the CambridgeSoft SDK
web pages at:
http://sdk.camsoft.com/
234 • Appendix G: Automation Chem3D

Appendix H: Parameter Tables
Parameter Table Parameter Table Use
Overview 4-Membered Ring Bond angles for bonds in
Chem3D uses the parameter tables, containing Angles.TBL 4-membered rings. In force
information about elements, bond types, atom types, field analysis, angle bending
and other parameters, for building and for analyzing portion of the force field for
your model. bonds in 4-membered rings.
The parameter tables must be located in the
4-Membered Ring Computes the portion of the
C3DTABLE directory in the same directory as the
Torsionals.TBL force field for the torsional
Chem3D application.
angles in your model for
atoms in 4-membered rings.
Parameter Table Use
Chem3D uses several parameter tables to calculate Angle Bending Standard bond angles. In
bond lengths and bond angles in your model. To Parameters.TBL force field analysis, angle
apply this information, select Apply Standard bending portion of the force
measurements in the Building Control panel. field for bonds.
Calculating the MM2 force field of a model requires
Atom Types.TBL Contains atom types available
special parameters for the atoms and bonds in your
for building models.
model. The MM2 force field is calculated during
Energy Minimization, Molecular Dynamics, and
Bond Stretching Standard bond lengths. In
Steric Energy computations.
Parameters.TBL force field analysis, bond
The use of the parameter tables are described in the stretching and electrostatic
following table: portions of force field for
bonds.
Parameter Table Use
Conjugated Bond lengths for bonds
3-Membered Ring Bond angles for bonds in Pisystem involved in Pi systems. Pi
Angles.TBL 3-membered rings. In force Atoms.TBL system portion of the force
field analysis, angle bending field for pi atoms.
portion of the force field for
bonds in 3-membered rings. Conjugated Pi system portion of the force
Pisystem field for pi bonds.
Bonds.TBL
Chem3D Appendix H: Parameter Tables • 235

Parameter Table Use Parameter Table Fields
Most of the tables contain the following types of
Electronegativity Adjusts optimal bond length
fields:
Adjustments.TBL between two atoms when one
Administrator
atom is attached to an atom • Atom Type Numbers

that is electronegative. • Quality
Elements.TBL Contains elements available • Reference

for building models.
Atom Type Numbers
MM2 Atom Type van der Waals parameters for The first column in a parameter table references an
Parameters.TBL computing force field for each atom type using an Atom Type number. An Atom
atom. Type number is assigned to an atom type in the
Atom Types table. For example, in Chem3D, a
MM2 Constants used for computing dihedral type field, 1–1–1–4, in the Torsional
Constants.TBL MM2 force field. Parameters table indicates a torsional angle between
carbon atoms of type alkane (Atom Type number 1)
Out-of-Plane Parameters to assure atoms in and carbon atoms of type alkyne (Atom Type
Bending trigonal planar geometry number 4). In the 3-membered ring table, the angle
Parameters.TBL remain planar. In force field type field, 22-22-22, indicates an angle between
analysis, parameters to assure three cyclopropyl carbons (Atom Type number 22)
atoms in trigonal planar in a cyclopropane ring.
geometry remain planar.
Quality
References.TBL Contains information about
where parameter information The quality of a parameter indicates the relative
is derived. accuracy of the data.
Substructures.TBL Contains predrawn Quality Accuracy Level

substructures available for
speeding up model building. 1 Parameter guessed by Chem3D.
Torsional Computes the portion of the 2 Parameter theorized but not

Parameters.TBL force field for the torsional confirmed.
angles in your model.
3 Parameter derived from
VDW Adjusts specific VDW experimental data.
Interactions.TBL interactions, such as hydrogen
bonding. 4 Parameter well confirmed.
236 • Appendix H: Parameter Tables Chem3D

Reference NOTE: Adding or changing parameter tables is not
The reference for a measurement corresponds to a recommended unless you are sure of the information
reference number in the References table. your are adding. For example, new parameter
References indicate where the parameter data was information that is documented in journals.
derived.
Estimating Parameters NOTE: A method for guessing at missing MM2

Parameters can be found in “Development of an
Under some circumstances Chem3D may estimate Internal Searching Algorithm for Parameterization
parameters. of the MM2/MM3 Force Fields”, Journal of
For example, during an MM2 analysis, a non-MM2 Computational Chemistry, Vol 12, No. 7, 844–849
atom type is encountered in your model. Although (1991).
the atom type is defined in the Atom Types table, the
necessary MM2 parameter will not be defined for To add a new parameter to a parameter table:
that atom type. For example, torsional parameters
are missing. This commonly occurs for inorganic 1. From the View menu, choose the parameter
complexes, which MM2 does not cover adequately. table to open.
More parameters exist for organic compounds. The Table Editor opens and the parameter table
In this case, Chem3D makes an educated “guess” appears.
wherever possible. A message indicating an error in 2. From the Edit menu, choose New Record.
your model may appear before you start the analysis.
If you choose to ignore this, you can determine the 3. Type the information for the new parameter.
parameters guessed after the analysis is complete.
The new parameter is added to the file.
To view the parameters used in an MM2 analysis:
• From the MM2 menu, choose Show Used NOTE: Do not include duplicate parameters. If
Parameters.
duplicate parameters exist in a parameter table it is
indeterminate which parameter will be used when
Estimated parameters have a Quality value of 1. called for in a calculation.
Creating Parameters
NOTE: If you do want to make changes to any of
The MM2 force field parameters are based on a
the parameters used in Chem3D, we strongly
limited number of MM2 atom types. These atom
recommend that you make a back up copy of the
types cover the common atom types found in
original parameter table and remove it from the
organic compounds. As discussed in the previous
C3DTABLE directory.
section, parameters may be missing from structures
containing other than an MM2 atom type.

The Elements Table Color
The Elements table (Elements.TBL) contains the The colors of elements are used when the Color by
elements for use in building your models. Element check box is selected in the control panel.
Administrator
To use an element in a model, type its symbol in the To change the color of an element:
Replacement text box (or paste it, after copying the
• Double-click the current color.
cell in the “Symbol” field to the Clipboard) and
press Enter when an atom is selected, or double- The Color Picker dialog box appears in which
click an atom. If no atom is selected, a fragment is you can specify a new color for the element.
added.
In Chem3D, three fields comprise a record in the Atom Types
Elements table: the symbol, the covalent radius, and The Atom Types table Atom Types.TBL) contains
the pattern. the atom types for use in building your models.
Symbol Normally you use only the first column of the Atom
Normally you use only the first column of the Types table while building models. To use an atom
Elements table while building models. If you are not type in a model, type its name in the Replacement
currently editing a text cell, you can quickly move text box (or paste it, after copying the name cell to
from one element to another by typing the first letter the Clipboard) and press Enter when an atom is
or letters of the element symbol. selected, or when you double-click an atom. If no
atom is selected, a fragment is added.
Covalent Radius Twelve fields comprise an atom type record: name,
The covalent radius is used to approximate bond symbol, van der Waals radius, atom type number,
lengths between atoms. charge, the maximum ring size, rectification type,
geometry, number of double bonds, number of triple
Pattern bonds, number of delocalized bonds, bound-to order
and bound-to type.
The pattern is used to shade atoms of each element
when displaying Ball & Stick, Cylindrical Bonds, or Name
Space Filling models.
The records in the Atom Types table are ordered
To change the pattern of an atom: alphabetically by atom type name. Atom type names
must be unique.
1. Point to the current pattern and double-click.
The Pattern Picker dialog box appears. Symbol
2. Select a new pattern. The symbol of an atom type corresponds to a symbol
of an element in the Elements table.
3. Click OK.

van der Waals Radius Rectification Type
The van der Waals radius is used when displaying The rectification type is an atom type assigned to the
the Ball & Stick, Cylindrical Bonds or Space Filling atoms which automatically fills open valences on
models. the selected atom. The rectification atoms are added
The Close Contacts command in the Analyze menu or deleted when you have selected the
also determines close contacts by comparing the Automatically Rectify check box from the Building
distance between pairs of non-bonded atoms to the control panel. Typically, rectification atom types are
sum of their van der Waals radii. hydrogen atom types.
To change the rectification type for a specific atom

NOTE: The van der Waals radii specified in the type:
Atom Types table do not affect the results of an MM2
computation. The radii used in an MM2 1. Double-click the rectification type cell in the
computation are specified in the MM2 Atom Types appropriate atom type record.
table.
A dialog box appears that contains a list of all
atom types.
Atom Type Number
2. To choose a new rectification type, select the
Atom Type Atom Type numbers are used to
new type from the list.
determine which measurements apply to a given
group of atoms. 3. Click OK.
For example, to determine the standard bond length
When you specify a rectification type, the
of a bond between a C Alkane atom (atom type
number 1) and an O Alcohol atom (atom type bound-to type of the rectification type should
number 6), you should look at the 1-6 record in the not conflict with the atom type. If there is no
Bond Stretching table. rectification type for an atom, it is never
rectified.
Charge For example, if the rectification type of O Carboxyl
The charge of an atom type is used when assigning is H Carboxyl, the bound-to type of H Carboxyl
atom types to atoms in a model. should be either O Carboxyl or empty. Otherwise,
when assigning atom types, hydrogen atoms bound
When the information about an atom is displayed,
to O Carboxyl atoms are not assigned H Carboxyl.
the atom symbol is always followed by the charge.
Charges can be fractional. For example, the charge
of a carbon atom in a cyclopentadienyl ring should
Geometry
be 0.200. The geometry for an atom type describes both the
number of bonds that extend from this type of atom
Maximum Ring Size and the angles formed by those bonds.
The maximum ring size field indicates whether the To view the menu of geometries:
corresponding atom type should be restricted to
atoms found in rings of a certain size. If this cell is 1. Double-click a geometry cell.
zero or empty, then this atom type is not restricted. A dialog box containing geometries appears.
For example, the maximum ring size of C
Cyclopropane is 3. 2. Select a geometry within the dialog box.

3. Click OK. For an atom to be of the type being defined, it must
be bonded to an atom of the bound-to type by a bond
NOTE: Standard bond angle parameters are used of the bound-to order.
only when the central atom has a tetrahedral,
To change the bound-to type:
Administrator
trigonal or bent geometry.

1. Double-click the current bound-to type in the
Atom Types table window.
Number of Double Bonds,
A dialog box appears that contains a list of all
Triple Bonds, and Delocalized
atom types.
Bonds
2. Select the new type from the list.
The number of double bonds, number of triple
bonds, and number of delocalized bonds are integers 3. Click OK. If an atom type is not restricted by a
ranging from zero to the number of ligands as bound-to type, click the cell in the table
specified by the geometry. Chem3D uses this window, and press the Delete key.
information both to assign atom types based on the
bond orders and to assign bond orders based on atom
types. Substructures
The Substructure table (Substructures.TBL)
Bound-to Order contains substructures to use in your model.
Chem3D uses the Bound-to Order field in To use a substructure simply type its name in the
conjunction with the Bound-to Type field to assign Replacement text box (or paste it, after copying the
atom types to atoms. name cell to the Clipboard) and press Enter when an
atom(s) is selected, or double-click an atom. You
To change a bound-to order: can also copy the substructures picture to the
1. Double-click the current bound-to order. Clipboard and paste it into a model window. The
substructure is attached to selected atom(s) in the
A dialog box appears containing a list of the
model window. If no atom is selected, a fragment is
possible bound-to orders.
added. You can also define your own substructures
2. Select a new bound-to order for the atom type. and add them to the table. The table below shows the
substructure table window with the substructure
3. Choose OK. records open (triangles facing down). Clicking a
The bound-to order should be consistent with triangle closes the record. The picture of the
the number of double, triple, and delocalized substructure is minimized.
bonds for this atom type. If the bound-to type of
an atom type is not specified, its bound-to order References
is ignored. The References table (References.TBL) contains
information concerning the source for other
Bound-to Type parameters. Use of the References table does not
CS Chem3D uses the Bound-to Type field in affect the other tables in any way.
conjunction with the Bound-to Order field to assign Two fields are used for each reference record: the
atom types to atoms. reference number and the reference description.

Reference Number The larger the value of KS for a particular bond
between two atoms, the more difficult it is to
The reference number is an index by which the compress or to stretch that bond.
references are organized. Each measurement also
contains a reference field that should contain a Length
reference number, indicating the source for that
measurement. The third field, Length, contains the bond length for
a particular bond type. The larger the number in the
Reference Description Length field, the longer is that type of bond.
The reference description contains whatever text Bond Dipole

you need to describe the reference. Journal
references or bibliographic data are common The Bond Dpl field contains the bond dipole for a
examples of how you can describe your references. particular bond type. The numbers in this cell give
an indication of the polarity of the particular bond.
Bond Stretching A value of zero indicates that there is no difference
in the electronegativity of the atoms in a particular
Parameters bond. A positive bond dipole indicates that the atom
The Bond Stretching Parameters table (Bond type represented by the first atom type number in the
Stretching Parameters.TBL) contains information Bond Type field is less electronegative than the atom
about standard bond lengths between atoms of type represented by the second atom type number.
various atom types. In addition to standard bond Finally, a negative bond dipole means that the atom
lengths are information used in MM2 calculations in type represented by the first atom type number in the
Chem3D. Bond Type field is more electronegative than the
atom type represented by the second atom type
The Bond Stretching table contains parameters number.
needed to compute the bond stretching and
electrostatic portions of the force field for the bonds For example, the 1-1 bond type has a bond dipole
in your model. of zero since both alkane carbons in the bond are of
The Bond Stretching Parameters record consists of the same electronegativity. The 1-6 bond type has a
six fields: Bond Type, KS, Length, Bond Dpl, bond dipole of 0.440 since an ether or alcohol oxy-
Quality, and Reference. gen is more electronegative than an alkane carbon.
Finally, the 1-19 bond type has a bond dipole
Bond Type of - 0.600 since a silane silicon is less
The Bond Type field contains the atom type electronegative than an alkane carbon.
numbers of the two bonded atoms.
For example, Bond Type 1-2 is a bond between an NOTE: The 1-5 bond type has a dipole of zero,
alkane carbon and an alkene carbon. despite the fact that the carbon and hydrogen atoms
on this bond have unequal electronegativity. This
KS approximation drastically reduces the number of
dipoles to be computed and has been found to
The KS, or bond stretching force constant field, produce acceptable results.
contains a proportionality constant which directly
impacts the strength of a bond between two atoms.

Record Order compute the angle bending portions of the MM2
force field for any bond angles in your model which
The order of the records in the Bond Stretching table occur in 4-membered rings.
window is as follows: The 3-membered Ring Angles table contains the
Administrator
1. Records are sorted by the first atom type

parameters that are needed to determine the bond
angles in your model that are part of 3-membered
number in the Bond Type field. For example,
rings. In Chem3D, additional information is used to
the record for bond type 1-3 is before the record
compute the angle bending portions of the MM2
for bond type 2-3. force field for any bond angles in your model which
2. For records where the first atom type number is
occur in 3-membered rings.
the same, the records are sorted by the second Each of the records in the Angle Bending table, the
atom type number in the Bond Type field. For 4-Membered Ring Angles table and the 3-
example, bond type 1-1 is before the record for Membered Ring Angles table consists of seven
fields: Angle Type, KB, –XR2–, –XRH–, –XH2–,
bond type 1-2.
Quality, and Reference.
Angle Bending, Angle Type

4-Membered Ring Angle The first field, Angle Type, contains the atom type
Bending, 3-Membered numbers of the three atoms which describe the bond
angle.
Ring Angle Bending For example, angle type 1-2-1 is a bond angle
The Angle Bending table (Angle Bending formed by an alkane carbon bonded to an alkene
Parameters.TBL) contains information about bond carbon which is bonded to another alkane carbon.
angles between atoms of various atom type. In Notice that the alkene carbon is the central atom of
addition to standard bond angles are information the bond angle.
used in MM2 Calculations in Chem3D. Angle
bending parameters are used when the central atom KB
has four or fewer attachments and the bond angle is
not in a three or four membered ring. In three and The KB, or the angle bending constant, contains a
four membered rings, the parameters in the measure of the amount of energy required to deform
3-Membered Ring Angles.TBL and 4-Membered a particular bond angle. The larger the value of KB
Ring Angles.TBL are used. for a particular bond angle described by three atoms,
the more difficult it is to compress or stretch that
The Angle Bending table contains the parameters bond angle.
used to determine the bond angles in your model. In
CS Chem3D Pro, additional information is used to –XR2–
compute the angle bending portions of the MM2
force field for the bond angles in your model. –XR2–, the third field, contains the optimal value of
a bond angle where the central atom of that bond
The 4-membered Ring Angles table contains the
angle is not bonded to any hydrogen atoms. In the –
parameters that are needed to determine the bond
XR2– notation, X represents the central atom of a
angles in your model that are part of 4-membered
bond angle and R represents any non-hydrogen atom
rings. In Chem3D, additional information is used to
bonded to X.

For example, the optimal value of the 1-1-3 angle Record Order
type for 2,2-dichloropropionic acid is the –XR2–
bond angle of 107.8°, since the central carbon (C-2) When sorted by angle type, the order of the records
has no attached hydrogen atoms. in the Angle Bending table, the 4-Membered Ring
The optimal value of the 1-8-1 angle type for Angles table and the 3-Membered Ring Angles table
N,N,N-triethylamine is the –XR2– bond angle of is as follows:
107.7°, because the central nitrogen has no attached 1. Records are sorted by the second atom type
hydrogen atoms. Notice that the central nitrogen has
number in the Angle Type field. For example,
a trigonal pyramidal geometry, thus one of the
the record for bond angle type 1-2-1 is before
attached non-hydrogen atoms is a lone pair, the other
non-hydrogen atom is a carbon. the record for bond angle type 1-3-1.
2. For multiple records where the second atom

–XRH– type number is the same, the records are sorted
The –XRH– field contains the optimal value of a by the first atom type number in the Angle Type
bond angle where the central atom of that bond field. For example, the record for bond angle
angle is also bonded to one hydrogen atom and one type 1-3-2 is listed before the record for bond
non-hydrogen atom. In the –XRH– notation, X and angle type 2-3-2.
R are the same as –XR2–, and H represents a
hydrogen atom bonded to X. 3. For multiple records where the first two atom
For example, the optimal value of the 1-1-3 angle type numbers are the same, the records are
type for 2-chloropropionic acid is the –XRH– bond sorted by the third atom type number in the
angle of 109.9°, since the central carbon (C-2) has Angle Type field. For example, the record for
one attached hydrogen atom. The optimal value of bond angle type 1-1-1 is listed before the record
the 1-8-1 angle type for N,N-diethylamine is the – for bond angle type 1-1-2.
XRH– value of 107.7°, because the central N has
one attached hydrogen atom. In this case the –XR2–
and –XRH– values for the 1-8-1 angle type are
Pi Atoms
identical. As in the N,N,N-triethylamine example The Pi Atoms table (Conjugated Pisystem
above, the only attached non-hydrogen atom is a Atoms.TBL) contains the parameters which are used
lone pair. to correct bond lengths and angles for pi atoms in
your model. In Chem3D, additional information is
–XH2– used to compute the pi system portions of the MM2
force field for the pi atoms in your model.
–XH2– is the optimal value of a bond angle where
the central atom of that bond angle is also bonded to The records in the Pi Atoms table are comprised of
two hydrogen atoms. six fields: Atom Type, Electron, Ionization,
Repulsion, Quality, and Reference.
For example, the optimal value of the 1-1-3 angle
type for propionic acid is the –XH2– bond angle of Atom Type
110.0°, since the central carbon (C-2) has two
attached hydrogen atoms. The Atom type number field contains the atom type
number to which the rest of the Conjugated
Pisystem Atoms record applies.

Electron of a pi system. In Chem3D, additional information is
used to compute the pi system portions of the MM2
The Electron field contains the number of electrons force field for the pi bonds in a model.
that a particular pi atom contributes to the pi system.
There are five fields in records in the Pi Bonds table:
Administrator
For example, an alkene carbon, atom type number 2, Bond Type, dForce, dLength, Quality, and
contributes 1 electron to the pi system whereas a Reference.
pyrrole nitrogen, atom type number 40, contributes
2 electrons to the pi system. Bond Type
Ionization The Bond Type field is described by the atom type
numbers of the two bonded atoms.
The Ionization field contains the amount of energy
For example, bond type 2-2 is a bond between two
required to remove a pi electron from an isolated pi
alkene carbons.
atom. The units of the ionization energy by electron
volts (eV). The magnitude of the ionization energy
is larger the more electronegative the atom.
dForce
For example, an alkene carbon has an ionization The dForce field contains a constant used to
energy of -11.160 eV, and the more electronegative decrease the bond stretching force constant of a
pyrrole nitrogen has an ionization energy of -13.145 particular conjugated double bond. The force
eV. constant Kx for a bond with a calculated pi bond
order x is:
Repulsion Kx = K2 - (1 - x) * dForce
The Repulsion field contains a measure of: where K2 is the force constant for a non-
conjugated double bond, taken from the Bond
• The energy required to keep two electrons, each
Stretching table.
on separate pi atoms, from moving apart and
The higher the value of Kx for the bond between two
• The energy required to keep two electrons,
pi atoms, the more difficult it is to compress or
occupying the same orbital on the same pi atom, stretch that bond.
from moving apart.
The units of the repulsion energy are electron dLength
volts (eV). The repulsion energy is more The dLength field contains a constant used to
positive the more electronegative the atom. increase the bond length of any conjugated double
For example, an alkene carbon has an repulsion bond. The bond length lx for a bond with a
energy of 11.134 eV, and the more electronegative calculated pi bond order x is:
pyrrole nitrogen has an repulsion energy of 17.210 lx = l2 + (1 - x) * dLength
eV.
where l2 is the bond length of a non-conjugated
Pi Bonds double bond, taken from the Bond Stretching
table. The higher the value of lx for the bond
The Pi Bonds table (Conjugated PI System between two pi atoms, the longer that bond is.
Bonds.TBL) contains parameters used to correct
bond lengths and bond angles for bonds that are part

Record Order Cubic and Quartic Stretch
When sorted for Bond Type, the order of the records Constants
in the Conjugated Pisystem Bonds table is as
Integrating the Hooke's Law equation provides the
follows:
Hooke's Law potential function which describes the
1. Records are sorted by the first atom type potential energy of the ball and spring model. The
number in the Bond Type field. For example, shape of this potential function is the classical
potential well.
the record for bond type 2-2 is listed before the
record for bond type 3-4. dV
– ------- = F = – dx
2. For records where the first atom type number is dx
the same, the records are sorted by the second The Hooke's Law potential function is quadratic,
atom type number in the Bond Type field. For thus the potential well created is symmetrical. The
example, the record for bond type 2-2 is listed real shape of the potential well is asymmetric and is
before the record for bond type 2-3. defined by a complicated function called the Morse
Function, but the Hooke's Law potential function
works well for most molecules.
Electronegativity
Adjustments x x 1 2
The parameters contained in the Electronegativity
V(x)=
°∫0 dV = k°∫0 xdx = --- kx
2
Adjustments table (Electronegativity
Adjustments.TBL) are used to adjust the optimal Certain molecules contain long bonds which are not
bond length between two atoms when one of the described well by Hooke's Law. For this reason the
atoms is attached to a third atom which is MM2 force field contains a cubic stretch term. The
electronegative. cubic stretch term allows for an asymmetric shape of
the potential well, thereby allowing these long
For example, the carbon-carbon single bond length bonds to be handled. However, the cubic stretch
in ethane is different than that in ethanol. The MM2 term is not sufficient to handle abnormally long
parameter set has only a single parameter for bonds. Thus the MM2 force field contains a quartic
carbon-carbon single bond lengths (1.523Å). The stretch term to correct for problems caused by these
use of electronegativity correction parameters abnormally long bonds.
allows the C-C bond in ethanol to be corrected. The
electronegativity parameter used in the Type 2 (-CHR-) Bending Force
Electronegativity Corrections table is the 1-1-6
angle type, where atom type 1 is a C Alkane and Parameters for C-C-C Angles
atom type 6 is an O Alcohol. The value of this -CHR- Bending K for 1-1-1 angles -CHR- Bending
parameter is -0.009Å. Thus the C-C bond length in K for 1-1-1 angles in 4-membered rings -CHR-
ethanol is 0.009Å shorter than the standard C-C Bending K for 22-22-22 angles in 3-membered rings
bond length.
These constants are distinct from the force constants
specified in the Angle Bending table. The bending
MM2 Constants force constant (K) for the 1-1-1 angle (1 is the atom
The MM2 Constants table (MM2 Constants.TBL) type number for the C Alkane atom type) listed in
contains parameters which Chem3D uses to the MM2 Angle Bending parameters table is for an
compute the MM2 force field. alkane carbon with two non-hydrogen groups

attached. Angle bending parameters for carbons Chem3D uses the sextic bending constant to
with one or two attached hydrogens differ from increase the energy of angles with large
those for carbons with no attached hydrogens. deformations from their ideal value.
Because carbons with one or two attached
Dielectric Constants
Administrator
hydrogens frequently occur, separate force constants

are used for these bond angles.
Dielectric constant for charges Dielectric constant
The -CHR- Bending K for 1-1-1 angles allows more for dipoles
accurate force constants to be specified for the Type
The dielectric constants perform as inverse
1 (-CH2-) and Type 2 (-CHR-) interactions. In
proportionality constants in the electrostatic energy
addition, the -CHR- Bending K for 1-1-1 angles in
terms. The constants for the charge and dipole terms
4-membered rings and the -CHR- Bending K for 22-
are supplied separately so that either can be partially
22-22 angles (22 is the atom type number for the C
or completely suppressed.
Cyclopropane atom type) in 3-membered rings
differ from the aforementioned -CHR- Bending K The charge-dipole interaction uses the geometric
for 1-1-1 angles and thus require separate constants mean of the charge and dipole dielectric constants.
to be accurately specified. For example, when you increase the Dielectric
constant for dipoles, a decrease in the Dipole/Dipole
Stretch-Bend Parameters energy occurs. This has the effect of reducing the
X-B,C,N,O-Y Stretch-Bend interaction force contribution of dipole-dipole interactions to the total
constant X-B,C,N,O-H Stretch-Bend interaction steric energy of a molecule.
force constant X-Al,S-Y Stretch-Bend force
constant X-Al,S-H Stretch-Bend force constant X- Electrostatic and van der Waals
Si,P-Y Stretch-Bend force constant X-Si,P-H Cutoff Parameters
Stretch-Bend force constant X-Ga,Ge,As,Se-Y
Cutoff distance for charge/charge interactions
Stretch-Bend force constant
Cutoff distance for charge/dipole interactions Cutoff
The stretch-bend parameters are force constants for distance for dipole/dipole interactions Cutoff
the stretch-bend interaction terms in the prior list of distance for van der Waals interactions
elements. X and Y represent any non-hydrogen
atom. These parameters define the minimum distance at
which the fifth-order polynomial switching function
When an angle is compressed, the MM2 force field is used for the computation of the listed interactions.
uses the stretch-bend force constants to lengthen the
bonds from the central atom in the angle to the other
two atoms in the angle.
MM2 Atom Types
The MM2 Atom Types table (MM2 Atom
For example, the normal C-C-C bond angle in
Types.TBL) contains the van der Waals parameters
cyclobutane is 88.0°, as compared to a C-C-C bond
used to compute the force field for each atom in your
angle of 110.8° in cyclohexane. The stretch-bend
model.
force constants are used to lengthen the C-C bonds
in cyclobutane to 1.550Å, from a C-C bond length of Each MM2 Atom Type record contains eight fields:
1.536Å in cyclohexane. Atom type number, R*, Eps, Reduct, Atomic
Weight, Lone Pairs, Quality, and Reference.
Sextic Bending Constant
Sextic bending constant (* 10**8)

Atom type number Any atom in a van der Waals potential function must
possess a spherical electron cloud centered about its
The Atom Type number field is the atom type to nucleus. For most larger atoms this is a reasonable
which the rest of the MM2 Atom Type Parameter assumption, but for smaller atoms such as hydrogen
record applies. The records in the MM2 Atom Type it is not a good assumption. Molecular mechanics
table window are sorted in ascending order of Atom calculations based on spherical electron clouds
Type Atom type number. centered about hydrogen nuclei do not give accurate
results.
R*
However, it is a reasonable compromise to assume
The R* field is the van der Waals radius of the that the electron cloud about hydrogen is still
particular atom. The larger the van der Waals radius spherical, but that it is no longer centered on the
of an atom is, the larger that atom. hydrogen nucleus. The Reduct constant is multiplied
by the normal bond length to give a new bond length
NOTE: Chem3D uses the van der Waals radius, which represents the center of the repositioned
R*, in the MM2 Atom Types table for computation. It electron cloud.
is not the same as the van der Waals radius in the The value of the Reduct field for all non-hydrogen
Atom Types table, which is used for displaying the atoms is zero.
model.
Atomic Weight
Eps The fifth field, Atomic Weight, is the atomic weight
of atoms represented by this atom type number.
The Eps or Epsilon field is a constant which is
proportional to the depth of the potential well. As
the value of epsilon increases, the depth of the NOTE: The atomic weight is for the isotopically
potential well increases, as does the strength of the pure element, i.e. the atomic weight for atom type
repulsive and attractive interactions between this number 1 is 12.000, the atomic weight of 12C.
atom and other atoms.
Lone Pairs
NOTE: For specific VDW interactions, the R* and
Eps values from the VDW Interactions table are The Lone Pairs field contains the number of lone
used instead of values in the MM2 Atom Types table. pairs around a particular atom type. Notice that an
See “VDW Interactions” later in the chapter for amine nitrogen, atom type number 8, has one lone
more information. pair and an ether oxygen, atom type number 6, has
two lone pairs. Lone pairs are treated explicitly for
atoms such as these, which have distinctly
Reduct non-spherical electron distributions. For atom types
such as O Carbonyl, which have more nearly
Reduct, the fourth field, is a constant used to orient
spherical electron distributions, no explicit lone
the center of the electron cloud on a hydrogen atom
pairs are necessary.
toward the nucleus of the carbon atom to which it is
bonded by approximately 10% of the distance
between the two atoms. NOTE: Lone pairs are added automatically to
atoms which require them at the beginning of an
MM2 computation.

Torsional Parameters V2
The Torsional Parameters table (Torsional The V2, or 180° Periodicity Torsional constant, field
Parameters.TBL) contains parameters used to contains the second of three principal torsional
constants used to compute the total torsional energy
Administrator
compute the portions of the MM2 force field for the

torsional angles in your model. The 4-Membered in a molecule. V2 derives its name from the fact that
Ring Torsional Parameters (4-membered Ring a torsional constant of 180° periodicity can have
Torsionals.TBL) contains torsional parameters for only two torsional energy minima and two torsional
atoms in 4-membered rings. energy maxima within a 360° period.
Each of the records in the Torsional Parameters table A positive value of V2 indicates there are minima at
and the 4-Membered Ring Torsional Parameters 0° and +180°, and there are maxima at -90° and +90°
table consists of six fields: Dihedral Type, V1, V2, in a 360° period. A negative value of V2 causes the
V3, Quality, and Reference. position of the maxima and minima to be switched,
as in the case of V1 above. The significance of V2 is
Dihedral Type explained in the following example.
The Dihedral Type field contains the atom type A good example of the significance of the V1 and
numbers of the four atom types which describe the V2 torsional constants exists in the 1-2-2-1 torsional
dihedral angle. parameter of 2-butene. The values of V1 and V2 in
the Torsional Parameters table are -0.100 and 10.000
For example, angle type 1-2-2-1 is a dihedral angle
formed by an alkane carbon bonded to an alkene respectively.
carbon which is first bonded to a second alkene Because a positive value of V2 indicates that there
carbon which is bonded to another alkane carbon. In are minima at 0° and +180°, these minima signify
other words, angle type 1-2-2-1 is the dihedral angle cis-2-butene and trans-2-butene respectively. Notice
between the two methyl groups of 2-butene. that V2 for torsional parameters involving torsions
The two alkene carbons are the central atoms of the about carbon-carbon double bonds all have values
dihedral angle. ranging from approximately V2=8.000 to
V2=16.250. In addition, V2 torsional parameters
V1 involving torsions about carbon-carbon single
The V1, or 360° Periodicity Torsional constant, field bonds all have values ranging from approximately
contains the first of three principal torsional V2=-2.000 to V2=0.950.
constants used to compute the total torsional energy The values of V2 for torsions about carbon-carbon
in a molecule. V1 derives its name from the fact that double bonds are higher than those values for
a torsional constant of 360° periodicity can have torsions about carbon-carbon single bonds. A
only one torsional energy minimum and one consequence of this difference in V2 values is that
torsional energy maximum within a 360° period. the energy barrier for rotations about double bonds
The period starts at -180° and ends at 180°. is much higher than the barrier for rotations about
single bonds.
A positive value of V1 means that a maximum
occurs at 0° and a minimum occurs at ±180° in a The V1 torsional constant creates a torsional energy
360° period. A negative value of V1 means that a difference between the conformers represented by
minimum occurs at 0° and a maximum occurs at the two torsional energy minima of the V2 constant.
±180° in a 360° period. The significance of V1 is As discussed previously, a negative value of V1
explained in the example following the V2 means that a torsional energy minimum occurs at 0°
discussion. and a torsional energy maximum occurs at 180°. The

value of V1=-0.100 means that cis-2-butene is a 120°, 0°, and +120°, the minima at ±60° signify the
torsional energy minimum that is 0.100 kcal/mole two conformers of n-butane in which the methyl
lower in energy than the torsional energy maximum groups are gauche to one another. The +180°
represented by trans-2-butene. minimum represents the conformer in which the
The counterintuitive fact that the V1 field is methyl groups are anti to one another. The
negative can be understood by remembering that maximum at 0° represents the conformation in
only the total energy can be compared to which the methyl groups are eclipsed. The maxima
experimental results. In fact, the total energy of at ±120° conform n-butane in which a methyl group
trans-2-butene is computed to be 1.423 kcal/mole and a hydrogen are eclipsed.
lower than the total energy of cis-2-butene. This The V1 and V2 torsional constants in this example
corresponds closely with experimental results. The affect the torsional energy in a similar way to the V1
negative V1 term has been introduced to torsional constant for torsions about a carbon-
compensate for an overestimation of the energy carbon double bond (see previous example).
difference based solely on van der Waals repulsion
between the methyl groups and hydrogens on NOTE: The results of MM2 calculations on
opposite ends of the double bond. This example hydrocarbons do not correspond well with the
illustrates an important lesson: experimental data on hydrocarbons when only the
There is not necessarily any correspondence V3 torsional constant is used (when V1 and V2 are
between the value of a particular parameter used in set to zero). However, including small values for the
MM2 calculations and value of a particular physical V1 and V2 torsional constants in the MM2
property of a molecule. calculations for hydrocarbons dramatically improve
the correspondence of the MM2 results with
V3 experimental results. This use of V1 and V2 provides
little correspondence to any particular physical
The V3, or 120° Periodicity Torsional constant, field property of hydrocarbons.
contains the third of three principal torsional
constants used to compute the total torsional energy
in a molecule. V3 derives its name from the fact that Record Order
a torsional constant of 120° periodicity can have
three torsional energy minima and three torsional When sorted by Dihedral Angle, the order of the
energy maxima within a 360° period. A positive records in the Torsional Parameters table and the
value of V3 indicates there are minima at -60°, +60° 4-Membered Ring Torsional Parameters table is as
and +180° and there are maxima at -120°, 0°, and follows:
+120° in a 360° period. A negative value of V3
1. Records are sorted by the second atom type
causes the position of the maxima and minima to be
reversed, as in the case of V1 and V2 above. The number in the Dihedral Type field. For
significance of V3 is explained in the following example, the record for dihedral type 1-1-1-1 is
example. listed before the record for dihedral
type 1-2-1-1.
The 1-1-1-1 torsional parameter of n-butane is an
example of the V3 torsional constant. The values of 2. For records where the second atom type number
V1, V2 and V3 in the Torsional Parameters table are is the same, the records are sorted by the third
0.200, 0.270 and 0.093 respectively. Because a
atom type number in the Dihedral Type field.
positive value of V3 indicates that there are minima
at -60°, +60° and +180° and there are maxima at -

For example, the record for dihedral planar. The larger the value of Force Constant for a
type 1-1-1-1 is listed before the record for particular atom, the more difficult it is to coerce that
dihedral type 1-1-2-1. atom to be non-planar.
Record Order
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3. For multiple records where the second and third

atom type numbers are the same, the records are
sorted by the first atom type number in the When sorted by Bond Type, the order of the records
Dihedral Type field. For example, the record for in the Out-of-Plane Bending Parameters table is as
dihedral type 5-1-3-1 is listed before the record follows:
for dihedral type 6-1-3-1. 1. Records are sorted by the first atom type
number in the Bond Type field. For example,
4. For multiple records where the first, second and
the record for bond type 2-1 is before the record
third atom type numbers are the same, the
for bond type 3-1.
records are sorted by the fourth atom type
number in the Dihedral Type field. For 2. For records where the first atom type number is
example, the record for dihedral type 5-1-3-1 is the same, the records are sorted by the second
listed before the record for dihedral atom type number in the Bond Type field. For
type 5-1-3-2. example, the record for bond type 2-1 is before
the record for bond type 2-2.
Out-of-Plane Bending
The Out-of-Plane Bending table (Out-of-Plane NOTE: Out-of-plane bending parameters are not
Bending Parameters.TBL) contains parameters symmetrical. For example, the force constant for a
which are used to ensure that atoms with trigonal 2-3 bond refers to the plane about the type 2 atom.
planar geometry remain planar in MM2 The force constant for a 3-2 bond refers to the plane
calculations. about the type 3 atom.
There are four fields in records in the Out-of-Plane
Bending Parameters table: Bond Type, Force
Constant, Quality and Reference.
VDW Interactions
The parameters contained in the VDW parameters
Bond Type table (VDW Interaction.TBL) are used to adjust
specific VDW interactions in a molecule, such as
The first field is the Bond Type which is described hydrogen bonding, to provide better correspondence
by the atom type numbers of the two bonded atoms. with experimental data in calculating the MM2 force
For example, Bond Type 2-3 is a bond between an field.
alkene carbon and a carbonyl carbon. For example, consider the VDW interaction
between an Alkane carbon (Atom Type 1) and a
Force Constant hydrogen (Atom Type 5). Normally, the VDW
The Force Constant field, or the out-of-plane energy is based on the sum of the VDW radii for
bending constant , field contains a measure of the these atoms, found for each atom in the Atom Types
amount of energy required to cause a trigonal planar table (1.900Å for Atom type number 1 + 1.400Å for
atom to bend out-of-plane, i.e., to become non- Atom type number 2 = 3.400Å). However, better
correspondence between the computed VDW
energy and experimental data is found by

substituting this sum with the value found in the
VDW Interactions table for this specific atom type
pair (Atom Types 1-5 = 3.340Å). Similarly, an Eps
parameter is substituted for the geometric mean of
the Eps parameters for a pair of atoms if their atom
types appear in the VDW Interactions table.
Record Order
When sorted by Atom Type, the order of the records
in VDW Interactions table window is as follows:
Records are sorted by the first atom type number in
the Atom Type field. For example, the record for
Atom Type 1-36 is before the record for atom type
2-21.
For records where the first atom type number is the
same, the records are sorted by the second atom type
number in the Atom Type field. For example, the
record for atom type 2-21 is before the record for
atom type 2-23.

Administrator

Appendix I: File Formats
Editing File Format Name
Atom Types Each atom type is described by a name. This name
is a number found in files of the format described
Some file formats contain information describing by the file format. All names must be unique. The
the atom types that the file format understands. records in the table window are sorted by name.
Typically, these atom types are ordered by some set
NOTE: While names are similar to atom type
of numbers, similar to the atom type numbers used
numbers, they do not have to correspond to the atom
in the Atom Types table. If the file format needs to
type numbers of atom types. In some cases, however,
support additional types of atoms, you can supply
they do correspond.
those types by using editing the file format atom
types using the CS Table Editor.
The atom types appear in table windows that you Description
can edit using the CS Table Editor.
The second field contains a description of the atom
To open atom types table associated with a file type, such as C Alkane. This description is included
format: for your reference only.
The remaining fields (Symbol, Charge, Maximum
1. From Explorer, open C3DFILTR.
Ring Size, Rectification type, Geometry, Number of
2. Double-click the table to open. Double Bonds, Number of Triple Bonds, Number
of Delocalized Bonds, Bound to Order and Bound
The file format appears in a table. The to Type) contain information corresponding to the
information in a file format is similar to that information in an Atom Types table.
found in an atom type table with the addition of
a Name field and a Description field. NOTE: When setting the rectification type and the
bound to type of an atom type, the dialog box that
3. Edit the cells in the table window. appears when you click the cell contains a list of
codes rather than a list of descriptions.
The Atom Type records for the file format is
saved with your changes.
Chem3D • 253
File Format Examples 27 7 2 10 SINGLE
28 8 3 4 SINGLE
The following sections provide examples of the
29 9 3 11 SINGLE
files created when you save Chem3D files using the
30 10 3 12 SINGLE
Administrator
provided file formats.

31 11 4 5 SINGLE
Alchemy File 32 12 4 13 SINGLE
33 13 4 14 SINGLE
The following is a sample Alchemy file1 (Alchemy)
34 14 5 6 SINGLE
created using Chem3D for a model of
cyclohexanol. The numbers in the first column are 35 15 5 15 SINGLE
line numbers that are added for reference only. 36 16 5 16 SINGLE
1 19 19 37 17 6 17 SINGLE
ATOMS BONDS 38 18 6 18 SINGLE
2 1 C3 -1.1236 -0.177 0.059 40 19 7 19 SINGLE
3 2 C3 -0.26 -0.856 -1.0224
Each line represents a data record containing one or
4 3 C3 1.01 -0.0491 -1.3267 more fields of information about the molecule.
5 4 C3 1.838 0.1626 -0.0526 Each field is delimited by spaces or a tab. The fields
6 5 C3 0.9934 0.8543 1.0252 used by Chem3D are described below:
7 6 C3 -0.2815 0.0527 1.3275
1. Line 1 contains two fields. The first field is the
8 7 O3 -2.1621 -1.0585 0.3907 total number of atoms in the molecule and the
9 8H -1.4448 0.8185 -0.3338 second field is the total number of bonds.
10 9H -0.8497 -0.979 -1.9623
11 10 H 0.0275 -1.8784 -0.6806 2. Lines 2–20 each contain 5 fields of information
12 11 H 1.6239 -0.5794 -2.0941 about each of the atom in the molecule. The first
field is the serial number of the atom. The
13 12 H 0.729 0.9408 -1.7589
second field is the atom type, the third field is
14 13 H 2.197 -0.8229 0.3289
the X coordinate, the fourth field is the
15 14 H 2.7422 0.7763 -0.282
Y coordinate and the fifth field is the
16 15 H 1.5961 0.9769 1.9574 Z coordinate.
17 16 H 0.7156 1.8784 0.679
18 17 H -0.8718 0.6068 2.0941 NOTE: Atom types in the Alchemy file format
19 18 H -0.004 -0.9319 1.7721 are user-definable. See “Editing File Format
20 19 H -2.7422 -0.593 0.9688 Atom Types” on page 253 for instructions on
21 1 1 2 SINGLE modifying or creating an atom type.
22 2 1 6 SINGLE
23 3 1 7 SINGLE 3. Lines 21–40 each contain 4 fields describing
24 4 1 8 SINGLE information about each of the bonds in the
molecule. The first field is the bond number
25 5 2 3 SINGLE
(ranging from 1 to the number of bonds), the
26 6 2 9 SINGLE
second field is the serial number of the atom
1. Alchemy III is a registered trademark of Tripos
where the bond begins, the third field is the
Associates, Inc.
254 • Chem3D
serial number of the atom where the bond ends, Atom Types in Cartesian Coordinate
and the fourth field is the bond type. The Files
possible bond types are: SINGLE, DOUBLE,
Two file formats are supplied with Chem3D that
TRIPLE, AMIDE, or AROMATIC. Note that
interpret Cartesian coordinate files. The difference
all the bond order names are padded on the right
between the two file formats are the codes used to
with spaces to eight characters. convert atom type numbers in the file into atom
types used by Chem3D.
FORTRAN Formats
In Cartesian coordinates 1, atom types are
The FORTRAN format for each record of the numbered according to the numbering used by N.L.
Alchemy file is as follows: Allinger in MM2. These numbers are also generally
followed by the program PC Model.
Line FORTRAN
In Cartesian coordinates 2, the atom type number
Number Description Format
for all atom types is computed by multiplying the
atomic number of the element by 10 and adding the
1 number of atoms, I5, 1X,
number of valences as specified by the geometry of
number of bonds ATOMS,1X,I5,1
the atom type. These numbers are also generally
X, BONDS
followed by the program MacroModel.
2–20 atom serial number, I6,A4,3(F9.4) For example, the atom type number for C Alkane (a
type, and tetrahedral carbon atom) is 64.
coordinates
To examine the atom types described by a file
format, see “Editing File Format Atom Types” on
21–40 bond id, from atom, I6,I5,I6,2X,A8
page 253.
to atom, bond type
The Cartesian Coordinate File Format
Cartesian Coordinate Files
The format for Cartesian coordinate files is as
The Cartesian coordinate file format (Cart Coords, follows:
Cart Coords 2) interprets text files that specify
1. The first line of data contains the number of
models in terms of the X, Y, and Z coordinates of
the atoms. This file format can also interpret atoms in the model.
fractional cell coordinates in orthogonal or non- Optionally, you can follow the number of atoms
orthogonal coordinate systems. in the file with crystal cell parameters for the
crystal structure: a, b, c, α, β, and γ. Following
the cell parameters, you can also include an
exponent. If you include an exponent, then all
of the fractional cell coordinates will be divided
by 10 raised to the power of the exponent.
2. The first line of a Cartesian coordinate file is

followed by one line of data for each atom in the
model. Each line describing an atom begins
with the symbol for the atom. This symbol must
Chem3D • 255
correspond to a symbol in the Elements table. Connection tables by serial number use the
The symbol can include a charge, such as N+. serial number of each atom to determine the
The symbol is followed by the serial number. number that appears in the connection table of
other atoms. All serial numbers must, therefore,
Administrator
3. The serial number is followed by the three

be unique.
coordinates of the atom. If you have specified
crystal cell parameters in the first line of the Connection tables by position use the relative
file, then these numbers are the fractional cell positions of the atoms in the file to determine
coordinates. Otherwise, the three numbers are the number for each atom that will appear in the
X, Y, and Z Cartesian coordinates. connection table of other atoms. The first atom
is number 1, the second is 2, etc.
4. Following the coordinates is the atom type
number of the atom type for this atom. This 6. To create multiple views of the same set of
number must correspond to the code of an atom atoms, you can flow the descriptions of the
type record specified in the file format atom atoms with an equal number of lines
type table. For more information, see “Editing corresponding to the same atoms with different
File Format Atom Types” on page 253. coordinates. Chem3D generates independent
views using the additional sets of coordinates.
5. Following the atom type number is the
Samples of Cartesian coordinate files with
connection table for the atom. You can specify
connection tables by position and serial number for
up to ten other atoms. The connection table for a model of cyclohexanol are shown below. To
a Cartesian coordinate file can be listed in one clearly illustrate the difference between the two
of two ways: by serial number or by position. formats, the serial number of the oxygen has been
19
C 1 0.706696 1.066193 0.50882 1 2 4 7 8
C 2 -0.834732 1.075577 0.508789 1 1 3 9 10
C 3 -1.409012 0.275513 -0.668915 1 2 6 11 12
C 4 1.217285 -0.38632 0.508865 1 1 5 13 14
C 5 0.639328 -1.19154 -0.664444 1 4 6 15 16
C 6 -0.89444 -1.1698 -0.646652 1 3 5 17 18
O 101 1.192993 1.809631 1.59346 6 1 19
H 9 1.052597 1.559525 -0.432266 5 1
H 10 -1.211624 2.125046 0.457016 5 2
H 11 -1.208969 0.640518 1.465607 5 2
256 • Chem3D
H 12 -2.524918 0.2816 -0.625809 5 3
H 13 -1.11557 0.762314 -1.629425 5 3
H 14 0.937027 -0.8781 1.470062 5 4
H 15 2.329758 -0.41023 0.437714 5 4
H 16 1.003448 -2.24631 -0.618286 5 5
H 17 1.005798 -0.76137 -1.627 5 5
H 18 -1.295059 -1.73161 -1.524567 5 6
H 19 -1.265137 -1.68524 0.271255 5 6
H 102 2.127594 1.865631 1.48999 21 7
Chem3D • 257
Following is an example of a Cartesian Coordinate
file with Connection table by Position for
Cyclohexanol.
Administrator
lement X, Y and Z Positions of Other Atoms

Symbol Coordinates to which C(1) is Bonded
C 1 0.706696 1.066193 0.508820 1 2 4 7 8
Serial Atom Type

Number Text Number
An example of a Cartesian Coordinate File with

Connection Table by Serial Number for
Cyclohexanol follows.
19
C 1 0.706696 1.066193 0.50882 1 2 4 9 10
C 2 -0.834732 1.075577 0.508789 1 1 3 10 11
C 3 -1.409012 0.275513 -0.668915 1 2 6 12 13
C 4 1.217285 -0.38632 0.508865 1 1 5 14 15
C 5 0.639328 -1.19154 -0.664444 1 4 6 16 17
C 6 -0.89444 -1.1698 -0.646652 1 3 5 18 19
O 101 1.192993 1.809631 1.59346 6 1 102
H 9 1.052597 1.559525 -0.432266 5 1
H 10 -1.211624 2.125046 0.457016 5 3
H 11 -1.208969 0.640518 1.465607 5 3
H 12 -2.524918 0.2816 -0.625809 5 4
H 13 -1.11557 0.762314 -1.629425 5 4
H 14 0.937027 -0.8781 1.470062 5 5
H 15 2.329758 -0.41023 0.437714 5 5
H 16 1.003448 -2.24631 -0.618286 5 6
H 17 1.005798 -0.76137 -1.627 5 6
H 18 -1.295059 -1.73161 -1.524567 5 7
H 19 -1.265137 -1.68524 0.271255 5 7
H 102 2.127594 1.865631 1.48999 21 10
1
258 • Chem3D
Components of a Cartesian coordinate File with Cartesian coordinate File (Connection Table by
Connection Table by Serial Number for C(1) of Serial Number or Position):
Cyclohexanol is shown below.
Line FORTRAN
lement X, Y and Z Serial Numbers of Other Atoms Number Description Format
Symbol Coordinates to which C(1) is Bonded
1 Number of I3
C 1 0.706696 1.066193 0.508820 1 2 4 9 101
Atoms
Serial Atom Type
Number Text Number 2 to End Atom coordinates A3, 1X, I4, 3(1X,
F11.6), 1X, I4,
10(1X, I4)
Components of a Cartesian coordinate File with
Crystal coordinate Parameters for C(1) is shown Cartesian coordinate File (Fractional Crystal Cell
below. Parameters):
Number
of Atoms a b c α β γ Exponent
Line FORTRAN
43 10.23 12.56 8.12 90.0 120.0 90.0 4
C 1 1578 -2341 5643 1 20 21 22

1 Number of I3, 6(1X, F), I
Atoms, Crystal
Fractional Cell
Coordinates Cell Parameters
2 to End Atom coordinates A3, 1X, I4, 3(1X,

FORTRAN Formats
F11.6), 1X, I4,
The FORTRAN format for the records in a 10(1X,I4)
Cartesian coordinate file with a connection table by
serial number or position and a Cartesian
coordinate file with fractional crystal cell
Cambridge Crystal Data Bank
parameters are listed in the following tables: Files
The specific format of Cambridge Crystal Data
Bank files (CCDB) used by Chem3D is the FDAT
format, described on pages 26–42 of the data file
specifications of the Cambridge Structural
Database, Version 1 File Specifications from the
Cambridge Crystallographic Data Centre. For
further details about the FDAT format, please refer
to the above publication or contact the Cambridge
Crystallographic Data Centre.
As described in the specifications of the Cambridge
Crystal Data Bank format, bonds are automatically
added between pairs of atoms whose distance is less
Chem3D • 259
than that of the sum of the covalent radii of the two 4. Beginning with line 4, the distance is followed
atoms. The bond orders are guessed based on the by the serial number of the first angle-defining
ratio of the actual distance to the sum of the atom and the angle between the newly defined
covalent radii. The bond orders, bond angles, and atom, the distance-defining atom, and the first
Administrator
the atom symbols are used to determine the atom angle-defining atom. All angles are measured in
types of the atoms in the model.
degrees.
Actual Distance / Sum of 5. Beginning with line 5, the serial number of a
Bond Type Covalent Radii second angle-defining atom and a second
defining angle follows the first angle. Finally, a
Triple 0.81
number is given that indicates the type of the
second angle. If the second angle type is zero,
Double 0.87
the second angle is a dihedral angle: New Atom
Delocalized 0.93 – Distance-defining Atom – First Angle-
defining Atom – Second Angle-defining Atom.
Single 1.00 Otherwise the third angle is a bond angle: New
Atom – Distance-defining Atom – Second
Internal Coordinates File Angle-defining Atom. If the second angle type
is 1, then the new atom is defined using a Pro-
Internal coordinates files (INT Coords) are text files R/Pro-S relationship to the three defining
that describe a single molecule by the internal atoms; if the second angle type is -1, the
coordinates used to position each atom. The serial relationship is Pro-S.
numbers are determined by the order of the atoms
in the file. The first atom has a serial number of 1, NOTE: You cannot position an atom in terms
the second is number 2, etc. of a later-positioned atom.
The format for Internal coordinates files is as
follows:
1. Line 1 is a comment line ignored by Chem3D.

Each subsequent line begins with the atom type
number of an atom type.
2. Line 2 contains the atom type number of the

Origin atom.
3. Beginning with line 3, the atom type number is

followed by the serial number of the atom to
which the new atom is bonded and the distance
to that atom. In an Internal coordinates file, the
origin atom is always the first distance-defining
atom in the file. All distances are measured in
Angstroms.
260 • Chem3D
The following is a sample of an Internal coordinates
output file for cyclohexanol which was created
from within Chem3D:
1 1 1.54146
1 2 1.53525 1 111.7729
1 1 1.53967 2 109.7132 3 -55.6959 0
1 4 1.53592 1 111.703 2 55.3112 0
1 3 1.53415 2 110.7535 1 57.0318 0
6 1 1.40195 2 107.6989 3 -172.6532 0
5 1 1.11742 2 109.39 4 109.39 -1
5 2 1.11629 1 109.41 3 109.41 1
5 2 1.11568 1 109.41 3 109.41 -1
5 3 1.11664 2 109.41 6 109.41 -1
5 3 1.11606 2 109.41 6 109.41 1
5 4 1.11542 1 109.41 5 109.41 1
5 4 1.11493 1 109.41 5 109.41 -1
5 5 1.11664 4 109.41 6 109.41 1
5 5 1.11617 4 109.41 6 109.41 -1
5 6 1.11664 3 109.41 5 109.41 1
5 6 1.11606 3 109.41 5 109.41 -1
21 7 0.942 1 106.8998 2 59.999 0
5 6
Chem3D • 261
Bonds connected to C(2) with a bond of length 1.53525 Å,
and at a bond angle of 111.7729 degrees with C(1),
Bonds are indicated in Internal coordinates files in defined by C(3)-C(2)-C(1). C(4) is attached to C(1)
two ways. with a bond of length 1.53967 Å, and at a bond
Administrator
First, a bond is automatically created between each angle of 109.7132 degrees with C(2), defined by
atom (except the Origin atom) and its distance- C(4)-C(1)-C(2). C(4) also forms a dihedral angle of
defining atom. -55.6959 degrees with C(3), defined by C(4)-C(1)-
C(2)-C(3).
Second, if there are any rings in the model, ring-
closing bonds are listed at the end of the file. If This portion of the Internal coordinates file for C(1)
there are ring-closing bonds in the model, a blank through C(4) of Cyclohexanol can be represented
line is included after the last atom definition. For by the following structural diagram:
each ring-closure, the serial numbers of the two
atoms which comprise the ring-closing bond are 1.540 Å 4
listed on one line. The serial number of the first
atom is 1, the second is 2, etc. In the prior Internal 1
coordinates output example of cyclohexanol, the 109.713°
numbers 5 and 6 are on a line at the end of the file, 1.541 Å -55.698° Dihedral Angle
and therefore the ring closure is between the fifth 111.771°
atom and the sixth atom. 2
If a bond listed at the end of an Internal coordinates

format file already exists (because one of the atoms 1.535 Å 3
on the bond is used to position the other atom on the
bond) the bond is removed from the model. This is
useful if you want to describe multiple fragments in
FORTRAN Formats
an internal coordinates file.
The FORTRAN formats for the records in an
Atom Type Internal coordinates file are as follows:
Text Numbers
Bond
Lengths
FORTRAN
Origin Atom 1 First
Angles Line Number Description Format
Second Atom 1 1 1.54146 Second
Angles
Comment Ignored by
Chem3D
Third Atom 1 2 1.53525 1 111.7729
Origin Atom I4
Fourth Atom 1 1 1.53967 2 109.7132 3 -55.6959 0
Second Atom I4, 1X, I3,
Distance-defining First Angle- Second Angle- Indicates
1X, F9.5
Atoms defining Atoms defining Atoms Dihedral
Third Atom I4, 2(1X, I3,
1X, F9.5)
Components of an Internal coordinates File for C(1)
Fourth Atom to I4, 3(1X, I3,
through C(4) of Cyclohexanol
Last Atom 1X, F9.5), I4
In this illustration, the origin atom is C(1). C(2) is Blank Line
connected to C(1), the origin and distance defining
Ring Closure 2(1X, I4)
atom, by a bond of length 1.54146 Å. C(3) is
Atoms
262 • Chem3D
MacroModel “MacroModel Structure Files” version 2.0
documentation. The following is a sample
MacroModel is produced within the Department of MacroModel file created using Chem3D. The
Chemistry at Columbia University, New York, N.Y. following file describes a model of cyclohexanol.
The MacroModel file format is defined in the
19 cyclohexanol
3 2 1 6 1 7 1 18 1 0 0 0 0 -1.396561 0.350174 1.055603 0
3 1 1 3 1 8 1 9 1 0 0 0 0 -0.455032 -0.740891 1.587143 0
3 2 1 4 1 10 1 11 1 0 0 0 0 0.514313 -1.222107 0.49733 0
3 3 1 5 1 12 1 13 1 0 0 0 0 1.302856 -0.04895 -0.103714 0
3 4 1 6 1 14 1 15 1 0 0 0 0 0.372467 1.056656 -0.627853 0
3 1 1 5 1 16 1 17 1 0 0 0 0 -0.606857 1.525177 0.4599 0
41 1 1 0 0 0 0 0 0 0 0 0 0 -2.068466 -0.083405 0.277008 0
41 2 1 0 0 0 0 0 0 0 0 0 0 -1.053284 -1.603394 1.96843 0
41 2 1 0 0 0 0 0 0 0 0 0 0 0.127151 -0.3405 2.451294 0
41 3 1 0 0 0 0 0 0 0 0 0 0 1.222366 -1.972153 0.925369 0
41 3 1 0 0 0 0 0 0 0 0 0 0 -0.058121 -1.742569 -0.306931 0
41 4 1 0 0 0 0 0 0 0 0 0 0 1.972885 0.38063 0.679077 0
41 4 1 0 0 0 0 0 0 0 0 0 0 1.960663 -0.413223 -0.928909 0
41 5 1 0 0 0 0 0 0 0 0 0 0 0.981857 1.921463 -0.992111 0
41 6 1 0 0 0 0 0 0 0 0 0 0 -1.309372 2.283279 0.037933 0
41 6 1 0 0 0 0 0 0 0 0 0 0 -0.033539 2.031708 1.272888 0
41 1 1 0 0 0 0 0 0 0 0 0 0 -2.052933 0.717285 1.881104 0
42 15 1 0 0 0 0 0 0 0 0 0 0 0.275696 0.374954 -2.411163 0
Each line represents a data record containing one or pairs of numbers describing the bonds that this
more fields of information about the model. Each atom makes to other atoms. The first number of
field is delimited by space(s) or a tab. each pair is the serial number of the other atom,
and the second number is the bond type. The
The fields in the MacroModel format file used by
Chem3D are: fourteenth field is the X coordinate, the
1. Line 1 contains 2 fields: the first field is the

number of atoms and the second field is the
name of the molecule. The molecule name is
the file name when the file is created using
Chem3DChem3D.
2. Lines 2-19 each contain 17 fields describing

information about one atom and its attached
bond. The first field contains the atom type. The
second through thirteenth fields represent 6
Chem3D • 263
fifteenth field is the Y coordinate, the sixteenth FORTRAN Formats
field is the Z coordinate and finally, and the
The FORTRAN format for each record of the
seventeenth field is the color of the atom.
MacroModel format is as follows:
Administrator
NOTE: Atom colors are ignored by Chem3D. This

field will contain a zero if the file was created using Line FORTRAN
Chem3D. Number Description Format
1 number of atoms 1X,I5,2X,A

NOTE: Atom types are user-definable. See and molecule
“Editing File Format Atom Types” on page 253 for name (file name
instructions on modifying or creating an atom type.
MDL MolFile
For example, the following illustrates the atom and
bond components for C6 and bond 3 of The MDL MolFile1 format is defined in the article
cyclohexanol: “Description of Several Chemical Structure File
Formats Used by Computer Programs Developed at
Each pair of numbers represents an Molecular Design Limited” found in the Journal of
atom to which this atom is bonded Atom Color
Chemical Information and Computer Science,
3 1 1 5 1 16 1 17 1 0 0 0 0 -0.606857 1.525177 0.459900 0 Volume 32, Number 3, 1992, pages 244–255. The
following is a sample MDL MolFile file created
Atom Type Serial Number Bond Type X Y Z using Chem3D Pro. This file describes a model of
Coordinates
cyclohexanol (the line numbers are added for
reference only):
1. MDL MACCS-II is a product of MDL
Information Systems, Inc. (previously called
Molecular Design, Limited).
1 cyclohexanol
2
3
4 19 19 0 0 0
5 -1.3488 0.1946 1.0316 C 0 0 0 0 0
6 -0.4072 -0.8965 1.5632 C 0 0 0 0 0
7 0.5621 -1.3777 0.4733 C 0 0 0 0 0
8 1.3507 -0.2045 -0.1277 C 0 0 0 0 0
9 0.4203 0.9011 -0.6518 C 0 0 0 0 0
10 -0.559 1.3696 0.4359 C 0 0 0 0 0
11 -0.3007 0.4266 -1.7567 O 0 0 0 0 0
12 -2.0207 -0.239 0.253 H 0 0 0 0 0
13 -2.0051 0.5617 1.8571 H 0 0 0 0 0
264 • Chem3D
14 -1.0054 -1.7589 1.9444 H 0 0 0 0 0
15 0.1749 -0.4961 2.4273 H 0 0 0 0 0
16 1.27 -2.1277 0.9014 H 0 0 0 0 0
17 -0.0103 -1.8981 -0.3309 H 0 0 0 0 0
18 2.0207 0.225 0.6551 H 0 0 0 0 0
19 2.0084 -0.5688 -0.9529 H 0 0 0 0 0
20 1.0296 7659 -1.0161 H 0 0 0 0 0
21 -1.2615 2.1277 0.0139 H 0 0 0 0 0
22 0.0143 1.8761 1.2488 H 0 0 0 0 0
23 0.3286 0.2227 -2.4273 H 0 0 0 0 0
24 1 2 1 0 0 0
25 1 6 1 0 0 0
26 1 8 1 6 0 0
27 1 9 1 1 0 0
28 2 3 1 6 0 0
29 2 10 1 0 0 0
30 2 11 1 1 0 0
31 3 4 1 0 0 0
32 3 12 1 0 0 0
33 3 13 1 6 0 0
34 4 5 1 0 0 0
35 4 14 1 1 0 0
36 4 15 1 6 0 0
37 5 6 1 1 0 0
38 5 7 1 6 0 0
39 5 16 1 0 0 0
40 6 17 1 0 0 0
41 6 18 1 1 0 0
42 7 19 1 6 0 0
Each line represents either a blank line, or a data 2. Line 2 continues the Header block, and is a
record containing one or more fields of information blank line.
about the structure. Each field is delimited by a
space(s) or a tab. 3. Line 3 continues the Header block, and is
another blank line.
The fields in the MDL MolFile format used by
Chem3D Pro are discussed below: 4. Line 4 (the Counts line) contains 5 fields which
1. Line 1 starts the header block, which contains describes the molecule: The first field is the
the name of the molecule. The molecule name number of atoms, the second field is the number
is the file name when the file was created using
Chem3D Pro.
Chem3D • 265
of bonds, the third field is the number of atom Limitations
lists, the fourth field is an unused field and the
The MDL MolFile format does not support
fifth field is the stereochemistry.
non-integral charges in the same way as Chem3D
Pro. For example, in a typical MDL MolFile format
Administrator
NOTE: Chem3D Pro ignores the following fields: file, the two oxygens in a nitro functional group
number of atom lists, the unused field and (NO2) contain different charges: -1 and 0. In
stereochemistry. These fields will always contain a Chem3D models, the oxygen atoms each contain a
zero if the file was created using Chem3D Pro. charge of -0.500.
5. Lines 5–23 (the Atom block) each contain 9 FORTRAN Formats

fields which describes an atom in the molecule: The FORTRAN format for each record of the MDL
The first field is the X coordinate, the second MolFile format is as follows:
field is the Y coordinate, the third field is the Z
coordinate, the fourth field is the atomic Line FORTRAN
symbol, the fifth field is the mass difference, the Number Description Format
sixth field is the charge, the seventh field is the
1 Molecule name A
stereo parity designator, the eighth field is the (file name)
number of hydrogens and the ninth field is the
center. 2 Blank line
3 Blank line
NOTE: Chem3D Pro ignores the following fields:
4 Number of atoms 5I3
mass difference, charge, stereo parity designator,
Number of bonds
number of hydrogens, and center. These fields
contain zeros if the file was created using Chem3D 5–23 Atom coordinates, 3F10.4,1X,A2,5I3
Pro. atomic symbol
24–42 Bond id, from 6(1X,I2)
6. Lines 24–42 (the Bond block) each contain 6 atom, to atom, and
fields which describe a bond in the molecule: bond type
the first field is the from-atom id, the second
field is the to-atom id, the third field is the bond
type, the fourth field is the bond stereo
MSI MolFile
designator, the fifth field is an unused field and The MSI MolFile1 is defined in Chapter 4,
the sixth field is the topology code. “Chem-Note File Format” in the Centrum:
Chem-Note™ Application documentation, pages
NOTE: Chem3D Pro ignores the unused field and 4-1 to 4-5. The following is a sample MSI MolFile
topology code. These fields will contain zeros if the
file was created using Chem3D Pro.
1. Molecular Simulations MOLFILE (ChemNote) is

a product of Molecular Simulations, Inc.
266 • Chem3D
file created using Chem3D Pro for cyclohexanol
(the line numbers are added for purposes of
discussion only):
1 ! Polygen 133
2 Polygen Corporation: ChemNote molecule file (2D)
3 * File format version number
4 90.0928
5 * File update version number
6 92.0114
7 * molecule name
8 cyclohexanol-MSI
9 empirical formula
10 Undefined Empirical Formula
11 * need 3D conversion?
12 0
13 * 3D displacement vector
14 0.000 0.000 0.000
15 * 3D rotation matrix
16 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000
17 * 3D scale factor
18 0
19 * 2D scale factor
20 1
21 * 2D attributes
22 100000000000000
23 * 3D attributes
24 00000000000
25 * Global display attributes
26 1 0 1 12 256
27 * Atom List
28 * Atom# Lbl Type x y x y z bits chrg ichrg frag istp lp chrl ring frad name seg grp FLAGS
29 1 C 10 0 0 -1 0.46 0.2 0 0 0 0 0 0 0 0 0 C 1 0 -1 0 0 0 0 0 0 [C]
30 2 C 10 0 0 1.2 -1.1 0.2 0 0 0 0 0 0 0 0 0 C 2 0 -1 0 0 0 0 0 0 [C]
30 2 C 10 0 0 1.2 -1.1 0.2 0 0 0 0 0 0 0 0 0 C 2 0 -1 0 0 0 0 0 0 [C]
31 3 C 10 0 0 0.1 -1.6 0.7 0 0 0 0 0 0 0 0 0 C 3 0 -1 0 0 0 0 0 0 [C]
32 4 C 10 0 0 1.3 -1.1 0 0 0 0000000C40-1000000[C]
33 5 C 10 0 0 1.2 0.48 0 0 0 0 0 0 0 0 0 0 C 5 0 -1 0 0 0 0 0 0 [C]
34 6 C 10 0 0 0 1.01 -1 0 0 0 0 0 0 0 0 0 C 6 0 -1 0 0 0 0 0 0 [C]
Chem3D • 267
35 7 O 45 0 0 0 2.42 -1 0 0 0 0 0 0 0 0 0 O 7 0 -1 0 0 0 0 0 0 [O]
36 8 H 8 0 0 0.6 2.72 -1 0 0 0 0 0 0 0 0 0 H 7 0 -1 0 0 0 0 0 0 [H]
37 9 H 1 0 0 2.1 0.86 -1 0 0 0 0 0 0 0 0 0 H 8 0 -1 0 0 0 0 0 0 [H]
38 10 H 1 0 0 1.4 0.86 0.8 0 0 0 0 0 0 0 0 0 H 9 0 -1 0 0 0 0 0 0 [H]
Administrator
39 11 H 1 0 0 1.1 -1.4 -1 0 0 0 0 0 0 0 0 0 H 10 0 -1 0 0 00 00[H]

40 12 H 1 0 0 2.2 -1.4 0.2 0 0 0 0 0 0 0 0 0 H 11 0 -1 0 0 0000 [H]
41 13 H 1 0 0 0 0.72 -2 0 0 0 0 0 0 0 0 0 H 12 0 -1 0 0000 0 [H]
42 14 H 1 0 0 0.1 -2.7 0.7 0 0 0 0 0 0 0 0 0 H 13 0 -1 0 0 0000 [H]
43 15 H 1 0 0 0.3 -1.3 1.7 0 0 0 0 0 0 0 0 0 H 14 0 -1 0 0 0 00 [H]
44 16 H 1 0 0 -1 -1.5 -1 0 0 0 0 0 0 0 0 0 H 15 0 -1 0 0 0000 [H]
45 17 H 1 0 0 -2 -1.5 0.9 0 0 0 0 0 0 0 0 0 H 16 0 -1 0 0 0000 [H]
46 18 H 1 0 0 -1 0.85 1.2 0 0 0 0 0 0 0 0 0 H 17 0 -1 0 0 0000 [H]
47 19 H 1 0 0 -2 0.83 0 0 0 0 0 0 0 0 0 0 H 18 0 -1 0 0 0000 [H]
48 * Bond List
49 * Bond# bond_type atom1 atom2 cis/trans length locked ring Sh_type Sh_nr Qorder Qtopol Qs
50 11120 0.000 0 0 0 0 [S] 0 0
51 21160 0.000 0 0 0 0 [S] 0 0
52 3 1 1 18 0 0.000 0 0 0 0 [S] 0 0
53 4 1 1 19 0 0.000 0 0 0 0 [S] 0 0
54 51230 0.000 0 0 0 0 [S] 0 0
55 6 1 2 16 0 0.000 0 0 0 0 [S] 0 0
56 7 1 2 17 0 0.000 0 0 0 0 [S] 0 0
57 81340 0.000 0 0 0 0 [S] 0 0
58 9 1 3 14 0 0.000 0 0 0 0 [S] 0 0
59 10 1 3 15 0 0.000 0 0 0 0 [S] 0 0
60 11 1 4 5 0 0.000 0 0 0 0 [S] 0 0
61 12 1 4 11 0 0.000 0 0 0 0 [S] 0 0
62 13 1 4 12 0 0.000 0 0 0 0 [S] 0 0
63 14 1 5 6 0 0.000 0 0 0 0 [S] 0 0
64 15 1 5 9 0 0.000 0 0 0 0 [S] 0 0
65 16 1 5 10 0 0.000 0 0 0 0 [S] 0 0
66 17 1 6 7 0 0.000 0 0 0 0 [S] 0 0
67 18 1 6 13 0 0.000 0 0 0 0 [S] 0 0
68 19 1 7 8 0 0.000 0 0 0 0 [S] 0 0
69 * Bond Angles
70 * bond1 bond2 angle locked
71 * Dihedral Angles
72 * at1-cons at1 at2 at2-cons angle locked
268 • Chem3D
73 * Planarity data
74 * User data area
75 * End of File
The MSI MolFile format is broken up into several 11. Lines 11–24 each contains information
sections. Section headers are preceded by a “*”. concerning conversions from 3D to 2D.
Blank lines also contain a “*”. Each line is either a
12. Line 25 is the header for the Global display
blank line, a header line or a data record containing
attributes section.
one or more fields of information about the
structure. Individual fields are delimited by space(s) 13. Line 26 contains 5 fields describing the global
or a tab. The fields in the MSI MolFile format file display attributes: Line thickness (1), font style
used by Chem3D Pro are discussed below. (0), type face (1), type size (12), font (256).
These values are specific to the platform that is
The field value for Carbon 6 from the example file
is included in parentheses for reference: generating the file.
14. .Line 27 contains the header for the Atom Lists
1. Line 1 is a standard header line for MSI MolFile
section.
format files.
15. Line 28 contains a listing of all the possible
2. Line 2 normally indicates the application which fields for the atom list section. When the file is
created the file. created using Chem3D Pro the following fields
are used: Atom#,Lbl, Type, and x,y,z.
3. Line 3 is the header for the File format version
number section. 16. Lines 29–47 each contains 28 fields describing
information about each of the atoms in the
4. Line 4 indicates the file format version number. structure: the first field is the atom number (6),
The format for this field is YY.MMDD. the second field is the atom label (C), the third
field is the atom type (10), the fourth field and
5. Line 5 is the header for the File update version
fifth fields contain 2D coordinates, and contain
number section.
zeros when the file is created using Chem3D
6. Line 6 indicates the file update version number. Pro, the sixth field is the X coordinate (-0.113)
The format for this field is YY.MMDD. and the fifth field is the Y coordinate (1.005),
the sixth field is the Z coordinate (-0.675), the
7. Line 7 is the header for the molecule name
seventh through fifteenth fields are ignored and
section.
contain zeros when the file is created by
8. Line 8 contains the field molecule name. This Chem3D Pro, the sixteenth field is, again, the
field contains either the file name, or atom label (C), the eighteenth field is, again, the
“Undefined Name”. atom number (6), the nineteenth field is the
segment field, the twentieth field is the
9. Line 9 is the header for the empirical formula. coordination field, the twenty first field is
10. Line 10 contains the empirical formula field. ignored, the twenty-second field is called the
This field contains either the empirical formula saturation field: if the atom is attached to any
or “Undefined Empirical Formula”. single, double or delocalized bonds this field is
1 (not saturated) otherwise this field is 0. The
Chem3D • 269
twenty-third through the twenty-sixth fields are 22. Line 75 is a header that indicates the End of
ignored and contain zeros when the file is File.
created using Chem3D Pro, the twenty-seventh
field is, again, the atom label (C). FORTRAN Formats
Administrator

NOTE: Atom types in the Molecular Molecular Simulations MolFile format is as
Simulations MolFile format are user-definable. follows:
For more information, see “Editing File
Format Atom Types” on page 253.
Line FORTRAN
17. Line 48 contains the header for the Bond List
section. 29-47 atom list, field I,1X,A,3(1X,I),3F9
18. Line 49 contains a listing of all the possible value .3,1X,I,F4.1,7(1X,I
fields for the bond list section. When the file is ),1X,A,I,8(1X,I),
created by Chem3D Pro the following fields are “[“,A, “] “
used: Bond#, Bond_type, atom 1, atom 2 and
cis/trans and Qorder. 50-68 bond list, field I,4(1X,I),F9.3,4(2X
values ,I),1X, “[“,A1, “]
19. Lines 50–68 each contain 4 fields describing “,2(1X,I)
information about each of the bonds in the
structure: the first field is the internal bond
number (6), the second field is the bond type
MOPAC
(1), the third and fourth fields are the atom The specific format of the MOPAC files used by
serial numbers for the atoms involved in the Chem3D is the MOPAC Data-File format. This
bond [atom 1 (2), atom 2 (16)], the fifth field is format is described on pages 1-5 through 1-7 of the
the cis/trans designator (this is 0 if it does not “Description of MOPAC” section and page 3-5 of
apply), the sixth through tenth fields are the “Geometry Specification” section in the
ignored, and contain zeros if the file is created MOPAC Manual (fifth edition). For further details
about the MOPAC Data-File format, please refer to
using Chem3D Pro, the eleventh field contains
the above publication.
the bond order ([S] meaning single), the twelfth
and thirteenth fields are ignored and contain
zeros if the file is created using Chem3D Pro.
20. Lines 69–73 are each a section header for 3D
conversion use. This section only contains the
header name only (as shown) when the file is
created using Chem3D Pro.
21. Line 74 is a header for the section User data
area. This section contains the header name
only (as shown) when the file is created using
Chem3D Pro.
270 • Chem3D
The following is a sample MOPAC output file from
Chem3D for cyclohexanol:
Line 1:
Line 2: Cyclohexanol
Line 3:
Line 4a: C 0 0 0 0 0 0 0 0 0
Line 4b: C 1.54152 1 0 0 0 0 1 0 0
Line 4c: C 1.53523 1 111.7747 1 0 0 2 1 0
Line 4d: C 1.53973 1 109.7114 1 -55.6959 1 1 2 3
Line 4e: C 1.53597 1 111.7012 1 55.3112 1 4 1 2
Line 4f: C 1.53424 1 110.7535 1 57.03175 1 3 2 1
Line 4g: O 1.40196 1 107.6989 1 -172.662 1 1 2 3
Line 4h: H 1.11739 1 107.8685 1 62.06751 1 1 2 3
Line 4I: H 1.11633 1 110.0751 1 -177.17 1 2 1 4
Line 4j: H 1.11566 1 109.4526 1 65.43868 1 2 1 4
Line 4k: H 1.11665 1 109.9597 1 178.6209 1 3 2 1
Line 4l: H 1.1161 1 109.5453 1 -63.9507 1 3 2 1
Line 4m: H 1.11542 1 109.4316 1 -66.0209 1 4 1 2
Line 4n: H 1.11499 1 110.549 1 176.0838 1 4 1 2
Line 4o: H 1.11671 1 109.93 1 -178.296 1 5 4 1
Line 4p: H 1.11615 1 109.4596 1 64.43501 1 5 4 1
Line 4q: H 1.11664 1 110.0104 1 -178.325 1 6 3 2
Line 4r: H 1.11604 1 109.6082 1 64.09581 1 6 3 2
Line 4s: H 0.94199 1 106.898 1 -173.033 1 7 1 2
The following illustrates the components of the The internal coordinates section of the MOPAC
MOPAC Output File from Chem3D for C(1) Data-File format contains one line of text for each
Through C(4) of Cyclohexanol atom in the model. Each line contains bond lengths,
bond angles, dihedral angles, action integers, and
Element Bond Action Bond Action Dihedral Action Connectivity
Symbol Lengths Integers Angles Integers Angles Integers Atoms connectivity atoms.
As shown in the illustration above, C(1) is the
1st Atom C 0.000000 0 0.000000 0 0.000000 0 0 0 0
origin atom. C(2) is connected to C(1) with a bond
2nd Atom C 1.541519 1 0.000000 0 0.000000 0 1 0 0 of length 1.541519 Å. C(3) is connected to C(2)
with a bond of length 1.535233 Å, and is at a bond
3rd Atom C 1.535233 1 111.774673 1 0.000000 0 2 1 0
angle of 111.774673 degrees from C(1). C(4) is
4th Atom C 1.539734 1 109.711411 1 -55.695877 1 1 2 3 connected to C(1) with a bond of length 1.539734
Chem3D • 271
Å, and is at a bond angle of 109.711411 degrees
from C(2). C(4) also forms a dihedral angle of
Protein Data Bank Files
-55.695877 degrees with C(3). The Protein Data Bank file format (Protein DB) is
taken from pages 3, 14–15, and 17–18 of the
The action integers listed next to each measurement
Administrator
Protein Data Bank Atomic coordinate and

are instructions to MOPAC which are as follows:
Bibliographic Entry Format Description dated
1Optimize this internal coordinate January, 1985.
0Do not optimize this internal coordinate A Protein Data Bank file can contain as many as 32
different record types. Only the COMPND, ATOM,
-1Reaction coordinate or grid index
HETATM, and CONECT records are used by
When you create a MOPAC file from within Chem3D; all other records in a Protein Data Bank
Chem3D, an action integer of 1 is automatically file are ignored. The COMPND record contains the
assigned to each non-zero bond length, bond angle, name of the molecule and identifying information.
and dihedral angle for each atom record in the file.
The ATOM record contains atomic coordinate
FORTRAN Formats records for “standard” groups, and the HETATM
record contains atomic coordinate records for “non-
The description of the MOPAC Data-File format for standard” groups. The CONECT record contains
each line is as follows: the atomic connectivity records.
Written NOTE: The COMPND record is created by

Line Read by by Chem3D to include the title of a Chem3D model
Number Description Chem3D Chem3D only when you are saving a file using the Protein
Data Bank file format. This record is not used when
1 Keywords for No No
opening a file.
Calculation
Instructions
2 Molecule No Yes
Title
3 Comment No No
4a-s Internal Yes Yes
coordinates
for molecule
5 Blank line, Yes Yes
terminates
geometry
definition
The FORTRAN format for each line containing
internal coordinate data in the MOPAC Data-File is
FORMAT(1X, 2A, 3(F12.6, I3), 1X, 3I4).
272 • Chem3D
The following is an example of a Protein Data Bank atom whose connectivity is being described, then
Output File from Chem3D for L-Alanine. the serial numbers of the first atom, second atom,
third atom and fourth atom to which the described
atom is connected.
COMPND Alanine.pdb
HETATM 1 N 0 -0.962 1 Record Chem3D
Name File Title
HETATM 2 C 0 -0.049 0
HETATM 3 C 0.6 0.834 -1 COMPND Alanine.pdb
HETATM 4 C -2 0.834 1 Record Serial Element X Y Z

Name Number Symbol Coord. Coord. Coord.
HETATM 5 O 0.3 1.737 -1
HETATM 6 O 1.8 0.459 0 HETATM 1 N 0.038 -0.962 0.943
HETATM 7 H 0.9 -1.398 1

Record Serial 1st Atom 2nd Atom 3rd Atom 4th Atom
HETATM 13 H -1 -1.737 1 Name Number Serial Serial Serial Serial
Number Number Number Number
HETATM 8 H -1 -0.642 -1
HETATM 9 H -2 1.564 0 CONECT 2 1 3 4 8
HETATM 10 H -1 1.41 1
HETATM 11 H -2 0.211 1 FORTRAN Formats
HETATM 12 H 2.4 1.06 -1
The full description of the COMPND record format
CONECT 1 2 7 13 in Protein Data Bank files is as follows:
CONECT 2 1 3 4 8
CONECT 3 2 5 6 Column Column Used by
CONECT 4 2 9 10 11 Number Description Chem3D
CONECT 5 3
CONECT 6 3 12 1-6 Record Name Yes
(COMPND)
CONECT 7 1
CONECT 13 1 7-10 UNUSED No
CONECT 8 2
CONECT 9 4 11-70 Name of Molecule Yes
CONECT 10 4
CONECT 11 4 The full description of the ATOM and HETATM
record formats in Protein Data Bank files is as
CONECT 12 6
follows:
END
The ATOM or HETATM record contains the record Column Column Used by
name, followed by the serial number of the atom Number Description Chem3D
being described, the element symbol for that atom,
then the X, Y, and Z Cartesian coordinates for that 1-6 Record Name Yes
atom. (HETATM or ATOM)
A CONECT record is used to describe the atomic 7-11 Atom Serial Number Yes
connectivity. The CONECT records contain the 12 UNUSED No
record name, followed by the serial number of the
Chem3D • 273
13–16 Atom Name (Element Yes 17–21 Serial Number of Yes
Symbol) Second Bonded Atom
17 Alternate Location No
22–26 Serial Number of Third Yes
Administrator
Indicator
Bonded Atom
18–20 Residue Name Optional
21 UNUSED No 27–31 Serial Number of Yes
Fourth Bonded Atom
22 Chain Identifier No
23–26 Residue Sequence No 32–36 Hydrogen Bonds, No
Number Atoms in cols. 7–11 are
Donors
27 Code for insertions of No
residues 37–41 Hydrogen Bonds No
28–30 UNUSED No
42–46 Salt Bridge, Atoms in No
31–38 X Orthogonal Å Yes cols. 7–11 have
coordinates Negative Charge
39–46 Y Orthogonal Å Yes
coordinates 47–51 Hydrogen Bonds, No
Atoms in cols 7–11 are
47–54 Z Orthogonal Å Yes Acceptors
coordinates
55–60 Occupancy No 52–56 Hydrogen Bonds No
61–66 Temperature Factor No 57–61 Salt Bridge, Atoms in No

67 UNUSED No cols. 7–11 have Positive
Charge
68–70 Footnote Number No
The FORTRAN formats for the records used in the
The full description of the CONECT record format
Protein Data Bank file format are as follows:
in Protein Data Bank files is as follows:
Line Description FORTRAN Format

Column Used by
Number Column Description Chem3D
COMPND ‘COMPND’, 4X, 60A1
1–6 Record Name Yes
ATOM ‘ATOM’, 2X, I5,1X,A4,
(CONECT)
1X, A3,10X, 3F8.3,16X
7–11 Atom Serial Number Yes
HETATM ‘HETATM’,
I5,1X,A4,14X,3F8.3,16X
12–16 Serial Number of First Yes
Bonded Atom
CONECT ‘CONECT’, 5I5, 30X
274 • Chem3D
ROSDAL files are for export only. The following is a sample
Rosdal format file created using Chem3D Pro for
The Rosdal Structure Language1 file format is cyclohexanol:
defined in Appendix C: Rosdal Syntax, pages 1-2-3-4-5-6,1-6,2-7H,3-8H,4-9H,5-10H,6-11H,1-
91–108, of the MOLKICK User’s Manual. The 12O-13H,1-14H,2-15H, 3-16H,4-17H,5-18H,6-
Rosdal format is primarily used for query searching 19H.@
in the Beilstein Online Database. Rosdal format
SMD
The Standard Molecular Data 2SMD file) file
format is defined in the SMD File Format version
4.3 documentation, dated 04-Feb-1987. The
following is a sample SMD file produced using
Chem3D Pro for cyclohexanol (the line numbers
are added for purposes of discussion only).
1. Rosdal is a product of Softron, Inc. 2. SMD format - H. Bebak AV-IM-AM Bayer AG.
Line 1 >STRT Cyclohexane
Line 2 DTCR Chem3D 00000 05-MAY-92 12:32:26
Line 3 >CT Cyclohexan 00039
Line 4 19 19 (A2,5I2) (6I3)
Line 5 C 0 0 0
Line 6 C 0 0 0
Line 7 C 0 0 0
Line 8 C 0 0 0
Line 9 C 0 0 0
Line 10 C 0 0 0
Line 11 H 0 0 0
Line 12 H 0 0 0
Line 13 H 0 0 0
Line 14 H 0 0 0
Line 15 H 0 0 0
Line 16 O 0 0 0
Line 17 H 0 0 0
Line 18 H 0 0 0
Line 19 H 0 0 0
Line 20 H 0 0 0
Line 21 H 0 0 0
Line 22 H 0 0 0
Line 23 H 0 0 0
Chem3D • 275
Line 24 1 2 1
Line 25 1 6 1
Line 26 1 12 1
Line 27 1 14 1
Administrator
Line 28 2 3 1
Line 29 2 7 1
Line 30 2 15 1
Line 31 3 4 1
Line 32 3 8 1
Line 33 3 16 1
Line 34 4 5 1
Line 35 4 9 1
Line 36 4 17 1
Line 37 5 6 1
Line 38 5 10 1
Line 39 5 18 1
Line 40 6 11 1
Line 41 6 19 1
Line 42 12 13 1
Line 43 >CO ANGSTROEM 0020
Line 44 4 (3I10)
Line 45 -6903 13566 -4583
Line 46 -14061 808 125
Line 47 -4424 -8880 7132
Line 48 7577 -12182 -1855
Line 49 14874 594 -6240
Line 50 5270 10234 -13349
Line 51 -18551 -4300 -8725
Line 52 -9815 -18274 9852
Line 53 4047 -17718 -10879
Line 54 19321 5600 2685
Line 55 10636 19608 -16168
Line 56 -2794 21139 6600
Line 57 2876 15736 11820
Line 58 -14029 20018 -10310
Line 59 -22477 3450 6965
Line 60 -806 -4365 16672
Line 61 14642 -18918 3566
276 • Chem3D
Line 62 23341 -2014 -13035
Line 63 1740 5536 -22837
Each line is either a blank line, a block header line field is the stereo information about the atom
or a data record containing multiple fields of and the fourth field is the formal charge of the
information about the structure. The SMD file is atom.
broken down into several blocks of information.
The header for each block starts with a > sign. NOTE: If the file is created using Chem3D
Individual fields are delimited by space(s) or a tab. Pro, the number of hydrogens, the stereo
The fields in the SMD format file used by Chem3D information and the formal charge fields are not
Pro are discussed below: used, and will always contain zeros.
1. Line 1 starts the block named STRT. This block 6. Lines 24–42 of the CT Block each contains 3
contains the molecule name. The molecule fields describing a bond between the two atoms.
name is the file name when the file was created The first field is the serial number of the atom
using Chem3D Pro. from which the bond starts, the second field is
2. Line 2 starts the block named DTCR. The
the serial number of atom where the bond ends,
information in this line includes the name of the and the third field is the bond order.
application that created the file and the date and 7. Line 43 starts the block named CO, The
time when the file was generated. information in this block includes the Cartesian
3. Line 3 starts the block named CT which
coordinates of all the atoms from the CT block
contains the connection table of the and indicates the type of coordinates used,
compound(s). Also on this line is a 10 character Angstroms in this example. Also in this line is
description of the connection table. This will be the number of lines in the block, 20 in this
the same as the file name when the file is example.
generated using Chem3D Pro. Finally, the 8. Line 44 contains two fields. The first field
number of records contained within the CT contains the exponent used to convert the
block is indicated, 39 in the above example. coordinates in the lines following to the
4. Line 4 of the CT Block contains four fields. The coordinate type specified in line 43. The second
first field is the number of atoms, the second field is the FORTRAN format of the atom
field is the number of bonds, the third field is coordinates.
the FORTRAN format for the number of atoms, 9. Lines 45–65 each contains three fields
and the fourth field is the FORTRAN format for describing the Cartesian coordinates of an atom
the number of bonds. indicated in the CT block. The first field is the
5. Lines 5–23 of the CT Block each contain 4
X coordinate, the second field is the Y
fields describing an atom. The first field is the coordinate and the third field is the Z
element symbol (first letter uppercase, second coordinate.
lowercase). The second field is the total number
of hydrogens attached to the atom, the third
Chem3D • 277
SYBYL MOL File
The SYBYL MOL File format (SYBYL) is defined
in Chapter 9, “SYBYL File Formats”, pages 9–1
Administrator
through 9–5, of the 1989 SYBYL Programming

Manual.
The following is an example of a file in SYBYL
format produced from within Chem3D. This file
describes a model of cyclohexanol.
19 MOL Cyclohexanol0
1 1 1.068 0.3581 -0.7007C
2 1 -0.207 1.2238 -0.7007C
3 1 -1.473 0.3737 -0.5185C
4 1 1.1286 -0.477 0.5913C
5 1 -0.139 -1.324 0.7800C
6 1 -1.396 -0.445 0.7768C
7 8 2.1708 1.2238 -0.7007O
8 13 1.0068 -0.343 -1.5689H
9 13 -0.284 1.7936 -1.6577H
10 13 -0.147 1.9741 0.1228H
11 13 -2.375 1.032 -0.4983H
12 13 -1.589 -0.314 -1.3895H
13 13 1.2546 0.202 1.4669H
14 13 2.0091 -1.161 0.5742H
15 13 -0.077 -1.893 1.7389H
16 13 -0.21 -2.076 -0.0419H
17 13 -2.308 -1.081 0.8816H
18 13 -1.372 0.2442 1.6545H
19 13 2.9386 0.6891 -0.8100H
19 MOL
1 1 2 1
2 1 4 1
3 1 7 1
4 1 8 1
5 2 3 1
6 2 9 1
7 2 10 1
8 3 6 1
9 3 11 1
278 • Chem3D
10 3 12 1
11 4 5 1
12 4 13 1
13 4 14 1
14 5 6 1
15 5 15 1
16 5 16 1
17 6 17 1
18 6 18 1
19 7 19 1
0 MOL
The following illustration shows the components of 2. The atom records (lines 2–20 in the
the SYBYL Output File from Chem3D for C(6) and cyclohexanol example) contain the Atom ID in
Bond 3 of Cyclohexanol. column 1, followed by the Atom Type in
column 2, and the X, Y and Z Cartesian
coordinates of that atom in columns 3–5.
Number Molecule
of Atoms Name Center 3. The first record after the last atom records
contains the number of bonds in the molecule,
19 MOL Cyclohexanol 0
followed by the word “MOL”.
6 1 -1.3959 -0.4449 0.7768C
4. The bond records (lines 22–40 in the

Atom Atom X Y Z
ID Type Coord Coord Coord cyclohexanol example) contain the Bond
Number
of Bonds Number in column 1, followed by the Atom ID
of the atom where the bond starts (the “From-
19 MOL
Atom”) in column 2 and the Atom ID of the
3 1 7 1
atom where the bond stops (the “To-Atom”) in
Bond From-Atom To-Atom Bond column 3. The last column in the bond records
Number Type
is the bond type. Finally the last line in the file
Number
of Features is the Number of Features record, which
contains the number of feature records in the
0 MOL
molecule. Chem3D does not use this
information.
The format for SYBYL MOL files is as follows:
1. The first record in the SYBYL MOL File

contains the number of atoms in the model, the
word “MOL”, the name of the molecule, and
the center of the molecule.
Chem3D • 279
FORTRAN Formats The following is a sample SYBYL MOL2 file
created using Chem3D Pro. This file describes a
The FORTRAN format for each record of the model of cyclohexanol (the line numbers are added
SYBYL MOL File format is as follows: for reference only):
Administrator
Line Description FORTRAN Format
Number of Atoms/File I4,1X,'MOL',20A2,11

Name X,I4
Atom records 2I4,3F9.4,2A2
Number of Bonds record I4,1X,'MOL'
Bond records 3I4,9X,I4
Number of Features I4,1X,'MOL'

record
SYBYL MOL2 File

The SYBYL MOL21 file format (SYBYL2) is
defined in Chapter 3, “File Formats”, pages 3033–
3050, of the 1991 SYBYL Programming Manual.
1. SYBYL is a product of TRIPOS Associates, Inc., a
subsidiary of Evans & Sutherland.
Line 1 # Name: CYCLOHEXANOL
Line 2
Line 3 @<TRIPOS>MOLECULE
Line 4 CYCLOHEXANOL
Line 5 19 19 0 0 0
Line 6 SMALL
Line 7 NO_CHARGES
Line 8
Line 9
Line 10 @<TRIPOS>ATOM
Line 11 1 C -1.349 0.195 1.032 C.3
Line 12 2 C -0.407 -0.896 1.563 C.3
Line 13 3 C 0.562 -1.378 0.473 C.3
Line 14 4 C 1.351 -0.205 -0.128 C.3
Line 15 5 C 0.42 0.9 -0.652 C.3
Line 16 6 C -0.559 1.37 0.436 C.3
280 • Chem3D
Line 17 7 H -2.021 -0.239 0.253 H
Line 18 8 H -1.005 -1.759 1.944 H
Line 19 9 H 0.175 -0.496 2.427 H
Line 20 10 H 1.27 -2.128 0.9 H
Line 21 11 H -0.01 -1.898 -0.331 H
Line 22 12 H 2.021 0.225 0.655 H
Line 23 13 H 2.008 -0.569 -0.953 H
Line 24 14 H 1.03 1.766 -1.016 H
Line 25 15 O -0.3 0.427 -1.757 O.sp
Line 26 16 H -1.262 2.128 0.014 H
Line 27 17 H 0.014 1.876 1.249 H
Line 28 18 H -2.005 0.562 1.857 H
Line 29 19 H 0.329 0.223 -2.427 H.sp
Line 30 @<TRIPOS>BOND
Line 31 1 31 2 1
Line 32 2 1 6 1
Line 33 3 1 7 1
Line 34 4 1 18 1
Line 35 5 2 3 1
Line 36 6 2 8 1
Line 37 7 2 9 1
Line 38 8 3 4 1
Line 39 9 3 10 1
Line 40 10 3 11 1
Line 41 11 4 5 1
Line 42 12 4 12 1
Line 43 13 4 13 1
Line 44 14 5 6 1
Line 45 15 5 14 1
Line 46 16 5 15 1
Line 47 17 6 16 1
Line 48 18 6 17 1
Line 49 19 15 19 1
Each line is either a blank line, a section header or a
data record containing multiple fields of
information about the compound. The SYBYL
MOL2 file is broken down into several sections of
information. Record type indicators (RTI) break the
Chem3D • 281
information about the molecule into sections. RTI’s 7. Line 7 describes the charge type associated with
are always preceded by an “@” sign. Individual the molecule. This field contains
fields are delimited by space(s) or a tab. NO_CHARGES if the file is created using
Chem3D Pro.
The fields in the SYBYL MOL2 format file used by
Administrator
Chem3D Pro are as follows: 8. Line 8, blank in the above example, might
1. Line 1 is a comment field. The pound sign contain internal SYBYL status bits associated
preceding the text indicates a comment line. with the molecule.
Name: is a field designating the name of
9. Line 9, blank in the above example, might
molecule. The molecule name is the file name contain comments associated with the
when the file is created using Chem3D Pro.
molecule.
2. Line 2 is a blank line.
NOTE: Four asterisks appear in line 8 when
3. Line 3, “@<TRIPOS>MOLECULE”, is a there are no status bits associated with the
Record Type Indicator (RTI) which begins a molecule but there is a comment in Line 9.
section containing information about the
molecule(s) contained in the file. 10. Line 10, “@<TRIPOS>ATOM”, is a Record
Type Indicator (RTI) which begins a section
NOTE: There are many additional RTIs in the containing information about each of the atoms
SYBYL MOL2 format. Chem3D Pro uses only associated with the molecule.
@<TRIPOS>MOLECULE,
11. Lines 11–29 each contain 6 fields describing
@<TRIPOS>ATOM and @<TRIPOS>BOND.
information about an atom: the first field is the
atom id, the second field is the atom name, the
4. Line 4 contains the name of the molecule. The third field is the X coordinate, the fourth field is
name on line 4 is the same as the name on line 1. the Y coordinate, the fifth field is the Z
5. Line 5 contains 5 fields describing information coordinate and the sixth field is the atom type.
about the molecule: The first field is the number
of atoms, the second field is the number of NOTE: Atom types are user-definable See
“Editing File Format Atom Types” on page 253
bonds, the third field is the number of
for instructions on modifying or creating an
substructures, the fourth field is the number of
atom type.
features and the fifth field is the number of sets.
12. Line 30, “@<TRIPOS>BOND”, is a Record
NOTE: Chem3D Pro ignores the following fields: Type Indicator (RTI) which begins a section
number of substructures, number of features and
containing information about the bonds
number of sets. These fields will contain zeros if the
associated with the molecule.
file was created using Chem3D Pro.
13. .Lines 31–49 each contain 4 fields describing
6. Line 6 describes the molecule type. This field
information about a bond: the first field is the
contains SMALL if the file is created using bond id, the second field is the from-atom id,
Chem3D Pro. the third field is the to-atom id, and the fourth
field is the bond type.
282 • Chem3D
FORTRAN Formats
SYBYL MOL2 File format is as follows:
Line FORTRAN
1 Molecule name (file “# “,5X,

name) “Name:
“,1X,A
5 Number of 4(1X,I2)
atoms/number of
bonds
11–29 Atom type, name, I4,6X,A2,3X,3

coordinates and id F9.3,2X,A5
31–49 Bond id, from-atom, 3I4,3X,A2

to-atom, bond type
Chem3D • 283
Chem3D
•
284
Administrator
Index
Symbols Alchemy 254
Fortran format 255
(-CHR-) Bending Force Parameters 245 Alchemy file format 115
ALCSee Alchemy 254
Numerics Aligning 69
parallel to an axis 69
1/2 electron approximation 141, 163 parallel to plane 69
2D to 3D conversion 53, 225 to center 71
3DMF file format 115 Allinger’s Force Field
3RINGANG.TBLSee Angle Bending table 242 changes 228
4-Membered Ring Torsionals 235 Alpha amino acids 52
4RINGANG.TBLSee Angle Bending table 242 Alpha helix, tutorial example 24
AM1 143, 188
A Amino acids 52
alpha conformation 52
beta conformation 52
aaa file extension 182
Angle bending energy 131
Ab initio methods
Angle bending force constant field 242
speed 125
Angle Bending table 235, 242
uses 125
3-membered ring 235, 242
vs. semiemperical 140
4-membered ring 235, 242
About
Angle defining atom 72
CS MOPAC 1
Angle Type field 242
Extended Huckel 140
Apple Events 233
Gaussian 1
AppleScript 233
geometry optimization 128
Apply Standard Measurements
molecular dynamics 136
bond angles 59
potential energy surfaces 126
bond lengths 59
single point calculations 127
building control 45
this manual 1
Applying standard measurements 45
Active window 37
Atom Display control panel 75
Actual field
Atom labels
editing 96
element symbols 49
measurements 14
overview 9
Add-in, ChemSAR for Excel 205
pop-ups 93
Adjacent atoms
serial numbers 9
selecting 65
tutorial example 22
showing/hiding 66
Atom pairs 102, 105
alc file extension 38, 112
Atom Size % control 82
alc file format 115
Chem3D Index • 285

Atom Size By control 82 solid coloring 81
Atom spheres, hiding and showing 81 tinting 80
Atom Type field 243, 247 Automatically
Atom Type number 236 apply standard measurements 45
Atom Type Number field 236, 239 correct atom types 45
Atom types fit model to window 46
Index
assigning automatically 11 rectify 45

automatic application of standards 13 Automatically Rectify check box 239
automatic rectification 11 Available properites 203
changing 50 Axes, origin 6
changing in model 55
charges 59 B
creating 220
number field 12 Background color 79
overview 10 Ball & Stick display 76
pop-up information 93 Basis set 139, 142
relation to bond order 56 Bending constants 245
Atom Types table 235, 238 Bending Energy, MM2 200
Atom Weight field 247 Beta amino acids 52
Atoms BFGS 167
aligning to plane 69 Bitmap file format 113
changing 54 Black model 67
changing atom types 55 bmp file format 113
changing element types 54 Boiling Point, ChemProp Pro 198
color 75, 79 Bond angles
coloring 80 parameters 13
coloring black 79 setting 57
coloring by depth 79 showing 97
coloring by element 78 tutorial example 18
coloring by group 78, 101 Bond Dipole field 241
coloring by partial charge 78 Bond Display control panel 75, 80
colorizing individually 79 Bond lengths
depth ratio 81 parameters 13
display options 83 pop-up information 93
displaying element symbols 83 setting 57
displaying serial numbers 83 showing 96
fill pattern 80 tutorial example 18, 25
mapping colors onto surfaces 91 Bond order matrix 183
moving 58, 66 Bond orders
moving to an axis 69 changing 55
patterning by depth 80 pi systems 135
patterning by element 80 pop-up information 93
selecting 14, 48, 63 relation to atom type 56
shadowed coloring 81 tutorial example 18
size 75, 82 Bond Proximate Addition
286 • Index Chem3D

command 56 Building Parameters 235
control 56
Bond stretching energy 131 C
Bond stretching force constant field 241
Bond Stretching table 236, 241 C3D file format 115
Bond tools C3DFILTR 253
description 46 C3DTABLE 237
tutorial example 17 Calculate force Constants At Each Point control 188
Bond Type field 241, 244, 250 Calculate Initial Force Constants control 188
Bond Width control 82 Calculation, with ChemSAR for Excel 205
BONDS 183 Cambridge Crystal Data Bank file 259
Bonds CambridgeSoft web site, accessing 212
adding 47 Camsoft.com 212
creating 47 Cart Coords 1See Cartesian coordinates file 255
creating between nearby atoms 56 Cart Coords 2See Cartesian coordinates file 255
cylindrical bond pattern 82 Cartesian coordinate file 255
depth ratio 75, 81 Cartesian coordinates
fill pattern 75, 80 atom movement on import 185
moving 66 displaying 101
removing 48 file format 185
selecting 48, 63 overview 15
tapering cylindrical bonds 82 pop-up information 93
thickness 75 positioning 69
uncoordinated 48 Cartesian Coordinates command 101
width 81, 82 Cartesian coordinates file
BONDS keyword 183 Fortran format 259
Born-Oppenheimer approximation 138 Cartesian Coordinates file format 115
Bound-to Order field 240 Cartesian coordinates format 115
Bound-to Type field 240 Cartesian coordinates table 15
Bound-to-order field, atom types 13 cc1 file format
Bound-to-type field, atom types 13 exporting 112
Break Bond command 56 opening 38
Building saving 115
modes 45, 46 CC1See Cartesian coordinates file 255
order of attachment 50 cc2 file format
polymers 53 exporting 112
polypeptides 52 opening 38
rings 50 saving 115
using 2D structures 53 CC2See Cartesian coordinates file 255
Building control panel ccd file format 38
automatically apply standards 45 CCDB file format 39
automatically bond proximate 45 CCDSee See Cambridge Crystal Data Bank file 259
automatically correct atom types 45 CCITT Group 3 and 4 114
automatically fit model in window 45 cdx file extension 38, 112
automatically rectify 45 Cell 8

Changes, discarding 43 CIS 184
Changing Clear All Other Frames command 108
atom types 55 Clear Molecular Surfaces command 88
elements 54 Clear Previous Frames command 108
substructures 54 Clear Subsequent Frames command 108
Charge field 239 Click 2
Index
Charge field, atom types 12 Clipboard

Charge property 172 copying to 120
Charge-Charge Energy, MM2 200 exporting with 120
Charge-Dipole Energy, MM2 200 importing 2D structures 53
Charge-dipole interaction term 228 Close command 43
Charges Close contacts 98
adding 49, 53 Close Contacts command 239
changing 59 Closed shell system 164
pop-up information 93 Closing
removing 59 Chem3D 16
Chem3D Stationery file format 115 models 43
Chem3D Template file format 115 Color
chem3d.h 16 applying to individual atoms 79
chem3d.tlb 16 atoms 80
ChemClub.com 213 background 79
ChemDraw black 79
creating structures 53 by depth 79
transferring models to 120 by element 78
tutorial example 30 by group 78
Chemicals, purchasing online 211 changing for groups 102
ChemNews.Com 212 dialog box 80
ChemOffice SDK, accessing 214 settings 78
ChemProp Color field 238
Error Messages 199 Column divider 8
limitations 199 Column heading 8
ChemProp Std Server properties 197 Comparing 105
ChemSAR for Excel Compression 114
configuring 205 Computational chemistry, definition 123
descriptors 208 Computational methods
overview 205 choosing the best method 124
statistics 209 defined 123
wizard 205 limitations 124
ChemStore.com 211 model size 124
chm file extension 38 parameter availability 124
Choose 3 potential energy surfaces 124
CI RAM 124
microstates used 183 Compute Properties
overview 141 dialog box 203
selecting wavefunction 163 Gaussian 191

MM2 155 atom types 220
MOPAC 170 bonds 47
removing properties 203 fragments 57
selecting properties 203 movies 107
con file format new models 37
exporting 116 substructures 215
opening 38 Creating models
Configuration interaction 141 using stationery 38
Configuring ChemSAR for Excel 205 using templates 38
Conformation, tutorial example 24 creating parameters 237
Conjugated pisystem bonds table 235 Critical Pressure, ChemProp Pro 199
Connection Table file format 116 Critical Temperature, ChemProp Pro 198
Connolly Accessible Surface Area, description 197 Critical Volume, ChemProp Pro 199
Connolly molecular surface CS MOPAC Pro 1
displaying 90 CS MOPAC Std 1
overview 90 ct file format 38, 112, 116
Connolly Molecular Surface Area, ChemProp STD cub file format 38, 117
197 Cutoff distances 246
Connolly Solvent-Excluded Volume, ChemProp Cutoff parameters
STD 197 electrostatic interactions 134
Constraining movement 66 van der Waals cutoffs 133
Context-sensitive Help 2 Cylindrical Bond Patterns controls 82
Coordinates 14 Cylindrical Bonds display 76
Coplanarity 100 CYMK Contiguous 114
Copy As Bitmap command 120
Copy As ChemDraw Structure D
exporting 120
tutorial example 30 dat file format
Copy command 120 opening 38
Copy Measurements to Messages control saving 118
GAMESS 194 Default Minimizer 167
Gaussian 188 Default settings 9
MM2 146 Define Group command 66
Copying from other programs 53 Defining atom types 220
Core-core repulsion energy 183 Defining substructures 215
Correct Atom Types control 45 Delocalized Bonds field 240
Correcting atom types 45 Depth Ratio control 81
Correlation Matrix 210 Descriptive Statistics 209
COSMO solvation 177 Descriptors
Covalent Radius field 238 ChemSAR for Excel 208
Create Input File command definition 197
Gaussian 191 Deselecting
MOPAC 184 changes in rectification 63
Creating definition 3
atom pairs 102, 105 description 63

DFORCE 183 E
dForce field 244
Dielectric constants 246 Editing
Dihedral angles bond orders 55
rotating 67 bonds 55
setting 57 Cartesian coordinates 15
Index
showing 98 colors of groups 102

tutorial example 19 display type 75
Dihedral Driver command 157 measurements 96
Dihedral Type field 248 movies 108
Dipole Moment selections 63
MM2 200 serial numbers 59
MOPAC Server 201 size of all frames 71
Dipole moment 171 size of window 71
Dipole-Dipole Energy, MM2 200 stereochemistry 60
Direct or Cross-eyed control 83 window font 15
Discarding changes 43 Z-matrix 71
Display control panel 75 EF 167
Display Every Iteration control 104, 107 EGO 121
GAMESS 194 Eigenvector Following 167
Gaussian 188 Eigenvectors 183
MM2 146, 162, 187, 192 Electron field 244
Display Stereo View 83 Electronic energy 183
Display types 75 Electronic Energy (298 K), MOPAC 201
Distance defining atom 72 Electrostatic cutoff distance 246
dlength field 244 Electrostatic cutoff term 229
Dock command 102 Electrostatic cutoffs 134
Dock dialog box 104 Electrostatic energy 133
Docking Electrostatic potential
movies 104 derived charges 175
overview 102 mapping onto surfaces 91
stopping 104 overview 175
Dot density 77 Element symbols
Dot surfaces displaying 83
dot density 77 overview 83
hiding and showing 77 Elements
Dots surface type 86 adding to model 50
Double Bond tool changing in model 54
description 47 color 78
tutorial example 19 highlighting 80
Double Bonds field 240 selecting 64
Double-click 2 Elements table 236, 238
Drag 3 emf format 113
Dragging 46 Enantiomers, creating using reflection 61
Dummy atom 48

Encapsulated postscript file 113 MacroModel 263
Energy Components, MOPAC 183 MDL MolFile 264
Energy Correction table 235 MOPAC 270
Energy Corrections table 245 MSI MolFile 266
Energy minimization 128 Protein Data Bank file 272
Enhanced Metafile format 113 ROSDAL 275
ENPART 183 SMD File 275
ent file extension 38 SYBYL MOL File 278
Eps field 247 SYBYL MOL2 280
eps file format 113, 121 File formats
Eraser tool 47, 48 3DMF 115
Error Message, ChemProp 199 Alchemy 115
ESR spectra simulation 178 Bitmap 113
Estimating parameters 237 Cartesian Coordinates 115
Even electrons 164 Cartesian coordinates 115
Exact Mass, ChemProp STD 197 ccd 38
Excel, ChemSAR 205 Chem3D 115
Excited state 165 Chem3D Stationery 115
Exit command 16 Chem3D Template 115
Expansion button 6 Connection Table 116
Exporting 112 Enhanced Metafile 113
Extended Huckel EPS 113
definition 140 Gaussian Checkpoint 117
description 84 Gaussian Cube 117
molecular surface types available 85 Gaussian Input 116
Extended Huckel Surfaces, tutorial example 31 GIF 115
External Tables, overview 235 Internal coordinates 117
Extrema 126 Job Description file 120
Job Description Stationery 120
F MacroModel 118
MDL MolFile 118
FAQs Molecular Design Limited 118
online, accessing 213 MOPAC 118
Technical Support 221 MOPAC Graph 119
fch file format MOPAC graph 119
opening 38 MOPAC Input 118
saving 117 Movie 115
fchk file fromat MSI 118
opening 38 MSI ChemNote 118
Field name 8 PICS 115
File format PICT 113
Cambridge Crystal Data Bank 259 PNG 115
Cartesian coordinates file 255 Postscript 113
editing atom types 253 Protein Data Bank 119
Internal coordinates fileSee 260 QuickTime 115

ROSDAL 119 specifying methods 193
SMD 120 Gaussian
Standard Molecular Data 120 Compute Properties command 191
SYBYL 120 Copy Measurements to Messages control 188
TIFF 114 Create Input File command 191
WMF 113 Cube file format 117
Index
Fileformat Display Every Iteration control 188

Alchemy 254 file formats 116
Filters, property 203 General tab 189
First button 6 Job Type tab 187
Fit Model to Window Minimize Energy command 187
building control 46 molecular surface types available 85
command 71 overview 1, 187
Fit Model to Window control 46 Properties tab 191
Fit Selection to Window command 71 specifying basis sets 188
Fock matrix 138, 229 specifying keywords 189
Font 15 specifying methods 188
Font size 15 specifying path to store results 190
Force Constant field 250 specifying population analyses 189
Force Constants 188 specifying solvation models 189
Formal Charge specifying spin multiplicites 188
ChemProp STD 197 specifying wave functions 188
definition 33 Theory tab 188
Fragments tutorial example 31
creating 57 Unix, visualizing surfaces 92
rotating 67 Gaussian Checkpoint file format 117
selecting 65 Gaussian Input file format 116, 191
Frame Interval control 152 Gaussian, Inc. 1
Frames General tab
scaling active only 71 GAMESS 195
scaling all 71 Gaussian 189
Free Energy, ChemProp Pro 199 MOPAC 166
Freehand drawing mode 46 Geometry field 239
Freehand rotation 68 Geometry field, atom types 13
Fujitsu, Ltd. 1, 231 Geometry optimization
Full Report, ChemProp Pro 199 definition 124
overview 128
G Gibbs Free Energy, ChemProp Pro 199
GIF file format 115
GAMESS gjc file format 38, 112, 116
installing 193 gjf file format 38, 116, 191
Minimize Energy command 193 gjt file format 191
overview 193 Global minimum 126
Property Server 201 gpt file format 38, 119
Property server 201 Gradient norm 171

Graphics Interchange Format 115 Hydrophobicity
Grid 87 mapping onto surfaces 91
density 87 scale 89
editing 87 Hyperfine Coupling Constants 178
length of axes 88 Hyperpolarizability 176
origin 87
Grid Settings dialog 87 I
Ground state 164
Group Ideal Gas Thermal Capacity, ChemProp Pro 199
mapping colors onto surfaces 91 Importing
Groups Cartesian coordinates files 185
colors 78, 102 ChemDraw structures 53
defining 66 ISIS/Draw structures 53
displaying 101 supported file formats 38
Groups command 101 Include PostScript Commands in Pictures 121
Groups table Inertia, ChemProp Std 198
defining 66 Installation
selecting 64 Chem3D requirements 3
substructures 51 GAMESS 193
Guessing parameters 147, 237 Int CoordsSee Internal coordinates file 260
int file extension 38, 112
H Interface 5
Internal axis rotation 67
Hamiltonian 137 Internal coordinates
Heat of Formation changing 71
ChemProp Pro 199 file format 117
definition 171 overview 14
Heating/Cooling Rate control 152 pop-up information 93
Help table 15, 101
context-sensitive 2 Internal coordinates file 260
Windows 2 Fortran format 262
Henry’s Law Constant, ChemProp Pro 199 Internal rotation 67
Hide Selected command 65 Internet, CambridgeSoft web site 212
Hide Surface button 88 INTSee Internal coordinates file 260
Hide Unselected command 65 Invert, tutorial example 23
Highlighting atoms 80 Ionization field 244
Home page, CambridgeSoft 212 Ionization potential 183
HOMO ISIS/Draw 53
Energy, MOPAC 201 Isocharge 91
overview 92 Isopotential 92
tutorial example 30 Isospin 91
HOMO/LUMO energies 183 Isovalues
Hooke's Law Equation 245 editing 87
Hooke's Law Potential Function 245 overview 87
Huckel 84

J Magnfiy button 7
Magnify button 71
jdf file format 120, 185, 190, 192 Magnify command 71
jdt file format 120, 190 Map Property control 91
Job Description file format 120, 185, 190, 192 Mapping properties
Job Description Stationery 120 description 91
Index
Job Description Template file format 120, 190 onto surfaces 91

Job Type tab tutorial example 32
GAMESS 194 Maximum Ring Size field 239
Gaussian 187 mcm file extension 38, 112
molecular dynamics 153 mcm file format 118
MOPAC 161 MCMSee MacroModel 263
MDL MolFile 118, 264
K Fortran format 266
MDL MolFile file format 118
KB field 242 Measurements
Keywords actual field 14
BOND 183 deleting 96
Keywords, additional editing 96
Gaussian 189 non-bonded distances 95, 96
MOPAC 183 optimal field 14
KS field 241 overriding standards 62
setting 57
L Measurements table
overview 95
Lab supplies, purchasing online 211 tutorial example 24
Last button 6 Melting Point, ChemProp Pro 199
Length field 241 Message command 102
LET 168, 169 Message controller 6
Local minima 126 Message Table Height bar 6
LOCALIZE 183 Microstates 141
Localized orbitals 183 MINDO/3 142, 188
LogP, ChemProp Pro 199 Minimizations, queuing 147
Lone Pairs field 247 Minimize Energy command
LUMO GAMESS 193
Energy, MOPAC 201 Gaussian 187, 188
overview 92 MM2 145
tutorial example 30 MOPAC 161
Minimize Energy dialog
GAMESS 193
M Gaussian 188
MM2 145
MacroModel 263
Minimizer 167
Fortran format 264
Minimum RMS Gradient
MacroModel file format 118
MM2 146, 162

ml2 file extension 38 saving 41
MM2 mol file extension 38
applying constraints 14 mol file format
bond orders 135 description 118
Compute Properties command 155 exporting 112
Copy Measurements to Messages control 146 importing 38
Display Every Iteration control 146, 162, 187, Molar Refractivity, ChemProp Pro 199
192 Molecular Dynamics
editing parameters 227 Job Type tab 153
Guessing parameters 147 overview 151
Minimize Energy dialog 145 settings 152
Minimum RMS Gradient 146, 162 Molecular electrostatic potential surface
overview 145 calculation types required 85
Properties tab 155 definition 92
property server 200 Molecular Electrostatic Potential Surface dialog 92
References 227 Molecular Formula, ChemProp STD 198
Restrict Movement of Select Atoms 146, 153 Molecular mechanics
tutorial example 21, 25 brief theory 129
MM2 Atom Types table 235, 246 limitations 124
MM2 Constants table 236, 245 parameters 129
MNDO 188 speed 125
MNDO-d 144 uses 125
Model Molecular orbitals
area 6 calculation types required 85
data 93 definition 92
parts 9 mapping onto surfaces 91
Settings control panels 75 tutorial example 31
settings, changing 75 Molecular shape 91
size 70 Molecular Surfaces
turns black on rotation 67 calculation types 85
type 75 clearing all 88
window 6 color 86
Model Display control panel 78, 80 definition 176
Model Tables dots surface type 86
area, description 7 grid 87
closing 14 hiding 88
showing 13 isovalues 87
types 11 must be calculated before displaying 84
Models overview 84
closing 43 showing 88
creating 37 smoothness 87
creating with templates 38 solid surface type 86
discarding changes 43 surface types 86
new 37, 38 translucent surface type 86
opening 37 tutorial example 30, 31

types available from Extended Huckel 85 Move to Y-Z Plane command 69
types available from Gaussian 85 Move to Z-Axis command, tutorial example 29
types available from MOPAC 85 Movie control panel 108
wire mesh surface type 86 Movie Controller
Molecular Weight, ChemProp Std 198 illustration 107
MOLSee MDL MolFile 264 overview 107
Index
Moments of Inertia, ChemProp Std 198 slider knob 107

Monochrome 114 speed control 108
Monochrome rotations 67, 108 Movie file format 115
mop file extension 38, 112 Movies
MOPAC 270 docking 104
aaa file 182 editing 108
approximations 141 overlaying 107
Compute Properties command 170 overview 107
Create Input File command 184 track rotations in monochrome 67
file formats,mop file format 118 tutorial example 26, 27
Fortran format 272 Moving
General tab 166 atoms 66
Graph file format 119 models 66
graph file format 119 mpc file format 38
Hamiltonians 142 description 118
history 231 MSI ChemNote file format 118
input file 185 MSI MolFile 266
Job Type tab 161 msm file format 118
keywords sent automatically 167, 169 exporting 112
methods, choosing 142 importing 38
Minimize Energy command 161 MSMSee MSI MolFile 266
molecular surface types available 85 Mulliken Charges 173
Optimize to transition state 168 Multiple models 57
ouput file 183
out file 182 N
overview 161
parameters, editing 232 Name field 238
Property server 201 Naming a selection 66
quits 183 New Model command 37
references 231 Next button 6
specifying electronic state 163 NOMM keyword 184
specifying keywords 166, 183 Non-bonded distances
specifying wave functions 163 constraints 136
Stopping 167 displaying 95
Theory tab 162 displaying in tables 96
MOPAC Input file format 118 setting 57
MOPSee MOPAC 270 Non-bonded energy 133
Move to X-Y Plane command 69
Move to X-Z Plane command 69

O overview 235
types 11
Odd electron 165 Parameters 11
OLE Automation 16, 234 bond angle 13
Online Help, see Help bond length 13
Online Menu creating 237
Browse ChemStore.com 211 estimating 237
CambridgeSoft Home Page 212 guessing 147, 155
ChemOffice SDK 214 MM2 155, 227
CS Chem3D Technical Support 213 MOPAC 232
Lookup Suppliers on ChemStore.com 211 Parameters, setting 204
Overview 211 Pariser-Parr-Pople pi orbital SCF computation 229
Register online 213 Partial Charge
Open shell 165 atom size control 82
Opening models 37 colors 78
Optimal field definition 33
editing 96 description 95
measurements 14 pop-up information 93, 95
Optimize to Transition State, MOPAC 168 Partition coefficient 199
Optimizing to a transition state 128 Paste command 53, 120
Orbital, setting 91 Pasting from other programs 53
Origin 6 Pattern by Depth control 80
Origin atoms, Z-matrix 72 Pattern by Element control 80
out file extension 182 Pattern field 238
Out of Plane Bending pdb file extension 38, 112
equations 135 pdb file format 119
Out-of-Plane Bending PDBSee Protein Data Bank file 272
table 236, 250 Physiochemical properties, calculating 205
Out-of-Plane Bending constant 250 PI 184
Output file 183 Pi Atoms table 229, 243
Ovality, ChemProp Std 198 Pi Bonds table 235, 244
Overlay command 105 Pi orbital SCF computation 229
Overlay dialog 106 Pi system SCF equations 135
Overlaying 105 PIATOMS.TBLSee Pi Atoms table 243
movies 107 PIBONDS.TBLSee Pi Bonds table 244
stopping 107 PICS file format 115
Overriding, standard measurements 62 PICT file format 113
Planarity 100
P PM3 144, 188
PNG file format 115
Packbits, compression 114 Pointing information 10
Page size 111 POLAR (E=n) 177
Parameter Tables Polarizability
fields 236 overview 176
Polymers, building 53

Pop-up Information rdl file extension 112
control panel 94 RDLSee ROSDAL 275
overview 93 RECALC=5 168, 169
Position by Bond Angles command 74 Record button 7, 108
PostScript files, background color 79 Record Each Iteration control 104, 107
Potential Energy Function, choosing 142 Record selector 8
Index
Potential energy surfaces 124, 126 Recording

PRECISE 168, 169, 184 minimization 147
Preferences file 9 molecular dynamics 154
Press 2 movies 108
Previous button 6 Rectification
Principal Moments of Inertia, ChemProp Std 198 automatic 11
Print command 112 building control 45
Printing change in bond order 56
background color 79 definition 45
overview 111 when deselecting 63
Properties Rectification Type field 239
selecting 203 Rectification type, atom types 12
sorting 203 Rectify
Properties tab command 61
GAMESS 194 definition 45
Gaussian 191 Reduce button 7, 71
MM2 155 Reduce command 71
Property calculation definition 124 Reduct field 247
Property filters 203 Reference Description field 241
Pro-R 61, 73 Reference field 237
ProR/ProS 260 Reference Number field 241
Pro-S 61, 73 References
Protein Data Bank File MM2 227
Fortran format 273 MOPAC 231
Protein Data Bank file 272 scripting 233
Protein Data Bank file format 119 References table 236, 240, 241
Protein DBSee Protein Data Bank file 272 Reflect command 60
Refractivity, ChemProp Pro 199
Q Registration, online 213
Removing
Quality field 236 bonds 48
Quartic stretching term 229 messages 102
QuickTime file format 115 using Eraser tool 47
Quit command 16 Rendering types 75
Repeat GAMMES Job command 196
R Repeat Gaussian Job command 192
Repeat MOPAC Job command 185, 192
R* field 247 Replacing atoms
RAM 3 tutorial example 22

Replaying Save command 41
molecular dynamics 154 Saving
Repulsion field 244 a copy of a model 42
Requirements in different file formats 42
RAM 3 models 41
system 3 when closing 43
Reserializing 59 Scaling
Resolve density matrix 184 active frame 71
Restrict Movement of Select Atoms, MM2 146, 153 all frames 71
Revert to Saved command 43 overview 70
RGB Indexed color 114 Scripts, references 233
RHF 139, 141, 163 SDK Online, accessing 214
RHF spin density 180 sdl file format 120
Ribbons display 77 Select 3
Ring closures 99 Select Adjacent command 65
RMAX=n.nn 168, 169 Select Element command 64
RMIN=n.nn 168, 169 Select Fragment command 65
ROSDAL 275 Select Orbital dialog box 91
ROSDAL file format 119 Select Reverse command 64
Rotate dialog box 68 Select tool 46, 48, 63
Rotating 46, 67 Selected axis rotation 67
dihedral angle 67 Selecting
fragments 67 adding atoms to a selection 63
internal angle 67 adjacent atoms 65
specific amount 68 atoms 48, 63
tutorial example 25, 26 bonds 48, 63
using trackball 68 by clicking 63
X/Y-axis rotation 68 by dragging 64
Z-axis rotation 68 defining a group 66
Rotation bars 6 description 46
Row Count 8 fragments 65
Run GAMESS Input File command 195 groups 64
Run Gaussian Input File command 191 moving 66
Run Gaussian Job command 192 multiple atoms or bonds 63
Run MOPAC Input file command 185 reversing the selecting 64
Run MOPAC Job command 185, 192 selection rectangle 64
Rune Plots 210 specific elements 64
Selection rectangle 64
S Self consistent field 140
Semiempirical methods
Saddle point 126 brief theory 137
Sample code, SDK web site 214 limitations 124
SAR descriptors, definition 197 speed 125
Save All Frames checkbox 118 uses 125
Save As command 113 Serial numbers

adding 59 smd file extension 38, 112
changing 59 SMD file format 120
displaying 83 SMDSee SMD file 275
overview 9 sml file extension 38, 112
Set Bond Order command 55 SMLSee SYBYL MOL File 278
Set Distance command 103 Solid Colors control 81
Index
Set orbital 91 Solid Spheres Size % control 82

Set Z-matrix commands 14, 74 Solid Spheres Size By control 82
Setting measurements Solid surface type 86
atom movement 58 Solubility, ChemProp Pro 199
overview 57 Solution affects 177
Settings Solvent accessible surface
changing defaults 9 calculation types required 85
changing structural display 75 definition 88
default 9 map property 91
Sextic bending constant 246 mapping atom colors 91
Shadowed Colors control 81 mapping group colors 91
Shift+click 3 mapping hydrophobicity 91
Shift+drag 3 solvent radius 89
Shift+selecting 63 Solvent Accessible Surface dialog 89
Show Adjacent Atoms command 66 Solvent radius 89
Show Bond Angles command 97 Sorting properties 203
Show Bond Lengths command 14, 96 Space Filling display 76
Show Close Contacts command 98 Speed control 108
Show Dihedral Angles command 98 Spin About Selected Axis command 109
Show H’s and Lp’s Spin density
setting 65 mapping onto surfaces 91
tutorial example 19, 21 overview 180
Show Internal Coordinates command 71 Spin Torsional Angles command 109
Show Pop-up Information check box 94 Standard Gibbs Free Energy, ChemProp Pro 199
Show Reverse command 66 Standard Measurement 235
Show Ring Closures command 99 Bond Angle 242
Show Surface button 85, 88 Bond Length 241
Show Used Parameters command 155, 157, 237 Standard measurements 13
Showing messages 102 bond angle 13
Single bond tool 46 bond length 13
Single point calculations overriding 62
definition 124 Standard Molecular Data file format 120
MOPAC 170 Standard Molecular DataSee SMD file 275
overview 127 Start button 7, 108
Size of window 70 Stationery point 126
Slider 7 Stationery submenu 38
sm2 file extension 38, 112 Step Interval control 152
SM2See SYBYL MOL2 File 280 Stereo Offset control 83
SMD File 275 Stereo View control panel 83

Stereochemistry Synchronize control 87
changing 60 System requirements 3
fusion atoms 60
Steric energy T
computing 155
equations 130 Tables
parameters 155 external 11
terms 156 internal 11
tutorial example 25, 29 Taper Cylindrical Bonds control 82
Stewart, Dr. James 1, 231 Technical support 221
Sticks display 76 Template submenu 38
STN Express 120 Templates
Stop button 7, 108 creating 38
Stopping saving settings in 9
docking 104 Terminate After control 152
minimization 147 Text Building tool
molecular dynamics 154 definition 47
MOPAC 167 description 49
movie replay 109 tutorial example 20, 21
overlaying 107 Theory tab
Stretch-bend cross terms 136 GAMESS 193
Stretch-Bend Energy, MM2 200 Gaussian 188
Stretch-bend parameters 246 MOPAC 162
Structure displays Thermal Capacity, ChemProp Pro 199
changing 75 TIFF
overview 75 description 114
Structure-activity relationships 197 file format 114
Substructures 215 Tools palette 7, 46
adding to model 54 ToolTips 2
tutorial example 23 Torsion energy
Substructures table 236, 240 constraints 136
Supplier, finding online 211 equation 132
Surface Types 85 MM2 200
Switching between open models 37 Torsional Parameters table 248
SYBYL file format 120 Torsional Parameters table, 4-membered ring 248
SYBYL MOL File 278 Torsionals table 236
Fortran format 280 Torsionals table, 4-membered ring 236
SYBYL MOL2 File 280 Torsion-Stretch Energy, MM2 200
Fortran format 283 Total charge density surface
SYBYL2See SYBYL MOL2 File 280 calculation types required 85
SYBYLSee SYBYL MOL File 278 definition 91
Symbol field 238 map property 91
Symmetry mapping electrostatic potential 91
MOPAC 201 mapping molecular orbitals 91
summary file 183 mapping spin density 91

tutorial example 32 cutoffs 133
Total spin energy 133, 201
calculation types required 85 Energy, MM2 200
definition 91 Radius field 239
tutorial example 31 surface, definition 88
Total Spin Density Surface dialog 91 Van der Waals radii
Index
Track Rotations in Monochrome control 67, 108 atom size control 82

Trackball tool dot surfaces display display 77
description 46 Vapor Pressure, ChemProp Pro 199
overview 68 VDW field, atom types 12
tutorial example 17 VDW Interactions table 236, 250
Trackball, Z-axis rotation 68 VDWINT.TBLSee VDW Interactions table 250
Transition state 126 VECTORS 183
Translucent surface type 86 Vibrational Energies 183
Triple bond tool 47
Triple Bonds field 240 W
Troubleshooting
atoms shift on MOPAC input 185 Wang-Ford charges 175
background color 79 Water Solubility, ChemProp Pro 199
Chem3D 222 Wave equation 138
MOPAC quits 183 Web site, CambridgeSoft, accessing 212
online 213 When 116
Window menu 16
U Window size 70
Windows Help 2
UHF 139, 141, 163 Wire Frame display 76
UHF spin density 180 Wire mesh surface type 86
Uncoordinated bond tool 47 WMF file format 113
Uncoordinated bonds 48 WWW, technical support 221
Undo command 43
Unix, Gaussian files 92 X
Use Current ZMatrix button 117
Use Tight Convergence Criteria X-axis rotation 67
description 188 –XH2– field 243
GAMESS 194 –XR2– field 242
UV energies 184 –XRH– field 243
V Y
V1 field 248 Y-axis rotation 67
V2 field 248
V3 field 249 Z
van der Waals
cutoff distance 246 Zero Point Energy 183
cutoff term 229

Z-matrix
changing 71
overview 14, 101
pop-up information 93
using dummy atoms 48
zmt file extension 38
zmt file format 118
Zwitterions 53

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ChemDraw Plugin
Advanced WWW Structure Client
• Embed live ChemDraw documents in WWW pages
• Works with Netscape & MS Internet Explorer
• Included with ChemDraw Pro & Ultra
SYSTEMS & LANGUAGES

Windows & Macintosh English & Japanese
Windows: 95/98 or NT 4.0, 486, 16 MB
Macintosh: System 7.5, PowerPC, 16 MB
All specifications subject to change without notice.
CS Chem3D
®

NEW
MOPAC 97
Gaussian
Chem3D Pro brings powerful computational chemistry and

3D publishing to your desktop. Join the tens of thousands of
chemists who make Chem3D the most widely used modeling
package in the world. Use molecular mechanics to find low ener-
gy conformations and semi-empirical methods to visualize molec-
ular surface properties and calculate partial charges. Convert your
ChemDraw or ISIS Draw sketches into 3D models.
Chem3D add-ons: expand the capabilities of Chem3D Pro with
Gaussian for ab initio calculations, Conformer for conformational search and analysis,
SciLogP and SciQSAR for property prediction and analysis.
Chem3D Ultra includes MOPAC Pro to compute physical properties and transition
state geometries using AM1, PM3, MNDO, MINDO/3 & MNDO/d potential functions.
Use Chem3D’s surface property mapping with MEP , charge density, and spin density to
visualize MOPAC results. Add Gaussian calculations to Chem3D with direct client interface.
Molecular Orbital Calculations
Surface Visualization
Chem3D Ultra
Ultimate Modeling, Visualization & Analysis
• Adds MOPAC Pro, Chem3D Plugin & ChemDraw Std to Chem3D Pro
• Includes Gaussian Client interface
• ChemProp Pro—advanced property predictions including LogP
Chem3D Pro
Premier Modeling, Visualization & Analysis
• Model types: space filling CPK , ball & stick, stick, ribbons, vdW dot surfaces & wire-frame
• Compute & visualize partial charges
• 3D surface properties including MEP & orbital mapping
• Creates 3D models from ChemDraw or ISIS Draw
• Polypeptide builder with residue recognition
• Supports: PDB , MDL Molfile, Beilstein ROSDAL , Tripos SYBYL MOL , EPS , PICT , GIF , 3DMF , TIFF , PNG & more
• ChemProp—Basic property predictions with Connolly volumes and surface areas
• Accepts output from other 3D graphics modeling packages
Computation & Analysis

• MM2 minimization & molecular dynamics
• Extended Huckel MO calculations
• Dock ligand and substrate molecules
MOPAC Pro
Advanced Semi-Empirical Computation
• Calculate ∆Hf, solvation energy, dipoles, charges, UHF & RHF spin densities, MEP , charge densities & more
• Optimize transition state geometries
• AM1 , PM3 , MNDO , MINDO/3 & MNDO/d methods
Chem3D Plugin
Advanced WWW Model Client
• Works with Netscape Navigator and Internet Explorer
• Interactive visualization of 3D molecules on Internet
• Included with Chem3D Ultra
SYSTEMS AND LANGUAGES

Windows: 95/98 or NT 4.0, Pentium, 32 MB
Macintosh: System 7.5.5, PowerPC, 32 MB
CS ChemFinder ®
NEW
Searching and Information Integration ChemInfo
MS Excel
ChemFinder Pro is a fast, chemically intelligent database

search engine for personal, group or enterprise-wide use.
ChemFinder can read and write to MDL ISIS databases in SD file
format for easy desktop access. ChemFinder can be integrated into
Excel to provide in-place active database capabilities.
An ever-increasing number of chemical databases are available in
ChemFinder format, putting the world’s scientific literature at your
fingertips. ChemFinder can also be used as a chemical inventory tracker,
to create SAR tables in Excel, and more. ChemFinder is multi-user and network friendly.
ChemOffice WebServer, including ChemFinder WebServer, enables you to serve
chemical data over your Corporate Intranet, Extranet or the WWW Internet using the
ChemDraw Plugin for query information to provide global institution-wide access to
chemical database information. Try out the ChemFinder WebServer using the ChemDraw
Plugin for substructure input and output on PC and Macintosh systems. Available at
www.ChemFinder.com
Table View
Relational Data
ChemFinder.Com
Ultimate Web Searching & Information
• Access chemical information for tens of thousands of compounds
• Searching by name, CAS number, formula, MW and boiling & melting points
• Use ChemDraw plugin to perform substructure searches
ChemFinder Pro for Windows

Premier Searching & Information
• Fully relational database engine
• Fully integrated, native MS Excel interface
• Manages hundreds of thousands of compounds
• Use with ChemInfo Pro—a library of thousands of structures, models and information
• Query refinement and unlimited hits
• Simple user-definable forms for custom displays
• Allows multiple structures per record
• Compound perception & search algorithms
• Connects to MS Access and ODBC servers
• Information integration with ChemOffice, Microsoft Office and Grams
• Simultaneous multi-user access
• Visual Basic OLE Automation, DDE & scripting
• Allows dataform security and authoring constraints
• Share group data across a network, the Internet or intranet
• Connects to Oracle and Sybase relational databases
• Access tens of thousands of compounds from ChemFinder WebServer
ChemFinder Pro for Windows & Macintosh

• Advanced search & structure query features
• Complete integration with ChemDraw & Chem3D
• Stores structures & models for easy retrieval
• Stores physical and calculated data
• Search by substructure (including stereochemistry) using ChemDraw
• Search and store chemical reaction data
• Import data from MDL standard SD files
• Sort by formula, MW , or any text or number field
SYSTEMS & LANGUAGES
Macintosh: System 7.5.5, PowerPC, 32 MB
CS ChemInfo TM
NEW
Structures, Models and Information ChemACX
ChemRXN
ChemInfo Pro is a collection of high-quality, substructure-

searchable chemical databases for all types of reference work. The
ChemACX directory of commercially available chemicals lists
products from over 70 leading suppliers, including the complete
catalogs of Sigma-Aldrich, Fisher-Acros, Lancaster, TCI America,
and others. ChemRXN contains two databases of over 13,000
chemical reactions each. The ChemINDEX set of structure and
property databases includes the complete contents of
CambridgeSoft’s award-winning ChemFinder WebServer, the NCI database, and others.
ChemMSDX has Material Safety Data Sheets for over 7,000 pure compounds.
ChemFinder Ultra includes ChemInfo databases with ChemFinder, which features
rapid structure and substructure searching, a flexible forms-based interface, and seamless
integration with ChemDraw and Chem3D. ChemFinder runs on your Windows PC , with
no need for expensive server hardware.
The ChemInfo WWW Subscription Editions provide subscription access to the ChemInfo
databases using the ChemDraw Plugin for substructure input and output on PC and
Macintosh client systems. Available at www.ChemFinder.com
Reaction Searching
Locate Commercial Chemicals

ChemFinder Ultra
Ultimate Structure & Model Information
• Adds ChemDraw Std, ChemDraw Plugin, Chem3D Std & ChemInfo Pro to ChemFinder Pro
ChemInfo Pro
Professional Structure & Model Information
• ChemACX database of commercially available chemicals lists over 120 catalogs offering over 250,000 products—over
160,000 different chemicals
• ChemRXN includes ChemSelect from InfoChem GmbH and a sample from ISI’s ChemPrep—over 29,000 organic reactions in all
• ChemINDEX is a compendium of structures and properties for over 180,000 compounds. It contains the NCI small molecule
database and the complete contents of CambridgeSoft’s ChemFinder WebServer database
• ChemMSDX provides full Material Safety Data Sheets for over 7,000 pure compounds
• Additional databases are available from ISI , InfoChem, & other information providers
ChemFinder Pro
• Windows-based database search and query engine for all ChemInfo databases
• Sophisticated structure– and substructure search by reactant, product, or functional group transformation
• Displays results as forms or in spreadsheet-style table view
• Native MS Excel interface
• Imports data from MACCS , REACCS , ISIS , and MS Access
ChemFinder.Com
WWW Searching & Information
• WWW ChemInfo databases available by subscription at www.ChemFinder.com
• Use ChemDraw Plugin to enter structural queries and obtain results as live chemical structures
• Works with Netscape & MS Internet Explorer
• Import/export results from & to other applications
SYSTEMS & LANGUAGES

Windows Only English & Japanese
ChemOffice WebServer ™
Enterprise Solutions, Applications and Databases
ChemOffice WebServer is the leading application platform for enter-

prise, corporate intranet, and WWW Internet scientific information manage-
ment. Compatible with all major databases including Oracle, SQL Server,
MDL ISIS , and MS Access, ChemOffice WebServer is used throughout the
industry for e-commerce, e-laboratory notebook, chemical registration, chem-
ical databases, and custom web applications. ChemOffice WebServer supports
structure and substructure searching, and comes with the ChemACX, ChemINDEX,
ChemRXN, and ChemMSDX databases, and a chemical registration application.
ChemOffice Browser, including ChemDraw Java and the ChemDraw

and Chem3D Plugins, bring the power of ChemOffice to the WWW Internet and corporate intranets. With
the ChemOffice Browser, Microsoft Explorer and Netscape Navigator browsers become instantly chemi-
cally aware. Search by structure and text and analyze 3D models, including molecular surfaces.
Web Oracle Solutions built with ChemOffice WebServer integrate chemical structures and Oracle
data such as biological test results and spectra. To access web Oracle applications, just click on a hyperlink
that displays compound databases, reaction database, and in-house applications. The ChemOffice
WebServer rapidly returns results, which can be manipulated, saved, or exported to MS Excel.
E-Laboratory Notebook
ChemACX.Com—Chemicals & Biologicals
Chemical Catalog
Electronic Commerce
Searching, Purchasing and Inventory
• ChemACX, over 500,000 chemical & biological products and supplies
• Scientists can search by structure, product name, part number & more
• Intranet or Internet purchasing system
• Handles sub-accounts, charge backs, and project billing
• Integrates with inventory and existing procurement systems
Enterprise Solutions
E-Notebook, Registration and CombiChem
• Web browser front end with ChemOffice & ChemDraw integration
• Electronic notebook application with structure, reaction, and text searching
• Visualize results on the Web or in MS Excel
• Registration system with robust data model and Oracle back end
• Reaction based combinatorial application speeds library building in MS Excel
• Spectral integration available with all WebServer applications
Chemical Databases
Chemicals, Reactions and Patents
• ChemACX, over 500,000 chemical & biological products and supplies
• ChemINDEX, full contents of www.ChemFinder.com, plus NCI & more!
• ChemRXN, over 30,000 chemical reactions from ISI & InfoChem
• ChemMSDX, materials safety data for over 7,000 pure compounds
• Derwent World Drug Index & World Drug Alerts for current awareness and patents
• ISI Current Chemical Reactions
• InfoChem ChemReact & ChemSynth for 400,000 reactions summarizing 2.5 million reaction database
• Current Drugs ID db drug intelligence
SYSTEMS & LANGUAGES

Windows & Macintosh English, Japanese, French, German
Server: Windows NT 4.0, sp3, option pack 4 (IIS 4.0); 128Mb RAM; 4Gb disk
Client: standard Win/Mac ChemOffice Ultra client spec’s; Netscape Navigator 4.0 or
MS Internet Explorer 4.0
Enterprise Solutions
E–Lab Notebook, Registration and Combinatorial
E–Laboratory Notebook
The ChemOffice laboratory notebook application does for the scientific notebook what Microsoft Word
did for the office memo. Notebook pages can be written with ChemOffice and Microsoft Office (Word,
Excel, and PowerPoint). The results are stored in Oracle for later retrieval and are indexed by chemical
structure, reaction, text, author’s name, and other customizable fields. Notebooks are searchable by
structure, reaction, scientist, etc., and are protected with Oracle’s security. Entering reaction schemes is
speeded by automatic stoichiometry calculations and ChemDraw’s powerful reaction-mapping tools.
With the notebook, you can also store your spectra in electronic form.
Chemical Registration
ChemOffice WebServer provides a powerful, web-based registration solution. The web browser interface,
with the popular ChemDraw Plugin, provides an easy and intuitive user interface. There is no new soft-
ware to learn, and scientists are at home with their favorite web browser. The registration system
includes a robust data model for pure compounds, batches, salt management, automatic duplicate
checking, and unique ID assignments. Compounds may be entered individually or with SD files. The
data model resides entirely in Oracle and uses Oracle’s security and transaction framework. For compa-
nies intending to modify or construct their own registration system, ChemOffice WebServer includes a
powerful Software Developer’s Kit (SDK ) to add custom functionality. Instead of inventing a proprietary
language, the ChemOffice WebServer SDK extends the Microsoft Intranet and Oracle languages for
chemistry, allowing information scientists to use the industry’s most powerful development tools like
Microsoft Visual Studio and Oracle Designer 2000.
Combinatorial Chemistry
The combinatorial extension to ChemOffice is designed for the increasing number of chemists who seek
to utilize combinatorial techniques to build libraries of reasonable size on a regular basis. Since many
chemists manage their combinatorial experiments with MS Excel, the ChemOffice solution integrates
ChemDraw with Excel and thereby provides combinatorial chemists with the chemistry functions they
require inside the software they prefer to use. Draw reactions in ChemDraw, find reagents with
ChemFinder and design experiments in Excel. Unsurpassed level of integration between products and the
smart, natural reaction-based approach to synthesis set the new standard for usability and effectiveness
for combinatorial chemistry software.
E-Laboratory Notebook
Chemical Registration
Combinatorial Chemistry
Electronic Commerce
Searching, Purchasing, Saving and Inventory
E-Commerce
The ChemACX.Com Internet and intranet procurement systems allow chemists and biologists to order
reagents and laboratory supplies right from their web browser. Available over the web or on your local
network, this purchasing system is a complete solution for searching, sourcing and fulfillment.
Internet Procurement
Researchers using ChemACX.Com have access to the most current pricing and availability information.
This information helps scientists make informed buying decisions unattainable with out-of-date catalogs
and database files. Scientists search from hundreds of catalogs from top chemical vendors by substruc-
ture, chemical name, formula, and part number. Search www.ChemACX.com, find the products and
availability from the industry’s top suppliers, and buy online with purchase order or credit card.
Financial Control
The purchasing system, whether used over the Internet or deployed on an intranet, has the ability to man-
age multiple accounts, sub-accounts, charge backs, order tracking, and much more. It provides flexible
reporting on accounts, vendor purchasing and shipping charges. Add custom financial reports with ease!
The ChemOffice WebServer with ChemACX.Com purchasing system also works with existing purchasing
systems and inventory tracking systems. With the ChemOffice WebServer ChemACX purchasing system,
scientists use the software and databases they’re familiar with to search for chemicals and supplies they
need. At the same time, the system provides information about pricing, budget levels, and buying patterns.
Intranet Procurement
On a local intranet, ChemACX.Com has the ability to add specialty suppliers, custom pricing, and fully-
configurable sign-off procedures for purchases. It easily integrates with existing purchasing and inventory
systems, providing tracking and safety information from the loading dock to the laboratory.
Consolidated Invoicing
Purchase reagents and supplies directly from vendors, or consolidate your ordering through the
ChemACX.Com Internet service. When purchases are consolidated through ChemACX.Com, products
from multiple vendors can be combined on one electronic purchase order. The ChemACX.Com sourcing
system also provides monthly consolidated billing and reports.
Inventory Management
ChemOffice WebServer with ChemACX purchasing integrates with in-house or commercial inventory sys-
tems. For example, CIS Pro, the Chemical Inventory System available from ChemSW, offers a flexible
solution which meets the requirements of all organizations that maintain chemical inventories.
Search for Chemicals and Biologicals
Purchase Online
Chemical Databases
Chemicals, Reference, Reactions, Patents and MSDS
Databases
ChemOffice WebServer provides a full range of compound and reaction databases essential for research.
Databases are available over the WWW Internet at www.ChemFinder.com, or over corporate intranets.
Chemicals
ChemACX, Available Chemicals Xchange, is a large and rapidly growing source for information on com-
pound availability. It includes compounds from Aldrich, Fisher, Acros, ICN , Lancaster, TCI , ALFA
ÆSAR, Avacado, and Maybridge with over 200 suppliers and over 500,000 products. Available for busi-
ness-to-business e-commerce. Also included is a library for screening and combinatorial chemistry.
Reference
ChemINDEX includes ChemFinder.Com, the public NCI compounds and other collections, which
together include more compounds and structures than the Merck Index and CRC Properties of Organic
Compounds combined.
World Drug Index (WDI ) from Derwent contains over 58,000 compounds with known biological
activity either available as drugs or submitted for clinical development. WDI classifies compounds
according to type of biological activity, mechanisms of action, synonyms, trade names, manufacturers,
references and more.
Reactions
Current Chemical Reactions (CCR ) from ISI is both a current awareness and a data mining applica-
tion used to design chemical syntheses. Renowned for its quality, CCR contains information from over
300,000 articles reporting the complete synthesis of molecules. Updated daily, the CCR is also an excel-
lent way to stay on top of recent developments.
ChemReact and ChemSynth from InfoChem are carefully selected from a database of over 2.5 million
reactions through an automated process of reaction classification. With over 390,000 reactions,
ChemReact is designed for expert synthetic chemists designing novel syntheses. Entries in ChemSynth
are limited to reactions from ChemReact with over 50% yield and which have been reported at least
twice in the literature.
ChemRXN is a refined selection of over 29,000 fully atom-mapped reactions. Including carefully select-
ed reactions from InfoChem’s ChemSelect database and ISI ’s ChemPrep database, ChemRXN is a terrific
combination of utility.
Patents
World Drug Alerts (WDA ) from Derwent is a current awareness application providing information on
patents, new biologically active compounds, new methods for synthesizing drugs and other data gath-
ered after careful review. It is a requirement for effective decision making in all stages of drug design.
Investigational Drugs Database (ID db) from Current Drugs is the world's leading competitor intelli-
gence service on drug R&D. Updated weekly, it covers all aspects of drug development world wide, from
first patent to eventual launch or discontinuation.
Safety MSDS
ChemMSDX provides over 7,000 material safety datasheets.
ISI Reactions
Derwent Patents
CS Software Problem Report
For faster response and accuracy, use the Web:
www.camsoft.com/support/suppProbRep.cfm
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Name WWW www.camsoft.com/support/suppProbRep.cfm
Title EMAIL support@camsoft.com
Firm FAX 617 588–9360
Street MAIL CambridgeSoft, 100 CambridgePark Dr.
City State Zip Cambridge, MA 02140 USA
Country
Tel Fax
Email
DETAILS OF THE PROBLEM
ATTEMPTED SOLUTION
SYSTEM CONFIGURATION
SOFTWARE ChemOffice ChemDraw Chem3D ChemFinder ChemInfo ChemDraw Chem3D Other
Plugin Plugin
Please cut here or photocopy page.
Version Number
Serial Number
SYSTEM
Computer Model
Windows (version)
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WWW www.camsoft.com TEL 617 588–9300 MAIL 100 CambridgePark Dr.

EMAIL support@camsoft.com FAX 617 588–9360 Cambridge, MA 02140 USA
ChemOffice.Com
CS Chem3D
®
for Windows Quick Reference

SCREEN ELEMENTS
Application Selected Axis
Control Menu Title Bar Status Bar Rotation Bar Minimize Button Maximize Button
Quit Button
Menu Bar Close Button
Element H(3) Serial Number

Symbol
Tools Palette
C(1)
H(4)
H(6)
®
C(2)
Atom Label
Measurements
Model Window Selected Table
Internal Atom
Rotation Bar
Shrink Button H(5)
Grow Button
Message
Window
Start Button Record Button Movie Controller X-axis Rotation Bar

Stop Button Movie Slider Knob Y-axis Rotation Bar
TOOLS PALETTE
Select Tool
Trackball Tool
Single Bond Tool
Double Bond Tool
Triple Bond Tool
Text Tool
Eraser Tool
MENUS
Create a new model window.
Display templates for creating new models.
Open or import a model.
Close the active window.
Save the active model to a file.
Save a copy of the active model with a different
Discard changes to the active model since last save. name, location, or file type.
Change default to current settings.
Set printing options.
Set print options and print your model.
Reopen a recently opened model.
Close Chem3D.
Undo the last action.

Remove selection and copy it to the Clipboard.
Copy selection to the Clipboard.
Place contents of the Clipboard into active window.
Delete selection from the active window.
Copy the active model to the Clipboard as a ChemDraw
Select all atoms and bonds in a model, all text in the structure or bitmap or movie.
text box, or all records in a table window. Select specific atoms in your model.
Delete stored frames.
Delete unneeded Hückel, MOPAC, or Gaussian
Delete Hückel, MOPAC, or Gaussian computations. molecular surfaces computations.
Specify options and minimize the active

model using the MM2 force field.
Run a job stored in a Job file.
Repeat the last MM2 job performed.
Toggle standard
Windows display toolbar. Toggle Tool
Palette display.
Set building, analyzing,
and displaying options.
Show selected
molecular
surface. Display the parameters used in an
MM2 analysis of the current model.
Specify properties to compute for the

active model using the MM2 force field.
Perform a Molecular Dynamics run

Display atom types table
for building models. Display tables
of parameters
for building
models and Search chemical databases on
performing CambridgeSoft’s web site.
Display elements table
for building models. analyses.
Access chemical supplier
information online.
Access CambridgeSoft’s store.
Display substructures
table for building models.
Access CambridgeSoft’s
Tech Support web site.
Access CambridgeSoft’s
SDK web site.
Register Chem3D electronically.
Access CambridgeSoft’s web site.
Center the selected atoms in the active window.
Move selected atoms parallel to the X-Y, Y-Z, or X-Z plane.
Change the color of selected atoms.
Show element symbols for selected atoms.
Show serial numbers for selected atoms.
Show atoms as spheres.
Show van der Waals dot surfaces for selected atoms.
Display the measurement for selected atoms.
Break bonds between selected atoms.
Change bond order of selected atoms to single, double,
Create bonds between atoms that are close together. or triple.
Add a dummy atom (Du) to the center of the selection.
Invert stereochemistry at selected atoms.
Position an atom relative to other atoms.
Remove selected atoms and bonds from view.
Remove atoms and bonds that are not selected from view.
Show all hidden atoms.
Show hidden atoms that are next to selected atoms.
Show hidden and hide visible atoms.
Create a group definition for the current selection.
Display Status Bar.

Display Rotation Bars.
Display Movie Controller.
Open Messages window.
Show Model Table items.
Show hydrogens and lone pairs while building.
Enlarge model.
Reduce model.
Correct atom types and number of hydrogens
for the selected atoms. Minimize the error in your model based on its geometry.
Orient one fragment relative to another by atom pairs
(specified by the Set Distance command). Overlay fragments by atom pairs.
Reflect selected atoms through a plane.
Resize the model to fit in Model window.
Resize the selected atoms and bonds to fill
the Model window. Resize all model frames to fit in Model window.
Perform a series of rotations around the X-axis.

Perform a series of rotations around the Y-axis.
Perform a series of rotations around the Z-axis.
Perform a series of rotations around a specified axis.
Perform a series of rotations that vary
the specified dihedral angle.
Display bond lengths and angles, dihedral angles, close
Compute orbitals for surfaces or partial charges contacts, and ring closures.
display using Extended Hückel theory.
Show the deviation of selected atoms
Compute a variety of physical properties. from the normal plane.
You must own Gaussian™, GAMESS™, or CS MOPAC™

for the respective menus to appear.
Repeat the last job.

Run a job that is stored in a Job file.
Specify options and minimize the active model.
Specify properties to compute for current conformation of active model.
Create Input file for external use or editing.
Run an external input file.
Display information about Client.
Optimize the geometry of a model to a saddle point using MOPAC Pro.

WORKING WITH SELECTIONS
If you want to … Here’s how …
Select an atom or bond With Select Tool, click an atom or bond
Add atoms or bonds to the selection With Select Tool, shift+click atoms or bonds not currently selected
Remove atoms or bonds from the selection With Select Tool, shift+click atoms or bonds currently selected
Select several atoms and bonds With Select Tool, drag diagonally across model
Deselect all atoms and bonds Click in an empty space in the Model Window
BUILDING TECHNIQUES
Change a bond type Drag over the bond using a different bond tool
Change an atom type using the Replacement Text box With Text Tool, click atom, type atom type (e.g. H Enol), press ENTER
Change an element using the Replacement Text box With Text Tool, click atom, type an element (e.g. N), press ENTER
Reserialize atoms using the Replacement Text box With Text Tool, click atom, type a starting number, press ENTER
Add a substructure using the Replacement Text box With Text Tool, click atom, type a substructure (e.g. OEt), press ENTER
Create a dummy atom using a bond tool Click and drag using the Uncoordinated Bond Tool
Move an atom Select and drag an atom
Pull atoms towards you CTRL+drag the atoms down
Push atoms away from you CTRL+drag the atoms up
Convert a ChemDraw structure into a model Copy the structure to Clipboard and Paste into Chem3D
Place a picture of a model in ChemDraw Copy the model to Clipboard and Paste into ChemDraw
Convert a model into a ChemDraw structure Choose Copy ChemDraw Structure from Edit Menu
ROTATING TECHNIQUES
Open the Rotate dialog box Double-click a Rotation bar
Rotate using the last entered rotation amount Triple-click a Rotation bar
Rotate selected fragments Drag a Rotation bar
Rotate all fragments regardless of selection Shift+drag a Rotation bar
Save rotation frames as a movie Click the Record button before performing a rotation
Stop recording frames Click the Stop button
Replay recorded frames Click the start button or drag the Movie Controller Slider knob
WWW www.camsoft.com/support/ TEL 617 588–9100 MAIL 100 CambridgePark Dr.

EMAIL support@camsoft.com FAX 617 588–9360 Cambridge, MA 02140 U S A
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft.Com © 2000
IWE 07381 0009
ChemOffice.Com
CS Chem3D
®
for Macintosh Quick Reference

SCREEN ELEMENTS
Application Selected Axis
Control Menu Close Button Title Bar Status Bar Rotation Bar Maximize Button Minimize Button
Menu Bar
Element H(3) Serial Number

Symbol
Tools Palette
C(1)
H(4)
H(6)
®
C(2)
Atom Label
Measurements
Model Window Table
Internal Selected
Rotation Bar Atom
H(5)
Shrink Button
Grow Button
Message
Window
Start Button Record Button Movie Controller X-axis Rotation Bar

Stop Button Y-axis Rotation Bar Movie Slider Knob
TOOLS PALETTE
Select Tool
Trackball Tool
Single Bond Tool
Double Bond Tool
Triple Bond Tool
Text Tool
Eraser Tool
MENUS
Create a new model window.
Display a submenu containing templates for creating new
Open or import a model. models.
Close the active window.
Save the active model to a file.
Save a copy of the active model with a different name,
Discard changes to the active model location, or file type.
since it was last saved. Change default to current settings.
Set paper size and other options affecting the printed
output of your model. Set print options and print your model.
Close the Chem3D application.
Undo your last action.

Remove selection and copy it to the Clipboard.
Copy selection to the Clipboard.
Place contents of the Clipboard into active window.
Delete selection from the active window.
Display a submenu with a command for copying the active
Select all atoms and bonds in a model, all text in the model to the Clipboard as a ChemDraw structure or bitmap.
text box or all records in a table window. Display a submenu with commands for selecting specific
Display a submenu where you can choose to delete atoms within your model.
stored frames. Display a dialog where you can delete unneeded Hückel,
Display a dialog where you can choose to delete unneeded MOPAC or Gaussian molecular surfaces computations.
Hückel, MOPAC or Gaussian computations.
Specify options and minimize the active

Run an MM2 job that

is stored in a Job file.
Set options that affect
building, analyzing, and
displaying your model. Repeat the last MM2 job performed.
Display dialog for showing

selected molecular surface.
Display a table of atom

types you can use for
building models.
Display tables containing
Display a table of all parameters for building
elements you can use for models and performing
building models. analyses. Information in Calculate a series of steric energy
tables can be edited using values by varying the angle of a
the Table Editor selected dihedral.
Display a table of application.
substructures you can use Display a list of parameters used in an
for building models. MM2 analysis of the current model.
Specify properties to compute for the

current conformation of the active
Perform a Molecular Dynamics run

Center the selected atoms in the active window.
Display a submenu where you can move selected atoms
Change the color of selected atoms. parallel to the X-Y, Y-Z, or X-Z plane.
Display a submenu where you can show element symbols
Display a submenu where you can show for selected atoms.
serial numbers for selected atoms. Display a submenu where you can show atoms as spheres.
Display a submenu where you can show van der Waals
dot surfaces for selected atoms. Display the measurement for selected atoms.
Break bonds between selected atoms.
Display a submenu where you can change the bond
Create bonds between atoms that are close together. order of selected atoms to single, double, or triple.
Add a dummy atom (Du) to the center of the selection.
Invert stereochemistry at selected atoms.
Display a submenu for positioning an atom relative to
Remove from view atoms and bonds that are selected. other atoms.
Remove from view atoms and bonds that are not selected.
Show all hidden atoms.
Show hidden atoms that are next to selected atoms.
Show hidden and hide visible atoms.
Create a group definition for the current selection.
Display Status Bar.

Display Rotation Bars.
Display Movie Controller.
Open Messages window.
Display submenu to show Model Table items.
Show hydrogens and lone pairs automatically as building
Enlarge model. progresses.
Reduce model.
Correct atom types and number of hydrogens
for the selected atoms. Minimize the error in your model based on its geometry.
Orient one fragment relative to another by atom pairs
(specified by the Set Distance command). Overlay one fragment on another by atom pairs (specified
Display a submenu for reflecting selected atoms by the Set command in the Object menu).
through a plane.
Resize the model to fit within the bounds of the Model
Resize the model so that selected atoms and bonds fill the window.
Model window. Resize all frames of the model to fit within the bounds of
the Model window.
Perform a series of rotations around the X-axis.

Perform a series of rotations around the Y-axis.
Perform a series of rotations around the Z-axis.
Perform a series of rotations around an axis specified by two
Perform a series of rotations that vary the dihedral angle selected atoms.
specified by selection of the dihedral’s central bond. Display bond lengths and angles, dihedral angles, close
Compute orbitals for surfaces display using Extended contacts, and ring closures.
Hückel theory. Compute partial charges using Extended Hückel theory.
Show the deviation of selected atoms from the normal
plane.
Compute a variety of physical properties.
You must own Gaussian™ You must own CS MOPAC™

for this menu to appear. for this menu to appear.
Repeat the last job.

Run a job that is stored in a Job file.
Specify options and minimize the active model.
Specify properties to compute for the current conformation of the active model.
Create Input file for external use or editing.
Run an external input file.
Display information about Client.
Optimize the geometry of a model to a saddle point using MOPAC Pro.

SCRIPTS FOLDER AND CUSTOMIZED MENUS
The menu bar in Chem3D is customizable. You can create additional menus and add commands that are compiled scripts, documents or other appli-
cations. The additional menus and the items that the menu contains correspond to the contents of the Chem3D Scripts folder, located in the same
folder as the Chem3D. For instance, within the Chem3D Scripts folder is a folder named “Help” which contains, among other things, the document
“About Chem3D Scripts”. The Help menu appears in the Chem3D menu bar with this document as a command. Several additional menus, such as
the Net and MOPAC, were created this way.
WORKING WITH SELECTIONS

If you want to … Here’s how …
Select an atom or bond With Select Tool click an atom or bond
Add atoms or bonds to the selection With Select Tool shift+click atoms or bonds not currently selected
Remove atoms or bonds from the selection With Select Tool shift+click atoms or bonds currently selected
Select several atoms and bonds With Select Tool drag diagonally across model
Deselect all atoms and bonds Click in an empty space in the Model Window
BUILDING TECHNIQUES
Change a bond type Drag over the bond using a different bond tool
Change an atom type using the Replacement Text box With Text Tool click atom, type atom type (e.g. H Enol), press ENTER
Change an element using the Replacement Text box With Text Tool click atom, type an element (e.g. N), press ENTER
Reserialize atoms using the Replacement Text box With Text Tool click atom, type a starting number, press ENTER
Add a substructure using the Replacement Text box With Text Tool click atom, type a substructure (e.g. OEt), press ENTER
Create a dummy atom using a bond tool Click and drag using the Uncoordinated Bond Tool
Move an atom Select and drag an atom
Pull atoms towards you Option+drag the atoms down
Push atoms away from you Option+drag the atoms up
Convert a ChemDraw structure into a model Copy the structure to Clipboard and Paste into Chem3D
Place a picture of a model in ChemDraw Copy the model to Clipboard and Paste into ChemDraw
Convert a model into a ChemDraw structure Choose Copy ChemDraw Structure from Edit Menu
ROTATING TECHNIQUES
Open the Rotate dialog box Double-click a Rotation bar
Rotate using the last entered rotation amount Triple-click a Rotation bar
Rotate selected fragments Drag a Rotation bar
Rotate all fragments regardless of selection Shift+drag a Rotation bar
Save rotation frames as a movie Click the Record button before performing a rotation
Stop recording frames Click the Stop button
Replay recorded frames Click the start button or drag the Movie Controller Slider knob
WWW www.camsoft.com/support/ TEL 617 588–9100 MAIL 100 CambridgePark Dr.

EMAIL support@camsoft.com FAX 617 588–9360 Cambridge, MA 02140 U S A
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft.Com © 2000
IME 07369 0009
Contents
ChemOffice Manual Introduction Chapter 2: ChemSAR for Excel
About the ChemOffice Manual ..................................7 ChemSAR for Excel Overview ...............................21
Conventions................................................................7 Configuring ChemSAR for Excel ............................21
Additional Help ..........................................................7 The ChemSAR Wizard.............................................21
CambridgeSoft Web Pages ..................................7 Selecting ChemSAR Descriptors .............................24
Installation and System Requirements .......................8 Adding Calculations to an Existing Worksheet .......24
Windows Requirements.......................................8 Customizing Calculations ........................................24
Macintosh Requirements .....................................8 Calculating Statistical Properties .............................25
Descriptive Statistics..........................................25
Chapter 1: ChemDraw for Excel Correlation Matrix .............................................26
Overview ...................................................................9 Rune Plots ..........................................................26
Starting ChemDraw for Excel ....................................9
Importing Tables ......................................................10 Chapter 3: CombiChem
Converting and Updating a Worksheet ....................10 Overview .................................................................27
Importing Hit Lists ...................................................10 Starting CombiChem................................................27
Importing a Hitlist..............................................10 Using Help................................................................27
Error Messages ..................................................11 Creating a New CombiChem Worksheet .................28
Exporting Tables ......................................................11 Working with Reaction Templates...........................28
Adding Molecules ....................................................12 Reaction Template Basics..................................28
Adding Molecules with ChemOffice .................12 Adding a Reaction Template to the Reaction
Adding Structure Files .......................................12 Worksheet ..........................................................28
Adding SMILES Strings ....................................12 Editing the Reactions in a Workbook ................29
Adding Molecules by Name.....................................13 Processing the Reaction Template .....................29
Saving Molecules .....................................................13 Working with Reactant Lists....................................30
Searching..................................................................13 Searching ChemFinder Databases............................30
Filter Tables .......................................................13 Searching Manually ...........................................30
Similarity Searches ............................................14 Searching Automatically....................................30
Working with Structures ..........................................15 Adding Databases .........................................31
Naming Molecules .............................................15 Editing the Search ChemFinder List .............31
Using the Clipboard ...........................................15 Searching the ChemFinder Database List .....32
Viewing Structures...................................................15 Searching Other Databases.......................................32
Showing and Hiding Structures .........................15 Imported Data Format ..............................................33
Aligning Structures ............................................16 Structure Column ...............................................33
Resizing Structures ............................................16 Use (Y/N)...........................................................33
Using ChemDraw for Excel Functions ....................16 MOL_ID ............................................................33
Using ChemProp Pro Functions...............................18 Imported Data ....................................................33
ChemProp Properties .........................................18 Creating Experiments ...............................................33
Inserting Functions ............................................18 Working With Experiments ...............................34
Configuring Plates....................................................34
Browsing Plates .................................................35
Viewing Related Structures ...............................35
ChemOffice Contents • 1
Chapter 4: Purchasing for Excel Removing a Collection ......................................60
Duplicating a Collection ....................................61
Overview ..................................................................37
Organizing a Collection.....................................61
Starting Purchasing for Excel ..................................37
Moving Items Within a Collection ...............62
Opening a Chemfinder Worksheet...........................37
Moving Items Between Collections..............62
Administrator
Placing a Chemical Structure in a Worksheet..........38

Referencing Collection Items ............................62
Getting Catalog Information ....................................38
Archiving Collection Items................................63
Shopping for Chemicals...........................................38
Viewing and Hiding Collections .......................63
Ordering Chemicals From ChemACX.Com ............39
Browsing Collections.........................................63
Chapter 5: ChemFinder for Word Limiting Collection Browsing ......................63
Browsing from Home ...................................64
Overview .................................................................41 Browsing to a Specific Page or Collection ...64
Opening ChemFinder for Word ...............................41 Browsing the Entire Collection Tree ............65
Searching by Chemical Structure.............................42 Browsing Up a Level ....................................65
Searching by Multiple Properties.............................43 Viewing Collection Properties...........................65
Selecting Files to Search ..........................................44 Working with Page and Template Sections .............66
Selecting Files With the Look In Tab................44 Creating a Section..............................................67
Selecting Files With the Open File Menu Viewing Sections in Card or List View.............67
Item ....................................................................45 Changing Sections .............................................68
Browsing Search Results .........................................45 Removing a Section ......................................68
Saving Files or Data Sources ...................................47 Renaming a Section ......................................68
Saving Search Results as .sdf Files ...................47 Duplicating a Section....................................69
Saving Data Sources as .dsd Files .....................47 Editing an MS Word Section.............................69
Saving Lists of Directory Paths as .dsd Files ....48 Editing an MS Excel Section.............................70
Searching .dsd Files .................................................48 Exporting a Section............................................70
Sending a File to Another Application ....................48 Recording Reactions ................................................71
Refining Your Search...............................................50 Resizing Reaction Section Parts in Card
Refining Your Query With the Search Tools ....50 View...................................................................71
Refining Your Query With the Search Creating and Editing Chemical Structures ........72
Options...............................................................50 Changing Reaction Properties ...........................72
Changing ChemFinder for Word Settings ...............52 Adding Properties .........................................72
Customizing the ChemFinder for Word Removing Properties.....................................73
Window .............................................................52 Setting and Editing Property Values.............73
Changing the ChemFinder for Word Analyzing a Reaction.........................................74
Preferences.........................................................53 Changing Information in the Stoichiometry
Closing ChemFinder for Word ................................54 Table ..................................................................74
Chapter 6: E-Notebook Adding Information to the Stoichiometry
Table .............................................................74
Overview of the E-Notebook Application ...............55 Removing Reactants and Products from
Terminology.............................................................55 the Stoichiometry Table................................75
Starting E-Notebook ................................................57 Recording Experiment Procedures ....................76
Opening E-Notebook .........................................57 Creating Reactants in the Database ...................77
Logging In .........................................................57 Removing Reactants from the Database............77
Refreshing E-Notebook Information .......................58 Recording Spectra Data............................................78
Working with Collections ........................................58 Resizing Spectra Section Parts in Card View....78
Understanding the Contents of a Collection......58 Changing a Spectrum.........................................79
Creating a Collection .........................................59 Adding a Spectrum .......................................79
Creating a Page Collection from a Template.....60 Removing a Spectrum...................................79
Renaming a Collection ......................................60 Replacing a Spectrum ...................................79
2 • Contents CambridgeSoft
Changing Spectrum Properties ..........................80 Setting Default Reaction Properties.................102
Recording Notes ................................................80 Setting the Chemical Structure File Path ...............102
Organizing Chemical Properties in Table Configuring the Database Options .........................103
Sections ....................................................................81 Setting Multi-User Access ...............................103
Adding Columns ................................................81 Connecting to Chemical Registration ..............104
Removing Columns ...........................................81
Organizing Columns ..........................................82 Chapter 8: Document Manager
Adding Rows .....................................................82 Overview ................................................................105
Removing Rows.................................................82 Logging In ..............................................................105
Organizing Rows ...............................................83 Submitting Documents ...........................................106
Resizing Rows and Columns .............................83 Creating Searches for Documents ..........................106
Changing Information in a Cell .........................83 Understanding Basic Text Searching...............106
Adding Information to a Cell ........................84 Exact Phrase Matching................................106
Registering Chemical Compounds...........................84 Wildcard Searching.....................................107
Searching..................................................................84 Understanding Advanced Text Searching .......107
Printing .....................................................................86 ABOUT .......................................................108
Closing E-Notebook.................................................87 AND (&) .....................................................108
Appendix of Collection Definitions .........................88 EQUIValence (=) ........................................109
Fuzzy (?) .....................................................109
Chapter 7: E-Notebook MINUS (-)...................................................110
Administrator NEAR (;) .....................................................110
Overview of E-Notebook Administrator..................89 NOT (~).......................................................111
Installing E-Notebook Administrator.......................89 OR (|)...........................................................112
Setting up in MS Access ....................................89 Soundex (!)..................................................112
Setting up in Oracle ...........................................90 Stem ($).......................................................113
Starting E-Notebook Administrator .........................91 Performing a Search.........................................113
Opening E-Notebook Administrator..................91 Changing Your Password.......................................114
Logging In..........................................................91 Managing Users......................................................115
Changing User Information......................................92 Logging Off............................................................115
Creating a User ..................................................92
Chapter 9: BioAssay Manager
Changing General Properties .............................93
Changing Security Properties ............................93 Overview ................................................................117
Adding Permissions for a User .....................94 Terminology ...........................................................117
Removing Permissions for a User.................94 System Requirements .............................................118
Retiring a User ...................................................94 Getting Started for the First Time ..........................118
Changing Group Information ...................................95 Opening BioAssay Manager for the First
Creating a Group................................................95 Time .................................................................118
Adding a User to a Group ..................................95 Choosing a Database........................................119
Changing a Group Name ...................................95 Choosing MS Access ..................................119
Removing a User from a Group.........................96 Choosing Oracle..........................................119
Setting Properties .....................................................96 Logging In with MS Access ............................120
Creating a Property ............................................96 Logging In with Oracle....................................120
Changing a Property ..........................................99 Maximizing the BioAssay Manager
Deleting a Property ..........................................100 Window............................................................121
Changing Enumerated Values .........................100 Creating Your First Assay ...............................121
Adding Enumerated Values ........................101 Opening BioAssay Manager ..................................121
Removing Enumerated Values....................101
Organizing Enumerated Values ..................101
Creating and Editing Assay Description Filtering Results .....................................................135
Information.............................................................121 Defining a Filter...............................................136
Creating a New Assay .....................................121 Applying a Filter..............................................136
Renaming an Assay .........................................122 Viewing Filtered Data......................................137
Assigning a Version to an Assay .....................122 Clearing a Filter ...............................................137
Administrator
Viewing Different Assays ......................................122 Using the Help Menu .............................................137

Moving Between Assays .................................123 Using the Admin Dialog Box ..........................137
Searching for an Assay ....................................123 Viewing the Version Information About
Using a Procedures Document ...............................123 BioAssay Manager...........................................138
Opening a Procedures Document ....................123
Saving Procedures ...........................................124 Chapter 10: Chemical Registration
Deleting Procedures.........................................124 Overview ................................................................139
Using a Layout Spreadsheet...................................125 Starting Chemical Registration ..............................139
Opening a Layout Spreadsheet ........................125 Adding New Records to the Temporary Table ......140
Saving a Layout ...............................................125 Adding a Compound........................................140
Deleting a Layout ............................................125 Adding a Reagent ............................................142
Using a Calculations and Variables Document......126 Adding a Batch ................................................143
Opening a Calculations and Variables Reviewing Records from the Temporary Table.....144
Document.........................................................126 Editing Records from the Temporary Table ..........145
Saving Calculations and Variables ..................127 Deleting Records from the Temporary Table ........145
Deleting Calculations and Variables ...............127 Registering Records ...............................................146
Setting Up an Assay Model in the Database Registering Records.........................................146
Tab .........................................................................127 Adding Identifier Information to Records .......146
Adding Tier Information .................................129 Adding Analytics Data to a Record .................147
Adding a Row to Tier Tables ..........................129 Searching Chemical Registration...........................148
Analyzing and Viewing Data with the Searching for Records in the Temporary
Aggregate View ...............................................129 Table ................................................................148
Opening the Aggregate View Dialog Box ..130 Searching for Registered Compounds .............148
Defining an Aggregate View ......................130 Viewing Details of Records.............................148
Choosing Tier One Results to Analyze.......131 Viewing BioAssay Manager Data ...................148
Choosing Calculations to Perform ..............131 Marking Records....................................................149
Naming the Aggregate View Results Viewing Marked Records ......................................149
Column........................................................131 Clearing Marked Records ......................................149
Seeing the Aggregate View Results............132 Exporting Search Results .......................................149
Clearing the Define Aggregate View Viewing Experiments in Spreadsheets...................150
Dialog Box ..................................................132 Managing Tables....................................................151
Opening an MS Excel Spreadsheet .................132 Defining Projects .............................................151
Importing an MS Excel Spreadsheet Defining Notebooks.........................................152
Template From BioAssay Manager.................133 Defining Registration Numbers .......................153
Loading Data Into BioAssay Manager Defining Structure Comments .........................154
From an MS Excel Spreadsheet.......................133 Defining Chemical Registration People ..........154
Changing the Width of Results Columns ........134 Defining Sites ..................................................155
Closing an MS Excel Spreadsheet...................134 Defining Salts ..................................................156
Viewing Tier One Results......................................134 Managing Users and Roles.....................................157
Viewing Tier Two Results .....................................134 Defining Users .................................................157
Graphing Tier Two Results....................................135 Defining Roles .................................................158
Choosing Data for the X- and Y-Axes ............135 Changing Passwords ..............................................159
Viewing a Standard or Log Graph of Tier Defining New Experiments....................................159
Two Results .....................................................135
Managing Analytics Data.......................................160 Chapter 13: ChemACX-SC
Defining Result Type.......................................160
What Is It? ..............................................................187
Defining Experiment Type ..............................161
ChemACX Screening Compound Databases .........187
Defining Parameter Type.................................161
How Is It Useful? ...................................................187
Managing Workgroups...........................................162
ChemACX-SC Participants....................................189
Importing SDFiles ..................................................162
Choosing Preferences.............................................165 Chapter 14: The Merck Index
Printing ...................................................................166
Logging Off............................................................166 What Is It? ..............................................................191
Appendix of Role Definitions ................................167 How Is It Useful? ...................................................191
Chapter 11: ChemInfo Introduction Chapter 15: ChemINDEX

What is ChemInfo?.................................................169 What Is It? ..............................................................193
Conventions............................................................169 How Is It Useful? ...................................................193
Terminology ...........................................................169 ChemINDEX Net ...................................................193
Additional Help ......................................................169 BuckyBase..............................................................194
Online Help......................................................169 National Cancer Institute........................................194
ToolTips...........................................................170 Chapter 16: ChemRXN
Status Bar.........................................................170
Technical Support ............................................170 What Is It? ..............................................................197
System Requirements.............................................170 How Is It Useful? ...................................................197
Installation..............................................................170 ChemPrep ...............................................................197
ChemInfo and ChemOffice ....................................171 ChemSelect.............................................................198
Using ChemInfo .....................................................171
Chapter 17: ChemMSDX
Chapter 12: ChemACX What Is It? ..............................................................201
What Is It? ..............................................................173 How Is It Useful? ...................................................201
ChemACX Database ..............................................173
Appendix: Technical Support
How Is It Useful? ...................................................173
Using ChemACX with ChemOffice Webserver ....174 Overview ...............................................................203
Opening ChemACX.........................................175 Serial Numbers ......................................................203
Searching ChemACX Catalogs .......................175 Troubleshooting .....................................................204
Searching Without the Plug-in.........................176
Creating and Editing Your List of Favorite
Index
Vendors ............................................................177
Saving Search Results to the Shopping Cart ...177
Viewing Your Shopping Cart ..........................178
Removing Items from Your Shopping Cart.....179
Ordering Chemicals Through ChemACX .......179
ChemACX 2000 Participants .................................180
What If My Favorite Supplier Isn’t Listed
Here? ......................................................................185
Administrator
ChemOffice Manual Introduction
About the ChemOffice NOTE: Notes such as this are used to highlight
information supplemental to the main text.
Manual
The ChemOffice Manual is a collection of
instructions for different CambridgeSoft products. Additional Help
Because the ChemOffice Manual is a You can find additional help in the following places:
comprehensive collection, you may not have every
product represented in it. • In “Technical Support” on page 203.
• CambridgeSoft Web Pages in the next section.
This guide assumes you are familiar with your
computer’s operating system. For details about
using your operating system, refer to the user
CambridgeSoft Web Pages
documentation provided with that system. The following table contains the addresses of
For information about ChemOffice, see the ChemDraw and ChemOffice-related web pages.
ChemOffice Manual.
For Access
For information about Chem3D, see the Chem3D information
Manual. about
For information about ChemFinder, see the Technical http://www.cambridgesoft.com/

ChemFinder Manual. Support support/
ChemDraw http://doc.cambridgesoft.com/
Conventions Plugin
The following notations are used throughout this
ChemDraw for http://java.cambridgesoft.com/
user’s guide:
Java
The Ultra symbol indicates that a
ChemOffice feature is available in CS ChemOffice Software http://sdk.cambridgesoft.com/
Ultra only. Developer’s kit
The Pro symbol indicates that a feature is Active X http://sdk.cambridgesoft.com/

available in CS ChemOffice Pro. Features available control
in CS ChemOffice Pro are also included in CS
ChemOffice Ultra. Purchasing http://store.cambridgesoft.com/
CambridgeSoft
Features that are available in CS ChemOffice Std are products and
not indicated by a symbol. chemicals
ChemOffice ChemOffice Manual Introduction • 7

About the ChemOffice Manual
Requirements
Administrator
To install ChemOffice, see the “Read Me First”

document that came with your software. Late
breaking information about installation is contained
in the Read Me file (Macintosh) or Install.txt
(Windows) on the installation CD-ROM.
Windows Requirements
• Windows 95, 98, 2000, Me, XP, or NT
• Disk Space:
• Std: 30 MB
• Pro: 40 MB
• Ultra: 70 MB
Macintosh Requirements
• MacOS 8.6–9.1, MacOS X 10.1
• Disk Space:
• Std: 8 MB
• Pro: 32 MB
8 • ChemOffice Manual Introduction CambridgeSoft

Chapter 1: ChemDraw for Excel
Overview The Add-Ins dialog box appears.
The ChemDraw for Excel add-in is an extension of

Microsoft Excel 97 for Windows. ChemDraw for
Excel allows you to perform the following functions
in an Excel spreadsheet:
• Add molecules and other data from a
ChemDraw database.
• Search using the same search features as
ChemFinder.
• Perform calculations on molecules.
3. Select ChemDraw for Excel and click OK.
NOTE: Any commands you use operate on the A ChemDraw menu is added to the Excel menu
cells, not the pictures in the cells. bar and a ChemDrawtoolbar appears.
These procedures assume you are familiar with

Microsoft Excel 97 for Windows. For more
information about using Excel, see the Excel User’s
Guide. To create a ChemDrawworksheet:
• From the ChemDraw menu, choose New
Starting ChemDraw for ChemDraw Worksheet or click .
Excel A ChemDraw worksheet appears. When a
ChemDraw worksheet is active, ChemDraw for
When you install ChemFinder, ChemDraw for Excel appears in the title bar and the
Excel is automatically installed. ChemDraw toolbar is active.
To start ChemDraw for Excel:
1. Open Microsoft Excel 97 or 2000.
2. From the Tools menu, choose Add-ins.
ChemOffice ChemDraw for Excel • 9

Starting ChemDraw for Excel
Importing Tables Converting and
ChemDraw for Excel allows you to import the Updating a Worksheet
following types of files:
Administrator
You can convert an existing worksheet into a

• MDL SDFiles—Imports all records in the ChemDraw for Excel worksheet. You can do this
database. Each molecule is given the name instead of copy and pasting information from a
stored in the SDFile. The molecules are stored
worksheet into a ChemDraw for Excel worksheet.
in the first column under the heading Structure.
All other columns are named for the properties You can also update an old ChemDarw for Excel
they represent. worksheet so that it has the same format as the new
• ChemDraw databases (.cfw files)—Imports ChemDraw for Excel worksheets.
all records in the main form. Molecular weight
To convert or update a worksheet:
and formula fields are not imported because
ChemDraw for Excel calculates them. • From the ChemDraw menu, choose
Each structure is named Structure <n>, where n Convert/Update Worksheet.
is a unique number.
The work sheet is converted or updated
When you import files, the molecule information is
appropriately.
added as molecules and non-molecular information
is added as separate columns.
Importing Hit Lists
To import a file:
You can perform a search in ChemDraw and then
1. Select the cell from where you want the import
to start. The upper left corner of the import is at import the hitlist structures with data into Excel
this cell. Data in filled down and in columns to using the Get ChemDraw List command.
the right. To use the Get ChemDraw List command, you
2. From the ChemDraw menu, choose Import ChemDraw must be open with a hitlist present.
Table or click .
The Import table dialog box appears. Importing a Hitlist
To import a hitlist:
1. From the ChemDraw menu, choose Get
ChemDraw List.
A dialog box similar to the one below appears
appears:
3. Type or choose the file name to import and

click Open.
2. Click Yes to return to Excel.
All records are added to your spreadsheet.
10 • ChemDraw for Excel CambridgeSoft

Importing Tables
The records are imported into Excel, where the 11. Open a database and perform a search.
first record is put in the currently selected cell. 12.Return to Excel and from the ChemDraw menu,
choose Get ChemDraw List, or click .
Error Messages
If all conditions required to use the Get ChemDraw Exporting Tables
List command are not met, one of the following
error messages may appear. ChemDraw for Excel allows you to export MDL
SDFiles.
ChemDraw is not running, would you like to
start it up? Selected cells are exported to a specified file. If no
cells are selected, the entire spreadsheet is exported.
ChemDraw is not running. Do the following: The area to export must include a column named
3. Click Yes. STRUCTURE in the first row before a blank cell.
The message “After loading your desired

database and performed your search, return to
Excel and redo the operation.” appears
4. Click OK.
ChemDraw opens.
5. Open a database and perform a search.
6. Return to Excel and from the ChemDraw menu,
No database loaded in ChemFinder. Load a
database and perform your search. Then return
to Excel and redo the operation.
ChemDraw is running, but no database is loaded. Do

the following: To export data:
7. Click OK. 1. Select the information to export:
ChemDraw moves to the front.
8. Open a database and perform a search. If you want to export Then
9. Return to Excel and from the ChemDraw menu,

a specified area of your Select the area to
spreadsheet export.
Form has no database or hitlist has no records.
Load a database and perform your search. Then the entire spreadsheet Do not make any
return to Excel and redo the operation. selection.
10.Click OK.
2. From the ChemDraw menu, choose Export
ChemDraw moves to the front. Table or click .

Exporting Tables
The Save Table To dialog box appears. 4. From the ChemDraw File menu, click Exit and
Return to Excel.
The new molecule appears in the cell.
Administrator
Adding Structure Files

To add structure files:
5. Select the cell into which you want to add the
molecule.
3. Type the file name and select the file type. 6. From the ChemDraw menu, choose Load
4. Click Save. Molecule or click .
The file is saved to the destination you The Choose Molecule to Load dialog box
specified. appears.
Adding Molecules
You can add molecules in all file formats supported
by ChemDraw to a spreadsheet. The names of added
molecules are retained. If the molecule does not
have a name, ChemDraw assigns the name:
Structure <n>, where n is a number unique to the
worksheet.
Adding Molecules with ChemOffice NOTE: You can use the sample molecule file,
The most direct way to insert a new molecule into a “SAMPLE.MOL,” contained in the ChemDraw
cell is by using ChemOffice. system directory or any .cdx file to load.
To add a molecule with ChemOffice: 7. Type the file name of the molecule to add and
1. Double-click in a cell. click Open.
The ChemDraw for Excel dialog box appears: The information is stored in the selected cell.
Adding SMILES Strings

You can insert SMILES strings into cells and
convert them to molecules.
To insert SMILES strings:

8. Type or paste SMILES strings into cells.
2. Click Yes.
ChemDraw opens.
3. Draw the molecule in ChemOffice.

Adding Molecules
9. Select the range of cells or single cell to If all cells cannot be converted, a message box
convert. appears.
4. Click OK to dismiss the message box.
NOTE: If you want to keep the original text,
copy it and paste it elsewhere. Saving Molecules
You can save a single molecule structure to a
10.From the ChemDraw menu, choose Convert
separate file.
SMILES To Structure.
1. In the spreadsheet, select the cell containing the
If the cell contains a valid SMILES string, it is
molecule structure.
replaced by a text string starting with a
Structure followed by a number. 2. From the ChemDraw menu, choose Save
Molecule or click .
If the cell did not contain a valid SMILES
string, the SMILES string remains. The Choose Molecule to Save dialog box
appears.
Adding Molecules by
Name
You can type or paste the names of molecules into
cells and convert them into molecules as follows:
1. Type the names into cell.
2. Select the range of cells or single cell to
convert. 3. Select the appropriate options and click Save.
The molecule is saved with the name and in the
NOTE: If you want to keep the original text, location you selected.
copy it and paste it elsewhere. Note that this
command can also convert names generated Searching
from Excel formulas.
You can perform the same types of searches in
ChemDraw for Excel as you can in ChemFinder:
3. From the ChemDraw menu, choose Convert
Name To Molecule. • Exact structure searching
If the cell contains a name supported by • Substructure searching
ChemDraw Name To Structure, the cell is • Similarity searching
converted to a ChemDraw for Excel molecule
with the given chemical as the name of the new Filter Tables
cell. For more information about Name to
Filter tables allows you to search for exact structures
Structure, see the ChemDraw User’s Guide.
and substructures.

Adding Molecules by Name
To perform a structure search:
If you want to Then
1. Select a cell containing the label Structure.
2. From the ChemDraw menu, choose Filter
see the R- click the Show R-Group
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Table and click . Group Analysis box.

The Search Query dialog box appears. Analysis
3. Select the search options:
see the click Restore Previous
previous query Query.
If you want to Then
4. Click Search.
search for a a. To load a structure,
The hit list is displayed in a column named
structure right-click and
choose Read Match. Items matching the search criteria are
Structure. labeled as TRUE.
b. To edit the structure, Similarity Searches

double-click it.
You can perform similarity searches to find
c. Select the Search structures with features corresponding to your
Type. search structure. For more information about
similarity searching, see the ChemDraw Webserver
d. Select the Filter User’s Guide.
Type.
To search for similarity:
search for a a. Type the molecular 5. Select a cell containing the label Structure.
formula formula or formula
query in the And/Or 6. From the ChemDraw menu, choose Similarity
Formula Query box. Table or click .
The Similarity Query dialog box appears.
b. Choose Clear.
search for a a. To edit the structure,

structure and a double-click it.
formula
b. Select the Search
Type.
c. Select the Filter

Type.
d. Type the molecular

formula in the
And/Or Formula 7. Select the Search Type.
Query box.
8. Select the Similarity Is value.

Searching
9. Select the Sort order. 5. From the ChemDraw menu, choose Cut
10.Click Search. Molecule or click .
The hit list is displayed in a column named The structure is removed from the cell and is
Match. Items matching the search criteria are placed on the clipboard.
labeled as TRUE. To copy a molecule from a cell:
7. From the ChemDraw menu, choose Copy
ChemDraw for Excel allows you to rename Molecule or click .
molecules and use the clipboard to cut, copy, and
The structure remains in the cell and a copy is
paste molecules.
placed on the clipboard.
Naming Molecules To paste a molecule:
Excel recognizes certain characters as formulas. To 8. Select the area into which you want to paste the
prevent the system from interpreting a molecule structure.
name as an Excel formula, you can rename a
9. From the ChemDraw menu, choose Paste
molecule.
Molecule or click .
To name a molecule: The structure is pasted from the clipboard.
2. From the ChemDraw menu, choose Name
Viewing Structures
Molecule or click . ChemDraw for Excel allows you to select whether
The Name Molecule dialog box appears. to display structures in a cell. You can also adjust the
height and width of cells to display their entire
contents.
Showing and Hiding Structures

To show structures:
1. Select the cells in which you want to display
3. Type the name and click OK. pictures.
2. From the ChemDraw menu, choose Show
Using the Clipboard Picture or click .
You can cut, copy, and paste structures using the
The structures are displayed in the selected
clipboard. After you cut or copy a molecule, it is
cells.
placed on the clipboard. You can then paste it into
another cell or another application. To hide structures:
To cut a molecule from a cell: 3. Select the cells in which you do not want to
display pictures.

4. From the ChemDraw menu, choose Hide 9. Click-drag the resize handles to resize a picture.
Picture or click . Any changes you make to a picture is
The structures are hidden and the cells resize. proportionately reflected in the other pictures.
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10.To end resizing, click a cell and the pictures are

Aligning Structures deselected.
A structure may fall outside the boundaries of its cell
because it is too big or because it is improperly Using ChemDraw for
positioned within the cell. Use Align Pictures to
enlarge the cell or reposition the structure. If the Excel Functions
entire structure is within the cell, regardless of its
ChemDraw for Excel supplies nine functions that
position, it is not affected by the Align Pictures return information about chemistry objects in a
command. Always align pictures to the whole table.
specified cell. Seven of these functions take only
To align structures: one argument—the cell to which the function refers.
The remaining two functions may also take an
5. Select the cells to align.
optional second argument as a string.
6. From the ChemDraw menu, choose Align
The function ISSTRUCTURE is an example of a
Pictures or click .
function that takes only one argument. To determine
The cells adjust to display their entire contents. whether the content of cell A1 in an Excel
spreadsheet is a ChemDraw for Excel chemistry
Resizing Structures object, you type “=ISSTRUCTURE(A1)” into a
You can resize a single structure by click-dragging. second cell. The second cell then displays TRUE or
To resize multiple pictures use the Resize Picture FALSE depending on whether A1 contains a
command. chemistry object.
The function CHEM.COMPOSITION is one of the
NOTE: When pictures are resized larger than their functions that may take an optional second
cells, use Align Pictures to enlarge the cells. Align argument. It works in one of two ways:
Pictures does not make cells smaller.
With First Argument Only—
To resize pictures: Without the second argument, it displays elemental
7. Select the chemistry cells whose pictures you composition by weight percent of the entire
want to resize. molecule in cell A1 when you type
“=CHEM.COMPOSITION(A1)” into a second cell.
It is not necessary to only select chemistry cells.
For benzene, it displays “C, 92.26; H, 7.74".
Non-chemical cells or chemical cells without
pictures will be ignored. With Both Arguments—The second argument lets
8. From the ChemDraw menu, choose Resize you find the percent composition of a single element
Picture or click . in the molecule. Typing
“=CHEM.COMPOSITION(A1, “C”)” returns the
Resize handles appear on the selected weight percent of carbon in the molecule. For
structures.

Using ChemDraw for Excel Functions
benzene it would display “0.922582”. Notice that
the display format for a single element is different Function Action
from that of the whole molecule.
CHEM.NUM. Returns number of
The following table outlines the ChemDraw for
HBACCEPTORS hydrogen bond
Excel functions. Only CHEM.COMPOSITION and acceptors based on
CHEM.NUM.ATOMS take an optional second topology. Returns #N/A
argument. The others only take the reference cell error if cell doesn’t
argument. contain ChemDraw
molecule.
Function Action
CHEM.NUM. Returns number of
ISSTRUCTURE Returns TRUE if cell HBDONORS hydrogen bond donors
referred to is any based on topology.
ChemDraw for Excel Returns #N/A error if
chemistry object cell doesn’t contain a
including reactions; molecule.
otherwise it returns
FALSE. CHEM.SMILES Returns SMILES string
for molecule. Returns
ISREACCTION Returns TRUE if cell #N/A error if cell
reference is any doesn’t contain
ChemDraw for Excel ChemDraw molecule.
chemistry object and
reaction; otherwise it CHEM.COMPOSITIO Returns elemental
returns FALSE. N percent by weight for all
elements in molecule
unless optional second
CHEM.FORMULA Returns formula for argument specifies a
molecule in cell single element symbol
reference; it returns as a string. In this case
#N/A error if cell the elemental percent is
doesn’t contain a expressed as a decimal
ChemDraw molecule. number between 0 and
1. (75.1% would be
0.751) Returns #N/A
CHEM.MOLWEIGHT Returns molecular
error if the cell
weight for molecule in referenced in first
cell reference. Returns argument doesn’t
#N/A error if cell contain a ChemDraw
doesn’t contain molecule, or if second
ChemDraw molecule. argument is not a valid
element symbol.

Using ChemDraw for Excel Functions
Function Action Property Function
CHEM.NUM.ATOMS Returns total number of Boiling Point CHEMPROP.BOILING

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atoms in the molecule

unless optional second
argument specifies a Freezing CHEMPROP.FREEZING
single element symbol Temperature
as a string. In this case, it
returns the number of
Critical Temperature CHEMPROP.CRITICAL.
atoms of that element
only. Returns #N/A error TEMP
if the cell referenced in
first argument doesn’t Critical Pressure CHEMPROP.CRITICAL.
contain a ChemDraw PRESSURE
molecule or if second
argument is not a valid
element symbol. Critical Volume CHEMPROP.CRITICAL.
VOLUME
Using ChemProp Pro Heat of Formation CHEMPROP.HOF
Functions
Gibbs Free Energy CHEMPROP.GIBBS
If you are using ChemDraw Ultra with the
ChemProp Pro add-on installed, you can calculate
physical and thermodynamic properties in Ideal Gas Thermal CHEMPROP.IDEAL.GAS
Capacity
ChemDraw for Excel. For detailed information on
the properties calculated and how ChemProp
calculates them, see the ChemDraw manual. NOTE: Using ChemProp Pro requires that you
have a version of ChemDraw that includes
ChemProp Properties ChemProp Pro installed.
In ChemDraw for Excel, you can use the ChemProp
Pro functions to calculate the following properties: For a description of the ChemProp Pro properties,
see the ChemDraw manual.
Property Function Inserting Functions

LogP CHEMPROP.LOGP To insert a ChemProp Pro function into your
worksheet:
Molar Refractivity CHEMPROP.MR 1. Select a cell.
2. From the Insert menu, select Function.
Henry’s Law CHEMPROP.HENRY.
Constant LAW.CONSTANT

Using ChemProp Pro Functions
The Paste Functions dialog box appears.
3. Select ChemDraw Functions.

4. Select the function to insert and click OK.
A dialog box appears.
5. Enter the structure cell reference for which you

want to calculate properties in the Structure
box.
6. Click OK.
Each property is calculated using the “best
available” method. For more information about
calculation methods, see the ChemDraw manual. If
the cell reference argument does not point to a valid
structure cell, #N/A appears in the cell.

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ChemSAR for Excel The Add-Ins dialog box appears.
Overview
ChemSAR for Excel is Chem3D Ultra for Windows
add-in for Microsoft Excel 97 and higher.
ChemSAR for Excel enables you to calculate the
physiochemical properties (descriptors) for a set of
structures in an Excel worksheet.
ChemSAR for Excel provides statistical tools to
help identify trends in the calculated properties and 3. Click ChemFinder for Excel and ChemSAR
correlate the data. for Excel.
To run ChemSAR for Excel, you must have the 4. Click OK.
following installed on your computer: 5. Click New ChemFinder Worksheet .
• Chem3D The ChemSAR toolbar appears.
• ChemFinder Select Mark Dependent Rune Options
• MS Excel Descriptors Columns Plots
Configuring ChemSAR
for Excel
To make the ChemSAR for Excel menu appear in Calculate Mark Independent Descriptive
the Excel menu bar: Now Columns Statistics
1. Open MS Excel.
The ChemSAR Wizard
2. From the Tools menu, choose Add-Ins.
The ChemSAR wizard leads you through the steps
required to perform property calculations on a set of
molecules.
To perform property calculations using the

ChemSAR Wizard:
1. From the ChemSAR menu, choose Wizard.
ChemOffice Chapter 2: ChemSAR for Excel • 21

Configuring ChemSAR for Excel
The Step 1 of 4 dialog box appears. 5. Click Next.
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The buttons on the right are active when you use
If you want to Then click a range of cells in your worksheet. To make the
buttons available, type a cell range.
create a new New ChemFinder The buttons are active as shown below.
ChemFinder worksheet Worksheet.
convert the current Convert

Excel worksheet to a Worksheet.
ChemFinder worksheet
3. Click Next.
6. To display graphics of your structures in the

worksheet, choose Show Structures As 2D
Pictures.
4. Type the cell to be the heading cell for the

structure column.
22 • Chapter 2: ChemSAR for Excel CambridgeSoft

The ChemSAR Wizard
If you want to Then
If you want to Then
use structures entered a. Select the text to
as text. include.
use data from a a. Click Import
ChemFinder ChemFinder b. Click Convert
database Database. From Chemical
Name.
b. In the Import Table
dialog box choose
the database and use specific a. Type the range of
click Open. structures in cells containing the
worksheet structures to use.
use an active a. Click Get Current b. Click Use
ChemFinder hit list List from Selected Range.
ChemFinder.
8. Click Next.
b. Click Yes.
import a structure a. Click Import SD
data file into the File.
ChemFinder
worksheet b. In the Importable
dialog box choose
the database and
click Open.
import a file of one of a. Click Load from

the following format File.
types: .CDX, .MOL,
.SKC, .f1d, .f1q, or b. In the Choose
.RXN. Molecule to Load
dialog box, choose 9. Click Select Descriptors.
the file.
10. In the Select Descriptors dialog box, select the
appropriate descriptors.
use structures entered a. Select the strings to
as SMILES strings. include. For more information on using the Select
Descriptors dialog box, see “Selecting
b. Click Convert ChemSAR Descriptors” on page 24.
From SMILES.
11. Click Finish.
The calculations are performed and the results
appear in the worksheet.

The ChemSAR Wizard
Selecting ChemSAR 7. To view the calculation method of a property,
select it and click Parameters.
Descriptors 8. Click OK.
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The Select Descriptors dialog box allows you to The calculations are performed.
specify which physical properties to calculate for
your worksheet. Properties are calculated for entire Adding Calculations to
molecules. If you want to calculate the properties of
a molecule fragment, you must add that fragment to an Existing Worksheet
your worksheet. When you add structures to a worksheet that already
To select descriptors: has calculated properties, you can calculate the
properties for only the added structures without
1. From the ChemSAR menu, choose Select
recalculating the entire worksheet.
Descriptors.
The Select Descriptors dialog box appears: To calculate properties for added structures:
1. In a worksheet with calculated properties, add
the structures for which you want to calculate
properties.
2. Click Calculate Now .
The properties are calculated and added to the
worksheet.
Customizing
Calculations
2. Select the calculation type from the Class You can use the ChemSAR Options dialog box to
drop-down list. customize a calculation by changing the default
3. Select the computational model from the Server settings.
drop-down list. To change the defaults:
4. Use the Cost and Accuracy sliders to set the
1. From the ChemSAR menu, choose Options.
appropriate ratio.
The ChemSAR Options dialog box appears.
The greater the cost number, the greater the
time it takes for the calculation.
The greater the accuracy number, the greater the
accuracy of method used to perform the
calculations.
5. Select the properties to calculate and click Add.
6. To delete a property from the list, click
Remove.

Selecting ChemSAR Descriptors
2. To populate any unfilled valences with 5. Do one of the following:
hydrogen atoms, select Hydrogen Fill All
Atoms. To perform the calculation Click …
3. To customize the partial charge calculation, on …
click Calculate Partial Charges using.
a. Select a type of method from the drop-down a selected molecule Now.
list.
the entire worksheet OK.
Options and then select a Charge Method
and Theory to use. Calculating Statistical
4. To customize the how the 3D geometry is
Properties
optimized, select Optimize 3D Geometry ChemSAR for Excel allows you to calculate the
using. following statistical properties:
a. Select a type of method from the drop-down • Descriptive Statistics
list.
• Correlation matrix
• Rune Plot
Options and then select a Optimization
Method, Theory, and RMS Gradient to use. Descriptive Statistics
ChemSAR calculates the following statistics for
every column in the data set:
• Mean
• Minimum
• Maximum
• Range
• Count
• Sum
• Standard deviation
• Median
To perform the statistical calculations:
• From the ChemSAR menu, choose Descriptive
Statistics.
The results are added as a separate worksheet.

Calculating Statistical Properties
Correlation Matrix
ChemSAR calculates scatter plots for each property
to every other property.
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To calculate the correlation matrix:

• From the ChemSAR menu, choose Correlation
Matrix.
The results are displayed on a separate
worksheet. correlating cells are colored.
Rune Plots
Rune plots are used to compare data and visualize
how normally the data is distributed. The data is
transformed on a scale of zero to one. Each data set
is then plotted next to each other. You can then
identify data sets that are not normally distributed
and exclude them from any further calculation.
To create Rune plots:
• From the ChemSAR menu, choose Rune Plots.
The plot is added as a separate worksheet.

Calculating Statistical Properties
Chapter 3: CombiChem
The CombiChem add-in is an extension of

Microsoft Excel for Windows. It enables you to
perform the following tasks:
• Add worksheets to Excel workbooks to contain
combinatorial library syntheses.
• Search for reactants (starting materials) in
available chemicals databases and import them
into Excel.
• Choose which reactants to use to create product
libraries (experiments). 3. Select CSCombi and click OK.
• Find related structures in reactant and product The CombiChem toolbar appears:
listings.
• Assign reactants and products to automated
synthesis well plates.
• Calculate properties of reactants and products Using Help
to determine which ones might be the most
The CombiChem Help provides you with stepwise
desirable.
procedures for the following processes:
The following procedures assume you are familiar
with Microsoft Excel 97 or Excel 2000 for • Editing reaction templates
Windows. For more information about using Excel, • Searching for reactants
see the Excel User’s Guide. • Enumerating products
Starting CombiChem To open Help:

• From the CombiChem menu, choose Help.
When you install ChemFinder, the CombiChem
add-in is automatically installed.
To start the CombiChem:

1. Open Microsoft Excel 97 or 2000.
2. From the Tools menu, choose Add-ins.
ChemOffice Chapter 3: CombiChem • 27

Starting CombiChem
The CombiChem Help dialog box appears.
Working with Reaction
Help drop-down list
Templates
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CombiChem is a reaction-based combinatorial

product. You first enter a reaction template with
R-groups at the variable sites in your starting
materials, and then search for reactants based on
these structures. CombiChem puts your final
product structures together and creates a virtual
library.
Reaction Template Basics

The example of a reaction template that follows is
supported by CombiChem:
Navigation buttons
To use Help, do one of the following:

• Choose a topic from the drop-down list.
• Browse through the topics using the navigation
buttons, and .
To close Help:
• Click Exit. NOTE: ChemDraw automatically adds the Rxn
designations shown in the above drawing. You do
Creating a New not need to add them.
CombiChem Worksheet A reaction template must meet the following

specifications:
To use CombiChem, you first create a Reaction
worksheet in which to store your reaction templates. • All sites of variability require unique R-group
designations.
To create a Reaction worksheet:
• Solvents, catalysts, and other “real-world”
• From the CombiChem menu, choose New elements should not be included in the reaction
Reactions. template drawing.
A new worksheet, Reactions, appears in your • Multi-step reaction templates are supported.
workbook.
Adding a Reaction Template to
the Reaction Worksheet
To add a reaction template to your worksheet:
28 • Chapter 3: CombiChem CambridgeSoft

Creating a New CombiChem Worksheet
1. Click the Reactions worksheet in your To create Reactant worksheets:
workbook. • From the CombiChem menu, choose Make
2. Double-click the cell labeled Reactions- Reactant Worksheets.
Double Click to Edit. New worksheets are added to your reaction
The following dialog box appears: workbook.
NOTE: This process can take longer if

ChemFinder is not running. If ChemFinder is
not running, it opens. Keep ChemFinder open
to be used for other CombiChem operations.
3. Click Yes.
ChemDraw opens. The Reactant worksheets are named Reactant1,
Reactant2, and so on, up to the number of starting
4. Draw a reaction or cut and paste a reaction from reactants in your reaction. If your reaction is a
a different ChemDraw document. multi-step reaction, intermediates (products of a
5. When you are finished, from the ChemDraw prior step in the reaction) are not included. Only
File menu, choose Exit and Return to Excel. reactants that come from outside sources are
Excel appears with the reaction in the first cell included.
in the Reactions sheet. When you create worksheets, note the following:
Editing the Reactions in a • If you edit the reaction template by

double-clicking on the structure in Excel, it is
Workbook not automatically reprocessed. You must
To edit the reaction template that a workbook manually choose this option after editing your
contains: template.
1. Double-click the cell that contains the reaction • If you choose to process a reaction template,
template. and there are already Reactant sheets in the
workbook, a message appears asking if you
ChemDraw opens.
want to delete the pre-existing sheets. If you
2. Edit the reaction. want to keep this data, save a copy of the
3. When you are finished, from the ChemDraw workbook under a different name before
File menu, choose Exit and Return to Excel. deleting the sheets.
Excel appears with the edited reaction.
Processing the Reaction

Template
CombiChem analyzes your reaction and creates
Reactant worksheets in your workbook.

Working with Reaction Templates
Working with Reactant 3. Switch to ChemFinder.
Lists NOTE: Be sure that only one instance of

ChemFinder is running on your computer.
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After you process a reaction template, the reactant

worksheets have the R-group structure of the
appropriate reactant at the top. These worksheets 4. In ChemFinder, click to switch to query
hold your reactant lists. mode.
Reactant lists contain the building blocks from 5. Select the structure field and from the Edit
which your product library is created. The source of menu, choose Paste.
these reactants can be a ChemFinder database, or 6. Add any information in other fields to narrow
any datasource in your institution capable of your search.
exporting MDL SDFiles. When CombiChem
7. Click to perform the search
processes the reaction template, it creates query
structures. These structures are set up with all the
proper parameters to perform a general search on NOTE: For detailed instructions on
any structure-searchable database. Searching, see the ChemFinder manual.
You can edit the query structures that CombiChem
stores. For example, to create a more specific search, When you have a list of reactants in ChemFinder
double-click on the cell that contains the query that you want to use:
structure you want to edit.
1. Switch back to Excel.
Searching ChemFinder 2. From the Reactants menu, choose Import

Current ChemFinder Hitlist.
Databases
NOTE: Do not use the ChemFinder for Excel
You can search ChemFinder databases in two ways:
function “Get ChemFinder List” to do this—the
• Manually, by cutting or copying a structure, and CombiChem function does several necessary things
then pasting it into ChemFinder. that the ChemFinder for Excel option does not.
• Automatically, by accessing ChemFinder
Your list of reactants are imported into the current
databases from Excel.
Reaction worksheet.
Searching Manually Searching Automatically
To manually perform a ChemFinder search: To search a ChemFinder database automatically you
1. Select the cell that contains the query structure, access the database to search from the CombiChem
at the top of the Reactant worksheet. Search ChemFinder menu. You can add, edit, and
delete databases in this menu.
2. From the ChemFinder menu, choose Copy
Molecule or click Copy Molecule on the
ChemFinder toolbar.

Working with Reactant Lists
Adding Databases Editing the Search ChemFinder List
You can add up to 10 databases to the Search You can edit a database entry. For example, you can
ChemFinder list for automatic searching. change the short name of the database or enter a new
path for a database that has moved. You can also
To add a ChemFinder database: delete entries from the list.
1. From the CombiChem Reactants menu, point
to Search ChemFinder, and then choose Edit To edit a database entry:
Database List. 1. From the CombiChem Reactants menu, point
The Edit Database List dialog box appears. to Search ChemFinder, and then choose Edit
Database List.
The Edit Database List dialog box appears.
2. Click Add.
The Edit Database dialog box appears.
If you want to Then
edit a database a. Select the database to

edit and click Edit.
b. Make your changes in

3. Type in a short name for the database in the the Edit Database dialog
Name box. You can use any characters except box, and then click OK.
ampersand (&).
delete a database • Select the database, and
then click Delete.
• Type the path to the ChemFinder form (.cfw)
file in the Path box. 3. When you are finished, click Close.
• Click to browse for the ChemFinder Your database changes appear in the database
form (.cfw). list in the Search ChemFinder menu.
5. Click OK.
The database you added appears in the Edit
Database List.

Searching ChemFinder Databases
Searching the ChemFinder Database Searching Other
List
To search a ChemFinder database that appears on
Databases
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the list: You cannot search databases from other vendors

1. Ensure that the query structure associated with
directly with CombiChem. To use reactants from
other databases, you must first export the hitlist from
the current Reactant sheet is the query structure
the database as an MDL SDFile, and then import it
you want to use. To edit the query structure,
“Editing the Reactions in a Workbook” on page into Excel.
29. If your database application allows structure
2. From the Reactants menu, point to Search searching, you can use the query structure stored in
ChemFinder Database, and choose the your workbook to query the database as follows:
database to search. 1. Select the cell containing the query structure at
ChemFinder appears in front, your selected the top of the Reactant sheet.
database will be searched, and the search results 2. From the ChemFinder menu, choose Copy
appear. Molecule or click Copy Molecule on the
You can prune the hitlist using the tools in ChemFinder toolbar.
ChemFinder. For more information, see the 3. Paste the structure into your application’s
ChemFinder manual. structure window and perform your search.
When you have a hitlist that you want to import into
Excel: NOTE: You can also export the molecule to a
1. Switch back to Excel. file type supported by your database and use it
for searching.
2. From the CombiChem Reactants menu,
choose Import Current ChemFinder Hitlist.
3. A dialog box similar to the one below appears: When you have a hitlist in your remote database
application that you want:
1. Export it to an SDfile, using your database
application.
2. In Excel, from the CombiChem Reactants
menu, choose Import SDFile.
4. Click Yes.
Your hitlist is imported into the currently active
NOTE: Do not use the ChemFinder For Excel
Reactant sheet. Import Table function to import the SDFile. Use
the CombiChem menu item.
Your hitlist is imported into the Reactant sheet.

Searching Other Databases
Imported Data Format Use (Y/N)
CombiChem adds a Use (Y/N) column to your
A Reactant sheet with imported data contains the
following columns: imported data. When you create experiments, you
choose Y or N in this field to select whether you
• Structure want to use that reactant in that experiment. For
• Use (Y/N) more information, see “Creating Experiments” on
page 33.
• MOL_ID
• Imported data MOL_ID
Structure Column The MOL_ID column contains a unique numerical
identifier for each reactant. If a MOL_ID field is not
The Structure column is headed by the generic found in the imported data, CombiChem
structure that represents all of the reactants on this automatically assigns one.
sheet. By default, all reactant structures are hidden
to conserve system resources and speed up Imported Data
operations like row moving, copying, and scrolling.
Columns 4 and higher contain the data in the SDFile
To view the structures on your Reactant sheet: or ChemFinder database you imported. If there is
extraneous data, you can delete those columns.
If you want to Then
Creating Experiments
Show or hide a 1. Select the cell or
A experiment is a library of product molecules,
specific structure or cells that contain the
created from the reaction template and the reactant
range of structures structure or
lists you imported. You can use CombiChem to
structures you want
to view. create, or enumerate, multiple experiments per
workbook.
2. From the
For example, you can take all the reactants you
ChemFinder menu,
choose Show imported and enumerate a experiment containing all
Picture or Hide possible combinations of reactants. After
Picture or click performing some property calculations on these
or . products, you might decide that 10% of these
products are worth synthesizing in the lab. You
Show or hide all From the CombiChem could then create a new experiment with just those
structures on a Structures menu, choose products that the calculations show to be promising.
worksheet Show All Structures or
To create a new experiment:
Hide All Structures.
1. On each reactant sheet, select the reactants to
use by typing a Y in their Use(Y/N) column.
2. From the Experiment menu, choose New
Experiment.

Imported Data Format
The Excel status bar displays the current status The Configure Plates dialog box appears. The
of the enumeration. check boxes represent wells in the product or
reactant plates. Reactants and products are
NOTE: Enumeration of a product library may take placed in wells selected by check marks.
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a long time, especially if there are many reactants or

you are using slower processor.
After the experiment is created, several new sheets

are added to your workbook:
• Experiment Reactant sheets—contain lists of
the reactants actually used in the experiment.
• Experiment Product sheet—contains the
enumerated products in the experiment.
Working With Experiments

After enumerating a experiment, you can do several
things with it. For example, you can calculate
properties of the products in your experiment using
ChemFinder’s property calculation methods. For
more information, see the ChemFinder manual.
2. Type the number of rows and columns.
Configuring Plates 3. Take the appropriate action:
If you are going to use a robotic synthesizer to If you want to Then

perform an experiment on the bench, CombiChem
can assign your products to product wells and your
Place reactants or Select the well.
experiment reactants to reactant block plates. You products in a well
can configure plates that contain 1 to 8 rows and
1 to 12 columns.
Leave a well empty Deselect the well.
To set up assignments:
1. From the Plates menu, choose Configure. Use a well for a control Click the check box
twice. The check box
is checked with a gray
background.
4. When you are finished, click Save.

The template is used to assign experiment
Reactants or Products to plates.

Configuring Plates
To assign the products or reactants on a sheet to To view the product or reactant:
plates:
1. Select a row on a Experiment Reactant or
• From the Plates menu, choose Assign To Experiment Product sheet.
Wells. 2. From the Structures menu, choose Highlight
Three columns are added to the reactant or Related Records.
product worksheet: Plate No., Row No., and The related records on the Experiment Reactant
Column No. Reactant and Experiment Product sheet are
To remove the plate assignments: highlighted.
• From the Plates menu, choose Remove To show the structures in highlighted rows:
Assignments. • From the Structures menu, choose Show
Highlighted Structures.
Browsing Plates
To hide the structures in highlighted rows:
After assigning reactants or products to wells, you
can view them. • From the Structures menu, choose Hide
Highlighted Structures.
1. From the Plates menu, choose Browse Plates.
To remove the highlighting from all rows:
The Plate Browser dialog box appears:
• From the Structures menu, choose
Unhighlight All.
The numbered buttons represent the wells in

your plate.
2. Click the appropriate button to move to the
corresponding reactant or product worksheet
row.
3. To move between plates, click the navigation
buttons at the top of the dialog box.
Viewing Related Structures

After enumerating an experiment, you may want to
see which reactants went into a product or which
products arose from a given reactant.

Configuring Plates
Administrator

Configuring Plates
Chapter 4: Purchasing for Excel
Using Purchasing for Excel, you can access the

Available Chemicals eXchange (ChemACX) to look
up vendors and price information for chemicals
based on chemical structure information in your
Excel document. You can see catalog information in
a table so that you can easily evaluate pricing and
specifications of products from many vendors at the
same time. After comparing available quantities and
prices, you can actually place an order for chemicals
through ChemACX.com.
Starting Purchasing for

Excel 3. Click Purchasing for Excel and ChemDraw
for Excel, and then click OK.
Before you can use Purchasing for Excel, you must
enable the add-ins in Excel. The add-ins are enabled so that you can use
Purchasing for Excel.
To enable the Purchasing for Excel add-ins:
1. Open Excel. Opening a Chemfinder
2. From the Tools menu choose Add-ins. Worksheet
Before you can shop and purchase chemicals, you
must open a ChemFinder worksheet, or spreadsheet,
in Excel. After you open the worksheet, you can
create chemical structures and then shop for
chemicals.
To open a ChemFinder worksheet:
• From the ChemFinder menu, choose New
ChemFinder Worksheet.
A new spreadsheet, or worksheet appears in
Excel.
ChemOffice Chapter 4: Purchasing for Excel • 37

Overview
Placing a Chemical Getting Catalog
Structure in a Information
Worksheet
Administrator
After you have structure information in a

ChemDraw worksheet, you can check the Available
You can populate your worksheet with chemical Chemicals eXchange for all of the vendors of those
structures so that you can shop and purchase chemicals.
chemicals based on their structure.
To get catalog information:
For more information, see “ChemDraw for Excel”
on page 9. 1. On the worksheet, select cells with chemical
structures.
To populate your worksheet with chemical
2. From the ChemDraw menu, point to
structures:
Purchasing, and then choose Look Up
1. On the worksheet, double-click a cell. Suppliers on ChemStore.Com.
A ChemDraw for Excel dialog box appears. The new VendorInfo worksheet appears.
Pricing and catalog information for vendors
appear for each structure from your original
worksheet. Structures with catalog information
in the VendorInfo worksheet appear in red.
Shopping for Chemicals

2. Click Yes.
After you see the vendor information about
ChemDraw appears. chemicals, you can make a list of chemicals and
3. Draw a chemical structure with the ChemDraw quantities you want to purchase with the worksheet.
tools. You can use this list to order chemicals from
ChemACX.com.
For more information, see the ChemDraw
Manual. To create a your own list of chemicals in Excel:
4. Close ChemOffice. 1. In the VendorInfo worksheet, go to the
Your structure is automatically saved and Quantity column, and then type a quantity of
transferred to your ChemDraw worksheet in the chemical you want.
Excel. 2. Sort the VendorInfo worksheet by the Quantity
column.
Your list of chemicals appears at the top of the
worksheet.
For more information, see the Microsoft Excel
documentation.
38 • Chapter 4: Purchasing for Excel CambridgeSoft

Placing a Chemical Structure in a Worksheet
3. Take the appropriate action: 3. On ChemACX.com, follow the instructions to
place your order.
If you want to Then for more Your order is filled and shipped to you.
information, see
print your list from Microsoft Excel

the worksheet documentation.
export your list into the documentation for

your current your purchasing
purchasing system system.
purchase the “Ordering Chemicals

chemicals directly From
through ChemACX.Com” on
ChemACX.Com page 39.
Ordering Chemicals
From ChemACX.Com
You can purchase the chemicals and quantities on
your list of chemicals by sending your list to
ChemACX.com.
At ChemACX.com, you can turn your list of
chemicals into a Shopping Cart. With a ChemACX
account and your Shopping Cart, you can create an
order so that all of the chemicals are shipped to your
lab.
To order chemicals with your worksheet list through

ChemACX.com:
1. On your sorted VendorsInfo worksheet, select
the entire row for each chemical with a number
in the Quantity column.
2. From the ChemDraw menu, point to
Purchasing, and then choose Purchase From
ChemStore. Com.
ChemACX.com appears in a browser window.
ChemOffice Chapter 4: Purchasing for Excel • 39

Ordering Chemicals From ChemACX.Com
Administrator
40 • Chapter 4: Purchasing for Excel CambridgeSoft

Ordering Chemicals From ChemACX.Com
Chapter 5: ChemFinder for Word
Overview • Save frequently-used collections of data
sources (documents and databases) in Data
ChemFinder for Word allows you to search data Source Definition (.dsd) files. Instead of
sources (documents and databases) to find chemical checking many data sources that you want
structures so that you do not need to search ChemFinder for Word to search, ChemFinder
manually. for Word can search one .dsd file.
ChemFinder for Word can search the following data • Search through MS Word files to find each
sources for chemical information: place in the document that a particular structure
exists. ChemFinder for Word finds the structure
• ChemFinder databases
and shows a list of where the structure exists in
• ChemDraw files the Hit List. Double-click a record in the Hit
• MS Word documents List to see the structure in the Word file.
• MS Excel speadsheets • Build databases by extracting information from

different sources and exporting to other sources.
• SD files
• Isis/Draw files Opening ChemFinder
You can also use ChemFinder for Word to do the
following: for Word
• Draw structures you want to find with ChemFinder for Word is installed when you install
ChemDraw or the ChemFinder for Word ChemOffice Ultra.
internal ChemDraw tools. ChemFinder for To open ChemFinder for Word, do one of the
Word can search for the whole structure, a following:
substructure, or a structure similar to the one
you draw. • From the Start menu, choose Find, and then
choose Chemical Structures.
• Search for chemical structures using the
following criteria:
• Chemical structures
• Substructures
• Similar structures
• Chemical formula
• Molecular weight
ChemOffice Chapter 5: ChemFinder for Word • 41

Opening ChemFinder for Word
• From the Start menu, choose Programs, CS
ChemOffice, and then ChemFinder for Word.
Chemfinder for Word opens and the Data
Source - Find Chemical Structures window
Administrator
appears, as shown below:
ChemFinder for Word

title bar Menu bar
Standard Toolbar
Record/Search toolbar
Structure tab
Find Now button
Structure window
Stop button
Look In tab New Search button
Search Options tab
Molecular Weight text box

Edit Structure button
Formula text box
Show/Hide Hit List
Status bar
Searching by Chemical The Data Source - Find Chemical Structures

window, appears.
Structure
You can find chemicals based on their structure with
ChemFinder for Word.
NOTE: Any search method that you use in

ChemFinder you can also use in ChemFinder for
Word.
To search by chemical structure only:

1. Open ChemFinder for Word.
2. Click New Search or Enter Query .

• From the Look In tab, select files to search.
42 • Chapter 5: ChemFinder for Word CambridgeSoft

Searching by Chemical Structure
For more information about the Look In tab, ChemFinder for Word shows all of the files
see “Selecting Files to Search” on page 44. with the structure that you specify in the Hit List
• Open a file to search. window shown below. Each entry in the Hit List
is a record or a hit.
For more information about opening files to
search through, see “Searching .dsd Files” on
page 48.
• From the File menu, choose a file name from
the most recently used list of files.
For more information about opening files to
search through, see “Searching .dsd Files” on
page 48.
• In the Data Source - Find Chemical
Structures window, click Edit Structure.
• From the Edit menu, click Edit Structure.
NOTE: All of the items in the Edit menu of

ChemFinder for Word will be available in If ChemFinder for Word finds no hits, a
future versions. warning message appears. To refine your search
so that ChemFinder has a greater possibility of
• Double-click in the structure box. finding hits, use the Search Options tab. For
more information, see “Refining Your Search”
ChemDraw appears.
on page 50.
5. In the ChemDraw window, draw a structure
For information about browsing records in the
with the ChemDraw tools.
Hit List, see “Browsing Search Results” on
For more information about ChemOffice, see page 45.
the ChemDraw User’s Guide.
8. To cancel the current search, click Stop.
6. Click the ChemFinder for Word window.
The search stops.
The structure you drew in ChemDraw appears
in the Structure window of ChemFinder for Searching by Multiple
Word.
7. In ChemFinder for Word, click Find Now.
Properties
You can search for a chemical structure, chemical
formula, molecular weight, or any combination of
these properties simultaneously.

Searching by Multiple Properties
To search for other properties or more than one ChemFinder for Word shows all of the files
property at a time: with the properties that you specify in the Hit
1. Open ChemFinder for Word. List window below the Structures window.
If ChemFinder for Word finds no hits, a
Administrator
The Data Source - Find Chemical Structures

window appears. warning message appears.
2. Click New Search or Enter Query . To refine your search so that ChemFinder has a
greater possibility of finding hits, use the
Search Options tab. To expand your search, use
the Look In tab. For more information, see
If you want to Then in the “Refining Your Search” on page 50.
search for Structure window
Selecting Files to
a specific molecular in the Mol. Wt. text
weight box, type a molecular Search
weight (g).
Use the Look In tab or the Open File menu item to
tell ChemFinder for Word where to look for a
a molecular weight in the Mol. Wt. text
structure.
within a range box, type a range of
molecular weights (g)
with < or >.
Selecting Files With the Look In
Tab
a chemical formula in the Formula text The Look In tab window shows all the documents
box, type a chemical and databases (data sources) on your mapped
formula. network, CD-ROM, floppy, and hard drives.
more than one enter the appropriate To look for a structure in specific files or data
criterion (structure, criteria. sources:
formula, or molecular 1. Click the Look In tab.
weight)
NOTE: When you search by chemical

structure, formula, and molecular weight,
ChemFinder for Word uses all the criteria
together. The information about each property
adds to the search criteria of the other
properties.
4. Click Find Now.

Selecting Files to Search
The files and data sources appear in a tree For example, you want to find a specific benzene file
directory. you saved. However, you are not sure what part of
ChemDraw you saved it in. Click the ChemDraw
Minus sign box and all of the ChemDraw files are searched.
Selecting Files With the Open

File Menu Item
Plus sign
To look for a structure in a specific file or data
source:

Check box
Look In 2. Select a file or data source you want to search
window
by doing one of the following:
• In the File Name text box, type the name of
the file to search.
NOTE: You can set Preferences to keep the file • Use the directory tree in the Open window to
names hidden in the directory tree. For more browse to a file to search.
information, see “Changing the ChemFinder
3. Click Open.
for Word Preferences” on page 53.
The structure associated with the last saved
version of the file appears in the Structure
2. In the Select files of type box, choose types of
window.
files in which to search.
You can select all data sources or files with the Browsing Search
following extensions:
• .cdx and .mol
Results
• .doc and .xls You can view the search results in the Hit List.
• .cfw To view the search results:
• .sdf • To view the entire Hit List, use the scroll bars.
3. Click the plus sign to expand that file or data • Click a record in the Hit List to display it in the
source. If there is a minus sign or no sign at all, Structure window.
then you cannot expand the file or data source.
• Double-click on file names in the Hit List with
4. Click the box next to the file or data source that the following extensions to see the actual file:
you want to search. A check mark appears.
• .doc—MS Word
All of the files under your selection are also
• .xls—MS Excel
searched.
• .cdx—ChemOffice

Browsing Search Results
• .cfw—ChemFinder
If you want to see Then click
The application appears in which the structure
was saved. In MS Word, the application opens
directly to the structure in the document. the record listed after Next .
Administrator
the one you are

When you view the structure in the application currently looking at
in which it was originally saved by this method,
the Hit List record is not copied to the other
the last record on the Last .
application. Hit List
To see a specific record (hit on the Hit List):
In the Structure window, the structure
• From the Record menu or Record toolbar, take associated with that hit appears. The hit is
the appropriate action: highlighted in the Hit List.
You can use the Hit List menu to browse and move
If you want to see Then click Hit List records.
the first record on the First . To browse move Hit List records with the Hit List
Hit List menu:
1. In a Hit List with records, right-click a record.
the record listed Previous .
The record is selected and the Hit List menu
before the one you are
appears.
currently looking at
a specific record a. Move to
Specified If you want to Then in the Hit List
Record . menu, choose
The Enter Record

place a file in the Hit a. Add.
Number dialog
List The Open
box appears.
window appears.
b. In the Record
b. In the File Name
text box, type the
text box, type the
number of the
name of the file
record (hit on the
you want to add
Hit List) you
to the Hit List.
want to see.
c. Click Open.
c. Click OK.
The file appears
as a record at the
end of the Hit
List.

Browsing Search Results
To save search results in the .sdf format after a
If you want to Then in the Hit List search:
menu, choose
1. From the File menu, choose Export SDFile.
take a record off the Remove. The Save As dialog box appears.
hit list 2. In the File Name text box, type a name for the
The record is removed file.
from the Hit List.
3. Click Save.
open a record in the Activate. The file is saved with an .sdf extension.
application it was For more information about exporting files to other
saved in and view the The structure appears applications, see “Sending a File to Another
structure in the application it
Application” on page 48.
was saved in.
Saving Data Sources as .dsd
view the MolServer Properties.
driver properties Files
You can save a group of data sources from a search
Saving Files or Data as a Data Source Definition (.dsd) file. After you
complete a search, save all the records from the Hit
Sources List as a .dsd file so that you can search through
them again. When you save a .dsd file with the Save
A data source, or file, can be any of the following: Source As menu item, the .dsd file has a structure
• A document, like an MS Word document or an associated with it.
MS Excel spreadsheet. You can use .dsd files to search for structures,
• A database, like a ChemFinder database. substructures, or structures similar to your previous
• Any combination of documents or databases. search through the .dsd file.
You can save search results as a file to search To save the results of a search as a .dsd file:
through again.
1. Click New Search or Enter Query .
Saving Search Results as .sdf 2. From the Look In window, choose the files you
Files want to group together.
3. Draw a structure to search for.
You can save search results as a .sdf file. This format
saves the Hit List records as complete structures in 4. Click Find Now.
MDL SDFile format. You can export .sdf files from ChemFinder for Word shows all of the files
ChemFinder for Word into applications like with the structure that you specify in the Hit List
ChemFinder. window below the Data Source - Find Chemical
Structures window.
5. After the search, from the File menu, choose
Save Source As.

Saving Files or Data Sources
Searching .dsd Files
6. In the File Name text box, type a name for the
group of files. To search for a structure in the .dsd file:
Administrator
7. Click Save. 1. From the File menu, choose Open.

The files are saved with a .dsd extension. The Open dialog box appears.
2. In the File Name text box, type the .dsd file
Saving Lists of Directory Paths name.
as .dsd Files 3. Click Open.
NOTE: Only advanced users familiar with text The first structure associated with the last saved
editors should use this procedure. version of the .dsd file appears in the Structure
window.
You can save lists of directory paths that you search 4. Click New Search or Enter Query .
as .dsd files. You can create these lists with a text ChemFinder for Word clears the Structure
editor such as Notepad. When you save a .dsd file window.
with the Save Source As menu item, the .dsd file has
a structure associated with it. Saving a list of 5. Draw a structure to search for.
directory paths as a .dsd file saves the directories in 6. Click Find Now.
which you search frequently. ChemFinder for Word searches through the
To save a list of directory paths: files specified in the .dsd file. Any hits appear in
the Hit List.
1. Open a Notepad.
2. Type the directory or database paths you want Sending a File to
to search.
Another Application
3. From the File menu in Notepad, choose Save
As. You can send a structure or a file of structures (like
.sdf files) to another application. Instead of cutting a
structure from one application and pasting it into
4. In the File Name text box, type a name for the another, you can send more than one structure
file and include a .dsd extension. directly into another application.
For example, type a File Name like Use the items in the Send To menu to send files to
“search1.dsd.” these applications:
5. Click Save.
• MS Word
6. Close Notepad.
• MS Excel
• CS ChemFinder
• CS ChemDraw Files
• ChemACX.Com Search

Searching .dsd Files
To send a file to another application: 4. From the Document section, select one of the
1. In the Data Source - Find Chemical following, if available:
Structures window, click the Send To menu.
The Send To menu appears.
2. From the Send To menu, choose an application
send structures to a Send molecule(s) to
to send a file to.
new (untitled) a new document.
The Send To box dialog box appears. document in an
application
NOTE: When you send files to

Chem.ACX.Com, The Send To dialog box does send structures to a Send molecule(s) to
not appear. The structure associated with the document you already a currently open
file is sent directly to ChemACX.Com. have open in an document.
application
5. In the Document section, type the name of the

file you want to send to another application, if
necessary.
If the text box in the Document section is not
available, skip this step.
6. Click OK.
If you choose Send To MS Word or MS Excel,
the document type opens with the file you sent
to it. The structures you send to the application
appear in that application.
3. From the Molecules section, select one of the To send a file to CS ChemFinder or CS ChemOffice,
following: you must save the file you want to send:
1. From the Save As dialog box, in the File Name

text box, type a name for the file you want to
send.
send the current Send current
structure in the molecule. 2. Click Save.
Structure window If you send a file to ChemFinder, ChemFinder
opens and the file you save appears as a form.
send all the structures Send all molecules If you send a file to ChemOffice, a warning
listed in the Hit List in current hit list. appears to tell you the path of the file you saved.

Sending a File to Another Application
Refining Your Search To use the search tools:
• From the Search menu or Search toolbar, take
You can refine your search so that you have a greater
the appropriate action:
chance of finding the structure you want. Use the
Administrator
Search tools and the Search Options tab to change

your query to refine your search. If you want to Then click
To refine your search: begin a new search Enter Query .

1. From the Search menu, choose Restore
Previous Query or click . search for the current Find Current
2. Change your query with the Search tools or the properties (chemical Query .
Search Options.
structure, chemical
formula, molecular
3. Select the files and data sources you want to weight)
search.
For more information, see “Selecting Files to see all the records in Retrieve All .
Search” on page 44. the search, including
records without a
4. Click Find.
match to your search
ChemFinder for Word shows all of the files
with the structure that you specify. These files search for the current Find Current
appear in the Hit List window below the Data structure, but ignore Structure .
Source - Find Chemical Structures window. any other search
Each entry in the Hit List is a record or a hit. properties like
molecular weight
For more information about the records in the
Hit List, see “Browsing Search Results” on
set up the previous Restore Previous
page 45.
search, usually so you Query .
If ChemFinder for Word finds no hits, refine can modify the search
your search more.
For more information about the Search tools, see the
Refining Your Query With the “Searching” chapter in the ChemFinder User’s
Search Tools Guide.
Some ChemFinder tools used to refine your search Refining Your Query With the
can also be used in ChemFinder for Word.
Search Options
You can refine your ChemFinder for Word search
with them Search Options.

Refining Your Search
To use the Search Options:
1. Click the Search Options tab. search for a
The Search Options window appears.
structure that partially a. Similarity.
matches your query
and set a percentage b. In the
of how much the Similarity% box,
query must match the do one of the
structure you specify. following:
• Click the Up and

Down Arrows
until the number
you want
appears.
• Type a whole
number.
structure with Match tetrahedral

matching tetrahedral stereo.
stereo
If you want to Then click structure with Match double bond

search for a matching double bond stereo.
stereo
part of a structure Substructure.
structure in which the Fragments may
complete structure Full Structure. fragments may overlap.
overlap
structure that overlaps Hit must overlap

the reaction center so reaction center.
that you know the
structure is part of the
reaction
structure which has Extra fragments may

more fragments than be present in hit.
the structure you draw

Refining Your Search
search for a
If you want to Then from the
View menu, click
Administrator
structure that matches Match any charge on

carbons with any carbon.
show the Standard Toolbar.
charge
toolbar, with these
icons: The Standard toolbar
structure that matches Match any charge on Open File, Save, Cut, appears above the
any charge on the heteroatom. Copy, Paste, and Help Data Source - Find
heteroatom Chemical Structures
window.
Changing ChemFinder hide the Standard Toolbar.

for Word Settings toolbar
The Standard toolbar
You can change ChemFinder for Word settings so disappears.
that ChemFinder for Word appears the way you
want. You can customize the way the ChemFinder show the Status bar Status bar.
for Word window appears with the items on the with these categories:
View menu. You can change some of the search status, record The standard
number, list number, ChemFinder for Word
ChemFinder for Word display features with the
query mode, and status bar appears
Preferences window.
database number below the Data
Source - Find
Customizing the ChemFinder Chemical Structures
for Word Window window.
Use the View menu to change the appearance of the
ChemFinder for Word window. hide the Status bar Status bar.
To use the View menu: The status bar

disappears.
1. In the Data Source - Find Chemical
Structures window, click the View menu.
show the Hit List, Show List.
The View menu appears. which shows all of the
places that The ChemFinder for
Chemfinder for Word Word Hit List window
has found the appears below the
structure you want to Data Source - Find
find Chemical Structures
window. Until you
begin or complete a
search it is empty.

Changing ChemFinder for Word Settings
Changing the ChemFinder for
If you want to Then from the
View menu, click Word Preferences
To change the ChemFinder for Word preferences:
hide the Hit List Hide List.
The Hit List
The Preferences window appears.
disappears.
show the hit list Hide List.
The Hit List appears.
customize features, a. Customize.

including:
Commands, Toolbars, The Customize
Menu, and Keyboard window appears.
options
b. Change the 2. Take the appropriate action:
features you
want.
If you want to Then
c. Click Close.
choose a specific Type the path in the
The Customize directory for the Look Startup directory text
window closes, In tab to open box or click
and the changes to browse to a file in
you made appear. (This setting does not the Startup directory.
affect any query
For more properties.)
information, see
the MS Word
specify the number of In the Number of
online Help.
most recently open recently used files to
files to show in the show on the File
File menu menu box, type the
number or click the
Up and Down Arrows
to set a whole number
from zero to 10.
open the last file you Click Reopen last

used when you start source on startup.
ChemFinder for Word

Changing ChemFinder for Word Settings
If you want to Then
show all files in the Click Show files in

Administrator
directory tree directory tree.
use the ChemDraw Click Use internal

tools provided with ChemDraw for
ChemFinder for Word editing.
instead of opening
ChemDraw to draw
and edit structures
display structures Click Use internal

with ChemDraw ChemDraw for
instead of structure display.
ChemFinder (default)
3. Click OK.
The Preferences window closes.
Closing ChemFinder for

Word
To close ChemFinder for Word:
• From the File menu, choose Exit.
ChemFinder for Word closes.
If ChemDraw or any other application is still
open when you close ChemFinder for Word,
that application stays open.

Closing ChemFinder for Word
E-Notebook
Overview of the You can use E-Notebook Administrator to configure
E-Notebook. For more information, see the
E-Notebook Application E-Notebook Administrator manual.
Up keeping your laboratory notebook is made easy

with E-Notebook. You can use E-Notebook instead
Terminology
of your paper laboratory notebook. With E- Although E-Notebook uses many of the same
Notebook, you can make notes about experiments, concepts as a paper notebook, it does have its own
projects, reactions, and other laboratory tasks and terminology. In some cases, familiar words have
data. You can also see the notes of other people who different meanings, such as Collection and
share the E-Notebook database. Notebook.
E-Notebook organizes organic syntheses and The following terminology is used in the E-
associated information such as: Notebook application and this manual:
• stoichiometry calculations Collection—A group of almost anything in
• reaction preparations E-Notebook that contains information you can view.
For example, a Group is a Collection of Users; a
• analytical methods Notebook is a Collection of Pages.
• notes
Client Application—An application, such as
• spreadsheets E-Notebook, that relies on a server for controls and
You can use electronic pages, analogous to the pages data storage.
of a paper laboratory notebook, to store information.
E-Notebook Database—The database in which all
You can search E-Notebook, unlike a paper
E-Notebook information is stored. This can have an
laboratory notebook, by: MS Access format or be an Oracle database. You
• substructure can control the database with E-Notebook
Administrator. For more information, see the
• reaction transformation
E-Notebook Administrator manual.
• Collection name
Experiment—A Collection of data. For example,
• Page name
an Experiment may contain a Collection of
E-Notebook also fully automates stoichiometric Notebooks.
calculations. These capabilities make E-Notebook
easier to work with than paper notebooks. Group—A Collection of Users who can view each
other’s Notebooks.
E-Notebook is a standalone application, but you can
Home Collection—A Collection from which you
use it with Microsoft Word and Microsoft Excel to
interpret and manage data. can start browsing Notebooks and other Collections.
ChemOffice E-Notebook • 55
Overview of the E-Notebook Application
MS Excel Section—A Page Section. You can use an can record for that property. For example, the
MS Excel Section to store calculations such as pressure property can have a number data type so
structure-activity relationship (SAR) tables or that you can only record numbers for pressure.
combinatorial library enumerations in a spreadsheet.
Reaction Scheme—A Collection.
Administrator
You can edit the content with MS Excel.

Reaction Section—A Page Section where you can
MS Word Section—A Page Section. You can use
record a single step in a reaction. You can include
an MS Word Section to record data. For example,
information about the reaction, such as chemical
you can type comments about an experiment and
structures, conditions for the reaction, and
paste a scan of a TLC plate into an MS Word
stoichiometry data about the reactants and products.
Section.
Section—A Section is part of a Template or a Page.
Multi User—An environment with more than one
You can create the following Sections:
User. In a Multi User environment, Users can see
each other’s Notebooks and Collections. You can • Reaction
configure E-Notebook for a Single User or Multi • MS Word
User environment with E-Notebook Administrator.
• MS Excel
Notebook—A place to record your data about • Spectra
experiments and other information. A Notebook,
just like a paper notebook, contains the following: • Table
Single User—An environment with one User. You
• a Collection of Pages.
can configure E-Notebook for a Single User or
• places to record data. Multi User environment with E-Notebook
• areas to view data. Administrator.
Page—A part of a Notebook that contains Sections. Spectra Section—A Page Section where you can
You can record all reaction steps, notes about record spectra. You can include information about
reactions, and other data in Page Sections. Page the spectra.
information is stored in a database that you manage
Synthesis—A Collection.
with E-Notebook Administrator. For more
information, see the E-Notebook Administrator Table Section—A Page Section where you can
manual. record property values for chemical structures,
reaction, and other data in a table format.
Project—A Collection of data. For example, a
Project may contain a Collection of Notebooks. Template—A part of a Notebook. You can use a
Template to regulate the information that you put
Property—A series of characteristics given to a
into Page Sections. For example, in a Template
Page Section. For example, you can record pressure,
Reaction Section, you can include specific Reaction
temperature, and atmospheric properties in a
Properties. When you use that Template to create a
Reaction Section.
Reaction Section in a Page, the Section will be
Property Data Type—A property has a designated created with the Reaction Properties from the
data type, such as text, date, number, or structure. Template.
The data type controls the kind of information you
Therapeutic Area—A Collection.
56 • E-Notebook CambridgeSoft
Terminology
User—A person who uses E-Notebook. User is also 2. In the E-Notebook Login dialog box, click
the name that E-Notebook uses to identify a person. Single User, and then click Login.
E-Notebook opens.
Starting E-Notebook
The first step to using E-Notebook is starting the
application. When you start E-Notebook, you must
follow a multi-step process. First, open E-Notebook
and then log in. After you log in, you can use E-
Notebook for recording experiment tasks and data or
viewing other Users’ Notebooks.
Opening E-Notebook
Opening E-Notebook is almost as simple as opening
a paper notebook, open the application to use it.
To open E-Notebook:
• From the Start menu, point to ChemOffice 6.2,
and then click E-Notebook.
The E-Notebook Login dialog box appears.
To log in as a Multi User:
1. Open E-Notebook.
2. In the E-Notebook Login dialog box, click
Multi User.
3. Type your User Name and Password, and then
click Login.
Logging In
When you log in to E-Notebook, you use your User
Name and Password. E-Notebook uses this
information to locate your Notebook and data. You
can log in as a Single User or a Multi User,
depending on how your system administrator
configures E-Notebook.
To log in as a Single User:

1. Open E-Notebook.
Starting E-Notebook
E-Notebook opens. When you create a Collection of Pages, Notebooks
or other E-Notebook groups, you place that
Collection in the Collection tree. After you create a
Collection, you can reference, or duplicate it, within
Administrator
other Collections. You can also rename, archive, and

browse Collections.
Understanding the Contents of

a Collection
The Collection tree appears along the left side of the
E-Notebook window. Each Collection, and all of the
groups within that Collection appear in the tree.
You can create Collections and populate those
Collections with items that you want related. This is
the relationship between Notebooks and Pages. For
example, you can create a Collection that contains
all of the reaction steps for a specific synthesis,
Refreshing E-Notebook regardless of what notebook those Pages appear in,
or which chemists created the Notebook. You might
Information also want to create a Collection of all of the
syntheses that lead to a certain product, or all of the
Multi Users must refresh E-Notebook periodically.
Users that are working on a specific project. E-
When other Users add information to E-Notebook,
Notebook links Collections and pages together,
you must refresh the application so that you can see
enabling you to navigate from Collection to
the new information.
Collection.
To refresh E-Notebook:
You can change the contents of a Collection so that
• From the View menu, choose Refresh. any group becomes a Collection. For example, an
E-Notebook updates all information. Experiment can be a Collection of Notebooks. A
Notebook can be a Collection of Experiments. A
Working with Project can be a Collection of Experiments. A
Collection may contain a Collection that also
Collections contains it.
You can organize a group of Notebooks and other The following are common Collections:
information into Collections. • Notebook and Page
A Collection is a group of almost anything in • Template and Page
E-Notebook. For example, a Group is a Collection • Therapeutic Area
of Users; a Notebook is a Collection of Pages.
• Project
• Experiment
Refreshing E-Notebook Information
• Reaction Scheme Pages and Templates can only be Collections for
• Synthesis Sections. For more information, see “Creating a
Section” on page 67.
In Multi User environments, each User has a
Collection of Notebooks. Users in a Group, which is
NOTE: Users are always the root for Notebooks.
created by the system administrator in E-Notebook
Administrator, can see the entire Collection of
Notebooks in the Group. To create a Collection:
1. Choose an item on the Collection tree.
Creating a Collection The item in the Collection tree becomes
You can create a Collection of E-Notebook groups, highlighted. This is the root for your Collection.
such as Notebooks, Pages, and Projects. You can The following illustration shows Notebook 2 as
organize Collections so that you can use the the root for a Collection of Pages.
information in them more easily.
When you create a Collection, you must choose a
[graphic]
root for the Collection. The root is the starting point
in the Collection tree for the Collection. For
example, a User can be the root for the Notebook
Collection. All the Notebooks that belong to the
User have the User as a root. When you want to see 2. From the File menu, point to New, and take the
the Notebooks that belong to a User, go to the User appropriate action:
in the Collection tree, and then you can see
everything in that User’s Collection.
if you want your Then if it is
Every Collection has a root that you specify. You Collection to available, choose
can choose a root by going to an item in the contain
Collection tree. Knowing the root of a Collection
makes it easier for you to organize Collections based Notebooks Notebook.
on their root.
After you choose a root, you add items under the Pages Page.
root. All items in the Collection appear under the
root in the Collection tree. Templates Template.
When you create a Collection, you must have write

Therapeutic Areas Therapeutic Area.
permission. For more details, contact your system
administrator.
Projects Project.
You must make all Collection, Page, and Template
names within the E-Notebook database unique.
Experiments Experiment.
Reaction Schemes Reaction Scheme.
Working with Collections
To create a Page Collection from a Template:
if you want your Then if it is
Collection to available, choose 1. In the Collection tree, click a Template.
contain 2. Duplicate the Template. For more information,
Administrator
see “Duplicating a Collection” on page 61.

Syntheses Synthesis.
The duplicate Template appears with a a name
based on the root Collection name.
NOTE: Page Sections, such as Reaction
Section or MS Word Section, do not appear in 3. Click and drag the duplicate Template to a
Collections because they are already a Notebook.
Collection for a Page.
The duplicate Template appears as a Notebook
A new, untitled Collection appears in the Page. It is renamed accordingly.
Collection tree. The User who is logged in
becomes the owner of the Collection. Renaming a Collection
3. Add more items to your Collection by repeating You can rename any Collection so that each
step 2. Collection has a unique name. For example, after
Your Collection appears in the Collection tree. you make duplicate a Collection, you can rename it
so that it has a more meaningful name to you and
Creating a Page Collection anyone viewing your Notebook.
from a Template When you rename a Collection, you must have write
You can create a Page and all the Sections in it from permission. For more details, contact your system
a Template. By creating Pages and Page Sections administrator.
from a Template, you can ensure that all your To rename a Collection:
information is uniform between all your Pages. For
example, you can create a Template with a Reaction 1. From the Collection tree, choose the name of a
Section. In the Reaction Section, you draw a protein. Collection.
Instead of drawing the protein in every Reaction 2. From the File menu, choose Rename.
Section in Your Notebook, you can copy the
3. Type the new name for the Collection.
Template Reaction Section and the protein you
already drew appears. 4. Press Enter.
You can create a Template the same way you create The Collection is renamed.
any other Collection. You can add Sections to a
Template the same way you add Sections to a Page.
Removing a Collection
For more information, see “Creating a Section” on You can remove, or delete, a Collection from the
page 67. Collection tree so that you only see the Collections
you use. You can also remove Collections that are no
longer relevant to your current needs.
When you remove a Collection, you must have write The following rules apply to duplicating
permission. For more details, contact your system Collections:
administrator.
• A duplicate Collection is not archived, even if
The following rules apply to removing Collections: the original Collection is archived.
• Other references to the Collection in the • The duplicate Collection belongs to the User
Collection tree are not removed automatically. who creates it, regardless of who owns the
You can remove these references manually, the original Collection.
same way you remove any Collection. • The duplicate Collection is renamed
• Only Users who create a Notebook can remove automatically. The original name is appended
that Notebook from their User Collection. by the word “copy.”
• Users in a Notebook Collection are permanent. To duplicate a Collection within the same
• Archived Collections are permanent. You can Collection:
not add items to or remove items from an
1. From the Collection tree, choose the name of a
archived Collection.
Collection.
To remove a Collection: 2. From the Edit menu, choose Duplicate.
1. From the Collection tree, choose the name of a A copy of the Collection appears in the
Collection. Collection tree.
2. From the File menu, choose Delete. To duplicate a Collection in a different Collection:
The Collection is removed from the Collection
1. From the Collection tree, click the name of a
tree.
Collection.
Duplicating a Collection 2. Hold the Control key and drag the Collection
into a different Collection.
You can duplicate, or copy, an entire Collection so
that you can move information to a different A copy of the Collection appears in the
Collection without changing the information. this Collection tree.
ensures that all information in duplicate Collections
is the same. Organizing a Collection
You can organize items in the Collection tree so that
The Collection copy contains references to all of the
Collections and Pages that are in the original their order makes more sense to you and other Users
who view your Collections.
Collection.
You can organize Collection items by moving them
You can duplicate a Collection within the same
Collection, or move the duplicate to a different up or down in a Collection. You can also copy items
from one Collection to another.
Collection.
When you organize a Collection, you must have
When you duplicate a Collection, you must have
write permission. For more details, contact your write permission. For more details, contact your
system administrator.
system administrator.
Moving Items Within a Collection To move a Collection item to a different Collection
You can move items in a Collection up or down. You in the Collection tree:
can move items to different Collections. For more 1. From the Collection tree, click the name of a
information, see “Moving Items Between
Administrator
Collection.
Collections” on page 62.
2. Drag the item to the Collection where you want
To move Collection items within a Collection: to add the reference.
1. From the Collection tree, choose the name of a

The item appears in the new position in the
Collection tree.
Collection.
2. From the Tools menu, take the appropriate Referencing Collection Items
action:
You can reference an item from one Collection to
another in the Collection tree. You can use
If you want to Then choose referenced Collections in different Notebooks and
move the item in
other Collections so that you can see the same exact
the Collection
information in other Collections of E-Notebook.
up one space Move Up. Referencing is slightly different from duplicating an

item. When you duplicate an item, the item appears
down one space Move Down. as “copy.” For more information, see “Duplicating a
Collection” on page 61. When you reference an
The item is moved in the Collection tree. item, the item appears in the new position exactly
the same as the original.
Moving Items Between Collections You cannot add a reference to a Page into a
You can move items from one Collection to another Notebook Collection.
on the Collection tree.
When you reference an item, you must have write
Archived items cannot be moved to a different permission. For more details, contact your system
Collection, but you can make a reference to the administrator.
archived item. For more information, see
“Referencing Collection Items” on page 62. To reference an item:
You cannot remove a Page from a Notebook, but 1. From the Collection tree, choose the name of
you can duplicate the Page and move the duplicate an item.
to a different Collection. For more information, see 2. Hold the Shift and Control keys and drag the
“Duplicating a Collection” on page 61. item to a Collection.
A reference to the original item appears in the
Collection tree.
Archiving Collection Items You can also hide a Collection or the contents of a
Collection so that you can focus on other
You can archive a Collection item so that no one can
Collections more easily.
change the information in that Collection. An
archived Collection is the same as an archived page To view the contents of a Collection:
in a paper Notebook. A Collection can only be • From the Collection tree, click the expansion
archived once. symbol of the Collection you want to see.
You can find out if an item is archived by viewing its The Collection expands so that you can see the
properties. For more information, see “Viewing items it contains.
Collection Properties” on page 65.
To hide the contents of a Collection:
When you archive an item, you must have write
• From the Collection tree, click the contraction
symbol of the Collection you do not want to
administrator.
see.
CAUTION The Collection contracts so that you cannot see
the items it contains.
After you archive an item, no one can make any
changes to it, including changing the archive status.
Browsing Collections
To archive a Collection item: You can browse to different parts of the Collection
tree so that you can find the information you want.
1. From the Collection tree, click the name of an
Browsing includes limiting which Collections you
item.
browse, going to the home Collection, going to a
2. From the Tools menu, choose Archive. specific Collection, browsing up the Collection tree
The Archive dialog box appears. by one Level, and viewing all of the Collection tree.
Limiting Collection Browsing

You can browse over the whole Collection tree, but
you can also limit the Collections over which you
want to browse. By limiting the Collection you can
browse, it becomes easier to find specific
3. Click Yes.
Collections.
The Collection is archived and can no longer be
changed by anyone. You can limit the Collection over which you browse
by setting a root for the Collection tree. You do this
Viewing and Hiding Collections by choosing the highest level Collection you want to
browse.
With the Collection tree, you can view Collections
in the database, so that you can find information
easily. After you go to a Collection through the
Collection tree, you can view that Collection and
then find data or make changes to information.
To set the root for the Collection tree: 3. Take the appropriate action:

If you want to go Then in the
Collection.
to a specific
Administrator
2. From the View menu, choose Browse From

Here.
Notebook Notebook box, type a
The Collection appears at the top of the Notebook name.
Collection tree.
Page number in a Page Number box,
Browsing from Home Notebook type a Page number.
You can browse from your User Home Collection,
which is what you usually see first when you start 4. Click Go.
E-Notebook. The Page appears in the Collection tree.
To go to your User Home Collection: To go to a specific Collection:
• From the View menu, choose Go Home.
1. From the View menu, choose Go To.
Your User Home Collection appears at the top
The Go To dialog box appears.
of the Collection tree.
Browsing to a Specific Page or

Collection
You can browse to a specific Collection or Page, if
you know the name or other details about it.
To go to a specific Page:
1. From the View menu, choose Go To.

The Go To dialog box appears.
2. Click the Collection tab.
The Page tab appears.
3. In the Collection box, type the name of the
Collection you want to go to.
4. Click Go.
The Collection appears in the Collection tree.
2. Click the Page tab.

The Page tab appears.
Browsing the Entire Collection Tree Viewing Collection Properties
You can browse through the entire Collection tree, You can view General Collection properties, so that
so that you can see all parts of the tree, and where you can see specific information about each
you want to go. Collection.
To browse the entire Collection tree: The General tab contains the following information
• From the View menu, choose Browse All. about the Collection:
The Database Collection appears at the top of • Name—name of the Collection.
the Collection tree. • Owner—User who created the Collection.
Browsing Up a Level • Type—type of the Collection.
You can browse up a level higher. For example, you • Contents—number of items in the Collection.
are in a Page and you want to browse the whole • Created—when the Collection was created.
Notebook Collection. You can browse up one level • Last Modified—when the Collection was
to see the Notebook Collection because a Notebook changed last.
is one level higher than a Page.
• Status—status of the Collection, active or
To browse up one level: archived and the date the Collection was
archived.
1. In the Collection tree, right-click an item.
The shortcut menu appears. NOTE: Not every Collection has information for
each property in the General Collection properties
tab.
To view Collection properties:

Collection.
2. From the File menu, choose Properties.
2. Point to Go Up To, and then choose a

Collection.
The Collection appears at the top of the
Collection tree.
The Properties dialog box appears. You can use Templates to set up the structure of
Pages automatically, or you can use Pages without
Templates. Page and Template Sections appear in
the Page area of the E-Notebook window.
Administrator
You can create Pages from Templates so that all

Pages are uniform.
Pages and Templates have the following
characteristics:
• You can assign them to a Notebook, Project,
therapeutic Area, Reaction Scheme, Synthesis,
or Experiment.
• When you create a Page or Template, it has a
unique, fixed number.
• When you create a Page or Template, it has a
single owner. Only the owner of a page can
modify it.
If you want to see Then click the
• When you create a Page or Template, it is
active, which means that the owner can change
General properties for General tab.
the content of the page. Later, you can archive a
the Collection
Page or Template. After the it is archived, it
cannot be changed.
Security properties Security tab, if
for the Collection available. You treat Templates and Pages the same way as any
other Collection. For more information, see:
4. Click Close when you finish viewing the • “Creating a Collection” on page 59.
Collection Properties.
• “Renaming a Collection” on page 60.
The Properties dialog box closes.
• “Duplicating a Collection” on page 61.
Working with Page and • “Organizing a Collection” on page 61.

• “Referencing Collection Items” on page 62.
Template Sections • “Archiving Collection Items” on page 63.
You can keep your data on Page Sections so that you • “Viewing Collection Properties” on page 65.
can add, change, and view data easily. Just as you
use pages in a paper notebook for recording different Different Page and Template Sections are designed
data, you can use Page Sections to record reactions, for different data, such as the following Sections:
spectra, and other information. • Reaction—For more information, see
“Recording Reactions” on page 71.
Working with Page and Template Sections
• MS Word—For more information, see “Editing
an MS Word Section” on page 69. If you want to Then choose
create
• MS Excel—For more information, see “Editing
an MS Excel Section” on page 70.
an MS Word Section MS Word Section.
• Spectra—For more information, see
“Recording Spectra Data” on page 78.
an MS Excel Section MS Excel Section.
• Table—For more information, see “Organizing
Chemical Properties in Table Sections” on page a Spectra Section Spectra Section.
81.
You can create a Page Section, and then view it in a Table Section Table Section.
Card view or List view. You can change a Section by
removing, renaming, or duplicating it. The Section appears in the Page area in Card
view. For more information about Card view,
Creating a Section see “Viewing Sections in Card or List View”.
You can keep your data in Page Sections. Just as you
use pages in a paper notebook for recording different
Viewing Sections in Card or
data, you can use Page Sections to record reactions, List View
spectra, and other information. You can create a new You can see one Section of one Page at a time in
Page Section, or copy a Template Section so that the Card view, so that you can see all the information on
information in the Page Section is uniform. that Section easily. Each Section of a Page has a tab
You can create a Page directly from a Template. For with the name of the Section on it. You can use the
more information, see “Creating a Collection” on Section tabs to view different Sections of a Page in
page 59. Card view.
When you create a Section, you must have write You can see a list of all of the Page Sections in List
permission. For more details, contact your system view so that you know which Section belong to a
administrator. Page. The list appears in a table.
You can also resize the different parts of a Reaction
To create a new Section:
Section so that you can see all the parts more easily.
1. In the Collection tree, click a Page or For more information, see “Resizing Reaction
Template. Section Parts in Card View” on page 71.
2. From the File menu, point to New, and take the
You can change how you view a Page even after you
appropriate action:
archive the Page.

create
a Reaction Section Reaction Section.
To see a Section in Card or List view: To remove a Section:
1. Go to a Page. 1. In Card view, go to the Section you want to

2. From the View menu, take the appropriate remove, and right-click the Section tab.
Administrator
action: The Shortcut menu appears.
If you want to see Then choose

Page Sections in
Card view, with tabs Card.
List view, in a table List.
The Sections of the Page appear in the view you

choose.
2. Choose Delete.
Changing Sections The Delete Section dialog box appears.
You can change, or modify, Sections based on how
you want to use them for recording data. Changing [graphic]
Sections includes the following:
• Removing a Section
3. Click Yes.
• Renaming a Section
The Section is removed from the Page.
• Duplicating a Section
When you change a Section, you must have write Renaming a Section
permission. For more details, contact your system You can rename, a Section from a Page or Template.
administrator.
Removing a Section
You can remove, or delete, a Section from a Page or
Template.
To rename a Section: To duplicate a Section within a Page or Template:
1. In Card view, go to the Section you want to 1. In Card view, go to the Section you want to
rename, and right-click the Section tab. duplicate, and right-click the Section tab.
The Shortcut menu appears. The Shortcut menu appears.
2. Choose Rename. 2. Choose Duplicate.

The Rename Section dialog box appears. The Section is duplicated on the Page.
To duplicate a Section in a different Page or

Template:
[graphic]
1. In Card view, go to the Section you want to
duplicate.
2. Drag the Section tab into the other Page or
3. Click Rename.
Template.
The Section is renamed.
The duplicate Section appears as a referenced
Section in the other Page or Template.
Duplicating a Section
You can duplicate, or copy, a Section within a Page Editing an MS Word Section
or Template. You can also duplicate a Section and
You can keep information that you usually record in
reference it in a different Page or Template.
MS Word in the MS Word Section of a Page. You
You can duplicate a Section and then move it to can edit this data as you normally edit any MS Word
another Collection. For more information, see document.
“Organizing a Collection” on page 61.
When you edit a Section, you must have write
administrator.
To edit an MS Word Section:
1. Go to an MS Word Section.
2. Double-click the MS Word Section area.
MS Word opens and the contents of the Section You can also export the first Section of a set of pages
appear there. by selecting a Collection that contains those pages.
3. Edit the MS Word document as you normally
do. NOTE: Spectra images are exported exactly as
Administrator
they appear in E-Lab Notebook.

4. Save and close MS Word. For more
information, see the Microsoft documentation.
To export a Page into MS Word:
MS Word closes and E-Notebook appears.
1. Go to a Page.
Editing an MS Excel Section 2. From the File menu, choose Export to MS
You can keep information that you usually record in Word.
MS Excel in the MS Excel Section of a Page. You The Export to MS Word dialog box appears.
can edit this data as you normally edit any MS Excel
document.
When you edit a Section, you must have write
administrator. [graphic]
To edit an MS Excel Section:
1. Go to an MS Excel Section.
2. Double-click the MS Excel Section area.
MS Excel opens and the contents of the Section 3. Specify you want to save the Page and then
appear there. click Save.
3. Edit the MS Excel spreadsheet as you normally The Save File dialog box closes, and the second
do. Export to MS Word dialog box appears.
4. Save and close MS Excel. For more
information, see the Microsoft documentation.
MS Excel closes and E-Notebook appears.
[graphic]
Exporting a Section
You can export a Page to MS Word so that you can
save a file outside of E-Notebook. You can edit this
file as you usually edit any MS Word document.
4. Take the appropriate action: • Stoichiometry, in a Stoichiometry table. You
can use the table to calculate and store
If you want to Then click information such as amount, formula mass,
export molarity, density, volume, and many other
values.
the entire Section All. • Preparation for the reaction. You can type the
preparation or procedure for the reaction.
specific Sections Pages, and then • Reactants in the Reactants table. You can use a
specify a page range. reactant that already exists in the E-Notebook
database.
the current Section Current Page.
NOTE: All additions or changes to a Reaction
the file to a different in the File name box, Section are automatically saved. However, you
location and type a file name. cannot change any part of a Page that you archive.
For more information, see “Archiving Collection
5. Click Export. Items” on page 63.
The Page is exported to MS Word. This may

take several minutes. Resizing Reaction Section
Parts in Card View
Recording Reactions You can reposition the parts of a Reaction Section,
You can use a Reaction Section to show one step of such as the Structure or Stoichiometry table, so that
a reaction. You can keep all the Reaction Sections in you can see information more easily. The Section
one Page Collection so that you can refer to any part parts adjust when you move one part. You can only
of the reaction easily. You can also record the do this in Card view.
following information about a reaction in a Reaction
To resize a Section part:
Section:
1. On a Reaction Section, go to Card view. For
• Chemical structure of all the compounds
more information, see “Viewing Sections in
involved in the reaction. You can draw the
Card or List View” on page 67.
chemical structure in E-Notebook with
ChemDraw tools and commands. You can view 2. On a Section part, move your mouse pointer
chemical structures in Card view or without in around the borders until the pointer becomes a
List view. For more information, see “Viewing double-headed arrow.
Sections in Card or List View” on page 67. 3. Drag the mouse pointer so that the border of the
• Reaction properties, such as pressure, Section part moves to where you want it.
temperature, and any others you want. You can The parts are resized.
even note multiple reaction properties of the
same type associated with a reaction, such as
two solvent properties that represent a mixture
of solvents.
Recording Reactions
Creating and Editing Chemical Changing Reaction Properties
Structures You can include reaction properties in a Reaction
You can create chemical structures in a Reaction Section, so that you can see which properties are
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Section by drawing or copying it in the Reaction associated with that step of the reaction. Reaction
box. You can use standard editing commands, such properties can include information such as
as Copy and Paste. temperature, reaction type, and pressure.
When you draw a chemical structure, you must have You can change, or modify, reaction properties.
write permission. For more details, contact your Changing properties includes the following:
system administrator. • Adding properties to the Reaction Section from
the properties list.
To draw a chemical structure:
• Removing properties from the Reaction
1. Go to a Reaction Section, and then click the Section.
Reaction box.
• Setting property values.
The ChemDraw toolbar appears.
• Organize the properties table
2. Draw the reaction with the ChemDraw tools.
When you change a Section, you must have write
For more information about the ChemDraw
tools, see the ChemDraw User’s Guide.
administrator.
The chemical structure appears in the Reaction
box.
NOTE: You can change Spectra properties the
To draw or edit a chemical structure in a larger same way you change Reaction properties. Make
window: sure that you change the appropriate property. For
example, when you are instructed to “go to a
1. Go to a Reaction Section, and then from the Reaction Section,” you go to a Spectra Section
Edit menu, choose Edit Structure. instead.
The Edit Structure dialog box and the
ChemDraw tools appear. Adding Properties
2. Draw the reaction with the ChemDraw tools. You can add a reaction property to a Reaction
For more information about the ChemDraw Section.
To add a property to a Reaction Section:
The chemical structure appears in the Reaction
box. 1. Go to a Reaction Section.
3. Click OK. 2. From the Reaction menu, choose Add

Property.
The Edit Structure dialog box closes. The
Reaction Section appears, and the chemical
structure appears in the Reaction box.
Recording Reactions
The Add Property dialog box appears. Setting and Editing Property Values
You can set and edit values for reaction properties in
the Reaction Properties box on a Reaction Section.
For searching purposes, numeric values for
[graphic] properties are interpreted by evaluating the longest
possible set of characters that are converted into a
number, starting with the first character. For
example, the text “37.5 g” is interpreted as 37.5. The
text “2 ATM/50” is interpreted as 2.
To set or edit the value of a property:

3. Click a property and then click Add.
The Add Property dialog box closes and the 1. Go to a Reaction Section.
property appears in the Reaction Properties 2. In the Reaction Properties box, click a cell in
table in the Reaction Section. the table.
Removing Properties
You can remove a reaction property from a Reaction
Section.
To remove a property from a Reaction Section:
1. Go to a Reaction Section.
2. In the Reaction Properties box, click a 3. Take the appropriate action:
property.
3. From the Reaction menu, choose Remove If the property has Then in the value
Property. cell,
The Remove Property dialog box appears.
the data type of Date click the date box,
and then type a date
and time.
the data type of Text then type text.
4. Click Yes. the data type of then type a number.

The property is removed from the Reaction Number
Section.
enumerated values from the menu,
choose a value.
Recording Reactions
4. Press Enter. Changing Information in the
The new value is saved. Stoichiometry Table
Analyzing a Reaction You can use the stoichiometry table to calculate and
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store stoichiometric data for the reaction. You can

After you create a chemical reaction in the Reaction get the reactants and products from the chemical
box on a Reaction Section, you can analyze the structure drawing automatically. For more
reaction. By analyzing the reaction, all the information, see “Analyzing a Reaction” on page
information about the reaction automatically 74. You can also type stoichiometric data manually.
appears in the Stoichiometry table of the Reaction
Section, if it is not there already. For more You can add reactants to the stoichiometry table
information about manually typing stoichiometric from a list from the database.
data and adding reactant information automatically, E-Notebook makes the following calculations with
see “Adding Information to the Stoichiometry data in the Stoichiometry table:
Table” on page 74.
• Moles = (amount x 1000) / formula mass x
New reactants and products are added to the percent weight
stoichiometry table based on the chemical drawing.
• Limiting Moles = moles of limiting reactant /
By default, the names of the reactants and products
equivalence of limiting reactant
are determined by the molecular formulas of the
drawing. • Molarity = moles / volume
If the stoichiometry table contains reactants and • Volume = amount / density

products, then the new analysis values take their For non-limiting reactants:
places. Reactants added from the reactants table are
• Equivalents = amount x percent weight /
not removed when you analyze a reaction.
formula mass x 1000 / limiting moles
The number of significant digits for any calculated • Moles = equivalents x limiting moles
data is determined by the maximum number of
• Amount = (moles / 1000) x formula mass /
significant digits for any entered data per reactant or
percent weight
product. The minimum number of significant digits
for any calculated data is 2. For products:
When you change a Section, you must have write • Moles = equivalents x limiting moles
permission. For more details, contact your system • Expected yield = formula mass x moles / 1000
administrator.
To analyze a reaction: permission. For more details, contact your system
administrator.
2. From the Reaction menu, choose Analyze Adding Information to the
Reaction.
The Stoichiometry table is automatically filled
in.
Recording Reactions
Stoichiometry Table The Add Reactant dialog box appears.
You can manually type stoichiometric information
into the Stoichiometry table of a Reaction Section,
and you can add reactants from a list from the
database. [graphic]
When you add reactant information automatically,
the name of the reactant in the stoichiometry table is
the same as the reactant in the database. Reactants
added from the database are not removed when you
analyze a reaction.
The number of significant digits for any calculated 3. Choose a reactant, and then click Add.
data is determined by the maximum number of The Add Reactant dialog box closes and the
significant digits for any entered data per reactant or reactant is added to the reactant Stoichiometry
product. The minimum number of significant digits table.
for any calculated data is 2.
For more information about calculating
Removing Reactants and Products
stoichiometric data, see “Analyzing a Reaction” on from the Stoichiometry Table
page 74. You can remove all the information about a product
or reactant from the Stoichiometry table
To manually type information into the automatically.
Stoichiometry table:
If the reactant is the limiting reactant of the reaction,
1. Go to a Reaction Section. the first remaining reactant becomes the limiting
2. In the Stoichiometry table, type information reactant for the reaction.
into the appropriate cells.
To remove products and reactants from the
Stoichiometry table:
[graphic] 1. Go to a Reaction Section.
2. From the Stoichiometry table, click a product
or a reactant.
3. From the Reaction menu, take the appropriate
action:
The information is saved.
To automatically enter reactant information into the If you want to Then choose
Stoichiometry table: remove
a product and all Remove Product.
2. From the Reaction menu, choose Add related information
Reactant.
Recording Reactions
The Text Formatting toolbar appears in the E-
If you want to Then choose Notebook window.
remove
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a product and all Remove Reactant.

3. Choose the text you want to format, and take the
related information
appropriate action:
The information is removed from the
Stoichiometry table. If you want to Then click
Recording Experiment remove the text from Cut .

Procedures and paste it on the
clipboard
You can use the Preparation box of a Reaction
Section to record experiment procedures for a
duplicate the text onto Copy .
reaction. You can keep the experiment preparation
the clipboard
with the reaction for the experiment, so that the data
is easily accessible. When you type a procedure, you
add text from the Paste .
can also format the text.
clipboard
permission. For more details, contact your system make text appear in Bold .
administrator. bold style
To record preparation procedures:
make text appear in Italics .
1. Go to a Reaction Section, and click the italicized style
Preparation box.
A cursor appears in the Preparation box. underline the text Underline .
2. Type the preparation procedure.
add a superscript Superscript .
The Preparation information is automatically
saved with the Reaction Section.
add a subscript Subscript .
To format the Preparation text:
align the text to the Left Justify .
1. Go to a Reaction Section, and click the left margin
Preparation box.
A cursor appears in the Preparation box. center the text Center .
2. From the View menu, choose Toolbar.
align the text to the Right Justify .
right margin
Recording Reactions
The Preparation information is automatically 4. Draw the reaction with the ChemDraw tools.
saved with the Reaction Section. For more information about the ChemDraw
Creating Reactants in the The chemical structure appears in the Reaction
Database box.
You can add reactants to the database so that you can 5. Click Create.
include them in reactions, without drawing them or The molecular formula and weight appear
typing them into the Stoichiometry table again. You below the drawing box, and the reactant is
can add more reactants to this list at any time. After added to the database.
you add a reactant to the E-Notebook database, it is
6. Click Close when you finish adding reactants.
available to all users.
The Reactants dialog box closes.
To create a reactant in the database:
1. From the View menu, choose Reactants.

Removing Reactants from the
The E-Notebook - Reactants dialog box
Database
appears. You can remove reactants from the database so that
you do not use extra database space. After you
remove a reactant from the E-Notebook database, it
is no longer available for any user.
[graphic]
2. In the Name box, type the name of a reactant.

3. In Create a New Reactant, click the drawing
box.
The ChemDraw toolbar appears.
Recording Reactions
To remove a reactant from the database:
Recording Spectra Data
1. From the View menu, choose Reactants.
You can maintain your spectra data in E-Notebook
The E-Notebook - Reactants dialog box easily and effectively with Spectra Sections. Spectra
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appears. Sections can contain one or more spectra images, a

set of properties for each spectra, and notes about the
spectra all in one area. You can also keep the Spectra
Section in a Page Collection with other Sections that
have information about the same experiment,
project, or other group.
You can use the same tools and commands that are
used in Galactic’s GRAMS32 software to analyze
the spectrum image.
[graphic]
administrator.
Resizing Spectra Section Parts

in Card View
You can reposition the parts of a Spectra Section,
such as the Structure or Stoichiometry table, so that
you can see information more easily. The Section
parts adjust when you move one part. You can only
2. Click a reactant, and then click Delete. do this in Card view.
The ELN Client dialog box appears. To resize a Section part:
1. On a Spectra Section, go to Card view. For
[graphic] more information, see “Viewing Sections in
Card or List View” on page 67.
2. On a Section part, move your mouse pointer
around the borders until the pointer becomes a
3. Click Yes. double-headed arrow.
The reactant is removed from the database. 3. Drag the mouse pointer so that the border of the
4. Click Close. Section part moves to where you want it.
The Reactants dialog box closes. The parts are resized.
Changing a Spectrum The New Spectrum dialog box closes and the
spectrum appears in the Spectra Section.
You can include spectra images in a Spectra Section
so that you can see different images easily. Removing a Spectrum
You can change, or modify, the placement of the You can remove a spectrum image from a Spectra
spectra images so that you organize them in a way Section.
that is useful to you. Changing properties includes
the following: To remove a spectrum to a Spectra Section:
• Adding images to the Spectra Section. 1. Go to a Spectra Section, and go to a specific

spectra.
• Removing images from the Spectra Section.
2. From the Spectra menu, choose Remove
• Replacing images in the Spectra Section.
Spectrum.
The spectrum is removed from the Spectra
Section.
administrator.
Replacing a Spectrum
Adding a Spectrum
You can replace a spectrum image with a different
You can add a spectrum image to a Spectra Section.
image on a Spectra Section. The properties and
If GRAMS32 is installed, then a dialog appears that notes for the spectrum do not change when you
contains an image of the spectrum file, as well as an replace the image.
extensive set of file formats you can import.
If GRAMS32 is installed, then a dialog appears that
To add a spectrum to a Spectra Section: contains an image of the spectrum file, as well as an
extensive set of file formats you can import.
1. Go to a Spectra Section.
To replace a spectrum on a Spectra Section:
2. From the Spectra menu, choose Add
Spectrum. 1. Go to a Spectra Section, and got to a specific
The New Spectrum dialog box appears. spectra.
2. From the Spectra menu, choose Replace
Spectrum.
[graphic]
3. Select a spectrum, and click Open.
The Replace Spectrum dialog box appears. To record notes:
1. Go to a Spectra Section, and click the Notes

box.
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A cursor appears in the Notes box.

[graphic]
2. Type the notes.
The Notes information is automatically saved
with the Spectra Section.
To format the Notes text:
3. Select a spectrum, and click Open. 1. Go to a Spectra Section, and click the Notes
box.
The Replace Spectrum dialog box closes and
the spectrum appears in the Spectra Section. A cursor appears in the Notes box.
2. From the View menu, choose Toolbar.
Changing Spectrum Properties The Text Formatting toolbar appears in the E-
Spectrum properties are associated with a spectrum, Notebook window.
such as spectra type, instrument, and date. You can
have multiple spectrum properties associated with a
spectrum. 3. Choose the text you want to format, and take the
You can add properties to the database, remove appropriate action:
properties, and set property values. For more
information, see “Changing Reaction Properties” on If you want to Then click
page 72. Spectra properties are different form
Reaction properties, so make sure that you are remove the text from Cut .
changing the correct property. When you are and paste it on the
instructed to “go to a Reaction Section,” you go to a clipboard
Spectra Section instead.
When you change a Section, you must have write duplicate the text onto Copy .
permission. For more details, contact your system the clipboard
administrator.
add text from the Paste .
Recording Notes clipboard
You can use the Notes box of a Spectra Section to
record additional information for a spectrum, so that make text appear in Bold .
bold style
the notes and the spectra are kept together.
When you change a Section, you must have write make text appear in Italics .
permission. For more details, contact your system italicized style
administrator.
• Remove columns, or properties
• Resize columns and rows
underline the text Underline . • Organize rows

• Organize columns
add a superscript Superscript . When you change a Section, you must have write
add a subscript Subscript . administrator.
align the text to the Left Justify . Adding Columns

left margin You can add columns to your Table in the form of
properties. Each column heading has a property
center the text Center . name, automatically. This is how you add properties
to a Table Section.
align the text to the Right Justify .
To add a property to a Table Section:
right margin
1. Go to a Table Section, and then click the
The Notes information is automatically saved heading cell of a column.
with the Spectra Section.
2. From the Table menu, choose Add Property.
Organizing Chemical The Add Property dialog box appears.
Properties in Table
Sections [graphic]
Table Sections contain one or more rows of data in a
spreadsheet format. Each row contains data for the
same set of properties. You can organize the
properties that appear in Table Sections so that you
can see the data which you interests you more easily.
Table Sections appear on Pages and contain tables of 3. Choose a property, and Click Add.
data. The data is organized in two dimensions by
The Add Property dialog box closes and the
property, or column, and by row. Information that is
property appears in the heading cell.
associated with a particular property and a particular
row appears in a cell of the table. Properties can be
one of the following types: text, number, chemical
Removing Columns
structure or date. You can remove columns, or properties, from your a
Table Section, so you only see the properties that
You can do the following on a Table Section:
you use.
• Add columns, as table properties
Organizing Chemical Properties in Table Sections
To remove a column from a Table Section: The column moves according to your choice.
1. Go to a Table Section, and then click the Adding Rows

heading cell of a column.
You can add rows to your Table, so that you can add
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2. From the Table menu, choose Remove

more information to each property, or column. Each
Property.
row is automatically numbered.
The Remove Property dialog box appears.
To add a row to a Table Section:
[graphic] 1. Go to a Table Section, and then click a row

number.
2. From the Table menu, choose Add Row.
The row appears in the Table Section, and are
3. Click Yes.
re-numbered if necessary.
The Remove Property dialog box closes and the
column is removed from the table. All of the Removing Rows
data in the column is also removed. You can remove rows from your Table, so that you
only see the rows you use. Each row is automatically
Organizing Columns re-numbered, if necessary.
You can organize columns in a Table Section by
moving an entire column to the left or right. When To remove a row from a Table Section:
you organize columns you move properties so that 1. Go to a Table Section, and then click a row
you can use them more easily. number.
To move a column: 2. From the Table menu, choose Remove Row.
1. Go to a Table Section, and then click the The Remove Rows dialog box appears.
heading cell of a column.
[graphic]
2. From the Table menu, take the appropriate
action:

move the column 3. Click Yes.
by one column The Remove Rows dialog box closes and the
space to the row is removed from the table.
left Move Property Left.
right Move Property

Right.
Organizing Rows To resize a row or column:
You can organize rows in a Table Section by moving 1. Go to a Table Section.

an entire row up or down, and by choosing the order 2. Take the appropriate action:
that they appear. When you organize rows, you
arrange information so that you can see it more
If you want to Then move your
easily.
resize mouse pointer to
To move rows: the
1. Go to a Table Section, and then click a row the height of a row horizontal line
number. between row numbers
2. From the Table menu, take the appropriate
action: the width of a column vertical line between
column headings
The mouse pointer becomes a double-headed
move the row up one Move Row Up. arrow.
row space 3. Drag the pointer in the direction you want.
The row or column is resized.
move the row down Move Row Down.
one row space Changing Information in a Cell
All of the information on a Table Section is in cells
sort the rows from the Sort Ascending.
of the Table. The information in each cell is
top downwards
determined by the data type for that cell. Each cell
has one of the following data types:
sort the rows from the Sort Descending.
bottom upwards • Text
• Date
The rows move according to your choice, and
• Number
are re-numbered if necessary.
• Structure
Resizing Rows and Columns You can put information into a cell by choosing a
You can resize rows and columns so that you can see value form a menu that appears in the cell, typing a
the information in the Table more easily. value, or drawing a chemical structure.
For purposes of searching, numeric values are
interpreted by evaluating the longest possible set of
characters that can be converted into a number,
starting with the first character. For examples, the
text “37.5 g” is interpreted as 37.5; The text “2
ATM/50” is interpreted as 2.
Adding Information to a Cell Registering Chemical
You can add information to a cell in the following
ways: Compounds
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• Choose a value form a menu that appears in the You can submit a compound drawn within
cell E-Notebook to Chemical Registration. For more
information about chemical Registration, see
• Type a value
“Chapter 10: Chemical Registration” on page 139.
• Draw a chemical structure
When you submit compounds, they are stored in the
NOTE: The information you add to a cell depends temporary tables in Chemical Registration. You can
on the data type of the cell. For example, you can edit information about compounds in Chemical
only draw a chemical structure in a cell with a Registration before you actually register them.
structure data type. You must specify the location of the Chemical
Registration database with E-Notebook
To add information to a cell: Administrator so that you can export compounds to
Chemical Registration.
1. Go to a Table Section, and click a cell.
2. Take the appropriate action: To export a compound to Chemical Registration:
If you want to Then 2. From the Reaction menu, choose Register
Compound.
add an enumerated from the menu in the A dialog box appears.
value from a menu cell or dialog box that
appears, choose a 3. Click Submit.
value. The dialog box closes. A notification message
appears when the compound is successfully
type a value type a value in the cell submitted.
add a chemical in the Edit Structure Searching

structure dialog box that
appears, draw a You can search for Collection items or Pages that
structure with the match some common criteria, such as the following:
ChemDraw tools.
• The name of an item
For more information • The owner of an item
about ChemOffice, • The type of an item (such as notebook, page,
see the ChemDraw
therapeutic area, or experiment)
User’s Guide.
• The last modified date of an item
The information is saved in the cell. • The status of an item
• A substructure in a reaction Section of a page
Registering Chemical Compounds
• A reaction property in a reaction Section of a
page If you want to find Then click the
items that match
To search for Collection items or Pages:
1. From the Tools menu, choose Search. a data type Type box, and specify
the criteria you want
The Search dialog box appears.
to match.
the creation date Creation Date box,

and specify the
criteria you want to
match.
the last modified date Last Modified Date

box, and specify the
criteria you want to
match.
[graphic]
status Status box, and
specify the criteria
you want to match.
chemical structures Sections contain

box, click the
Reaction Structure
tab, and then draw a
structure you want to
match.
Reaction properties Sections contain
box, click the
If you want to find Then click the Reaction Properties
items that match tab, and then specify
the criteria you want
an item name Name box, and to match.
specify the criteria
you want to match. a spectrum Sections contain
box, click the
a User’s last name Owner Last Name Spectra Properties
box, and specify the tab, and then specify
criteria you want to the criteria you want
match. to match.
Searching
3. Click Search Now. 3. Take the appropriate action:
The Search dialog box expands, and the results
of your search appear in a list. If you want to Then
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To go to a specific Collection or Page:

print to a printer From the Name menu,
1. From the search results list, choose an item. other than the one choose a printer.
in the Name menu
2. Click the Go To button. box
The Search dialog box closes, and the item you
choose appears in the E-Notebook window. see the printer Click Properties.
property settings
To create a new Collection containing the results of
your search:
print all the pages All.
• From the Search dialog box, click Save in the Collection
Results.
The Search dialog box closes and a new print a range of a. Click Pages.
Collection appears as the root of the Collection Sections from the
tree. All the items from the search results list Page b. In the from text box,
use this new root. type the page number
of the first page you
want to print.
Printing
c. In the to text box,
You can print a Page in Card view, so that the
type the page number
Sections appear on one printed page. You can print of the last page you
a Page in List view, so that the Sections appear in want to print.
continuous output.
You can also print the first Section of a set of Pages print the pages you Click Selection.
by choosing a Collection that contains those Pages. are currently
viewing
To print a Page:
1. Go to a Page. print a specific In the Number of copies
2. From the File menu, choose Print. number of copies box, do one of the
following:
The Print dialog box appears.
• Type a number.
• Use the up and down

arrows to select a
number.
Printing
If you want to Then
have the printer Select Collate.

collate the copies
4. Click Print or OK.

The Sections are printed.
Closing E-Notebook
You can close E-Notebook when you finish using it.
To close E-Notebook:
• From the File menu, choose Close.
E-Notebook closes.
Closing E-Notebook
Appendix of Collection The following table shows which Collection types
(in the columns) can contain specific Collection
Definitions items (in the rows), noted with an X. This table
shows the possible relationships between
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You can use E-Notebook Collections to group Collections so that you can understand how to create
almost any information together. You can create and organize Collections more efficiently.
Collections and populate those Collections with
items that you want related. For more information
about Collections, see “Working with Collections”
on page 58. Collection Types
Are apeutic
e nt
Sect plate
S c h t i on
k
is
e
ions
e ri m
eboo
i on s
pl a t
eme
t he s
ect
c
e
Tem
Rea
Pag
e
r
Sect
Tem
T he
a
P r oj
E xp
S yn
Use
P ag
N ot
Notebook X X X X X X
Page X X X X X X X
Collection Items
Page X
Sections
Template X X X X X X
Template X
Sections
Therapeutic X X X X X X
Area
Project X X X X X X
Experiment X X X X X X
Reaction X X X X X X
Scheme
Synthesis X X X X X X
User
Appendix of Collection Definitions
Chapter 7: E-Notebook Administrator
Overview of E-Notebook Setting up in MS Access
When you set up E-Notebook in the MS ACCess
Administrator format, you must install E-Notebook and then
E-Notebook is an electronic notebook that you can configure the client system to connect with the file
use to do the following: server.
• Store your data in an electronic notebook. When you install E-Notebook, you must move the
database folder contents. This folder contains the
• Create MS Word, MS Excel, spectra, table, and
following files:
reaction sections for your data.
• View data from any other notebook stored in the • ELabNotebook.mdb
E-Notebook database. • ELabNotebook.mst
• View data from any other experiment stored in • ELabNotebook.msi
the E-Notebook database.
When you create a Data Source for the client system,
You can control access to E-Notebook with the it must do the following:
E-Notebook Administrator.
• Use the MS Access ODBC driver
E-Notebook works in a Single-User or a Multi-User
• Be able to reference the database on the server.
environment. In a Single-User environment, all
setup operations are automatic, but you must use the For more information about moving .mst and .msi
E-Notebook Administrator to set up the Multi-User files, see“Setting the Chemical Structure File Path”
environment. on page 102.
E-Notebook supports two database formats: For more information about connecting to Chemical
Microsoft Access (.mdb) and Oracle. The Access Registration, see “Connecting to Chemical
version of the E-Notebook database is included with Registration” on page 104.
the E-Notebook software. To acquire the Oracle To install the E-Notebook database on a file server:
version of the E-Notebook database, please contact
1. Install ChemOffice 6.2 on a client system.
info@camsoft.com.
2. Move the contents of the folder
Installing E-Notebook ChemOffice2001/ChemFinder/
ELabNotebook/database to the file server.
Administrator E-Notebook database is installed.
You can install E-Notebook for the MS Access
format or the Oracle format. You must set up
E-Notebook for one of these database formats.
ChemOffice Chapter 7: E-Notebook Administrator • 89

Overview of E-Notebook Administrator
To configure a client system to connect to the file For more information about connecting to Chemical
server: Registration, see “Connecting to Chemical
Registration” on page 104.
• Create a Data Source named “E-Notebook
6.2.”
Administrator
To install the E-Notebook database into an Oracle

The Data Source can be a User or System Data System:
Source. 3. Create the user CS_NOTEBOOK with
You can use E-Notebook Administrator to set password CS_NOTEBOOK and include DBA
the Administrator password, create new users, privileges.
and create groups. 4. Log in as CS_NOTEBOOK.
5. Run the SQL script ELN_DB.sql.
Setting up in Oracle
There are three parts to an Oracle configuration: To install E-Notebook software to connect to the
Oracle database:
• The Oracle database
6. Install ChemOffice 6.2 on the administrator
• The client systems system.
• The chemical structure index files 7. Create a Data Source named “E-Notebook
The ChemOffice 6.2 installer contains the software 6.2.”
for the client systems and the chemical structure
index files. To configure an E-Notebook client to talk to the
Oracle back end:
You must install the ODBC driver for Oracle before
8. Create a folder on a Windows file server. This
you connect to the Oracle database. For Windows
folder contains the chemical database indexes.
98/Office 97, this requires installing the Oracle
client, version 7.3 or later. 9. Copy the ELabNotebook.mst and
ELabNotebook.msi files from the database
You must have an available Oracle Service Name. folder to the folder on the file server.
With Oracle8i, service names can be managed on a
10.Run E-Notebook Administrator.
local machine using the Net8 Assistant.
Alternatively, your system may have Oracle Name 11. Log in with the user name Administrator, but
Servers installed that are used to publish Oracle no password.
Names across your network. 12.From the View menu, choose Chemical
When you create a Data Source, it must do the Structure File Path.
following: 13.Specify a path to the .mst file.
• Use the Oracle ODBC driver For more information, see “Setting the
• Be able to connect to the Oracle database that Chemical Structure File Path” on page 102.
contains the user CS_NOTEBOOK You can use E-Notebook Administrator to set
When you run E-Notebook Administrator, you must the Administrator password, create new users,
and create groups.
run it on a machine that can connect to the Oracle
back end.
90 • Chapter 7: E-Notebook Administrator CambridgeSoft

Installing E-Notebook Administrator
Starting E-Notebook The E-Notebook Administrator appears.
Administrator
You must open and then log in to E-Notebook
Administrator so that you can use it.
Opening E-Notebook
Administrator
You must open E-Notebook Administrator before
you can log in.
To open E-Notebook Administrator:
• From the Start menu, point to Programs, point
to ChemOffice 7.0, and then choose E-
Notebook Administrator.
The E-Notebook Login dialog box appears. To log in as a Multi-User:
3. Open E-Notebook Administrator.
Multi-User.
5. Type your User Name and Password, and then
click Login.
The E-Notebook Administrator appears.
Logging In
You can log in as a Multi-User, with a user name and
password, or a Single-User.
To log in as a Single-User:
Single-User, and then click Login.

Starting E-Notebook Administrator
Changing User 2. Click the General tab and take the appropriate
action:
Information
If you want to Then
Administrator
You can create a user account. Each user has specific

properties that you can change. You can also retire a
user, but you cannot delete a user. include the title of the in the Title box, type a
user title.
Creating a User
include the first name in the First Name
You can create a user account with properties for
of the user box, type a first name.
that specific user.
After you begin creating a user account, you cannot include the middle in the Middle Name
undo the action. You can retire a user if the account name of the user box, type a middle
is not active. name.
To create a user:
include the last name in the Last Name
1. From the File menu, point to New, and then of the user box, type a last name.
click User.
The User Properties dialog box appears. assign a user name in the Login ID box,
type a user name.
assign a password in the Password box,

type a password.
confirm the password in the Confirm

Password box, type
the password for the
user again.
include the email in the E-mail

address of the user Address box, type an
email address.
grant administrator click Administrator.

privileges
3. Click the Security tab.

The Security tab appears.

Changing User Information
The Security panel is used to specify the The User Properties dialog box appears.
Default Security for collections and pages
created by the user.
3. Follow step 2 in “Creating a User” on page 92.

4. Click Apply.
4. Click Add.
The changes are applied to the user.
The Add Permissions dialog box appears. For
5. Click Close.
more information, see “Adding Permissions for
a User” on page 94. The User Properties dialog box closes.
5. Click Add.
Changing Security Properties
The Add Permissions dialog box closes. The
You can change, or edit, the security properties
Security tab appears.
associated with a User.
6. Click Close.
When a user has security permissions, they have
The User Properties dialog box closes.
access to specific Notebooks. You can control which
Notebooks users can access by adding or removing
Changing General Properties
the user from permissions lists.
You can change, or edit, the properties associated
with a User. To open the security properties for a user:
To change the properties of a user: 1. From the Users list, click the name of a user.
1. From the Users list, click the name of a user.
The User Properties dialog box appears.
3. Click the Security tab.

The Security tab appears. The Add Permissions dialog box shows all the
Users in E-Notebook Administrator.
4. From the Groups and Users list, click a user.
Administrator
5. From the Type of Access menu, take the

appropriate action:
If you want the Then choose

User to be able to
read files without Read.

changing them
read and change files Read and Write.
6. Click Add.
Adding Permissions for a User The Add Permissions dialog box closes.
You can add a user to a list of other users who have
the same security privileges. Removing Permissions for a User
To add a user to a permissions list: You can remove a user from the list of Groups and
User who share the same permissions. When you
1. In the User Properties dialog box, click the remove a user from the list, the user does not have
Security tab. the permissions.
The Security tab appears. To remove a user from the permissions list:
2. Click Add.
1. In the User Properties dialog box, click the
The Add Permissions dialog box appears. Security tab.
The Security tab appears.
2. From the Share New Pages and Collection
With list, click a user.
3. Click Remove.
The user is removed from the permissions list.
Retiring a User
When a user account becomes inactive, you can
retire the user. A retired user cannot log in to the
database, and you can assign the login ID to a
3. Click Show Users. different user.

To retire a user: A temporary group name, Untitled Group,
appears in the Groups list.
1. From the Users list, choose a user.
2. From the Edit menu, choose Retire User.
The E-Notebook Administrator dialog box
appears.
3. Click Yes.
The user is retired.
Changing Group
Information
You can create a group account. You can also 2. Type a name for the group.
rename a group, add, and delete a users from the The name appears in the Groups list.
group.
Adding a User to a Group
An E-Notebook group is a collection of users who
can all access specific Notebooks. You can add users to a group, which is a collection
of users.
Groups do not a set of properties because a group is
only a collection. Individual users have properties To add a user to a group:
which are separate from a group. For more
1. From the Users list, click a user.
information, see “Changing General Properties” on
page 93 and “Changing Security Properties” on page 2. Drag the user to a group.
93. The expansion symbol, , appears to the left
of the group and the user who now belongs to
Creating a Group the group.
You can create a group, which is a collection of
users. Changing a Group Name
You can change, or edit, the name of a group.
To create a group:
1. From the File menu, point to New, and then To change the name of an existing group:
click Group.
1. From the Groups list, click the group you want
to edit.
The name of the group appears in a text box.

Changing Group Information
2. Type a new name. • Tables—Controls the Table properties in a
3. Press Enter. reaction that appear in the Table section of a
Notebook Page. Table properties include
The group name is changed. compound ID, chemical structure, and
Administrator
molecular weight.
Removing a User from a Group
Each type of information has a property dialog box
You can remove a user from a group. User that you
associated with it, in which you manage the
remove do not have permissions for the Notebooks
properties. You can do the following from each
of that group. property dialog box:
To remove a user from a group: • Create properties
1. From the Groups list, click a user. • Rename properties
2. From the Edit menu, choose Remove User • Deactivate properties
from Group. • Remove properties
The user is removed from the group. • Add enumerated values to properties
• Set defaults for properties
Setting Properties
The following types of information have different Creating a Property
properties associated with them: You can create a property in any of the property
• Reaction—Controls the Reaction properties dialog boxes.
that appear in the Reaction section of a When you create a property, you assign it a data
Notebook Page. Reaction properties include type. The data type specifies what kind of data you
solvent, temperature, and pressure. You can associate with the property. For example, you can
also set enumerated values for Reaction assign a structure data type to a Table property.
properties. When you enter information for that Table property
• Reaction Reactants—Controls the Reactant in E-Notebook, you can only enter a structure.
properties in a reaction that appear in the Different properties have different data types you
Stoichiometry section of a Notebook Page. can use. The following table shows the data types
Reactant properties include sources for you can assign to each type of property, denoted by
reactants. an X:
• Reaction Products—Controls the Product
properties in a reaction that appear in the Type of Text Number Date Structure
Stoichiometry section of a Notebook Page. Property
Product properties include disposition.
• Spectra—Controls the Spectra properties in a Reaction X X X –
reaction that appear in the Spectra section of a
Notebook Page. Spectra properties include Reactant X X – –
type, date, and frequency.

Setting Properties
A Property dialog box opens. The following
Type of Text Number Date Structure illustration shows the Reaction Property dialog
Property box.
Product X X – –
Spectra X X X –
Table X X X X
Text data types can have values with up to 50

characters. Date data types contain both date and
time parts.
To create a property:
1. From the View menu, take the appropriate
action:

create a
2. In the Name box, type a name for the new
reaction property Reaction Properties. property.
3. From the Type menu, take the appropriate
reactant property for a Reactant Properties. action:
reaction
If you want the Then if possible,

product property for a Product Properties. new property to choose
reaction have a data type of
spectra property Spectrum text Text.

Properties.
number Number.
table property Table Properties.
date Date.
structure Structure.

Setting Properties
If you want the Then click

property to
Administrator
appear automatically Default.

in a Page section
be able to appear, but Active.

not automatically in a
Page section
NOTE: For a Reactant property or Product

property to appear for new reactants, you must
make the property both the default and active.
5. Click Create.
The new property appears in the table in the
Property dialog box.

Setting Properties
Changing a Property
You can change, or edit, a property.
To change a property:

action:

change a
Reaction property Reaction Properties.
Reactant property for Reactant Properties.

a reaction
Product property for a Product Properties.

reaction 2. Take the appropriate action:
Spectra property Spectrum If you want to Then

Properties. change
Table property Table Properties. the name of the in the Name box, type
property a new name.
A Property dialog box opens. The following
illustration shows the Reaction Property dialog the data type of the from the Type menu,
box. property choose a different
data type.
default status click Default.
active status click Active.
the enumerated click Enumerated

values Values. For more
information, see
“Changing
Enumerated Values”
on page 100.
3. Click Change.

Setting Properties
The property changes. A Property dialog box opens. The following
illustration shows the Reaction Property dialog
Deleting a Property box.
You can completely remove, or delete, a property.
Administrator
You cannot remove a property that is currently in

use, but you can deactivate it. For more information
about changing the Active status of a property, see
“Changing a Property” on page 99.
To delete a property:

action:

change a
Reaction property Reaction Properties.
Reactant property for Reactant Properties.

a reaction 2. Click the property you want to delete.
3. Click Delete.
Product property for a Product Properties.
The E-Notebook Administrator dialog box
reaction
appears.
Spectra property Spectrum

Properties.
Table property Table Properties.

4. Click Yes.
The property is deleted.
Changing Enumerated Values

You can add, remove, and organize enumerated
values.
When you add enumerated values to a property,
users can only choose those values when they use
the property. They cannot create their own values for
the property.

Setting Properties
You can only add enumerated values to Reaction A blank row appears in the Enumerated Values
properties with a text data type. dialog box.
To open the Enumerated Values dialog box so that
you can change the values:
• In a Property dialog box, click Enumerated
Values.
The Enumerated Values dialog box appears.
The following illustration shows the
Enumerated Values for “Reaction Type” dialog
box.
3. In the blank row, type a value.

4. Click OK.
The Enumerated Value dialog box closes and
the Reaction Properties dialog box appears.
Removing Enumerated Values

You can remove, or delete, enumerated values from
properties with the text data type.
To remove enumerated values:
Adding Enumerated Values
1. Open the Enumerated Values dialog box for a
You can add enumerated values to Reaction
property.
properties with the text data type.
2. Click a row.
To add enumerated values to Reaction properties:
3. Click Remove Value.
1. Open the Enumerated Values dialog box for a
The value is removed from the dialog box.
Reaction property.
4. Click OK.
2. Click Add Value.
The Enumerated Value dialog box closes and
the Properties dialog box appears.
Organizing Enumerated Values

You can change the organization of enumerated
values by moving them up or down in the
enumerated values table.

Setting Properties
To organize enumerated values: To set a default reaction:
1. Open the Enumerated Values dialog box for a 1. From the View menu, choose Default Reaction.
property. The Default Reaction dialog box appears.
Administrator
2. Click a row.

move a row
down the table by one Move Value Down.

row
up the table by one Move Value Up.

row
2. Create a default reaction and specify any other
The row is moved. default settings.
3. Click OK.
4. Click OK.
The Enumerated Value dialog box closes and The Default Reaction dialog box closes and the
the Properties dialog box appears. E-Notebook Administrator appears.
Setting Default Reaction Setting the Chemical

Properties Structure File Path
You can set a specific chemical reaction, or default
You can set the chemical structure index file path,
reaction, to appear when you use a Reaction section
which is used to search for chemicals. The chemical
in E-Notebook. The default reaction automatically
structure index file is an .mst file.
appears when you open a Reaction section.
You must specify the chemical structure file path
You use ChemDraw through E-Notebook
before entering any chemical information into the
Administrator to set the default reaction. You can
database. If you change the chemical structure file
also save other default reaction settings, such as a
path after the chemical information has been
default font for atom labels or type and length of the
entered, then searching for structure content does
reaction arrow.
not work properly.
For more information about using the ChemDraw
Choose a path relative to the entire network for the
controls, see the ChemDraw manual.
machine running E-Notebook Administrator, not a
specific drive, such as “G:”

Setting the Chemical Structure File Path
For Access databases, the chemical structure file is In Single-User mode, the user does not specify a
in the same folder as the Administrator application username or password. The user has administrative
database. You can choose a chemical structure file privileges over all of the content of the database.
path if you want to move the .mst and .msi files to a
You can configure the database to require Multi-
different location.
User access so that users cannot access the E-
For an Oracle database, the chemical structure file Notebook database. A Single-User cannot connect
path must be specified before you can use E- to a Multi-User database because the connection
Notebook. fails.
To specify the chemical structure file path: To configure the database to require Multi-User
1. From the View menu, choose Chemical access:
Structure File Path. 1. Open E-Notebook Administrator.
The Chemical Structure File Path dialog box 2. From the View menu, choose Configure
appears. Database.
The Configure Database dialog box appears.
2. Find the .mst file and click Open.

The chemical structure file path is set.
Configuring the
Database Options 3. Click the Login tab.
4. Click Require Multi-User Login.
This section describes additional configuration
options available when you set up your database. 5. Click OK.
The Configure Database dialog box closes.
Setting Multi-User Access
After you configure a DSN on a client system, that
client can log into E-Notebook databases as a
Single-User or Multi-User.

Configuring the Database Options
Connecting to Chemical
Registration
You can set E-Notebook so that it connects to
Administrator
To set E-Notebook to connect to Chemical

Registration:

2. From the View menu, choose Configure
Database.
The Configure Database dialog box appears.
3. Click the Chemical Registration tab.

4. In the Web Server box, type the name of the
Chemical Registration web server.
5. In the Web Page box, type
//chem_reg/reg/reg_post_action.asp.
6. Click OK.
The Configure Database dialog box closes.

Configuring the Database Options
Chapter 8: Document Manager
Overview The Document Manager Log In window
appears in your browser.
You can use Document Manager to do the
following:
• Create a central area, or repository, for chemical
documents in .doc or .txt formats for your entire
organization, over the web.
• Search MS Word and .txt documents in the
repository. You can perform a Boolean search
over the web by chemical structure or text.
• Add, or submit, documents to the system over
the web. The document submitted is securely
stored in a database, indexed by both structure
and text for Document Manager users to search
and view. 2. In the User name box, type your user name.
• Remove documents that are no longer shared. 3. In the Password box, type your password.
• Manage users and groups as the system 4. Click Login .
administrator. You can add and remove users, The Document Manager Main Menu page
and manage user privileges over the web. appears.
Logging In
You must log in to Document Manager so that you
can use the system.
To log in to Document Manager:

1. Type http://hostname into your web browser.
Hostname is the name of the Document
Manager machine. You can contact your server
administrator to get this name.
ChemOffice Chapter 8: Document Manager • 105

Overview
Submitting Documents When you create a text search, you type search
criteria or parameters into the search Text box.
You can submit documents to Document Manager When you create a structure search, draw a structure
over the web. in the Structure box. After you type or draw your
Administrator
search criteria, you can start the search.

You can search submitted documents for specific
structure or text information, and then view the For more information about search features, such as
document. Retrieve All and New Query, see the ChemOffice
WebServer User’s Guide.
To submit a document:
1. On the Main Menu page, click Submit Understanding Basic Text
Documents . Searching
The Submit Document page appears.
You can use basic text searching, or querying, to find
information in documents within Document
Manager. When you use basic text searching with
specific characters, you can narrow or increase your
search parameters, depending on how sure you are
about the information you want to find. When you
narrow your search, you create a more unambiguous
2. In the Document box, type the directory search which gives you more precise results, making
location and file name of the document you it easier to find the information you want. When you
want to submit or Browse to the document. increase your search, you create a broader search so
that you have many different documents in which to
3. Click View Document.
find information.
Your document appears in the browser window.
You can use different types of basic text searching
4. Click Submit This Document
depending on your needs, such as exact word or
.
phrase matching and wildcard characters.
The Submit Documents page appears with a
message that the documents was submitted Exact Phrase Matching
successfully. You can use exact word or phrase matching when
you want to find information that identically
Creating Searches for matches what you use to search. This is the most
simple search, or query, which returns exactly the
Documents information you request through search parameters.
You can search submitted documents for specific
structure or text information, and then view the
document with the information in it.
Document Manager supports Basic and Advanced
Text searching characters and operators as well as
structure searching.
106 • Chapter 8: Document Manager CambridgeSoft

Submitting Documents
For example of what to type and what you get from For example of what to type and what you get from
the search: the search:
Searching for Returns documents Searching for Returns documents

with with
thymidine syn- the words thymidine synth* words like synthesis,

thesis synthesis in them, in that synthetic, and syntheses
exact order. in them.
cyclohexane the word cyclohexane in *ethane words like ethane, and

them. methane in them.
(phrase with and, or or (wildcards at both

in it) ends?)
Wildcard Searching Understanding Advanced Text

When you do not know a prefix or a suffix for a Searching
word, you can use the wildcard characters to return
You can use advanced text searching, or querying, to
all word with the same word root. You can use
find information in documents within Document
wildcard characters in a basic text search when you
Manager. When you use advanced text searching
want to search for all documents that contain a part
with specific operators, you can narrow your search
of a word. This kind of search returns more matches
parameters dramatically. When you narrow your
to your search criteria than the exact phrase search,
search, or query, you create a more unambiguous
so that you have a larger number of documents in
search which gives you more precise results, making
chich to find information.
it easier to find the information you want.
You can use different types of advanced text
searching depending on your needs, such as the
following types:
• ABOUT
• AND (&)
• EQUIValence (=)
• fuzzy (?)
• MINUS (-)
• NEAR (;)
• NOT (~)
• OR (|)

Creating Searches for Documents
• soundex (!) For example, you can issue the following combined
• stem ($) ABOUT and word queries:
ABOUT Searching for Returns documents

Administrator
You can use the ABOUT operator in an advanced with

text search, or query, so that you can find documents
that contain information related to a word or phrase. ABOUT (carbon)
An ABOUT search increases the precision of the AND diamond
same search without this operator. Increased
precision means more relevant documents are ABOUT (carbon)
returned. NOT ABOUT
(diamond)
When you use the ABOUT operator, type the word
ABOUT in all capital letters, and then type
Information for advanced Oracle users: The word or
parentheses around the word or phrase on which you
phrase specified in your ABOUT query does not
want to perform an ABOUT search.
have to exactly match the themes stored in the index.
ABOUT searches are always case-sensitive. The Oracle automatically normalizes the word or phrase
text string inside the parentheses is interpreted with before performing lookup in the Text index.
respect to case.
AND (&)
For examples of what you type and what you get
from the search: You can use the AND operator in an advanced text
search, or query, so that you can find documents that
contain information about specific multiple words
Searching for Returns documents
or phrases. You can use the AND operator to search
with
for documents that contain at least one occurrence of
each of the query terms.
ABOUT (carbon)
When you use the AND operator, type the first term,
ABOUT (carbon then type the word AND in all capital letters or type
bi-products from the ampersand (&), and then type another phrase on
syntheses at 25 which you want to perform an AND search.
degrees Celcius)
You can use other operators, such as AND or NOT,

to combine ABOUT queries with word queries.

For examples of what you type and what you get For examples of what you type and what you get
from the search: from the search:

with with
carbon AND the words carbon, graphite EQUIV the words graphite or
diamond diamond, and both in diamond diamond in them.
them.
graphite = the words graphite or
carbon & diamond the words carbon, diamond diamond in them.
diamond, and both in
them. carbon the words carbon
dioxide=monoxide dioxide, carbon
carbon & diamond the words carbon, monoxide, or both terms
& graphite diamond, graphite, and in them.
any combination of the
terms in them.
NOTE: The EQUIValent operator has higher
thymidine syn- the words thymidine precedence than all other operators except the
thesis AND synthesis, carbon expansion operators (fuzzy, soundex, stem).
carbon dioxide dioxide, and both terms
in them.
Fuzzy (?)
You can use the fuzzy operator in an advanced text
EQUIValence (=) search, or query, so that you can find documents that
You can use the EQUIValence operator in an contain words similar to the word you use in a
advanced text search, or query, so that you can find search. You can use the fuzzy operator to expand
documents that contain information about words queries to include words that are spelled similarly to
that can be used in place of each other, alone or in a the specified term. This type of expansion is helpful
phrase. You can use the EQUIValence operator to for finding more accurate results when there are
specify an acceptable substitution for a word in a frequent misspellings in the documents in the
query. database.
When you use the EQUIValence operator, type When you use the fuzzy operator, type a question
EQUIV in all capital letters or type the equals sign mark (?), and then type the word on which you want
(=), and then type the phrase on which you want to to perform a fuzzy search.
perform an EQUIValence search.

For examples of what you type and what you get For examples of what you type and what you get
from the search: from the search:

Administrator
with with
?boron the words boron and carbon - diamond the words carbon and
baron in them. diamond in them, but
documents with
?read the words read, lead and diamond are listed last.
real in them.
carbon MINUS the words carbon and
?chemist the words chemist, diamond diamond in them, but
chemistry, and chemists documents with
in them. diamond are listed last.
MINUS (-) NEAR (;)

You can use the MINUS operator in an advanced You can use the NEAR operator in an advanced text
text search, or query, so that you can find documents search, or query, so that you can find documents that
that contain two phrases, with the first phrase taking contain two phrases that are close together. You can
precedence. You can use the MINUS operator to specify the maximum distance between the two
search for documents that contain two query terms, terms if you want.
but you want the second query term to cause the When you use the NEAR operator, type NEAR in all
document to be ranked lower than documents capital letters or type a semicolon (;), then inside
without the second term. The MINUS operator is parentheses, type the words or phrases on which you
useful for lowering the score of documents that want to perform a NEAR search.
contain “noise.”
Use the NEAR operator to return documents based
When you use the MINUS operator, type the first on the proximity of two or more query terms.
term, then type MINUS in all capital letters or type
the minus sign or hyphen (-), and then type another NOTE: You cannot use NEAR in ABOUT queries.
term on which you want to perform a MINUS
search.

For example of what to type and what you get from You can use the NEAR operator with other
the search: operators, such as AND, OR, and EQUIValence.
For example of what to type and what you get from
Searching for Returns documents the search:
with

NEAR (carbon, the words carbon and with
diamond) diamond in them, but
only when they appear
less than 100 words NEAR ((carbon, the words carbon,
apart and in no specific diamond), 10) diamond, and benzene
order. AND benzene in them, but only when
carbon and diamond
appear less than 10
;(carbon, the words carbon and words apart and in no
diamond) diamond in them, but specific order.
only when they appear
less than 100 words
apart and in no specific NEAR ((carbon, the words carbon,
order. diamond = diamond, and graphite
graphite), 10) in them, but only when
carbon and diamond or
NEAR ((carbon, the words carbon and carbon and graphite
diamond), 20, diamond in them, less appear less than 10
FALSE) than 20 words apart, in words apart and in no
no specific order. specific order.
NEAR ((carbon, the words carbon and

diamond), 20, diamond in them, less NOT (~)
TRUE) than 20 words apart, in You can use the NOT operator in an advanced text
this specific order. search, or query, so that you can find documents that
contain a word or phrase, but only when it appears
NEAR uses the following defaults: without a second word or phrase. When you use the
NOT operator, type the term you want to find, then
• Search terms are found if they are 100 words
type NOT in all capital letters or type a tilde (~), and
apart or less, unless you specify otherwise. Use
whole numbers between 1 and 100. then type the term you do not want included in the
NOT search.
• Search terms are found in any order, unless you
specify otherwise. Use TRUE or FALSE. Use the NOT operator to search for documents that
contain one query term and not another.

For example of what to type and what you get from For example of what to type and what you get from
the search: the search:

Administrator
with with
carbon NOT the word carbon, but not carbon OR the words carbon,
diamond with diamond in them. diamond diamond, or both in
them.
carbon ~ diamond the word carbon, but not
with diamond in them. carbon | diamond the words carbon,
diamond, or both in
carbon NOT the word carbon, but not them.
(diamond OR with diamond or
graphite) graphite in them. carbon OR the words carbon,
diamond OR diamond, graphite, or
graphite any combination of the
NOTE: The NOT operator does not affect other terms in them.
logical operators.
thymidine syn- the words thymidine
thesis OR carbon synthesis, carbon
OR (|)
dioxide dioxide, or both terms in
You can use the OR operator in an advanced text them.
contain information about any words in a phrase, but
not necessarily all words in a phrase. When you use Soundex (!)
the OR operator, type the first term, then type the You can use the soundex operator in an advanced
word OR in all capital letters or type the pipe (|), and text search, or query, so that you can find documents
then type another term on which you want to that contain words that sound like the word you use
perform an OR search. in a search. When you use the soundex operator,
type an exclamation point (!), and then type the
Use the OR operator to search for documents that
word on which you want to perform a soundex
contain at least one occurrence of any of the query
search.
terms.
Use the soundex (!) operator to expand queries to
include words that have similar sounds; that is,
words that sound like other words. This function
allows comparison of words that are spelled
differently, but sound alike in English.

For example of what to type and what you get from Performing a Search
the search:
To search documents for specific information:
Searching for Returns documents 1. On the Main Menu page, click Search
with Documents .
The Search Documents page appears.
!carben the words carbon and
carboxcylic in them.
?read the words read and lead

in them.
Stem ($)
You can use the stem operator in an advanced text
contain words similar to the word you use in a
search. When you use the fuzzy operator, type a
dollar sign ($), and then type the word on which you
want to perform a stem search.
Use the stem operator to search for terms that have
the same linguistic root as the query term. Stem
expands a query to include all terms with the same 2. Take the appropriate action:
stem or root word as the search term.
For example of what to type and what you get from If you want to Then
search for
the search:
text in the document in the Full-Text box,

type the text you want
with
to find
$commit the words commits,

committing, committee,
and committed in them.
$chemist the words chemist,

chemistry, and chemists
in them.

To change your password:
If you want to Then
1. On the Main Menu page, click Change
search for
Password .
Administrator
a chemical structure a. in the Structure The Change Password page appears.

box, draw a
chemical
structure with the
ChemDraw
tools. For more
information, see
the ChemDraw
manual.
2. In the Password box, type a new password.
b. from the Match
Structure menu, 3. In the Password Confirm box, type your new
choose the exact password again.
level that you 4. Click Update User .
want the
structures to The Update User dialog box appears.
match. For more
information, see
ChemOffice
WebServer
User’s Guide.
3. Click Search .
5. Click OK.
Changing Your The Main Menu appears and the password is
Password changed.
You can change your password so that Document

Manager remains secure.

Changing Your Password
Managing Users
As system administrator, you can manage different
users and their accounts.
You can manage Users, their Roles, and People.
To manage users:
• On the Main Menu page, click Manage Users
.
The Manage Users page appears.
For more information about Users, Roles, and

People, see “Managing Users and Roles” on
page 157.
Logging Off
When you finish using Document Manager, you can
log off.
To log off Document Manager:
• On any page in Document Manager, click Log
Off .
The Document Manager Log In window
appears in your browser. You are successfully
logged off Document Manager, and my log in
again if you want.

Managing Users
Administrator

Logging Off
Chapter 9: BioAssay Manager
Overview Aggregate View—The Tier One results that
BioAssay Manager analyzes according to your
BioAssay Manager manages data from biological preferences. For more information, see “Analyzing
experiments. It is designed for biologists working on and Viewing Data with the Aggregate View” on
research projects to discover new pharmaceuticals, page 129.
or for other scientists who test drugs or genes against
Assay—The record of laboratory experiments or
samples in different types of research.
tests. In BioAssay Manager, all data and results are
Chemists synthesize molecules and biologists grouped by assays.
develop assays to test these molecules for biological
Calculations and Variables document—An MS
activity. These assays model different physiological
Word document that you can use to keep track of all
processes, such as the maintenance of ion
the calculations and variables that go with an assay.
concentration gradients across a cell membrane.
You can open and close through the Layout tab in
Assays differ dramatically from model to model.
BioAssay Manager.
BioAssay Manager provides an application
framework to set up these different models in a Database—A part of BioAssay Manager that holds
database, to load and update data, and to perceive the data from your experiemnts.
relationships between data. BioAssay Manager is of Database Tab—A part of BioAssay Manager where
special value for researchers performing in vivo
you set up Tier One and Tier Two information for
experiments with complex models.
the BioAssay Manager database and the MS Excel
BioAssay Manager is designed to be used in spreadsheet template. For more information, see
conjunction with ChemFinder and ChemOffice “Setting Up an Assay Model in the Database Tab”
WebServer. These products are the main report tools on page 127.
for analyzing data entered through BioAssay Description Tab—A part of BioAssay Manager
Manager, although BioAssay Manager does provide
where you enter and view the description
some simple report functionality. Data input through
information for each assay. For more information,
BioAssay Manager is designed to be viewed through see “Creating and Editing Assay Description
ChemFinder and ChemOffice WebServer.
Information” on page 121.
BioAssay Manager is available for either Microsoft
Field—A section of a database that holds data. You
Access or Oracle. can put data into fields. Fields have names such as
Type, Date, or Name.
Terminology
The following terms have specific definitions in
BioAssay Manager:
ChemOffice Chapter 9: BioAssay Manager • 117

Overview
Filter—A function in BioAssay Manager that you Tier Two—The raw results from one experiment.
define. A filter sorts through data according to the For more information, see “Setting Up an Assay
parameters you set to find the pieces you want to Model in the Database Tab” on page 127.
see. For more information, see “Filtering Results”
Version—A way of identifying a different edition of
Administrator
on page 135.
an assay. You can use versions to track amendments
Graph Tab—A part of BioAssay Manager where to an assay. For more information, see “Assigning a
you view Tier One and Tier Two results. You can Version to an Assay” on page 122.
also see a standard or log graph for Tier Two results.
For more information, see “Graphing Tier Two System Requirements
Results” on page 135.
You must have the following to use BioAssay
Layout spreadsheet—An MS Excel spreadsheet Manager on your system:
that you can use to keep track of all the results that
are not essential for the assay. You can open and • Microsoft Office 2000
close the MS Excel spreadsheet through the Layout • Microsoft Access 2000 or Oracle 8.x
tab in BioAssay Manager.
Layout Tab—The part of BioAssay Manager where Getting Started for the
you open and use an MS Excel spreadsheet that is
separate from the other spreadsheets for BioAssay
First Time
Manager. You can also open and MS Word The first time you use BioAssay Manager, you must
document that is separate from the other documents do the following:
for BioAssay Manager. For more information, see
• Open BioAssay Manager.
“Using a Layout Spreadsheet” on page 125 and
“Using a Calculations and Variables Document” on • Choose a database.
page 126. • Log in.
Procedure document—An MS Word document • Maximize the BioAssay Manager window.
that you can use to keep track of the actual • Create an assay.
procedural steps for an assay. You can open and
After the first time you use BioAssay Manager, you
close the MS Word file through the Description tab
do not need to perform all of these tasks.
in BioAssay Manager.
Results Tab—The part of BioAssay Manager that Opening BioAssay Manager for
shows Tier One and Aggregate View results. For the First Time
more information, see “Viewing Tier One Results”
on page 134. To open BioAssay Manager for the first time:
• From the Start menu, point to Programs, point
Tier One—The final analysis, or summary, of many
to CS BioAssay Manager, and then choose CS
raw results from one experiment. For more
BioAssay Manager.
information, see “Setting Up an Assay Model in the
Database Tab” on page 127. BioAssay Manager opens and the CS BioAssay
Manager: Alert dialog box appears.
118 • Chapter 9: BioAssay Manager CambridgeSoft

System Requirements
Choosing a Database The Choose the database file to open dialog box
appears.
The first time you use BioAssay Manager, you are
prompted to choose a database to use, either MS
Access or Oracle.
NOTE: Before you choose a database, you must be

sure MS Access or Oracle has already been
installed.
Choosing MS Access
CAUTION 3. Click CSBioAssay Manager.mdb.
MS Access does not provide any security for your 4. Click Open.
database.
The Login dialog box appears.
To choose MS Access to run your database: Choosing Oracle

1. From the CS BioAssay Manager: Alert dialog
To choose Oracle to run your database:
box, click OK.
1. From the CS BioAssay Manager: Alert dialog
box, click OK.
The CS BioAssay Manager dialog box appears.
The CS BioAssay Manager dialog box appears.
2. Click Access 2000.
2. Click Oracle 8.x.

Getting Started for the First Time
The CS BioAssay Manager: Request dialog box The Login dialog box appears.
appears.
Logging In with MS Access
Each time you open BioAssay Manager, you must
Administrator
log in.
To log in with MS Access:
• In the Login dialog box, click OK.
3. Type the Oracle Net 8 service name you want to Do not type a user name or password.
use.
4. Click OK.
The CS BioAssay Manager confirm dialog box
appears.
BioAssay Manager opens and the Description

tab appears.
Logging In with Oracle
If you Than click Each time you open BioAssay Manager, you must
log in.
do not want to create No.
To log in with Oracle:
SQL scripts
want to create SQL Yes.

scripts
The CS BioAssay
Manager: Request
dialog box appears.
1. In the Login dialog box, type your user name.

2. Type your password.
3. Click OK.
BioAssay Manager opens and the Description
tab appears.
• Type a directory
path, if NOTE: For your user name and password, see
necessary, and your System Administrator.
click OK.

Getting Started for the First Time
Maximizing the BioAssay Opening BioAssay
Manager Window
Manager
When you open BioAssay Manager, you may not be
able to see the bottom of the window. To view the To open BioAssay Manager any time after the first
whole window, maximize it. time you open it:
To maximize the BioAssay Manager window: 1. From the Start menu, point to Programs, point
to CS BioAssay Manager, and then choose CS
• In the upper right corner of the BioAssay
BioAssay Manager.
Manager window, click Maximize Window
. The Log In dialog box appears.
The BioAssay Manager window fills the whole 2. Take the appropriate action:
screen on your monitor.
for your database, Then
Creating Your First Assay if you use
All the information you store in BioAssay Manager
is grouped by assay. You must create an assay to Oracle type your user name
store any information. and password.
When you create an Assay, you must name it and MS Access skip this step.
then save it. For more information, see “Creating
and Editing Assay Description Information” on
3. Click OK.
page 121 and “Viewing Different Assays” on page
122. BioAssay Manager opens and the Description
tab appears.
To create an assay:
1. Click the Description tab.

Creating and Editing
2. From the File menu, choose New Assay. Assay Description
The CS BioAssay Manager: Request dialog box
appears.
Information
3. Type the name of your new assay.
All the information you store in BioAssay Manager
is grouped by assay. Before you create or edit an
4. Click OK. assay, you must turn on Edit mode.
closes. The new assay name appears in the Creating a New Assay
Assay box. You must create an assay to store any information in
5. From the File menu and choose Save Assay. BioAssay Manager.
You have created a new assay. To create a new assay:

Opening BioAssay Manager
2. From the Edit menu, choose Edit On/Off. Assigning a Version to an
You are now in Edit mode so that you can edit Assay
assay information.
You can assay versions to keep track of amendments
Administrator
3. From the File menu, choose New Assay. made to the assay. For example, several people may
The CS BioAssay Manager: Request dialog box contribute to the information for one assay. After
appears. each person amends or changes any part of an assay,
4. Type the name of your new assay. they can update the version.
5. Click OK. To assign a version to an assay:

The CS BioAssay Manager: Request dialog box 1. Click the Description tab.
closes. The new assay name appears in the
2. From the Edit menu, choose Edit On/Off.
Assay box.
You are now in Edit mode so that you can edit
6. Click the File menu and choose Save Assay.
assay information.
You have created a new assay.
3. Click a row in the Version box.
Renaming an Assay The box is selected.
You can change the name of an assay by renaming it.
To rename an assay:

assay information.
3. Click Rename.
appears.
4. Type a new version name or number.
4. Type the name of your new assay.
5. Click OK.
The CS BioAssay Manager: Request dialog box Viewing Different
closes. The new assay name appears in the
Assay box.
Assays
6. Click the File menu and choose Save Assay. You can see information from different assays by
changing which assay you view. You can choose
You have renamed an assay.
which assay you want to see by moving between
assays and by searching for assays.

Viewing Different Assays
Moving Between Assays 2. In the Assay name box, type the name or part of
the name of the assays you want to find.
When you create a new assay, BioAssay Manager
places it after the last one created. You can move 3. Click Go.
from one assay to the next assay in the sequence, or BioAssay Manager finds the assays closest to
to the end or the beginning of all the assays. your search criteria.
To move between assays: To turn off Search mode and return to the normal
assay view:
1. Click any tab in the BioAssay Manager
window. • From the View menu, choose All.
2. Take the appropriate action: The Search mode turns off and the first assay
appears.
If you want to see Then click
the Using a Procedures
first assay in BioAssay First .
Document
Manager You can write up the test procedure for your assay as
a Procedure document in a new or exisitng MS Word
last assay in BioAssay Last . file through BioAssay Manager. The procedure is
Manager always linked to an assay.
You can edit the MS Word file just as you normally
assay after the one you Next . do.
currently see
Opening a Procedures
assay before the one Previous . Document
you currently see
When you use a Procedure document, BioAssay
The assay view changes to the assay you Manager opens an MS Word file.
specify.
To open a Procedure document:
Searching for an Assay 1. Click the Description tab.
You can search for a specific assay by the name of 2. From the Edit menu, choose Edit On/Off.
the assay. Before you search for an assay, you must You are now in Edit mode so that you can edit
turn on Search mode and turn off Edit mode. Before assay information.
you move to another assay, you must turn off Search 3. Click the Procedure check box.
mode.
To search for an assay:
1. From the View menu, choose Search.

The Search Description tab appears.

Using a Procedures Document
The Procedure Editing tools appear to the left of To save a Procedure document:
the Procedure box.
1. From the MS Word file that BioAssay
Manager opened, save and close the file as you
Administrator
do normally.
The Description tab appears.
2. On the Description tab, click Save Procedure
.
3. From the File menu, choose Save Assay.
BioAssay Manager saves the Procedure
4. Click New Procedure . document as part of the assay.
appears. Deleting Procedures
5. Take the appropriate action: You can delete the Procedure document from an
assay. This does not delete the whole MS Word file
from your computer, only from this particular assay.
To delete a Procedure document:
open an MS Word file Yes. The Choose the
that already exists Word file dialog box 1. Click the Description tab.
appears. 2. From the Edit menu, choose Edit On/Off.
• Click Open. You are now in Edit mode so that you can edit
assay information.
open a new MS Word No. 3. Click the Procedure check box.
file
BioAssay Manager opens an MS Word file.
Saving Procedures
You must save the Procedure document with an
assay, you must do the following:
• Save the MS Word file.
The Procedure Editing tools appear to the left of
• Save the Procedure in BioAssay Manager. the Procedure box.
• Save the assay. 4. Click Delete Procedure .
appears.
5. Click Yes.

Using a Procedures Document
Another CS BioAssay Manager confirm dialog 4. Click New Layout .
box appears to double-check your action. The CS BioAssay Manager confirm dialog box
6. Click Yes. appears.
The text in the Procedure box is deleted, but the 5. Take the appropriate action:
MS Word file still exists on your computer
where ever you originally saved it. If you want to Then click
Using a Layout open an MS Excel file Yes.

that already exists
Spreadsheet
You can link an MS Excel spreadsheet to the Layout open a new MS Excel No.
spreadsheet to keep track of your testing results. file
This spreadsheet is not directly linked to any other
part of BioAssay Manager. BioAssay Manager opens an MS Excel file.
You can edit the MS Excel file just as you normally
Saving a Layout
do.
You must save the Layout spreadsheet in several
Opening a Layout Spreadsheet ways so that BioAssay Manager associates it with an
assay.
When you use a Layout spreadsheet, BioAssay
Manager opens an MS Excel spreadsheet and saves To save a Layout spreadsheet:
your Layout in the file.
1. From the MS Excel file that BioAssay
To open a Layout spreadsheet: Manager opened, save and close the file as you
1. Click the Layout tab. do normally.
2. From the Edit menu, choose Edit On/Off. The Description tab appears.
You are now in Edit mode so that you can edit 2. Click Save Layout .
assay information. 3. From the File menu, choose Save Assay.
3. Click the Layout check box. BioAssay Manager saves the Layout
spreadsheet as part of the assay.
Deleting a Layout
You can delete the Layout spreadsheet from an
assay. This does not delete the whole MS Excel file
from your computer, only from this particular assay.
To delete a Layout spreadsheet:

The Layout Editing tools appear to the left of
1. Click the Layout tab.
the Layout box.

Using a Layout Spreadsheet
You are now in Edit mode so that you can edit Opening a Calculations and
assay information.
Variables Document
3. Click the Layout check box.
When you use a Calculations and Variables
Administrator
document, BioAssay Manager opens an MS Word

file.
To open a Calculations and Variables document:

1. Click the Layout tab.
The Layout Editing tools appear to the left of assay information.
the Layout box. 3. Click the Calculations and Variables check
4. Click Delete Layout . box.
appears.
5. Click Yes.
Another CS BioAssay Manager confirm dialog
box appears to double-check your action.
6. Click Yes.
The text in the Layout box is deleted, but the
The Calculations and Variables Editing tools
MS Excel file still exists on your computer.
appear to the left of the Calculations and
Variables box.
Using a Calculations 4. Click New Calculations and Variables .
and Variables Document The CS BioAssay Manager confirm dialog box
You can use the Calculations and Variables appears.
document to keep track of all the equations and other 5. Take the appropriate action:
useful notes for the assay in an MS Word file that
BioAssay Manager links to an assay. If you want to Then click
You can edit the MS Word file just as you normally
do. open an MS Word file Yes.
that already exists
open a new MS Word No.

file
BioAssay Manager opens an MS Word file.

Using a Calculations and Variables Document
Saving Calculations and The Calculations and Variables Editing tools
appear to the left of the Calculations and
Variables Variables box.
You must save the Calculations and Variables
4. Click Delete Calculations and Variables .
document in several ways so that BioAssay
Manager associates it with an assay. The CS BioAssay Manager confirm dialog box
appears.
To save a Calculations and Variables document: 5. Click Yes.
1. From the MS Word file that BioAssay Another CS BioAssay Manager confirm dialog
Manager opened, save and close the file as you box appears to double-check your action.
do normally. 6. Click Yes.
The Description tab appears.
The text in the Calculations and Variables
2. Click Save Calculations and Variables . box is deleted, but the MS Word file still
3. From the File menu, choose Save Assay. exists on your computer.
BioAssay Manager saves the Calculations and
Variables document as part of the assay.
Setting Up an Assay
Deleting Calculations and
Model in the Database
Variables Tab
You can delete the Calculations and Variables BioAssay Manager represents assay models, or
document from an assay. This does not delete the experiments, in the database with two tiers, in which
whole MS Word file from your computer. you can place any parameters. The two tiers are
independent of each other, but they are related in
To delete a Calculations and Variables document: that there is one record in the first, Tier One, for
1. Click the Layout tab. many records in the second tier, Tier Two.

assay information.
3. Click the Calculations and Variables check
box.

Setting Up an Assay Model in the Database Tab
For example, an assay model has six results: 1, 2, 3 Before you enter any test results into BioAssay
and A, B, C. Each result, or piece of raw data, goes Manager, you must set up a spreadsheet template in
into Tier Two. Tier One is the summary of all the which to enter your data. Your template is the frame
raw data in Tier Two. for an MS Excel spreadsheet, which you can use to
Administrator
import data into BioAssay Manager.

Tier One
On the Database tab in BioAssay Manager, you can
Sample_ID, Date make your template by adding information in the
Total_Results (1-3)
Average_Results (A-C)
Tiers. You can add information by typing it into the
tables for each Tier. Each cell in each table becomes
a field in the BioAssay Manager database.
The Tier One table has the following columns:
Result 1 Result 2 Result 3
Result A Result B Result C • Name—The name of an MS Excel spreadsheet
column and a BioAssay Manager database
Tier Two field. For example, you can use Ki, IC50,
Sample ID, and Units for the Name.
NOTE: You can store more than one result
parameter per tier.
NOTE: You cannot use any spaces in a Name.
Some common Tier Two parameters are: You can use an underscore (_) instead.For
example, use Corporate_ID instead of
• Concentration
Corporate ID.
• %INH
• Time • Type—The category, or data type, for each
• Units Name. You must choose one definition from the
menu that appears when you click in this
You can further specify which two parameters in the
Tier Two records should serve as the (x,y) column:
coordinate pair for graphing. For more information, • Date—Any date in any format.
see “Graphing Tier Two Results” on page 135. • Number—Any number, including decimal
Some common Tier One parameters are: points. You cannot use any other characters.
To express units of measurement and
• Ki operators. Designate a Text (Units) field to
• IC50 be next to a Number (Concentration) field.
• Sample_ID • Text—Any character.
• Corporate_ID • Width—The width of the columns for results
• Date tables on the Results and Graph tabs. You can
only change this value on the Results and Graph
• Total_Time
tabs. For more information, see “Changing the
• Units Width of Results Columns” on page 134.

The Tier Two table has the following columns: Adding a Row to Tier Tables
• Name—The same as the Name column for Tier The Tier tables have one row each when you open
One. the Database tab. You can add more rows to each
• Type—The same as the Type column for Tier Tier table.
One.
To add a row to a Tier table:
• Axis—You can use this column to assign
information to a graph. The graph appears in the 1. Click the Database tab.
Graph tab of BioAssay Manager and has no 2. From the Edit menu, choose Edit On/Off.
relation to the MS Excel spreadsheet template. You are in Edit mode and can edit assay
• x-axis—The results from this field are on the information.
x-axis of the graph on the Graph tab.
3. Click a cell in the Name column to select it.
• y-axis—The results from this field are on the
y-axis of the graph on the Graph tab.
Adding Tier Information

4. Click the asterisk (*) to the left of the bottom
You can create information in each Tier table on the
row.
Database tab to do the following:
A blank row appears in the table.
• Make a spreadsheet template for an MS Excel
spreadsheet. Analyzing and Viewing Data
• Create fields for the BioAssay Manager with the Aggregate View
database that hold your data.
You can analyze Tier One data in the Aggregate
To create information in the Tier tables: View with the following process:
1. Click the Database tab. • Define which Tier One fields you want the
2. From the Edit menu, choose Edit On/Off. Aggregate View to show. You can rename the
You are in Edit mode and can edit assay fields for the Aggregate View analysis if you
information. want.
3. Click a cell in the Name column to select it. • Choose which Tier One fields to analyze.
4. Type a name in the Name cell. • Choose which calculations to perform on your
data.
5. Click a cell in the Type or Axis columns.
• Choose a heading for the column in which
6. Choose a Type or an Axis from the menu that
results are shown.
appears in that cell.
• Save the Aggregate View definitions and view
the analysis in the Results tab.
Edit mode is turned off and the assay is saved.

You can define the Aggregate View before or after To define an Aggregate View:
you load your MS Excel spreadsheet data into
1. In the Define aggregate view dialog box, under
BioAssay Manager. For more information, see
Group data around these fields section,
“Loading Data Into BioAssay Manager From an MS
Administrator
choose a Tier One field Name from the menu.

Excel Spreadsheet” on page 133.
Opening the Aggregate View Dialog

Box
This field appears in the Aggregate View
To open the Aggregate View definition dialog box: Results the same way it appears in the MS Excel
spreadsheet template.
1. Click the Database tab of an assay that already
2. In the box to the right of (optional) subgroup
has an MS Excel spreadsheet template saved.
by, choose another Tier One field Name from
For more information about spreadsheet
the menu that appears there.
templates, see “Setting Up an Assay Model in
the Database Tab” on page 127.
2. From the Edit menu, choose Edit On/Off. This definition is optional.
You are now in Edit mode so that you can edit 3. In the box to the right of (optional) and again
assay information. by, choose another Tier One field Name from
3. Click Define aggregate view. the menu.
This definition is also optional.
To rename an Aggregate View definition:

4. In the Define aggregate view dialog box, under
Group data around these fields section, in the
box to the right of shown as, you can type a
The CS BioAssay Manager - Define aggregate different name for the Tier One field Name.
view dialog box appears.
Defining an Aggregate View

You can define up to three Tier One fields you want 5. Repeat step 4 for all of the boxes to the right of
the Aggregate View to show. You can rename the the respective shown as sections.
fields for the results of the Aggregate View analysis
The Tier One field Names are renamed for the
if you want.
Aggregate View results only.

Choosing Tier One Results to Analyze • Sum—The sum of the numerical values.
You can choose different Tier One results, by field, To choose a function for BioAssay Manager to
for BioAssay Manager to analyze. perform to analyze Tier One data:
NOTE: BioAssay Manager can only analyze Tier To choose Tier One results for BioAssay Manager to
One fields that are defined as Number Types. For use in calculating an Aggregate View analysis:
more information about Types, see “Setting Up an
1. In the Define aggregate view dialog box, look
Assay Model in the Database Tab” on page 127.
at the table under and perform these
calculations on the aggregates.
To choose Tier One results for BioAssay Manager to
2. In the Function column, click a cell.
use in calculating an Aggregate View analysis:
1. In the Define aggregate view dialog box, look

at the table under and perform these
calculations on the aggregates.
3. From the menu in that cell, choose a function
2. In the Input column, click a cell.
you want BioAssay Manager to use for that
particular field in the row.
4. Repeat step 2 and step 3 if you want to use more
than one function for more than one field.
3. From the menu in that cell, choose a field Name The functions you choose are used for
you want to use in the Aggregate View Aggregate View calculations.
calculation.
4. Repeat step 2 and step 3 if you want to use more Naming the Aggregate View Results
than one field. Column
The values in the fields you choose are used for You can give a name to the column that shows the
Aggregate View calculations. Aggregate View results.
Choosing Calculations to Perform To name the Aggregate View results column:
You can choose which calculation you want 1. In the Define aggregate view dialog box, go to
BioAssay Manager to perform on your Tier One the table under and perform these
fields. BioAssay Manager can calculate values for calculations on the aggregates.
Tier One data with the following functions: 2. In the Caption column, click a cell.
• Average—The average, or mean, of a field you
define.
• Count—The number of values.
• Max—The highest numerical value. 3. Type a name for the Aggregate View results
• Min—The lowest numerical value. column.
• SD—The standard deviation from the average.

4. Repeat step 2 and step 3 if you want to name To clear the Define aggregate view dialog box:
more than one results column.
• In the Define aggregate view dialog box, click
The names you choose are used for the Clear.
Aggregate View results column.
Administrator
Seeing the Aggregate View Results

You must close the Define aggregate view dialog
box, save the assay from the Database tab, and then
click the Results tab to see the Aggregate View
results.
To see the Aggregate View results: All text boxes and tables in the dialog box
become blank.
1. In the Define aggregate view dialog box, click
OK.
Opening an MS Excel
The Define aggregate view dialog box closes.
Spreadsheet
You can open an MS Excel spreadsheet directly
The assay is saved and Edit mode is turned off. from BioAssay Manager.
3. Click the Results tab.
The Aggregate View results appear in the new NOTE: You can only open an existing MS Excel
Results tab table. spreadsheet from BioAssay Manager.
Clearing the Define Aggregate View To open an MS Excel spreadsheet from BioAssay
Dialog Box Manager:
You can clear the entire Define aggregate view 1. From the Edit menu, choose Edit On/Off to turn
dialog box so that you can enter new Aggregate off Edit mode.
View criteria.
2. From the Import menu, choose Open.
NOTE: When you clear the dialog box, any The Open dialog box appears.
information in the dialog box is deleted 3. Choose an MS Excel spreadsheet to open.
permanently.
4. Click Open.
An MS Excel spreadsheet opens.

Importing an MS Excel For more information about importing a spreadsheet
template into an MS Excel spreadsheet, see
Spreadsheet Template From “Importing an MS Excel Spreadsheet Template
BioAssay Manager From BioAssay Manager” on page 133.
After you create a spreadsheet template, you can Before you load the spreadsheet data into BioAssay
load it into an MS Excel spreadsheet. For Manager, you can choose to have BioAssay
information about creating an MS Excel spreadsheet Manager run faster by not checking for duplicate
template, see “Setting Up an Assay Model in the information in the database.
Database Tab” on page 127.
To set BioAssay Manager to not check incoming
To import a spreadsheet template into an MS Excel data for duplicates in the database:
spreadsheet:
• From the Import menu, choose Don’t check for
1. From the Edit menu, choose Edit On/Off to turn duplicates (faster).
off Edit mode. When you load spreadsheet data into the
2. From the Import menu, choose Make BioAssay Manager database, BioAssay
Template. Manager does not check for duplicate
information.
A CS BioAssay Manager confirm dialog box
opens. To load data from an MS Excel spreadsheet into
3. Click Yes. BioAssay Manager:
An MS Excel spreadsheet opens with the fields 1. From the Edit menu, choose Edit On/Off to turn
that you define in your spreadsheet template. off Edit mode.
You can type or paste data into this new
2. From the Import menu, choose Open.
spreadsheet. For more information about
creating a spreadsheet template, see “Setting The Open dialog box appears.
Up an Assay Model in the Database Tab” on 3. Choose an MS Excel spreadsheet to open.
page 127.
4. Click Open.
Loading Data Into BioAssay An MS Excel spreadsheet opens.

Manager From an MS Excel 5. From the MS Excel spreadsheet, select all of the
data, including the column headings, but not the
Spreadsheet
column types that appear in the row above the
After you create and export a spreadsheet template column headings.
into an MS Excel spreadsheet, you can import the
6. Go back to BioAssay Manager.
spreadsheet data back into BioAssay Manager for
more analysis. 7. From the Import menu, choose Load.
For more information about creating a spreadsheet The data from the MS Excel spreadsheet is
imported into the BioAssay Manager database.
template, see “Setting Up an Assay Model in the
Database Tab” on page 127.

For more information about seeing the data in Closing an MS Excel
BioAssay Manager, see “Viewing Tier One
Results” on page 134 and “Viewing Tier Two
Spreadsheet
Results” on page 134. You can close an open MS Excel spreadsheet
Administrator
directly from BioAssay Manager.

NOTE: If BioAssay Manager cannot interpret any To close an MS Excel spreadsheet from BioAssay
part of the data, that part is noted with red text in the
Manager:
MS Excel spreadsheet. BioAssay Manager cannot
import any data if any of the spreadsheet text is red. 1. From the Edit menu, choose Edit On/Off to turn
off Edit mode.
Changing the Width of Results 2. From the Import menu, choose Close.
Columns An MS Excel spreadsheet closes.
You change the width of any of the columns in the
Results or Graph tabs. Viewing Tier One
To change the width of columns in tables: Results
1. Click the Results or Graph tabs. You can see your Tier One results in the Results tab.
For more information, see “Setting Up an Assay
2. On a table, point to the divider between each
Model in the Database Tab” on page 127.
column heading.
To see your Tier One Results:
• In BioAssay Manager, click the Results tab.
NOTE: You can view Aggregate View calculation

The arrow pointer turns into a column change
results in the Results tab also.
pointer.
3. Drag the pointer left or right to make the
columns wider or narrower. Viewing Tier Two
The column divider stays where you move it. Results
To get confirmation that the column width has You can see your Tier Two results in the Graph tab.
changed for Tier One results: For more information, see “Setting Up an Assay
1. Click the Database tab.
Model in the Database Tab” on page 127.
2. In the Tier One information table, look at the To see your Tier Two Results do one of the
Width column. If the Width column is empty, following:
the width of the result table columns was not • In BioAssay Manager, click the Graph tab.
changed. If the Width column has a value in it,
the result table columns were changed.

Viewing Tier One Results
• In BioAssay Manager, click the Results tab 6. From the menu that appears in the cell, choose
and double-click the Tier One results table. X-axis or Y-axis, whichever you did not choose
in step 4.
NOTE: If you specified any axes when you created 7. Click the File menu and choose Save Assay.
Tier Two information, the fields you specified
appear as a graph on the Graph tab. The graphing information for Tier Two data is
saved.
Graphing Tier Two Viewing a Standard or Log

Results Graph of Tier Two Results
You can see a standard or log graph in the Graph tab.
You can graph the data from two of your Tier Two
fields. For more information, see “Setting Up an To see a graph:
Assay Model in the Database Tab” on page 127.
1. Click the Graph tab.
NOTE: You can only graph Tier Two results in 2. Take the appropriate action:
BioAssay Manager. You can only graph two Tier
Two fields at one time because BioAssay Manager If you want to see a Then click
does not generate more than one graph at a time.
standard graph Std.
Choosing Data for the X- and
Y-Axes log graph Log.
To graph the data from any two fields of Tier Two: A graph of your Tier Two data appears below
1. Click the Database tab. the Tier Two results table.

Filtering Results
assay information. You can filter your Tier One and Tier Two data so
that you can view only the data you want to see.
3. In the Tier Two table, click a cell in the Axis
column. For example, you can see all of your Tier Two
results that have a concentration above a specific
level.
First, you can define a filter so that you can specify
the criteria for data you want to see. Then you apply
the filter so that BioAssay Manager filters the data.
Finally, you can view the data that BioAssay
4. From the menu that appears in the cell, choose Manager filters.
X-axis or Y-axis.
5. Click another cell in the Axis column.

Graphing Tier Two Results
Defining a Filter
If you want to see Then from the
To define a filter: data that is menu for each
field, choose
1. From the View menu, point to Filter, and then
Administrator
choose Define.
equal to or less than a >=.
The CS BioAssay Manager - Define filters specific value
dialog box appears.
2. Maximize the dialog box by clicking between specific < >.
Maximize . values
a value of zero Null.
If you want to Then

not a value of zero NotNull.
filter Tier One data click the Main tab of

the Define filter similar to a value Like in the Text Type
dialog box. column only.
5. Type values for each field you want to filter.

filter Tier Two data click the Details tab
of the Define filter 6. Click Done when you finish defining the filter.
dialog box. The Define filter dialog box closes.
4. Take the appropriate action to see data from the Applying a Filter
Numbers, Text, or Dates Type results column:
You must apply a filter so that BioAssay Manager
filters the data you want to see.
If you want to see Then from the
data that is menu for each To apply a filter to the data:
field, choose • From the View menu, point to Filter, and then
choose On/Off.
equal to a specific = from the menu for
The filter you define is applied to the data for
value each field.
one assay.
greater than a specific < . To take a filter off the data:
value
• From the View menu, point to Filter, and then
choose On/Off.
equal to or greater than <= .
a specific value The filter is removed from the data for one
assay.
less than a specific >.
value

Filtering Results
Viewing Filtered Data The CS BioAssay Manager admin dialog box
opens.
You can see the filtered data in the Results and
Graph tabs, depending on whether you want to see
Tier One or Tier Two data.
To view filtered data for Tier One:
• Click the Results or the Graph tabs.
The table shows the filtered data.
To view filtered data for Tier Two:
To change the database directory path:
• Click the Graph tab. 1. In the CS BioAssay Manager admin dialog
The table shows the filtered data. box, click Set.
The Dialog Caption dialog box appears.
Clearing a Filter
1. From the View menu, point to Filter, and then
choose Define.
The CS BioAssay Manager - Define filters
dialog box appears.
2. Maximize the dialog box by clicking Maximize
.
3. Click Reset.
All text boxes in the dialog box become blank.
2. From the directory menu, choose the path that
Using the Help Menu you want the database to use.

3. Click OK.
You can open the Admin and About BioAssay
The Dialog Caption dialog box closes.
Manager information from the Help menu.
To have Oracle start or stop creating scripts:
Using the Admin Dialog Box
4. In the CS BioAssay Manager admin dialog
The Admin dialog box contains the following: box, click Oracle Scripts.
• The path for the database directory. The CS BioAssay Manager Confirm dialog box
• The ability to change the database directory appears.
path.
• The ability to create Oracle scripts, if you use
Oracle as the database.
To open Admin:
• From the Help menu, choose Admin.

Using the Help Menu
5. Take the appropriate action: To close About BioAssay Manager:
• In the CS BioAssay Manager Confirm dialog
If you Than click box, click OK.
Administrator
The CS BioAssay Manager Confirm dialog box

do not want to create No.
closes.
SQL scripts
want to create SQL Yes.

scripts
The CS BioAssay
Manager: Request
dialog box appears.
• Type a directory
path, if
necessary, and
click OK.
6. The CS BioAssay Manager Confirm dialog box

closes.
Viewing the Version

Information About BioAssay
Manager
The About box shows you information about the
version of BioAssay Manager you are using.
To open About BioAssay Manager:
• From the Help menu, choose About BioAssay
Manager.
The CS BioAssay Manager Confirm dialog box
opens.

Using the Help Menu
Chapter 10: Chemical Registration
Overview Starting Chemical
Chemical Registration is an application that runs on Registration
You must open Chemical Registration and then log
With Chemical Registration you can: in when you start using Chemical Registration.
• Register chemical compounds temporarily, and
To open and log in to Chemical Registration:
then permanently to the database. For more
information, see “Adding New Records to the 1. Type http://hostname into your web browser.
Temporary Table” on page 140 and Hostname is the name of the ChemOffice
“Registering Records” on page 146. WebServer machine. You can contact your
• View information about any chemical records server administrator to get this name.
in your Chemical Registration database. For The main ChemOffice WebServer window
more information, see “Searching Chemical appears.
Registration” on page 148. 2. Click Chemical Registration.
• Include chemical information with each record, The Chemical Registration log in page appears.
such as chemical structure. For more
information, see “Adding a Compound” on
page 140.
• Search and manage records in the database. For
more information, see “Searching Chemical
Registration” on page 148 and “Managing
Tables” on page 151.
• Control privileges of all Chemical Registration
3. Type your Username and Password, and then
users. For more information, see “Managing
click Log In.
Users and Roles” on page 157 and “Managing
Workgroups” on page 162.
• Configure the system for the needs of each user.
For more information, see “Choosing
Preferences” on page 165 and “Managing Users
and Roles” on page 157.
• Import .sdf files or ChemFinder databases into
Chemical Registration as chemical records. For
more information, see “Importing SDFiles” on
page 162.
ChemOffice Chapter 10: Chemical Registration • 139

Overview
The Chemical Registration main menu appears. To add a Compound record to Chemical
Registration:
1. From the Main Menu, click Add Compound.
Administrator
The New Compound Submission Form

appears.
From the Main Menu you can start using

NOTE: Your Administrator may set different

privileges for different users, so your Main Menu
may not look like the previous illustration.
Adding New Records to

the Temporary Table
You can add a new record to the temporary table, or
temporary database, as a Compound or a Batch of
compounds.
You can also add Salts at the Compound or Batch
levels. For more information about using a
configuration for Salts, contact CambridgeSoft at
support@cambridgesoft.com.
Adding a Compound
You can add a record to the temporary table in
Chemical Registration that contains information
about a chemical compound.
140 • Chapter 10: Chemical Registration CambridgeSoft

Adding New Records to the Temporary Table
2. In the New Compound Submission Form,
take the appropriate action: If you want add Then
information to the
record about
If you want add Then
information to the
record about synonyms for the in the Synonym box,
compound type synonyms.
a chemical structure in the Structure box,
draw a chemical a salt name from the Salt Name
structure of the menu, choose a salt.
compound. For more
information, see the a notebook from the Notebook
ChemDraw manual. assignment menu, choose a
notebook name.
a project name from the Project
menu, choose a a notebook page in the Page box, type
project name. assignment a page number.
a registration number from the Prefix menu, the date the batch was in the Creation Date
prefix choose a registration created box, type the date that
number prefix. the compound was
created.
a CAS number in the CAS No box,
type a CAS number. the amount in the in the Amount box,
batch type the amount of the
a molecular weight in the MW text box, compound in the
type a molecular batch.
weight.
comments about the in the Batch
a molecular formula in the MF text box, batch Comment box, type
type a molecular comments about the
formula. batch.
a place holder instead from the Structure comments about an in the Experimental
of a structure Comment menu, experiment box, type comments
choose a place holder. about an experiment.
chemical names for in the Chemical

the compound Name box, type
chemical names.

If you want add Then If you want add Then
information to the information to the
record about record about
Administrator
references and in the Reference and the melting point of in the MP °C box,
vendors Vendor Data box, the compound type comments about
type information HNMR results.
about references and
vendors. mass spectrometer in the MS box, type
comments comments about mass
safety concerns, such in the Storage spectrometer results.
as storage Requirements and
requirements and Warnings box, type infrared comments in the IR box, type
warnings comments safety comments about
concerns. infrared results.
HNMR comments in the HNMR box,

type comments about NOTE: You may be required to include specific
HNMR results. information about a record. For more
information, see your system administrator.
CNMR comments in the CNMR box,
type comments about
3. Click Add Record.
CNMR results.
The dialog box appears that confirms you added
comments about the in the Form box, type a record to the temporary table.
state of the compound comments about the
state of the
compound.
HPLC comments in the HPLC box, type

comments about
4. Click OK.
HPLC results.
the color of the in the Color box, type appears.
compound comments about the
color of the Adding a Reagent
compound. You can add a Reagent record to the temporary table
in Chemical Registration that contains information
about a reagent.

You may not have this option on your system. For
more information, see your system administrator. If you want add Then
information to the
To add a Reagent record to Chemical Registration: record about
1. From the Main Menu, click Add Reagent.

a place holder instead from the Structure
The New Compound Submission Form of a structure Comment menu,
appears. choose a place holder.
chemical names for in the Chemical

the compound Name box, type
chemical names.
synonyms for the in the Synonym box,

compound type synonyms.
2. In the New Compound Submission Form, The dialog box appears that confirms you added
take the appropriate action: a record to the temporary table.
If you want add Then

information to the
record about
a chemical structure in the Structure box, 4. Click OK.

draw a chemical
structure of the
compound. appears.
Adding a Batch
a CAS number in the CAS No box,
type a CAS number. You can add a Batch record to the temporary table in
Chemical Registration that contains information
a molecular weight in the MW text box, about a batch of a compound. The compound is
type a molecular assigned a suffix to its registration number that
weight. identifies it as part of a Batch.
You can keep track of compounds in Batches for
a molecular formula in the MF text box, various reasons. For example, you might prepare a
type a molecular compound, then later repeat the preparation to make
formula. more of the compound; or the organization might
purchase a compound from two different suppliers.

Batch information is important because different Common compound information for all the
batches may contain different impurities or behave Batches is retained.
differently in tests. 3. In the New Batch Submission Form, take the
appropriate action from step 2 from “Adding
Administrator
To add a Batch record to Chemical Registration:

New Records to the Temporary Table” on page
1. From the Main Menu, click Add Batch. 140, for all the necessary areas.
The Batch Registration Number page appears. 4. Click Add Record.
The dialog box appears that confirms you added
a record to the temporary table.
2. Type a Registry Number and then click OK.

The New Batch Submission Form appears.
5. Click OK.
The Batch Registration Number page appears.
Reviewing Records
from the Temporary
Table
You can view the records that are in the temporary
table before you register them in the permanent
tables.
To review records from the temporary table:

1. From the Main Menu, click Review/Register.
The Search Temporary Table appears.

Reviewing Records from the Temporary Table
2. Take the appropriate action: For more information about finding a record,
see “Reviewing Records from the Temporary
If you want to Then Table” on page 144.
3. Click Review/ Register.
search for records that a. in the Search The Register Compound Results Form appears.
have specific Temporary
attributes Table, type or 4. Click Edit , if it is available.
choose the The Registered Compounds Results Form
attributes of the changes to so that you can edit the record.
records you want
5. Make the necessary changes to the record and
to review.
then click Update Record .
b. Click Search. The Registered Compounds Results Form
changes back to its view-record mode.
see all of the records click Retrieve All.
in the temporary table Deleting Records from
A list of records appears reflecting the search. the Temporary Table
3. Click the Review/Register button of a specific You can delete records from the temporary table
record. instead of adding them to the permanent database.
The Commit Compound form appears. You cannot undo a delete operation.
For more information, see “Registering
Records” on page 146. To delete a record from the temporary table:
1. From the Main Menu, choose Register/Review.
Editing Records from The Search Temporary Table appears.
the Temporary Table 2. Go to a record that you want to delete from the
temporary table.
You can edit records in the temporary table before
The Registered Compounds Results List
you register them in the permanent database.
appears.
You cannot undo an edit operation. For more information about finding a record,
To edit records that are in the temporary table: see “Reviewing Records from the Temporary
Table” on page 144.
1. From the Main Menu, choose Register/Review.
3. Click Review/ Register.
The Search Temporary Table appears.
The Register Compound Results form appears.
2. Go to a record that you want to edit.
4. Click Edit , if it is available.
The Registered Compounds Results List
appears. The Registered Compounds Results List
changes to so that you can edit it.
5. Click Delete Record .

Editing Records from the Temporary Table
A dialog box appears so that you can reconfirm 3. Take the appropriate action:
your action.
If you want to Then
register
Administrator
all the compounds in click the Register All

the Registered button.
6. Click OK. Compounds Results
List The processing
The record is deleted from the temporary table. window appears.
Registering Records compounds a. go to the

individually compound you
After you review a record in the temporary table, want to register
you can register it. Registering a record moves it and then click
from the temporary table to the permanent tables, Register/
and assigns the record a unique registry number. Review.
Anyone using Chemical Registration can see
records in the permanent database. The Register
Compounds
You can also add Analytics data to a permanent Results List
record. For more information, see “Managing appears.
Analytics Data” on page 160.
b. Click Register.
Registering Records
The Register Compounds Results List changes
When you register a record, you can review it to to show that you successfully registered
make sure it has the information you want. compounds. The Registration Numbers and
You may also choose to do the following to a record: Batch numbers appear for each record.
• Delete it, so that you do not add it to the For more information about changing
permanent database. information about the compound before you
register it, see “Editing Records from the
• Add extra information with identifiers. For
Temporary Table” on page 145.
more information, see “Adding Identifier
Information to Records” on page 146. Adding Identifier Information to
To add records to the permanent database: Records
1. From the Main Menu, choose Register/Review. You can add more chemical names and synonyms to
The Search Temporary Table appears. records to help identify compounds more easily.
This additional information make up identifiers.
2. Go to a records that you want to register. For
more information, see “Reviewing Records
from the Temporary Table” on page 144.

Registering Records
To add information to permanent records with A dialog box appears that confirms you added a
identifiers: record to the permanent database, or table.
1. From the Main Menu, choose Add Identifiers.

The Add Record Form appears.
5. Click OK.
The Add Record Form page appears.
2. Type a Registry Number and then click OK. Adding Analytics Data to a
The New Identifiers Submission Form appears. Record
You can add analytics data to a record to help
identify compounds more easily.
For more information, see “Defining New
Experiments” on page 159.
To add analytics data to permanent records:
1. From the Main Menu, choose Add Analytics

Data.
The Add Record Form appears.
If you want to Then in the

add a
2. Type a Registry Number with a batch number
chemical name to the Chemical Name box, and then click OK.
record type a chemical name.
synonym for the Synonym box, type a

compound synonym.

Registering Records
The Results Form View appears. The chemical Searching for Registered
structure, batch ID, and registration number
vary according to your records.
Compounds
You can search for records which have been
Administrator
registered. These records do not appear in the

temporary table.
For more information about the different kinds of
queries you can create, see “Searching” in the
ChemOffice WebServer User’s Guide.
Viewing Details of Records

When you complete a search, records are returned
3. From the Experiment Type menu, choose an and appear in a table format, or a list. You can view
experiment type, and then click Add Data. more details about each record by viewing it in a
The Results View Form changes. form.
4. Add parameters and results data to the record To view details about a record:
and then click Commit Data.
1. Go to a record retrieved from a search.
The analytics data is added to the record.
2. Click Show Details.
Searching Chemical The record changes from Results List View to

Results Form View.
Registration
Viewing BioAssay Manager
You can search all the records in chemical
registration. When you search, you must create a
Data
query and then search for records. You can view BioAssay Manager data from
different assays.
ChemOffice WebServer User’s Guide. NOTE: This an optional module.
Searching for Records in the To view BioAssay Manager data:

Temporary Table 1. From the Main Menu, choose SAR Table.
You can search for records in the temporary table. The Select BioReg Assay dialog box appears.
These records have not yet been registered into the
permanent tables.
ChemOffice WebServer User’s Guide.

Searching Chemical Registration
2. In the Select BioReg Assay dialog box, take To view marked records:
the appropriate action:
• Go to a record that you marked and then click
Show Marked.
If you want to see Then
All the marked records appear in a new Results
List View.
a specific BioAssay from the Select
Manager Assay BioReg Assay menu,
choose an assay. Clearing Marked
Records
structures on the click the Show
assay Structures box. You can unmark records so that they do not appear
with the other marked records. You can unmark
3. Click SAR Table. record individually, or unmark all of them at once
which clears the viewing table.
BioAssay Manager assay results appear.
To unmark, or clear individual records:
Marking Records • Go to a record that you marked and then click
When you search Chemical Registration, you can Unmark Record.
mark specific records to view again later. The Unmark Record button changes to Mark
These are saved in the client and are client-specific Record.
lists. To unmark, or clear all records:
To mark records: • Go to the list of marked records and then click
Clear Marked.
1. Perform a search. For more information,
see“Searching Chemical Registration” on page All marked records are unmarked.
148.
2. Next to a record that you want to view again Exporting Search
later, click Mark Record.
Results
The Mark Record button changes to Unmark
Record. The record is marked so that you can You can export records, or hits, to your client
view it later with other marked records. system.
To export a records to your system:

Viewing Marked 1. From the result list, and click Export Hits.
Records
You can view all of the records you already marked
in one table.

Marking Records
The Export Hits window opens. The Save As dialog box appears.
Administrator
5. Choose a directory in which to save the record

and then click Save.
The record is saved as an .sdf file on your
system.
2. Click the boxes of the fields that you want to

Viewing Experiments in
export with the record and then click OK. Spreadsheets
3. Click Click to Download. You can see records grouped by experiment in a
The File Download dialog box opens. spreadsheet, or list, format.
To view records by experiment:

1. From the Main Menu, choose Show S/Sheet.
The Query Input Form appears.

4. Click Save this file to disk, and then click OK.
structures in the click the Structures
spreadsheet box.

Viewing Experiments in Spreadsheets
Defining Projects
You can include a project name with a record when
records from from the Experiment you create a record for a compound. You can use the
solubility Type menu, choose Projects table to define the Projects that appear
experiments Solubility. when any user of the system creates a record.
This information appears in the Project menu when
records from optical from the Experiment any user creates records for compounds.
rotation experiments Type menu, choose
Optical Rotation. To open the Projects tables:
• From the Manage Table page, click Projects.
records from NMR from the Experiment
A table that defines the Projects appears.
experiments Type menu, choose
1H NMR. To add a new project to the Projects table:
3. Click Show S/Sheet. 1. From the Projects table, click new.
A spreadsheet appears with the experiment A dialog box where you define a new project
data. appears.
Managing Tables
You can change, or manage, the following parts of 2. Take the appropriate action:
Chemical Registration with the Tables:
• Projects If you want to Then
• Notebooks
name the project in the Project Name
• Sequence
box, type a name for
• Structure Comments the project.
• People
stop this project name from the Active
• Sites
from appearing in the menu, choose False.
• Salts Project menu when a
To open a table you want to change: user creates a record
• From the Main Menu, choose Registry Tables.

make this project from the Active
The Manage Tables page opens. name appear in the menu, choose True.
Project menu when a
user creates a record

The Projects table appears with the new project.

Managing Tables
To edit a project in the Projects table: 2. Take the appropriate action:
4. From the Projects table, click the ID number
that corresponds to the project you want to edit. If you want to Then
Administrator
An area where you redefine a project appears.

name the notebook in the
Notebook_Name
box, type a name for
the notebook.
5. Follow step 2 from the previous section.
name the location of in the Location box,
6. Click Update Record. the notebook type a location for the
The Projects table is updated. notebook.
Defining Notebooks name the microfiche in the Microfiche

You can include a notebook name with a record of the notebook box, type the
microfiche name for
when you create a record for a compound. You can
the notebook.
use the Notebooks table to define the Notebooks that
appear when you create a record.
associate the from the User Last
This information appears in the Notebook menu notebook with the last Name menu, choose a
when you create records for compounds. name of a Chemical user.
Registration user
These all pertain to all users, not just a personal
setting.
stop this notebook from the Active
To open the Notebooks tables: name from appearing menu, choose False.
in the Notebook menu
• From the Manage Table page, click when you create a
Notebooks. record
A table that defines the Notebooks appears.
make this notebook from the Active
To add a new notebook to the Notebooks table: name appear in the menu, choose True.
Notebook menu when
1. From the Notebooks table, click new.
you create a record
An area where you define a new notebook
appears. 3. Click Add Record.
The Notebooks table appears with the new
notebook.

Managing Tables
To edit a notebook in the Notebooks table: 2. Take the appropriate action:
4. From the Notebooks table, click the ID number
that corresponds to the notebook you want to If you want to Then
edit.
An area where you redefine a notebook appears. name prefix for the in the Prefix box, type
compound a prefix.
registration numbers
specify the number in the Next in

with which to start the Sequence box, type a
compound number.
registration
numbering
6. Click Update Record. stop this prefix name from the Active
The Notebooks table is updated. from appearing in the menu, choose False.
Prefix menu when
Defining Registration Numbers you create a record
You can include a prefix and a starting number for

make this prefix name from the Active
compound registration numbers when you create a appear in the Prefix menu, choose True.
record. You can use the Sequences table to define menu when you
the compound registration numbers for each record. create a record
This information appears in the Prefix menu when
you create records for compounds. 3. Click Add Record.
The Sequence table appears with the new
To open the Sequence tables:
information.
• From the Manage Table page, click Sequence.
To edit a sequence in the Sequence table:
A table that defines the Sequence appears.
1. From the Sequence table, click the ID number
To add a new registration number prefix and starting that corresponds to the sequence you want to
number to the Sequence table: edit.
1. From the Sequence table, click new. An area where you redefine a sequence appears.
An area where you define a new sequence
appears.

Managing Tables
If you want to Then
3. Click Update Record.
The Sequence table is updated. stop this structure from the Active
Administrator
comment name from menu, choose False.

Defining Structure Comments appearing in the
You can include a comment about the structure of a Struct Comment
compound when you create a record. You can use menu when you
the Structure Comments table to define the structure create a record
comments that appear when you create a record.
make this structure from the Active
This information appears in the Struct Comment comment name menu, choose True.
menu when you create records for compounds. appear in the Struct
Comment menu when
To open the Structure Comments tables:
you create a record
• From the Manage Table page, click Structure
Comments. 3. Click Add Record.
A table that defines the Structure Comments The Structure Comments table appears with the
appears. new structure comment.
To add a new structure comment to the Structure To edit a structure comment in the Structure
Comments table: Comments table:
1. From the Structure Comments table, click 1. From the Structure Comments table, click the
new. ID number that corresponds to the structure
comment you want to edit.
An area where you define a new structure
comment appears. An area where you redefine a structure
comment appears.

If you want to Then
name the structure in the Structure The Structure Comments table is updated.
comment Comment box, type a
name for the structure Defining Chemical Registration
comment. People
You can include the name of a person with a record.
You can use the People table to define the properties
of each person.

Managing Tables
This information appears in the People menu when
you create records. If you want to Then
To open the People tables: name the location of in the Location box,
• From the Manage Table page, click People. the notebook type a location for the
notebook.
A table that defines the People appears.
To add a new person to the People table: include the first name in the First Name
of the person box, type a name.
1. From the People table, click new.
An area where you define a new person appears. include the middle in the Middle Name
name of the person box, type a name.
include the last name in the Last Name

of the person box, type a name.
choose a site for the from the Site menu,

person choose a work site
location.
include the phone in the Telephone box,

number of the person type a phone number.
2. Take the appropriate action: include the email in the Email box, type
address of the person an email address.
If you want to Then
stop this person from from the Active
include the code of in the Chemist Code appearing in the menu, choose False.
the person box, type a name for People menu
the notebook.
make this person from the Active
choose an unbound from the Unbound appear in the People menu, choose True.
user identification User_ID menu, menu
choose an ID.
choose a supervisor from the Supervisor/ The People table appears with the new person.
or workgroup Workgroup_ID
identification menu, choose an ID. Defining Sites
You can include a site name with a record. You can
use the Sites table to define the Sites that appear
when you create a record.

Managing Tables
This information appears in the Site menu when you To edit a site in the Sites table:
create records.
1. From the Sites table, click the ID number that
To open the Sites tables: corresponds to the site you want to edit.
Administrator
• From the Manage Table page, click Sites. An area where you redefine a site appears.
A table that defines the Sites appears.
To add a new site to the Sites table:
1. From the Sites table, click new.

An area where you define a new site appears. 2. Follow step 2 from the previous section.
The Sites table is updated.
2. Take the appropriate action: Defining Salts

You can include a salt with a record when you create
If you want to Then a record for a compound. You can use the Salts table
to define the Salts that appear when you create a
name the site in the Site Name box, record.
type a name for the This information appears in the Salt menu when you
site. create records for compounds.
name the code of the in the Site Code box, To open the Salts tables:
site type a code for the • From the Manage Table page, click Salts.
site.
A table that defines the Salts appears.
stop this site name from the Active To add a new salt to the Salts table:
from appearing in the menu, choose False.
Site menu when you 1. From the Salts table, click new.
create a record An area where you define a new salt appears.
make this site name from the Active

appear in the Site menu, choose True.
menu when you
create a record

The Sites table appears with the new site.

Managing Tables
2. Take the appropriate action: 3. Click Update Record.
The Salts table is updated.
If you want to Then
Managing Users and
name the salt in the Salt_Name
box, type a name for Roles
the salt.
You can change, or manage, the privileges of all of
the people who use Chemical Registration with the
give the molecular in the Salt_MW box, following:
weight of the salt type a weight for the
salt. • Users table
• Roles table
give the molecular in the Salt_MF box,
To open a table you want to change:
formula of the salt type a formula for the
salt. • From the Main Menu, choose Manager Users.
The Manage Users page opens.
stop this salt name from the Active
from appearing in the menu, choose False. Defining Users
Salt menu when you
create a record You can define privileges for different users. You
can use the Users table to define their privileges by
assigning roles.
make this salt name from the Active
appear in the Salt menu, choose True. To open the Users table:
menu when you
create a record • From the Manage Users page, click Users.
A table that defines the Users appears.
To add a new user to the Users table:
The Salts table appears with the new salt.
1. From the Users table, click new.
To edit a salt in the Salts table: An area where you define a new user appears.
1. From the Salts table, click the ID number that
corresponds to the salt you want to edit.
An area where you redefine a salt appears.

Managing Users and Roles
2. Take the appropriate action: To add a new role to the Roles table:
1. From the Roles table, click new.

If you want to Then
An area where you define a new role appears.
Administrator
The following illustration shows a partial list of

name the user in the User Name
box, type a name for role definitions.
the user.
assign a password to in the Password box,

the user type a password for
the user.
confirm the password in the Password

you assign to the user confirm box, type the
password for the user
again.
3. Click Add User.

The Users table appears with the new user. For more information, see “Appendix of Role
Definitions” on page 167.
Defining Roles 2. In the Role_Name box, type a name for the new
You can define roles to assign to different users. You Role.
can use the Roles table to define privileges by 3. Choose role definitions to assign to the new
choosing roles. Role. For more information about role
To open the Roles table: definitions, see “Appendix of Role Definitions”
on page 167.
• From the Manage Users page, click Roles.
4. Click Add Role.
A table that defines the Roles appears.
The Roles table appears with the new role.

Managing Users and Roles
To edit a role in the Roles table: To change your password in the Passwords table:
1. From the Roles table, click the Role Name that 1. Take the appropriate action:
corresponds to the role you want to edit.
An area where you redefine a role appears. The If you want to Then
following illustration shows a partial list of role
definitions. change your in the Password box,
password type a new password.
confirm your in the Password

password confirm box, type the
password again.
2. Click Update User.

The Passwords table appears with the new
password.
Defining New
For more information, see “Appendix of Role
Experiments
Definitions” on page 167. You can include an experiment name with a record.
2. Follow step 2 from the previous section. You can use the Experiments table to define the
Experiments that appear when you create a record.
3. Click Update Role.
The Roles table is updated. This information appears in the Experiments menu
when you create records.
Changing Passwords To open the Experiments table:
You can change the password for yourself. You can • From the Main Menu, click New Experiment.
use the Passwords table to edit your password.
A table that defines the experiments appears.
To open the Passwords table:
To add a new experiment to the Experiments table:
• From the Main Menu, click Change Password.
1. From the Experiments table, click new.
An area where you redefine your password
An area where you define a new experiment
appears.
appears.

Changing Passwords
2. Take the appropriate action: To edit an experiment in the Experiments table:
1. From the Experiments table, click the

If you want to Then
Experiment_type_id that corresponds to the
Administrator
experiment you want to edit.

name the experiment in the Name box, type
a name for the An area where you redefine an experiment
experiment. appears.
describe the in the Description

experiment box, type a
description for the
experiment.
include the date you in the Created box,

create this experiment type a date.
include the date you in the Modified box,

change this type a date.
experiment 2. Follow step 2 from the previous section.
include a version in the Version box,
The Experiments table is updated.
identifier for this type a way to identify
experiment the different version.
Managing Analytics
Data
The Experiments table appears with the new
experiment. You can define different parts of information for
experiments with the analytics data, such as:
• Result type
• Parameter type
Defining Result Type

You can include a result type with an experiment
when you create a record for a compound. You can
use the Result Types table to define the Result Types
that appear when you create a record.
This information appears in the Result Type menu.

Managing Analytics Data
To open the Result Types tables: To edit a result type in the Result Types table:
• From the Analytics Table page, click Result 1. From the Result Types table, click the ID
Types. number that corresponds to the result type you
A table that defines the Result Types appears. want to edit.
An area where you redefine a result type
To add a new result type to the Result Types table:
appears.
1. From the Result Types table, click new.
An area where you define a new result type
appears.

The Result Types table is updated.
If you want to Then Defining Experiment Type

For more information, see “Defining New
name the result type in the Name box, type Experiments” on page 159.
a name for the result
type. Defining Parameter Type
describe the result in the Description You can include a parameter type with an
type box, type a experiment when you create a record for a
description for the compound. You can use the Parameter types table to
result type. define the Parameter Types that appear when you
create a record.
describe the units of in the Units box, type This information appears in the Parameter Type
the result type a description for the menu.
units of the result
type. To open the Parameter Types tables:
• From the Analytics Table page, click
Parameter Types.
The Result Types table appears with the new
A table that defines the Parameter Types
result type.
appears.

Managing Analytics Data
To add a new parameter type to the Parameter Types To edit a parameter type in the Parameter Types
table: table:
1. From the Parameter Types table, click new. 1. From the Parameter Types table, click the ID
Administrator
An area where you define a new parameter type number that corresponds to the parameter type
appears. you want to edit.
An area where you redefine a parameter type
appears.
If you want to Then

name the parameter in the Name box, type 3. Click Update Record.
type a name for the
The Parameter Types table is updated.
parameter type.
describe the in the Description

Managing Workgroups
parameter type box, type a To open the Workgroups tables:
description for the
parameter type. • From the Main Menu, click Managing
Workgroups.
describe the units of in the Units box, type A table that defines the Workgroups appears.
the parameter type a description for the For more information about adding workgroups, see
units of the parameter “Defining Chemical Registration People” on page
type.
154.

Importing SDFiles
The Parameter Types table appears with the
new parameter type. You can import chemical data stored as .sdf files
through ChemFinder and into Chemical
Registration or directly from ChemFinder
databases. These files become records in the
temporary table or the permanent database in
Chemical Registration, depending on the options
chosen.

Managing Workgroups
When you import an .sdf file into Chemical The ChemLoader dialog box appears.
Registration, you must do the following:
• Import an .sdf file into a ChemFinder database.
For more information, see the ChemFinder
Manual.
• Open ChemLoader on a server machine.
• Choose an input database, that is the
ChemFinder database where you already
imported the .sdf file.
• Choose an output database: the server where
Chemical Registration exists.
• Match the fields from the input to the output
databases.
To choose input and output databases:
• View the matched fields.
1. From the Input Database section, click
• Import the records.
Browse.
You must have ChemOffice installed on your
machine so that you can use ChemFinder. For more
information about ChemFinder, see the ChemFinder
Manual. ChemOffice is installed by default with the
You can customize database fields with generec
names such as FIELD_1 and FIELD_2. Each field
name can contain up to 2000 characters.
To open ChemLoader:
• From the directory
\\Inetpub\wwwrootChemOffice\chem_reg\,
open MatchDatabase.exe. 2. Choose an input database and click Open.
The database appears in the Input Database
section of MatchDatabase. All of the
information, such as tables and fields,
associated with the input database appear in the
appropriate sections.
3. From the Output Database section, click
Browse.

Importing SDFiles
The Select Server dialog box appears. 5. From the list, choose a server and click OK.
The server appears in the Output Database
section of ChemLoader. All of the information,
such as tables and fields, associated with the
Administrator
server appear in the appropriate sections.
To match the fields from the input database to the

output database and then view the matches:
1. In the Input Database Fields section, click a

field.
The field you choose becomes highlighted.
2. In the Output Database Fields section, click a
field.
The field you choose becomes highlighted.
3. Click Match Fields.
If you want Then The fields in the separate databases become

linked, shown by a line between them.
to choose a server that in the Server box,
does not appear on the type a server name.
list of servers
to include a user name in the User ID box,

type a user name.
to include a password in the Password box,

type a password.
the imported records click Add data to

to appear as records in temporary table
the temporary table of only.
Chemical 4. Repeat step 1 through step 3 to match more
Registration fields.
the imported records click Add data to NOTE: Some fields automatically match each
to appear as records in permanent table. other, such as MOL_ID in the input database
the permanent and STRUCTURE in the output database.
database of Chemical
Registration

Importing SDFiles
5. Take the appropriate action: The Matching field list appears.
If you want to Then
include records from click the Start index

the input database box and type a record
that start at a specific number from the
place in the database database. 7. Click OK.
To import the records into Chemical Registration:
include records from click the Stop index
the input database box and type a record • Click Import.
that end at a specific number from the The Dialog dialog box appears.
place in the database database.
record the importing click the Log file box,

process in a log file and type the location
of a directory in
which the log file is
saved.
include a sequence in from the Sequence

the imported files menu, choose a When the import is complete, ChemLoader
sequence. appears.
You can use the new records as you normally do
include a project from the Project in Chemical Registration.
name in the imported menu, choose a
To abort the import:
files sequence.
• In the Dialog dialog box, click Cancel.
include a compound from the Compound The import stops and ChemLoader appears.
name in the imported menu, choose a
Records already imported remain.
files sequence.
include a notebook from the Notebook

Choosing Preferences
name in the imported menu, choose a For more information, see the ChemOffice
files sequence. WebServer User’s Guide.
include a salt name in from the Salt menu,

the imported files choose a sequence.
6. Click View Matches.

Choosing Preferences
Printing
You can print records from Chemical Registration.
Administrator
To print records:
1. Click Print.
The Print dialog box appears.
2. Check the settings and then click OK.
A Chemical Registration record is printed.
Logging Off
You can end your Chemical Registration at anytime
by logging off.
To log off:
• Click Log Off.
The Chemical Registration Log In dialog page
appears. You can log back in and continue using
chemical Registration, or browse to a different
site.

Printing
Appendix of Role
Definitions
You can choose role definitions to define privileges
for different users. Each definition grants a different
privilege.
The following shows a table of each Chemical
Registration Role:
If you want the user to be able to Then choose the role definition
add batch information to a compound that is in the temporary table ADD_BATCH_TEMP.

add a compound to the temporary table ADD_COMPOUND_TEMP.
add entries to the Compound Type table ADD_COMPOUND_TYPE_TABLE.
add Analytics data to a batch ADD_EVAL_DATA.

add salt information to a compound that is in the temporary table ADD_SALT_TEMP.
add an identifier to a compound that is in the temporary table ADD_IDENTIFIER_TEMP.
add entries to the People table ADD_PEOPLE_TABLE.
add entries to the projects table ADD_PROJECTS_TABLE.

add entries to the workgroup table ADD_WORKGROUP.
open Chemical Registration by logging on CAMSOFT_LOG_ON.
delete entries from the Compound Type table DELETE_COMPOUND_TYPE_TABLE.
delete entries from the People table DELETE_PEOPLE_TABLE.

delete entries from the projects table DELETE_PROJECTS_TABLE.
delete a compound from the registry DELETE_REG.
delete a compound from the temporary table DELETE_TEMP.
delete entries from the workgroup table DELETE_WORKGROUP.
edit batch information about a compound that is in the registry EDIT_BATCH_REG.
edit batch information about a compound that is in the temporary EDIT_BATCH_TEMP.
table
edit information about a compound that is in the registry EDIT_COMPOUND_REG.
edit information about a compound that is in the temporary table EDIT_COMPOUND_TEMP.

edit the Compound Type table EDIT_COMPOUND_TYPE_TABLE.

Appendix of Role Definitions
If you want the user to be able to Then choose the role definition
edit Analytics data EDIT_EVAL_DATA.

Administrator
edit identifiers for a compound that is in the registry EDIT_IDENTIFIERS_REG.
edit identifiers for a compound that is in the temporary table EDIT_IDENTIFIERS_TEMP.

edit the notebooks table EDIT_NOTEBOOKS_TABLE.
edit the table of people who are known to the system EDIT_PEOPLE_TABLE.
edit the projects table EDIT_PROJECTS_TABLE.
edit salt information about a compound that is in the registry EDIT_SALT_REG.

edit the salt form table EDIT_SALT_TABLE.
edit salt information about a compound that is in the temporary table EDIT_SALT_TEMP.
apply all of the edit/register features to everyone at a site EDIT_SCOPE_ALL.
apply all of the edit/register features to their person_id EDIT_SCOPE_SELF.

apply all of the edit/register features to their person_id, and to EDIT_SCOPE_SUPERVISOR.
anyone who uses it as their supervisor_id
edit the compound numbering table EDIT_SEQUENCES_TABLE.
edit the table of sites that are known to the system EDIT_SITES_TABLE.
edit Users table EDIT_USERS_TABLE.

edit workgroup information EDIT_WORKGROUP.
remove a compound from the temporary table and place it REGISTER_TEMP.
permanently in the Chemical Registration registry
view the Analytics spreadsheet data SEARCH_EVAL_DATA.
search for a compound that is in the temporary table SEARCH_TEMP.

search for registered compounds SEARCH_REG.
SET_APPROVED_FLAG.
SET_QUALITY_CHECK_FLAG.
set ability to edit/register all entries for all sites on or off SITE_ACCESS_ALL.
set approval flag on or off TOGGLE_APPROVED_FLAG.
TOGGLE_QUALITY_CHECK_FLAG

Appendix of Role Definitions
Chapter 11: ChemInfo Introduction
What is ChemInfo? • Select—Highlight an object or choose an
option. Selecting an object does not initiate an
ChemInfo is a library of chemical information action, but selects the item upon which to act.
databases of compounds and chemical reactions. Deselect is the opposite of select.
You search ChemInfo with tools provided in the • Choose—Select a command from a menu or
ChemOffice software suite. submenu. Choosing an item performs a
ChemInfo brings a wealth of chemical information command.
to your desktop personal computer. With the click of • Key+click—Hold the specified key and click
a mouse you can find names, structures, physical the mouse button. For example, Shift+click
data, suppliers, safety data, and literature references means hold down the Shift key while clicking
for hundreds of thousands of chemicals and the mouse button.
chemical reactions.
• Key+drag—Hold down the specified key and
drag a selection. For example, Shift+drag
Conventions means to hold down the Shift key while
dragging the pointer.
The following convention is used throughout the
former ChemInfo user’s guide:
Additional Help
NOTE: Notes such as this are used to highlight Additional sources of help for using ChemInfo
information supplemental to the main text. include the following:
• Quick Reference Card
Terminology • ChemFinder and ChemDraw online Help
The following terminology is used in this User’s • ToolTips
Guide: • Status Bar
• Point—Move the mouse pointer over the item • CambridgeSoft Technical Support
you want.
Online Help
• Click—Quickly press and then release the
mouse button while pointing to an object. Access to online help is provided from the
• Double-click—Click the mouse twice in rapid ChemFinder and ChemDraw Help menus.
succession. To learn about using the online Help:
• Drag—Hold down the mouse button, move the • From the Help menu, choose How to Use Help.
mouse, and then release the mouse button.
ChemOffice Chapter 11: ChemInfo Introduction • 169

What is ChemInfo?
To access online Help: The following table lists the RAM required for
ChemFinder Pro using the following databases:
• From the Help menu, choose Contents.
ToolTips Database Required Recommended

Administrator
ChemFinder and ChemDraw provide ToolTips as an

additional form of online Help. Rest your pointer on ChemACX 32 MB 64 MB
a tool to display a message box with a brief
description of the tool. ChemACX-SC 32 MB 64 MB
ChemRXN 64 MB 128 MB
ChemMSDX 32 MB 64 MB
Status Bar
The bottom left corner of the ChemFinder and ChemINDEX 64 MB 128 MB
ChemDraw Status Bars display a slightly more
detailed description of the tool icons.
Installation
You do not need to install the ChemInfo databases,
but can use them directly from the CD-ROMs.
Technical Support
When you use the databases from the CD-ROMs,
For information about Technical Support at they are Read-only. If you have sufficient hard disk
CambridgeSoft Corporation, see “Technical space, you can copy the databases from the
Support” on page 203
CD-ROMs. This not only makes searching faster but
allows you to edit the databases, except ChemACX
System Requirements and ChemACX-SC.
CS ChemInfo runs on IBM-compatible computers ChemInfo may be packaged with various
with the following: applications. For example, if you purchased
• Windows 95/98/NT ChemOffice Ultra, you receive ChemInfo with
ChemOffice, Chem3D, and ChemFinder. The
• Pentium processor
installation procedure on the ChemOffice Ultra CD-
• 32 MB RAM ROM installs these applications.
• 52 MB Disk space
170 • Chapter 11: ChemInfo Introduction CambridgeSoft

System Requirements
ChemInfo and 3. From the File menu, select Open and select a
form for one of the databases.
ChemOffice
ChemInfo works with ChemOffice, an integrated
suite of software tools for chemists with personal
computers. The ChemOffice applications,
ChemFinder, ChemDraw , and Chem3D help
ChemInfo deliver information.
ChemOffice includes the following:
ChemFinder—The primary application used by
ChemInfo. It provides the engine for searching the
data the forms and tables for viewing it. Relational
databases and Structured Query Language are Alternatively, you can explore the CD-ROM with
supported by ChemFinder. the Windows Explorer and open ChemFinder by
double-clicking one of the ChemFinder form icons.
ChemDraw—The chemical drawing standard
allows structures to be drawn and edited in
ChemFinder. It can represent individual structures
or chemical reactions, complete with atom-to-atom
mapping and absolute or relative stereochemistry,
for detailed structure-based queries.
Chem3D—A molecular modeling and
computations application featuring molecular
mechanical and quantum mechanical computational
capability. Featuring an intuitive graphical user
interface, it displays molecules as three-dimensional
models that you can rotate and translate to reveal
details of a structure not evident in two dimensions.
Using ChemInfo
To use ChemInfo:
1. Insert one of the ChemInfo CD-ROMs into

your CD drive.
2. Start ChemFinder.
ChemOffice Chapter 11: ChemInfo Introduction • 171

ChemInfo and ChemOffice
Administrator
172 • Chapter 11: ChemInfo Introduction CambridgeSoft

Using ChemInfo
Chapter 12: ChemACX
What Is It? How Is It Useful?
ChemACX (Available Chemicals Exchange) is a ChemACX is your guide to commercially available
class of databases available from chemical chemicals worldwide. Whether you are planning a
manufacturers and distributors, featuring complete bench synthesis, scale-up, or a commercial process,
catalogs of major world suppliers of fine research, you can search these databases to determine the
specialty, and industrial chemicals. ChemACX is a availability and sources for the chemicals you need.
read-only database.
You can search ChemACX by any of the following:
ChemACX Database • Chemical structure

• Chemical substructure
Directory: ChemACX
• Compound name
Filenames: Acx2000Index.cfw, Acx2000Prod.cfw,
Acx2000Supplier.cfw • Molecular formula
• CAS Registry Number
Number of Suppliers: 227
• Molecular weight range
Number of Unique Chemical Entities: >187, 000
• Combinations of the above criteria
Number of Chemical Products: >360, 000
For information about searching, see the
Key Fields: ChemFinder manual.
• Structure ChemACX has three linked forms:
• Formula • Index form
• ACX Number • Product form
• Product Name • Supplier form
• Molecular Weight
• CAS Registry Number
• Synonym
• Product ID
• Catalog Number
• Supplier ID
• Property
• Supplier Name
ChemOffice Chapter 12: ChemACX • 173

What Is It?
If you want to search over the entire database for a To return to the Index form:
chemical, start with the Index form.
• Click Index.
To view information about the supplier of the

Administrator
chemical:
• Click Info.
The Supplier form appears.
If you start your search with the Index form and find
some matching compounds:
• A list of synonyms in the Synonyms subform
appears. To display a list of products for the displayed
• A list of suppliers in the Products subform supplier:
appears.
• Click Products.
To view product information: The Products form appears.
• On the Index form, click a product name.
The Product form appears. Using ChemACX with
ChemOffice Webserver
ChemACX (Available Chemicals Exchange) is a
database of commercially available chemicals. The
database contains catalogs from research and
industrial chemical vendors.
You can search for chemicals from the ChemACX
vendors. After you find the chemicals you want, you
can save them to a list, or Shopping Cart. You can
print your Shopping Cart list and then send or fax
your order to CambridgeSoft.
174 • Chapter 12: ChemACX CambridgeSoft

Using ChemACX with ChemOffice Webserver
Opening ChemACX Searching ChemACX Catalogs
To open ChemACX: You can search all of the catalogs for all of the
vendors on ChemACX or a specific list of vendors’
Type http://servername into your web browser. catalogs.
Servername is the name of the ChemOffice
You can create a search query with any combination
WebServer machine. You can contact your
of the following criteria:
server administrator to get this name.
• Substance Name (text search)
The main ChemOffice WebServer window
appears. • CAS Registry Number
• Click ChemACX. • ACX Number
The ChemACX.com Query Input Form • Mol. Formula (formula search)

appears. • MW Range (molecular weight search)
• Catalog Number
For more information, see the ChemOffice
To search for information from ChemACX vendors:
1. Open ChemACX.
2. Type or draw search criteria, and then take the
appropriate action:

search
all of the ChemACX Search all vendors.

vendors’ catalogs
your specific list of Search your favorite

vendors’ catalogs vendors.
3. Click Search.

The Search Results page appears. The
following illustration shows the results from a If you want to Then
search for cyclohexane. search
Administrator
by CAS number in the text box, type

Search your favorite
vendors.
with the full query click Advanced

page, including Query with Plugin.
structures and other
criteria
3. Click Search.
The Search Results page appears. The
following illustration shows the results from a
search for cyclohexane.
Searching Without the Plug-in

You can search for a chemical name or a CAS
number only, to simplify your search. You can do
this by searching without using the plug-in.
To search without the plug-in:
1. Open ChemACX and then click Click for Non-

Plugin Search.
The Non-Plug-in Search page appears.
If you want to Then

search
by chemical name in the text box, type

Search all vendors.

Creating and Editing Your List
If you want to Then
of Favorite Vendors
You can create a list of your favorite vendors’ remove a vendor from click the box with a
catalogs to search. You can add vendors to your list your favorite vendors checkmark in it. The
list checkmark is
by following the same steps as creating the list.
removed from the
To select vendors to create or edit the list of your box.
favorite vendors:
3. Click Save as Preferred List.
1. On the main ChemACX page, click Edit
Your list of favorite vendors list is saved and the
Favorite Vendors List.
Vendor Selector box closes.
The Vendor Selector box appears.
Saving Search Results to the
Shopping Cart
You can save information from your search in the
Shopping Cart. You can also use your Shopping Cart
list to order chemicals. For more information, see
“Ordering Chemicals Through ChemACX” on page
179.
To save your information to the Shopping Cart:
1. Search for a chemical on ChemACX.

For more information, see the ChemOffice
If you want to Then
create your favorite click the blank box

vendors list next to a vendor
name. A checkmark
appears in the box.
add a vendor to your click the blank box

favorite vendors list next to a vendor
name. A checkmark
appears in the box.

The Search Results page appears. The 5. From the catalog list, click the box next to Add
following illustration shows the results from a to Cart and type a quantity.
search for cyclohexane.
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The order is added to your Shopping Cart.
Viewing Your Shopping Cart

You can see your Shopping Cart list from the main
ChemACX page and the Search Results page.
To view your Shopping Cart:
If you are on the Then click
ChemACX Query
Input page
2. For a specific record, click Details.
The Detailed View appears. ChemACX Search
Results page or
Your Shopping Cart list appears with the

chemical information from your search.
3. From Online Vendors, Your Favorite

Vendors, or Other Vendors, choose a vendor.
4. Click Catalog View.

Removing Items from Your
Shopping Cart
To remove an item from your Shopping Cart list:
• On the Shopping Cart page, click Remove
.
The item is removed from your Shopping Cart
list.
Ordering Chemicals Through

ChemACX
You cannot order chemicals directly through
ChemACX. You can order chemcals by printing
your Shopping Cart and then mailing or faxing it to
CambridgeSoft.
To order chemicals with information from

ChemACX:
1. Open ChemACX and then perform a search.

2. Save chemicals you want to order to your
Shopping Cart.
3. Open your Shopping Cart and then click Print.
Your Shopping Cart appears and then it is
printed.
4. Mail or fax your Shopping Cart to

CambridgeSoft.

ChemACX 2000
Participants
Administrator
ChemACX 2000 suppliers are listed below.
A.G. Scientific AccuStandard Acros Organics - Acros Organics - USA

International
Advanced ChemTech Air Products & Ajinomoto - Amino Albemarle Corporation

Chemicals, Inc. Acid Department
Albright & Wilson Alchymars SpA Aldrich Aldrich Flavors and

Americas Fragrances
Alfa Aesar AlliedSignal Inc. American Radiolabeled Angelini Fine

Specialty Chemicals Chemicals, Inc. Chemicals
ARCO Chemical Array BioPharma, Inc. Asahi Glass Company - Ashwood Chemicals
Company Fluorochemicals Ltd.
Division
Asymchem BASF Chemical Bayer Corporation Bedoukian Research,

Intermediates Inc.
Biddle Sawyer Biomol Biosynth International, Boehringer Ingelheim

Corporation Inc. KG
Borregaard Synthesis Boulder Scientific Burdick & Jackson, Inc. Bush Boake Allen Inc.
Company
Callery Chemical Cambrex Corporation Carbomer Cayman Chemical

Company Company
Celanese, Ltd. Central Glass Co. Ltd.- Charkit Chemical Chattem Chemicals,
Fine Chemical Corporation Inc.
Department
Chem-Impex ChemDesign Corp. Chemetall GmbH, Chemisphere Limited

International, Inc. Lithium Division
ChemPacific ChemService, Inc. Chemtec Leuna - China National

Specialty Chemicals Chemical Construction
and Fine Chemicals Corporation

ChemACX 2000 Participants
Chiragene Corporation ChiRex Ltd. ChiroTech Technology Chugai Kasei Co., Ltd.
Limited
Cilag AG Clariant Corporation Classic Flavors & Coalite Chemicals

Fragrances
CreaNova, Inc. CU Chemie Uetikon D&O Chemicals, Inc. D.F. Goldsmith

Chemicals & Metals
Co.
Daicel Chemical Daikin Industries Ltd Daiso Co., Ltd. Davos Chemical Corp.
Industries, Ltd.
De Voit Associates Deepwater Chemicals Degussa Corp. Diagnostic Chemicals

Limited
Diaz Digital Specialty Dinamite Dipharma Diosynth b.v.

Chemicals, Inc. SpA
Dishman USA Dixie Chemical DSM Fine Chemicals Dynamit Nobel GmbH
Company, Inc. Inc.
Eastman Chemical Elan Chemical Electron Microscopy EMS Dottikon AG

Company Company, Inc. Services
Esprit Chemical Exchem Organics Expansia S.A. F2 Chemicals Ltd.

Company
FAR Research Fine & Performance Fine Chemicals Fine Organics Ltd., Seal
Chemicals Ltd. Corporation (PTY) Ltd. Sands
First Chemical Corp. Fisher Scientific Fluorochem USA Fluka
Frinton Laboratories Frinton Laboratories Frontier Scientific, Inc. FrutArom (laboratory

ChemStore chemicals)
FrutArom Ltd (aroma FTech, Inc. FujiHunt G.J. Chemical

chemicals) Company, Inc.
Ganes Chemicals Inc. Gaylord Chemical Gelest Inc. Generichem Corp.

Corporation
Genzyme George Uhe Company, GFS GNI Chemicals

Pharmaceuticals Inc. Corporation

Great Lakes Chemical H&S Chemical Co. Inc. Halocarbon Hokko Chemical
Corp. Industry Co., Ltd. - Fine
Chemicals Division
Administrator
ICN Biomedical Ihara Chemical Industry Ihara Nikkei Chemical Inabata America Corp.
Research Products Co., Ltd. Industry Co., Ltd.
INDOFINE Chemical Industria Chimica INSPEC Group PLC & Interchem Corp.
Company, Inc. Milanese S.p.A. Int’l Specialty
Chemicals Ltd
ISOCHEM, Groupe Isotec Inc. ISP Fine Chemicals J.T. Baker

SNPE
Jost Chemical Jupiter Chemicals, Inc. K-I Chemical Industry Kaden Biochemicals
Co., Ltd. GmbH
Kaneka Corporation - Katwijk Chemie bv Kemira Fine Chemicals KingChem

Fine Chemicals
Division
KOEI Chemical Kyowa Hakko Kogyo Lancaster Synthesis Lonza Ltd.

Company, Ltd Co., Ltd. Inc.
Mallinckrodt Marker Gene Maybridge Chemical Menai Organics

Laboratory Chemicals Technologies, Inc Company, Ltd.
MillionLink (Tianjin) Mitchell Cotts Miteni SpA Mitsui Chemicals, Inc.

International Trade Chemicals
Co., Ltd.
Molecular BioSciences Moravek Biochemicals MORFLEX, Inc. Morton International,

Inc.
Nichimen America Inc. Nihon Nohyaku Co., NIPA Hardwicke Inc. Nippoh Chemicals Co.,
Ltd. Ltd.
Norchim S.A. Norquay Technology NSC Technologies Oakwood Products, Inc.

Inc. USA
Omega Chemical Co., Optima Chemical ORGANICA Organix, Inc.

Inc. Group LLC Feinchemie GmbH
Wolfen
Orgasynth Palindent Organic Parish Chemical PCAS

Intermediates Company

Peakdale Fine PepTech Corporation Pfaltz & Bauer, Inc. Pharmacia & Upjohn
Chemicals Limited Company
Pharmco Products Inc. Phoenix Chemicals PNK United, Inc. PolyCarbon Inds., Inc.
PPG-SIPSY Queen’s University of Raschig AG Regis Technologies,

Belfast Inc.
Reilly Industries, Inc. RELAX Ltd Research Organics Rhodia Fine Organics
Richman Chemical Robinson Brothers Rohner Ltd. ROMIL Ltd

Inc. Limited
RSP Amino Acid Ruetgers-Nease S.I.M.S. s.r.l. Salford Ultrafine

Analogues, Inc. Corporation Chemicals & Research
Ltd.
Sanfur USA, Inc. Sanochemia Surefabrik SEAC

Pharmazeutika AG Schweizerhall
Sigma Aldrich Library Sigma Chemical Silar Laboratories - A Simafex

of Rare Chemicals Company Division of Wright
Corporation
SK Energy and SNPE Chemicals, Soltec Ventures, Inc. Spectrum Quality

Chemical, Inc. Groups SNPE Products, Inc.
Spherotech, Inc. Stanford Materials Strem Chemicals, Inc. Sumitomo Seika

Company Chemcials Co., Ltd.
SynChem, Inc. Syntai Chemicals & Synthetech Synthon Corp.

Pharmaceuticals, Ltd.
Taizhou Kangduo Sea Takasago International TCI Tocris Cookson Ltd.

Biochemical & Corp.
Pharmaceutical Co.
Ltd.
Toronto Research Tosoh Corporation Trans World Chemicals Tyger Scientific Inc.
Chemicals, Inc. Inc.
UBE Industries, Ltd. - Ubichem plc VanDeMark Group VIS Farmaceutici SpA
Fine Chemicals
Division

Wacker Chemicals Whyte Chemicals William Blythe Ltd Wilshire Chemical Co.,
(USA) Limited Inc.
WYCHEM Limited Zambon Group ZENECA Specialties

Administrator

What If My Favorite
Supplier Isn’t Listed
Here?
CambridgeSoft is always adding new companies to
ChemACX. The one you want might be in the next
release of ChemInfo, or it might already be
CambridgeSoft’s WWW subscription service,
ChemInfo Pro.
Contact your supplier and ask them to participate in
ChemACX. To participate, your supplier sends
CambridgeSoft its product list. The preferred format
for submission is a ChemFinder database with
structures. They can also use other electronic
formats such as Access databases or Excel
spreadsheets. They can use a brochure for short
product lists. Send the information to one of the
following:
• csinfo@camsoft.com
• ChemACX Data, CambridgeSoft Corporation,
100 CambridgePark Drive, Cambridge, MA
02140 (USA)

What If My Favorite Supplier Isn’t Listed Here?
Administrator

What If My Favorite Supplier Isn’t Listed Here?
Chapter 13: ChemACX-SC
What Is It? search and compare compounds.Using the database,
you can easily choose the most useful and
ChemACX-SC is designed to complement interesting compounds for screening.
ChemACX with structures from high-throughput
You can search ChemACX-SC by any of the
screening sample providers. ChemACX_SC is a
following:
collection of fully structure-searchable catalogs
from leading screening compound suppliers. • Chemical structure
ChemACX-SC is a read-only database. • Chemical substructure
• Compound name
ChemACX Screening
• Molecular formula
Compound Databases • CAS Registry Number
Directory: ChemACX_SC • Molecular weight range
Filenames: AcxSC2000Index.cfw, • Combinations of the above criteria
AcxSC2000Prod.cfw, AcxSC2000Supplier.cfw For information about searching, see the
Number of Suppliers: 15 ChemOffice WebServer User’s Guide
documentation.
Number of Compounds: >603, 000
ChemACX-SC has three linked forms:
Key Fields:
• Index form
• Structure
• Product form
• Formula
• Supplier form
• ACX Number
• SC Number
• Molecular Weight
• Supplier
• Catalog
How Is It Useful?
ChemACX-SC allows you to locate and order
compounds used for high-throughput screening
programs. The database provides consolidated
supplier data to enable you to quickly and easily
ChemOffice Chapter 13: ChemACX-SC • 187

What Is It?
If you want to search over the entire database for a To view information about the supplier of the
chemical, start with the Index form. chemical:
• Click Intro.
Administrator
The Supplier form appears.
To view product information: To display a list of products for the displayed

• On the Index form, click a product name. supplier:
The Product form appears. • Click Products.
The Products form appears.
To return to the Index form:

• Click Index.
188 • Chapter 13: ChemACX-SC CambridgeSoft

How Is It Useful?
ChemACX-SC
Participants
ChemACX-SC suppliers are listed below:
AsInEx BIONET Research Ltd. Butt Park Ltd ChemBridge

Corporation
ChemStar, Ltd. Contact Service Florida Center for G&J Research

Company -ReFine(TM) Heterocyclic Chemistry Chemicals Ltd
Collection
Maybridge Chemical Menai Organics Molecular Diversity OAK Samples Trading,

Company, Ltd. Limited Preservation Intl. Ltd.
Orion Research Ltd. Sherk Chemicals sas Sigma Aldrich Library

of Rare Chemicals
ChemOffice Chapter 13: ChemACX-SC • 189

ChemACX-SC Participants
Administrator
190 • Chapter 13: ChemACX-SC CambridgeSoft

ChemACX-SC Participants
Chapter 14:The Merck Index
What Is It? you directly to the relevent monographs without
your having to flip through a three-inch-thick book.
The Merck Index is a one-volume encyclopedia of Physical properties can be quired directly as well,
chemicals, drugs and biologicals that contains more and so can all of the other data fields. As with the
than 10,000 monographs. The entries are not a other ChemInfo databases, The Merck Index also
listing of Merck & Co., Inc. products, but rather allows searching by structure, substructure, and
cover a wide range of compounds that have been similarity, all of which are virtually impossible
selected by the editors on the basis of present or when using the printed edition alone.
historic importance and interest. Since the
All of the supplementary data present in the printed
publication of its Twelfth Edition in 1996, over
edition, including the Organic Name Reactions, is
5,000 monographs have been significantly revised
available in separate files on the CD-ROM also.
and updated. Each monograph is a concise
description of a single substance or a small group of Directory: The Merck Index CD-ROM
closely related compounds. The information Filenames: The Merck Index.cfw
provided includes chemical, common and generic
names, trademarks and their associated companies, Number of Compounds: 10,250
Chemical Abstracts Service (CAS) Registry
Numbers, molecular formulas and weights, physical
and toxicity data, therapeutic and commercial uses,
citations to the chemical, biomedical and patent
literature, and chemical structures.
How Is It Useful?
For more than 100 years, the printed edition of The
Merck Index has been the premier reference for
validated data about many compounds of general
interest. The subjects covered include human and
veterinary drugs, biologicals and natural products,
agricultural chemicals, industrial and laboratory
chemicals, and environmentally significant
compounds. The electronic version includes all of
the information in the printed edition, and enhances
it by allowing direct and rapid searching over all
data fields. Where the printed edition offers indexes
of names and CAS Registry Numbers, the electronic
version lets enter them as search terms, and takes
ChemOffice Chapter 14:The Merck Index • 191

What Is It?
Administrator
192 • Chapter 14:The Merck Index CambridgeSoft

How Is It Useful?
Chapter 15: ChemINDEX
What Is It? Key Fields:
• Structure
ChemINDEX is a class of chemical reference
databases composed of the BuckyBase, • Formula
ChemINDEX Net, and NCI databases. Its databases • ACX Number
are found in the ChemINDEX CD-ROM.
• SC Number
How Is It Useful? • Molecular Weight

• Supplier
This class of databases serves as an extensive
chemical reference for finding general information • Catalog
about commonly used compounds, such as • Name
structure, name, molecular weight, CAS Registry • Vapor Pressure
Number, synonyms, and physical data (melting
• Synonym
point, boiling point, vapor pressure, etc.).
ChemINDEX Net contains active hyperlinks to • CAS Registry Number
WWW sites with further information about the • Boiling Point
compounds.
• Melting Point
ChemINDEX Net • Site ID
We believe the WWW server at

www.chemfinder.com, to be the most heavily used
public-access chemical information site on the
Internet. ChemINDEX Net is the ChemFinder
database of small molecule information presented at
this site. Many of the individual compound records
also contain lists of hyperlinks (URLs) to other
WWW sites containing additional information
about the compound. To go to a site, click its link.
The default web browser on your system will be
activated and directed to the target URL.
Directory: IndexNet
Filename: Indexnet.cfw
Number of compounds: >78, 000
ChemOffice Chapter 15: ChemINDEX • 193

What Is It?
Each data field on this form is labeled. Melting To view any of the buckyballs or building blocks as
points and boiling points are presented as three a 3-dimensional model using Chem3D:
fields:
• Right-click the structure and select View
• If only a single value is available, it is placed in Model. Chem3D starts and displays the
Administrator
the first field. molecule.

• If a range is available, the low and high limits of
the range are placed in the first two fields.
• The third field is for a note, such as (dec) for
decomposes.
Synonyms and hyperlinks are displayed in the
subforms on the right side of the form. You must
have an internet connection to use the hyperlink
features. If you are connected to the internet, the GO
button at the upper right connects to
CambridgeSoft’s WWW server for this database.
Click the button or one of the hyperlinks, and
ChemInfo attempts to start your system’s default National Cancer
web browser and direct it to the appropriate URL. Institute
BuckyBase The National Cancer Institute (NCI) database is
provided with CambridgeSoft-generated 2-
The subfolder BUCKYBSE within ChemINDEX dimensional structures. Access to AIDS screening
contains two databases. BUCKBALL is a file of 132 results is provided for compounds for which they are
buckminsterfullerenes, and BUILDING is a file of available.
99 building blocks which can be joined together to
make new or existing buckminsterfullerenes. Directory: nci
Directories: buckybse, balls, buildingFilenames: Filenames: NCI2000.cfw, AIDSresults.cfw

Buckball.cfw, Building.cfw Number of compounds: >246,000
Number of compounds: 132 buckyballs; 99 Key Fields:
building blocks
• Structure
Key Fields:
• Formula
• Structure • Molecular Weight
• Formula • NSC NumberMolecular Weight
• Molecular Weight • CAS Number
• Name • Synonym
194 • Chapter 15: ChemINDEX CambridgeSoft

BuckyBase
A file containing definitions appears.
To return to the main database:
• Click Back.
To view the AIDS screening results for a compound:

• Click AIDS Results.
The AIDS Results form is displayed.
To view information about the screening

terminology used in the results:
• Click Screening_Explanations.
ChemOffice Chapter 15: ChemINDEX • 195

National Cancer Institute
Administrator
196 • Chapter 15: ChemINDEX CambridgeSoft

National Cancer Institute
Chapter 16: ChemRXN
What Is It? Key Fields:
• Structure (reaction)
ChemRXN is a class of databases of chemical
reactions which include literature citations, • Reaction Formula
products, reactants, solvent and catalyst data, yields, • Abstract
and reaction conditions. ChemRXN consists of
• Molecular Weight (components)
ChemPrep and ChemSelect.
• Atmosphere
How Is It Useful? • Reaction text
ChemRXN provides ready access to information • Time

useful in planning a chemical synthesis. A reaction • Key phrases
query can search for all reactions that: • Pressure
• Yield a particular product • Reflux
• Use a particular catalyst or solvent ChemPrep has a principal form or main screen,
• Consume a particular reactant Chemprep.cfw, and three associated forms:
• Have been published by a certain author • Reaction.cfw

For example, you can search for reactions which • Solvent.cfw
produce benzofurans in greater than 90% yield. • Catalyst.cfw
Reaction.cfw shows the reaction diagram in a larger
ChemPrep window. It is useful in case the reaction is
ChemPrep is a carefully prepared chemical reaction complicated or has large molecules or many
database from the Institute for Scientific components. Reaction.cfw is called from the main
Information (ISI). ISI is one of the largest and most screen by clicking the zoom Reaction button. The
reputable providers of scientific information, and “view Solvents” and “view Catalysts” buttons
has a number of scientific databases available provide larger views of the solvent (form
including exhaustive reaction and molecular Solvent.cfw) and catalyst (form Catalyst.cfw)
literature databases. molecules which appear in the scrolling lists on the
right of the main screen. Each of these associated
Directory: ChemPrep forms has a button to return to the main screen.
Filenames: Chemprep.cfw, Catalyst.cfw,
Reaction.cfw, Solvent.cfw
Number of Reactions: 16,761
ChemOffice Chapter 16: ChemRXN • 197

What Is It?
The reactions in ChemPrep were selected by ISI • Molecular Weight (components)
from their larger reaction databases and were • PageNumber
provided with full literature references. The reaction
centers and atomic transformation matrices were • Journal
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computed with ChemFinder. • Yield

• Reaction Text
• Pressure
• Reflux
• Literature text
• Author
• Type
• Title
• Language
• Volume
ChemSelect has a main form, ChemSelect.cfw, and
ChemSelect three associated forms:
• Reaction.cfw
ChemSelect is a collection of the most commonly
cited reactions from the literature, selected by • Solvent.cfw
InfoChem GmbH of Germany. The ChemSelect data • Catalyst.cfw
is taken from the VINITI project of the former
The associated forms show the data in a larger
Soviet Union, in which over 2 million chemical
window.
reactions were compiled. The 13,037 reactions of
ChemSelect were obtained using a defined To access Reaction.cfw:
statistical methodology which selects the most
• From the main screen, click Zoom Reaction.
representative reactions from the database. All
reactions contain full literature citations. To display larger views of Solvent.cfw and
Catalyst.cfw molecules:
Directory: ChemSelect
• Click Zoom Solvent(s) or Zoom Catalyst(s).
Filenames: ChemSelect.cfw, Catalyst.cfw,
To return to the main screen:
Reaction.cfw, Solvent.cfw
• Click Return or Return to main screen.
Number of reactions: 13,037
InfoChem is a major provider of scientific
Key Fields:
information, and has also created selections called
• Structure (reaction) ChemReact41 (41,000 reactions), ChemSynth
• Reaction Formula (100,000 reactions), and ChemReact (400,000
• Year
198 • Chapter 16: ChemRXN CambridgeSoft

ChemSelect
reactions). These will also be available as
ChemFinder databases. For further information,
contact CambridgeSoft or InfoChem GmbH.
Selection Criteria
For inclusion in ChemSelect, each reaction must
typify at least five different reactions. Two reactions
are considered to be of the same type if the reaction
centers and the groups around the reaction centers
are identical. Each reaction in ChemSelect has been
cited in at least five different journal articles, has a
yield of at least 50%, and has been published in a
generally available journal.
ChemOffice Chapter 16: ChemRXN • 199

ChemSelect
Administrator
200 • Chapter 16: ChemRXN CambridgeSoft

ChemSelect
Chapter 17: ChemMSDX
What Is It? Number of Compounds: 7,364
Key fields: Varies by form.
CS ChemMSDX is a collection of over 7,000
Material Safety Sheets presented on six linked
forms:
• Compound Information
• Transportation
• Health Hazards & First Aid
• Handling
• Manufacturer Information
• Spill Procedures
Each form has buttons linking it to the other forms.
The current form button is labeled with dimmed text
and the other buttons are labeled with bold text.
Every form has the same structure, name, and CAS
Number fields to identify the material, but the other
fields vary according to the type of form. We suggest
that you search using the compound information
form, Msdx.cfw shown below.
How Is It Useful?
ChemMSDX provides rapid access to
comprehensive health and safety information to aid
in the safe handling, storage, and transportation of
materials, and provides precautionary and
emergency medical information. Like other
ChemInfo databases, the ChemMSDX forms can be
searched by name, structure, CAS Number, and
other fields.
Directory: ChemMSDX
Filenames: handling.cfw, hazard.cfw,
manufact.cfw, Msdx.cfw, spill.cfw, transprt.cfw
ChemOffice Chapter 17: ChemMSDX • 201

What Is It?
Administrator
202 • Chapter 17: ChemMSDX CambridgeSoft

How Is It Useful?
Appendix A: Technical Support
support to all registered users of this software WWW:
through the World Wide Web (web), and through http://www.cambridgesoft.com/support/mail
Internet: support@cambridgesoft.com
Our Technical Support pages on the web contain Fax: 617 588-9360
access our Technical Support page using the ATTN: Technical Support
If you don’t find the answers you need on the web,
please complete the following tasks before Serial Numbers
contacting the Technical Support. When contacting Technical Support, you must
1. Check the Readme file for known limitations or always provide your serial number. This serial
conflicts. number was on the outside of the original
ChemOffice box, and is the number that you entered
2. Check the system requirements for the software when you launched ChemOffice for the first time. If
at the beginning of this User’s Guide. you have thrown away your box and lost your
3. Read the Troubleshooting section of this installation instructions, you can find the serial
appendix and follow the possible resolution number in the following way:
With ChemOffice launched, choose About CS
4. If all your attempts to resolve a problem fail, fill ChemOffice from the Help menu. The serial number
out a copy of the CS Software Problem Report appears at the bottom left of the about box.
Form at:
http://www.cambridgesoft.com/support/mail. For more information on obtaining serial numbers
and registration codes, see:
• Try to reproduce the problem before http//www.cambridgesoft.com/support/
contacting us. If you can reproduce the codes.cfm
problem, please record the exact steps that
you took to do so.
• Record the exact wording of any error
messages that appear.
• Record anything that you have tried to correct
the problem.
ChemDraw 7 Technical Support • 203

Troubleshooting System Crashes
This section describes steps you can take that affect ChemOffice should never crash, but below are the
the overall performance of ChemOffice, as well as steps you should go through to try to resolve issues
Administrator
steps to follow if your computer crashes when using that cause computer crashes while using a CS
a CS software product. software product.
1. Restart your computer (Macintosh) or restart

Launching
Windows and try to reproduce the problem. If
If ChemOffice can’t find the ChemOffice Items the problem recurs, continue with the following
folder, you are not able to launch the program. steps.
2. Take the steps appropriate for your system:
Performance
• Macintosh OS 8/ 9: Use your Extensions
Below are some ways you can optimize the
Manager control panel to restart your
performance of ChemOffice:
computer with MacOS base extensions on.
• (Macintosh): Increase the total amount of
If the problem no longer occurs, then you likely
memory that the application can use:
have an extension conflict. You should
• Select the ChemOffice application icon in determine which extension is causing the
the Finder when ChemOffice is not running. conflict, and then not have it load when using
• From the Edit menu, choose Get Info. ChemOffice. To isolate an extension, disable
Increase the memory allocation in the half of your extensions using the Extensions
Preferred size text box in the Memory Manager and test the problem again. Keep
Requirements section of the dialog box. disabling half of your extensions until you find
which extensions are causing the problem.
• (Windows) In the Performance tab in the
System control panel (Windows NT 4.0),
extensions are causing the problem.
allocate more processor time to ChemOffice.
• Windows: The most common conflicts for
• Install more physical RAM. The more you
have, the less ChemOffice will have to access
your hard disk to use Virtual Memory.
• Increase the Virtual Memory (VM). Virtual sure to determine what type and version of
memory extends RAM by allowing space on drivers you are using.
Video Driver related problems: If you are
ChemOffice, try restarting your computer in
physical RAM.
Safe Mode (VGA mode for WinNT users).
Change the VM as follows: See your Windows Help for restarting in Safe
• Macintosh OS 8/ 9: Memory control panel. Mode. If Safe (or VGA) mode helps, your
original video driver may need to be
• Windows 95/98 and Windows NT 4.0:
updated—contact the maker of the driver and
System control panel, Performance tab.
204 • Technical Support CambridgeSoft

Troubleshooting
have trouble contact us with the relevant
resulting problem.
resulting problem.
page on the WWW.
4. If the problem still occurs, use our contact form
at:
http://www.cambridgesoft.com/support/mail
and provide the details of the problem to
Technical Support.
ChemDraw 7 Technical Support • 205

Troubleshooting
Administrator
206 • Technical Support CambridgeSoft

Troubleshooting
Index
A Appendix of role definitions 167
Archiving collection items 63
Add-in, ChemSAR for Excel 21 Assay
Adding assigning a version 122
analytics data to records 147 creating for first time 121
batches to temporary table 143 creating new 121
ChemACX description information 121
Shopping cart 178 renaming 122
vendors list 177 term 117
compounds to temporary table 140
identifiers to records 146 B
new experiments 159
notebooks 152 BioAssay Manager
parameter type 161 Adding
people 154 rows to tier tables 129
projects 151 tier information 129
reagents to temporary table 142 Aggregate View
records to temporary table 140 choosing calculations 131
registration numbers 153 choosing data 131
result type 160 clearing dialog box 132
roles 158 defining 130
rows to tier tables 129 definition 117
salts 156 naming results column 131
sites 155 opening the dialog box 130
structure comments 154 seeing results 132
structures in ChemDraw for Excel 12 Assay
tier information 129 assigning a version 122
users 157 creating for first time 121
Aggregate View creating new 121
choosing calculations 131 definition 117
choosing data 131 description information 121
clearing dialog box 132 renaming 122
defining 130 Calculations document definition 117
naming results column 131 Changing
opening the dialog box 130 database directory path 137
seeing results 132 width of results columns 134
term 117 Choosing a database 119
AIDS Results, NCI database 193 Closing MS Excel 134
Analytics data 147 Creating Oracle scripts 137
ChemOffice Index • 207

Database tab Tier Two
definition 117 adding information 129
setting up assay model 127 adding rows to tier tables 129
Database, definition 117 common parameters 128
Administrator
Defining Aggregate View 130 definition 118

Description tab definition 117 graphing results 135
Field, definition 117 template table 129
Filter definition 118 viewing results 134
Getting started for the first time 118 Version
Graph tab definition 118 assigning 122
Graphing Tier Two results 135 definition 118
Importing information 138
from MS Excel 133 Viewing
spreadsheet template into MS Excel 133 Aggregate View results 132
Layout spreadsheet definition 118 Tier One results 134
Layout tab definition 118 Tier Two results 134
Loading from MS Excel 133 Browse Plates 35
Maximizing window 121 Browsing search results 45
MS Access Buckminsterfullerenes 192
choosing 119 BuckyBase 192
logging in 120 Buying chemicals 39
Opening
after first time 121 C
Aggregate View 130
for first time 118 Calculation, with ChemSAR for Excel 21
MS Excel 132 Calculations document, definition 117
Oracle CAS registry number 191
choosing 119 Catalog information for Purchasing for Excel 38
creating SQL scripts 137 Changing
logging in 120 chemical properties 81
Overview 117 database directory path, BioAssay Manager 137
Procedure document definition 118 enumerated values 100
Results tab definition 118 group information in E-Notebook Administra-
Spreadsheet template tor 95
adding a row 129 password for Chemical Registration 159
adding information 129 password for Documentation Manager 114
using 128 reaction properties 72
System requirements 118 section in E-Notebook 68
Terminology 117 spectrum information 79
Tier One spectrum properties 80
adding information 129 stoichiometry 74
adding rows to tier tables 129 user information in E-Notebook Administrator
common parameters 128 92
definition 118 width of results columns 134
template table 128 ChemACX 187

adding vendors list 177 a reagent 142
opening 175 clearing marked records 149
ordering chemicals 179 defining password 159
removing from shopping cart 179 deleting a record 145
saving search results 177 editing a record 145
searching 175 identifiers 146, 147
using 174 importing sdfiles 162
viewing search results 178 Log in 139
ChemACX-SC 187 Log off 166
ChemDraw 16 marking records 149
ChemDraw for Excel MatchDatabase 162
adding new experiments 159
structure files 12 notebooks 152
structures 12 opening 139
structures as SMILES 12 Overview 139
structures by name 13 parameter type 161
structures with ChemDraw 12 people 154
aligning structures 16 printing records 166
exporting 11 projects 151
Get ChemDraw List command 10 registering records 146
importing tables 10 registration numbers 153
naming molecules 15 result type 160
searching 13 reviewing a record 144
starting 9 role definitions 167
viewing structures 15 roles 158
ChemFinder for Word salts 156
closing 54 searching
customizing 52 records 148
customizing the window 52 temporary table 148
Find window 42 sites 155
Look In tab 44 structure comments 154
opening 41 temporary table 140
Overview 41 users 157
preferences 53 viewing
Search Options tab 50 BioAssay Manager data 148
Send To menu 48 details of records 148
settings 52 experiment spreadsheets 150
starting 41 marked records 149
Chemical file structure path in E-Notebook Admin- Chemical synthesis database 195
istrator 102 Chemicals database 187
Chemical properties in E-Notebook 81 ChemIndex 191
Chemical Registration ChemInfo 171
adding ChemMSDX 199
a batch 143 ChemOffice 171
a compound 140 ChemPrep 195, 196

ChemProp, using with ChemDraw for Excel 18 setting up assay model 127
ChemRXN 195 Database, BioAssay Manager term 117
ChemSAR for Excel Defining
configuring 21 Aggregate View 130
Administrator
descriptors 24 new experiments 159

overview 21 notebooks 152
statistics 25 parameter type 161
wizard 21 password 159
ChemSelect 196 people 154
Choosing a database for BioAssay Manager 119 projects 151
Clearing marked records 149 registration numbers 153
Closing result type 160
ChemFinder for Word 54 role definitions 167
MS Excel in BioAssay Manager 134 roles 158
Collection salts 156
archiving items 63 sites 155
browsing items 63 structure comments 154
creating 59 users 157
duplicating 61 Deleting records from temporary table 145
E-Notebook 55 Description tab definition 117
organizing 61 Descriptive Statistics 25
referencing items 62 Descriptors in ChemSAR for Excel 24
removing 60 Documentation Manager
renaming 60 managing users 115
Viewing properties 65 overview 105
Collection definitions, appendix 88 password 114
Commonly cited reactions 196 searching 106
Configuring ChemSAR for Excel 21 submitting documents 106
Conventions 7, 169 Duplicating collection 61
Correlation Matrix 26
Creating E
collection 59
notebook 59 Editing
Oracle scripts, BioAssay Manager 137 favorite vendors list 177
page 59 notebooks 152
page from template 60 parameter type 161
reactants in the E-Notebook database 77 projects 151
section 67 records 145
template 59 registration numbers 153
result type 160
D roles 158
salts 156
Data Source - Find Chemical Structures window 42 sites 155
Database tab structure comments 154
definition 117 users 157

E-Notebook removing a collection 60
appendix of collection definitions 88 renaming a collection 60
archiving collection items 63 searching 84
browsing collection items 63 Section, definition 56
changing Spectra section, definition 56
a section 68 spectrum information 79
chemical properties properties 81 Synthesis, definition 56
reaction properties 72 Table section, definition 56
spectrum properties 80 Template, definition 56
stoichiometry information 74 terminology 55
closing 87 therapeutic Area, definition 56
Collection, definition 55 viewing collection properties 65
creating E-Notebook Administrator
a collection 59 changing
a notebook 59 enumerated values 100
a page 59 group information 95
a page collection from a template 60 user information 92
a section 67 chemical file structure path 102
a template 59 configuring the database 103
reactants in the database 77 installation 89
database, definition 55 opening 91
duplicating a collection 61 overview 89
Experiment, definition 55 setting properties 96
exporting a section 70 Enumerated values 100
Group, definition 55 Excel, see ChemDraw for Excel, CombiChem, or
logging in 57 ChemSAR for Excel
MS Excel section 70 Experiment procedures in E-Notebook 76
MS Word section 69 Experiments
Notebook, definition 56 defining 159
opening 57 viewing spreadsheets 150
organizing 61 Exporting
overview 55 from ChemFinder for Word 48
Page, definition 56 from Purchasing for Excel 39
printing 86 in ChemDraw for Excel 11
Project, definition 56 section in E-Notebook 70
Property, definition 56
Reaction scheme, definition 56 F
Reaction section, definition 56
recording Field, BioAssay Manager term 117
experiment procedures 76 Files
reactions 71 dsd 47, 48
spectra 78 sdf 47
referencing collection items 62 selecting with Look In tab 44
refreshing 58 selecting with Open File menu 45
registering chemicals 84 Filter, BioAssay Manager term 118

Filtering tables 13 M
Form, see Query Input Form
Formula, searching by 44 Macintosh, system requirements for ChemOffice 8
Functions in ChemDraw for Excel 16 Managing users in Documentation Manager 115
Administrator
Marked records, viewing 149

G Marking records 149
MatchDatabase 162
Get ChemDraw for Excel List 10 Maximizing window, BioAssay Manager 121
Getting started for first time, BioAssay Manager Molecular weight, searching by 44
118 MS Access, BioAssay Manager
Graph tab definition 118 choosing 119
Graphing Tier Two results 135 logging in 120
Group in E-Notebook 55 MS Excel section in E-Notebook 70
MS Word section in E-Notebook 69
H MSDS database 199
Multi-User log in 57
Hit List results 45
N
I
National Cancer Institute database 192
Identifiers 146 New experiments, defining 159
Importing Notebook
from MS Excel to BioAssay Manager 133 Chemical Registration 152
sdfiles into Chemical Registration 162 creating 59
spreadsheet template into MS Excel from Bio- E-Notebook 56
Assay Manager 133
tables in ChemDraw for Excel 10 O
Index form
ChemACX 174 Online help 169
ChemACX-SC 188 Opening
IndexNet 191 BioAssay Manager
Input form, see Query Input Form after first time 121
Installation 8, 170 Aggregate View 130
Installing E-Notebook Administrator 89 for first time 118
MS Excel 132
L ChemACX 175
ChemCombi 27
Layout spreadsheet definition 118 ChemDraw for Excel 9
Layout tab definition 118 ChemFinder for Excel 27
Loading from MS Excel into BioAssay Manager ChemFinder for Word 41
133 ChemFinder worksheet in Purchasing for Excel
Log in, Chemical Registration 139 37
Log off, Chemical Registration 166 Chemical Registration 139
Look In tab 44 E-Notebook 57

E-Notebook Administrator 91 Projects, defining 151
Purchasing for Excel 37 Property in E-Notebook 56
Oracle, BioAssay Manager Purchasing chemicals 39
choosing 119 Purchasing for Excel
creating SQL scripts 137 buying chemicals 39
logging in 120 catalog information 38
Ordering chemicals 39 ChemFinder worksheet use 37
Ordering chemicals through ChemACX 179 chemical structures in worksheets 38
Organinzing a collection 61 exporting worksheet 39
Overview 27 opening 37
BioAssay Manager 117 ordering chemicals on ChemACX.com 39
Chemical Registration 139 overview 37
ChemInfo 169 printing worksheet 39
Documentation Manager 105 purchasing chemicals 39
E-Notebook 55 shopping for chemicals 38
E-Notebook Administrator 89 suppliers on ChemStore.com 38
Purchasing for Excel 37 VendorInfo worksheet 38
P Q
Page Query Input form
creating in E-Notebook 59 accessing 175
from an E-Notebook template 60 opening 175
Pages, definition 56
Parameter type, defining 161 R
People, defining 154
Permanent database RAM 8
adding analytics data 147 Reactants in the E-Notebook database 77
adding identifiers 146 Reaction properties in E-Notebook 72
clearing marked records 149 Reaction Scheme in E-Notebook 56
marking records 149 Reaction Section in E-Notebook 56
registering records 146 Reaction Template
searching 148 adding to workbook 28
viewing details of records 148 creating 28
Physiochemical properties, calculating 21 editing 29
Plates, browsing 35 overview 28
Preferences in ChemFinder for Word 53 Reactions recording in E-Notebook 71
Printing in E-Notebook 86 Reagent Lists 30
Printing records, Chemical Registration 166 Reagent sheet, viewing structures on 33
Procedure document definition 118 Reagents, assigning to block plates 34
Product form Record
ChemACX 174 buttons 46
ChemACX-SC 188 menu 46
Product Wells, assigning products to 34 toolbar 46
Project in E-Notebook 56 Recording reactions in E-Notebook 71

Referencing collection items 62 by selected files 44
Refining your search ChemACX 175
overview 50 ChemDraw for Excel 13
search options 50 Chemical Registration 148
Administrator
search tools 50 directory paths 48

Refreshing E-Notebook 58 Documentation Manager 106
Registering chemicals in E-Notebook 84 dsd files 48
Registering records in permanent database 146 E-Notebook 84
Registration numbers, defining 153 enter query 50
Removing collection 60 options 50
Removing orders from ChemACX shopping cart records in permanent database 148
179 records in the temporary table 148
Renaming collection 60 refining 50
Requirements restore previous query 50
Macintosh 8 save results 47
RAM 8 start 50
system 8, 170 tools 50
Windows 8 Section
Result type, defining 160 changing 68
Results tab definition 118 creating 67
Reviewing records 144 E-Notebook 56
Roles, defining 158, 167 exporting 70
Rune Plots 26 Sending to another application 48
Runsets Setting
creating 33 chemical file structure path 102
working with 34 properties in E-Notebook Administrator 96
Settings 52
S Shopping cart
removing entries 179
Salts, defining 156 saving to 177
Saving viewing 178
ChemACX search results 177 Shopping for chemicals 38
data sources 47 Similarity searching in ChemDraw for Excel 14
directory paths to search 48 Single-User log in 57
files 47 Sites, defining 155
search results 47 Spectra data in E-Notebook 78
structures in ChemDraw for Excel 13 Spectra Section in E-Notebook 56
to Shopping cart 177 Spectrum properties in E-Notebook 80
Search options 50 Spreadsheet template, BioAssay Manager
Search results 45 adding a row 129
Searching adding information 129
by chemical formula 43 using 128
by chemical structure 42 Starting ChemDraw for Excel 9, 27
by molecular weight 43 Stoichiometry in E-Notebook 74
by multiple properties 43 Structure comments, defining 154

Structure searching, in ChemDraw for Excel 13 searching 148
Submitting documents 106 Terminology 169
Substructure searching, in ChemDraw for Excel 13 BioAssay Manager 117
Supplier form ChemInfo 169
ChemACX 174 E-Notebook 55
ChemACX-SC 188 Therapeutic Area in E-Notebook 56
Suppliers Tier One, BioAssay Manager
adding to ChemACX 185 adding information 129
ChemACX 180 adding rows to tier tables 129
ChemACX-SC 189 common parameters 128
ChemStore.com 38 template table 128
Synthesis database 195 term 118
Synthesis in E-Notebook 56 Tier Two, BioAssay Manager
System requirements 8, 170 adding information 129
adding rows to tier tables 129
T common parameters 128
graphing results 135
Table Section in E-Notebook 56 template table 129
Tables term 118
new experiments 159 viewing results 134
notebooks 152 ToolTips 7, 170
parameter type 161 Troubleshooting 202
password 159
people 154 U
projects 151
registration numbers 153 Users, defining 157
result type 160 Using ChemACX shopping cart 177
roles 158
salts 156 V
sites 155
structure comments 154 VendorInfo worksheet 38
users 157 Version, BioAssay Manager
Technical support 201 assigning 122
Template term 118
creating 59 Viewing
E-Notebook 56 Aggregate View results 132
Temporary table BioAssay Manager data 148
adding ChemACX shopping cart 178
a batch 143 experiment spreadsheets 150
a compound 140 marked records 149
a reagent 142 records in permanent database 148
adding records 140 Tier One results 134
deleting a record 145 Tier Two results 134
editing a record 145 Viewing collection properties in E-Notebook 65
reviewing a record 144 Views in ChemDraw for Excel 15

W
Worksheet printing in Purchasing for Excel 39
Administrator

Handbook of Chem Office

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Contents

Introduction Using Documents .................................................... 12

Drawing Bonds ....................................................... 52 Specifying Line Spacing ...................................66

ChemDraw Contents • iii

Displaying the Color Palette ...........................114 Removing Atom Properties ............................132

Settings dialog or columns

Drawing File menu File menu,

Online Help ChemDraw for http://java.cambridgesoft.com/

To install ChemDraw, see the “Read Me First”

ChemDraw 7 Chapter 1: ChemDraw Basics • 5

Magnification Minimize Maximize

Status Bar Resize

The Macintosh OS 9 version of ChemDraw is shown below.

Menu Bar Magnification Control Zoom Collapse/Expand

6 • Chapter 1: ChemDraw Basics CambridgeSoft

Multiple Bonds Text Objects that are selected can be further

Hashed Bond Arrows

Cycloheptane Ring Cyclooctane Ring

Orbital Draw orbitals. Orbitals of different

Drawing Draw annotations that lack chemical

ChemDraw 7 Chapter 1: ChemDraw Basics • 7

Chemical Draw chemically significant symbols To dock a tool palette:

Rings Quickly draw common structural Setting the Default Tool

To show or hide a tools palette: To set the default tool:

8 • Chapter 1: ChemDraw Basics CambridgeSoft

The Status Bar or Message

A check mark appears next to the item when the

Docking and Undocking Toolbars

ChemDraw 7 Chapter 1: ChemDraw Basics • 9

• Apply settings to the entire current document

Default Style Sheet or Stationery Pad

10 • Chapter 1: ChemDraw Basics CambridgeSoft

2. Open the appropriate folder and select a

ChemDraw 7 Chapter 1: ChemDraw Basics • 11

If you want to apply the Then click …

selected object only No

selected object and any new Yes

The settings are applied.

Location Creating a Document

1. From the File menu, click Open Special.

12 • Chapter 1: ChemDraw Basics CambridgeSoft

Stationery Pads located in the ChemDraw Items

Setting the Default Open File Format Saving Changes Automatically

ChemDraw 7 Chapter 1: ChemDraw Basics • 13

1. Remove the rotation.

14 • Chapter 1: ChemDraw Basics CambridgeSoft

a Document The title of the document window changes to

ChemDraw 7 Chapter 1: ChemDraw Basics • 15

1. From the File menu, choose Save As.

NOTE: When you select some formats, the Options

16 • Chapter 1: ChemDraw Basics CambridgeSoft

The ChemDraw Items Folder

ChemDraw 7 Chapter 1: ChemDraw Basics • 17

In general, to print a ChemDraw document: If you are transferring information to another

18 • Chapter 1: ChemDraw Basics CambridgeSoft

To transfer ChemDraw pictures to another

For more information, see “Transferring PostScript

ChemDraw 7 Chapter 1: ChemDraw Basics • 19

20 • Chapter 1: ChemDraw Basics CambridgeSoft

Create a ChemDraw Document:

ChemDraw 7 Chapter 2: Tutorials • 21

document window and click.

2. Drag as shown below over the existing single

Add a second bond: