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 User’s Guide

CS ChemDraw 6.0
for Windows and Macintosh

CS ChemDraw is a stand alone application within

CS ChemOffice, an integrated suite including
CS Chem3D for molecular modeling and analysis,
CS ChemFinder for searching and information integration, and
CS ChemInfo for chemical and reference databases.

ChemDraw
Chemical Structure Drawing Standard
®
License Information

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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
At my company, we pass disks around all the
A
time. We all assume that this must be okay
since it was the company that purchased the
software in the first place.
Many employees don’t realize that corporations
are bound by the copyright laws, just like every-
one else. Such conduct exposes the company (and
possibly the persons involved) to liability for copyright
infringement. Consequently, more and more corporations concerned
about their liability have written policies against such “softlifting”. Em-
ployees may face disciplinary action if they make extra copies of the
company’s software for use at home or on additional computers within
the office. A good rule to remember is that there must be one autho-
Q
rized copy of a software product for every computer upon which it is
run.
A
Do the same rules apply to bulletin boards and
user groups? I always thought that the reason they
got together was to share software.
Yes. Bulletin boards and user groups are bound by the
copyright law just as individuals and corporations.
However, to the extent they offer shareware or public
domain software, this is a perfectly acceptable practice.
Similarly, some software companies offer bulletin boards and user
groups special demonstration versions of their products, which in
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
Q
to ensure that it is not used as a vehicle for unauthorized copying or
distribution.
A
What about schools and professional
training organizations?
The same copyright responsibilities that apply to
Q
individuals and corporations apply to schools
and professional training organizations. No one
is exempt from the copyright law.
A
I’ll bet most of the people who copy software
don’t even know that they’re breaking the law.
Because the software industry is relatively new, and be-
cause copying software is so easy, many people are either
unaware of the laws governing software use or choose to
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
excuse. If you are part of an organization, see what you can do to ini-
tiate a policy statement that everyone respects. Also, suggest that your
management consider conducting a software audit. Finally, as an indi-
vidual, help spread the word that the users should be “software legal.”
The SPA also offers a number of
other materials designed to help
you comply with the Federal
Copyright Law. These materials
include:
• SPA Software Management
Guide. This guide, available for $80,
contains SPA’s 8 point program for
maintaining copyright compliance, an
internal controls analysis and questionnaire,
a software audit guide, SPAudit, “It’s Just
Not Worth the Risk” video and other
educational materials.
• SPAudit (DOS and Macintosh). This Kit,
available free of charge, will audit hard disks
to inventory programs and summarize the
number and location of each application.
• “It’s Just Not Worth the Risk” video. This 12-
minute video, available for $10, has helped
over 20,000 organizations dramatize to their
employees the implications and conse-
quences of software piracy.
• “Don’t Copy that Floppy” video. This 9
minute rap video, available for $10, is
designed to educate students on the ethical
use of software.
• Other educational materials including,
“Software Use and the Law,” a brochure
detailing the copyright law and how software
should be used by educational institutions,
corporations and individuals; and several
posters to help emphasize the message that
unauthorized copying of software is illegal.
To order any of these materials, please send
your request to:
“SPA Anti-Piracy Materials”
Software Publishers Association
1730 M Street, NW, Suite 700, Washington,
D.C. 20036
(202) 452-1600
Special thanks to Aldus Corporation for their
contribution to this brochure. We urge you to
make as many copies as you would like in
order to help us spread the word that unautho-
rized copying of software is illegal.
Reprinted by CambridgeSoft Corporation with
permission from the Software Publishers
Association.
Contents
Introduction
About ChemDraw ..................................................... 1
About this User’s Guide............................................ 1
Conventions............................................................... 1
Terminology .............................................................. 1
Additional Information.............................................. 2
Quick Reference Card .........................................2
Windows Online Help ........................................2
Online Help .................................................... 2
ToolTips ......................................................... 2
Context-sensitive Help................................... 2
Macintosh Online Help .......................................2
Online Help .................................................... 2
Balloon Help .................................................. 2
CambridgeSoft Web Pages .................................3
Installation/System Requirements............................. 3
Windows Requirements ......................................3
Macintosh Requirements ....................................3
Chapter 1: ChemDraw Basics
Overview ................................................................... 5
Starting ChemDraw................................................... 5
Creating a Document................................................. 5
Creating a New Document............................. 5
Creating a Document Using a
Style Sheet or Stationery Pad......................... 5
Opening a Document................................................. 6
Switching Between Open Documents....................... 6
Saving a Document ................................................... 6
Saving a Document with a
Different Name or Location ................................7
Saving a Document in a Different File Format ...7
Closing a Document ............................................8
Discarding Recent Changes to a Document.............. 8
Viewing the Location of a
Document (Macintosh only)...................................... 8
Accessing Documents Quickly ................................. 8
The MRU List .....................................................8
The ChemDraw Folder (Macintosh) ...................9
The Windows Menu (Macintosh Only) ......... 9
The cd_items Directory (Windows) .................10
The Open Special Submenu (Windows)...... 10
The Window Menu (Windows) ........................10
ChemDraw
Changing the Default Directory (Windows) ........... 10
Printing .................................................................... 11
Setting Print Preferences ...................................11
Printing Background Color .......................... 11
Macintosh-only Print Preferences ................ 11
Optimize Pictures for High-Resolution
Non-PostScript Printing (Macintosh)........... 11
Include PostScript (Macintosh).................... 12
Include ChemDraw
Laser Prep (Macintosh) ................................ 12
Quitting or Exiting ................................................. 12
ChemDraw’s Graphical User Interface (GUI) ........ 13
The Tools Palette ..............................................15
Status Bar or Message Area ..............................16
m/e................................................................ 16
Toolbar (Windows) ...........................................16
Menus and Commands ......................................17
Using Dialog Boxes ..........................................18
Undoing Actions ..................................................... 19
Redoing Actions ...................................................... 19
Repeating Actions ................................................... 19
Customizing Your Environment ............................. 19
Preferences ........................................................19
Document Settings ............................................22
Drawing Settings ...............................................23
Text Settings ....................................................24
Macintosh..................................................... 24
Windows ...................................................... 25
Color Palette .....................................................25
Saving Customized Settings .............................26
Applying Settings From Other Documents .......26
Default Style Sheet or Stationery Pad ...............27
Scripts (Macintosh Only) ........................................ 27
Chapter 2: Tutorials
Overview ................................................................. 29
Tutorial 1: Reaction Schemes ................................. 29
Tutorial 2: Drawing an Intermediate ....................... 36
Tutorial 3: Using Rings ........................................... 40
Tutorial 4: Fischer Projections ................................ 45
Tutorial 5: Perspective Drawings ............................ 49
Tutorial 6: Newman Projections ............................. 53
Contents • i
 Chapter 3:
Drawing Chemical Structures
Overview ................................................................. 57
Drawing Bonds ....................................................... 57
Bond Tools .......................................................57
Contents
Drawing with Fixed Lengths ............................57
Drawing with Fixed Angles ..............................57
Drawing Unconstrained Bonds .........................58
Toggling Fixed Lengths and Fixed Angles ......58
Message Area ...................................................58
Dative Bonds and Wedged Bonds ....................58
Specifying Units ...............................................59
Adding a Bond by Clicking ..............................59
Adding Bonds by Dragging ..............................59
Changing the Highlight Box Size .....................59
Multiple Bonds .................................................60
Double Bonds .............................................. 60
Double Either Bonds.................................... 60
Triple Bonds ................................................ 60
Quadruple Bonds ......................................... 60
Ring Tools............................................................... 61
Drawing a Ring .................................................61
Drawing a Ring by Clicking .............................61
Drawing Cyclohexane Chair Rings ..................62
Drawing Resonance Delocalized Rings ...........62
Drawing Cyclopentadiene and
Benzene Rings ..................................................62
Drawing Acyclic Chains ......................................... 63
Drawing Chains ................................................63
Adding Chains ..................................................63
Changing Chain Direction ................................64
Changing the Chain Angle ...............................64
Bond Drawing Settings ........................................... 64
Changing the Line Width .................................64
Changing the Bold Width .................................64
Changing the Hash Spacing ..............................65
Changing the Bond Spacing .............................65
Editing Bonds.......................................................... 65
Changing Bond Types ......................................65
Changing Double Bonds ...................................65
Changing Orientation of Wedged
and Dative Bonds ..............................................66
Changing Alignment of Double Bonds ............66
Moving Atoms ..................................................66
Changing Bond Crossings ................................67
Adjusting Margin Width ...................................67
Changing the Bond Order .................................67
Automatic Error Checking ...................................... 68
ii • Contents
Automatic Drawing—Structures from
Chemical Names ..................................................... 68
Converting Names to Structures .......................69
Inserting Names ........................................... 69
Paste Special ................................................ 69
Converting Captions to Structures ....................69
Chapter 4:
Drawing Captions and Atom Labels
Creating Text........................................................... 71
Formatting Text....................................................... 71
Using the Format Dialog Box
(Windows Only)........................................... 71
Creating Captions.................................................... 72
Changing the Caption Width ............................72
Editing a Caption ..............................................73
Specifying Caption Label Text Format ............73
Specifying Caption Settings for
New Captions............................................... 73
Changing Caption Settings .......................... 74
Justifying Captions....................................... 74
Specifying Caption Line Spacing ................ 75
Adding Chemical Names ........................................ 75
Using HotKeys to Label Atoms .............................. 76
Method 1: Labeling the last atom drawn ..........76
Method 2: Labeling an atom by pointing .........76
Method 3: Labeling an atom with a
selection tool .....................................................77
Method 4: Labeling multiple atoms ..................77
Hard-Coded HotKeys .......................................77
Creating HotKeys .............................................77
Labeling Atoms with the Text Tool ........................ 78
Specifying the Margin Width ...........................79
Editing Atom Labels .........................................79
Deleting an Atom Label ....................................79
Specifying Atom Label Text Format ................79
Changing Default Settings ........................... 79
Setting Default Atom Label
Font, Size, and Style .................................... 79
Changing Text Label Settings...................... 80
Justifying Atom Labels .....................................81
Justifying Automatically.............................. 81
Setting Automatic Justification.................... 82
Justifying with Stacked Above ................... 82
Justifying Flush Left .................................... 82
Justifying Flush Right .................................. 82
Justifying Centered ...................................... 83
Specifying Atom Label Line Spacing ..................... 83
ChemDraw
Repeating an Atom Label........................................ 83
Typing Non-Roman Text ........................................ 84
Labeling Atoms With a Bond or Ring Tool............ 84
Using the Text Tool with the Lasso Tool................ 84
Creating a New Line and Closing Text Boxes ........ 85
Using Bitmap Fonts When Available (Macintosh) . 85
Creating Tables ....................................................... 85
Creating the First Row (column headings) .......85
Creating a New Row .........................................86
Adjusting Row or Column Spacing ..................86
Moving Around Within Tables .........................86
Inserting a New Row ........................................87
Chapter 5: Drawing
Orbitals and Chemical Symbols
Overview ................................................................. 89
The Orbital Tool...................................................... 89
s-orbitals ............................................................89
Sigma Orbitals ..................................................89
Single Lobe Orbitals .........................................90
p-orbitals ...........................................................90
Hybrid Orbitals .................................................90
d-orbitals ...........................................................91
dz2-orbitals .......................................................91
The Chemical Symbols Tool................................... 91
H-dot and H-dash ..............................................91
Lone Pair ...........................................................92
Radical ..............................................................92
Radical Cation and Radical Anion ....................92
Charge Symbols ................................................93
Stereochemical Symbols ...................................93
Free Sites ...........................................................93
Rotating a Symbol ............................................94
Chapter 6: Drawing
Arrows, Arcs, and Other Shapes
Overview ................................................................. 95
Selecting Tools from the Palette ............................. 95
The Arrow Tool....................................................... 95
Selecting an Arrow ...........................................95
Drawing an Arrow ............................................96
Editing an Arrow ..............................................96
The Drawing Elements Tool ................................... 96
Selecting a Drawing Element ...........................96
Drawing Boxes .................................................97
Drawing Circles and Ovals ...............................97
Drawing Brackets .............................................97
ChemDraw
Single Brackets ............................................ 97
Drawing Paired Brackets ............................. 97
Drawing Lines ...................................................97
Drawing Daggers ..............................................98
Resizing or Rotating Drawing Elements ...........98
Distorting Circle and Ovals ..............................98
The Arc Tool ........................................................... 98
Drawing Arcs ....................................................98
Editing Arcs ......................................................99
The Pen Tool ........................................................... 99
Drawing Bézier Curves by Dragging ................99
Drawing Segments by Clicking ......................100
Editing a Curve ...............................................100
Changing the Shape of a Curve.................. 101
Adding a Segment ...................................... 101
Deleting a Segment .................................... 101
Applying a Style to a Shape ............................101
Filled and Closed Styles............................. 102
Shaded Style............................................... 102
Plain Style .................................................. 102
Chapter 7: Manipulating Drawings
Overview ............................................................... 103
Using a Selection Tool .......................................... 103
Selecting Objects with the Lasso Tool ............103
Selecting Objects with the Marquee Tool .......103
Toggling Between Selection Tools .................104
Toggling Between Other Tools .......................104
Selecting Objects by Clicking .........................104
Setting the Highlight Box Tolerance ..............104
Selecting Entire Structures ..............................104
Making Multiple Selections ............................105
Removing Objects from the Selection ............105
Selecting All Objects ......................................105
Deselecting All Objects ..................................105
Deleting Objects ..............................................105
Moving Objects ...............................................106
Using the Clipboard ........................................106
Cutting........................................................ 106
Pasting........................................................ 106
Moving Atoms ................................................107
Duplicating Objects ........................................107
Rotating Objects .................................................... 108
Reflecting Objects Through Planes....................... 108
Flipping Objects ......................................... 109
Creating Mirror Images.............................. 109
Resizing Objects.................................................... 109
The Resize Handle ..........................................109
Scaling Objects ...............................................110
Distorting a Selection ......................................110
Contents • iii
 Joining Objects...................................................... 111
Setting the Maximum Distance Tolerance .....111
Grouping Objects ............................................111
Ungrouping Objects ........................................112
Chapter 8:
Contents
Advanced Drawing Techniques
Overview ............................................................... 113
Using Nicknames .................................................. 113
Applying Nicknames ......................................113
Defining Nicknames .......................................114
Troubleshooting Nicknames ...........................115
Viewing Nicknames .......................................116
Deleting Nicknames .......................................116
Contracting Labels ................................................ 116
Expanding Labels.................................................. 117
Using Multi-Center Bonds .................................... 117
Creating a Multi-Center Bond ........................117
Viewing Attachment Points ............................118
Multi-Attached labels............................................ 119
Adding Bonds to an Atom Label ....................119
Using Clean Up Structure ..................................... 119
Using Variable Attachment Positions ................... 120
Working with Color .............................................. 121
Color Menu .....................................................122
Coloring Objects .............................................122
Coloring Text ..................................................122
Changing the Color Palette .............................123
Windows Color Settings ............................ 123
Adding or Customizing Colors .................. 124
Macintosh Color Settings........................... 124
Adding or Customizing Macintosh Colors 125
Removing Colors ....................................... 125
Templates and Color .......................................125
Saving Color Palette Settings .........................125
Chapter 9: Working With Structures
Overview ............................................................... 127
Checking Chemistry.............................................. 127
Check Structure ..............................................127
Check Structure when Copying to Clipboard or Ex-
porting .............................................................128
Analyzing a Structure............................................ 128
Analysis Information ......................................128
Viewing Analysis Information .......................128
iv • Contents
Atom-to-Atom Mapping ....................................... 129
Always Display and Print Atom Mapping ......129
Automatic Mapping ........................................130
Manual Mapping .............................................130
Clearing Reaction Mapping ............................131
Exporting Reaction Mapping ..........................131
Showing Stereochemistry...................................... 131
Spectrum-Structure Assignments.......................... 132
Assigning Structures to Spectra ......................132
Viewing Spectral Assignments .......................132
Removing Spectral Assignments ....................132
Chemical Property Information............................. 133
Calculating Properties .....................................133
Changing the Calculation Method (Windows only)
134
NMR Shift Information—ChemNMR Pro........... 134
Chapter 10:
Drawing Query Structures
What Are Query Structures? ................................. 137
Atom Properties .................................................... 137
Viewing Atom Property Values ......................138
Removing Atom Properties ............................139
Atom Property Options ...................................139
Substituents ................................................ 139
Implicit Hydrogens .................................... 140
Ring Bond Count ............................................140
Unsaturation ....................................................140
Reaction Change .............................................141
Reaction Stereo ...............................................141
Translation ......................................................141
Abnormal Valence ..........................................142
Bond Properties..................................................... 142
Viewing Bond Property Values ......................143
Removing Bond Properties .............................143
Bond Property Options ...................................143
Bond Types ................................................ 143
Topology .................................................... 144
Reaction Center.......................................... 144
Generic Nicknames ............................................... 145
Element Lists......................................................... 146
Element Not-Lists ................................................. 147
Alternative Groups ................................................ 147
Defining an Alternative Group .......................148
Defining Attachment Points ...........................148
Multiple Attachment Points ............................149
Showing Attachment Rank Indicators ............149
Attachment Point Numbering .........................150
Anonymous Alternative Groups ........................... 150
Export Compatibility............................................. 151
ChemDraw
Chapter 11:
Drawing With Templates
Overview ............................................................... 155
The Templates Tool .............................................. 155
Choosing a Template............................................. 155
Using Templates.................................................... 156
Drawing a Template ........................................156
Fusing a Template With An Existing Structure 156
Drawing with the Same Template ..................156
Creating Templates and Template Documents ..... 156
Creating Templates .........................................157
Orientation of Templates ................................157
Resizing Template Panes ................................158
Template Panels ..............................................158
Saving Template Documents ..........................158
Chapter 12:
Working with Page Layout
Overview ............................................................... 159
Controlling the Drawing Area............................... 159
Page Setup .......................................................159
Page Orientation .............................................160
Margins ...........................................................160
Reduce or Enlarge ...........................................160
Saving Page Setup Settings .............................161
35mm Slide Boundary Guides .............................. 161
Multiple-Paged Documents................................... 161
Paged Document Setup ...................................161
Poster Documents Setup .................................162
Creating Headers and Footers .........................162
Changing Perspectives .......................................... 163
Magnifying with the Tools Menu ..................163
Magnify ...................................................... 163
Actual Size ................................................. 163
Reduce........................................................ 163
Show Page.................................................. 164
Using the Magnification Control ............... 164
Arranging Objects ................................................. 164
Using Rulers ...................................................164
Showing Rulers ...............................................164
Hiding Rulers ..................................................165
Using the Crosshair .........................................165
Displaying the Crosshair .................................165
Moving the Crosshair ......................................165
Aligning Objects using the Crosshair .............166
Hide Crosshair ................................................166
Centering on a Page ........................................166
ChemDraw
Aligning Objects .............................................166
Distributing Objects ........................................167
Front to Back Ordering ...................................167
Picture Layers ............................................ 167
Send to Back .............................................. 168
Bring to Front............................................. 168
Chapter 13: Sharing Information
Overview ............................................................... 169
Transferring Between ChemDraw Documents ..... 169
Using the Clipboard ........................................169
Copying ...................................................... 169
Cutting........................................................ 169
Pasting........................................................ 169
Using the Drag-and-Drop Feature ..................170
Autoscaling .....................................................170
Bonds ..............................................................171
Atom Labels ....................................................171
Captions ..........................................................171
Non-bond Objects and Color ..........................171
Pasting to an Empty Document Window ........172
Transferring ChemDraw Documents Across Platforms
172
Transferring from Macintosh to Windows .....172
Transferring from Windows to Macintosh .....173
Transferring Files to ChemDraw/Plus 3.1 for the
Macintosh................................................... 173
Embedding Objects ............................................... 173
OLE (Windows Only) .....................................174
Transferring PostScript
(Macintosh Only) ............................................174
Publishers, Subscribers, and Editions (Macintosh
only) ................................................................175
Creating a Publisher ................................... 175
Subscribing to an Edition File.................... 176
Publisher Options ....................................... 176
Publisher to ................................................ 176
Send Editions ............................................. 177
Updating Automatically ............................. 177
Updating Manually .................................... 177
Cancel Publisher ........................................ 177
Subscriber Options ..................................... 177
Subscriber to .............................................. 177
Get Editions................................................ 177
Open Publisher ........................................... 178
Cancel Subscriber ...................................... 178
The Edition File ......................................... 178
Open Publisher ........................................... 178
Contents • v
 Importing and Exporting....................................... 178 Appendix A:
Exporting Using the Clipboard .......................179 The Chemistry of ChemDraw
SMILES and SMIRKS Strings .......................179
Creating SMILES Strings .......................... 179 Appendix B: Specifying Paths
Pasting SMILES from Clipboard............... 180
Creating SLN Strings................................. 180 Appendix C: Technical Support
Contents

Exporting and Importing Using File Formats ....... 180

Bitmap (.bmp) Export Only ............................181 Appendix D: Document Settings
ChemDraw Template (*.ctp, *.ctr) .................181
ChemDraw (*.cdx) .........................................181 Appendix E: Automation
ChemDraw XML (*.xml) ...............................181
ChemDraw 3.5 (*.chm) ..................................181 Appendix F: How ChemNMR Pro
ChemDraw 2.0 and ChemDraw 2.1 (*.chm) ..182 Works
ChemDraw Stationery/Style Sheet (*.cds) .....182
Connection Table (*.ct) ..................................182 Appendix G: How ChemProp Works
DARC-F1 Format (*.f1d) ...............................182
DARC-F1 Query (*.f1q) .................................182 Index
Encapsulated PostScript (Text) (Macintosh)
PostScript, *.eps (Windows) Export only ......182
Encapsulated PostScript (Mac) (Macintosh) and
PostScript with Preview (Windows) ...............182
GIF Image (*.gif) Export only ........................183
ISIS/SKC and ISIS/TGF .................................183
ISIS/Reactions (*.rxn) ....................................183
JDX (*.jdx, *.dx) Import only ........................184
MDL MolFile (*.mol) .....................................184
Molecular Simulations MolFile (*.msm) .......184
PICT (Macintosh) ...........................................185
PICT scaled 4X (Macintosh) ..........................185
PNG file (*.png) Export only .........................185
SMD (*.smd) ..................................................185
SPC (.*spc) Import only .................................185
Template Style Sheet (*.cts) ...........................185
Windows Metafile (Windows Only) (*.wmf) 185
TIFF file (*.tif) Export only ...........................185
Resolution ................................................. 186
Color .......................................................... 186
Compression .............................................. 186
Setting TIFF options .................................. 186

vi • Contents ChemDraw
Introduction
About ChemDraw
ChemDraw is a tool to enable professional
scientists, science students, and scientific authors to
communicate chemical structures. It is designed to
work according to conventions we found most
intuitive for such users. Our goal has been to make
ChemDraw as easy to use as possible while
providing superior drawing quality.
About this User’s Guide
This user’s guide contains information for the
Windows and Macintosh platforms. Illustrations are
taken from both platforms, so they may differ from
what you see on your screen.
This guide assumes you are familiar with your
computer’s operating system. For details about
using your operating system, refer to the user
documentation provided with that system.
Conventions
The following notations are used throughout this
User’s Guide:
The Ultra symbol indicates that
ChemDraw feature is available in CS ChemDraw
Ultra only.
The Pro symbol indicates that a feature is
available in CS ChemDraw Pro. Features available
in CS ChemDraw Pro are also included in CS
ChemDraw Ultra.
Features that are available in CS ChemDraw Std are
not indicated by a symbol.
NOTE: Notes such as this are used to highlight
information supplemental to the main text.
ChemDraw
Terminology
The following terminology is used throughout this
User’s Guide:
Point—Move the mouse until the pointer is
over the item you want.
Click—Press and release the mouse button. In
Windows, this refers to the left mouse button.
Double-click—Click the mouse twice in rapid
succession.
Drag—Hold down the mouse button, move the
mouse, and release the mouse button.
Select—Highlight an object or choose an
option. Selecting something does not initiate an
action, it marks the item upon which you want
to act. Deselect is the opposite of select.
Choose—Select a command from a menu or
submenu, or click a Toolbar button, or click a
button in a dialog box that completes or cancels
a command. 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 specified key and
drag a selection. For example, Shift+drag
means to hold down the Shift key and drag the
pointer.
Introduction • 1
 Right-click—
• Windows: Press and release the right mouse
button.
Administrator
• Macintosh: Hold the Control key while
pressing the mouse button.
NOTE: Right-clicking an object or area
displays a shortcut menu with options
pertaining to the object or area.
Additional Information
Additional ChemDraw information is available in
the following formats:
• A Quick Reference Card.
• Online Help. The type of online Help available
depends on the platform you are using.
• CambridgeSoft Web Pages.
Quick Reference Card
The ChemDraw Quick Reference Card is located in
the back of the manual. The card provides
summaries of ChemDraw commands and features.
Use the Quick Reference Card as you perform the
tutorials in “Chapter 2: Getting Started Tutorials”
because the card contains information about the
elements of the interface.
Windows Online Help
The Windows platform provides the following types
of online information:
• Online Help—An online version of this guide.
• Context-sensitive Help—Displays Help topics
related to user interface objects.
• ToolTips—Displays a short description of user
interface objects.
2 • Introduction
Online Help
To access the online Help:
• From the Help Menu, choose Contents.
A web browser is required to view the Help.
You can use Internet Explorer version 4.0 or
greater or Netscape Navigator version 4.0 or
greater.
ToolTips
To access ToolTips:
• Point at an item in the Tool bar, or Tool palette.
A description of the item appears.
Context-sensitive Help
To access context-sensitive help:
1. Press Shift+F1.
2. Click any menu item or tool.
Information about the selected item appears.
Macintosh Online Help
The Macintosh platform provides the following
types of online information:
• Online Help—An online version of this guide.
A web browser is required to view the Help.
You can use Internet Explorer version 4.0 or
greater or Netscape Navigator version 4.0 or
greater.
• Balloon Help—Displays a short description of
user interface objects.
Online Help
To access online Help:
• From the Help Menu, choose CS ChemDraw
Help.
Balloon Help
To access Balloon Help:
• From the Help menu, choose Show Balloons.
ChemDraw
CambridgeSoft Web Pages Installation/System
The following table contains the URLs of web pages
related to ChemDraw.
Requirements
To install ChemDraw, see the “Read Me First”
For information Access … document that came with your software. Late
about …
breaking information about installation is contained
in the Read Me file (Macintosh) or Install.txt
Technical Support http://www.camsoft.com/
support/ (Windows) on your installation disk or CD-ROM.

Windows Requirements
ChemDraw Plugin http://doc.camsoft.com/
Windows 95, 98, or NT 4.0:
ChemDraw for http://java.camsoft.com/
• System: Pentium processor, 32 MB RAM
Java
(64 MB recommended)
• Disk Space:
Software http://sdk.camsoft.com/
Developer’s kit • Std: 30 MB
• Pro: 40 MB
Active X control http://sdk.camsoft.com/
• Ultra: 70 MB

Purchasing http://store.camsoft.com/ Macintosh Requirements

CambridgeSoft
products and MacOS 8.1 or later
chemicals
• System: PowerPC, G3, or compatible, 32 MB
RAM (64 MB recommended)
• Disk Space:
• Std: 8 MB
• Pro: 32 MB
• Ultra: 55 MB

ChemDraw Introduction • 3
Administrator

4 • Introduction ChemDraw
Chapter 1: ChemDraw Basics
Overview
The information required to begin using ChemDraw
includes how to do the following:
• Start ChemDraw
• Create, open, and save documents
• Identify the parts of the ChemDraw interface
• Set printing preferences
• Customize parts of the user environment
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.
Windows 95, 98, or NT:
• From the desktop, double-click the ChemDraw
application icon
• From the Start menu, choose ChemDraw.
ChemDraw opens and a new document is
created.
Creating a Document
You can create a new, blank document using the
ChemDraw default settings, or use a Style Sheet
(Windows) or Stationery pad (Macintosh) with
customized settings.
ChemDraw
Creating a New Document
To create a document:
• From the File menu, click New Document.
Creating a Document Using a Style
Sheet or Stationery Pad
To create a new document using a different Style
Sheet (Windows):
1. From the File menu, click Open Special.
2. Choose a Style Sheet from the list.
A new document is created with the settings
(and objects) stored in the Style Sheet.
To create a new document using a Stationery Pad
(Macintosh):
• From the Windows menu, choose a stationery
document.
A new document is created with the settings
(and objects) stored in the Stationery Pad.
ChemDraw provides pre-defined Style Sheets and
Stationery Pads located in the cd_items directory
(Windows) or the ChemDraw Folder (Macintosh).
For example, the ACS-1996 document is configured
to create documents that are set with the bond
lengths, bond width, spacing, and fonts used in the
2-column format within the Journal of the American
Chemical Society. For a list of the settings stored in
these documents, see “Appendix D: Document
Settings”.
Chapter 1: ChemDraw Basics • 5
 Opening a Document
To open a recently used document:
• From the File menu, choose the document form
Administrator
the list at the bottom of the menu.
For more information, see “The MRU List” on
page 8.
To open other ChemDraw document:
1. From the File menu, choose Open.
The Open dialog box appears. The Windows
version is shown below.
2. Select the location where the file is stored.
3. To open a non-ChemDraw file, choose the file
format from the list at the bottom of the dialog
box. For more information, see “Exporting and
Importing Using File Formats” on page 180.
4. Select the file name.
5. Click Open or OK.
6 • Chapter 1: ChemDraw Basics
Switching Between
Open Documents
Each time you open a document, a document
window appears. If you have opened more than one
document, the document windows are stacked. The
top document is the active window where you can
do work. The Window menu (Windows) or
Windows menu (Macintosh) lists the open
documents.
To set an open document as the active window, do
any one of the following:
• From the Window or Windows menu, choose
the document.
• Click any exposed area of the window you want
to be the active window.
• In Windows only, press Ctrl+Tab to switch
between the open windows.
Saving a Document
To save a ChemDraw document in the default
ChemDraw cdx file format:
1. From the File menu, choose Save As.
The Save As dialog box appears. The
appearance of the dialog box depends on the
platform you are using.
NOTE: The Macintosh version includes a Go To
ChemDraw Folder button. For more information,
see “The ChemDraw Folder (Macintosh)” on page
9.
2. Choose a folder in which to store the file.
ChemDraw
 3. Type a file name in the File name (Windows) or
Save As (Macintosh) text box.
MacOS 9 allows you to type up to 255
characters for a file name, including spaces. For
example: “my first structure in ChemDraw”.
The Windows operating system allows you to
type up to 255 characters for a file name,
including the entire path of directories in which
the file is stored.
4. Click Save or OK to create the file.
The title of the document window changes to
name of the saved file. The file is added to the
MRU list.
NOTE: ChemDraw uses the *.cdx file format to
accurately store chemical information with a
structure drawing. Other file formats may be
capable of storing a picture of your drawing, but
they might lose chemically relevant information
about the structure. For example, if you save a
ChemDraw drawing in the .eps file format, you will
store only a picture of the structure without storing
the chemical significance of the connections
between atoms and bonds.
To save a document that has previously been saved:
• From the File menu, choose Save.
The contents of the file are updated to reflect the
information currently in the window without
displaying the Save As dialog box.
Saving a Document with a
Different Name or Location
You can save a copy of your document under a
different name, location, or file format. Saving a
copy under a different name or location is useful for
keeping earlier revisions of your document. Saving
a file as a different format is useful for creating Style
Sheets or Stationery Pads and for exporting
information to other applications.
ChemDraw
To save a copy of a ChemDraw document under a
different name or in a different location:
1. From the File menu, choose Save As.
2. Choose a new location in which to save the
document.
3. Type a new file name.
4. Click Save or OK.
Saving a Document in a
Different File 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 the TIFF or EPS file
formats, the Options button appears. Click it to open
a dialog box for setting color resolution and
compression options. For more information about
TIFF and EPS options, see “Chapter 13: Sharing
Information”.
5. Click Save or OK.
If you type a name that already exists in the same
directory, the existing document is replaced. If you
do not want to replace the original ChemDraw
document, use a different name. For information
about other file formats, see “Chapter 13: Sharing
Information”.
The original document in the ChemDraw format is
the active window. The document in the other
format is saved with the name and in the location
you specified.
Chapter 1: ChemDraw Basics • 7
 Closing a Document
To close a ChemDraw document:
• From the File menu, choose Close.
Administrator
If the document contains unsaved information, you
are prompted to save the file.
Discarding Recent
Changes to a Document
To retrieve the last saved version of a file:
• From the File menu, choose Revert.
All changes made to the file since it was saved
last are discarded and the previous version of
the file appears.
NOTE: You can use the Undo command in the Edit
menu to remove each individual action since the last
save.
Viewing the Location of
a Document (Macintosh
only)
To view the folders where the document in the front
window is located:
1. Point to the document name in the title bar.
2. Hold Command down and click.
8 • Chapter 1: ChemDraw Basics
A menu appears describing the location of the
document.
The second item from the top in the list is the name
of the folder (or the disk if there are no folders) that
contains the document. The last item in the list is the
name of the disk that contains the document.
The example menu tells us that the document named
“Glucose” is within a folder named “John’s Stuff,”
which is the innermost of five nested folders on the
drive named “Borodin.”
Accessing Documents
Quickly
You can quickly access ChemDraw documents
using the following features:
• MRU list
• ChemDraw Folder (Macintosh)
• cd_items directory (Windows)
The MRU List
You can quickly access the last six previously
opened documents by using the File menu. When
files are opened or saved they are added the most
recently-used (MRU) list. As new items are added,
they appear at the top of the list. The most
recently-used documents appear at the bottom of
the file menu as shown in the following illustration.
ChemDraw

Most recently
used documents
To access files from the MRU:
• Click the File menu and select the document.
The selected file opens. If the file is already
open, the window is activated.
The ChemDraw Folder
(Macintosh)
The ChemDraw Folder is a special folder found 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
elements ChemDraw uses), and the generic
nicknames file. In ChemDraw Pro, it also contains
Template documents and Template Stationery Pads.
NOTE: You can place aliases of template files or
Stationery Pads in the ChemDraw Folder. The
originals can come from another folder on your
computer or another computer on your network. You
can then access the alias from the Windows menu.
ChemDraw
The Windows Menu (Macintosh Only)
The Windows menu contains three groups of
documents, as shown below:
• Currently open documents
• Template Stationery Pads
• ChemDraw and Template Documents
Open documents
Stationery Pads
ChemDraw and
Template
Documents
NOTE: The Stationery Pads only appear
in ChemDraw Pro.
Documents within each of the three segments of the
Windows menu appear alphabetically. The first
segment contains documents that are currently open,
both ChemDraw documents and Template
documents. The open document that is the active
window has a check mark next to it.
The second segment lists all Stationery Pads
contained within the ChemDraw Folder, both
ChemDraw stationery, and Template Stationery
Pads.
Chapter 1: ChemDraw Basics • 9
 The third segment lists any other ChemDraw The Window Menu (Windows)
documents or Template documents contained within
The Window menu lists all open ChemDraw
the ChemDraw Folder. The icons for each of the
document types are slightly different. documents and open Template documents. The
Administrator

Window menu contains other standard Windows

The cd_items Directory commands for organizing your document windows
and icons within the Application window, such as
(Windows) tiling and cascading. The document you choose
The cd_items directory is usually located in the from the Windows menu becomes the active
same directory as the ChemDraw application. window.
However, it can also be located within the System
directory within the Windows directory. To change Changing the Default
the path to the cd_items folder, see “Appendix B:
Specifying Paths”. Directory (Windows)
When you choose to open or save a file, ChemDraw
The Open Special Submenu
automatically displays the directory that contains
(Windows) the ChemDraw application in the Open or Save
To select documents from the cd_items directory: dialog box. You can change the default directory by
• On the File menu, point to Open Special, and modifying the ChemDraw icon.
select the file to open. To change the default directory:
The Open Special submenu, listing documents
1. Right-click the ChemDraw application icon in
that you commonly use, appears as follows:
the Windows Explorer.
2. From the File menu, choose Create Shortcut.
3. Select the Shortcut to ChemDraw icon.
4. Press Alt+Enter.
Style Sheets
5. Click the Shortcut tab.
6. Enter the desired default directory in the Start
In field.
7. Click OK.
ChemDraw and
Template You can now use this modified icon or shortcut
Documents to launch ChemDraw.

10 • Chapter 1: ChemDraw Basics ChemDraw

Printing
ChemDraw uses the standard system commands to
print ChemDraw documents. The options that you
have available to you depend on the printer that you
are using. Refer to your printer’s documentation for
more information.
In general, to print a ChemDraw document:
1. From the File menu, choose Page Setup.
2. Make all appropriate selections for the printer
you are using and click OK.
3. From the File menu, choose Print.
4. Make your selections in the Print dialog box
and click OK.
To print a document from the File Manager or from
the Finder:
1. Select the document you want to print.
2. From the File menu, choose Print.
The ChemDraw application is opened and the
Print dialog box appears.
3. Make your selections in the Print dialog box
and click OK.
Setting Print Preferences
The Print Preferences dialog box contains settings
that affect how your ChemDraw document is
printed. Changing these settings affects all
documents.
Printing Background Color
Print Background Color controls whether the
Background Color contained in your ChemDraw
document is printed.
To change whether the Background color is printed:
1. From the File menu, choose Preferences.
2. Click Print Background Color.
3. Click OK.
ChemDraw
Macintosh-only Print Preferences
When you print a document, ChemDraw creates
both a QuickDraw representation and a PostScript
representation of the document’s contents.
QuickDraw is the graphical format that is supported
by the Macintosh Operating System. Every printer
that supports the MacOS can convert QuickDraw
representations into printed output. However,
QuickDraw does not support some features (for
example, high-resolution printing) that are available
only on some printers.
If you are transferring information to another
application from which you print ChemDraw
pictures, you should consider including PostScript
commands and the ChemDraw LaserPrep File with
the pictures. To learn about special situations to
consider, see “Transferring PostScript (Macintosh
Only)” on page 174.
Optimize Pictures for High-Resolution
Non-PostScript Printing (Macintosh)
The Macintosh High Resolution Clipboard supports
high-resolution printers. Although ChemDraw
supports the use of this High-Resolution Clipboard,
it also needs to be supported in the program into
which you are pasting your pictures. Some other
applications that support the High Resolution
Clipboard include PageMaker, MacDraw,
KaleidaGraph, and IGOR Pro. Microsoft Word,
through version 98, is an example of a program that
does not support the High-Resolution Clipboard.
If you are unsure if the application uses a High
Resolution Clipboard, try transferring pictures with
this check box selected and deselected, and see
which picture prints with higher quality.
Chapter 1: ChemDraw Basics • 11
 To use the High Resolution Clipboard:
1. From the File menu, choose Preferences.
2. Select Optimize Pictures for High-Resolution
Administrator
Non-PostScript Printing.
3. Click OK.
If you are printing to a PostScript printer, select
Include PostScript instead. PostScript always
offers the highest-quality output. For more
information, see “Transferring PostScript
(Macintosh Only)” on page 174.
If you are printing to a non-PostScript printer,
deselect Include ChemDraw LaserPrep and
Include PostScript to reduce the size of each
picture. Do not deselect this option if the
document will ever be printed to a PostScript
printer.
Printers that use the PostScript page definition
language use the PostScript representation. The
PostScript representation describes objects by using
mathematical shapes that can be precisely imaged at
whatever resolution is used by your printer. The
PostScript representation created by ChemDraw is
composed of two parts, the PostScript commands
and the ChemDraw Laser Prep. The ChemDraw
Laser Prep contains specific instructions that enable
the printer to interpret the PostScript commands
contained in a ChemDraw document.
Include PostScript (Macintosh)
To transfer ChemDraw pictures to another
document that will be printed on a PostScript
printer:
1. From the File menu, choose Preferences.
2. Click Include PostScript.
3. Click OK.
When Include PostScript is deselected, no
PostScript commands are generated. This usually
results in lower quality printing, particularly of
12 • Chapter 1: ChemDraw Basics
drawings cut and pasted into other applications.
However, because the representation used for
printing when Include PostScript is not selected is
the same as that used for drawing to the screen,
better correspondence between the screen and
printed output may be observed.
For more information, see “Transferring PostScript
(Macintosh Only)” on page 174.
Include ChemDraw Laser Prep
(Macintosh)
Selecting the include ChemDraw Laser Prep allows
you to print to a printer that cannot be initialized
using ChemDraw. If you create drawings with this
option off, they will not print on PostScript printers
without the use of ChemDraw. If you do not select
this check box, you must choose the Initialize
LaserWriter command from within ChemDraw
before you print.
To Include ChemDraw Laser Prep:
1. From the File menu, choose Preferences.
2. Click Include ChemDraw Laser Prep.
3. Click OK.
NOTE: When you select Include ChemDraw Laser
Prep, you should also select Include PostScript.
For more information, see “Transferring PostScript
(Macintosh Only)” on page 174.
Quitting or Exiting
To close the ChemDraw application:
• From the File menu, choose Quit ChemDraw
(Macintosh) or Exit ChemDraw (Windows).
If you have unsaved document windows open,
you are prompted to save them before you can
close the application.
ChemDraw
ChemDraw’s Graphical
User Interface (GUI)
ChemDraw’s graphical user interface (GUI) is the
part of the application that you interact with.
Although the Macintosh and Windows versions
differ, the essential ChemDraw GUI consists of a the
same elements.
The Macintosh version of ChemDraw is shown below.

Menu Bar Zoom Collapse/Expand

Box Box
Title Bar

Close Box

Tools Palette
Scroll Bars
Document Window

Resize

Message Area Magnification Control

ChemDraw Chapter 1: ChemDraw Basics • 13

 The Windows version of ChemDraw is shown below.

Toolbar Magnification Minimize Maximize

Administrator

Control Button Button

Title Bar

Close
Menu Bar
Button

Tools Palette

Scroll
Document Window Bars

Status Bar Resize

14 • Chapter 1: ChemDraw Basics ChemDraw

The Tools Palette The following table describes the functions of the
tools.
The Tools palette contains the tools that allow you to
create and manipulate drawings. The Windows
Tool Name Description
version of the tool palette is shown below.

Bond Tools Use to draw single, double and

NOTE: If you are using a monitor with a resolution
triple bonds of various types.
of 640 x 480 or less, the Tool palette appears
differently than the one shown. At lower resolutions,
some tools are included on palettes extending from Acyclic Chain Use to draw chains of any
other tools. A triangle on a button indicates a palette Tool length.
is available.
Arc Tool Use to draw arcs. Arcs of
different degrees can be
Lasso Marquee
selected from the Arc Tool’s
palette.
Solid Bond Eraser

Dashed Bond Text

Alternative In ChemDraw Pro, use
Hashed Bond Pen
Group Tool to create alternative group
Hashed Wedged Bond Arrow definitions (R, G, etc.) that
Bold Bond Orbital represent a set of substituents,
Bold Wedged Bond Drawing Elements
any one of which will match the
query.
Hollow Wedged Bond Chemical Symbol

Dative Bond Arc

Reaction Atom- In ChemDraw Pro, use
Wavy Bond Reaction Atom-Atom Map
Atom Map Tool to create correspondences
Alternative Group Attachment Point between atoms in different
Acyclic Chain Template structures for use in creating
Cyclopropane Ring Cyclobutane Ring
queries for searching a reaction
database.
Cyclopentane Ring Cyclohexane Ring

Cycloheptane Ring Cyclooctane Ring

Cyclohexane Chair (1)
Cyclopentadiene Ring
Attachment Point In ChemDraw Pro,
Cyclohexane Chair (2)
Tool use to specify attachment points
Benzene Ring in an alternative group
definition.

Arrow Tool Use to draw arrows. Arrows of

different types can be selected
from the Arrow Tools palette.

ChemDraw Chapter 1: ChemDraw Basics • 15

 Tool Name Description
Chemical Used to draw chemically
Administrator
Symbols Tool significant symbols such as
charges, radicals and lone pairs.
Drawing Used to draw objects common
Elements Tool to reaction schemes, such as
brackets and lines. Drawing
Elements of different types can
be selected from the Drawing
Element Tools palette.
Eraser Tool Used to delete objects.
Orbital Tool Used for drawing orbitals.
Orbitals of different types can
be selected from the Orbital
Tools palette.
Ring Tools Used for quickly drawing
common structural
components.
Pen Tool Used to draw freehand shapes
such as custom arrows and
orbitals.
Lasso Tool Used to select objects by
dragging around them. Objects
that are selected can be further
manipulated using menu
commands.
Marquee Tool Used to select objects by
dragging diagonally across
them. Objects that are selected
can be further manipulated
using menu commands.
16 • Chapter 1: ChemDraw Basics
Tool Name Description
Templates Tool Used for drawing structures
using templates stored in
template documents. Templates
can be selected from the
Templates tools palette.
Text Tool Used to create atom labels and
captions.
Status Bar or Message Area
The status bar or message area displays information
about the task you are performing.
m/e
When you select a structure in a document, the m/e
(mass/charge, where charge =1) for that structure is
displayed in the Status bar or Message area.
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.
The weights of the three most common isotopes are
shown. Low abundance combinations (whether
because the isotope is in low abundance or because
it includes many moderate-abundance
contributions) are not taken into account.
Toolbar (Windows)
The toolbar contains buttons and lists that provide
shortcuts for menu commands. You can choose
whether to display or hide the toolbar as follows:
• From the Tools menu, choose Show Toolbar.
A check mark appears next to the item when the
toolbar is displayed.
ChemDraw
Menus and Commands The appearance of the commands in a menu may
change. The different appearances of commands are
The menus in the menu bar contain the commands
described in the following table.
that you use to perform tasks on a document.
There are four ways to access commands within Menu Convention Description
menus in ChemDraw:
• Mouse—Display the commands in a menu by Check mark next to a The command is
pointing to a menu name, holding down the command selected, or in effect.
mouse button, and dragging to the command Selecting the command
again removes the check
you want to choose. In Windows, you may
mark.
alternatively point to the menu name, click it to
select and open the menu, then point to the
command you want to choose and click the Partial Selection marks Each selected command
mouse button. next to several applies to part of the
• Shortcut menus—Right-click objects or an commands current selection (these
empty area of a document to display a shortcut appear as hyphens on
the Macintosh)
menu containing commands appropriate for
that object or area.
• Alt, letter, letter (Windows only)— Press the
Alt key and then type the underlined letter in the
menu name you want to open, release this key Dimmed command The command is not
and type the underlined letter in the command (grayed out command) available for the current
you want to choose. For example, Alt, F, X selection, or for the state
opens the File menu and chooses the Exit of the active document
ChemDraw command. If you open a menu and or is not available in this
version.
decide not to choose a command, you can press
the Alt or ESC key to close the menu or use an
Arrow key to open another menu.
Ellipsis (…) after a A dialog box appears
• Command shortcuts—You can execute command that requires user input
commands that have keyboard equivalents before the command is
directly without first opening the menu. For executed.
example, on the Macintosh, is equivalent
to choosing New from the File menu. In
Windows, Alt+F4 is equivalent to opening the
Key combination next to Use the combination
File menu and choosing Exit ChemDraw. The a command command keys to
command key equivalents are listed next to the execute a command
menu commands. instead of choosing it
from the menu.

ChemDraw Chapter 1: ChemDraw Basics • 17

 Menu Convention Description Option Description

Triangle next to a Indicates a submenu Drop-down List Drop-down list boxes

Administrator

command with further options that
appear if you point to
the triangle.
Using Dialog Boxes
Dialog boxes appear when additional information is
required to complete commands.
You can navigate within a dialog box in the
following ways:
• Mouse—Click an option to select it, or click a
command button to complete or cancel a
command.
• Keyboard—Move within the dialog box by
pressing the Tab key to go to the next button or
option group. Press Shift+Tab to move back to
the last button or option group. Option groups
and their navigation techniques are discussed in
the following table.
• Alt key—Hold the Alt key while typing an
underlined letter to move to that option.
Option Description
Check Boxes Check boxes are selected
when a check mark appears in
the box. You can select
multiple check boxes. Check
boxes without a check mark
are deselected.
Boxes or Pop-up (Windows) or pop-up menus
Menus (Macintosh) provide a list of
possible options from which
you can choose, much like the
menus in the menu bar.
Command Buttons Command buttons execute
commands or operations, or
cancel changes.
In most dialog boxes, a default
button exists. The default
button has a bolder outline
and you can choose it by
clicking it or by pressing the
Enter or Return key.
Option Button or The items in a group of option
Radio Button buttons (Windows) or Radio
buttons (Macintosh) are
mutually exclusive. You can
only select one option button
in a group.
Spin Button or Spin buttons (Windows) or
Control Arrows Control Arrows (Macintosh)
provide a range of values from
which you can select. To
select a value, click the up or
down arrow, or type a value in
the text box.
Text Box You use text boxes to enter
textual information. To enter
information in a text box,
point to the box, click to select
the text, and then type the text.

18 • Chapter 1: ChemDraw Basics ChemDraw

Undoing Actions
ChemDraw keeps track of the actions you perform.
You can reverse actions one at a time by choosing
the Undo command. The number of actions that can
be undone or redone is limited only by the amount
of memory (RAM and virtual memory) available for
use by ChemDraw. When you save your document
the Undo queue is reset and starts over.
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.
For example, if you draw cyclohexane, create an
atom label text box, type a label, and select and
rotate the structure, you will be able to remove the
actions as follows:
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. You can reverse the effect of the
Undo command by choosing the Redo command.
To redo the last action undone:
• From the Edit menu, choose Redo.
The last action undone is reinstated. The Undo
command changes to reflect that action. The
Redo command changes to reflect the next
action that can be redone.
ChemDraw
Repeating Actions
You can repeat some actions you perform on objects
by using the Repeat command on the Edit Menu. If
the action performed is repeatable, the name of the
action appears next to the Repeat command.
To repeat an action:
• From the Edit menu, choose Repeat.
The last action performed is repeated.
Customizing Your
Environment
Preferences allow you to change the default
behavior of certain options that apply to every open
document. Document Settings allow you to change
the default behavior of options that will affect only
the active document.
Preferences
Preferences affect the way the ChemDraw
application works, regardless of the document with
which you are working. Preferences are saved in the
ChemDraw Preferences file located in the System
folder (Macintosh) or chemdraw.ini located in the
Windows directory (Windows).
To open the Preferences dialog box:
• From the File menu, choose Preferences.
Chapter 1: ChemDraw Basics • 19
 The Preferences dialog box appears:
Preference Description

Tolerance The size of the highlight box

Administrator

that appears when you point at

any object in the document
window. The tolerance affects
how close the cursor needs to
be for selecting or joining.

For more information see

“Setting the Highlight Box
Tolerance” on page 104.

Macintosh Preferences Include PostScript Transfers ChemDraw

(Macintosh only) drawings to other applications
that print to a PostScript
printer. Drawings can be
transferred through the
Clipboard or Publish.

If you print only to non-

Postscript printers, you can
reduce the file size of the
pictures by deselecting this
option.

Windows Preferences NOTE: PostScript

information adds 11K to 12K
The following table describes the Preferences. per drawing to the destination
document. However, it ensures
Preference Description you can print the document
containing the drawings. This
affects Clipboard, Publish,
Units The units used in the Drawing and EPS files.
Settings dialog box,
Document Setup, the Rulers, For more information, see
and the Crossphair. Available “Include ChemDraw Laser
units include inches, Prep (Macintosh)” on page 12.
centimeters, and points.

For more information see

“Specifying Units” on page
59.

20 • Chapter 1: ChemDraw Basics ChemDraw

Preference Description
Include Prints to a printer that cannot
ChemDraw be initialized using Chemdraw
LaserPrep (for example, a service
(Macintosh only) bureau). If you print to a
PostScript printer, select this
option.
For more information
see“Include PostScript
(Macintosh)” on page 12.
Show 35mm Slide Displays boundary guides to
Boundary Guides help keep your drawing in the
appropriate ratio for the
standard 35 mm slide
dimensions. The boundary
guides are not printed.
For more information see
“35mm Slide Boundary
Guides” on page 161.
Require Uses the Enter key (or Return
Ctrl-Enter to key for Macintosh users) to
Create New Line close caption and label text
(Windows) or boxes.
Require Option +
When this option is selected,
Return to Create
hold down the Ctrl key and
New Line
press the Enter key (Option
(Macintosh)
and Return keys on
Macintosh) to add a new line.
For more information see
“Creating a New Line and
Closing Text Boxes” on page
85.
ChemDraw
Preference Description
Optimize Pictures Transfers ChemDraw pictures
for High to another application that
Resolution Non- uses a High Resolution
PostScript Clipboard and will be printing
Printing the document to a non-
(Macintosh only) PostScript (QuickDraw)
printer.
For more information see
“Optimize Pictures for
High-Resolution Non-
PostScript Printing
(Macintosh)” on page 11.
Use Bitmap Fonts Displays text on screen using
When Available Bitmap fonts rather than
(Macintosh only) TrueType fonts. The text will
appear more quickly and for
some fonts, such as Helvetica,
the on-screen display is more
readable. If this option is
deselected, text may be less
readable on the screen, but
will more accurately represent
the size and position of the
printed text.
For more information see
“Using Bitmap Fonts When
Available (Macintosh)” on
page 85.
Chapter 1: ChemDraw Basics • 21
 Preference Description
Automatic Atom Applies Automatic
Administrator
Labels justification to new labels.
With this option selected, new
labels are Flush Left,
Centered, Flush Right, or
Stacked Above, depending on
the positions of the bonds to
the atom.
For more information see
“Setting Automatic
Justification” on page 82.
Print Background Prints the background color.
Color With this option deselected,
the background is controlled
by the printer.
For more information see
“Printing Background Color”
on page 11.
Check Structure Invokes the Check Structure
When Copying to command when a structure is
Clipboard or copied to the Clipboard or
Exporting saved.
This provides a safety check
for structures that you will be
importing into other
applications, such as
ChemFinder.
For more information see
“Check Structure when
Copying to Clipboard or
Exporting” on page 128.
22 • Chapter 1: ChemDraw Basics
Preference Description
Show Attachment In ChemDraw Pro,
Rank Indicators shows visual indication of the
attachment point ordering in
alternative groups.
For more information see
“Showing Attachment Rank
Indicators” on page 149.
Always Display In ChemDraw Pro,
and Print Reaction shows visual indication of
Mapping atom mapping created using
the Reaction Atom-Atom Map
tool.
For more information see
“Always Display and Print
Atom Mapping” on page 129.
Automatic Atom In ChemDraw Pro,
Mapping automatically completes atom
mapping after an atom-atom
map is manually defined using
the Reaction Atom-Atom Map
tool.
For more information see
“Automatic Mapping” on
page 130.
Document Settings
Document settings are user definable settings that
are applied to the current document. Document
settings include Drawing Settings, Caption Text
Settings, Label Text Settings, Print/Page Setup, and
the Color Palette. Drawing Settings affect drawing
options such as the fixed length used to draw bonds.
Text Settings affect text options like the font used for
atom labels and captions. The default Color Palette
ChemDraw
affects the colors available to colorize objects. The
Print/Page Setup affects options like the page size
used.
As you become familiar with ChemDraw you can
change these settings to fit your needs. You can also
save different sets of document settings in Style
Sheets/Stationery Pads to be used for special
instances, such as journal articles, textbook
chapters, slide presentations and so on. For more
information, see “Saving Customized Settings” on
page 26.
Drawing Settings
Drawing Settings are document settings that affect
how bonds are drawn. Changes made in the Drawing
Settings dialog box take effect for all bonds already
drawn as well as those that are drawn later with the
exception of the fixed length setting, which only
applies to newly drawn bonds. Changes made affect
the active document window only. Drawing settings
can be saved in Style Sheets/Stationery Pads.
ChemDraw
A summary of each of the options is described in the
table below:
Adjust this If you want to …
setting …
Chain Angle Change the angle (from 1 to 179
degrees) between bonds created by
the Acyclic chain tool or modified
by the Clean Up Structure
command
For more information see,
“Drawing Acyclic Chains” on page
63 and “Using Clean Up Structure”
on page 119.
Bond Change the distance between the
Spacing lines in double or triple bonds. The
distance is set as the percentage of
the total length of the bond
(between 1 and 100). This allows
for proportional spacing to be used
if different bond lengths are used in
the drawing. For more information,
see “Drawing Settings for Bonds”
on page 65.
Fixed Length Constrain the length of the bonds
drawn to the length you specify
when the command Fixed Lengths
command in the Tools menu is
selected (a check mark is next to
it). This also adjusts the preferred
bond length for structures modified
by the Clean Up Structure
command.
For more information see
“Drawing with Fixed Lengths” on
page 58 and “Using Clean Up
Structure” on page 118.
Chapter 1: ChemDraw Basics • 23
 Text Settings
Adjust this If you want to …
setting … Text Settings (Macintosh) or Caption Text Settings
and Label Text Settings (Windows) affect how new
Administrator

Bold Width Change the width of the line used
when bold and wedge bonds are
drawn.
For more information see
“Drawing Settings for Bonds” on
page 65.
Line Width Change the width of all bonds,
lines and arrowheads in the
drawing.
For more information see
“Drawing Settings for Bonds” on
page 65.
Margin Change the amount of space
Width surrounding all atom labels that
will erase portions of the bonds to
which they are attached. The
margin width also determines the
amount of white space surrounding
the front bonds in a bond crossing.
For more information, see
“Creating Atom Labels” on page
75 and “Changing Bond
Crossings” on page 68.
captions and all atom labels for the current
document are drawn and formatted. Changing the
Text Settings in the Text Settings dialog box
(Macintosh), or Caption and Label Text Settings
(Windows), affects the current document only.
When you change settings for captions, all new
captions you create use the new settings. Previously
drawn labels are not changed.
When you change settings for atom labels, all new
atom labels you create use the new settings, but all
previously drawn atom labels are scaled to a size
that is proportional to the new size. This scaling
method prevents atom labels specifically sized to be
proportional relative to another atom label to lose
this relationship.
You can save text settings in Stationery Pad
Documents (Macintosh) or Style Sheets (Windows)
if you repeatedly use the same settings.
Macintosh
To display the Macintosh text settings:
• From the File menu, choose Text Settings.
The Text Settings dialog box appears.

Hash Spacing Change the spacing between the

hashed lines used when wedged
hashed bonds, hashed bonds,
dashed bonds, dashed arrows or
dashed curves are drawn.

For more information, see

“Drawing Settings for Bonds” on
page 65.

24 • Chapter 1: ChemDraw Basics ChemDraw

To change the spacing between characters as close to
proportional spacing as possible:
• Select Fractional Character Widths.
If you are printing to a PostScript printer this option
generally improves the font appearance. The screen
image of the font is also affected by this check box,
and the text may look irregular on the screen.

NOTE: If you copy structures to other applications,

make sure the character widths setting is the same in
the other application or printing problems may
occur.
Windows
To display the Windows text settings for captions:
• From the File menu, choose Caption Text
Settings.
The Caption Text Settings Dialog box appears.
Color Palette
The Color Palette allows you to add, remove, or
change the default foreground and background color
and specify the other colors available for coloring
objects. For more information, see “Changing the
Color Palette” on page 123.
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” on
page 26.

To display the Windows text settings for atom

labels:
• From the File menu, choose Label Text
Settings.
The Label Text Settings Dialog box appears.

ChemDraw Chapter 1: ChemDraw Basics • 25

 A summary of each of the options is described in the Applying Settings From Other
following table.
Documents
Click … If you want to … To apply document settings to the active window
Administrator

New Color Add a new color box and set its
color using the Color Picker or
Color Wheel dialog box.
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.
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.
that are contained in a Style Sheet located in the
cd_items directory or ChemDraw Folder:
1. From the File menu, choose Apply Settings.
2. From the Apply Settings submenu, choose a
Style Sheet or Stationery Pad.
The settings in the active document window
change to those found in the Style
Sheet/Stationery Pad that you choose.
To apply the document settings contained in a
ChemDraw document or Style Sheet/Stationery Pad
not contained in the cd_items directory (Windows)
or ChemDraw Folder (Macintosh) to the document
in the active window:

Saving Customized Settings 1. From the Apply Settings submenu, choose

Other.
Every new document created within ChemDraw
uses a Style Sheet or Stationery Pad to obtain its The following dialog box appears.
document settings. Style Sheets and Stationery Pads
can also contain predefined objects. When you
create a new document, you actually create an
untitled copy of the Style Sheet or Stationery Pad.
Any changes you make to the copy of the Style
Sheet does not affect the Style Sheet or Stationery
Pad itself.
By creating different Style Sheets and Stationery
Pads, you can avoid the need to specify the
document settings repeatedly when you switch
between projects that require different settings. As a
convenience, Style Sheets and Stationery Pads can
2. Select a ChemDraw document, Style Sheet, or
be stored in the cd_items directory (Windows) or
Stationery Pad.
ChemDraw Folder (Macintosh) so that they are
accessible from the Open Special submenu in the 3. Click Open.
File menu. The Apply Settings command preserves any style
differences within a document. For example, if your
original document has one short and one long bond,

26 • Chapter 1: ChemDraw Basics ChemDraw

it will still have one short and one long bond after • From the Scripts menu, choose About
you choose Apply Settings, even if the lengths of the ChemDraw Scripts.
bonds are different. For more information about AppleScript™ and the
To make different bonds within one document the Script Editor application see your system manuals.
same length, you must either scale them individually
or use the Clean Up Structure command. For more
information, see “The Resize Handle” on page 109
and “Using Clean Up Structure” on page 119.

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
file becomes the default.
To view the default Style Sheet or Stationery Pad:
• Point to the File menu.
The “New” menu item displays the name of the
Style Sheet or Stationery Pad.

Scripts (Macintosh
Only)
The Scripts menu contains scripts that you can use
to perform tasks within ChemDraw or between
ChemDraw and another scriptable application.
Scripts, found in the Scripts menu, are created using
Apple’s Script Editor application. With the proper
script extensions in conjunction with Apple’s Script
Editor application, you can create scripts using the
AppleScript™ scripting language and add scripts to
the Scripts menu by placing them in the ChemDraw
Folder.

NOTE: Scripts not stored within the ChemDraw

Folder are not accessible from the Scripts menu.

To read about the scripts that come with ChemDraw:

ChemDraw Chapter 1: ChemDraw Basics • 27

Administrator

28 • Chapter 1: ChemDraw Basics ChemDraw

Chapter 2: Tutorials
Overview
The tutorials are designed to teach you the
fundamental drawing techniques available in
ChemDraw. Before you begin, you may want to
review “Conventions” and “Terminology” on page 1
to familiarize yourself with the terminology used in
the tutorials. You may also want to use your Quick
Reference Card while you perform the tutorials.

Tutorial 1: Reaction
NOTE: Applying fixed lengths and fixed angles
Schemes enables you to create structures with consistent
bond lengths and angles. The fixed length dimension
In this tutorial, you will draw the following
is set in the Drawing Settings dialog box. The fixed
(simplified) reaction scheme:
angle dimension increments angles by 15 degrees.

O O Create a bond:
OH

OH
1. Click the Solid Bond tool icon.
2-propanone 4-hydroxy-4-methyl-2-pentanone
2 moles 1 mole

Create a ChemDraw Document:

1. Start ChemDraw.
2. From the File menu, choose Save As.
3. Type tut1.cdx in the appropriate text box. 2. Position the pointer (+) anywhere in the
document window and hold down the mouse
4. Select a folder in which to save the file.
button.
5. Click Save.
3. Drag the mouse diagonally upward toward the
6. Click the Tools menu and make sure there is a right at a 30-degree angle. Watch the message in
check mark next to the Fixed Lengths and the lower left corner of the document window to
Fixed Angles commands. If either command is determine when you reach 30 degrees.
not checked, choose it.

ChemDraw Chapter 2: Tutorials • 29

 4. Release the mouse button when the bond is Change a single bond into a double bond:
extended to its fixed length at a 30-degree
1. Point to the atom shown below and hold the
angle.
mouse button down.
Administrator

NOTE: When drawing with bond tools, you

must always draw the first bond in a structure
2. Drag as shown below over the existing single
by dragging as shown above.
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

2. Double-click the atom.
bonds is controlled by the Chain Angle setting
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 O in the text box that appears.
. .

2. Click the atom to add a bond.

30 • Chapter 2: Tutorials ChemDraw

 4. Close the text box by doing one of the 4. Drag the Selection Rectangle to the right.
following:
• Click in an empty area of the window.
• Click another tool.
Next, you duplicate a structure and then create
another structure from the duplicate.
Duplicate the structure: A copy of the structure appears as you begin
1. Click the Lasso Tool icon.
drag. The original structure remains in its
position. Release the mouse button when the
copy is clear of the original.

NOTE: When you create a copy as shown above

you can drag it anywhere in the document window.
If you want the copy to remain aligned with the
original, hold Shift while dragging.
The last structure drawn is automatically
selected.
Modify the duplicated structure:
2. Point over the Selection Rectangle.
1. Click the Solid Bond tool icon.

3. Press and hold Alt (Windows) or Option

(Macintosh).
2. Point, in the copied structure, to the atom
The hand pointer with a plus sign indicates that shown below and click.
you are in the duplication mode of a selection
tool. O

ChemDraw Chapter 2: Tutorials • 31

 Add several bonds to a single atom:
1. Point to the atom shown below.
O You should have the two structures below in your
Administrator
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
opens a text box or a triple-click, which
duplicates your last atom label.
Create an atom label using HotKeys. HotKeys are
keys on your keyboard that are linked to specific
atom labels.
1. Point to the atom shown below.
O
2. Type o.
OH
32 • Chapter 2: Tutorials
When you use HotKeys that represent a single
element, the correct number of hydrogen atoms is
added to the label.
document.
O O
OH
In the following steps, you use a different method
for selecting structures and then separate the
structures to make room for an arrow.
1. Click the Marquee Tool icon.
NOTE: Alternatively, you can select the Lasso
tool and hold Alt to use the Marquee tool.
The last object drawn is selected.
Drag the selection to make room for an arrow:
• Hold Shift to maintain the alignment of the
structure and drag the Selection Rectangle to
the right.
ChemDraw
Add arrows to the reaction scheme. 2. Drag the Arrow to the length you want. Release
the mouse button.
1. Click and hold the mouse button over the Arrow
tool to display the Arrow palette. O O

OH

NOTE: If you need to change the length (or the

NOTE: The triangle in the lower right corner
of the Arrow icon indicates it contains a palette.
2. Drag the cursor to the arrow shown below.
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 icon.

3. After the arrow is selected, release the mouse

button.
2. Point above the arrow. A text insertion point
appears as shown below.
NOTE: The arrow you choose from the palette O
O
becomes the default arrow type. To change to
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
mouse button. O
O

O O

OH

ChemDraw Chapter 2: Tutorials • 33

 4. Type OH. Objects added from the Chemical Symbols palette
are automatically associated with the structure they
O O are closest to.
Some objects, such as arrows, are not associated
Administrator

automatically. You can manually group objects

OH
NOTE: If you want to realign the caption,
select a selection tool and drag the caption.
using the Group command. You can then select the
grouped objects to manipulate or move them
together.
To group objects:

Add a charge symbol using the specialized symbols 1. Click a selection tool.
available in the Chemical Symbols tool palette:

1. Click and hold the mouse button over the

Chemical Symbol tool. Drag to the circled
negative charge symbol shown below and
release the mouse button.
2. Hold Shift and click the arrow, the OH caption,
and the charge symbol.

2. Point to the center of the OH label.

The Shift key allows you to add objects to a
O O selection without deselecting other objects.
OH

NOTE: If you click a selected object while

OH holding Shift, that object is deselected.
3. Click to add the charge symbol.

3. From the Object menu, choose Group.

O O
OH
NOTE: You can select individual objects
within a group by clicking them.
OH

NOTE: If you hold the mouse button down

after depositing the symbol, you can rotate the
symbol around the label in a fixed position by
dragging it.

34 • Chapter 2: Tutorials ChemDraw

Use the Text tool to create a caption containing the Type the caption:
name and amount of reactant, and then center the
1. Type 2-propanone.
caption under the structure.

1. Click the Text tool to select it. O

2-propanone

2. Press Enter or Return to insert a new line.

2. Point below the first structure.

O
2-propanone

3. Type 2 moles.

O
3. Click to create a text box. The default cursor is
flush left.

2-propanone
2 moles

Create an aligned caption for the other structure.

1. Press Tab to create another Text box that is

4. From the Text menu, choose Centered.
aligned adjacent to the first.
O
O

2-propanone
2 moles
The cursor moves to the center of the text box.

ChemDraw Chapter 2: Tutorials • 35

 3. Point to the upper left corner of the reaction
NOTE: You can use the Tab key in the caption scheme. Hold the down the mouse button and
mode of the text tool to create multiple aligned drag diagonally downward to the right to draw
captions with the same font, font size, style, and the box.
Administrator

justification as the previous caption.

2. Type 4-hydroxy-4-methyl-2-pentanone, press

Enter or Return, and then type 1 mole. O O
OH
If your captions are not aligned properly beneath the
structures you can move them using a selection tool. OH
2-propanone 4-hydroxy-4-methyl-2-pentatone
1. Click a selection tool. 2 moles 1 mole
The text box is automatically selected because
it is the last object drawn. Save and close the document:
2. Press the Left or Right Arrow to center the
caption beneath its structure. This method 1. From the File menu, choose Save.
maintains the alignment created by the Tab key. Your document is saved.
To complete the drawing, add a shadowed box 2. From the File menu, choose Close.
around the scheme:

1. Hold down the mouse button over the Drawing

Tutorial 2: Drawing an
Elements tool. Intermediate
In this tutorial you will draw the following
intermediate structure starting from a ring and then
add arrows with customized shapes using the Pen
tool:

O-
2. Select the shadowed box from the palette of
OH
drawing elements.

Create a new ChemDraw document:

1. From the File menu, choose New Document.

2. From the File menu, choose Save As.
3. Type tut2.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.

36 • Chapter 2: Tutorials ChemDraw

Draw a ring: 3. Click the atom.

1. Click the Cyclohexane Ring tool.

Add a bond:
2. Point in the document window. The
1. Select the Solid Bond tool.
Cyclohexane cursor appears.
3. Click to add a ring.

2. Point to the atom shown below.

Delete an atom and its bonds from the ring:

1. Select the Eraser tool.

3. Click to add a bond.

2. Point to the atom shown below.

Add second and third bonds:

1. Point to the atom shown below and click to

add another bond.

NOTE: You can delete a bond individually by

pointing at the center of the bond and clicking.

ChemDraw Chapter 2: Tutorials • 37

 2. Add a third bond by dragging to make sure it Change the orientation of the double bond:
has the desired orientation:
1. Point to the center of the double bond.
a. Continue pointing to C4.
Administrator

b. Hold the mouse button and drag diagonally 2. Click the bond to move the second line to the
upward toward the right. outside.

c. When the bond is oriented, release the mouse

button to deposit the bond. NOTE: You can move a double bond by
Create a double bond: clicking it when a bond tool is selected. The
cursor corresponding to the bond tool that is
1. Point to the atom shown below. selected appears.

Add an atom label:

1. Point to the atom to label shown below.

2. Drag diagonally downward over the existing

bond to create a double bond.

2. Double-click the atom to open a text box.

38 • Chapter 2: Tutorials ChemDraw

 3. Type O. On the Text menu, point to Style, and 3. Point near the double bond where you want to
then choose Superscript. Type “-”. indicate the start of electron flow.

O- O-
OH

Label an atom with “OH”:

4. Drag downward and to the left. Release the
1. Point to the atom shown below.
mouse button.

O-
O-
OH

2. Double-click the atom to open a text box.

O-

The hand with a “+” cursor indicates that you

are in the editing mode of the Pen tool.
3. Type OH.
5. Position the cursor where you want the
Next you will add an arrow that is not included in the
arrowhead to appear.
arrow palette to indicate electron flow.
To create a customized arrow using the Pen tool.
O-
1. Click the Pen tool. OH

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

ChemDraw Chapter 2: Tutorials • 39

 6. Drag upward to create a curve segment.
O-
Administrator
OH
Refine the shape of the arrow:
1. Point to the handle pointing away from and to
the right of the curve. This is a tangent handle
that controls the tangent of the curve that it
touches.
2. Drag the handle upward to the right to make the
arrowhead point more inward.
3. Press Esc when you are finished.
40 • Chapter 2: Tutorials
4. Create additional arrows as described above to
complete the intermediate as shown below.
O-
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 Tools menu.
Save and close the document:
1. From the File menu, choose Save.
2. From the File menu, choose Close.
Tutorial 3: Using Rings
In this tutorial you will draw more complex
structures by using rings.
O
CH
Open a new ChemDraw document:
1. From the File menu, choose New Document.
2. From the File menu, choose Save As.
3. Type tut3.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
ChemDraw
Create a ring: Fuse a third ring:
1. Point to the bond shown below.
1. Click the Cyclohexane Ring tool.

2. Point in an empty area of a document window.

2. Click to fuse another ring. Your document

should contain the structure shown below.

3. Click to add a ring.

Fuse a second ring to the first: Fuse a fourth ring:

1. Point to the center of lower right bond in the 1. Point to the bond shown below.
ring.

2. Click to fuse another ring.

2. Click to fuse another ring.

ChemDraw Chapter 2: Tutorials • 41

 Remove atoms and their bonds from the ring using 4. Click each of the atoms shown below to delete
the Eraser tool: the bonds.

1. Select the Eraser tool.

Administrator

2. Point to the atom shown below.

The resulting structure is shown below.

A highlight box appears on the atom to be

removed.
3. Click to delete the atom and its bonds.
Add double bonds to the structure and realign them:

1. Click the Solid Bond tool.

42 • Chapter 2: Tutorials ChemDraw

 2. Point to the atom indicated below. 2. Drag upward to draw a double bond.

3. Drag upward to draw a double bond.

Realign the double bonds so they are centered:

1. Point to the center of the lower double bond and

click to move the line to the other side of the
bond.

Add another double bond:

1. Point to the atom shown below.

2. Click again to center the bonds.

ChemDraw Chapter 2: Tutorials • 43

 3. Point to the center of the upper double bond. 2. Press the c key on your keyboard. “c” is a
HotKey assigned to the atom label “C”.
Administrator

CH

4. Click to move the line to the other side of the

bond. The atom label appears with the correct number
of hydrogen atoms.
Add an oxygen atom label to complete the structure:

1. Point to the atom shown below.

CH

5. Click again to center the bonds.

Add a carbon atom label:
1. Point to the atom shown below.

2. Press the o key on your keyboard. “o” is a

Hotkey assigned to the atom label “O”.

CH

Save and close the document.

1. From the File menu, choose Save.

2. From the File menu, choose Close.

44 • Chapter 2: Tutorials ChemDraw

Tutorial 4: Fischer 4. Select a folder in which to save the file.
5. Click Save.
Projections Draw the first bond:
In this tutorial you will draw a Fischer projection of
1. Click the Solid Bond tool.
glucose (shown below) by drawing a linear series of
bonds.

CHO

H OH

HO H

2. Point in the document window. Drag downward

H OH
vertically to draw the first bond.
H OH

CH2OH

1. Create document from a template by opening

the appropriate document template:
• Windows: From File menu, point to Open
Special, and then choose
ACS Document 1996.
Add a second bond:
• Macintosh: From the Windows menu,
choose ACS Document 1996. 1. Point to the lower atom.

The new document created is based on a Style

Sheet (Windows), or Stationery Pad
(Macintosh).

NOTE: These special documents allow you to have 2. Drag downward to draw the second bond.
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
(Drawing Setting)
• Atom Labels in Times font (Text Setting)

2. From the File menu, choose Save As.

3. Type tut4.cdx in the appropriate text box.

ChemDraw Chapter 2: Tutorials • 45

 3. Repeat step 1 and step 2 three times to draw a Add a horizontal bond in the opposite direction:
total of five bonds.
• Continue pointing to C2 and click the atom to
add a perpendicular bond in the opposite
direction.
Administrator

Add bonds to the next three carbon atoms:

1. Point at the third atom (C3) and click the atom

to add a perpendicular 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

string of bonds you created:

1. Point to C2 and click the atom to add a

perpendicular bond. 2. Continue pointing to C3 and click the atom to
add a perpendicular bond in the opposite
direction.

46 • Chapter 2: Tutorials ChemDraw

 3. Repeat steps 1 and 2 for the fourth (C4) and 3. Point to C6.
fifth (C5) atoms.

4. Double-click C6 to create a text box, then type

Add labels to C1 and C6: CH2OH.

1. Point to C1. CHO

5. Click outside the text box to deselect it.

2. Double-click C1 to create a text box, then type
CHO. Add the H and OH labels:

1. Point to the atom shown below.

CHO

CH2OH

ChemDraw Chapter 2: Tutorials • 47

 2. Type h to label the atom with hydrogen. Check the chemical syntax of the structure you drew
and automatically calculate the formula and
CHO
molecular weight:
H
Administrator

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 Structure menu, choose Analyze
Structure.
If drawn correctly, a dialog box with
CH2OH
information calculated from the structure
3. Repeat this labeling procedure for the appears.
remaining hydrogen atoms shown below.
If drawn incorrectly, a check structure message
CHO appears indicating the problem.
3. In the dialog box that appears, deselect all but
H
the Formula and Molecular Weight check
H boxes.
4. Click Paste to paste the information as a
H
caption below the structure.
H
5. Click outside the caption to deselect it.
CH2OH
CHO
4. Label the remaining atoms by typing o to label
them with OH. The result should appear as H OH
shown below.
O H

CHO
H OH

H OH
H OH

HO H
CH2OH

H OH C6H12O6
Mol. Wt.: 180.16
H OH
Save and close the document:
CH2OH
1. From the File menu, choose Save.
2. From the File menu, choose Close.

48 • Chapter 2: Tutorials ChemDraw

Tutorial 5: Perspective 3. Click to add a ring.

Drawings
In this tutorial you will learn how to create a
perspective drawing by drawing the following
α-D-glucose as a Haworth projection.
Rotate the ring:
CH2OH 1. Press Ctrl+Alt+Tab (Windows) or
O Control+Command+Tab (Macintosh) to select
OH
a selection tool and the last structure drawn.
H OH
OH
1. Create a new document using the ChemDraw
default style:
• Windows: From File menu, point to Open
Special, and then choose New Document.
• Macintosh: From the Windows menu, 2. Point to the upper right corner of the Selection
choose New Document. Rectangle (the Rotation handle).

2. From the File menu, choose Save As.

3. Type tut5.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
Draw a ring:

1. Click the Cyclohexane Ring tool.

NOTE: The cursor changes to a curved
double-sided arrow to indicate the rotation mode of
a selection tool is activated.

3. Drag the Rotation handle to the right about 30

degrees. Look at the Messages area at the lower
2. Point in an empty area of a document window. left of the window to determine the angle.

ChemDraw Chapter 2: Tutorials • 49

 Even though Fixed Angles is on, the angle is not 3. Drag upward to create a bond.
constrained. The Fixed Angles feature constrains
angles only when they are being drawn. For
example, if you created this ring by dragging instead O
Administrator

of clicking, the angle would be constrained when

Fixed Angles is on.
Change cyclohexane to tetrahydropyran:
4. Point to C1 again.
1. Click outside the structure to deselect it.
2. Point to the atom indicated below. O

5. Drag downward to create another bond.

3. Type o. O

Add vertical bonds: 6. Repeat for the atoms indicated by the arrows
below.
1. Click the Solid Bond tool.
O

2. Point to the atom shown below. The result appears as shown below.

O O

50 • Chapter 2: Tutorials ChemDraw

Draw one bond upward at C5: 2. Hold down the mouse button, press Shift, and
drag downward from C5. Stop dragging about
1. Point to the atom shown below.
half the distance to the upward bond on C3.

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.

1. Click the Lasso tool.

O

For the downward bond for C5, you must turn Fixed 2. Point to the Resize handle (lower right corner)
Lengths off or the bond will be joined to the upward and hold Shift.
bond of C3.
You can temporarily disable Fixed Lengths using a
modifier key:

1. Point to the atom shown below.

NOTE: The cursor changes to a cross with

arrows at each end indicating the distortion
function of a selection tool.

ChemDraw Chapter 2: Tutorials • 51

 3. Drag upwards until you have distorted the 3. Triple-click the remaining atoms (as shown
structure to about 50% (shown in the Messages below) to repeat the OH label.
area of the window).
Administrator

O
OH

OH OH
OH

NOTE: If you find it difficult to place the labels

because of the size of the drawing, choose
Next, you create OH labels. Because this label is Magnify from the Tools menu.
repeatedly used, you will learn how to repeat a label.
Only labels created by opening a text box are
Add the CH2OH label:
repeatable.
1. Triple-click the upper atom of C5.
1. Select the Solid Bond tool, point to the atom
shown below and double-click to open a text 2. Press Enter to open the atom label text box and
box. type CH2 before the OH.

CH2OH
O O
OH

OH OH
OH
2. Type OH, move the pointer to the next atom as
shown, and triple-click to repeat the atom label.
NOTE: The Enter HotKey opens a text box for
the last atom labeled. The definition for this
O particular HotKey cannot be changed.

OH Change the type of the front bonds:

1. Click the Bold Bond tool.

52 • Chapter 2: Tutorials ChemDraw

2. Point to the center of the bond shown below. The resulting structure is shown below.

CH2OH CH2OH
O O
OH
OH
OH OH
OH H OH
OH
3. Click to change to the new bond type

NOTE: If the wedge is pointed in the wrong

NOTE: The cursor changes to a bold arrow as direction, click the bond again to flip its
you point at the bond. orientation.

CH2OH Save and close the document:

O
OH 1. From the File menu, choose Save.
OH OH 2. From the File menu, choose Close.
OH
4. Click the Solid Wedge bond tool. Tutorial 6: Newman
Projections
In this tutorial shows you will draw a Newman
projection.

5. Point to each of the bonds shown below.

CH2OH
O
OH

OH OH
OH
Create a ChemDraw document:

6. For each bond, point slightly off center in the 1. From the File menu, choose New Document.
direction that you want the wide end of the 2. From the File menu, choose Save As.
wedge to be oriented and click.
3. Type tut6.cdx in the appropriate text box.
4. Select a folder in which to save the file.
NOTE: If you move the pointer too far, the
highlight box disappears. Choose Magnify from 5. Click Save.
the Tools menu if you find it difficult to place the
pointer.

ChemDraw Chapter 2: Tutorials • 53

 Create the first bond: 6. Point within the Selection rectangle and hold
Alt (Windows) or Option (Macintosh).
1. Click the Solid Bond tool.
Administrator

7. Hold the mouse button and drag a copy of the

2. Point in the document window and drag structure diagonally upward to the right of the
downward to create the first bond. original.

3. Continue pointing at the lower atom and click

again to add a second bond.

8. Release the mouse button and depressed key

when the copy is positioned.
Add a bond between the duplicated structures:

4. Continue pointing at the same atom and click 1. Click the Solid Bond tool.
again to add a third bond.

5. Click the Lasso tool. 2. Point to the central atom of the lower fragment.

The last structure you drew is automatically

selected. NOTE: When connecting existing atoms, the
Fixed Length and Fixed Angles commands are
ignored.

54 • Chapter 2: Tutorials ChemDraw

 3. Click and drag to the central atom of the upper
fragment.
4. Release the mouse button when the highlight
box over the central atom appears.
NOTE: Orbitals are not automatically
grouped with the closest structure. If you want
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:

1. Click the Marquee tool.

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. Hold the mouse button over the Orbital tool and

drag to the unfilled s orbital (first column, first
2. Point above the structure and drag around the
row).
upper fragment to select the three bonds.

2. Point to the left center carbon and drag outward.

The size of the orbital is constrained just like
bonds. The constraint is based on a percentage
of the Fixed Length setting in the Drawing
Settings dialog box.
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.

ChemDraw Chapter 2: Tutorials • 55

 Rotate the selection: 2. Drag the selection until the central atom of the
selection is centered within the orbital.
1. Double-click the Rotation handle in the upper
right of the Selection Rectangle to open the
Administrator

Rotate dialog box.

3. Release the mouse button and click outside the

Selection Rectangle to deselect the structure.
Save and close the document:

2. Type 180 in the text box and click Rotate. 1. From the File menu, choose Save.
2. From the File menu, choose Close.

Change the layering of the structure so that the

selection is in front:
• From the Object menu, choose Bring to Front.
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.

56 • Chapter 2: Tutorials ChemDraw

Chapter 3:
Drawing Chemical Structures
Overview Bold Bond

ChemDraw provides the following tools for drawing Hollow Wedged Bond
chemical structures:
• Bond tools Wavy Bond
• Ring tools
Dative Bond
• An acyclic chain tool
• Automatic error checking
Drawing with Fixed Lengths
• In ChemDraw Ultra, a menu item to draw
structures automatically from chemical names To draw bonds that are constrained to a fixed length:

1. From the Tools menu, choose Fixed Lengths.

Drawing Bonds
You can draw bonds that are constrained to:
• A fixed or variable length
• A fixed or variable angle relative to the X-axis
Bond Tools
The Tools palette contains nine single bond tool
icons. The icons representing each tool are shown
below:
Solid Bond
A check mark appears next to the Fixed Lengths
command indicating that it is selected. When
Fixed Lengths is selected, all the bonds drawn
are constrained to the fixed length specified in
the Drawing Settings dialog box.
2. Click a bond tool on the Tools palette.
3. Drag from one end of the bond to the other.
Drawing with Fixed Angles
To draw bonds with constrained angles that are
multiples of 15 degrees relative to the X-axis:

Dashed Bond 1. From the Tools menu, choose Fixed Angles.

A check mark appears next to the Fixed Angles
Hashed Wedged Bond command indicating that it is on.
2. Click a bond tool.
Bold Wedged Bond
3. Drag from one end of the bond to the other in a
Hashed Bond document window.

ChemDraw Chapter 3: Drawing Chemical Structures • 57

 4. Move the end of the bond to other angles.
The Message area shows that the bond angle is
constrained to 15-degree increments. For more
information, see “Message Area” on page 58.
Administrator
The number on the left indicates the length of the
bond you are drawing. The number on the right
indicates the counterclockwise angle between the
bond and the positive X-axis.

Drawing Unconstrained Bonds Dative Bonds and Wedged

To draw a bond that is not constrained to a fixed
Bonds
length or fixed angle: Dative bonds and wedged bonds are drawn with a
fixed orientation in a document window.
1. From the Tools menu, choose Fixed Lengths
and Fixed Angles. To draw a dative bond:
The absence of a check mark next to the Fixed 1. Click the Dative Bond tool.
Lengths or Fixed Angles command in the Tools
2. Drag from the positive to the negative end
menu indicates the commands are deselected.
(arrow head) of the dative bond.
2. Click a bond tool.
3. Drag from one end of the bond to the other in a
document window.
You can draw any bond length and create any
angle relative to the X-axis. The Message area
displays the bond length and angle as you drag
the bond.
To draw a wedged bond:
Toggling Fixed Lengths and 1. Click one of the wedged bond tools.
Fixed Angles 2. Drag from the narrow end of the wedged bond
If Fixed Lengths or Fixed Angles are selected, you to the wide end of the wedged bond.
can temporarily deselect them.
To toggle Fixed Lengths and Fixed Angles:
• Shift+drag from one end of a bond to the other
end in the document window. To change the orientation of the dative or wedged
bond:
Message Area
• Click the center of the dative or wedge bond
As you draw bonds, information appears in the using the appropriate tool.
Message area at the lower left corner of a document
The orientation of the bond is inverted.
window. The message area shows the bond length
and angle the bond makes with the X-axis.

58 • Chapter 3: Drawing Chemical Structures ChemDraw

Specifying Units To add a bond by dragging:

The units used in the Rulers, Crosshair, and Drawing 1. Click a bond tool.
Settings can be can set to centimeters, inches, or 2. Point to an atom.
points.
To change the units:

1. From the File menu, choose Preferences. A highlight box appears over the atom
2. Choose a unit of measure from the Units menu. indicating where the bond will be joined.

3. Click OK. 3. Drag from the atom at which you are pointing to
the end of the new bond.
This change affects all documents.
A new bond is drawn and joined to the atom
Adding a Bond by Clicking
where the highlight box appeared.
To quickly add a fixed length bond:

1. Click a bond tool.

2. Click an atom.

Changing the Highlight Box

A new bond is drawn and is joined to the atom Size
you clicked.
The size of highlight box is controlled by the value
in the box labeled “Tolerance” in the Preferences
dialog box. The default setting for the Tolerance is 5
Bonds drawn by this method are always drawn using pixels. This means that the highlight box appears on
the Fixed Length specified in the Drawing Settings atoms if the pointer is located in a square region 10
dialog box. The angle that the deposited bond makes pixels on a side or +/- 5 pixels from the atom.
with its nearest neighbor is equal to the Chain Angle To change the Tolerance:
set in the Drawing Settings dialog box. If this angle
cannot be established, a smaller angle is used. 1. From the File menu, choose Preferences.
2. Select or type the tolerance, and then click OK.
Adding Bonds by Dragging
To control the orientation of bonds that you draw,
you can add bonds by dragging.
By using this dragging method for drawing the
bond, you can control the orientation of the other
end of the bond.

ChemDraw Chapter 3: Drawing Chemical Structures • 59

 Multiple Bonds Double Either Bonds
You can use the Solid, Dashed, Wavy, and Bold To draw a double either bond:
Bond tools to create the following multiple bonds: 1. Draw a double bond using the Wavy Bond tool.
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Double 2. Point to the center of the double bond and click.

Tautomeric Triple Bonds

You can draw a triple bond by drawing another
Aromatic single bond on top of a double bond. All bonds in a
triple bond are solid bonds.
To draw a triple bond:
Double Bold
1. Click any bond tool.
Double Either 2. Drag from one end of an existing double bond
to the other.
Triple
Quadruple Bonds
Quadruple To draw a quadruple bond:

1. Click any bond tool.

2. Drag from one end of an existing triple bond to
NOTE: You can also draw multiple bonds by
the other.
right-clicking over a bond and selecting the bond
type from the shortcut menu or by using the bond The triple bond changes to a quadruple bond.
properties dialog box. For more information, see
“Bond Properties” on page 142.

Double Bonds To change a quadruple bond into a single bond:

To draw a double bond: 1. Click any bond tool.

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.
2. Drag from one end of an existing quadruple
bond to the other.
The quadruple bond changes into a single bond
corresponding to the tool used to draw over the
bond.

A double bond is created. NOTE: You can also use the Eraser tool to reduce
the bond order. For more information, see “Deleting
Objects” on page 105.

60 • Chapter 3: Drawing Chemical Structures ChemDraw

Ring Tools To draw a ring:

1. Click a ring tool.

The following ring tools allow you to draw ring
sizes and types: 2. Position the pointer in a document window.

Cyclopropane Ring Tool The cyclohexane tool is shown below:

Cyclobutane Ring Tool

3. Drag from the beginning to the end of the first
Cyclopentane Ring Tool bond.

Cyclohexane Ring Tool

Cycloheptane Ring Tool

Cyclooctane Ring Tool When you point in a document window, the

pointer changes to a ring tool pointer. The
Cyclohexane Chair Ring Tool (1) highlight box on the ring tool pointer indicates
the atom that is drawn first. The bond directly
Cyclohexane Chair Ring Tool (2) below the highlight box is the bond that is
drawn first.
Cyclopentadiene Ring Tool
First atom drawn
Benzene Ring Tool
First bond
drawn
NOTE: If you are using a monitor with a resolution
of 640 x 480 or less, some tools are included on
palettes extending from other tools. An arrow on a
button indicates a palette is available.
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 Bonds” on page 57. dialog box. The ring is deposited in the
orientation shown on the ring tool icon.

ChemDraw Chapter 3: Drawing Chemical Structures • 61

 If you click an atom, the ring is fused to that atom.
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If you click a bond, the ring is fused to that bond.
If you click an atom in a ring, a spiro-linkage is
formed.
Drawing Cyclohexane Chair
Rings
You can draw Cyclohexane chair rings in two
orientations: horizontal and vertical.When you draw
a cyclohexane chair ring by clicking, the chair is
drawn in a horizontal orientation.
To orient a cyclohexane chair ring to a vertical
orientation:
1. Click one of the Cyclohexane Chair Ring
tools.
2. Shift+click in the document window and
Shift+drag to the orientation you want.
62 • Chapter 3: Drawing Chemical Structures
Horizontal Orientation Vertical Orientation
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:
1. Click a Ring tool.
2. Hold down Alt or Option and drag or click to
draw the ring.
A circle appears inside the ring.
NOTE: The circle is automatically grouped with
the ring when drawn. For more information on
grouping objects, see “Grouping Objects” on page
111.
Drawing Cyclopentadiene and
Benzene Rings
The double bonds in the cyclopentadiene or benzene
ring tools can be drawn in either of two forms.
When you draw a cyclopentadiene or benzene ring a
double bond is drawn first. The Cyclopentadiene
and Benzene Ring tool pointers indicate this
orientation.
ChemDraw
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
single bond to the end of the single bond.
• Shift+click in a document window to draw the
bond with a Fixed Length.
In the figure below, the arrow indicates the
direction in which the first bond is drawn.
When Fixed Angles is on, the angle the acyclic
chain makes relative to the X-axis is constrained to
15-degree increments.
Adding Chains
To add an acyclic chain to an existing atom:
1. Click the Acyclic Chain tool.
2. Point to the atom to which you want to attach
the chain.

3. Drag in the direction you want the chain to

grow.
Drawing Acyclic Chains
You can draw long hydrocarbon chains with the 2
Acyclic Chain tool .

Drawing Chains
To draw an acyclic chain: To specify a chain length:

1. Click the Acyclic Chain tool.
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
document window.
The Add Chain or Attach Chain dialog box
appears.

A number appears at the end of the chain

indicating how many bonds 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 position of
the first bond, and all subsequent odd-numbered 3. Type the number of bonds in the chain.
atoms, depend on the direction you drag. Before 4. Click Attach.
releasing the mouse button, this position can be
changed by dragging in the opposite direction.

ChemDraw Chapter 3: Drawing Chemical Structures • 63

 To add another chain of the same length anywhere in These settings apply simultaneously to all the bonds
a document window: in the active document. Changes made to any of
these settings affect the current document only.
• Alt+click or Option+click an existing atom or
click in an empty area within the document
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Changing the Line Width

window.
The thickness of bonds, lines, and arrowheads is
Changing Chain Direction specified in the Line Width box in the Drawing
Settings dialog box.
To change the direction of the chain as you draw:
• Hold down Alt (Windows) or Option
Line Widths
(Macintosh) while drawing chains in the
direction you want.

0.5 Point 1 Point 1.5 Point

To change the Line Width:

Changing the Chain Angle 1. From the File Menu, choose Drawing Settings.

All of the bond angles in an acyclic chain are equal.
The size of this angle is controlled by the Chain
Angle value in the Drawing Settings dialog box. The
angle is measured in degrees. You can set the angle
at any integral value between 1° and 179° degrees.
To change the chain angle:
1. From the File menu, choose Drawing Settings.
2. Type or select the Chain Angle.
3. Click OK.
This change affects the current document only.
2. Type a value in the Line Width box, and then
click OK.
Changing the Bold Width
The thickness of bold, hashed, and wedged bonds is
specified in the Bold Width box in the Drawing
Settings dialog box. The Bold Width setting must be
greater than the Line Width setting. The end of a
wedge is 1.5 times the bold width.
Bold Widths

Bond Drawing Settings

2 Point 4 Point 8 Point
ChemDraw provides four Drawing Settings that
affect the appearance of bonds: To change the Bold Width:
• Line Width • Type a bold width value in the Bold Width box,
• Bold Width and then click OK.

• Hash Spacing This change affects the current document only.

• Bond Spacing

64 • Chapter 3: Drawing Chemical Structures ChemDraw

Changing the Hash Spacing Editing Bonds
The spacing between the hash marks in hashed
You can modify the appearance of chemical
bonds and the dash marks in dashed arrows in curves structures by:
is specified in the Hash Spacing box in the Drawing
Settings dialog box. • Changing bond types
• Changing bond alignment and orientation
Hash Spacing
• Moving atoms
• Layering bonds
2 Point 4 Point 8 Point • Changing the bond order

To change the Hash Spacing: Changing Bond Types

• Type a hash spacing value in the Hash To change a single bond from one type to another:
Spacing box, and then click OK.
1. Click a bond tool.
Changing the Bond Spacing 2. Point at the center of an existing bond and
click.
The spacing between bonds in double and triple
bonds is measured as a percentage of the bond
length. The spacing is specified using the Bond
Spacing control arrows in the Drawing Settings
dialog box. You can set the bond spacing from 1 to The bond that you click changes to the new
100% of the bond length. bond type.

Bond Spacing

10% 14% 18%

Changing Double Bonds
To change the bond spacing: To change one type of double bond to another:

• Select or type the Bond Spacing. 1. Click the Bold, Dashed, or Solid Bond tool.

This change affects the current document only. 2. Point to one of the bonds in the double bond.

ChemDraw Chapter 3: Drawing Chemical Structures • 65

 3. Click the bond. Changing Alignment of Double
Bonds
The bonds in a double bond can have any one of
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three alignments relative to other bonds:

The double bond changes to the new bond type.
One of the bonds in the double bond is always a
solid or dashed bond.
NOTE: If you click a tautomeric bond
(solid/dashed) a second time with the dashed bond
tool, you create an aromatic double bond
(dashed/dashed).
Changing Orientation of
Wedged and Dative Bonds
When you draw or change a bond to a wedged or
dative bond, the orientation of the bond is chosen
appropriately.
To change the orientation:
• Click the dative or wedged bond with the tool
used to create it.
• Above
• Below
• Centered
To change the alignment of a double bond:
1. Click the bond tool used to create the existing
double bond.
2. Click the center of the double bond.
The alignment changes.
3. Click the center of the double bond again to
change to the next alignment.
Moving Atoms
You can use any of the bond tools to move an atom
within acyclic or cyclic structures. You cannot use a
ring tool.
To move an atom in a chemical structure:

1. Click a bond tool.

CO2H
2. Point at the atom to move.
A highlight box appears over the atom.
H
O
CH3
The dative or wedged bond is changed to the
opposite orientation.

3. Shift+drag the atom.

CO2H

H
O
CH3

66 • Chapter 3: Drawing Chemical Structures ChemDraw

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.
To convert ring types:
1. Point at atom and Shift-Drag.
2. Release when one atom is on top of the other.
The bond between the atoms disappears.
NOTE: You can also move atoms using a selection
tool. For more information see “Moving Objects”
on page 106.
Changing Bond Crossings
When one bond crosses another, white space is used
to indicate which bond is in front of the other.
To change which bond is in front:
1. Click any bond tool.
2. Double-click the bond to bring it to the front.
ChemDraw
The bond appears in front.
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
167.
NOTE: You can magnify your view to make
changing the bond layering easier. For more
information, see “Changing Perspectives” on page
153.
Adjusting Margin Width
To adjust the white space that surrounds a bond in
the region where one bond crosses another:
1. From the File menu, choose Drawing Settings.
2. Type a value in the Margin Width box.
3. Click OK.
The units used are those specified in the
Preferences dialog box.
This change affects the current document only.
Changing the Bond Order
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:
Chapter 3: Drawing Chemical Structures • 67
 To reduce the bond order:
1. Point to the bond to change and right-click
(Windows) or control-click (Macintosh).
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2. Choose the appropriate bond type from the
shortcut menu that appears.
NOTE: You can also use the eraser tool to reduce
the bond order. For more information, see “Deleting
Objects” on page 105.
Automatic Error
Checking
ChemDraw automatically checks for correct
chemical syntax as you draw. If ChemDraw finds an
error, a red box is displayed around the erroneous
object. The red box is display only and does not
print.
To view a description of the error, do one of the
following:
• Right-click on the error and choose Explain
This Warning.
• Select the structure and from the Structure
menu, choose Check Structure or Analyze
Structure.
For more information, see “Checking
Chemistry” on page 127 or “Analyzing a
Structure” on page 128.
To disable the automatic error checking:
• On the Tools menu, deselect Show Chemical
Warnings.
This setting applies to all documents.
To disable the automatic error checking on a specific
object:
• Right-click the object and choose Display
Warnings.
68 • Chapter 3: Drawing Chemical Structures
When Display Warnings is deselected for an object:
• Red boxes are not displayed for errors.
Errors are not reported by the Analyze Structure or
Check Structure commands. For more information
on the Analyze Structure and Check Structure
commands, see “Chapter 9: Working With
Structures”.
Automatic
Drawing—Structures
from Chemical Names
In ChemDraw Ultra only, you can draw a structure
automatically from a chemical name, by using the
Convert Name to Structure feature.
ChemDraw Ultra recognizes most organic
nomenclature. Most inorganic chemistry is
recognized, especially when the rules closely match
those for organic chemistry.
The following are not supported:
• Coordination complexes
• Polyboranes
• Isotopically-labelled compounds, except
deuterated compounds
• Polymers
• Some highly-bridged ring systems, including
fullerenes and porphyrins/porphines
• Some stereochemistry designators: +, -, +/-, +-,
D, L, DL, endo, exo, syn, anti, r, t, c
ChemDraw
Converting Names to Paste Special
Structures The Paste Special command allows you to paste
names copied to the clipboard from other
You can insert a name as a structure in the document
applications as a structure in ChemDraw.
window by using the
To paste a name copied to the clipboard from
• Insert Structure dialog box
another application:
• Paste Special command
1. Click in the document window.
Inserting Names 2. From the Edit menu, point to Paste Special,
For example, to insert 2-bromobenzoic acid: and then choose Name as Structure.

1. From the ChemDraw Ultra Structure menu,

The structure appears in your document.
choose Convert Name to Structure.
Converting Captions to
The Insert Structure dialog box appears.
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,

2. Type 2-bromobenzoic acid. choose Convert Name to Structure.
The molecular structure and name appear in the
NOTE: You can also copy a name to the drawing area.
clipboard and then type CRTL+V (Windows) or
Command+V (Macintosh) to paste the name
into the dialog box.

3. Click OK.
The molecular structure and name appear in the
drawing area.

Br

OH
2-bromobenzoic acid

ChemDraw Chapter 3: Drawing Chemical Structures • 69

Administrator

70 • Chapter 3: Drawing Chemical Structures ChemDraw

Chapter 4:
Drawing Captions and Atom Labels
Creating Text
ChemDraw enables you to create the following
types of text:
• Caption text—Create annotations, chemical
names, chemical formulas, page titles, and
information in tables.
OH
Caption Text
Phenol
• Atom label text—Identify atoms and
substructures by their chemical symbols and
formulas.
OH
Atom Label
Text
The text formatting options available depend on the
type of text you create. You create and edit caption
and atom label text with the Text tool.
ChemDraw does not install its own fonts. If a
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 “Using HotKeys to Label
Atoms” on page 76.
ChemDraw
Formatting Text
You can format text in any of the following ways:
• Caption Text Settings or Label Text Settings
dialog box—Specify format settings for all new
captions or labels. See “Specifying Caption
Label Text Format” on page 73 and “Specifying
Atom Label Text Format” on page 79.
• Text Menu—Specify format settings for
individual captions or labels. See “Changing
Caption Settings” on page 74 and “Changing
Text Label Settings” on page 80.
• Format dialog box (Windows)—Specify
several format settings for individual captions
and labels. for more information, see “Using the
Format Dialog Box (Windows Only)” on page
71.
NOTE: You can change a style using the key
combinations listed to the right of the style
command in the Style menu. You can change the size
of text selected with the lasso using the Resize
handle or Scale command from the Object menu.
Using the Format Dialog Box
(Windows Only)
Use the Format command on the Text menu to make
several format changes at a time, instead of choosing
individual formats from submenus.
Chapter 4: Drawing Captions and Atom Labels • 71
 To change the font, size, and style using the format
dialog box:
1. Select the multiple captions or atom labels
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using a selection tool, or individual captions or
atom labels with the Text tool.
From the Text menu, choose Format.
The Format dialog box appears.
2. Select a font, size, and style.
3. Click OK.
The new formats are applied to the selection or to the
new text you type.
This change affects all documents.
Creating Captions
The format of any new captions you create are
specified in the Captions Settings dialog box. To
change the settings before you type, see “Specifying
Caption Settings for New Captions” on page 73.
To create a caption:
1. Click the Text tool .
2. Point in an empty space in a document window.
72 • Chapter 4: Drawing Captions and Atom Labels
A caption text box with a flashing insertion
point appears.
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.
You can also click outside the Caption text box
in a document window to close the current
Caption text box and open a new Caption text
box.
NOTE: You can verify the chemical significance of
captions using the Check Structure command. For
more information, see “Check Structure” on page
127. You can use the Analyze Structure command to
calculate information about the caption. For more
information, see “Analyzing a Structure” on page
128. You must format the captions in Formula style
to use these commands. For more information see
“Specifying Caption Label Text Format” on page
73.
Changing the Caption Width
To change the width of a caption:
1. Select a caption using the Text tool.
The Caption text box appears around the
caption. The right side of the text box contains
a Resize handle.
Resize handle
2. Drag the Resize handle.
The point at which the text wraps is adjusted as
you drag the Resize handle.
ChemDraw
Editing a Caption
To open a caption for editing:
1. Click the Text tool.
2. Point at a caption and click to open the text box.
The caption text is highlighted.
To change all of the highlighted text within an open
text box:
• Type the new caption text over the highlighted
text.
The highlighted text disappears as you type the
new caption.
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:
• Drag the insertion point over a part of the
caption.
ChemDraw
Specifying Caption Label Text
Format
Each new caption you create has the font, size, and
style specified in the Text Settings dialog box. You
can change these format settings so that all new
captions you type use these specifications or you can
apply settings to existing captions with the Text
menu.
Changing caption defaults changes the format for all
newly created captions in the active window.
Specifying Caption Settings for New
Captions
To specify the font, size, and styles for new captions:
1. From the File menu, choose Caption Text
Settings (Windows) or Text Settings
(Macintosh).
2. A text settings dialog box appears. The
Windows dialog box is shown below.
3. Choose a Font, Size, and Style. On the
Macintosh, the settings are located in the
section labeled “New Captions”.
4. Click OK.
These settings affect all new captions in the current
document window. To use these settings in new
documents save them in a Style Sheet or Stationery
Pad.
Chapter 4: Drawing Captions and Atom Labels • 73
 Changing Caption Settings
NOTE: If the captions you select have more than a
To change the font, size, or style for a specific single font or size, a hyphen appears next to each
caption or captions: font or size that is contained within the selection.
Choosing a new font or size changes all of the
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• Select the caption or captions to change with a

selection tool.
To change only a part of a single caption you must
use the Text tool:
• Select part of the caption with the Text tool.
To specify a font for a selected caption:
selected text to the new font or size.
You can specify the following baseline styles:
• Superscript—Reduces the font size of caption
text by twenty-five percent and raises its
baseline.

1. On the Text menu, point to Font, and then do

• Subscript—Reduces the caption text by
one of the following: twenty-five percent and lowers the baseline.
• Formula—Automatically subscripts numbers.
If the font you Then… To specify the style of the selected caption text:
want is …
• On the Text menu, point to Style, and then
choose a style.
displayed choose the font.
You can apply several styles to the same selected
caption. You can also apply multiple styles to
not displayed a. Choose Other.
different portions of a single caption.
b. Type the font. If the captions you select have more than one style,
a hyphen appears next to each style that is applied to
2. Click OK. a portion of the selection. A check mark appears
To specify the size for selected text: next to each style that applies to all of the selected
text. Choosing a style, except Plain, adds the new
1. On the Text menu, point to Size, and then do style to all of the selected captions. Previously
one of the following: applied styles are not affected.

If size you Then … Justifying Captions

want is … All new captions you create are Flush Left and the
line spacing is chosen automatically. You specify
displayed choose the size. different settings using the Justification and Line
Spacing commands on the Text menu. All text in a
not displayed a. Choose Other. single caption must have the same Justification and
Line Spacing.
b. Type the size.

2. Click OK.

74 • Chapter 4: Drawing Captions and Atom Labels ChemDraw

There are four available justifications: To specify the spacing between caption lines:
• Flush Left—creates left-justified caption text. 1. Select a caption with a selection tool.
2. From the Text menu, choose Line Spacing.
The Line Spacing dialog box appears.

• Centered—creates centered caption text.

• Flush Right—creates right-justified caption

text. 3. Take the appropriate action:

If you want to Click …

specify …

• Justified—creates right-left justified caption Automatic line Automatic.

text. spacing

Variable line spacing Variable.

Fixed line spacing a. Fixed.

To specify the justification of captions: b. Type a value in the

1. Select a caption with a selection tool.
2. From the Text menu, choose a justification.
Specifying Caption 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
spacing that you specify.
text box labeled
“Fixed at”.
Adding Chemical
Names
In ChemDraw Ultra only, you can insert the name of
a selected structure as a caption using the Convert
Structure to Name command from the Structure
menu.
The conversion of a structure to a name is limited by
the following:
• Stereochemical information is ignored
• Structures must contain fewer than 125 atoms
(excluding implicit hydrogens)

ChemDraw Chapter 4: Drawing Captions and Atom Labels • 75

 • Rings and chains must contain fewer than 44
atoms
• Isotopic variation, charged carbon atoms,
radicals and multi-component species are
Administrator
ignored
• 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:
1. Select the drawing for which you want to insert
a name.
2. From the Structure menu, choose Convert
Structure to Name.
Cyclohexane
The name of the structure appears as a caption
under your drawing.
The chemical naming features are provided by
AutoNom. To view information about Autonom:
• From the Structure menu, choose About
AutoNom.
76 • Chapter 4: Drawing Captions and Atom Labels
Using HotKeys to Label
Atoms
Use ChemDraw HotKeys to quickly label atoms and
apply atom properties. The file CS ChemDraw
Hotkeys.txt in the cd_items directory (Windows) or
CS ChemDraw HotKeys (Macintosh) in the
ChemDraw Folder (Macintosh), contains the
HotKeys provided with ChemDraw. You can add or
change HotKeys by editing the file in a text editor.
Use the following methods to label an atom with a
HotKey.
Method 1: Labeling the last
atom drawn
1. Draw a bond.
2. Press a HotKey.
The last atom drawn is labeled. Each time you
draw a bond, the last atom drawn is the HotKey
atom.
Method 2: Labeling an atom by
pointing
1. Using a bond tool or the Text tool, position the
pointer over an atom.
A highlight box appears over the atom.
2. Press a HotKey, for example, “c”.
H3C
The label is added to the atom highlighted. If
the label is a single element, such as “C”, then
the appropriate number of hydrogen atoms are
added to the label.
ChemDraw
Method 3: Labeling an atom HotKey Function
with a selection tool
/ (slash) Displays the Atom Properties
1. Using a selection tool, position the pointer over dialog box when pointing to an
an atom. atom or the Bond Properties
dialog box when pointing to a
Highlight boxes appear over the atom.
bond.

= (equal) Displays the List Nickname

dialog box.
2. Press a HotKey, for example, “c”.
. (period) add an attachment point.

C
H2
Creating HotKeys
To add or edit ChemDraw HotKeys:
Method 4: Labeling multiple • Open CS ChemDraw Hotkeys.txt in the
atoms cd_items directory (Windows) or
CS ChemDraw HotKeys (Macintosh) in the
1. Select several atoms using a selection tool. ChemDraw Folder.
The file contains a simple list using the format
shown below.

2. Press a HotKey, for example, “c”.

The selected atoms are labeled.

H 3C
C
H2

The element or label associated with the

HotKey is added to the structure.

Hard-Coded HotKeys
You cannot edit hard-coded HotKeys. The following
table contains a list of hard-coded HotKeys:

HotKey Function

Enter or Opens the atom label text box.

Return
space Removes an atom label.

ChemDraw Chapter 4: Drawing Captions and Atom Labels • 77

 You can use any uppercase or lowercase
alphanumeric key as a HotKey with the exception of
the hard coded HotKeys listed previously. If a
capital and lowercase HotKey do not exist, the
Administrator

HotKey is assigned to both. If a key is used more 3. Click the atom.

than once in the file, the one closer to the end of the
file takes precedence. An Atom Label text box appears over the atom.

To add a HotKey:

1. Add a new line and type the key you want to

use.
2. Type a space.
3. Type the letters to associate with the HotKey.
4. HotKeys defined for single elements always
result in the adding of the appropriate number
of hydrogen atoms.
To create a new HotKeys file:
1. Create a text file named CS ChemDraw
Hotkeys.txt (Windows) or ChemDraw
HotKeys (Macintosh).
2. Save the file in the cd_items directory
(Windows) or the ChemDraw Folder
(Macintosh).
3. Click OK or Save.
4. Type an atom label.
Numbers are automatically subscripted. The
justification you choose determines how the
letters in an atom label are positioned on a bond.
Numbers, leading open parentheses, and
trailing closed parentheses are ignored in the
positioning of atom labels. For more
information, see “Justifying Atom Labels” on
page 81.
5. Close the Atom Label text box.
You can also click outside the current Atom Label
text box on another unlabeled atom to open a new
Atom Label text box.

NOTE: You can use HotKeys to label an atom

Labeling Atoms with the instead of using the Text tool. You can also label
Text Tool atoms using Nicknames that are text representations
of substructures. For more information, see “Using
To place an atom label on an atom: HotKeys to Label Atoms” on page 76 and “Using
Nicknames” on page 113.
1. Click the Text tool .
2. Point to an atom.
The pointer changes when it is positioned
correctly over an atom to indicate that you will
create an atom label rather than a caption.

78 • Chapter 4: Drawing Captions and Atom Labels ChemDraw

Specifying the Margin Width
You can adjust the white space surrounding the atom
label can so some of the attached bond is hidden.
To adjust the white space:
1. From the File menu, choose Drawing Settings.
2. Type a new Margin Width value.
3. Click OK.
Editing Atom Labels
To edit an atom label:
1. Click an existing label using the Text tool or
double-click using a bond or ring tool.
The highlighted atom label text appears within
the Atom Label text box.
Specifying Atom Label Text
Format
Each new atom label uses default settings for the
font, size, and style of captions and atom labels. You
can change the format by choosing new formats
before you type, or by selecting text and applying
the new formats after you type.
Changing atom label defaults affects all existing
atom labels and newly created atom labels within
the active document.
Changing Default Settings
Use the Caption Text Settings and Label Text
Settings to change the default settings for captions
and atom labels. The default settings apply to the
active document only. To use these settings in other
documents you can save them in a Style Sheet.

Setting Default Atom Label Font, Size,

and Style
2. Type the new atom label text over the
To change the font, size and styles for all atom labels
highlighted text.
in the active document window:
If all the text is not highlighted, and you want to
select all of the atom label: 1. From the File menu, choose Label Text
Settings.
• From the Edit menu, choose Select All.
To edit part of the atom label: The Label Text Settings dialog box appears.

1. Drag the insertion point over part of the atom

label.
2. Type the new characters.
3. Close the Atom Label text box.

Deleting an Atom Label

To delete an atom label, leaving the underlying
bonds unchanged, do one of the following:
• Click the Eraser tool and then click the atom
label.
• With the atom label selected, press the
spacebar or delete HotKey.

ChemDraw Chapter 4: Drawing Captions and Atom Labels • 79

 2. Select a font, size, and style.
If the font you Choose …
NOTE: If you save a new style sheet, this also want is …
changes any atom labels you create in future
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documents. not displayed 1. Choose Other.

2. Type the font.

Changing Text Label Settings
You can change the text settings for individual labels 3. Click OK.
using the Text menu.
To specify the size for a selected caption text:
You can change the default Font, Size, or Style in
one of the following ways: 1. On the Text menu, point to Size, and then do
one of the following:
• For new text, before you begin typing, choose
the font style and size that you want from the If the size you Then …
Text menu. want is …

• To edit existing text, select the labels using a displayed • Choose the size.
selection tool or individual atom labels with the not displayed 1. Choose Other.
Text tool and specify settings with the Text
menu. 2. Type the size.

NOTE: If the labels you select have more than a
single font or size, a partial selection mark appears
next to each font, size, or style. Choosing a new font
or size changes all of the selected text to the new font
or size. Choosing a style adds the new style to all of
the selected atom labels without affecting styles
previously applied.
3. Click OK.
You can specify the following baseline styles:
• Superscript—Reduces the label text font size
by twenty-five percent and raises its baseline.
• Subscript—Reduces the label text by
twenty-five percent and lowers the baseline.

To specify a font for a selected caption: • Formula—Automatically subscripts numbers.

To specify the style of the selected caption text:
• On the Text menu, point to Font, and then do
one of the following: • On the Text menu, point to Style, and then
choose a style.
If the font you Choose … The superscript style is shown below.
want is …

displayed • Choose the font.

80 • Chapter 4: Drawing Captions and Atom Labels ChemDraw

Justifying Atom Labels
Use the Automatic, Centered, Flush Left, Flush
Right, and Stacked Above justifications from the NCH3
Text menu to create labels that identify atoms and
functional groups in your chemical structure without If you label C5, the tokens are placed from right to
obscuring any bonds or other atom labels. left because there are bonds to the right of the atom:

Examples of the atom label justifications are shown

below.
H3CN
OMe RNH
CH2 In ChemDraw Pro, you can force an entire
N multi-atom label to be a token by defining it as a
Nickname. This prevents the label from flipping
when applied to the left side of a structure.

Stacked Above Centered For example, if you define the Nickname “CH3”,
and label C-5 with the combined label and nickname
“NCH3”, the final orientation is “CH3N” instead of
“H3CN”. In this case, the Nickname, “CH3”, is a
N N token. For more examples, see “Using Nicknames”
CH2 H2C on page 113.
OMe MeO
If you label C-1, the second and third tokens are
Flush Left Flush Right
placed above the first token since there are bonds
below the atom.
Justifying Automatically
When you justify Atom labels automatically, CH3
ChemDraw breaks the label into tokens. A token N
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
without obscuring other parts of the chemical If you label C-4, the second and third tokens are
structure. placed below the first token.

For example, to create N-methylpiperidine, label an

atom in cyclohexane with the atom label “NCH3”,
which contains the three tokens, “N” and “C” and
“H3”. If you label C3, the tokens are placed from left N
to right because there are bonds to the left of the CH3
atom.

ChemDraw Chapter 4: Drawing Captions and Atom Labels • 81

 Setting Automatic Justification
The default atom label justification is Automatic. To
turn off automatic justification:
Administrator
1. From the File menu, choose Preferences.
2. Deselect Automatic Atom Labels.
3. Click OK.
To turn off Automatic Atom Labels for an individual
atom:
1. Select an atom label.
2. From the Text menu, choose a justification
other than Automatic.
Justifying with Stacked Above
To create an atom label using the Stacked Above
justification:
1. Select an atom to label.
2. From the Text menu, choose Stacked Above.
3. Type the top row of characters
4. Create a new line.
5. Type the next line of characters.
The atom label appears as a stack.
6. Repeat step 4 and step 5 until the entire stacked
atom label is created.
7. Close the Atom Label text box.
The bonds are drawn to the first character in the
last row that you typed.
82 • Chapter 4: Drawing Captions and Atom Labels
Justifying Flush Left
To create an atom label using the Flush Left
justification:
1. Select an atom to label.
2. From the Text menu, choose Flush Left.
3. Type the first row of characters.
4. Create a new line.
5. Type the second row of characters.
6. Repeat step 4 and step 5 until all rows in the
atom label are created.
7. Close the Atom Label text box.
Justifying Flush Right
To create an atom label using the Flush Right
justification:
1. Select the atom to label.
2. From the Text menu, choose Flush Right.
3. Type the first row of characters.
Flush Right justification attaches the last
uppercase character in the first line to the bond.
4. Create a new line.
5. Type the next row of characters
6. Repeat the step 4 and step 5 until all the atom
label rows are created.
7. Close the Atom Label text box.
ChemDraw
Justifying Centered 2. From the Text menu, choose Line Spacing.

Centered justification places the same number of The Line Spacing dialog box appears.
characters (including numbers) be on each side of
the atom label joining the bond. For example,
CH3NCH3 will be centered on the nitrogen, whereas
RNCH3 will be centered on the carbon.
To create an atom label that has Centered
justification:
1. Select an atom to label.
2. From the Text menu, choose Centered. 3. Take the appropriate action:

3. Type a row of characters so the center character If you want to Click …

is the character you want connected to the bond. specify …
Automatic line Automatic.
spacing
Variable line Variable.
spacing
Fixed line 1. Fixed.
spacing
4. Create a new line, if necessary. 2. Type a value in the
text box labeled
5. Type the second line of characters.
“Fixed at”.
6. Repeat step 4 and step 5 until the atom label is
completed.
NOTE: The line spacing of ChemDraw version 2.x
7. Close the Atom Label text box.
documents opened in ChemDraw version 6.0 is
automatically set to Fixed Line spacing to maintain
NOTE: For precise control of atom label vertical alignment.
alignment, see“Multi-Attached labels” on page 119.

Repeating an Atom
Specifying Atom Label
Label
Line Spacing
You can repeat an atom label using the text, bond, or
You can adjust the spacing between the lines of an ring tools.
atom label using the Line Spacing command in the
Text menu. Variable line spacing is the default for To label several atoms with the same text using the
atom labels. Text tool:

To specify the spacing between the lines of an atom 1. Click the Text tool.
label: 2. Label a single atom.
1. Select an atom label with a selection tool. 3. Double-click another atom to repeat the
previous label.

ChemDraw Chapter 4: Drawing Captions and Atom Labels • 83

 To label several atoms with the same text using a
bond, ring, or Acyclic Chain tool: NOTE: The characters available differ in different
fonts. A list of all characters available in each font
1. Click the tool. how to type them is available in the KeyCaps menu
item of the Macintosh Apple menu or the Character
Administrator

2. Triple-click an atom to repeat the previous

Map application in the Windows Accessories.
label.

Typing Non-Roman Text Labeling Atoms With a

ChemDraw uses standard methods for entering all Bond or Ring Tool
types of text, including the Greek characters and
other symbols commonly used in chemistry. To avoid switching back and forth between tools,
you can label atoms with a bond or ring tool.
To enter Greek characters:
To label an atom using a bond or ring tool:
1. Click in a text box with the text tool.
1. Click the Bond or Ring tool.
2. On the Text menu, point to Font, and then
2. Point to an atom and double-click.
choose Symbol.
3. Type the text. For example, an “a” is a lower-
case alpha, a “P” is a capital pi.
To enter additional non-Greek text in the same text
box:
An atom text label appears over the atom.
• On the Text menu, point to the Font, and select
the previously selected font.
To enter a degree symbol:

1. Click in a text box with the text tool.

2. Take the appropriate action:

If you’re Then …
Using the Text Tool with
using … the Lasso Tool
Macintosh • Press Option+Shift+8. The Text tool used in conjunction with a selection
Windows 1. Press Num Lock. tool enables you to perform additional edits, such as
simultaneously changing several captions or atom
2. Hold down ALT. labels. For more information about selection tools,
see “Chapter 7: Manipulating Drawings”.
3. Type 0, 1, 7, 6 using the
keypad.

4. Release ALT.

84 • Chapter 4: Drawing Captions and Atom Labels ChemDraw

You can toggle between the Text tool and the Lasso
tool as follows:
Using Bitmap Fonts
• Press Ctrl+Alt+Tab or When Available
Command+Option+Tab.
The text box is automatically selected when you
(Macintosh)
switch to the lasso tool. When text appears in a document on the screen, it
To switch from the Lasso tool to the Text tool when can appear using either a bitmap or a TrueType font.
a caption or atom label is selected: To use bitmap fonts if they are available:
• Press Ctrl+Alt+Tab or
1. From the File menu, choose Preferences.
Command+Option+Tab.
The Text tool is selected and the text box is 2. Select Use Bitmap Fonts When Available.
opened for editing. Text drawn using Bitmap fonts looks better and
appears more quickly than text drawn using
Creating a New Line and TrueType fonts. However, the size and position of
text drawn using Bitmap fonts change somewhat
Closing Text Boxes when printed.
The default way to create a new line in a Caption or For accurate correspondence between what you see
atom label text box is to press Enter or Return. To on the screen and what is printed:
close the text box, you click outside the text box or
• Deselect Use Bitmap Fonts When Available.
select another tool.
This change affects all documents.
You can change the default and use Enter or Return
to close the text box and press Ctrl+Enter or
Option+Return to create a new line by doing the
Creating Tables
following: ChemDraw allows you to create tables of text using
the Tab key with the Text tool.
1. From the File menu, choose Preferences.
2. Take the appropriate action: Creating the First Row (column
headings)
To change the Select …
default for … To create the first row and establish the columns of
a table:
Caption text • Require Ctrl+Enter to
1. Click the Text tool.
Create New Line in
Captions. 2. Click in a document window where you want
the table to start.
Atom Label text • Require Ctrl+Enter to 3. Choose a font, size, and style from the Text
Create New Line in
menu, and then type a caption.
Atom Labels.
4. Press Tab.
3. Click OK. A second caption box appears.

ChemDraw Chapter 4: Drawing Captions and Atom Labels • 85

 5. Choose a font, size, and style from the
appropriate submenu in the Text menu and then
type a second caption.
The second column is placed 20 points
Administrator
(20/72 inch, 0.71 cm) to the right of the first.
6. Press Tab again to create a third column, and so
on.
NOTE: The style, font, and size that you set in each
column are maintained in all the rows that follow.
The following illustration shows the creation of new
columns using the Tab key.
Compound M.W. LogP LD50
tab tab tab
To change the spacing between columns one point at
a time while editing a caption:
1. Select the caption.
The caption is automatically selected with a
selection tool.
2. Move the caption with the arrow keys.
For more information on moving objects, see
“Moving Objects” on page 106.
To create another column with this same spacing as
the previous:
• Press Tab.
A third caption text box appears.
Creating a New Row
To start a new row that is exactly aligned with the
first:
• Press Tab twice at the end of a row.
A caption text box appears exactly aligned
under the first caption positioned exactly 20
points below the first caption in the first row.
86 • Chapter 4: Drawing Captions and Atom Labels
The following diagram illustrates the creation of a
new row.
Compound M.W. LogP LD50
tab twice
1
To change the spacing between rows as you create
the table:
1. Select the captions in a row.
2. Move the captions using the arrow keys.
For more information on moving objects, see
“Moving Objects” on page 106.
To continue and fill in the row with captions:
• Press Tab to create another caption in the row,
and then press Tab twice to begin a new row.
The spacing between the newest row and the
row directly before it have the same spacing
that you specified between the previous two
rows.
Adjusting Row or Column
Spacing
To use a selection tool to adjust the spacing in a
table:
1. Select all of the captions with a selection tool.
2. Shift+drag the caption.
The movement is constrained to the X-axis or Y-axis
so that you can maintain the row or column
alignment.
Moving Around Within Tables
To move within an existing table:
1. Select the Text tool and select a caption.
2. Press Alt+Arrow or Option+Arrow to move to
the next caption in the direction of the arrow.
ChemDraw
Alternatively, you can use the following key To fill in the inserted row with caption text:
combinations:
1. Click the Text tool and select the first caption in
the inserted row.
Use … To move …
2. Type new text.
Tab (Windows) Option+Tab right 3. Press Tab to move to the second caption in the
(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.

Inserting a New Row

To insert a row:

1. Select a selection tool and select a row of

captions.
2. Shift+drag the selected row.
Shift constrains the movement to the Y-axis to
maintain the column alignment.
3. Select the first caption in the row above or
below the space you created.
4. Shift+Alt+drag or Shift+Option+drag to create
a copy of the caption and position it in the
empty space you created.
The placement of this copied caption sets the
position of the inserted row.

ChemDraw Chapter 4: Drawing Captions and Atom Labels • 87

Administrator

88 • Chapter 4: Drawing Captions and Atom Labels ChemDraw

Chapter 5: Drawing
Orbitals and Chemical Symbols
Overview To draw an s-orbital:

1. Hold down the mouse button over the Orbital

ChemDraw provides two tools that allow you to add
chemical symbols to your structures: tool and drag to select the s-orbital tool
from the palette.
• The Orbital tool
2. Point to an atom where the orbital will be
• The Chemical Symbols tool centered.

The Orbital Tool

Use the orbital tool to add orbitals to your chemical
structures. You draw orbitals so that the node 3. Drag outward.
appears first. Depending on the orbital type, fill
patterns of white, gray, or black are available.
The Message area shows the orbital’s length and
angle relative to the X-axis while you draw it. You
can constrain the length and angle of an orbital by
selecting Fixed Lengths and Fixed Angles on the
Tools menu.
Sigma Orbitals
The σ-orbital tools are shown below:
NOTE: Orbitals are not normally part of the
structure they are drawn near and are not selected
when you double-click a bond, atom, or atom label
with a selection tool. To group the orbitals with the
To draw a σ-orbital:
structure, use the Group command from the Object
menu. For more information, see “Grouping 1. Hold down the mouse button over the Orbital
Objects” on page 111. tool and drag to select the σ-orbital tool
from the palette.
s-orbitals 2. Point where the orbital will be centered.
The s-orbital tools are shown below: 3. Drag outward along the long axis of the orbital.

ChemDraw Chapter 5: Drawing Orbitals and Chemical Symbols • 89

 Single Lobe Orbitals 2. Point to an atom where the node of the orbital is
to be attached.
Single lobe orbitals are commonly used for
indicating a lone pair. The single lobe orbital tools
Administrator

are shown below:

3. Drag from the orbital node to the wide end of

the filled lobe.

To draw a single lobe orbital:

1. Hold down the mouse button over the Orbital

tool and drag to select the single lobe
orbital tool from the palette.
2. Point to an atom where the narrow end of the
Hybrid Orbitals
orbital is to be attached.
The hybrid-orbital tools are shown below:

3. Drag from the narrow end of the lobe to its wide

end. To draw a hybrid orbital:

1. Hold down the mouse button over the Orbital

tool and drag to select the hybrid-orbital
tool from the palette.
2. Point to an atom where the node of the orbital is
to be attached.

p-orbitals 3. Drag from the orbital node to the wide end of

the major lobe of the orbital.
The p-orbital tools are shown below:

To draw a p-orbital:

1. Hold down the mouse button over the Orbital

tool and drag to select the p-orbital tool
from the palette.

90 • Chapter 5: Drawing Orbitals and Chemical Symbols ChemDraw

d-orbitals 3. Drag from the center of the orbital to the wide
end of a lobe.
The d-orbital tools are shown below:

To draw a d-orbital:

1. Hold down the mouse button over the Orbital

tool and drag to select the d-orbital tool The Chemical Symbols
from the palette.
2. Point to an atom where the node of the orbital is Tool
to be attached. Use the Chemical Symbols tool to add
3. Drag from the center of the orbital to the wide chemical symbols to your structure. When you click
end of a filled lobe. the Chemical Symbols tool, the following palette
appears:

If you click an atom and then click the Symbol tool,

the charge, radical, or free site symbols are created
dz2-orbitals at a fixed distance from the atom they are associated
The dz orbital tools are shown below:
2-
with. If you immediately drag the symbol to any
position around an atom, it remains at that fixed
distance. You can, however, select a symbol
separately and move it anywhere or resize it.

To draw a dz orbital:
2- When you attach a symbol to an atom, it remains at
a fixed distance from the central character of the
1. Hold down the mouse button over the Orbital atom label.
tool and drag to select the dz2-orbital tool
from the palette. H-dot and H-dash
2. Point to an atom where the node of the orbital To represent a hydrogen atom that is coming out of
will be attached. the plane toward you along the Z-axis, use the H-dot
symbol .
To represent a hydrogen atom that is directed
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.

ChemDraw Chapter 5: Drawing Orbitals and Chemical Symbols • 91

 To draw an H-dot or an H-dash: The lone pair is offset from the atom at a fixed
position.
1. Hold down the mouse button over the
Chemical Symbols tool and drag to select
Administrator

the symbol from the palette.

OH
2. Point to the atom.

O
To deposit a lone pair symbol in a horizontal
orientation:
O
• Click in a document window.

Radical
3. Click the atom. Use the radical symbol to indicate a single
non-bonded electron.
O
To draw a radical symbol:

O
1. Hold down the mouse button over the
Chemical Symbols tool and drag to select
the radical from the palette.
H-dot symbol
O
2. Pooint to the atom where you want the radical
Lone Pair symbol to appear.
3. Click to draw the symbol.
Use the lone pair symbol to indicate a lone
pair of electrons common in Lewis structure
representations.
Radical Cation and Radical
Anion
To draw a lone pair:
Use the charge radical symbols to
1. Hold down the mouse button over the represent radicals that are charged.
Chemical Symbols tool and drag to select
the lone pair from the palette. To draw a radical cation or radical anion symbol:

2. Point to the atom where you want the lone pair 1. Hold down the mouse button over the
located and drag in the appropriate direction to Chemical Symbols tool and drag to select
position it. the symbol from the palette.
3. Release the mouse button. 2. Point to the atom where you want the symbol to
appear.
3. Drag from the charge portion of the symbol to
the radical portion of the symbol.

92 • Chapter 5: Drawing Orbitals and Chemical Symbols ChemDraw

To quickly deposit a radical cation or radical anion
symbol in a horizontal orientation.
• Click to deposit the symbol.
Charge Symbols
Use the charge symbols shown below to represent
charges on structures.
These symbols indicate that the molecule with
which they are associated represents on of the
following:
• A racemic mixture
• A pure enantiomer of known configuration
• A pure enantiomer of unknown configuration
The font and size for stereochemical flags is
determined by the default Atom Label size for the
document.

To draw a charge and associate it with a structure: To draw a stereochemical flag:

1. Hold down the mouse button over the 1. Hold down the mouse button over the
Chemical Symbols tool and drag to Chemical Symbols tool and drag to select
select the charge symbol from the palette. the flag you want from the palette.
2. Position the pointer next to the structure to
2. Click to the atom to which you want the charge
to correspond. which you want to assign the flag.
3. Click to deposit the symbol.
NH3
O
Free Sites
H2N
Use the Free Sites tool to increment or decrement
H OH
the number of free sites in a query structure.
The number of hydrogen atoms increases or
decreases as appropriate for the addition of the To increment the number of Free Sites:
charge. 1. Hold down the mouse button over the
Chemical Symbols tool and drag to select
NH3 the Free Site symbol from the palette.
O
H3N 2. Position the pointer over the atom to which you
H OH want to apply free sites.
3. Click to add the symbol.
Stereochemical Symbols
4. Continue to click the atom to increment the free
ChemDraw provides three types of stereochemical site number.
flags:
To decrement the number of free sites:
• Racemic • Hold the Alt key while clicking the atom.
• Absolute You can also change the free sites by using the Atom
• Relative Properties dialog box or the shortcut menu. For
more information see “Atom Properties” on page
137.

ChemDraw Chapter 5: Drawing Orbitals and Chemical Symbols • 93

 Rotating a Symbol
With the exception of the charge and the radical
symbols, you can rotate the symbols by selecting
Administrator

and dragging the Rotation handle on the Selection

Rectangle. All symbols are rotated around the same
end from which they were originally drawn. For
example, the radical cation symbol is rotated and
resized from the charge. The Message area shows
the angle that one of the ends of a symbol makes
with the X-axis as you rotate symbols.
To rotate a chemical symbol:

1. Select the chemical symbol with a selection

tool.
2. Drag the Rotation handle on the chemical
symbol.
For more information about rotating and resizing,
see “Rotating Objects” on page 108.

94 • Chapter 5: Drawing Orbitals and Chemical Symbols ChemDraw

Chapter 6: Drawing
Arrows, Arcs, and Other Shapes
Overview The Arrow Tool
ChemDraw provides four tools that enable you to Use the Arrow tool to add arrows to show the
add shapes to your documents: conversion of reactants to products and to indicate
electron flow.
• Arrow tool—to draw arrows
• Drawing Elements tool—to draw boxes,
NOTE: Use the Pen tool to make customized
circles, and brackets arrows. For more information, see“The Pen Tool”
• Arc tool—to draw arcs on page 99.
• Pen tool—to draw freehand shapes
Selecting an Arrow
Selecting Tools from the To select an arrow:
Palette • Hold down the mouse button over the Arrow
The Arrow, Arc, and Drawing Elements tools each tool and drag to select the arrow type
contain a palette with different types of that tool. from the palette.
When you choose a tool type from the palette, it
becomes the default. To use a different tool type,
select it.
To select a tool and use its default tool type:
• Click the tool’s icon to select it.
To choose a different tool type from the palette:

1. Point to the tool’s icon and hold down the

mouse button.
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.

ChemDraw Chapter 6: Drawing Arrows, Arcs, and Other Shapes • 95

 Drawing an Arrow The Drawing Elements
To draw an arrow:
Tool
1. Click the Arrow tool .
Administrator

The Drawing Elements tool provides shapes you can

2. Point in the document where you want the add to your drawing.
beginning of the arrow to appear.
Drawing elements are not a part of the structure they
3. Drag to where you want the arrowhead to be. are drawn near. If you double-click on a bond, atom,
or atom label with a drawing tool, they are not
Editing an Arrow selected. To group drawing elements with a
To lengthen, shorten, or rotate an arrow: structure, use the Group command in the Object
menu. For more information, see “Grouping
1. Click the Arrow tool . Objects” on page 111.
2. Hold down Shift and point to the head of the
Some drawing element types are available with fill
arrow.
patterns: hollow (no fill pattern), gray, and black.
A highlight box appears over the head of the You can change the type of box, circle, or oval using
arrow. the Curves menu.
3. Drag the arrowhead.
The Message area indicates the length and angle
The arrow is resized and rotated relative to its end. relative to the X-axis while you use any of the
The Message area indicates the change in length and drawing element types.
the angle the arrowhead makes with the X-axis as
you drag. Selecting a Drawing Element
You can resize and rotate an arrow using a selection To select a Drawing Element:
tool by dragging the Resize or Rotation handle on • Hold down the mouse button over the Drawing
the Selection rectangle. The resize or rotation occurs
Elements tool and drag to select the
around the center of the Selection rectangle. The
element from the palette.
Message area 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
more information, see “Rotating Objects” on page
108 and “Resizing Objects” on page 109.

96 • Chapter 6: Drawing Arrows, Arcs, and Other Shapes ChemDraw

Drawing Boxes 2. Point where you want the bracket to start.

To draw a box: 3. Drag from one end of the bracket to the other
end.
1. Select one of the box tools shown below.
Drawing Paired Brackets
Paired brackets can only be placed in a vertical
orientation. A rectangle or box defines their
position.
To draw a paired brackets:
2. Point where you want a corner of the box to be
located 1. Select a paired bracket tool.
3. Drag from one corner of the box diagonally to
the opposite corner.

Drawing Circles and Ovals 2. Point where you want a corner of the bracket to
To draw a circle or oval: be located.
3. Drag from one corner of the box diagonally to
1. Select one of the circle or oval tools shown
the opposite corner.
below.
Drawing Lines
Lines drawn with the line tool differ in two
significant ways from bonds drawn with the bond
tools:
2. Point where you want the center of the circle to • They are not included in chemical interpretation
be located. of the drawing.
3. Drag outward from the center. • Lines that cross appear solid.
To draw using line tool:
Drawing Brackets
Brackets includes braces {}, brackets [], and 1. Select a line tool.
parentheses ().

Single Brackets
2. Point where you want the line to start.
A single bracket can be drawn in any orientation.
3. Drag from one end of the line to the other end.
To draw a single bracket:

1. Select a single bracket tool.

ChemDraw Chapter 6: Drawing Arrows, Arcs, and Other Shapes • 97

 Drawing Daggers
To draw a dagger:
1. Select a dagger tool.
Administrator
2. Point where you want the symbol to be located.
3. Click to deposit the dagger.
NOTE: The size of the dagger symbol is
proportional to the Atom Label font size specified in
the Text Settings dialog box.
Resizing or Rotating Drawing
Elements
A drawing element is resized or rotated from the
same point that it was originally drawn. For
example, a shadowed box is resized from the corner
where the plain edges meet.
You cannot rotate Boxes, Brackets, or Daggers.
When a box or closed bracket is rotated along with
objects within its borders, the area of the box or
closed bracket increases to accommodate the
rotation of the contained objects.
To resize or rotate a drawing element:
1. Select the Drawing Element tool.
2. Hold down 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 Message area indicates percentage
enlarged or reduced when you drag the Resize
handle and the number of degrees the object
rotates when you drag the Rotation handle.
98 • Chapter 6: Drawing Arrows, Arcs, and Other Shapes
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
with fill the same color as the curve. You can also
distort boxes and closed brackets.
The remaining Drawing Element types cannot be
distorted. For more information, see “Rotating
Objects” on page 108 and “Resizing Objects” on
page 109.
The Arc Tool
Use the Arc tool to draw solid or dashed arcs of
different angles: 90°, 120°, 180°, and 270°.
Drawing Arcs
Where you access the arc tool depends on which
level of ChemDraw you are using.
To draw an arc:
1. Do one of the following:
• In ChemDraw Std, hold down the mouse button
over the Drawing Elements tool and drag
to select the angle from the palette.
• In ChemDraw Pro or Ultra, hold down the
mouse button over the Arc tool and drag to
select the angle from the palette.
2. Drag from the left edge of the arc to the
clockwise end of the arc in a document window.
The Message area indicates the length between
the ends, and the angle the clockwise end makes
with the X-axis while you draw an arc.
ChemDraw
Editing Arcs Some examples of shapes that you can draw using
the Pen tool are shown below.
To resize or rotate an arc using the Arc tool:
1. Select the Arc tool.
2. Hold down Shift and point to the clockwise end
of the arc.
A highlight box appears.
Customized orbitals Unique arrows
3. Drag the clockwise end of the arc.
The arc is resized and rotated relative to the end
from which it was drawn. The Message area
indicates the distance between the ends of the arc
and the angle the clockwise end makes with the
X-axis.
You can resize and rotate an arc by dragging the Curves and axes Geometric shapes
Resize or Rotation handle on the Selection To toggle between a selection tool and the Pen tool
rectangle. The resize or rotation occurs around the do one of the following:
center defined by the Selection rectangle. When you
drag the Resize handle, the Message area indicates • Press Ctrl+Alt+Tab (Windows) or
the percentage enlarged or reduced. When you drag Command+Tab (Macintosh).
the Rotation handle, the Message area indicates the • Click a selection tool.
degree rotated. For more information, see “Rotating
The last drawn curve and a selection tool are
Objects” on page 108 and “Resizing Objects” on
selected.
page 109.
Drawing Bézier Curves by
The Pen Tool Dragging
Use the Pen tool to draw shapes that are not provided A Bézier curve is a curve that is calculated to
in the Arrow, Orbital, or Drawing Elements palettes. connect separate points into a smooth line.You can
For example, you can draw irregularly shaped draw Bézier curves with the Pen tool by clicking and
arrows, curves depicting graphs or reaction dragging repeatedly to create curved segments.
coordinate diagrams, and other irregularly shaped
solids. 1. Select the Pen tool.
The Pen tool has two modes: 2. Point to where you want the beginning of the
curve to appear and click.
• Drawing—Used to create shapes. The hand
cursor appears with a “+” sign inside. An anchor point appears.
3. Move the cursor to another position.
• Edit—Used to edit shapes. In drawing mode,
press Esc or select a tool to enter edit mode.

ChemDraw Chapter 6: Drawing Arrows, Arcs, and Other Shapes • 99

 4. Hold down the mouse button and drag to create 4. Move the cursor and click again to add a second
an arc. point.
Administrator

5. Continue until you have the curve you want.

Anchor Point

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.
Direction points appear on the direction line. Use the Editing a Curve
direction points to adjust the curve from that point.
You can edit a curve by selecting it and manipulating
it with the direction lines.
Direction Point
To select an existing curve:

Direction Line 1. Select the Pen tool.

2. Point at the center of the curve.
A highlight box appears when you are
positioned correctly.

Drawing Segments by Clicking

You can draw shapes with corners by clicking
repeatedly in an outline of the shape you want.
To draw segments: 3. Click the highlight box to select the curve.
The direction lines appear.
1. Select the Pen tool.
2. Point to where you want the beginning of the
curve to appear.
3. Click to deposit an anchor point.

100 • Chapter 6: Drawing Arrows, Arcs, and Other Shapes ChemDraw

Changing the Shape of a Curve
Use the endpoints of the direction lines to increase
or decrease the breadth of the curve or change its
direction.
To change the shape of a curve:
1. Select the Pen tool and click the existing curve
you want to edit.
2. Drag the direction lines to create the shape you
want.
Alternatively, you can Ctrl-Shift-Click a direction
point and move it.
Adding a Segment
To extend an existing curve by adding a segment:
1. Select the Pen tool and click the existing curve
you want to edit.
2. Point to the endpoint of a curve until the cursor
appears as a hand.
3. Alt+click the endpoint.
The cursor appears as a hand with a “+” sign
inside.
ChemDraw
4. Click and drag to connect more segments to
your curve.
Deleting a Segment
To delete a curve segment:
• In the edit mode of the Pen tool, Alt+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
tool and the Eraser tool.
Applying a Style to a Shape
All curves are drawn with the last curve style chosen
until you change the selections. Certain styles are
mutually exclusive. For example, if you choose
Closed, you cannot also choose Arrow at Start.
To apply a style to a curve:
1. Select a curve using either the Pen tool or a
selection tool.
2. From the Curves menu, choose a style.
Chapter 6: Drawing Arrows, Arcs, and Other Shapes • 101
 Filled and Closed Styles Plain Style
The illustration below shows a shape with the Plain To remove all styles from a curve:
style applied.
• With a curve selected, from the Curves menu,
Administrator

choose Plain.

The following illustration shows the shape above

with the Filled and Closed styles applied.

Shaded Style
You can apply shading to any curve, however the
shaded style works best with convex or slightly
concave shapes. Shading may not appear as desired
in extremely concaved shapes.
The illustration below shows shapes with the Plain
style applied.

The following illustration shows the above shapes

with the Shaded style applied.

102 • Chapter 6: Drawing Arrows, Arcs, and Other Shapes ChemDraw

Chapter 7: Manipulating Drawings
Overview 3. Drag around a portion of a chemical structure or
other object.
The Lasso or Marquee tools enable you to select
objects to edit. You can select objects individually
or as groups. You can then duplicate, move, resize,
rotate, or delete the selected objects.

Using a Selection Tool

You can use the Lasso or the Marquee selection tool
to select all objects. The default Lasso is used to As you drag, a line appears which defines the
select freehand. The default Marquee is used to Selection area. Bonds, structures, or other
select rectangular regions. objects are selected only if they are entirely
within this area. The end points of the Lasso are
When you click a selection tool, the last object
automatically connected when you release the
drawn is selected. A selection rectangle appears
mouse button.
around the object.
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:
Selecting Objects with the
Lasso Tool 1. Select the Marquee tool .

Use the Lasso tool to make freehand selection of The pointer becomes a Marquee.
irregular areas. 2. Drag diagonally across the chemical structures
or other objects.
To select objects using the Lasso tool:

1. Select the Lasso tool .

2. Press the mouse button while the pointer is not
over any object.

ChemDraw Chapter 7: Manipulating Drawings • 103

 As you drag, a rectangle appears which defines 3. Click the object.
the Selection area. Bonds and other objects are
selected only if they are entirely within the
rectangle.
Administrator

You can use the Marquee to select several objects at

once if they can be surrounded by a rectangle. The selected objects appear within the Selection
Rectangle and the cursor changes to a hand.
Toggling Between Selection
NOTE: If the bond or other object is part of a group
Tools you can select it as an individual object. For more
You can set one selection tool to behave like the information, see “Grouping Objects” on page 111.
other as follows:
• Click the Lasso or Marquee tool and Setting the Highlight Box
hold down Alt. Tolerance
Toggling Between Other Tools You determine the size of the highlight box and how
close you must get to activate an object by setting
To quickly switch to a selection tool from some
the Tolerance. The standard setting for the
other tool:
Tolerance is 5 pixels. At this setting, the highlight
• Press Ctrl+Alt+Tab (Windows) or box appears on bonds if the pointer is located 5
Command+Option+Tab (Macintosh). pixels or less from any point on the bond.
A selection tool and the last drawn object are To set the Tolerance:
selected.
1. From the File menu, choose Preferences.
To switch from a selection tool to the last drawing
tool used: 2. Select or type the tolerance.
This change affects all documents.
• Press Ctrl+Alt+Tab (Windows) or
Command+Tab (Macintosh).
Selecting Entire Structures
Selecting Objects by Clicking To select an entire chemical structure:
To select an object by clicking: • Using a selection tool, double-click a bond or
atom within the structure.
1. Select the Lasso or the Marquee tool.
2. Point to an object in a document window.

A highlight box appears over the selected

object. If you point at a bond, the highlight box
appears over the length of the bond.

104 • Chapter 7: Manipulating Drawings ChemDraw

 The entire chemical structure is selected. Deselecting All Objects
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
group, the entire group is selected. For more • Select a different tool.
information, see “Grouping Objects” on page 111. • Select another object without holding down
Shift.
Making Multiple Selections The selected objects are deselected.
To make multiple selections or add more objects to
the selection: Deleting Objects
• Hold down Shift and select the other objects. To delete selected objects, do one of the following:
You can add objects to the Selection by clicking, • Press Delete.
double-clicking, or by using the selection tools.
• Press Backspace.
Removing Objects from the • From the Edit menu, choose Clear.
Selection • Use the Eraser tool:

To remove an object from the selection: a. Click the Eraser tool.

b. Click a single, double, or triple bond.
• Hold down 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.

NOTE: Objects may appear within the borders of The bond order is reduced by one.
the Selection rectangle, but not be selected. Only
objects that are shimmering are selected.

Selecting All Objects

To select all objects within a document window:
• From the Edit menu, choose Select All.

ChemDraw Chapter 7: Manipulating Drawings • 105

 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.
Administrator

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.

NOTE: For more information about aligning

objects, see “Chapter 12: Working with Page
Layout”.

3. Drag the object.

Using the Clipboard
Use the Clipboard to remove the objects contained
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.

To constrain the movement to the horizontal or Cutting

vertical direction:
To use the clipboard:
• Shift+drag the selected objects.
1. Select the object with a selection tool.
From the Edit menu, choose Cut.
The object is transferred to the Clipboard and
deleted from a document window.

To move selected objects a small distance using the
Arrow keys:
• Press an arrow key while an object is selected.
The selected object moves 1 point in the
direction of the arrow.
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.
NOTE: For information about transferring
ChemDraw pictures to other types of documents see
“Autoscaling” on page 170.

106 • Chapter 7: Manipulating Drawings ChemDraw

Moving Atoms
You can move the atoms within a chemical structure
using a selection tool.
To move a single atom:
1. Point to an atom using a selection tool.
2. Drag the atom.
The bonds connected to the atom stretch.
To move multiple atoms:
• Select only the bonds that have atoms on both
ends that you want to move.
The unselected bonds that are attached to the
selected atoms are stretched.
NOTE: You can also move atoms using the bond
tool that was used to draw the atom. For more
information, see “Moving Atoms” on page 66.
ChemDraw
Duplicating Objects
To duplicate objects with a selection tool:
1. Click a selection tool.
2. Select the objects.
3. Altl+drag to create a copy and position it.
A copy of the selected objects is moved to the new
position.
To duplicate the selected objects and constrain the
positioning of the copy to the same position as the
original objects:
1. Select a selection tool.
2. Select the objects.
3. Shift+Alt+drag (Windows) or
Option+Command+drag (Macintosh) to create
a copy and position it.
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.
NOTE: For information about transferring
ChemDraw pictures to other types of documents see
“Autoscaling” on page 170.
Chapter 7: Manipulating Drawings • 107
 Rotating Objects
To rotate objects:
Administrator
1. Select the objects to rotate using a selection
tool.
The Rotation handle is located on the upper
right corner of the selection rectangle
Rotation handle
2. Drag the Rotation handle clockwise or
counterclockwise.
The Message area indicates the magnitude of
the rotation around the center of the Selection
rectangle.
By default, atom labels do not rotate with the
structure.
To rotate an atom label with a structure:
• Hold down Alt or Option while dragging the
structure.
If a single atom is unselected when a structure is
rotated, the structure rotates around the unselected
atom.
NOTE: Captions and atom labels that contain
multiple colors change to the foreground color when
rotated. However, all colors contained in the
captions are printed.
108 • Chapter 7: Manipulating Drawings
To rotate the selected objects a specified number of
degrees:
1. Do one of the following:
• From the Object menu, choose Rotate.
• Double-click the rotation handle.
The Rotation dialog box appears.
2. Type a positive whole number for a clockwise
rotation or a negative whole number for
counterclockwise rotation.
3. If you want to rotate the atom label text, click
Rotate Atom Labels.
4. Click Rotate.
Objects are rotated around the center of the
Selection rectangle.
To repeat the same rotation on any object in the
document window:
1. Immediately after performing a rotation, select
the other objects to rotate.
2. From the Edit menu, choose Repeat Rotate.
Reflecting Objects
Through Planes
You can reflect structures through planes
perpendicular to the X-axis or Y-axis using a
selection tool. Used with duplicating, you can create
mirror images of chemical structures for
representing racemic mixtures and other
stereoisomers.
ChemDraw
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 rotating it.
To create a mirror image: 3. Drag the resize handle until the object is the size
you want.
1. Draw a structure with defined stereochemistry,
The Message area indicates the percentage
for example, wedged bonds.
enlarged or reduced.
2. Make a copy of the structure.
a. Select the structure
b. Alt+Drag the structure.
3. While the structure is selected, from the Object
menu, choose Flip Horizontal or Flip Vertical.

ChemDraw Chapter 7: Manipulating Drawings • 109

 Scaling Objects
To resize objects with the Scale command:
1. Select the objects to scale.
Administrator
2. Do one of the following:
• From the Object menu, choose Scale.
• Double-click the Resize handle.
The Scale Objects dialog box appears.
Use the first two options in the Scale Objects dialog
box to scale all selected objects so that the median
selected bond has a specified length based on the
following scale factor:
new median bond length
scale factor =
current median bond length
To scale bonds so that the Fixed Length becomes the
new median bond length:
1. Select the top option.
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.
110 • Chapter 7: Manipulating Drawings
To scale the bonds to a new fixed length that you
specify:
1. Select the middle option.
2. Type the new median bond length in the box
to the right of the button.
3. The current median bond length for the
selection is shown in the highlighted text box
when the dialog box initially appears.
4. Click Scale.
To scale objects by a percentage:
1. Select the bottom option/radio button.
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)
does not change. However, it is possible to change
the aspect ratio (distort) of certain objects including
chemical structures, circles, boxes, and ovals.
To distort an object in the horizontal or vertical
direction:
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.
ChemDraw
Joining Objects
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 Drawing Settings dialog box.
To join chemical structures along the length of a
bond:
1. Position the structures to join so the bonds you
want to join are nearly overlapping (within
tolerance).
2. Select the chemical structures to join.
3. From the Object menu, choose Join.
The structures are joined.
To join chemical structures at one atom to create a
spiro-linkage:
1. Position the two chemical structures so two
atoms nearly overlap.
.
2. Select both chemical structures.
ChemDraw
3. From the Object menu, choose Join.
NOTE: When you join two differently colored
bonds or atom labels, the color of the front object
becomes the color of the resulting joined object.
When you join two atoms that are labeled, the front
atom label becomes the atom label of the resulting
atom. For more information about front to back
ordering of objects, see “Chapter 12: Working with
Page Layout”.
Setting the Maximum Distance
Tolerance
The maximum distance required between two atoms
for joining to occur is controlled by the Tolerance
setting in the Preferences dialog box. 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:
1. From the File menu, choose Preferences.
2. Select or type the tolerance.
This change affects all documents.
Grouping Objects
You can group a number of objects drawn
separately. Grouping creates an association between
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.
Chapter 7: Manipulating Drawings • 111
 Grouping does not lock the position or orientation of Ungrouping Objects
objects. Grouped objects maintain their relative
To ungroup objects that are grouped:
positions when they are centered on the page,
aligned or distributed. 1. Double-click a group using a selection tool.
Administrator

Atoms and bonds making up a single chemical 2. From the Object menu, choose Ungroup.
structure are always grouped. If you group part of a
All the objects previously grouped become
structure with other objects, the resulting group
individual objects.
contains the entire structure. If you add atoms or
bonds to a grouped structure, the new atoms and
bonds are part of the group.

NOTE: Only one level of grouping is provided. For

example, if you create two grouped objects, group
these groups and then ungroup them, you return to
the individual objects—not the groups.

To group several objects:

1. Select the objects to group using a selection

tool.
2. From the Object menu, choose Group.
To select grouped objects:
• Double-click the grouped objects using a
selection tool.

To select an individual object within a group:

• Click the object using a selection tool.
The object is selected, not the group.

112 • Chapter 7: Manipulating Drawings ChemDraw

Chapter 8:
Advanced Drawing Techniques
Overview Applying Nicknames
To use a Nickname to label an atom:
ChemDraw provides advanced drawing features that
allow you to: 1. Create a structure.
• Label functional groups with Nicknames CH2CH3

• Expand Nicknames
• Add bonds to specific characters in atom labels
• Create bonds whose attachment is not explicitly
defined
NHOH
Using Nicknames 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 An atom label text box appears.
label. When an atom is labeled with a Nickname, the
chemical significance of the expanded structure is
retained.
Commonly used Nicknames, such as Me, Et, and Ph
are provided with ChemDraw in the nickname.dat or
ChemDraw Nicknames file located in your cd_items
directory (Windows) or ChemDraw Folder
(Macintosh). You can add to or delete from this list.
NHOH
You can assign HotKeys to Nicknames. For
3. Type a Nickname label such as “Et”.
example, in the Nicknames and HotKeys provided
with ChemDraw, the HotKey, “4” labels an atom Et
with “Ph” which is a Nickname representing a
phenyl group. For more information, see “Using
HotKeys to Label Atoms” on page 76.

NHOH

ChemDraw Chapter 8: Advanced Drawing Techniques • 113

 To select a Nickname to apply to an atom using a 3. From the Structure menu, choose Define
HotKey: Nickname.

1. Point to an atom. The number of connection points is shown by

radicals in the Formula. You can have only one
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2. Press the HotKey “=”.

or two connection points in a nickname.
The Nickname list appears.
3. Select a Nickname from the list.
4. Click OK.

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
“THPO”. For more information, see ““Justifying
Captions” on page 74.
Defining Nicknames
To define your own Nicknames, you must have
ChemDraw Pro.
You can define Nicknames with one or two
attachment points. The attachment points must be
single bonds.
4. Type a short name for the Nickname.
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
for an acetyl group replaces the element Actinium.
The Check Structure and Analyze structure
commands recognize the label as an acetyl group
rather than Actinium.
ChemDraw provides the following default
Nickname/Element conflicts:
Symbol Nickname Element

To define a new Nickname: Ac Acetyl Actinium

Am Amyl Americium
1. Create a structure containing the functional
group you want to define as a Nickname. Np para- Neptunium
Nitrophenyl
2. Select the functional group.
Pr Propyl Praeseodymium
You must indicate the connection point for the
functional group by selecting some bonds and not To remove the overriding Nicknames, choose List
selecting others. Nicknames from the File menu and delete the
overriding Nickname definition. For more
NOTE: If stereochemistry is indicated in a information, see “Deleting Nicknames” on page
structure that you are defining as a Nickname, the 115.
stereochemistry is retained.

114 • Chapter 8: Advanced Drawing Techniques ChemDraw

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
drawn and the entire group selected. Because there
is no atom that indicates a connection point, you
cannot define a Nickname.

incorrect definitions correct definitions

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—
In the example below, the sulfonamide group is Nitrogen on the left and Carbon on the right.
attached to an unselected bond, which defines a
bond from sulfur as the connection point for the
group. This allows you to define a Nickname.

You can draw a peptide chain by:

You must leave a bond unselected for each
connection point. You cannot define more than two
connection points or one attachment point on a
single atom in a nickname.
• Stringing Nicknames together.
H Gly Ala OH
• Stringing Nicknames together in an atom label
as long as there is a bond attached.

GlyAlaOH
• Stringing Nicknames together and not
including bonds.

HGlyAlaOH

ChemDraw Chapter 8: Advanced Drawing Techniques • 115

 Viewing Nicknames
To view the list of defined Nicknames:
• From the File menu, choose List Nicknames.
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The List Nickname dialog box appears.
Alternatively, you can use the “=” HotKey.
Deleting Nicknames
To delete a Nickname:
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.
116 • Chapter 8: Advanced Drawing Techniques
Contracting Labels
You can compress an area of a structure and replace
it with a text label by using the Contract Label
command. Contracted labels are similar to
Nicknames, but they are for one-time use only, in the
current document.
To create a contracted label:
1. Select the area of the structure to contract.
2. From the Structure menu, choose Contract
Label.
The Contract Label dialog box appears.
3. Type a label for the contracted structure and
click OK.
The label replaces the selected portion of the
structure.
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
ignore all errors or Stop to end the contract process.
molecule
ChemDraw
Expanding Labels
If your structures contain defined nicknames, long
atom labels, or contracted labels, ChemDraw can
restore your structures to the fully expanded form.
Contracted Form
Using Multi-Center
Bonds
The multi-center attachment feature allows you to
draw, with chemical significance, polyhapto
structures, for example, ferrocene ((Cp)2Fe).

Ph CH2 CH2CHCH3

CH3

Fe
Expanded Form

Creating a Multi-Center Bond

To create a multi-center attachment point:
To expand atom labels:
1. Select a selection tool.
2. Select the label to expand or double-click the
structure to expand all possible labels.
1. Select the structure whose center you want
defined as a multi-center attachment point.
2. From the Structure menu, choose Add
Multi-Center Attachment.
An asterisk is displayed with the fragment to
show that it contains a multi-center node.

3. From the Structure menu, choose Expand

Label.
Your structure is redrawn in its expanded form.
The asterisk is not visible once a bond is drawn to it.
You can view the attachment point with a bond or
selection tool. For more information, see “Viewing
Attachment Points” on page 118.

ChemDraw Chapter 8: Advanced Drawing Techniques • 117

 To draw a bond to a multi-center attachment point: Viewing Attachment Points
1. Select 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.
2. Select the downward bond. • Select the bond tool and position the cursor over
the attachment point.
3. Double-click on the cyclopentadienyl ring with
a selection tool. The attachment node and all the atoms it
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).

118 • Chapter 8: Advanced Drawing Techniques ChemDraw

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

ChemDraw Chapter 8: Advanced Drawing Techniques • 119

 If you select only part of a structure when you To use Clean Up Structure:
choose Clean Up Structure, the other atoms and
1. Select the structure or part of the structure you
bonds are not be affected.
want to clean up with a selection tool.
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NOTE: For some compounds, the Clean Up

Structure command produces a structure that
extends beyond the bounds of the page. To view the
entire structure, scale the structure or increase the
size of the printed page. For more information, see
“Resizing Objects” on page 109 and “Page Setup” 2. From the Structure menu, choose Clean Up
on page 159. Structure.

General Rules for Clean Up Structure are:

• The Fixed Length setting in the Drawing
Settings dialog determines optimum bond
lengths. NOTE: Clean Up Structure does not position
• A given ring is redrawn only if all of its bonds molecules relative to other objects. Overlap may
are selected. occur.
• Multi-attached atom labels and variable
attachment points cannot be cleaned. Using Variable
• Multi-center bonds cannot be cleaned.
Attachment Positions
• Structures are rotated so that as many bonds as
possible are directed at a multiple of 15 degrees. You can use the Add Variable Attachment command
to draw different positional isomers of a compound
• Clean Up Structure preserves stereochemical
using an abbreviated notation that retains chemical
meaning rather than the precise identity of any
significance.
wedged or hashed bonds, as shown below.
For example, you can draw explicitly the three
isomers of dibromobenzene shown below.
OH
Cl Br Br Br

Br

O
O
HO Cl Br

After Br
Before
o-Dibromobenzene m-Dibromobenzene p-Dibromobenzene

120 • Chapter 8: Advanced Drawing Techniques ChemDraw

You can express all three isomers as a single parent
structure by using a variable attachment.
Br
Br
To use variable attachment:
1. Draw the structural fragment to which you want
to assign a variable attachment node.
2. Select the fragment using a selection tool.
3. From the Structure menu, choose Add
Variable Attachment.
An asterisk appears in the center of your
fragment.
Br
You can treat this attachment node as you would
treat the end of a normal bond.
1. Click a Bond tool.
2. Point to the asterisk and drag to draw a bond.
Br
NOTE: In the example above, Fixed Lengths was
disabled using Shift, so a bond could be drawn
extending further from the ring.
After you draw a bond from the attachment
node, the asterisk disappears.
ChemDraw
To verify that the node is present, do one of the
following:
• Click a Selection tool and place the pointer on
the attachment point.
The attachment node is highlighted.
Br
• Click a Bond tool and place the pointer on the
attachment point.
The attachment node and the atoms it represents
are highlighted.
Br
For more information about viewing the attachment
points, see “Viewing Attachment Points” on page
118.
Working with Color
With the color capabilities of ChemDraw, you can
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
any one time may be limited by the particular
monitor and display card installed in your computer.
In ChemDraw you can choose from a palette
consisting of a Background Color, a Foreground
Color, and up to twenty additional colors for any
given drawing. A palette is stored in every document
Chapter 8: Advanced Drawing Techniques • 121
 and Style Sheet/Stationery Pad. You can use Style
Sheets/Stationery Pads to create a series of
documents with the same color scheme.
Using color you can:
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• Color atoms and bonds in a mostly
black-on-white drawing to highlight areas of
interest.
• Color parts of a structure in a reaction scheme
to indicate where starting materials end up in
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.
Color Menu
The Color menu contains the palette of colors that
you can use to color objects and text in the document
within the active window.
The Foreground color in the Color menu is the color
used for all newly drawn objects. The Other colors
in the Color menu can be used to change the color of
objects that you select.
You can customize the Color menu using the Color
Palette dialog box in the File menu. Colors can be
added, or existing colors can be changed. Changing
a color, for example Other #2, changes all objects
that are using the color.
122 • Chapter 8: Advanced Drawing Techniques
NOTE: If you select an individual or grouped
object that contains multiple colors, there is a check
mark next to each of the colors in the Color menu.
The purpose of the check marks is to alert you that a
change would affect more than one color.
Coloring Objects
Any object that you can select with a selection tool
can also be colored.
To color an object:
1. Select the object in a document window using a
selection tool.
2. From the Color menu, choose a color.
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
boxes in the Drawing Elements palette can be
colored, but the inside of the object cannot.
Coloring Text
You can color captions and atom labels before or
after they are typed, and as a whole or in part.
To color a caption or atom label:
1. Select the Text tool.
2. Click in the position where you want to place
the text.
3. From the Color menu, choose a color.
4. Type the caption or atom label.
ChemDraw
To color individual characters: Windows Color Settings
1. Select part of an existing caption or atom label To change the palette of colors used in the current
document:
using the Text tool.
2. From the Color menu, choose a color.
• From the File menu, choose Color Palette.
The Color Palette dialog box appears.
NOTE: Macintosh: Captions that contain multiple
colors change to the foreground color when rotated.
However, all colors contained in the caption are
printed.

To color several captions or atom labels at once:

1. Select the captions or atom labels using a

selection tool.
2. From the Color menu, choose a color.

Changing the Color Palette 3. Click the color you want to change.
You can change the palette of colors available in the The color is highlighted.
Color menu and the background and foreground 4. Click Set Background Color or double-click
color using the Color Palette dialog box in the File the color.
menu. The Color dialog box appears.
Use the Color Palette to specify the following
colors:
• Background Color—Fills the background of
the current document in the active window.
• Foreground Color—Default color used when
you draw a new object.
• Other Colors—Colors available in the Color
Menu for changing the color of individual
objects. The colors are represented in the same
order that they appear in the Color menu.

5. Click a color box in the Basic Colors or the

Custom Colors section.
A highlighted border appears around the color
you select.
6. Click OK.
The color is changed to the new color and added
to the Color menu.

ChemDraw Chapter 8: Advanced Drawing Techniques • 123

 Adding or Customizing Colors Macintosh Color Settings
To add colors or create customized colors: To change the palette of colors used in the current
document:
1. Within the Color dialog box, click Define
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Custom Colors or Set Other Color. 1. From the File menu, choose a Color Palette.
The Color dialog box appears. The Color Palette dialog box appears.

Color Refiner box Luminosity box

2. Double-click the color you want to change.

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 within the Luminosity box to set the
brightness of the color.
4. If necessary, change the hue, saturation,
luminosity, and RGB components by typing the
values in the text boxes.
5. Click Add. 3. Click a color to change to in the Color Wheel.
For more information about the Macintosh
Color Wheel, refer to your System
documentation.
4. Click OK.
The new color appears in the Color Palette
dialog box in place of the original color and is
added to the color menu.

124 • Chapter 8: Advanced Drawing Techniques ChemDraw

Adding or Customizing Macintosh Saving Color Palette Settings
Colors You can save the Color Palette in a Style Sheet or
To add a new color to the Color menu: Staionery Pad. The Color Palette is saved in addition
to other document settings such as Page Setup
1. Click New Color or Set Other Color.
settings, Text settings, and Drawing settings.
The Color Picker dialog box appears.
2. Click a color in the Color Wheel.
3. If necessary, adjust the hue, saturation,
brightness, and RGB components by typing the
values in
4. Click OK.
The new color is added to the list of Other
Colors.

Removing Colors
To remove a color from the Color menu:

1. Click the color you want to remove.

A highlight box appears around the color.
2. Click Remove Color.
The color disappears from the list of other
colors. Objects that were drawn in the removed
color are changed to the Foreground color

Templates and Color

The background and foreground colors used in a
template from the template pop-up palette are not
used when the template is drawn in a document
window. However, any other colors used in the
template are added to the color palette of the current
document if they are not already present. This is part
of the autoscale feature. For more information, see
“Autoscaling” on page 170.

ChemDraw Chapter 8: Advanced Drawing Techniques • 125

Administrator

126 • Chapter 8: Advanced Drawing Techniques ChemDraw

Chapter 9: 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
• Analyze a structure to determine its chemical
properties
• Assign Atom-to-Atom mapping
• In ChemDraw Pro, show stereochemistry and
calculate chemical properties
• In ChemDraw Ultra, assign structures to spectra
To continue checking the structure when a message
and calculate NMR Shift information
appears:

Checking Chemistry • Click Ignore.

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

1. Select a structure, part of a structure, or caption

with a selection tool.
2. From the Structure menu, choose Check
Structure.

ChemDraw Chapter 9: Working With Structures • 127

 Check Structure when Copying
to Clipboard or Exporting
To have ChemDraw perform a check structure
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analysis on any structure copied to the Clipboard:
1. From the File menu, choose Preferences.
2. Click the Check Structure When Copying to
Clipboard or Exporting check box.
This change affects all documents.
Analyzing a Structure
Analyze Structure calculates the chemical formula,
exact mass, molecular weight, and elemental
analysis for a structure, part of a structure, or a
caption (in Formula style). Before the calculation,
the Check Structure command is performed. For
more information, see “Check Structure” on page
127.
The Analyze Structure command accounts for
charge, radicals, and isotopes. For more
information, see “Appendix A: The Chemistry of
ChemDraw”.
In ChemDraw Ultra, you can calculate
chemical properties such as LogP and NMR data for
a selected structure. For more information, see
“Chemical Property Information” on page 133 and
“NMR Shift Information—ChemNMR Pro” on
page 134.
128 • Chapter 9: Working With Structures
Analysis Information
You can use the Analysis dialog box to calculate the
following types of information about a structure:s
Property Description
Formula The molecular formula showing the
exact number of atoms of each
element in the molecule and charges,
radicals, and isotopes.
Exact Mass The exact molecular mass of the
structure, where atomic masses of
each atom are based on the most
common isotope for the element.
Molecular The average molecular mass of the
Weight structure, where atomic masses are
based on the average of all isotope
masses for the element.
Elemental The percent by weight of each
Analysis element in the structure.
Viewing Analysis Information
To view information about a selected structure:
1. Select an entire structure, part of a structure, or
a caption (in Formula style).
2. From the Structure menu, choose Analyze
Structure.
ChemDraw
 The Analyze Structure dialog appears.
NOTE: In ChemDraw Pro for Windows,
the Analyze dialog box contains two tabs: Analysis
and Properties. Click the Analysis tab to see the
information discussed in this section.
If any of the valences or labels is not correct, a
message appears. For more information, see “Check
Structure” on page 127.
To paste information about a structure as a caption:
1. Click the check boxes for the information that
you want to paste.
2. Click Paste.
The information appears as a multiline caption
below the structure. You can edit this information
with the text tool.
C6H12
Exact Mass: 84.09
Mol. Wt.: 84.16
C, 85.63; H, 14.37
ChemDraw
Atom-to-Atom
Mapping
You can assign atom-to-atom mapping for creating
records for a reaction database and for creating
queries for searching a reaction database. You can
assign atom mapping in two ways:
• Automatic mapping, using the Map Reaction
Atoms command.
• Manual mapping, using the Reaction
Atom-Atom Map tool .
To be mapped properly, reactions must contain only
one step. Mapping does not support multi-step
reactions.
During either type of mapping process, the mapping
algorithm perceives and assigns a reaction center for
the reactants and products.
When a reaction map is established, you can point to
an atom in one structure with the Reaction
Atom-Atom Map tool selected to highlight the
mapped atom in the other structure.
Always Display and Print Atom
Mapping
If you want the symbols to always appear and print
on the atoms when reaction mapping has been
performed:
1. From the File menu, choose Preferences.
2. Select Always Display and Print Reaction
Mapping.
3. Click OK.
Deselect Always Display and Print Atom Mapping
to show the symbols only when you select the
Reaction Atom-Atom Map tool. When this option is
deselected, atom mapping symbols do not print,
even though a reaction map has been created.
Chapter 9: Working With Structures • 129
 Automatic Mapping The following figure shows how to amend the initial
mapping by using the Reaction Atom-Atom Map
To automatically create a reaction map:
tool.
1. Draw the reaction you want to map. For
Administrator

Rxn
7 7
example: O OH

OSiMe 3 6 6
∆
O O
1 5 1 5 Rxn
+
Ph
Ph
2 4 2 4
O 3 3

2. Select the reactants and products in the reaction.
3. From the Structure menu, choose Map
Reaction Atoms.
OSiMe3
Rxn
O O
Rxn Rxn
+
h Rxn
Ph Rxn
O
The symbol “Rxn” appears next to the bonds in
the reactant and product that are perceived by
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 142.
Manual Mapping
In situations that require manual mapping of atoms,
you can use the Reaction Atom-Atom Map tool.
This might be necessary when the automatic
mapping is applied to complicated reactions. In
these cases you can manually readjust the reaction
mapping.
When you perform manual mapping with the
Reaction Atom-Atom Map tool, you can suppress
automatic re-mapping of atoms other than your
target atom.
To suppress automatic re-mapping:
Rxn
Rxn
1. From the File menu, choose Preferences.
2. Deselect Automatic Reaction Mapping.
3. Click OK.
To use the Reaction Atom-Atom Map tool to
supplement the automatic mapping:
1. Click the Reaction Atom-Atom Map tool .
2. Point to the atom in the reactant whose mapping
you want to establish. For example, in the
following drawing you would point to the
acyclic carbon adjacent to the ether oxygen.
3. Drag from the reactant atom to the
corresponding product atom.
Rxn
7
O
7
OH
6 6
1 5 1 5 Rxn

2 4 2 4
3 3

130 • Chapter 9: Working With Structures ChemDraw

 The remaining atoms are automatically mapped the Cahn-Ingold-Prelog (CIP) priority rules. For
based on the manual mapping you performed. more information about the CIP rules, see
“Appendix A: The Chemistry of ChemDraw”.
1
Rxn Rxn 1
8
O 9 8 Rxn
9
Only tetrahedral and double-bond stereochemistry
OH
Rxn Rxn are supported, and only non-racemic
7 10 7
6
10 stereochemistry is interpreted. Stereochemical
2 6 2 Rxn
11 11 indicators for aromatic bonds are not shown.
3 5 3 5 ChemDraw calculates and displays the following
4 4
stereochemical terms:
You can continue to set or change the mapping for • (R, S)—Standard tetrahedral stereochemistry
other atoms in the reaction if necessary until you get
exactly the mapping you want. For this example • (r, s) —Tetrahedral stereochemistry determined
additional manual mapping is not necessary. by other stereochemical centers. For example:
cis-decalin and myo-inositol.
Clearing Reaction Mapping • (E, Z)—Standard double-bond stereochemistry
To clear all reaction mapping: The atom label settings determine the font style and
size of the terms.
1. Select the structures whose mapping you want
to remove. To show the stereochemistry of a structure:
2. From the Structure menu, choose Clear • From the Tools menu, choose Show
Reaction Maps. Stereochemistry.
The stereocenters are marked as shown in the
Exporting Reaction Mapping following example.
Reaction mapping and reaction center perception
information are stored in the native ChemDraw file
format (*.cdx) for reopening in ChemDraw and the
ISIS Reaction file format for transfer to other
applications that read atom mapping, such as
ChemFinder and ISIS/Base. You can also copy (R)

mapped reactions to these same applications using (R)

the Clipboard. H
(R)

(S) (S)

Showing (R)
H
(S)
H
(S)

Stereochemistry O (Z)

cholesterol
When the Show Stereochemistry option is selected,
ChemDraw calculates the absolute stereochemistry If you make changes to the drawing that affect the
for tetrahedral atoms and double bonds according to stereochemistry, the stereochemistry is recalculated.

ChemDraw Chapter 9: Working With Structures • 131

 To remove existing markers: 5. From the Structure menu, choose Make
Spectrum-Structure Assignment.
• On the Tools menu, deselect Show
Stereochemistry. The selected atoms and bonds in the structure
are associated with the selected spectral peaks.
Administrator

Spectrum-Structure Viewing Spectral Assignments

Assignments To view the spectral assignments:
ChemDraw Ultra enables you to assign structures to
spectra.You can then display the structure associated 1. Click the Lasso or Marquee tool.
with a specific peak by placing the pointer on that 2. Place the pointer over a peak.
peak.
The assigned atoms or bonds are highlighted.
Assigning Structures to
Spectra
To assign structures to a spectrum:
1. Open a spectral file.
2. Draw the structure or structures you want to
assign to the spectrum.
3. Select specific atoms and bonds in the structure.
4. Shift-click the peak or peaks to which you want
the structure assigned.
The selection rectangle surrounds the selected
objects.

O
Removing Spectral
Assignments
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.

10 8 6 4 2 0
PPM

132 • Chapter 9: Working With Structures ChemDraw

 Chemical Property Property Description
Information
Critical Volume The volume occupied at the
ChemDraw Ultra, using an add-on, compound’s critical
CS ChemPropPro, enables you to calculate temperature and pressure
predicted values for the following physical and (Vc). Reported in cm3/mol.
thermodynamic properties for a selected structure of
up to 100 atoms: Heat of Formation The heat of formation, ∆Hf,
for the structure. Reported in
Property Description kJ/mol at 1 atm and 298.15K.

LogP The logarithm of the partition Gibbs Energy The Gibbs free energy,∆G, for
coefficient for the structure. Reported in
n-octanol/water. kJ/mol at 1 atm and 298.15K.

MR The Molar Refraction index. Calculating Properties

Henry’s Law The logarithm of Henry’s law
constant (no units).
Boiling Point The boiling point for the
structure. Reported in Kelvin
at 1 atm.
Melting Point The melting point for the
structure. Reported in Kelvin
at 1 atm.
To calculate predicted properties for a selected
structure:
1. Select the structure to analyze.
2. From the Structure menu, choose Analyze
Structure.
A dialog box containing the basic properties:
Formula, Exact Mass, Molecular Weight, and
Elemental Analysis appears.

Critical The temperature above which

Temperature the gas form of the structure
cannot be liquefied, no matter
the applied pressure (Tc).
Reported in Kelvin.

Critical Pressure The minimum pressure that

must be applied to liquefy the
structure at the critical
temperature (Pc). Reported in
bars.

ChemDraw Chapter 9: Working With Structures • 133

 3. Take the appropriate action: Changing the Calculation
Method (Windows only)
If you are And you Then …
using … want to … In ChemDraw for Windows, you can change the
Administrator

method used to calculate the properties.

Windows view additional Click the Properties To change the calculation method:
properties tab.
• In the Properties dialog box, select the
appropriate option:
create a report Do one of the
following:
If you want to … Select …
• From the
Analysis tab, use the default method showing Best
click the all properties using the most Method
Properties reliable methods for calculation
button. for the given structure.
• From the
Properties tab, show Log P and MR values Literature
click Report. based on literature values rather Values
than a calculation.
paste the basic Click Paste.
properties into To view results for other fragmentation methods
your document including the Broto, Crippern, Viswanadhan,
Joback, and Joback/Stein methods:
Macintosh create a report Click Properties. • In the Properties dialog box, click Report.
and view
additional
properties
NMR Shift
Information—
paste the basic Click Paste.
properties into ChemNMR Pro
your document ChemNMR Pro is a feature of ChemDraw Ultra
only. ChemNMR Pro estimates and displays proton
When you create a report, a detailed list of and carbon-13 chemical shifts in ppm for a selected
information used for performing the calculation is molecule.
shown in a text file. The list includes additional
properties and literature references used to perform
the calculation.

134 • Chapter 9: Working With Structures ChemDraw

To view 1H or 13C NMR information: 2. From the Estimate menu (Windows) or the
Scripts menu (Macintosh), choose 1H NMR
1. Select the target chemical structure.
Shifts or 13C NMR Shifts.
ChemNMR Pro redraws the molecule with the
estimated shifts and displays the information
and line spectrum in a new window as shown
below.

ChemNMR H-1 Estimation

7.01 3.22
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
CH 7.02 7.26 1-benzene
-0.05 1 -C=C
-0.19 1 -C
CH 7.18 7.26 1-benzene
0.04 1 -C=C
-0.12 1 -C
CH 7.01 7.26 1-benzene
-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

ChemDraw Chapter 9: Working With Structures • 135

Administrator

136 • Chapter 9: Working With Structures ChemDraw

Chapter 10:
Drawing Query Structures
What Are Query
Structures?
Using a query structure to specify properties for
atoms and bonds provides an efficient way to search
chemical databases such as ChemFinder, DARC,
RS3, or ISIS/Base. You can use a query structure to
narrow or broaden your search.
For example, creating a query structure indicating a
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
search.
Because ChemDraw is not a chemical database
application, the interpretation of query structures
involves other programs. Not all databases support
the same query properties. If you use a query
structure containing properties not understood by a
given database, one of the following may happen:
• An error message appears
• The unsupported properties are ignored
To use query structures for searching you may do
either of the following:
• Paste the query structure into a database search
window and initiate a search.
• Save the structure in an appropriate file format
and open the file in the database application.
ChemDraw
For more information on query properties, see
“Chapter 13: Sharing Information”, or consult the
documentation for your chemical database.
NOTE: You can assign conflicting or nonsensical
properties. For example, you can require that one of
the atoms in benzene is not part of any ring, which is
inherently impossible. The results of the search
depend on the query system used, but usually no
matches are found.
Atom Properties
To assign properties to selected atoms in a structure:
1. Do one of the following:
• Select a single atom by clicking it with a
selection tool.
• Select multiple atoms by Shift+clicking the
atoms.
2. Do one of the following:
• Right-click, point to Atom, point to the
property you want, and then choose he
appropriate option.
• From the Structure menu, choose Atom
Properties. In the Atom Properties dialog
box, select the properties to associate with
the selected atoms.
• Point to an atom and press the HotKey “/ ”.
In the Atom Properties dialog box, select the
properties to associate with the selected
atoms.
Chapter 10: Drawing Query Structures • 137
 The Atom Properties dialog box appears.
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3. Select the atom properties to associate with the
selected atoms from the drop-down lists.
4. Click OK.
Small characters appear adjacent to atoms that
have associated atom properties.
X3
T *2HS
C R
S
The character that appears depends on which query
properties have been assigned. If more than one
property is assigned, more than one character
appears adjacent to the atom. The atom property
indicators are shown in the following table.
Character Query Property
* Substituents: Free Sites (followed
by the number of free sites)
U Substituents: Up to (followed by
the maximum number of
substituents)
138 • Chapter 10: Drawing Query Structures
Character Query Property
X Substituents: Exactly (followed by
the number of substituents)
H Implicit Hydrogens
R Ring Bond Count
S Unsaturation
C Reaction Change
T Reaction Stereo
L Translation
NOTE: The Abnormal Valence atom property does
not provide a visual indicator.
Viewing Atom Property Values
Except for the three Substituents query properties,
the characters indicate that a given property is
applied, but not the value of that property.
To find the value of a query property setting:
1. Select the atom.
2. Do one of the following:
• From the Structure menu, choose Atom
Properties and view the settings in the
drop-down lists.
• Right-click, point to Atom and then point to
the appropriate property.
ChemDraw
Removing Atom Properties
To remove all atom properties from an atom:
1. Select the atom.
2. From the Structure menu, choose Atom
Properties.
3. Click Use Defaults.
The atom properties are removed and the
characters no longer appear.
To remove specific atom properties:
1. Select the atom.
2. From the Structure menu, choose Atom
Properties.
3. Select the default value for the atom property to
remove.
Atom Property Options
The following topics describe the atom properties
you can associate with an atom.
Substituents
The three Substituents properties specify the
number of substituents that may be bonded to the
selected atoms. In ChemDraw, a substituent is
defined as a non-hydrogen atom connected by a
bond of any order.
For example, in the figure below, the carbonyl
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
oxygen counts as only one substituent and hydrogen
atoms never count as substituents.
O specified, up to 15 substituents.
ChemDraw
The substituent count atom property allows you to
specify the number of bonds to an atom in the target
structure. This includes bonds already drawn in the
query structure. The substituent options are
described in the following table.
Option Search Result
Unspecified Default. Search is determined by
the target database. Some
databases (including ISIS) find
compounds with any substitution
at this atom and some databases
(including DARC) find only
compounds with substitution
exactly as drawn.
Free Sites Finds compounds in which the
selected atoms may contain a
range of substituents up to the
number specified plus the
number of bonds as drawn. A
value of zero finds a substituent
count as drawn. You can also use
the Free Sites symbol in the
Chemical Symbols palette to
apply free sites. For more
information, see “Chapter 5:
Drawing Orbitals and Chemical
Symbols”.
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
Chapter 10: Drawing Query Structures • 139
 Implicit Hydrogens
Option Search Result
The Implicit Hydrogens property specifies whether
additional, implicit hydrogen atoms may be attached
As drawn Finds compounds in which the
to the selected atoms. If implicit hydrogen atoms are
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selected atoms reside in the same

not allowed, all valences to that atom must be filled
type and number of rings as drawn.
by bonds to non-hydrogen atoms. The implicit
hydrogen options are described in the following
table. Simple ring Finds compounds in which the
selected atoms is a member of only
one ring (the atom has two ring
Option Search Result bonds).

Allowed Default. Finds compounds Fusion Finds compounds in which the

regardless of whether hydrogen
atoms are attached to the selected
atoms.
Not allowed Finds compounds with no
additional hydrogen atoms
attached to the selected atoms.
selected atoms lies at ring fusions
(the atom has three ring bonds).
Spiro or Finds compounds in which the
higher selected atoms is a member of a
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
attached to an atom that are part of rings of any size.
For simple cases, this also specifies the maximum
number of rings in which an atom can reside. The
ring bond count options are described in the
following table.
The Unsaturation property specifies whether a
multiple bond is attached to the selected atoms. The
unsaturation options are described in the following
table.
Option Search Result

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.

No ring bonds Finds compounds in which the

selected atoms are acyclic.

140 • Chapter 10: Drawing Query Structures ChemDraw

 The reaction stereo options are described in the
Option Search Result following table.

Must be absent Finds compounds that do not Option Search Result

have a multiple bond attached to
the selected atoms.
Any Default. Finds all compounds
regardless of the stereochemistry
Must be Finds compounds that have at at the selected atoms.
present least one multiple bond (double,
triple or aromatic) attached to the
Inversion Finds compounds in which the
selected atoms.
selected atoms have an inverted
stereo configuration after a
Reaction Change reaction.
The Reaction Change property specifies whether a
change occurs at selected atoms after a reaction. Retention Finds compounds whose selected
This property is only meaningful when searching a atoms have an unchanged stereo
database containing chemical reactions. The configuration after a reaction.
reaction change options are described in the
following table. Translation
Option Search Result The Translation property specifies what is required
to match in the structure query and possible database
May be Default. Finds all reactions hits in a Markush DARC query.
anything regardless of any change to The translation options are described in the
selected atoms after a reaction. following table:

Must be as Finds all reactions that are

Option
specified changed at the selected atoms
exactly as specified by the
reaction center property in the Equal
Atom Properties dialog box.
Definition
Default. Matches specific to specific
or generic to generic terms.

Broad Translates specific query atoms to

Reaction Stereo corresponding superatoms in the
The Reaction Stereo property specifies that the database.
selected atoms are stereocenters in a reaction. This
property is only meaningful when searching a
database containing chemical reactions.

ChemDraw Chapter 10: Drawing Query Structures • 141

 Option Definition
Narrow Translates query superatoms to
Administrator
corresponding specific atoms or
groups in the database.
Any Translates generic or specific terms
to any term.
For more information, refer to the Markush DARC
User Manual.
Abnormal Valence
The Abnormal Valence property specifies whether
selected atoms can have a valence other than
normal. “Normal” valences for each element are
defined in the Isotopes Table file in the ChemDraw
Folder (Macintosh) or the cd_items directory
(Windows).
The Abnormal Valence options are described in the
following table.
Option Search Result
Not allowed Default. Finds compounds where
the selected atoms only have
valences that are normal for that
element. If necessary, hydrogen
atoms are automatically added to or
removed from the atom before
transferring it to the chemical
database. If the Check Structure
When Copying to Clipboard or
Exporting preference is turned on,
an error message warns of abnormal
valences.
Allowed Finds compounds with the specific
valence drawn.
142 • Chapter 10: Drawing Query Structures
NOTE: If Abnormal Valence is Allowed, any
Invalid Valence messages for those atoms are
ignored automatically by the Analyze Structure and
Check Structure commands.
Bond Properties
To define bond properties of selected bonds in a
structure:
1. Do one of the following:
• Select a bond using a selection tool.
• Shift+click to select multiple bonds.
2. Do one of the following:
• Right-click, point to Bond, point to the
property you want, and then choose the
appropriate option.
• From the Structure menu, choose Bond
Properties. In the Bond Properties dialog
box, select the bond properties to associate
with the selected bonds from the drop-down
lists.
• Point to an bond and press the HotKey “/ ”.
In the Bond Properties dialog box, select the
properties to associate with the selected
atoms.
3. Click OK.
Textual descriptors appear adjacent to bonds
that have associated bond properties.
S/D Any S/D
Rxn S/D
Any S/D
one bond many bonds
ChemDraw
The descriptor that appears depends on which query Removing Bond Properties
properties have been assigned. If more than one
To remove all bond properties from selected bonds:
property is assigned, more than one descriptor
appears adjacent to the atoms. The descriptors are 1. Select the bonds.
described in the following table.
2. From the Structure menu, choose Bond
Properties.
Descriptor Query Property
3. Click Use Defaults.

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

Rng Topology: Ring 3. Select the default value for the bond property
you want to remove.
Chn Topology: Chain
Bond Property Options
Rxn Reaction Center The following are the atom properties that you can
associate with an atom:

Viewing Bond Property Values Bond Types

The descriptor for the Reaction Center query This property specifies the bond type of the selected
property indicates that the property is applied, but bonds. The default bond type corresponds to the
not the value of the property. current type of the bond (single, double, etc.) as
drawn.
To find the value of a query bond property setting:
The Bond Type options are described in the
1. Select the bond. following table.
2. Do one of the following:
• From the Structure menu, choose Bond Option Search Result
Properties, and view the settings of the
drop-down list boxes. Single (all) and Finds compounds with the bond
Dative type you select for the selected
• Right-click, point to Bond, and then point to bonds.
the appropriate property.
Double or Finds compounds whose selected
Double Bold bonds are double.

ChemDraw Chapter 10: Drawing Query Structures • 143

 Topology
Option Search Result
The Topology property specifies the ring
Double Either Finds compounds whose selected environment of the selected bonds.
Administrator

bonds are double bonds and have The Topology options are described in the following
either cis/trans stereochemical table.
configuration.

Aromatic Finds compounds whose selected Option Search Result

bonds are aromatic.
Tautomeric Finds compounds whose selected
bonds are tautomeric.
Triple Finds compounds whose selected
bonds are triple.
Quadruple Finds compounds whose selected
bonds are quadruple.
Any Finds compounds regardless of
the bond type of the selected
bonds.
Unspecified Default. Finds compounds
regardless of environment.
Ring Finds compounds where the
selected bonds are part of a
ring.
Chain Finds compounds where the
selected bonds are part of a
chain (and are specifically not
part of a ring).

S/D Finds compounds whose selected

bonds are single or double.
D/A Finds compounds whose selected
bonds are double or aromatic.
Reaction Center
The Reaction Center property specifies how the
selected bonds are affected in a reaction. This
property is only meaningful when searching a
database containing chemical reactions.

S/A Finds compounds whose selected

bonds are single or aromatic.

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
equivalent that is supported.

144 • Chapter 10: Drawing Query Structures ChemDraw

The Reaction Center options are described in the
following table
Option Search Result
Unspecified Default. Finds compounds
regardless of whether the
selected bonds are affected by
the reaction.
Center Finds compounds where the
selected bonds are affected by
a reaction, but the type of
change is unspecified.
Make/Break Finds compounds where the
selected bonds are either
broken or created in a reaction.
Change Finds compounds where the
bond order of the selected
bonds changes in a reaction.
Make&Change Finds compounds where the
selected bonds are formed,
broken, or undergo a change in
bond order.
Not Center Finds compounds where the
selected bonds are not part of
the reaction center.
Not Modified Finds compounds where the
selected bond’s orders do not
change, but which may or may
not be part of the reaction
center.
ChemDraw
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
If you are using a query system that recognizes
generic nicknames, you can use these nicknames in
your ChemDraw query structure.
You can assign Generic nicknames, like other
nicknames, to HotKeys. For information on
assigning a HotKey to a nickname, see “Chapter 8:
Advanced Drawing Techniques”.
You cannot define the meaning of a generic
nickname in ChemDraw because generic nicknames
represent multiple (and perhaps an infinite number
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 Folder
(Macintosh) or the cd_items directory (Windows).
For definitions of the nicknames, see the “Nickname
Definitions” Help topic.
To edit the generic nickname files:
• Open the Generic Nicknames file in a text
editor and make your changes.
See the provided Generic Nicknames file for
examples of the correct format as shown below.
Chapter 10: Drawing Query Structures • 145
 Element Lists
The element list allows you to define your search
query more concisely. By labeling an atom position
Administrator

as a list of elements you specify that one of these

elements must match in the structure for which you
are searching. The elements in the element list must
be separated by commas. A space after each comma
and brackets are optional. An example of an element
list is shown below.

[S,Se,Te]

NOTE: An element list may contain only atomic

To label an atomic position with a generic nickname, symbols, plus D (deuterium) and T (tritium).
use the same procedures as labeling an atom:
To create an element list:
1. Do one of the following:
1. Open an atom label text box.
• Open a text box on an atom position by
clicking with the Text tool. 2. Type an open bracket ([) followed by a list of
elements separated by commas (Cl, Br, I),
• Double-click on an atom position with a
followed by a close bracket (]).
Bond tool.
2. Type the generic nickname.
3. Press Return or click outside the text box.

3. Close the text box.

[Br, I, Cl]

NOTE: If you perform “Analyze Structure” or

“Check Structure” on a structure with a generic
nickname, a message is displayed because the
structure contains variable substituents. If you
ignore this message, the generic nicknames are
ignored and ChemDraw reports the chemical
formula, mass, and so on as if the atom label
containing the generic nickname were not selected.

146 • Chapter 10: Drawing Query Structures ChemDraw

The following example shows a query structure For example:
created to find compounds matching the following NO T F,Cl,B r,I [- C, O, N]
criteria:
NOT[F,Cl,Br,I] [NOT C,O,N]
a. Non-oxygen chalcogenide bonded to another
atom.
NOTE: An element not-list may contain only
b. Not necessarily carbon (a generic nickname). atomic elements, plus D (deuterium) and T (tritium).
c. The bond type between the chalcogenide and
the other atom to be a single or double bond. To create an element not-list:

1. Open an atom label text box.

(b) (a)
2. Type an open bracket, the word NOT, and a
space (“[NOT”) followed by a list of elements
A [S, Se, Te]
S/D separated by commas (“Cl, Br, I”), followed by
a close bracket (“]”).

(c) Alternative Groups

The “A” label indicates that the atom may match any
atom except hydrogen. The mark near the bond
indicates that the bond has special properties. The
bond type specified in the Bond Properties dialog
box must be single or double, S/D. The “[S,Se,Te]”
specifies that one of these elements must match in
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.
The word NOT must be in all-caps and must be
The Alternative Group feature allows you to 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,
G-Groups, or Generic Groups, are shown below.
F
G
NH2

followed by a space. Alternatively, the word NOT G

may be replaced with a minus sign.

F

NH2
OH

OH

ChemDraw Chapter 10: Drawing Query Structures • 147

 Defining an Alternative Group
To define an alternative group:
1. Click the Alternative Group tool .
Administrator
2. Click and drag to create an area large enough to
draw the alternative groups.
The Alternative Group Title box appears.
3. Type a title, such as R1, in the Alternative
Group Title box.
4. Draw the substructure fragments in the
Alternative Group box.
148 • Chapter 10: Drawing Query Structures
Defining Attachment Points
Specify where the fragments should bond to the
parent structure at the alternative group label:
1. Select the Attachment Point tool .
2. Do one of the following:
• Click a substructure fragment where you
want to place the attachment point.
• Point to a substructure fragment where you
want to place the attachment point and press
the HotKey “.”.
An attachment point symbol appears.
Attachment
point symbol
3. Repeat step 2 for all fragments.
When you create a parent compound that contains
an alternative group you defined, an attachment
point symbol appears next to the label. The
attachment point number matches that found in the
definition.
ChemDraw
 By specifying the attachment points order, you can
R1
1 exclude the unwanted compounds. The parent
R1
structure below satisfies the necessary requirements.
To specify the attachment points order:
1 NH2
1. Draw the parent structure shown below.

1 OH
R1
NH2
1 F

The number displayed in the attachment point 2. Create an Alternative Group Box labeled “R1”.
symbol is the attachment rank order. See the
example in “Multiple Attachment Points” on page R1
149.

Multiple Attachment Points

If you have well-defined multiple attachment points 1 2

on your structure fragments, you can perform

searches for specific materials. This type of search is
especially useful for searching for conformationally 1 O 2

similar structures.
For example, you want to find the two compounds 3. Draw the structure fragments and label them
below: with attachment points.
When the alternative group definition is
complete, the attachment point symbols appear
in the parent compound.
NH2 NH2
O
By numbering your attachment points, you have
unambiguously specified that the methyl group must
be adjacent to the amine group. The conformations
However, you are not interested in the two
that are not of interest are excluded.
compounds below:
Showing Attachment Rank
Indicators
NH2
O
NH2 You can hide the attachment rank indicators if
required. For example, sometimes—particularly in
publication-quality drawings—the numbering of
attachment points is implicit and the numbered
attachment rank indicators are superfluous.

ChemDraw Chapter 10: Drawing Query Structures • 149

 To hide the attachment rank indicators and remove
the numbers from the attachment points:
Anonymous Alternative
1. From the File menu, choose Preferences.
Groups
Administrator

2. Deselect the Show Attachment Rank
Indicators check box.
The following illustration shows an alternative
group definition and a parent structure with the
attachment rank indicators hidden.
R1 R1
NH2
O you specify that one of these substructures must
This change affects all documents.
Attachment Point Numbering
An anonymous alternative group is a cross between
an element list and an alternative group. Element
lists are restricted to single elements, but
anonymous alternative groups can contain any
structure that can be represented by text. Nicknames
and generic nicknames are allowed in anonymous
alternative groups. Anonymous alternative groups
are shortcut notation for regular alternative groups,
eliminating the need to specify a name such as “R1”.
The anonymous alternative group allows you to
define your search query more concisely. By
labeling an atom position as a list of substructures
match in the structure for which you are searching.
Commas must separate the items in the anonymous
alternative group. A space after each comma and the
brackets are optional.

Numbered attachment points allow you to specify Examples of anonymous alternative groups follow:
precisely how the structure fragments are connected
to your parent structure. [OMe,OPh] [M,B,C]

The numbering of the attachment points is related to [OCH3,OH] X,S,Se

the front to back order of the attachment points.
To create anonymous alternative groups:
To set the order of the attachment points:
1. Open an atom label text box.
• Click the ends of the bonds in order.
2. Type an open bracket “[”followed by a list of
The last point clicked has the highest number.
elements, fragments, nicknames, or generic
To change the ordering of the attachment points do nicknames separated by commas, followed by a
one of the following: close bracket “]”.
• Click the attachment points with the
Attachment Point tool.
• Select an attachment point with a selection tool,
and from the Object menu, choose Bring to
Front or Send To Back.
The attachment point numbers are highest in the
front.

150 • Chapter 10: Drawing Query Structures ChemDraw

Export Compatibility Exported ISIS DARC Mol Rxn
Query F1-
Because query properties are only useful in a Properties Query
chemical database, you must transfer your structures
from ChemDraw into your search system. Not all Spiro or higher X X X
file formats support the same query properties and Unsaturation
not all chemical databases support the same file
Unspecified X X X
formats. Consult the documentation for your
database to see which file formats are supported. Must be absent
The following table lists the query properties that Must be X X X
ChemDraw writes to ISIS (SKC, TGF, and present
Clipboard) and DARC (F1, F1-Query, and Reaction Change
Clipboard) file formats. All query properties are
May be X X
written to the ChemDraw (CDX) file format. CDX
anything
is the preferred format to use to retain all query
properties in a drawing. Must be as X X
specified
Exported ISIS DARC Mol Rxn
Reaction Stereo
Query F1-
Properties Query Any X X

Atom Properties Inversion X X

Substituents Retention X X

Unspecified X X X X Translation
b X b b Equal X
Free Sites
a c a a Broad X
Up to
d d d Any X
Exactly X X X

Implicit Hydrogens Narrow X

Not allowed X X X X Abnormal Valence

Allowed X X X X Not Allowed X X X X

Ring Bond Count Allowed X X X X

Any X X X Bond Properties

No ring bonds X X X Bond Type
As drawn X X X Single X X X X

X e X X
Simple ring X X X Dashed
e e e e
Fusion X X X Hashed

ChemDraw Chapter 10: Drawing Query Structures • 151

 Exported ISIS DARC Mol Rxn Exported ISIS DARC Mol Rxn
Query F1- Query F1-
Properties Query Properties Query
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Wedged X X X X Make&Chang X X X
Hashed e
Bold X f f f Not Center X X X

Wedged X X X X Other Query Attributes

Wavy X g X X Generic Xn Xo Xn Xn
X
f f f f Nicknames
Hollow
Wedged Element Lists Xpu X Xpu Xpu
h h h h Xp
Dative Element Not- X Xp Xp
Lists
Double Xi X Xi Xi
Alternative X Xq Xs
Double Either X X X X
Groups
Double Bold j j j j
Anonymous t t t

Aromatic X k X X Alternative
X
l l l l Groups
Tautomeric
Atom-Atom X X X
Triple X X X X
mapping
Quadruple r r r r
Variable
Any X Xm X X Attachment
Positions
S/D X X X X

D/A X X X X
a
S/A X X X X Converted to the appropriate number of exact
substituents
Topology
b Free Sites counts of zero translated to
Unspecified X X X X
“Substitution as drawn”; all other Free Sites values
Ring X X X X written as substitution counts equal to the total
current valence plus the free sites value.
Chain X X X X
c
Reaction Center Converted to the appropriated number of Free
Sites
Unspecified X X X
d
Substituent counts of greater than 5 are translated
Center X X X
to “6 or more”
Make/Break X X X e Converted to Wedged Hashed
Change X X X f
Converted to Wedged

152 • Chapter 10: Drawing Query Structures ChemDraw

g
Converted to Racemic
h
Converted to a Single, with a positive charge
applied to that atom at the base of the dative bond
and a negative charge applied to the atom at the
point of the dative bond
i Interpreted by ISIS as unspecified cis/trans
stereochemistry
j
Converted to Double
k Converted to Normalized
l
Converted to S/D
m
Converted to Undefined
n Only M, X, Q, A; others written as aliases
o
Extensive list — see DARC manual
p
Truncated to the first 5 elements
qConverted to G-Groups and possibly renamed;
only 20 supported in one file.
r
Converted to single.
s An RGFile will be created automatically.
t
Converted to non-anonymous alternative groups.
u
Lists of greater than 5 elements converted to
alternative groups.

ChemDraw Chapter 10: Drawing Query Structures • 153

Administrator

154 • Chapter 10: Drawing Query Structures ChemDraw

Chapter 11:
Drawing With Templates
Overview
Template documents are collections of structures
organized by structural type or functionality. A
structure in a Template document is named a
template. Use an existing template instead of
drawing the structure to shorten the time required to
create documents.
The Template documents distributed with
ChemDraw are stored the “cd_items” folder
(Windows), or in the “ChemDraw Folder”
NOTE: In ChemDraw Pro the pop-up
(Macintosh) in the same folder/directory as the
menu is segmented if any Template documents are
ChemDraw application.
open for editing. The upper segment contains
Template documents that are currently open for
NOTE: In ChemDraw Pro, you can define editing.
your own commonly used structures as templates.
Any Template documents in the ChemDraw Folder
are listed in the Windows menu (Macintosh) or Open Choosing a Template
Special on the File menu (Windows).
To choose a template from the Template palette:

The Templates Tool 1. Hold down the mouse button over the
Templates tool .
The Templates tool contains a palette from which A menu listing the Template documents
you can select different types of structures or appears.
objects. The Templates tool has two levels:
2. Point to a Template document name.
• The first level displays the available Template
A palette containing the available templates
documents.
appears.
• The second level displays the templates within
3. Choose a template from the palette.
each Template document.
When you display the Template palette that was last
used, a blinking box appears around the currently
selected template until you drag to another template.

ChemDraw Chapter 11: Drawing With Templates • 155

 Using Templates
When you draw with templates, the first bond drawn
determines the position of the template in a
Administrator
document window. All remaining bonds are drawn
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.
After a template is drawn in a document window, the
structures or objects can be manipulated by standard
drawing and editing methods.
Drawing a Template
To draw a template:
• Click in a document window.
The template is drawn centered around the
pointer in the orientation that it appears in the
Templates palette.
Fusing a Template With An
Existing Structure
To draw a template and fuse it with an existing
structure:
• Click an existing bond in a document window.
156 • Chapter 11: Drawing With Templates
To deposit a template and create a spiro-linkage with
an existing structure:
• Click an existing atom in a document window.
To draw a template in a document window and
control the size and orientation:
• Drag from the beginning of the first bond in the
template to the end of the first bond.
When you drag upwards the bulk of the
template is drawn to the left, and when you drag
downwards the bulk of the template is drawn to
the right. Templates must contain at least one
bond in order to be drawn by the dragging
method.
Drawing with the Same
Template
To draw another template of the same type:
1. Click the Templates tool .
2. Draw the template in a document window.
Creating
Templates and Template
Documents
In ChemDraw Pro you can create new templates and
add them to existing Template documents or create
new Template documents.
To create a new Template document:
Windows:
• On the File menu, point to Open Special, and
then choose New Templates.
Macintosh:
• From the Window menu, choose the New
Template Stationery Pad.
ChemDraw
A new and untitled Template window appears. The
Template window is similar to a document window.
The Template window is divided into two halves by
a moveable, horizontal line:
• Template panel—Top half of the window
consists of individual panes where newly
created templates appear.
• Drawing area—Bottom half of the window
where you can draw new templates.
Template
Pane
Template
Panel
Template Template
Dividing Resizing
Line Handle
Drawing area
The templates you define are not limited to atoms
and bonds. Templates can contain any ChemDraw
objects such as captions, boxes, arcs, orbitals,
arrows, reaction mechanism symbols, and curves.
The ChemDraw objects in Template documents can
be colored. However, the colors do not appear in the
Templates tool palette. You can paste pictures from
other applications into a Template pane. Pasted
objects are scaled to the current Template document
settings. For more information, see “Autoscaling”
on page 170.
Creating Templates
To create a new template:
1. Select a Template pane by clicking it.
2. Draw a structure or object in the drawing area of
the Template window.
ChemDraw
The structure appears in the Template pane as
you draw. The tools in the Tools palette are used
to draw a template in the drawing area of the
Template window exactly as they are used to
draw structures in the drawing area of a
document window.
To select a different Template pane:
• Click another Template pane.
When you select a Template pane, the contents
of the pane appear in the drawing area.
As you define templates they become available for
use in your document without having to save the
Template document.
To view the newly-defined Template:
• Point at the Templates tool and hold
down the mouse button.
The name of the new Template document
appears in the menu.
Orientation of Templates
To make the templates that you create as easy to
draw with as possible, it is recommended that you
orient your structures so that the bond that
establishes the position of the template, for example,
the bond used for fusing is left and vertical. The
most vertical left bond is drawn first. For examples,
see “Using Templates” on page 156.
Chapter 11: Drawing With Templates • 157
 Resizing Template Panes
To resize the Template panes in the Template panel:
• Drag the Resize handle on the lower right
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Saving Template Documents
To save a Template document and have it available
in the Template pop-up menu and the Window

menu:
corner of the Template panel.
The percentage the block of Template panes is
enlarged or reduced appears in the Message
area.
Template Panels
To increase the size of the Template panel:
• Drag the Template dividing line.
1. From the File menu, choose Save As.
The Save As dialog box appears.
Saving a Template document in the cd_items
directory (Windows) or the ChemDraw Folder
(Macintosh) makes it accessible in the Open
Special submenu and in the Templates tools
palette.

To add a row of panes to the Template panel: 2. Type a name for the Template document and
click OK or Save.
1. Select a Template pane.
2. From the Tools menu, choose Add Row.
The new row is added at the below the Template
pane you selected.
To add a column to the Template panel:

1. Select a Template pane.

2. From the Tools menu, choose Add Column.
The new column is added to the right of the
Template pane you selected.
To delete a row of Template panes from the
Template panel:

1. Select a Template pane in the row you want to

delete.
2. From the Tools menu, choose Delete Row.
To delete a column of Template panes from the
Template panel:

1. Select a Template pane in the column you want

to delete.
2. From the Tools menu, choose Delete Column.
The column is removed and all other columns
are moved to the left.

158 • Chapter 11: Drawing With Templates ChemDraw

Chapter 12:
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
If you magnify a document, the drawing area size
structures and other objects are placed on the page
and drawing objects become bigger. If you increase
(layout). Effective layout of a drawing includes
the magnification so that the page size becomes
proper alignment of chemical structures and other
bigger than the screen, scroll bars become available.
objects, appropriate page size, and page orientation.
The page layout tools include: setup of the page and Page Setup
the use of the ruler, and the grouping, layering,
aligning, and distributing commands. The Page Setup parameters that affect the size of the
drawing area are:
Controlling the Drawing • Page size

Area • Orientation
• Margins
The size of a document window is not necessarily
the same as the size of the drawing area of the page. These parameters are specified in the Page Setup
A document window, in most cases, actually covers dialog box. The Page Setup dialog box and the
only a portion of the drawing area. options available vary depending on the printer you
have chosen. For the Macintosh, the version of the
The following options allow you to set the drawing printer driver for that printer is installed in your
area displayed on your screen. System Folder.
• Page Setup from the File menu allows you to set To set the paper size, orientation, and margins:
the size and orientation of the page.
1. From the File menu, choose Page Setup.
• View menu options: Actual Size, Show Page,
Magnify, and Reduce. The Page Setup dialog box appears. The dialog
box appears slightly different depending on the
• Magnification Controls: enlarge and reduce
printer and platform you have.
• 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 Chapter 12: Working with Page Layout • 159

 The Macintosh Page Setup dialog box with Page Orientation
common settings for a LaserWriter is shown
To choose the orientation of the page:
below.
• Click the vertical (portrait) or horizontal
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(landscape) orientation button.

The orientation of a document window changes
to the orientation you have chosen. This is
evident when the rulers are visible.

Margins
To change the margins for the selected paper size:
2. Select a paper size from the drop-down list.
1. Select the text next to the margin you want to
The available page sizes vary depending on the change.
type of printer. Listed below are common sizes
2. Type the new margin measurement.
available. The page orientation you choose
determines which of the measurements is height The units of the margins are set in the
and which is width: Preferences dialog box. The paper size minus
the margins determines the drawing area.
Paper Type Dimensions 3. Click OK.

US Letter 8.5 x 11 inches NOTE: Most printers do not use the Print/Page
Setup settings from other printers. If you change
printers, check the Print/Page Setup settings for all
US Legal 8.5 x 14 inches of your documents.

A4 Letter 21 x 29.7 cm
Reduce or Enlarge
B5 Letter 17.6 x 25 cm Some printers include an option to reduce or enlarge
your drawings by a variable percentage (25-400%).
Tabloid 11 x 17 inches This option scales all objects and text in the
document window by the percentage specified. This
International 8.5 x 12 inches is not a change in magnification. The size of objects
is changed relative to the paper size, margins, and
orientation you have specified.
Computer 14 x 11 inches
The enlarge or reduce option is useful for changing
the size of the available drawing area, while keeping
the images on the screen at the normal size when you
are drawing. If your document is set so that the
drawing fills the page on one printer and you use
another printer that requires larger margins, the

160 • Chapter 12: Working with Page Layout ChemDraw

drawing my disappear off the edge of the document
window. You can reduce the size of the drawing with
Multiple-Paged
the reduce option so that it fits in the document Documents
window.
You can create two types of multiple-paged
Saving Page Setup Settings documents:

You can save Page Setup settings in a Style Sheet or Paged—A single document containing two or more
Stationery Pad. Whenever you open a Style Sheet or sheets, each of which is printed on a single piece of
Stationery Pad, these settings are automatically paper.
used. The Page Setup settings are saved in addition Posters—A single large document, composed of as
to the Text settings, Drawing Settings, and the Color many pieces of paper as necessary.
Palette.
Paged Document Setup
35mm Slide Boundary To create a document with more than one page:
Guides 1. From the File menu, choose Document Setup.
If you make 35mm slides from a hard copy of a
ChemDraw document or from a screen shot, you can
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
help you keep your drawing within this region to
maintain the proper ratio, but are not printed. The
drawing area of the page must be at least 7 x 10.5
inches for these boundary lines to be visible.
To display the 35mm slide boundary lines:

1. From the File menu, choose Preferences.

2. Select the Show 35mm Slide Boundary
Guides check box.
3. Click the OK button.
Two 35mm Slide Boundary Guides appear in
the same orientation you have chosen in the
Page Setup dialog box. These guides appear in 2. Specify the number of pages in the Document
every document. Size section.
This preference affect all documents. The size of the pages is determined by the Page
Setup settings. For more information, see “Page
Setup” on page 159.
3. Type the Margin settings.

ChemDraw Chapter 12: Working with Page Layout • 161

 4. Create Headers and Footers as described in The number of pages and the margin
“Creating Headers and Footers” on page 162. dimensions are calculated.
5. Click OK. 4. Select whether to Print Registration Marks.
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A document is created using your settings. 5. Create Headers and Footers as described in
“Creating Headers and Footers” on page 162.
Poster Documents Setup 6. Click OK.
You can create a poster by creating a single large An example of a 19-inch by 14-inch poster,
drawing area, which will be printed on as many consisting of six 8.5-inch by 11-inch pieces of paper
separate pages as necessary. When you set the with a 1-inch overlap is shown below.
document size and how much each page overlaps,
ChemDraw calculates the number of pages needed 8.5"
and the margin sizes. You can set registration marks, 1" 1"
which mark the overlap setting on each page, to use
as a guide when assembling the poster from the 11"
separate pages.
1" 19" X 14" Poster
To create a poster document:

1. From the File menu, choose Document Setup.

2. Click Poster.

Creating Headers and Footers

You create headers and footers in the Document
Setup dialog box. In poster documents, only one
header and footer appear for the entire document.

1. In the Document Setup dialog box, type the

value of the position from the edge of the page
that you want the header or footer to appear.
2. Type the text to appear in the header or footer.
3. Add additional information as follows:

To include the… Type …

file name &f

page number &p

date printed &d

3. Type the Height, Width, and Page Overlap.
time printed &t

162 • Chapter 12: Working with Page Layout ChemDraw

 4. Position the text horizontally by typing the
characters in the table below. Any text
following these characters is appropriately
aligned.
2. From the Tools menu, choose Magnify.
NOTE: In Windows, you can also magnify by
clicking .

To align the Type …

text … The magnification occurs around the center of
the selected object. The magnification
centered &c percentage appears in the Magnification
drop-down list.
right &r
Windows Macintosh
left (default) &l
You can continue to magnify your view to a
Changing Perspectives maximum of 400%.

You can use a close-up view of objects in your Actual Size

reaction scheme to make sure they are properly To return to the actual size from any other
positioned. At times, you may want to reduce your magnification:
view so that you can move groups of objects around
the page. You can change the magnification to • From the Tools menu, choose Actual Size.
perform these functions by using the Magnify and The view is returned to the original size.
Reduce commands in the Tools menu or the
magnification controls. Reduce
To reduce the magnification:
Magnifying with the Tools
Menu 1. Select an object around which you want to
reduce the magnification.
When you use the tools menu to magnify or reduce,
the magnification is set to the next higher or lower
NOTE: If you do not select an object, the last
value. You can magnify up to 400% or reduce to
object drawn is the center point of the
25%.
magnification.
Magnify
2. From the Tools menu, choose Reduce.
To magnify using the Tools menu:
1. Select the object around which you want to
NOTE: In Windows, you can also reduce your
magnify your view. document by clicking .

NOTE: If you do not select an object, the last The reduction in magnification appears in the
object drawn is the center point of the Magnification drop-down list.
magnification.
Windows Macintosh

ChemDraw Chapter 12: Working with Page Layout • 163

 You can reduce the magnification until the entire
page fits on the screen. In the reduced view, you can
Arranging Objects
continue to use all of the drawing tools. In particular, This section describes methods for positioning,
you can use a selection tool to rearrange the drawing aligning, and layering objects in a document
Administrator

in order to take better advantage of the space window.

available.

Show Page
Using Rulers
The Show Page reduces the magnification until the You can use the rulers to position objects a measured
entire page is visible in the document window. distance away from some reference point or create
objects of an approximate size. The units used for
To view the entire drawing area in a document
the ruler are set in the Preferences dialog box, where
window at once:
you have the choice of inches, centimeters or points.
• From the Tools menu, choose Show Page.
The Message area shows the reduction in Showing Rulers
magnification that was required to have the To display the rulers:
entire page appear on the screen.
• From the Tools menu, choose Show Rulers.
Using the Magnification Control A check mark appears next to the Show Rulers
When you use the Magnification control, you can command, and the rulers appear along the top
display magnifications from 10% to 999% of the and left edges of a document window.
normal size of your page. The magnification control
allows you to select a specific value.
To use the Magnification controls:
Windows:
• Select a value from the drop-down list
or type a value.
Macintosh:
Do one of the following:
• Select a value from the drop-down list
.
As you move the pointer, Ruler Guides appear
• Select Other from the drop-down list. In the
on each ruler, indicating the position of the
dialog box that appears, type a value and click
pointer.
OK.

164 • Chapter 12: Working with Page Layout ChemDraw

 Ruler Guides
Ruler guides also appear when you drag selected
objects. In this case, however, there are two Ruler
guides that bracket the object. With this bracketing
you can quickly establish the height and width of the
selected objects.
Displaying the Crosshair
To show the Crosshair:
• From the Tools menu, choose Show Crosshair.
A check mark appears next to the Show
Crosshair command and the Crosshair appear
within a document window.
To assist you in aligning objects, the Crosshair
includes grid lines that extend from the major
division marks on each axis.

Ruler Guides

You can also show the Rulers while the Crosshair

are displayed so that you can see the unit
measurement associated with each of the divisions
on the Crosshair axes.

Moving the Crosshair

Hiding Rulers
To move the Crosshair:
To Hide the rulers:
1. Position the pointer where the Crosshair axes
• From the Tools menu, choose Show Rulers.
intersect.
The check mark disappears.
When the pointer is near to the center of the
Using the Crosshair Crosshair, it changes to an arrow.
2. Drag the Crosshair.
Use the Crosshair to align objects relative to each
other, and to space objects a consistent distance To constrain the movement of the Crosshair to the
apart. The axes of the Crosshair can be moved X- or Y-direction:
within a document window. • Shift+drag the crosshair.

ChemDraw Chapter 12: Working with Page Layout • 165

 Aligning Objects using the Centering on a Page
Crosshair To center an object (or group of objects) at the center
To use the Crosshair to align objects do one of the of the page:
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following: 1. Select the object you want to center using a

• Move the Crosshair axes and align it with the selection tool.
object. 2. From the Object menu, choose Center on
• Select an object and drag it until it is aligned Page.
with either axis of the Crosshair, or a grid line. The selected objects move so that the center of
In either case, if a bond or side of the object is the Selection rectangle is positioned at the
parallel to one of the axis, it disappears when it is center of the page.
exactly positioned over a Crosshair axis.
Aligning Objects
To align another object on the Crosshair:
Use the Align commands to align objects relative to
1. Select a second object. each other. Examples of the types of alignments are
2. Drag the second object to the Crosshair axis or shown on the menu.
grid line and align it to the first.
You can also move selected objects in small
increments to align them with the Crosshair using
the Arrow keys available on some keyboards:
To move 1 point in the direction of an Arrow key:

NOTE: 1 point equals 1/72 inch or 0.035 cm.

To align two or more objects:
• Select the objects and then press an Arrow key.
1. Select the objects with a selection tool.
To move 10 points using the Arrow key, for
example, to the right:
• Press Alt+Right Arrow.

Hide Crosshair
To hide the Crosshair:
• From the Tools menu, choose Show Crosshair.
The check mark next to the Show Crosshair
command disappears.

166 • Chapter 12: Working with Page Layout ChemDraw

 2. From the Align submenu, choose one of the
Align commands.
If you select only part of a structure or group
with a selection tool, only that part is used for
the alignment operation, but the entire structure
or group is moved.
Distributing Objects
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.
H
OH
CH2Br
2. On the Object menu, point to Distribute, and
then choose Vertically or Horizontally.
H
OH
CH Br
The space between the objects is equalized. The
upper, lower, right, and left positions of objects
in your selection remain unchanged.
ChemDraw
Front to Back Ordering
The front to back ordering is a useful method for
changing the orientation of one object relative to
another object within the same picture layer. For
additional information specific to the layering of
bonds, see “Changing Bond Crossings” on page 67.
Picture Layers
There are three layers within a ChemDraw
document. From back to front, they are: imported
pictures, graphical ChemDraw objects, and text. The
ordering of these layers cannot be changed.
However, the front to back ordering of objects
within each layer can be specified with the Bring to
Front and Send to Back commands in the Object
menu.
For example, if an imported picture is dragged onto
a ChemDraw structure, the structure is not hidden
because the imported picture resides in the back
layer.
An imported picture is any picture pasted into a
ChemDraw document from another application
such as a molecular model or a graph from a
graphing application, or a spectrum. The picture can
be imported into the ChemDraw document by using
the Paste command. A graphical ChemDraw object
is any structure or object created within ChemDraw,
excluding text. Text, including both atom labels and
captions, is always the front layer.
NOTE: When you point at an imported picture, a
highlight box appears around the periphery of the
object that helps distinguish it from a graphical
ChemDraw object. Text also has this type of
highlight box
Chapter 12: Working with Page Layout • 167
 Send to Back
To place one object behind another within a layer:

1. Select the object that you want to send to the

Administrator

back, in this example, the two upper orbitals.

2. From the Object menu, choose Send to Back.

The selected object appears behind all other

objects in the same layer.

Bring to Front
To place one object in front of another within a
layer:

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 in the same layer.

168 • Chapter 12: Working with Page Layout ChemDraw

Chapter 13: Sharing Information
Overview
ChemDraw includes many of the standard system
commands for transferring information within
ChemDraw documents, between ChemDraw
documents, and between documents created using
other applications. You can transfer information
using the Clipboard, drag and drop, object
embedding, and file formats.
ChemDraw does not install its own fonts. If a
ChemDraw document contains fonts that are not
available on a particular computer, they are
substituted with fonts that are available.
Cutting
To place ChemDraw objects on the Clipboard and
remove the objects from a document window:
1. Select the objects to remove with a selection
tool.
2. From the Edit menu, choose Cut.
The selected objects are placed on the clipboard
and removed from a document.
Pasting
To paste the contents of the Clipboard into a
ChemDraw document:

Transferring Between 1. From the Edit menu, choose Paste while a

ChemDraw Documents
You can use the clipboard or the drag-and-drop
feature to transfer ChemDraw pictures to other
ChemDraw documents.
Using the Clipboard
You can use the clipboard to copy or cut a
ChemDraw object for pasting into another
document.
selection tool is selected.
2. The contents of the clipboard are placed in the
center of the active document.
If the Clipboard contains ChemDraw structures, the
pasted information is scaled to the settings in the
current document. For more information, see
“Autoscaling” on page 170.
To view the contents of the Clipboard:
• Take the appropriate action:

Copying If you are Then…

To place a copy of a ChemDraw drawing on the using …
clipboard:
Windows • From the desktop, click
1. Select the objects to copy using a selection tool. Start, point to Programs,
2. From the Edit menu, choose Copy. point to Accessories, and
then choose the Clipboard
A copy of the selected objects is placed on the Viewer.
Clipboard. The selected objects remain in the
document.

ChemDraw Chapter 13: Sharing Information • 169


If you are Then…
using …
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Macintosh • From the Edit menu, choose
Show Clipboard.
See your operating system documentation for
information on using the Clipboard.
NOTE: You can paste the contents of the Clipboard
into another application by the same procedure. See
your application documentation for additional
information specific to the application. Macintosh:
If you are pasting the ChemDraw drawing in a
document from which you are planning to print to a
PostScript printer, see“Transferring PostScript
(Macintosh Only)” on page 174.
Using the Drag-and-Drop
Feature
You can use the drag-and-drop feature to copy
objects to place in other documents. To use this
feature in other applications, they must support
drag-and-drop.
To use the drag-and-drop feature to transfer
information between ChemDraw documents:
1. Select an object or structure in a ChemDraw
document.
2. Drag the selection into another ChemDraw
document window.
The selection is copied to the destination
ChemDraw document.
To drag and drop a selection to another application:
1. Select an object or structure in a ChemDraw
document.
2. Drag the selection into the other application’s
document window.
170 • Chapter 13: Sharing Information
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).
To create a clipping file or a scrap file:
1. Select an object in a ChemDraw document.
2. Drag the selection out of the ChemDraw
document window onto the desktop.
A clipping file or a scrap file is created on your
desktop.
To view the information within a clipping file or a
scrap file:
• Double-click the file’s icon.
A window appears showing the ChemDraw
drawing. Click the close box to close the
clipping file’s window.
To use the contents of a clipping or scrap file in a
document:
• Drag the clipping or scrap file into an open
window of an application that supports the
drag-and-drop feature.
The contents of the clipping or scrap file are
copied to the open window. The clipping or
scrap file is unchanged.
Autoscaling
When you transfer ChemDraw objects using the
Clipboard or drag and drop from one ChemDraw
document (the source document) to another
ChemDraw document (the destination document),
the objects are automatically scaled to match the
document settings of the destination document.
Automatic scaling assures that the objects being
transferred match the settings of the current
document.
ChemDraw
Bonds
All bonds drawn in the source document using the
values specified in the Drawing Settings dialog box
can be changed to use the Drawing Settings in the
destination document.
Any resized bond in the source document is scaled
in the destination document. The scale factor is
based on the ratio of the bond’s length after resizing
(source) to the Fixed Length in the Drawing Settings
dialog box (source). This scaling process maintains
the source document proportions in the destination
document. All values in the Drawing Settings dialog
box are scaled using this method.
For example, the Fixed Length is set to 1.0 cm in a
source document. A benzene ring is resized in to
200%. The bond length is then 2.0 cm: a ratio of 2.0
cm:1.0 cm or a scale factor of 2. In the destination
document, the Fixed Length set to 1.7 cm. When the
benzene ring is pasted into the destination
document, the bonds are scaled by a factor of 2 to a
final bond length of 3.4 cm.
Atom Labels
Atom labels are scaled the same way as bonds.
For example, in the source document, the atom label
font size is set to 16 points. One or two atom labels
in the source document are resized to 8 points, a
ratio of 8:16 or a scale factor of 0.5. The destination
document has an atom label font size is set to 14
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.
ChemDraw
Captions
ChemDraw autoscales captions are autoscaled using
the ratio of the fixed length in the destination
document to the fixed length in the source document
times the caption font size. The font size of the
caption can be any size and is not related to the
setting in the Caption Text Settings dialog box. This
assures that captions are always in proportion to the
bonds with which they are pasted.
For example, If the source document has a fixed
length of 1.0 cm and the destination document has a
fixed length of 2.0 cm, and the caption you are
pasting is 12 points, then the resulting caption size
after autoscaling is (2.0 cm /1.0 cm) x 12 points = 24
points.
Non-bond Objects and Color
All objects that are not affected by settings in the
Document Settings dialog boxes, such as arrows and
boxes, are scaled to maintain the same proportions
to bonds that were present in the source document.
With the exception of the foreground and
background color, the other colors present in the
selection to be pasted are added to the destination
document’s Color Palette if they are not already
present (up to a maximum of 20 total colors). The
background color in the destination document is
unchanged, and all objects colored using the
foreground color are changed to match the
foreground color in the destination document.
Chapter 13: Sharing Information • 171
 Pasting to an Empty Document Transferring ChemDraw
Window
Documents Across
If you paste a ChemDraw drawing into an empty
Platforms
Administrator

ChemDraw document and the settings between the

documents are different, the Change Settings dialog
box appears:
To change the settings in the destination document
to match the settings in the source document:
• Click Change Settings.
All of the settings in the destination document
are changed to match those of the source
document. All of the colors in the Color Palette
of the destination document are changed to
those specified in the source document.
To scale the objects from the source document to the
settings in the destination document:
• Click Don’t Change.
Use the following procedures to transfer ChemDraw
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
new platform.
Transferring from Macintosh to
Windows
To be able to open a ChemDraw file created on the
Macintosh in Windows, follow the instructions for
the appropriate versions shown in the table below.
From To Instructions
Mac Windows
Version Version

The settings from the source document are ≥ 4.0 ≥ 4.0 Save as ChemDraw and
scaled to those in the destination document add .cdx to the file
name.
using the ratios given above.
≥ 4.0 3.x Save as ChemDraw 3.x
NOTE: If the source document was created in a and add .chm to the file
ChemDraw version earlier than 3.0, the name of the name.
document appears as “Unknown” in the dialog box. = 3.5.x = 3.x Save as ChemDraw and
add .chm to the file
name.

172 • Chapter 13: Sharing Information ChemDraw

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

ChemDraw Chapter 13: Sharing Information • 173

 OLE (Windows Only)
When a drawing is transferred from ChemDraw into
another document type that supports OLE, you can
Administrator
open the drawing and it appears in a ChemDraw
document window. Any changes you make within
the ChemDraw document window are shown in the
other document when you close the ChemDraw
window.
For example, to edit a ChemDraw drawing pasted
into Microsoft Word for Windows version 6.0 or
later:
• Double-click the ChemDraw drawing that is
pasted into a Microsoft Word document.
The ChemDraw application opens. The
drawing opens in a window titled “From
Microsoft Word”.
You can use all the ChemDraw tools to edit the
drawing. When you have finished making changes:
• From the File menu, choose Close.
The ChemDraw document window closes and
the drawing in the Microsoft Word document is
updated with any changes you made.
Transferring PostScript
(Macintosh Only)
To obtain the highest quality drawings possible on a
PostScript printer, ChemDraw creates both a screen
representation and a PostScript representation of
your drawing. PostScript is a page-definition
language used to describe drawings. Many printers,
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
selected (default) when you copy and paste from
ChemDraw to other applications. The ChemDraw
174 • Chapter 13: Sharing Information
Laser Prep option adds approximately 11K to 12K to
each drawing, but these options give you the greatest
flexibility if you give your document to someone
else or later want to print it on a PostScript printer.
If you never plan to print to a PostScript printer or
never plan to give your document to someone who
uses a PostScript printer, you can turn the
preferences off.
To deselect the PostScript preferences:
1. From the File menu, choose Preferences.
2. Deselect Include PostScript and Include
ChemDraw LaserPrep.
You can produce high quality output from your
PostScript printer with these preferences off by
doing the following:
• From the File menu, choose Initialize
LaserWriter.
The ChemDraw Laser Prep is sent directly to
your printer. The ChemDraw Laser Prep setting
remains in the printer’s memory until the printer
is turned off or reinitialized.
We do not recommend that you use this option if you
plan to give the document to someone without
access to your printer or who does not have
ChemDraw.
To transfer only a few drawings to another
document:
NOTE: You can also transfer drawings to a
document in a remote location whose printer cannot
be initialized by ChemDraw.
• In the Preferences dialog box, select Include
PostScript and Include ChemDraw Laser
Prep.
ChemDraw
 The PostScript commands and the ChemDraw
Laser Prep are transferred with each drawing. NOTE: All colors, except for the Background
The transferred drawings can be printed Color, are contained within an edition file. The
Background Color is always removed.
independently of ChemDraw.
If you do not check the Include PostScript
check box when printing to a PostScript printer Creating a Publisher
ChemDraw sends QuickDraw commands to the To create a Publisher file:
printer. For more information, see “Setting Print
1. Select the objects to publish using a selection
Preferences” on page 11.
tool.
To print to a non-PostScript printer:
2. From the Edit menu, choose Create Publisher.

NOTE: You can also use this procedure to transfer The Create Publisher dialog box appears.
ChemDraw drawings to a drawing program that
does not use PostScript commands.

• Deselect both Include PostScript and Include

ChemDraw Laser Prep in the Preferences
dialog box.

Publishers, Subscribers, and

Editions (Macintosh only)
You can share information through a dynamic link
between a ChemDraw document and one or more
other application documents using the publish,
subscribe, and edition features.
To create a link, you designate a portion of a
ChemDraw document as a publisher and save a
drawing of the publisher in an edition file. You can
then designate an area within a document as a
subscriber and also link to this edition file.
Changes made to the publisher update the edition
file, which then updates the subscriber. You can
choose automatic or manual updating. Updating is
done in the background. The subscriber document
does not need to be open to be updated.
You cannot publish or subscribe from a Template
document.
3. Type an edition file name and choose a folder to
save it in.
4. Click Publish.
The Create Publisher dialog box closes. The
object you selected is enclosed in a gray
rectangle called a Publisher border.
The area contained the borders of the publisher is
included in the edition file. Any object or part of an
object in the edition file appears in any document
that subscribes to it. The publisher border is an
object and you can use a selection tool to select,
move, and resize it independent of its contents.

ChemDraw Chapter 13: Sharing Information • 175

 To resize a publisher border without changing its
height to width ratio:
1. Select the publisher border by clicking with a
Administrator
selection tool.
2. Drag the Resize handle.
To resize a publisher border in the X- or Y-direction
only:
• Hold down Shift and drag the Resize handle.
Publisher borders only appear on the screen.
They are not printed.
To hide the Publisher borders:
• From the Edit menu, choose Show Borders.
The check mark and the publisher borders
disappear.
Subscribing to an Edition File
To subscribe to the contents of an edition file:
1. From the Edit menu, choose Subscribe To.
The Subscribe To dialog box appears.
2. From the directory listing, select the edition file
you want to subscribe to.
The content of the edition file appears in the
Preview section.
3. Click Subscribe.
The Subscribe To dialog box closes. The most
recent edition appears in the document window
enclosed in a gray rectangle called a Subscriber
border.
176 • Chapter 13: Sharing Information
You can select, move, and resize a subscriber. If you
resize a subscriber, each time an edition file is
updated the contents appear resized.
The Subscriber border appears only on the screen. It
is not printed.
To hide the Subscriber borders:
From the Edit menu, choose Show Borders.
• The check mark and the subscriber border
disappear.
Publisher Options
You can use the Publisher Options command to:
• Specify when an edition file is updated with
changes made to the publisher.
• Display other information about the edition file.
To open Publisher Options do one of the following:
• Select a publisher by clicking the Publisher
border using a selection tool.
• From the Edit menu, choose Publisher
Options.
• Double-click the Publisher border.
The Publisher Options dialog box appears.
Publisher to
To display a pop-up menu listing the location of the
edition file linked to the publisher:
• Point to the Publisher to pop-up menu and hold
down the mouse button.
ChemDraw
Send Editions
You can specify when a publisher sends a new
edition to an edition file by setting options within the
Send Editions section of the Publisher Options
dialog box. In ChemDraw, each time a publisher
updates an edition file, the edition file contains the
most up-to-date drawing of the objects contained
within the publisher border.
Updating Automatically
To update an edition file automatically each time the
document is saved:
• Select On Save.
When you make changes to objects contained
within the Publisher border, the edition file is
automatically updated.
Updating Manually
To specify which revisions of the publisher are sent
to the edition file:
• Select Manually.
To update the edition file when the Manually radio
button is selected:
• Click Send Edition Now.
The Latest Edition is the last date and time the
edition file for the publisher was updated. The
Last Change appears below the Latest Edition
time and displays the last date and time that
changes were saved in the edition file.
Cancel Publisher
To delete a publisher and its corresponding edition
file:
• Click Cancel Publisher.
A message appears asking you if you are sure
that you want to remove the selected publisher.
When you cancel a publisher, the publisher
ChemDraw
border around the drawing is removed from the
document. The edition file is deleted when the
document is saved.
Subscriber Options
You can use the Subscriber Options command to
specify when a subscriber is updated with the
contents of the edition file.
To specify subscriber information:
1. Click the Subscriber border using a selection
tool.
2. From the Edit menu, choose Subscriber
Options.
3. Double-click the Subscriber border.
The Subscriber Options dialog box appears.
Subscriber to
To display a pop-up menu showing the location of
the edition file linked to the subscriber:
• Point to the Subscriber to pop-up menu and
hold down the mouse button.
Get Editions
You can specify when a subscriber receives the
updated edition by setting the options within the Get
Editions section.
To update the subscriber automatically each time the
document is opened and each time the edition file is
updated:
• Click Automatically.
Chapter 13: Sharing Information • 177
 To specify each time the subscriber is updated with A window appears containing a drawing of the
the most recent version of the edition file: contents of the edition file.
• Click Manually.
Administrator

To update the subscriber when the Manually radio

button is selected:
• Click Get Edition Now.
The Latest Edition Time is the last date and
time that the edition file for the selected sub-
scriber was updated.
When the Manually radio button is selected, the Last
Received time appears below the last edition time.
The Last Received time is the date and time the
contents of the edition file were used to update the NOTE: The word in the lower left corner refers to
subscriber. the type of information contained within the edition
file. In this example, it is PICT.
Open Publisher
To open the document containing the publisher:
Open Publisher
• Click Open Publisher. To open the document containing the publisher
linked to this edition file:
Cancel Subscriber
To break the connection between the selected • Click Open Publisher.
subscriber and the edition file.
Importing and Exporting
• Click Cancel Subscriber.
There are two ways to transfer ChemDraw drawings
A message appears asking you if you are sure
to and from other applications:
that you want to remove the selected subscriber.
When you break the connection, the subscriber • Using the Clipboard—The Clipboard is useful
is removed, but the drawing remains in your for transferring part or all of the information
document. within an active document window between
applications on the same computer or a
The Edition File networked computer.
To display the contents of an edition file: • Using different file formats—File formats are
useful for saving and opening the contents of a
1. Select the Edition File icon in the Finder.
ChemDraw document for transfer to other
2. From the File menu, choose Open, or double- chemistry, word processing, and desktop
click the icon. publication applications.

178 • Chapter 13: Sharing Information ChemDraw

Exporting Using the Clipboard
ChemDraw includes several formats on the
Clipboard during a normal copying operation.
ChemDraw supports the following formats:
• ChemDraw 4.0 or later (*.cdx)
• ChemDraw 3.5 (*.chm)
• PICT (Macintosh only)
• WMF (*.wmf, Windows only)
• 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
section under file formats.
To export a file using the Clipboard:
1. Select the structure using a selection tool.
2. From the Edit menu, choose Copy.
The structure is copied to the Clipboard. For
large structures you may see a status bar
indicating the progress.
SMILES and SMIRKS Strings
A SMILES string is a way to describe a chemical
structure in a line of text. Several software packages
use SMILES strings as a way to enter and store
chemical structure information.
A SMIRKS string is a way to describe chemical
reactions in text. If you select a reaction and use the
Copy As SMILES command, a SMIRKS string is
copied to the clipboard. If you use the Paste Special
SMILES command when a SMIRKS string is on the
clipboard, a reaction is pasted into your document.
ChemDraw
SMIRKS allows for agents, which are molecules
that do not contribute atoms to the product or accept
atoms form the reactants. ChemDraw does not allow
for agents. When you copy a reaction, everything
before the arrow is a reactant and everything after
the arrow is a product. When you paste a reaction,
any agents present are moved before the arrow.
Creating SMILES Strings
To create the SMILES string for the following
structure:
1. Select the structure using a selection tool.
2. From the Edit menu, point to Copy As, and then
choose SMILES.
The SMILES string corresponding to the
trans-2-amino-cyclohexanol molecule is
transferred to the Clipboard.
NH2
OH
N[C@@H]1[C@H](O)CCCC1
To display the SMILES string:
• Paste the string in a document window.
To view the SMILES string on the clipboard:
• In Windows, on the desktop, click Start, point
to Programs, then point to Accessories, and
choose Clipboard Viewer.
• On the Macintosh, from the Edit menu, choose
Show Clipboard.
When the SMILES string is on the Clipboard, you
can transfer it to another application that can
interpret and manipulate SMILES strings.
Chapter 13: Sharing Information • 179
 If you select more than one structure in ChemDraw,
and choose Copy SMILES from the Edit menu, the
SMILES string for each structure is copied to the
Clipboard and separated from the previous SMILES
Administrator
string by a period.
SMILES supports an alternate notation for aromatic
structures using lowercase letters. ChemDraw
generates this type of SMILES string for any
structure drawn with explicit aromatic bonds, either
by using the Aromatic bond type in the Atom
Properties dialog box, or by placing a circle within
any ring structure.
Pasting SMILES from
Clipboard
If you have a SMILES string, then you can
automatically convert that text string into a
ChemDraw structure.
To paste a SMILES string as a ChemDraw structure:
1. Select the SMILES string using the Text tool.
2. From the Edit menu, choose Copy.
3. From the Edit menu, point to Paste Special,
and then choose SMILES.
The SMILES string is drawn as a structure.
NOTE: Pasting SMILES uses the same routines as
the Clean Up structure command. For more
information, see “Using Clean Up Structure” on
page 119.
180 • Chapter 13: Sharing Information
Creating SLN Strings
You can copy a ChemDraw structure to the
Clipboard as an SLN string for export to a TRIPOS
application.
To copy a ChemDraw structure as an SLN string:
1. Select a structure.
2. From the Edit menu, point to Copy As, and then
choose SLN.
The Structure is copied to the clipboard as an
SLN String.
C[1]CCCCC@1
Exporting and Importing
Using File Formats
Many applications can use the information
contained within a ChemDraw document and saved
in one of the other file formats. File formats are
available in a pop-up menu at the bottom of the
Open and Save dialog boxes.
To export a file:
1. From the File menu, choose Save As.
2. In the Save As dialog box, do the following:
a. Type a name for the file and choose a
location in which to save it.
b. Select a file format from the bottom of the
dialog box.
c. Click OK or Save.
A copy of the current document is saved in the
format you specified. The current document
remains unchanged.
ChemDraw
Some file formats do not support atom labels that
contain nicknames or structural fragments. When
you save in these formats, ChemDraw automatically
expands all atom labels and saves the file using the
expanded form. For more information, see
“Expanding Labels” on page 117.
The following formats do not support nicknames or
structural fragments:
• Connection Table
• DARC F1
• DARC F1 Query
• MSI MolFile
• SMD
Bitmap (.bmp) Export Only
Bitmap (.bmp) files store raster graphics in an array
of individual bits. Bitmap images are the most
common format for continuous-tone images.
Because they represent a fixed number of pixels,
bitmaps are resolution dependent and may appear
jagged and lose detail if they are scaled on-screen or
printed on a higher resolution printer than they were
created for.
ChemDraw Template (*.ctp,
*.ctr)
Use the CD Template file format to save template
documents that appear in the template pop-up menu.
ChemDraw
ChemDraw (*.cdx)
The ChemDraw file format is the native format for
ChemDraw version 4.0 and later. This is a public
tagged file format that stores information about a
ChemDraw structure in a series of data blocks. This
format is designed to be easily generated and
interpreted by other programs. This format
accurately stores anything that can be drawn in
ChemDraw.
NOTE: Imported drawings saved within a
ChemDraw file created using ChemDraw for
Macintosh are lost when the file is opened using
ChemDraw for Windows. However, all ChemDraw
specific information is preserved. Imported
drawings include any graphics pasted into a
ChemDraw document from another Macintosh
application. The same applies for Windows to
Macintosh conversion.
ChemDraw XML (*.xml)
The cdxml file format is an interpreted version of
cdx that conforms to the XML specification unlike
binary cdx format. cdxml is text-based but contains
some data. For more information, see www.xml.org.
ChemDraw 3.5 (*.chm)
ChemDraw 3.5 file formats are used for saving or
opening ChemDraw documents using the version
3.5.x of ChemDraw. These documents can also be
opened in versions 3.0, 3.0.1, 3.0.2, and 3.1 of
ChemDraw as long as atom properties are not used
in the files.
NOTE: When you save a ChemDraw file in one of
these formats, all features specific to later versions
are lost. For example, multi-attached atom labels,
variable attachment points, and multicenter bonds
are not be saved.
Chapter 13: Sharing Information • 181
 ChemDraw 2.0 and ChemDraw
2.1 (*.chm)
ChemDraw 2.0 and ChemDraw 2.1 file formats are
Administrator
used for saving or opening ChemDraw documents
using the version 2.x file format of ChemDraw for
Macintosh.
NOTE: When you save a ChemDraw file in one of
these formats, all features specific to later versions
are lost. For example, color, dative bonds and
shaded orbitals are not saved.
ChemDraw Stationery/Style
Sheet (*.cds)
Use ChemDraw Stationery file format to save
document settings and other objects.
Connection Table (*.ct)
The Connection Table file format is a simple format
that saves a list of atom connectivities in terms of an
element, serial number, X and Y coordinates, bond
order, and bond type.
DARC-F1 Format (*.f1d)
The native file format for storing structures in the
Questel DARC system.
DARC-F1 Query (*.f1q)
The native file format for storing queries in the
Questel DARC system.
182 • Chapter 13: Sharing Information
Encapsulated PostScript (Text)
(Macintosh)
PostScript, *.eps (Windows)
Export only
Encapsulated PostScript (Text) files (EPS (Text)),
are ASCII text files containing the scalable
PostScript representation of a ChemDraw drawing
that can be opened using other applications and
platforms. No preview is included in this type of
EPS file. Programs that do not support the display of
raw PostScript can only print, not view an image on
screen.
Use EPS files to share ChemDraw drawings with
desktop publishing applications such as Adobe
PageMaker and QuarkXPress.
All colors are saved in the EPS file except for the
Background color. To save an EPS file with a
colored background, create a large colored
rectangular box using the Drawing Elements tool
and choose Send to Back before saving the file. For
more information, see “Drawing Boxes” on page 97
and “Working with Color” on page 121.
To include fonts in Windows EPS files, you must
have Adobe Type Manager (ATM) installed. Only
ATM fonts are saved in the EPS file.
Encapsulated PostScript (Mac)
(Macintosh) and PostScript
with Preview (Windows)
Macintosh Encapsulated PostScript (Mac) files
contain the scalable PostScript representation and
the QuickDraw (PICT) representation of a
ChemDraw drawing that other Macintosh
applications can translate and view.
ChemDraw
You can open and view ChemDraw drawings saved
in EPS (Mac) file format and PostScript with
Preview in various illustration, desktop publishing,
and desktop presentation applications.
Windows Postscript with Preview files contain the
scalable PostScript representation and the Windows
Metafile (WMF) representation of a ChemDraw
drawing that other Windows applications can
translate and view.
To include fonts in Windows EPS files, you must
have Adobe Type Manager (ATM) installed. Only
ATM fonts are saved in the EPS file.
All colors are saved in the EPS file except for the
Background color. To save an EPS file with a
colored background, create a large colored rectangle
and choose Send to Back before saving the file.
GIF Image (*.gif) Export only
Graphics interface format (GIF) is useful for
working with the hypertext markup language
(HTML) used in displaying information on the
World Wide Web. A GIF image can be displayed
directly on a Web page rather than having to
download the drawing for viewing in a Helper
application.
ChemDraw saves GIF files according to the GIF 89a
specifications with transparent backgrounds.
ISIS/SKC and ISIS/TGF
You can save a ChemDraw document in an ISIS file
format for export to an ISIS application, or import a
file created by an ISIS application into ChemDraw.
ChemDraw
ChemDraw Pro provides two ISIS file formats:
• ISIS/Sketch (*.skc)—For saving files as a
binary sketch file for transfer to another ISIS
application running on the same operating
system (this format is used on the Clipboard).
• ISIS/TGF (*.tgf)—For saving as an ASCII text
file (a Transportable Graphics File) for transfer
to ISIS applications on different platforms.
NOTE: When transferring between ChemDraw
and ISIS/Draw, if information in a file or on the
Clipboard contains only non-bond, unsupported
objects, the information is imported as a WMF
(metafile) or PICT graphic. However, if a supported
object, such as a bond, is also in the file or on the
Clipboard, then only the supported object appears.
NOTE: Object types in ISIS not supported in
ChemDraw, such as polymers, are not transferred.
Object types in ChemDraw not supported in ISIS are
not transferred. However, in some cases, such as
different arrow types, the arrow is converted to the
most similar form.
ISIS/Reactions (*.rxn)
The ISIS/Reactions format (RXN) is an MDL-
developed format for storing chemical reaction
information used by the ISIS family of products and
others.
For single step single or multi-line reactions,
ChemDraw uses the point of the reaction arrow as
the dividing line to determine which molecules in a
reaction are reactants and which are products.
NOTE: A reaction with an intermediate step cannot
be saved using the RXN file format.
Chapter 13: Sharing Information • 183
 Molecules whose centers are behind or above the tip
of the arrow are considered reactants, and all
remaining molecules are products. The reaction
arrow can be at any orientation; it does not have to
Administrator
be parallel to the x-axis. If a reaction contains
multiple arrows, then the largest arrow is used as the
reaction arrow.
NOTE: ChemDraw only recognizes structures.
Symbols, such as “+”, are ignored.
Reaction mapping and reaction center information is
stored in the rxn output file.
JDX (*.jdx, *.dx) Import
only
The Joint Commission on Atomic and Molecular
Properties (JCAMP) developed the JDX file format
for spectral data. JDX is a public, but not well
defined format that has numerous variations.
ChemDraw supports many of the more common
spectral variations with uniform x-axis spacing.
ChemDraw also supports Bruker NMR JCAMP
data, which is saved with a .dx file extension
When you import JDX files, they appear in the
window with a spectrum of a standard size that can
be re-sized by dragging.
You can export spectral data as part of a .cdx file
only.
MDL MolFile (*.mol)
MDL Information Systems, Inc. MolFile (MDL
MolFile) file format is used by several other
Windows, Macintosh, and UNIX chemical
databases and drawing applications such as
ISIS/Draw™, ISIS/Base™, MACCS™, and
REACCS™.
184 • Chapter 13: Sharing Information
ChemDraw Pro provides two MDL MolFile
formats:
• MDL MolFile (Text)
• MDL MolFile (Mac) for Macintosh only. This
file type is saved with an mmol file extension
and can be saved and opened with ISIS.
MDL MolFile files are ASCII text files that can be
created or edited in common word processing
applications or text editors. Atom and bond property
information is stored in the MolFile.
MDL RGFile (*.rgf) file format is used by several
other chemical databases and drawing applications.
The MDL File RGFile supports alternate groups
whereas an MDL Molfile cannot. When you save a
ChemDraw file that contains alternate groups as an
MDL MolFile, it is automatically saved as an MDL
RGFile.
For more information on MDL Molfile, see “MDL
MolFile (*.mol)” on page 184.
Molecular Simulations
MolFile (*.msm)
Molecular Simulations MolFile format is an ASCII
text file used by applications such as ChemNote™.
You can save a ChemDraw Pro document in
Molecular Simulations MolFile format for export to
one of these applications.
NOTE: ChemDraw uses the file extension “.msm”
for Molecular Simulations MolFiles rather than the
standard “.mol”, used by Molecular Simulation,
Inc. ChemDraw recognizes files with the “.mol” file
extension as MDL MolFiles. In addition, the
extension “.msi” used in earlier versions of
ChemDraw is no longer recognized in ChemDraw.
To open Molecular Simulations MolFiles that have
a “.mol” or “.msi” extension you must first change
the extension to “.msm”.
ChemDraw
PICT (Macintosh)
PICT files contain a QuickDraw representation of a
ChemDraw drawing that can be used by various
drawing applications. You can save a ChemDraw
document in the PICT format so it can be opened by
one of these other applications. The PICT file format
contains ChemDraw structural information. PICT
files created by ChemDraw version 6.0 or earlier can
be reopened and edited by ChemDraw version 6.0.
PICT files created by ChemDraw 6.0 can be edited
by ChemDraw 3.x, but not by earlier versions of
ChemDraw.
All colors are saved in the PICT file except for the
Background color.
PICT scaled 4X (Macintosh)
PICT scaled 4X files are the same as PICT files,
except that the drawing is four times larger. When
these larger files are placed into certain other
applications and shrunk back down to 1/4 size, they
may provide higher quality output than regular PICT
files.
PNG file (*.png) Export only
PNG (Portable Network Graphics) format is an
alternative to the GIF format for adding graphics to
web pages. You can save, but not open, files in PNG
format. The PNG format is fairly new and was
designed to address many of the shortcomings of the
GIF format. In particular, the PNG file format offers
true color images, is less prone to transmission
errors and offers a full alpha channel for specifying
background or transparency options.
For additional information about PNG visit:
http://www.boutell.com/boutell/png
SMD (*.smd)
Standard Molecular Data (SMD) file format, version
4.3, is an ASCII text file commonly used by
programs that search Chemical Abstracts Databases
such as STN Express™. You can save your
ChemDraw document in SMD format and use the
file for searching in a Chemical Abstracts database.
ChemDraw
SPC (.*spc) Import only
The SPC file format was developed by Galactic
Industries as part of the GRAMS software, which
reads spectral data from every type of spectrometer
and converts them to SPC format. SPC is a
well-defined, proprietary, but open standard format
for spectral data.
ChemDraw imports most one-dimensional spectral
spc formats. When you import an SPC file, it
appears in the window with a spectrum of a standard
size that can be re-sized by dragging.
You can export spectral data as part of a .cdx file
only.
Template Style Sheet
(*.cts)
The Template Style Sheet file format is used for
saving document settings and row and column
characteristics for creating ChemDraw Template
documents.
Windows Metafile (Windows
Only) (*.wmf)
The Windows Metafile file format saves the Graphic
Device Interface (GDI) representation of a
ChemDraw drawing. Using the WMF file format
you can transfer ChemDraw drawings to other
applications, such as Microsoft Word, that support
that WMF file format on the same or different
computers rather than using the Clipboard. The
WMF file format contains ChemDraw structural
information.
TIFF file (*.tif) Export only
TIFF format (Tagged Image File Format) is a high
resolution format commonly used for saving
graphics for importing into desktop publishing
applications on the same or on different computer
platforms. TIFF images can be saved using a variety
of resolution, color, and compression options. As
TIFF images can get rather large, choosing
appropriate options is important. The TIFF format is
for export only.
Chapter 13: Sharing Information • 185
 Resolution Compression
Available resolutions range from 72 (computer You can select from the following compression
monitor) to 1440 dpi (high resolution output). When options:
choosing a resolution, keep in mind that the size of
Administrator

• PackBits—Used to reduce files size by

the file increase as the square of the resolution.
encoding repeating bytes of information as
output when using the CMYK Planar color
Color
option. Below is a highly simplified
You can select from the following color options: representation of this compression scheme. For
• Monochrome—Forces all objects to black and a line of color information such as:
white. CCCCCMMMMMYYYYYKKKKK, the
compression yields a smaller file by
• RGB Indexed—Stores colors using computer
representing the information as C46M5Y5K.
monitor style of color encoding.
• CCITT Group 3—Used for fax transmissions
• CMYK Planar—Uses printing press style of
of images.
color encoding. Groups each color type
sequentially. This provides better compression. • CCITT Group 4—Used for fax transmissions
For example: of images.
CCCCCCMMMMMMYYYYYYKKKKK • Deflate—Similar to LZW compression. Works
rather than CMYKCMYKCMYKCMYK. This well with all Color and Resolution options.
option produces far better compression than
using the PackBits compression method. Setting TIFF options
However, many desktop publishing packages To set these options:
do not support CMYK Planar files.
1. Click the Options button in the Save dialog box
• CMYK Contiguous—Uses printing press style
to display the following dialog box.
of color encoding. Stores colors non-
sequentially. For example: CMYKCMYK. The
PackBits compression type provides no
compression for this type of file.

NOTE: If objects in your document are black and

white they are saved 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 2. Select the options you want and click OK.
Monochrome.
NOTE: In the Macintosh version you may want to
increase the memory allocated to ChemDraw if you
are saving large TIFF files.

186 • Chapter 13: Sharing Information ChemDraw

Appendix A:
The Chemistry of ChemDraw
Overview
ChemDraw automatically converts lines, characters,
and other symbols into chemically meaningful
figures as you work. This work occurs in the
background, but you can choose to view this
chemical data using Check Structure, Analyze
Structure, and Expand Atom Labels. ChemDraw
also uses this chemical data when exporting to file
formats that support only a subset of the notations
that ChemDraw does.
This appendix describes how ChemDraw interprets
what you draw and how you can help ChemDraw
better interpret what you mean.
ChemDraw’s Chemical
Intelligence
ChemDraw was designed as a tool to aid in chemical
communication. Most chemists would understand
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
ChemDraw’s chemical intelligence can be used as a
sophisticated “spelling” checker for chemical
compounds. For example, if you’re investigating
organic acids, a compound with the structural
formula CH3COO would probably represent acetic
acid. Present the same formula in a paper on
transition metal chemistry, and you might be
describing a novel methylated cobalt oxide. If you
had asked ChemDraw to interpret it beforehand, you
would have received a message reporting a valence
error, and you might have been prompted either to
add a negative charge or to change the
capitalization.
ChemDraw can offer only suggestions. If you and
your audience understand what you are trying to
depict, then you can ignore ChemDraw’s
suggestions. In many cases, you can teach
ChemDraw to understand the notation you’re using.
For more information, see “Applying Nicknames”
on page 113.
Appendix A: The Chemistry of ChemDraw • 187
 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.
Single bond, “down”
Fe
stereochemistry (into the plane of
the paper, away from the viewer),
Fe Fe from the first drawn atom to the
second drawn atom.
Fe Single bond, “up” stereochemistry
(out of the plane of the paper,
and 3 other isomers toward the viewer), from the first
Merck Index Beilstein drawn atom to the second drawn
atom.
Single bond, mixture of “up” and
HC CH “down” stereochemistries in some
HC CH unspecified proportion.
CH
Fe Dative bond. Often used to indicate
Fe CH
CH CH polar bonds, such as the in N-O
CH CH bond in pyridine N-oxide.
Double bond, with cis/trans
Aldrich MDL ACD stereochemistry as drawn.
Double bond, with cis/trans
A successful search in one database might not stereochemistry unknown.
produce any hits in another. When in doubt, consult
the documentation for your database, and see if it Tautomeric bond, either single or
double according to rules of
offers any clues to the conventions used.
tautomerism.
Aromatic bond, part of a
delocalized resonance system.
Triple bond.

Quadruple Bond.

188 • Appendix A: The Chemistry of ChemDraw ChemDraw

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
on the right if the atom label was in Automatic style
Atom Labels and on the left side of the original structure:
A simple atom label may contain any of the
A multi-attached label
following: O that is parsed from left
Cl A single to right.
element. CH2CCH3
O
A multi-attached label
CH3 An element and O that is parsed from
H some number of right to left.
N hydrogen atoms. H3CCH2C

Me A nickname. (C H2)4 OH A bond attached to the

open parenthesis of a
CH2 (CH2 )3OH
Ala repeating group is
treated as if bonded to
C(OCH3)3 Repeating units the first of those
within groups.
O(CH 2)4CH3 parentheses. (CH2)4 A bond attached to the
CH2 COOC (OPh)3 A series of any close parenthesis or
CH2 (CH2 )2CH 2
combination of repeat count of a
the above. repeating group is
treated as if bonded to
When analyzing an atom label, ChemDraw starts at the last of those
the left and continues to the right, applying standard groups.
rules of valence to determine which atoms are bound
to which. The exception is with an atom label in Multiple fragments within a single label can be
Automatic alignment on the left side of a compound. specified in the following ways:
This sort of atom label is displayed “backwards”
(H3CO instead OCH3) and is therefore parsed from COO-Na Implicitly, using standard
right to left. Standard valences for each atom are valence rules.
defined in the Isotopes Table.

ChemDraw Appendix A: The Chemistry of ChemDraw • 189

 Chemically-significant text must be entirely in
Explicitly, using a space, Formula or, for isotopes and charges, Superscript
COO- Na+
period (unsuperscripted
style. ChemDraw does not recognize a chemical
or unsubscripted), bullet,
formula embedded within a larger block of text.
or combination.
Administrator

COO-.Na+
NH4 + If you draw a bond, add an
atom label, and then delete the
COO-•Na+
bond, you have a chemically
meaningful text block whose
COO- . Na+ font, size, and style match
other atom labels.
(COO-)3 . 3Na+ An unsuperscripted, If you create a caption with the
unsubscripted integer at H 2O text tool and set it to Formula
(COO-)3 . Na+ Na+ Na+
the start of a fragment is style, you have a chemically
recognized as a meaningful text block whose
stoichiometric multiplier font, size, and style match
and is treated as if the other captions.
appropriate number of
fragments were drawn
explicitly.
Charges
Charges may be created as part of a textual atom
label or with the appropriate symbol from the
Chemically Significant Text Chemical Symbols Palette. Charges are always
Often it is simpler to write a chemical formula like assigned to a specific element in the atom label,
MeOH or H2O than it is to draw out an entire atoms- whose acceptable valences become those of the
and-bonds structure. ChemDraw correctly interprets similar isoelectronic neutral element.
any unambiguous structural formula. For example,
CH3COCH2CH3 is recognized as methyl ethyl O- A charge following an
element is assigned to that
ketone and MeOH is recognized as methanol. On the
element.
other hand, C6H6 might mean benzene, or it might
mean one of over 200 other isomers. C6H6 is not +NH3 A charge that does not
recognized by ChemDraw, and generates an error follow an element is
message if you try to analyze it. Generally, empirical assigned to the next
(N+)H3 element.
formulas (C2H6 and H2SO4) are not recognized, but
structural formulas (CH3CH3 and HOSO2OH) are. NH3 + Charges that follow a
monovalent element with a
Molecular weight and elemental analyses of
repeat count are assigned to
empirical structures is possible, but the Expand (N+)H3 the element before that
Label command does not work with them. Empirical element.
structures are discarded when they are transferred to
other applications that require unambiguous
structures.

190 • Appendix A: The Chemistry of ChemDraw ChemDraw

 CO2- Charges that follow other Isotopes can be
CH2 13COOH
repeating units are included anywhere
distributed among those that regular elements
CO(O-) units. can.

NH3
+ Charges may be O Deuterium and
superscripted. Tritium can be
T T
indicated by their
Fe++ Multiple charges are
one-letter symbols.
recognized appropriately. D 3C OD
2+ Charges may have repeat
Fe
counts as long as both the Radicals
Fe
+2 charge and the repeat count Radicals are indicated with the appropriate symbol
are superscripted. from the Chemical Symbols Palette. As with
A “floating” charge placed charges, they are assigned to the nearest atom.
with the Chemical Symbols Radicals always occupy one free valence, in
NH3
Tool is assigned to the addition to any charge effects.
nearest atom. If no atom is
(N+)H3 within the distance set as the
Fixed Length, the charge is Ph
ignored and not assigned to Ph C C O
any atom.
Ph
A “floating” charge placed
within a delocalized system
is recognized by the
H-Dot/H-Dash
Analyze Structure function, H-Dot and H-Dash symbols from the Chemical
but is discarded when saved Symbols Palette indicate the stereochemistry of a
to formats that require all single hydrogen atom. These symbols are most
charges to be associated commonly used in fused systems.
with specific atoms.
H
Isotopes and Elements
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
H
in the Isotopes Table file. You can edit this file to add
new isotopes in any text editor.

35 A superscripted
Cl
number before the
element symbol
indicates isotope
numbers.

ChemDraw Appendix A: The Chemistry of ChemDraw • 191

 Complexes Another
Compounds with electron pairs can act as Lewis representation of
heme.
bases, bonding with Lewis acids that are electron- N
Administrator

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 Multi-center Attachments
dative bond more accurately represents the electron
Multi-center attachments are meaningful only when
donation.
created using Add Multi-Center Attachment from
Complexes may also be represented with explicit the Structure Menu. This command creates a
lone pairs and without any bonds. pseudo-atom that is disregarded during chemical
calculations, but still allows you to create diagrams
If you use a plain bond to indicate a complex, you
that look meaningful to an experienced chemist.
may want to set Abnormal Valence to Allowed in the
Atom Properties dialog.

F3B NH3 Boron trifluoride-

ammonia complex.
O Boron trifluoride- M
acetic acid
complex. η3 or π-Allyl complex

HO

B
F
F
Fe
Heme, a compound
with two formal
N covalent bonds and
N Fe N
two formal donor-
acceptor pairs. Ferrocene, a π-Aryl complex
N

O
HO

192 • Appendix A: The Chemistry of ChemDraw ChemDraw

 • Rule 3—cis precedes trans
Cl Cl • Rule 4—Like pairs of descriptors precede
Ti unlike pairs
• Rule 5—R precedes S
ChemDraw checks differences up to 15 atoms
distant from the stereocenter.
Cp2TiCl2, another π-Aryl complex After the ligands are ranked, a descriptor is assigned
as shown in the following table.1
CO
C CO Stereocenter Descriptor

Mn Double bond Z if the highest ranking ligand

of each pair are on the same side
of the bond; otherwise E.

η-C5H5Mn(CO)3 Tetrahedral atom When the lowest-ranking ligand

is located behind the central
Stereochemistry atom:
Absolute stereochemistry is calculated for • R when remaining 3
tetrahedral atoms and double bonds according to the ligands are arranged
Cahn-Ingold-Prelog (CIP) priority rules. The CIP clockwise in descending
rules are designed to order ligands by their priority order
and determine a descriptor based on the orientation
of the ordered ligands in space. • S when remaining 3 ligands
are arranged
A ligand is an entity attached to a stereocenter. For counterclockwise in
example, a tetrahedral carbon has four ligands descending order
corresponding to its four substituents. When a
tetrahedral carbon is in a ring, it still has four • r or s is used for
ligands: the two ligands outside the ring, a third pseudoasymmetric atoms
consisting of the ring “unpeeled” clockwise, and a
fourth consisting of the ring “unpeeled” Stereochemical Flags
counterclockwise.
While the chirality of a specific stereocenter can be
Five rules are used to determine the priority of indicated with the appropriate wedged, hashed, or
ligands are summarized below in simplified form. plain bond, sometimes it is useful to indicate the
For more detailed information, see the references. relative stereochemistry of a molecule as a whole,
They are checked sequentially as follows: considering the relationship between all
• Rule 1—Higher atomic number precedes lower stereocenters. Stereochemical flags apply to the
• Rule 2—Higher atomic mass precedes lower

ChemDraw Appendix A: The Chemistry of ChemDraw • 193

 nearest structure; if no structure is within the Query Properties
distance specified by the Fixed Length value, the
By their nature, query properties do not represent
stereochemical flag is not assigned to any structure.
actual chemical features, but describe broad classes
Administrator

The Absolute or groups of features. For information on using

Abs
flag indicates query properties, see “Chapter 9: Working With
COOH
the exact Structures”.
NH2 stereoisomer as
drawn. Analysis Messages
COOH When ChemDraw is unable to analyze your
NH2
structure fully, two general types of messages are
The Relative displayed:
Rel

COOH
flag indicates • Status messages that report a problem that may
the exact not affect the final analysis
NH2
stereoisomer as
drawn, or its • Critical messages that may affect the final
COOH COOH
enantiomer. analysis
OR

NH2 NH2

The Racemic Message Description

Rac

COOH
NH2
COOH
AND
NH2 NH2
1.
R.S. Cahn, C.K. Ingold, and V. Prelog,
“Specification of Molecular Chirality”,
Angew. Chem., Int. Ed. Engl. 1966, 5, 385-
414 (errata: 1966, 5, 511); Angew. Chem.
1966, 78, 413-447.
V. Prelog and G. Helmchen, “Basic
Principals of the CIP-System and
Proposals for a Revision”, Angew. Chem.
1982, 94, 614-631; Angew. Chem. Int. Ed.
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.
flag indicates a
mixture of the There are too Displayed for every unlabeled
exact many bonds to atom with more than 4 filled
stereoisomer as this unlabeled valences. Filled valences
COOH drawn and its Carbon. include sum of bond orders,
enantiomer. charge, radicals, and free sites.
Aromatic bonds count 1.5 each,
rounded down unless it is the
only bond to the atom. Charge
is signed and includes charge
implied by dative bonds. The
Substituents query property
treats Free Sites, Up to and
Exactly the same way: an atom
with 2 explicit bonds and
“Substituents: Up To 3” or
“Substituents: Exactly 3” or
“Substituents: Free Sites 1” has
three filled valences.

194 • Appendix A: The Chemistry of ChemDraw ChemDraw

Message Description
An atom in this Displayed in a variety of cases
label has an where ChemDraw cannot find
invalid valence. a place to put a bond or cannot
find a bond to put on an atom.
Valid valences for each element
are listed in the Isotopes Table
file.
ChemDraw can’t Displayed when ChemDraw
interpret this finds text that it cannot identify
label. as an element, nickname,
generic nickname, or
alternative group name.
Parentheses don’t Displayed when parentheses
match. cannot be matched into nested
open-close pairs.
This label has Displayed when a plus and
conflicting or minus charge have been
unassignable assigned to the same element,
charges. charges have been assigned in
more than one way, or a charge
has been assigned to a
nickname, generic nickname,
or Alternative Group name.
Formula cannot Displayed for every label that
be computed for contains a generic nickname,
queries. an element list or an alternative
group. This is a status message
only; analysis continues as if
the problematic label were not
selected.
ChemDraw
Message Description
Text not in Displayed for the first caption
Formula style that is not an atom label or
won’t be Alternative Group name, and
interpreted. which contains any text not in
Formula, Subscript, or
Superscript style. This is a
status message only, and
appears only once regardless of
how many captions are in the
selection.
This named Displayed for any structure
alternative group within an Alternative Group
contains no Box where the structure lacks
attachment point. an attachment point. This is a
status message only.
This named Displayed for any Alternative
alternative group Group Box whose contained
contains structures have varying
fragments with numbers of attachment points.
inconsistent Since all structures within an
valences. Alternative Group Box are to
be used interchangeably, they
must have the same number of
attachments. This is a status
message only.
This named Displayed for any Alternative
alternative group Group Box that is empty. This
contains no is a status message only.
fragment.
Part of a molecule Displayed for any Alternative
is outside of the Group Box whose border
alternative group crosses part of a structure. This
definition. is a status message only.
Appendix A: The Chemistry of ChemDraw • 195
 Message Description

This isolated Displayed for unlabeled single

Administrator

bond is probably bonds unattached to other

not intended to bonds. All bonds are
have chemical interpreted chemically, usually
significance. as C2H6, and may cause
unexpected results if intended
as a graphical line only. This is
a status message only.

The atom is very Displayed for any atom that is

close to another nearly touching another atom
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.

The stereocenter Displayed for any asymmetric

has no center without attached
stereobonds wedged, hashed, dashed, or
specified. bold bonds. This is a status
message only, and appears only
when Show Stereochemistry is
tuned on and there is at least
one other wedged, hashed,
dashed, or bold bond in the
structure.

196 • Appendix A: The Chemistry of ChemDraw ChemDraw

Appendix B: Specifying Paths
Overview
This appendix describes the path information
necessary to locate the cd_items directory under
Windows or the ChemDraw Folder on the
Macintosh.
Windows
Normally, the cd_items directory is in the same
directory as the ChemDraw application and the path
is automatically set. However, if you want the
cd_items folder to reside in a different directory, you
must specify the path in the chemdraw.ini file. When
the path is not specified properly, ChemDraw
displays an error message and quits.
To change the path in the chemdraw.ini file if you
are using Windows:
• Open the chemdraw.ini file using a text editor.
NOTE: You should always create a backup of the
chemdraw.ini file before you make any edits. Use the
backup file if for any reason the edited file does not
work properly.
Normally, the chemdraw.ini file is located within
your Windows directory. The path information for
the cd_items directory is specified in the line
beginning with ChemDraw 6 Items Path=.
The following is an example of the text that appears:
ChemDraw 6 Items Path=C:\Program
Files\ChemOffice\ChemDraw\Cd_items\
If this line doesn’t exist, create it, otherwise
ChemDraw looks for the cd_items directory in your
local directory.
ChemDraw
To specify the path (information within the
chemdraw.ini file isn’t case sensitive):
• Type the path after “ChemDraw 6 Items Path=”
For example, if the cd_items directory is
located within a directory called “users” on
drive C, type:
c:\users\cd_items
The complete line should read:
ChemDraw 6 Items Path=c:\users\cd_items
After specifying the path:
• Save the changes and close the chemdraw.ini
file.
To implement the changes:
• Exit and restart ChemDraw.
Macintosh
When ChemDraw is installed the ChemDraw Folder
is placed in the same folder as the application.
However, if you are using ChemDraw from a file
server and you want to have your own ChemDraw
folder, place the ChemDraw folder in the
Preferences folder in your System folder.
ChemDraw always looks for the ChemDraw folder
in the Preferences folder first, followed by the
application folder second.
Appendix B: Specifying Paths • 197
Administrator

198 • Appendix B: Specifying Paths ChemDraw

Appendix C: Technical Support
Overview
CambridgeSoft Corporation (CS) provides technical
support to all registered users of this software
through the World Wide Web (WWW), and through
our Technical Support department.
You can deliver your CS Software Problem Report
Form to Technical Support by the following
methods:
WWW: http//www.camsoft.com/support
Internet: support@camsoft.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 ATTN: Technical Support
access our Technical Support page using the
100 CambridgePark Drive
following address:
http://www.camsoft.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 the back of this User’s Guide. This
ChemDraw 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
contacting us. If you can reproduce the • In the Finder, single-click on the ChemDraw
problem, please record the exact steps that application icon and choose Get Info from the
you took to do so. File menu. The serial number is listed
immediately after the version.
• Record the exact wording of any error
messages that appear.
• Record anything that you have tried to correct
the problem.

ChemDraw Appendix C: Technical Support • 199

 Windows
• With ChemDraw launched, choose About CS
ChemDraw from the Help menu. The serial
number appears at the bottom left of the about
Administrator
box.
• Open the chemdraw.ini file (in your Windows
directory) using any text editor. The serial
number appears in the line starting
“SERIAL_NO=”.
For more information on obtaining serial numbers
and registration codes, see:
http//www.camsoft.com/support/codes.cfm
Troubleshooting
This section describes steps you can take that affect
the overall performance of ChemDraw, as well as
steps to follow if your computer crashes when using
a CS software product.
Launching
If ChemDraw can’t find the ChemDraw Folder
(Macintosh) or cd_items directory (Windows) you
are not able to launch the program. For additional
information about the appropriate location, see
Appendix B: Specifying Path.
Performance
Below are some ways you can optimize the
performance of ChemDraw:
• (Macintosh): Increase the total amount of
memory that the application can use:
• Select the ChemDraw application icon in the
Finder when ChemDraw is not running.
• From the Edit menu, choose Get Info.
Increase the memory allocation in the
Preferred size text box in the Memory
Requirements section of the dialog box.
200 • Appendix C: Technical Support
• (Windows) In the Performance tab in the
System control panel (Windows NT 4.0),
allocate more processor time to ChemDraw.
• Install more physical RAM. The more you
have, the less ChemDraw will have to access
your hard disk to use Virtual Memory.
• Increase the Virtual Memory (VM). Virtual
memory extends RAM by allowing space on
your hard disk to be used as RAM. However,
the time for swapping between the application
and the hard disk is slower than swapping with
physical RAM.
Change the VM as follows:
• Macintosh: Memory control panel.
• Windows 95/98 and Windows NT 4.0:
System control panel, Performance tab.
System Crashes
ChemDraw should never crash, but below are the
steps you should go through to try to resolve issues
that cause computer crashes while using a CS
software product.
1. Restart your computer (Macintosh) or restart
Windows and try to reproduce the problem. If
the problem recur, continue with the following
steps.
2. Take the steps appropriate for your system:
• (Macintosh): Restart your computer while
holding Shift down to turn off all system
extensions. Try to reproduce the problem.
If the problem no longer occurs, then you likely
have an extension conflict. You should
determine which extension is causing the
conflict, and then not have it load when using
ChemDraw. To isolate an extension, disable
half of your extensions using the Extensions
Manager and test the problem again. Keep
disabling half of your extensions until you find
ChemDraw
 which extensions are causing the problem.
Please inform Technical support which
extensions are causing the problem.
• (Windows): The most common conflicts for
Windows users concern Video Drivers,
Printer Drivers, screen savers, and virus
protection. If you do need to contact us, be
sure to determine what type and version of
drivers you are using.
Video Driver related problems: If you are
having problems with the display of
ChemDraw, 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.
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
details about the original driver and the
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, Fax or E-mail the
details of the problem to Technical Support.

ChemDraw Appendix C: Technical Support • 201

Administrator

202 • Appendix C: Technical Support ChemDraw

Appendix D: Document Settings
Creating Style Sheets b. Type a name for the document.
c. Select the cd_items directory (Windows) or
and Stationery Pads ChemDraw Folder (Macintosh) as the
location for saving the template.
To create your own Style Sheet or Stationery Pad:
5. Click OK or Save.
1. Create a new document.
2. Enter the settings in the Page Setup, Drawing, ChemDraw Style Sheets
Text Settings, and Color Palette dialog boxes.
3. From the File menu, choose Save As.
and Stationery Pads
4. In the Save As dialog box: This following table contains drawing settings and
an example structure for each of the Style Sheets and
a. Select the CD Style Sheet (Windows) or CD
Stationery Pads ChemDraw provides.
Stationery (Macintosh) file format.

Drawing and Atom Label and Caption Text Settings in Journal Style Sheets/Stationery Pads

ACS 1996 ACS-1996

• Fixed Length: 14.4 pt

• Bold Width: 2 pt
O • Line Width: 0.6 pt
• Margin Width: 1.6 pt
O • Hash Spacing: 2.5 pt
• Chain Angle (degrees): 120
H N
H • Bond Spacing (% of length): 18
O • Atom Label Font (Win/Mac): Arial/Helvetica
• Atom Label Size: 10 pt
Morphine • Caption Font (Win/Mac): Arial/Helvetica
• Caption Size: 10 pt
• Drawing Area (Width x Height): 540 pt x 720 pt
• Page Size: US Letter
• Reduction (%): 100

ChemDraw Appendix D: Document Settings • 203

 Drawing and Atom Label and Caption Text Settings in Journal Style Sheets/Stationery Pads

Can. J. Chem Can. J. Chem

Administrator

• Fixed Length: 18 pt
O
• Bold Width: 2.5 pt
• Line Width: 0.8 pt
O • Margin Width: 2 pt

H • Hash Spacing: 3 pt
N • Chain Angle (degrees): 120
H
• Bond Spacing (% of length): 18
O
• Atom Label Font (Win/Mac): Arial/Helvetica
Morphine • Atom Label Size: 12 pt
• Caption Font (Win/Mac): Arial/Helvetica
• Caption Size: 12 pt
• Drawing Area (Width x Height): 540 pt x 720 pt
• Page Size: US Letter
• Reduction (%): 80

J. Mol. Mod.
. Mol. Mod.
• Fixed Length: 14.4 pt
• Bold Width: 2 pt
• Line Width: 0.6 pt
HO
• Margin Width: 1.6 pt

O • Hash Spacing: 2.5 pt

• Chain Angle (degrees): 120
H N
H • Bond Spacing (% of length): 18
HO • Atom Label Font (Win/Mac): Times New
Roman/Times
Morphine
• Atom Label Size: 10 pt
• Caption Font (Win/Mac): Times New Roman/Times
• Caption Size: 10 pt
• Drawing Area (Width x Height): 8.5 cm x 25.4 cm (1
column); 17 cm x 25.4 cm (2 column)
• Page Size: US Letter
• Reduction (%): 100

204 • Appendix D: Document Settings ChemDraw

Drawing and Atom Label and Caption Text Settings in Journal Style Sheets/Stationery Pads

RSC-1997
RSC-1997
• Fixed Length: 0.7 cm
• Bold Width: 0.092 cm
O
• Line Width: 0.025 cm
O • Margin Width: 0.071 cm
H N • Hash Spacing: 0.099 cm
H
O • Chain Angle (degrees): 120

Morphine • Bond Spacing (% of length): 20

• Atom Label Font (Win/Mac): Arial/Helvetica
• Atom Label Size: 7 pt
• Caption Font (Win/Mac): Arial/Helvetica
• Caption Size: 7 pt
• Drawing Area (Width x Height): 19.05 cm x 25.4 cm
• Page Size: US Letter
• Reduction (%): 60

YNTHESIS, SYNLETT SYNTHESIS/SYNLETT

• Fixed Length: 17 pt
• Bold Width: 2 pt
HO • Line Width: 0.8 pt
• Margin Width: 1.3 pt
O • Hash Spacing: 2.5 pt

H • Chain Angle (degrees): 120

N
H • Bond Spacing (% of length): 18
HO • Atom Label Font (Win/Mac): Arial/Helvetica
• Atom Label Size: 10 pt
Morphine
• Caption Font (Win/Mac): Arial/Helvetica
• Caption Size: 10 pt
• Drawing Area (Width x Height): 12 cm x 26.7 cm
• Page Size: A4
• Reduction (%): 100

ChemDraw Appendix D: Document Settings • 205

 Drawing and Atom Label and Caption Text Settings in Journal Style Sheets/Stationery Pads

New Document
Administrator

New Document • Fixed Length: 30 pt

• Bold Width: 2 pt

O
• Line Width: 1 pt
• Margin Width: 2 pt
• Hash Spacing: 2.7 pt
• Chain Angle (degrees): 120
O • Bond Spacing (% of length): 12
• Atom Label Font (Win/Mac): Arial/Helvetica
H • Atom Label Size: 10 pt
N
H • Caption Font (Win/Mac): Times New Roman/Times
• Caption Size: 12 pt
O
• Drawing Area (Width x Height): 7.5 in x 10 in
• Page Size: US Letter
Morphine • Reduction (%): 100

New Slide
New Slide
• Fixed Length: 30 pt
• Bold Width: 4 pt
HO • Line Width: 1.6 pt
• Margin Width: 2 pt
• Hash Spacing: 2.7 pt
• Chain Angle (degrees): 120
O
• Bond Spacing (% of length): 15
• Atom Label Font (Win/Mac): Arial/Helvetica
H
N • Atom Label Size: 12 pt
H • Caption Font (Win/Mac): Times New Roman/Times
• Caption Size: 16 pt
HO
• Drawing Area (Width x Height): 7.5 in x 10 in
• Page Size: US Letter
Morphine • Reduction (%): 100

206 • Appendix D: Document Settings ChemDraw

Appendix E: Automation
Macintosh For more information see the CambridgeSoft SDK
web pages at: http://sdk.camsoft.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 Appendix E: Automation • 207

Administrator

208 • Appendix E: Automation ChemDraw

Appendix F: How ChemNMR Pro Works
Overview
ChemNMR Pro estimates chemical shifts for all
hydrogen or carbon atoms for which additivity rules
are available. Following a hierarchical list, it first
identifies key substructures of a molecule. A
substructure provides the base value for the
estimated shift. For example, benzene would be
identified as the key substructure of trinitrotoluene.
When a substructure happens to be a ring system not
available in the data, ChemNMR approximates its
base shift using embedded rings and, if necessary, it
will even disassemble the ring into acyclic
substructures.
ChemNMR views remaining parts of the molecule
as substituents of a substructure. Each substituent
adds to or subtracts from the base shift of the
substructure to which it is attached. Additivity rules
determine the increment of each contribution. If an
increment for a substituent cannot be determined,
ChemNMR uses embedded substituents—smaller
structural units with the same neighboring atoms.
Or, it will use increments of identical or embedded
substituents of a corresponding substructure by
assuming that the effects of the substituents are of
the same magnitude.
ChemNMR provides a detailed protocol of the
estimation process applied. It gives substructures as
names, compound classes in most cases,
substituents in form of a linear code, respectively.
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
4000 parameters. It also implements models for
ethylenes (cis/trans) and cyclohexanes
(equitorial/axial).
ChemNMR Limitations
The program handles the following elements:
H, D, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si,
P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu,
Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc,
Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La,
Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb,
Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po,
At, Rn, Fr, Ra, Ac, Th, Pa, U, Nep, Pu, Am, Cm, Bk,
Cf, Es, Fm, Md, No, Lr. Functional groups are
expanded automatically.
In case of 1H NMR, it estimates shifts of about 90%
of all CHx-groups with a standard deviation of
0.2– 0.3 ppm. The use of polar solvents may
strongly increase these deviations. It does not
estimate shifts of hydrogen atoms bonded to
heteroatoms because they are significantly affected
by solvents, concentration, impurities, and steric
effects.
In case of 13C NMR, it estimates over 95% of the
shifts with a mean deviation of -0.29 ppm and
standard deviation of 5.5 ppm.
For more information see:
Fürst, A.; Pretsch, E. Anal. Chim. Acta 1990, 229,
17.
Pretsch, E.; Fürst, A.; Badertscher M.; Bürgin, R.;
Munk, M. E. J. Chem. Inf. Comp. Sci. 1992, 32, 291-
295.
Appendix F: How ChemNMR Pro Works • 209
 Bürgin Schaller, R.; Pretsch, E. Anal. Chim. Acta
1994, 290, 295.
Bürgin Schaller, R.; Arnold, C.; Pretsch, E. Anal.
Chim. Acta 1995, 312, 95-105.
Administrator

Bürgin Schaller, R.; Munk, M. E.; Pretsch, E.

J. Chem. Inf. Comput. Sci.1996, 36, 239-243.

210 • Appendix F: How ChemNMR Pro Works ChemDraw

 Appendix G: How ChemProp Works
ChemProp Values
ChemPropPro enables you to calculate predicted
values selected physical and thermodynamic
properties for structures of up to 100 atoms. The
following topics describe how ChemProp obtains its
values.
LogP
LogP (partition coefficient for n-octanol/water)—
three fragmentation methods are used to predict the
logP values.
1. Method one is based on 94 atomic contributions
evaluated from 830 molecules by least squares
analysis. This method works with a standard
deviation of 0.47 logP units and can handle
molecules containing hydrogen, oxygen,
nitrogen, sulfur and halogens.
2. Method two is an extension of method one that
is based on 120 atomic contributions evaluated
from 893 molecules by least squares analysis.
In addition to the atoms introduced for method
one, it can handle molecules that contain
phosphorus and selenium atoms. This method
works with a standard deviation of 0.50 logP
units.
3. Method three is based on 222 atomic
contributions calculated from 1868 molecules
by least squares analysis. This method allows a
calculation of logP with a standard deviation of
0.43 logP units and can handle molecules
containing hydrogen, oxygen, nitrogen, sulfur,
halogens and phosphorus atoms. If this method
is applied to molecules with internal hydrogen
bonds, the standard deviation is 0.83 logP units.
ChemDraw
Henry’s Law
Henry’s Law Constant—The air to water partition
coefficient that is expressed as ratio of vapor
pressure to water solubility or as a unitless
distribution coefficient that can be evaluated as a
ratio of the concentration in air to the concentration
in water.
Two methods are used to predict Henry's Law
constant.
1. The first is an approach based on the bond
contribution method. This method uses 59 bond
contribution values and 15 correction factors.
The contributions were calculated by least
squares analysis using a data set of 345
chemicals. This method estimates with a mean
error of 0.30 units and a standard deviation of
0.45 units and can handle molecules containing
carbon, hydrogen, oxygen, nitrogen, sulfur,
phosphorus and halogens.
2. In the second method, Henry's Law constant is
estimated from an equation found using linear
regression. Multifunctional compounds were
omitted from this study. This method should not
be used for compounds where distant polar
interaction is present.
Appendix G: How ChemProp Works • 211
 Molar Refractivity
Molar refractivity—Two fragmentation methods
are used to estimate the molar refractivity value.
Administrator

1. Method one includes 93 atomic contributions

evaluated from 504 molecules by using a
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.

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.
Normal Boiling Point and Melting Point—
Estimated in K using two methods.

1. Joback's fragmentation method.

2. The Joback method as modified by Stein. All
boiling points are estimated at a pressure of
1 atm.

212 • Appendix G: How ChemProp Works ChemDraw

Index
Numerics Analysis
messages 194
viewing results 128
13
C, 1H shifts, estimating 135
Analyze Structure
35 mm Slide Boundary lines 161 calculating 133
overview 128
A Anion, drawing 92
Anonymous Alternative Groups 150
Abnormal Valence 142 Apple Events
Abnormally shaped arrows, creating 102 description 207
Absolute flag, drawing 93 EGO 173
Accessing documents quickly 8 Apply Settings command 26
ACS Document 1996 203 Arc Tool
Active window 6 description 15
Actual Size command 163 using 98
Acyclic Chain Tool, description 15 Arcs
Acyclic chains drawing 98
adding 63 resizing 99
length 63 Arrow Tool
Add description 15
column to template 158 overview 95
row to template 158 palette 95
to selection 105 Arrows
Adding chemical names 75 autoscaling 171
Aligning objects changing hash spacing 64
Align Submenu 166 created with curves 102
overview 166 resizing 96
rulers 164 Aspect Ratio, changing 110
with crosshair 166 Assigning
Alpha symbol, typing 84 atom mapping 129
ALT key structures to spectra 132
and letter, letter 17 Atom
distorting objects 110 moving 107
Alternative Group Tool 15 query properties 138
Alternative Groups Atom Label text boxes, closing 85
attachment point numbering 150 Atom Labels
attachment point symbol 148 automatic justification 81
Attachment Rank indicators 149 centered justification 83
defining 148 creating 78
description 147 deleting 79
multiple attachment points 149 editing 79
Always Display and Print Atom Mapping 129 Flush Left justification 82
Always Display and Print Reaction Mapping 22 Flush Right justification 82

ChemDraw Index • 213

 Atom Labels (continued) Automation 207
font 71 AutoNom 75
format, setting 79 Autoscale
hotkeys 76 bonds 171
justification 81 empty document window 172
line spacing 83 template color 125
margin width 79
Index

when transferring 170

multi-attached 119
overview 71 B
repeating 83
size 71 Background color, printing 11
specification 189 Balloon Help 2
stacked above format 82
Baseline style, captions 74
text box 78
Benzene Ring
text boxes, creating new line 85
changing orientation 63
white space 79
drawing 62
Atom properties
Benzene Ring Tool 61
abnormal valence 142
Best Method, selecting 134
description 139
Beta symbol, typing 84
implicit hydrogens 140
Bezier curves 99
in query structures 137
BitMap 181
reaction changes 141
Bitmapped
reaction stereo 141
resetting defaults 139 Fonts 85
ring bond count 140 printing quality 11
substituents 139 bmp files 181
unsaturation 140 Boiling Point
viewing 138 calculation 212
Atom-To-Atom Mapping 129 definition 133
Attachment Point Bold Bond Tool icon 57
defining 148 Bold Wedge Bond Tool icon 57
multiple 149 Bold Width 24, 64
numbering 150 Bond crossings
symbol 148 changing 67
Attachment Point Tool 15 white space 67
Attachment Rank indicators, showing 149 Bond Properties
Automatic defining 142
atom labels 22, 82 descriptors 143
Atom Mapping 22 reaction center 144
drawing 68 removing 143
drawing of structure 68 topology 144
error checking 68 types 143
justification 81 viewing 143
justification, atom labels 81 Bond Spacing
Line Spacing 75, 83 changing 65
Mapping 130 description 23

214 • Index ChemDraw

Bond tool
icons 57
repeating a label 84
Bonds
adding 119
autoscaling 171
changing bond type 65
changing type 65
double either 144
drawing 57
drawing by clicking 59
editing 65
Fixed Length 57
layering 67
length and angle display 58
margin width 67
multi center attachment 117
orientation, changing 66
orientation, dative bond 58
orientation, wedge bond 58
quadruple 60
selecting 104
setting line width 64
spacing 65
types 188
variable angle 58
variable length 58
Border of page 159
Boxes
drawing 97
rotating 98
Braces 97
Bring to Front command 168
Bruker JCAMP file format 184
Bullet, typing 84
C file format 181
Calculating
changing method 134
chemical properties 133
elemental analysis 129
exact mass 129
formula 129
Molecular Weight 129
ChemDraw
Calculation method, changing 134
Can. J. Chem. Document 203
Caption text boxes
closing 85
creating new line 85
Captions
Analyze Structure 129
autoscaling 171
coloring 122
creating 72
creating tables 85
editing 73
font 71, 73
formula 74, 80
inserting from structure 75
inserting rows in tables 87
justification 74
line spacing 75, 83
setting Font, Size and Styles 73, 79
Size 73
size 71
styles 73
subscript 74, 80
superscript 74, 80
Table column spacing 86
text overview 71
width 72
Carbon-13 shifts, see 13C, 1H shifts, estimating
Cation, drawing 92
CCITT Group 3 and 4 186
CD Template 181
cd_items directory
description 10
Path 197
cds format 182
cdx
saving as 6
cdxml format 181
Center on Page command 166
Centered justification, atom labels 83
Centering objects 166
Chain Angle
description 23
setting 64
Index • 215
 Changing Chemical syntax checking 68
aspect ratio 110 Chemical Warnings
Bond orientation 66 overview 68
bond type 65 supressing 68
default directory 10 Chemically significant text 190
default settings 26 Chemistry
Index

perspective 163 checking 127

settings when transferring 172 of ChemDraw 187
tolerance 104 ChemNMR
Characters, special 84 limitations 209
Charges using 134
specifications 190 ChemProp
symbols, drawing 93 calculations 211
Check Boxes 18 description 211
Check mark 17 using 133
Check Structure chm files 181
overview 127 Choose, definition 1
when copying 128
CIP Rules 193
When Copying, description 22
Clean Up Structure command 119
Checking Chemistry 127
Clearing
ChemDraw
mapping 131
2.x file format 181, 182
spectrum-structure assignments 132
2.x, line spacing 75, 83
stereochemical markers 131
3.5 file format 181
cdx format 181 Click
closing 12 definition 1
ctp, ctr file formats 181 to select objects 104
HotKeys 9 Clipboard
HotKeys File 77 Check Structure 128
Nicknames 113 copy 107
opening 5 cutting 106
ChemDraw Folder Exporting 179
description 9 moving objects 106
path 197 pasting 106
scripts 26 transferring objects 169
ChemDraw Laser Prep 12 viewing contents 169
ChemDraw SDK 207 Clipping file 170
chemdraw.ini 197 Closed Brackets, rotating 98
Chemical properties Closed style, shapes 102
calculating 133 Closing
Chemprop 133 caption text box 85
description 128 ChemDraw 12
Chemical Symbols documents 8
palette 91 CMYK, Planar and Contiguous 186
rotating 94
tool 16, 91

216 • Index ChemDraw

Color Critical Temperature
autoscaling 171 calculation 212
menu 122 definition 133
overview 121 Critical Volume
saving settings 125 calculation 212
Color dialog box 123, 124 definition 133
Color Palette 25 Crosshair
Coloring displaying 165
captions 122 moving 165
objects 122 setting units 59
Column spacing 86 using to align objects 166
Command Buttons 18 CT file format 182
Commands, overview 17 CTP file format 181
Compression 186 CTR file format 181
Connection Table, file format 182 CTS file format 185
Context-sensitive Help 2 Curve Tool 16
Contract label 116 Curves
Control arrows, description 18 autoscaling 171
Conventions 1 dash spacing 64
Convert name to structure for creating arrows 102
limitations 68 Custom templates 156
using 68 Customizing
Convert structure to name, automatic captions 75 menu extension DLLs 207
Copy saving document settings 26
and Check Structure 128 using Scripts 27
As SLN command 180 Cut
As SMILES command 179 objects 106
drag and drop 170 using clipboard 169
duplicating objects 107 Cycloalkane rings, converting to delocalized rings
objects 107 62
transferring objects 169 Cyclobutane Ring Tool 61
Create Publisher command 175 Cycloheptane Ring Tool 61
Creating Cyclohexane Chair Ring Tool
HotKeys 77 (1) 61
mirror images 109 (2) 61
new document 5 orientation 62
SLN strings 180 Cyclohexane Ring Tool 61
Stationery Pads 203 Cyclooctane Ring Tool 61
Style Sheets 203 Cyclopentadiene Ring Tool 61
tables 85 Cyclopentadiene Ring, changing orientation 63
templates 157 Cyclopentadiene rings, drawing 62
Critical messages 194 Cyclopentane Ring Tool 61
Critical Pressure Cyclopropane Ring Tool 61
calculation 212
definition 133

ChemDraw Index • 217

 D Displaying
atom mapping 129
DARC-F1 cross hairs 165
Format 182 entire page 164
Query Format 182 reaction mapping 129
Dashed Bond Tool icon 57 rulers 164
Index

Databases Distorting objects 110

support for query structures 137 Distributing objects 167
supported 137 DLL 207
Dative Bond Document 203
drawing 58 creating 5
Tool icon 57 multi-paged 161
Default opening 6
atom properties, resetting 139 opening with MRU 8
bond properties, resetting 143 posters 162
changing 26 reverting to last saved 8
directory 10 saving 6
settings, text 79 viewing location of 8
Stationery pad 27 Document Settings, overview 22
Style Sheet 27 Document Setup
Defined Nickname 114 multiple-paged documents 161
Defining a Path 197 Posters 162
Deflate compression 186 Document window
Degree symbol, typing 84 Drawing area 159
Delete Column, from template 158 enlarging 159
Delete Row, from template 158 orientation 160
Deleting reducing 159
atom labels 79 viewing location 8
Backspace key 105 Double bond
Delete key 105 changing type 65
Nicknames 116 drawing 60
objects 105 orientation 66
Pen tool shapes 101 Double either bonds, drawing 60
Delocalized rings, drawing 62 Double-click 1
Deselect Drag 1
definition 1 drag and drop 170
objects 105 Drawing
Detecting errors acyclic chains 63
Automatic error checking 68 Arcs 98
Check Structure command 127 automatically with name 68
Dialog boxes 18 bonds by clicking 59
Dimmed command 17 boxes 97
Disable chemical warnings 68 charge symbols 93
Discarding changes 8 cyclopentadiene rings 62
double bonds 60

218 • Index ChemDraw

Drawing (continued) Duplicating
double either bonds 60 labels 84
dz2- orbitals 91 objects 107
fixed length bonds 57 dx file format 184
free sites 93 dz2- orbitals, drawing 91
H-dash Symbol 91
H-dot Symbol 91 E
mirror images 109
orbitals 89 Editing
quadruple bonds 60 atom labels 79
radicals 92 bond orientation 66
resonance delocalized rings 62 bond type 65
rings 61 bonds 65
rings with fixed length 61 captions 73
sigma orbitals 89 generic nickname file 145
single bonds 57 Edition
s-orbitals 89 access from Finder 178
stereochemical symbols 93 breaking publisher link 177
structure automatically from name 68 breaking subscriber link 178
triple bond 60 file 175
triple bonds 60 publishing information in 175
with templates 156 subscribing to 176
Drawing area 159 updating 176
Drawing Elements updating subscriber 177
autoscaling 171 EGO 173
color 96 Element
distorting 98 folder 9
fill patterns 96 list 146
ovals 98 not-list 147
resizing 98 recognized 191
rotating 98 Elemental Analysis
Drawing Elements Tool 16 caption 129
Drawing settings description 128
bond spacing 65 Ellipsis (…), description 17
chain angle 64 Embedding objects 173
changing defaults 26 Encapsulated PostScript, see EPS file format
command 23 Enlarge
dialog box 23 document window 159
Fixed Angles 58 page size 160
hash spacing 64 EPS file format
Line Width 64 Macintosh 182
margin width, effect on atom labels 79 overview 182
margin width, effect on Bond crossing 67 Text 182
units 59 windows with preview 183
Drop-down List Boxes 18 Eraser Tool 16

ChemDraw Index • 219

 Error checking 68 File format (continued)
Error Messages 194 native 6
Exact Mass PICT 185
caption 129 PICT scaled 4x 185
definition 128 PNG 185
Exiting 12 rxn 183
Index

Expanding labels 117 SMD 185

Exporting 178 SPC 185
checking structure 128 style sheet 182
compatibility 151 TGF 183
mapping 131 TIF 185
PNG 185 TIFF 185
query properites 151 TPL Style sheet 185
query structures 151 WMF 185
TIFF 185 Fill patterns, orbital tool 89
using Clipboard 179 Filled style, shapes 102
using file formats 180 Fixed Angles
bonds 58
F orbitals 89
toggling on/off 58
f1q format 182 Fixed Lengths
FAQs 199 bonds 57
File format description 23
Bitmap 181 drawing with 57
CD Template 181 scaling 110
cdx 6 toggling on/off 58
cdxml 181 Flags, stereochemical 93, 193
ChemDraw 181 Flip Horizontal command 109
ChemDraw 3.5 181 Flip Vertical command 109
ChemDraw Stationery 182 Flush Left justification
Connection Table 182 atom labels 82
CT 182 captions 75
CTP 181 Flush Right justification
CTR 181 atom labels 82
cts 185 captions 75
DARC-F1 182 Font
EPS (MAC) 182 caption 73
EPS (TEXT) 182 imaging speed 85
GIF 183 new captions 73, 79
ISIS 183 size 73
ISIS/Reactions 183 substitution 71
JDX 184 Footers, creating 162
MDL MolFile 184 Format
MDL RGFile 184 atom labels 81
MSI MolFile 184 text 71

220 • Index ChemDraw

Formula command Hashed Bond Tool icon 57
description 128 Hashed Wedge Bond tool icon 57
using 74, 80 H-dash Symbol, drawing 91
Free Energy H-Dot and H-Dash, specification 191
calculation 212 H-dot Symbol, drawing 91
definition 133 Headers, creating 162
Free Sites Heat of Formation
drawing 93 calculation 212
in queries 139 definition 133
Freezing Point, calculation 212 Help
Front to Back ordering 167 context-sensitive 2
Fusing templates 156 Macintosh 2
Windows 2
G Henry’s Law, definition 133
Hide Crosshair command 166
G Groups 147 Hide Rulers command 165
Galactic Industries file format 185 High resolution
Gamma symbol, typing 84 non-PS printing 11
Generic Groups 147 printing 11
Generic Nicknames 9 Highlight box
description 145 selecting 104
editing file 145 size 59
Getting Started Tutorial 29 Hollow Wedge Tool icon 57
Gibbs Free Energy HotKeys
calculation 212 HotKeys.txt 77
definition 133 overview 76
GIF format 183 Hydrogens, implicit 140
GRAMS software 185 Hyphens, Font submenu 74
Graphical ChemDraw object 167
Graphical User Interface 13 I
Grayed-out command 17
Greek text 84 Icon
Grouping Arc Tool 98
objects 111 Bond tools 57
orbitals 89 Ideal Gas Thermal Capacity, calculation 212
using 112 Implicit Hydrogens 140
GUI, see Graphical User Interface Imported objects, selecting 104
Imported Picture 181
H Importing
overview 178
Hard Coded HotKeys 77 picture layer 167
Hash Spacing recognizing 167
description 24 spectral data 184, 185
setting for Bond 64 using file formats 180
Include ChemDraw LaserPrep 174

ChemDraw Index • 221

 Initialize PostScript Printer command 174 Lasso tool
Insert Name as Structure 68 selecting objects 103
Inserting toggling with Text Tool 84
name as structure 68 Launching 5
rows in tables 87 Layering
Installation 3 atom labels 79
Index

Interface 13 objects 167

IR spectra, see spectra Layout, page 159
ISIS Lewis dot symbol, see Lone Pair Symbol
Reactions 183 Ligand, defined 193
SKC file format 183 Limitations, name-to-structure 68
TGF file format 183 Line Spacing
Isotopes atom labels 83
file location 9 automatic 75, 83
specifications 191 captions 75
Isotopes Table 142 command 83
isotopes.txt 142 CSChemDraw 2.x documents 75, 83
dialog box 83
J variable 75, 83
Line Width 24, 64
J. Mol. Mod. Lines, drawing 97
(1 Column) 203 List Nicknames command 116
(2 Column) 203 Literature values, LogP and MR 134
JCAMP file format 184 Location
JDX file format 184 Stationery pads 9
Joback’s Fragmentation Method 212 Style Sheets 10
Joining, structures 111 Template documents 9, 10
Justification LogP
atom labels 81 calculation 211
automatic atom labels 82 definition 133
captions 74 Lone Pair Symbol 92
stacked above 82
M
K
m/e, displaying 16
Kekule structures 62 Macintosh
Key combination, description 17 Help 2
system requirements 3
L Magnifying
with Magnification control 164
Labels with Tools menu 163
contracting 116 Make Spectrum-Structure Assignment 132
expanding 117 Manual Mapping
Landscape page orientation 160 clearing 131
overview 130

222 • Index ChemDraw

Mapping Monochrome 186
atom 129 Most recently used documents 8
automatic 130 Moving
clearing 131 atoms, bond tool 66
exporting 131 atoms, Selection Tool 107
manual 130 crosshair 165
reaction 129 in tables 86
Margin Width objects 106
adjusting 67 MR, see Molar Refraction index
description 24 MRU list 8
effect on Bond crossings 67 MS, see spectra
specifying 79 MSI MolFile format 184
Margins, page 160 Multi-attached atom labels command 119
Marquee tool 103 Multi-Center Attachments
Mass spectra command 117
importing as JDX 184 overview 192
importing as SPC 185 Multiple Attachment Points 149
mass/charge, displaying 16
Multiple Bond tool 60
Maximize objects 163
Multiple Undo 19
MDL MolFile 184
Multiple-paged documents, setup 161
MDL RGFile 184
Melting Point, definition 133
Menu Extension DLLs 207 N
Menus, overview 17
Message Area Name
bond info 58 as structure, inserting 68
display of fixed angles 58 converting to structure 68
units 58 of structure, inserting 75
Messages Name as Structure, Paste Special 69
analysis 194 Name-to-structure
critical 194 description 68
status 194 limitations 68
Mirror images, creating 109 Native file format 6
mol 184 New Color Button 26
mol file format 184 New Command 5
Molar refraction index New document 5
definition 133 New Slide 203
how calculated 212 New Template, creating 156
Molecular Design Limited, see MDL Nicknames 9, 113
Molecular mass, definition 128 defining 114
Molecular Simulations MolFile 184 deleting 116
Molecular Weight generic 145
caption 129 troubleshooting 115
definition 128 nicknames.dat 113
display in status bar 16 NMR, see ChemNMR, Spectra
how calculated 16

ChemDraw Index • 223

 Non-PostScript printing Orientation
high resolution 11 Benzene Ring Tool 63
Macintosh 175 Cyclohexane Chairs 62
Non-Roman text 84 Cyclopentadiene Ring Tool 63
Normal Boiling Point 212 double Bond 66
Normal view 163 of page 160
Index

rings 61
O templates 156
user-defined templates 157
Object embedding 173 Original view 163
Objects Overlap, multipaged documents 162
aligning 166
centering 166 P
deleting 105
distributing 167 Packbits, compression 186
joining 111 Page
moving 106 border 159
ordering 167 layout 159
reflecting 108 margins 160
selecting all 105 orientation 160
using crosshair with 165 overlap 162
using rulers with 164 setup 159
OLE 173 Page Definition Language
OLE automation 207 PostScript 11
QuickDraw 11
Online Help, see Help
Page Setup
Open command
page layout 159
default directory 10
saving settings 161
using 6
Paged documents 161
Open Special command 5 Paired brackets 97
Opening Palette
ChemDraw 5 Chemical Symbols 91
document 6 color 25
document with MRU list 8 single bonds 57
Optimize pictures for High Res printing 21 Paper Size 160
Option Button 18 Parentheses 97
Orbital Tool Partial Selection marks 17
description 16 Partition coefficient, definition 133
fill patterns 89 Paste
Fixed Angle 89 drag and drop 170
overview 89 Duplicating objects 107
Orbitals objects 106
drawing 89 using clipboard 169
grouping 89 Paste Special
type 89 name as structure 69
Ordering objects 167 SMILES 180

224 • Index ChemDraw

Path information 197
Pen tool shapes
deleting segments 101
selecting 100
Perspectives, changing 163
Pi symbol, typing 84
PICT file format 185
PICT scaled 4x file format 185
Picture Layers
atom labels 79
overview 167
Plain style, shapes 102
PNG file format 185
Portrait page orientation 160
Positioning
crosshair 165
grouping 111
objects 106
rulers 164
using the Clipboard 106
Posters, setup 162
PostScript
commands 174
EPS (MAC) 182
EPS (TEXT) 182
print quality 11
printing 11
Preferences 19
Automatic Atom labels 82
Check Structure 128
drawing, see Drawing Settings 26
highlight box 59
Include ChemDraw LaserPrep 174
Include PostScript 174
Initialize PostScript Printer 174
print 11
require CTRL+ENTER 85
require Option+Return 85
text, see Text Settings 26
tolerance, joining structures 111
Use Bitmap Fonts When Available 85
Print Background Color 22
Print Quality 11
ChemDraw
Printing
atom mapping 129
background color 11
ChemDraw Laser Prep 12
drawing elements fill 96
effect of PostScript commands 174
from other applications 174
high-resolution non-PostScript 11
include PostScript 12
margins 160
orientation (of page) 160
overview 11
page setup 159
paper size 160
postscript atom labels 12
preferences 11
reaction mapping 129
Properties
atom in searching 137
atom, abnormal valence 142
atom, description 139
atom, implicit hydrogens 140
atom, query 138
atom, reaction changes 141
atom, reaction stereo 141
atom, resetting defaults 139
atom, ring bond count 140
atom, substituents 139
atom, unsaturation 140
atom, viewing values 138
bond 142
bond descriptors 143
Bond types 143
bond, reaction center 144
bond, removing 143
bond, topology 144
bond, viewing 143
calculating 133
Proton shifts, see 13C, 1H shifts, estimating
Publish/Subscribe
canceling a publisher 177
canceling a subscriber 178
creating a publisher 175
edition file 178
opening the Publisher 178
Index • 225
 Publish/Subscribe (continued) Recently used files 8
overview 175 Red boxes on objects 68
subscribing to an edition 176 Redo 19
updating a publisher 176 Reduce
updating a subscriber 177 document window 159
Publisher border 175 object 163
Index

Publisher Options command 176 page size 160

Publisher to publisher option 176 Reflection 109
Registration marks 162
Q Relative flag, drawing 93
Remove
Quadruple bonds 60 Color Button 26
Queries, see searching colors 125
Query properties rulers 165
exported 151 Repeat command, rotations 108
overview 194 Repeating a Label, bond tool 84
Query Structures Require
description 137 Ctrl+Enter to create new line 21
exporting 151 Ctrl+Enter to Create New Line in Atom Labels
Quick Reference Card, descripiton 2 85
QuickDraw Ctrl+Enter to Create New Line in Captions 85
bitmapped image 11 Option+Return to create new line 21
print quality 11 Requirements
Quitting 12 Macintosh 3
RAM 3
R system 3
Windows 3
R Groups 147 Reset defaults
Racemic flag, drawing 93 atom properties 139
Radicals bond properties 143
drawing 92 Resize Handle 109
specification 191 Resizing
RAM 3 arcs 99
Reaction Atom-Atom Map Tool 15 arrows 96
Reaction Atom-To-Atom Mapping 129 drawing elements 98
Reaction center 144 handle, double-clicking 109
Reaction Changes 141 objects 109
Reaction mapping template panes 158
always display and print 129 Resolution, TIFF 186
automatic 130 Resonance Delocalized rings, drawing 62
clearing 131 Revert command 8
exporting 131 RGB Indexed color 186
manual 130 RGFile format 184
overview 129 Right-click, definition 2
Reaction Stereo 141 Ring Bond Count 140

226 • Index ChemDraw

Ring pointer icon appearance 61 Searching
Ring Tool 16 databases 137
Rings export compatibility 151
drawing 61 query properties supported 137
drawing with fixed length 61 Select All command 105
orientation 61 Select, definition 1
Rotate Selecting
chemical symbols 94 all 105
command 108 bonds 104
dialog box 108 Lasso 103
drawing elements 98 last object 104
objects 108 last tool 104
Rotation handle 108 Marquee 103
Rsc-1995 203 Pen tool shapes 100
Ruler Guides 164 several objects 105
Rulers structures 104
hiding 165 Selection Rectangle
setting units 59 Resize handle 109
showing 164 Rotation handle 108
RXN file format 183 Selection Tool 16
definition 16
S deleting with Delete key 105
deselecting objects 105
Save As command 7 distorting objects 110
Save command highlight box 104
default directory 10 joining 111
using 6 selecting all 105
Saving selecting several objects 105
a copy of a document 7 using 103
defaults 26 Selection, adding to 105
document 6 Send Editions, publisher option 177
in different file formats 7 Send to Back command 168
template documents 158 Set Color Button 26
with different name or location 7 Settings
Scale highlight box 59
command 110 tolerance 59
dialog box 110 units 59
Scaling Shaded style, shapes 102
by a percentage 110 Shapes
fixed length 110 closed 102
objects 110 filled 102
when Transferring information 170 plain 102
Scripts menu 27 shaded style 102
SDK 207 Sharing Information 169
Shift key, deselecting objects 105

ChemDraw Index • 227

 Shift+click 1 Stationery Pads
Shift+drag 1 creating 203
Show 35mm Slide Boundary Guides 21 default 27
Show Attachment Rank Indicators 22 document settings 22
Show Borders command 176 Page Setup settings 161
Show Crosshair 165 provided 203
Index

Show Page 164 saving document settings 26

Show Rulers command 164 Status bar 16
Show Stereochemistry 131 Status messages 194
sigma orbitals, drawing 89 Stereochemical flags 193
single bonds, drawing 57 Stereochemical symbols, drawing 93
Single brackets 97 Stereochemistry
skc format 183 descriptors 193
SLN strings 180 drawing mirror images 109
SMD file format 185 how calculated 193
SMILES removing markers 132
creating 179 showing 131
overview 179 terms supported 131
paste 180 Structure
viewing clipboard 179 analyzing 128
SMIRKS, overview 179 automatic error checking 68
Software Developer’s Kit 207 automatically checking 68
s-orbitals, drawing 89 checking 127
SPC file format 185 checking automatically 68
Special characters 84 converting name to 68
Spectra converting to name 75
assigning structures 132 selecting 104
exporting 184, 185 show stereochemistry 131
importing 184, 185 Structure Diagram Generation 119
importing as JDX 184 Style Sheets
importing as SPC 185 color palette 125
removing assignments 132 creating 203
Spectrum-structure assignments default 27
making 132 document settings 22
removing 132 file format 182
viewing 132 Page Setup settings 161
Spin button, description 18 provided 203
Spiro linkage, templates 156 saving document settings 26
Squiggly Bond tool see Wavy Bond tool 57 selecting 10
Stacked Above, atom label 82 Style, caption 74, 80
Standard Molecular Data, see SMD Subscribe To command 176
Starting 5 Subscriber borders 176
Subscriber Options dialog box 177
Subscript command 74, 80
Substituents 139

228 • Index ChemDraw

Superatom, ISIS 183 Text (continued)
Superscript command 74, 80 Caption line spacing 75, 83
Supress chemical warnings 68 Caption Size 73
Switching between open documents 6 Caption Style 73
Symbol font 84 caption, creating tables 85
Symbols, adding 84 coloring 122
Syntax Checking 127 formatting 71
Synthesis/Synlett Document 203 picture layer 167
System requirements 3 types 71
Text Box
T atom labels 78
closing 85
Tables creating new line 85
column spacing 86 description 18
creating 85 Text Settings
inserting rows 87 Atom Labels 79
moving in 86 automatic atom labels 82
Technical support 199 captions, font, size, and style 73, 79
Template Panels 158 changing defaults 26
Template Tool Text Tool
description 16 atom labels 78
using 155 description 16
Templates toggling with lasso tool 84
Autoscaling 156 Text, atom label
coloring 125 flush left 82
creating 156, 157 flush right 82
document location 9, 10 format 81
drawing with 156 stacked above 82
file format 185 TGF file format 183
fusing 156 Thermal Capacity, calculation 212
fusing with existing structure 156 TIFF
orientation 156, 157 description 185
overview 155 options 186
panel 158 resolution 186
resizing 158 Toggling
resizing template panes 158 between tools 104
reusing 156 fixed length/fixed angle 58
saving template documents 158 text tool with lasso tool 85
spiro linkage 156 Tolerance
Text changing 111
atom label text box 78 effect on highlight box 104
atom label, editing 79 joining 111
atom labels, automatic justification 81 setting 20, 59
Caption editing 73
Caption Font 73

ChemDraw Index • 229

 Tool Use Bitmap Fonts When Available 85
Acyclic Chain 63 Use Defaults
Alternative Group 148 atom properties 139
Arc 98 bond properties 143
Arrow 95 User-Defined Templates 156
Attachment Point 148 Using the clipboard 106
Index

Bond 57
Chemical Symbol 91 V
Drawing Elements 96
Lasso 103 Variable attachment command 120
Marquee 103 Variable Line Spacing 75, 83
Orbital 89 Viewing
Pen 99 analysis information 128
Reaction Atom-To-Atom Mapping 129 atom properties 138
Ring 61 bond properties 143
Templates 155 Spectrum-structure assignments 132
Text 71 Viewing document location 8
Tools Palette 15
Tools window 57 W
ToolTips 2
Topology 144 Warnings, chemical 68
TPL style sheet 185 Wavy Bond Tool icon 57
Transferring information Wedge Bond, drawing 58
across platforms 172 Window menu 9, 10
keeping in scale 170 Windows Help 2
overview 178 Windows menu
Triangle, next to command 18 description 9
Triple bond, drawing 60 stationery documents 5
Troubleshooting 200 Windows Metafile 185
Tutorial 29 WMF format 185
Types of bonds 188 WWW, technical support 199

U Z
Unavailable command 17 Zooming, see Changing Perspectives
Undo 19
command 19
lost on save 19
Ungroup command 112
Units
description 20
specifying 59
Unsaturation 140
Unspecified atom properties, in queries 139
Up to, in queries 139

230 • Index ChemDraw

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TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
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TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
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Windows & Macintosh English & Japanese
Windows: 95/98 or NT 4.0, Pentium, 32 MB
Macintosh: System 7.5.5, PowerPC, 32 MB
All specifications subject to change without notice.

TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
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

Premier Searching & Information
• 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
Windows & Macintosh English & Japanese
Windows: 95/98 or NT 4.0, Pentium, 32 MB
Macintosh: System 7.5.5, PowerPC, 32 MB
All specifications subject to change without notice.

TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
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
Premier Searching & Information
• 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
Windows: 95/98 or NT 4.0, Pentium, 32 MB
All specifications subject to change without notice.

TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
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
All specifications subject to change without notice.

TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
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

TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
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

TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
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

TEL 800 315–7300 INT’L 617 588–9300 EMAIL info@camsoft.com WWW www.camsoft.com
FAX 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
 CS Software Problem Report
For faster response and accuracy, use the Web:
www.camsoft.com/support/suppProbRep.cfm
USER INFORMATION (Please Print Legibly) Submit this form via…
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)
MacOs (version) PRINTER
Web Browser(s) (version) Printer Type
CPU Type Printer Driver Name
RAM (in MB ) Driver Version Number
Virtual Memory (in MB ) Printer RAM (in MB )
✁

WWW www.camsoft.com TEL 617 588–9300 MAIL 100 CambridgePark Dr.

EMAIL support@camsoft.com FAX 617 588–9360 Cambridge, MA 02140 USA
CS ChemOffice.Com

CS ChemDraw ®

for Windows Quick Reference

SCREEN ELEMENTS
Application
Control-menu Magnification Control Title bar Minimize button Maximize button
Close box
Menu bar
Tool bar
Scroll box
Rotation handle

Resize handle
Vertical scroll bar
Selection rectangle
Drawing area

Resize handle
Document Application
window window
®

Text box
Tools
palette Scroll
Status bar Horizontal scroll bar
arrow

TOOLS PALETTE * = Pro or higher

Ultra palette shown. ‡ = Ultra only
Lasso Marquee
Varies with Pro & Std.
Solid Eraser
Dashed Text
Hashed Pen
Bond
Hashed Wedged Arrow
Tools Bold Orbital
Bold Wedged Drawing Elements
Hollow Wedged Chemical Symbols
Dative Arc
Wavy Reaction Atom-Atom Map*
Alternative Group* Attachment Point*
Acyclic Chain Template
Cyclopropane Cyclobutane
Ring Cyclopentane Cyclohexane
Tools Cycloheptane Cyclooctane
Cyclohexane Chair (1) Cyclohexane Chair (2)
Cyclopentadiene Benzene
MENUS * = Pro or higher
‡ = Ultra only
Create a new document based on the last style sheet used.
Choose a document to open.
Choose a style sheet to use in new document
or open a Template document*
Close the document window.
Save changes to the document.
Save a copy of the active document in another location
or file format. Revert to the last saved version.
Specify settings for multi-paged documents and posters.*
Specify settings for printed page.
Specify options and print.
Specify settings for objects being drawn in the
Specify default character format for atom labels and current document.
captions in the current document.
Specify colors displayed in Color menu.
Use settings from another style sheet.
Set application-specific options.
View or delete nicknames.

Most recently used documents.

Exit and close CS ChemDraw.

Undo effect of the last command.

Redo last command undone.

Remove selection to the Clipboard.

Paste information from the Clipboard.
Select all objects (Lasso/Marquee).
Select all text in text box (Text tool).
Convert selection to smiles or sln*
string and place on the Clipboard.
Copy selection to the Clipboard.
Delete selection (not copied to the Clipboard).
Repeat the last command.
Paste a smiles string or a chemical name‡
as a chemical structure.

Display a movable grid.
Display rulers.
Toggle the display of a toolbar.
Constrain bond length to the fixed length drawing setting.
Constrain object orientation to 15 degree increments.
Display stereochemical markers.
Display automatic error checking.
Shortcut Menu
The menu commands displayed
depend on what object you right-
click in the application. The fol-
lowing menu appears when you
right-click anywhere in a
document window.

Return to 100% view.

Reduce view to show entire page.
Magnify view in increments up to 400%.
Reduce view in increments. (Minimum size is specific
to the dimensions of your monitor.)

Add and remove rows and columns in Template panel.* Commands from Edit Menu.
 Center selection on the page.
Align two or more selected objects.
Distribute three or more selected
objects horizontally or vertically.
Group objects for selecting.
Ungroup a selected group.
Join curves or structures to make a single object.

Change the front to back ordering of selected objects.

Flip selected objects across an axis.

Rotate a selection.
Resize a selection.

Apply properties to selected atoms in a query structure.*

Apply properties to selected bonds in a
Calculate MW and other chemical properties.* query structure.*
Check valences and labels in a selection.
Adjust bond angles and lengths of a selected structure.
Expand a structure containing a
Contract a structure and create label. nickname or atom label.
Add a node representing an attachment to two or
Add a node representing an attachment more atoms.*
any of several isomers.* Automatically create an atom-to-atom
Remove all existing atom-to-atom mapping of a selected reaction.
mapping from a selection. Create interactive spectrum-structure display.
Create a nickname for a selected structure.*
Type a chemical name and automatically draw a
Draw a chemical structure and automatically structure.
convert to name.

Specify character for- Select context-sensitive help.

mat of text selection. Apply a font to text Click a screen element or
Apply a style to text selection. menu command
selection. to view a topic.
Apply a size to text
Justify atom label or selection.
caption text. Display contents
(“Justified” applies to of the help file.
captions only. Display a topic on how
“Automatic” and to use the help file.
“Stacked Above” Display the tutorial
apply to atom Lists new features. topics in the help file.
labels only.)
Display information
Specify line spacing in a about CS ChemDraw.
text selection.

Choose an arrangement for open

Display 13C NMR chemical shifts document windows.
& line spectrum.‡

Display 1H NMR chemical shifts

& line spectrum.‡

Apply a style to a
selected shape created Display information about Choose an open document to
with the Pen tool. CS ChemNMR Pro.‡ display as the active window.
WORKING WITH SELECTIONS
If you want to …
Add items to a selection
Remove items from a selection
Duplicate a selection
Constrain dragging to X or Y direction
Duplicate and constrain dragging
Switch between selection and another tool
Resize selection excluding atom labels
Resize selection including atom labels
Rotate selection excluding atom labels
Rotate selection including atom labels
Distort aspect ratio of selection
Open Rotate or Resize dialog box
DRAWING TECHNIQUES
Draw a first bond
Add a bond to a structure
Label an atom using a bond or ring tool
Label an atom using the Text tool
Label an atom using a HotKey
Draw a double bond (solid, dashed, bold only)
Draw a triple bond (solid only)
Reduce bond order using Eraser tool
Change double bond alignment
Change double bond type
Move an atom
Change bond type
Change bond layering using bond tool
Draw a ring
Create a spiro-linkage
Create a fused ring
Change size of non-bond object
WWW www.camsoft.com/support/
EMAIL support@camsoft.com
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
IWE 05652 0001
Here’s how …
SHIFT+select items not currently selected
SHIFT+select items currently selected
ALT+drag Selection Rectangle
SHIFT+drag Selection Rectangle
SHIFT+ALT+drag Selection Rectangle
CTRL+ALT+TAB
Drag Resize handle of Selection Rectangle
ALT+drag Resize handle of Selection Rectangle
Drag Rotation handle of Selection Rectangle
ALT+drag Rotation handle of Selection Rectangle
SHIFT+drag Resize handle of Selection Rectangle
Double-click Resize handle or Rotation handle
Drag to draw the bond
Click an atom or drag from an atom
Double-click an atom (triple-click to repeat last label)
Click an atom (double-click to repeat last label)
Point at an atom and press a HotKey (e.g., “c”)
Select bond type from Shortcut menu
Select bond type from Shortcut menu
Select bond type from Shortcut menu
Click center of double bond using any bond tool
Click center of double bond using different bond tool
SHIFT+drag an atom using a bond or selection tool
Click center of bond using different bond tool
Double-click center of bond you want forward
Click or drag using a Ring tool
Click or drag from an atom using a Ring tool
Click a bond using a Ring tool
SHIFT+drag starting point of object (e.g., arrowhead)
CambridgeSoft
TEL 617 588–9300 MAIL 100 CambridgePark Drive
FAX 617 588–9360 Cambridge, MA 02140 U S A
CS ChemOffice.Com

CS ChemDraw ®

for Macintosh Quick Reference

SCREEN ELEMENTS
Close box Title bar Window title Maximize button Minimize button
Menu bar

Scroll box
Rotation handle

Resize handle

Selection rectangle
Drawing area Vertical scroll bar

Resize handle

Document
®

window Text box

Scroll arrow
Tools
palette Message area Magnification Horizontal Size box
control scroll bar

TOOLS PALETTE * = Pro or higher

Ultra palette shown. Lasso Marquee
Varies with Pro & Std. ‡ = Ultra only
Solid Eraser
Dashed Text
Hashed Pen
Bond
Hashed Wedged Arrow
Tools Bold Orbital
Bold Wedged Drawing Elements
Hollow Wedged Chemical Symbols
Dative Arc
Wavy Reaction Atom-Atom Map*
Alternative Group* Attachment Point*
Acyclic Chain Template
Cyclopropane Cyclobutane
Ring Cyclopentane Cyclohexane
Tools Cycloheptane Cyclooctane
Cyclohexane Chair (1) Cyclohexane Chair (2)
Cyclopentadiene Benzene
MENUS
* = Pro or higher
Create a new document based on the ‡ = Ultra only
last stationery pad used. Choose a document to open.
Close the document window.
Save changes to the document.
Save a copy of the active document in
another location or file format. Revert to the last saved version.
Specify settings for multi-paged documents and posters.*
Specify settings for printed page.
Specify options and print.
Download ChemDraw information to a printer.
Specify settings that affect the appearance
of the active document. Specify default character format for
Specify colors displayed in Color menu. atom labels and captions in the current document.
Use settings from another stationery pad.
Set application-specific options.
View or delete nicknames.
Most recently used documents.

Exit and close CS ChemDraw.

Undo effect of the last command.

Redo last command undone.
Remove selection to the Clipboard.
Copy selection to the Clipboard.
Paste information from the Clipboard.
Delete selection (not copied to the Clipboard.)
Select all objects (Lasso/Marquee).
Select all text in text box (Text tool). Repeat the last command.
Convert selection to smiles or sln*
string and place on the Clipboard. Paste either a smiles string or
Select options for publishing a selection. a chemical name‡ as a chemical structure.
Select a document containing a subscriber.
Set options for selected publisher/subscriber.
Display a visible border around a publisher/subscriber.
Display the contents of the Clipboard.

Choose an open document to display as

the active window.
Shortcut Menu
The menu commands displayed
depend on what object you con-
trol-click in the application. The
Choose a stationery pad to create a new document. following menu appears when
you control-click anywhere in a
document window.

Choose a Template document to open for editing.*

Commands from Edit Menu.
 Display a movable grid.
Display rulers.
Constrain bond length to the fixed
length drawing setting. Constrain object orientation to 15 degree increments.
Display stereochemical markers.
Display automatic error checking.
Return to 100% view.
Reduce view to show entire page.
Magnify view in increments up to 400%.
Reduce view in increments. (Minimum size is
specific to the dimensions of your monitor.)

Add and remove rows and columns in

Template panel.*

Center selection on the page.

Align two or more selected objects.
Distribute three or more selected objects
horizontally or vertically.
Group objects for selecting.
Ungroup a selected group.
Join curves or structures to make a single object.

Change the front to back ordering of selected objects.

Flip selected objects across an axis.

Rotate a selection.
Resize a selection.

Apply properties to selected atoms

in a query structure.* Apply bond properties to selected bonds
Calculate MW and other chemical properties.* in a query structure.*
Adjust bond angles and lengths of a selected structure. Check valences and labels in a selection.
Expand a structure containing
Contract a structure and create label. a nickname or atom label.
Add a node representing an attachment
Add a node representing an attachment to to two or more atoms.*
any of several isomers.*
Automatically create an atom-to-atom
Remove all existing atom-to-atom mapping of a selected reaction.
mapping from a selection.
Create interactive spectrum-spectrum display.
Create a nickname for a selected structure.*
Type a chemical name and automatically
Draw a chemical structure and draw a structure.
automatically convert to name.

How to use Balloon Help.

Display brief Help topics.
Display ChemDraw Help.

Scripts Menu
A customizable menu that can
contain compiled scripts. Drag
Apply a font to text selection. the icon of a compiled script
Apply a style to text selection. into the ChemDraw Folder to Apply a style to a selected shape
Apply a size to text selection. add it to the Scripts menu. created with the Pen tool.

Justify atom label or caption Display 13C NMR chemical shifts & line spectrum.‡
text. (“Justified” applies to Display 1H NMR chemical shifts & line spectrum.‡
captions only. “Automatic” Describes an item provided in ChemDraw folder.
and “Stacked Above” apply to Display information about CS ChemNMR Pro.‡
atom labels only.)

Specify line spacing

in a text selection.
WORKING WITH SELECTIONS
If you want to …
Add items to a selection
Remove items from a selection
Duplicate a selection
Constrain dragging to X or Y direction
Duplicate and constrain dragging
Switch between selection and another tool
Resize selection excluding atom labels
Resize selection including atom labels
Rotate selection excluding atom labels
Rotate selection including atom labels
Distort aspect ratio of selection
Open Rotate or Resize dialog box
DRAWING TECHNIQUES
Draw a first bond
Add a bond to a structure
Label an atom using a bond or ring tool
Label an atom using the Text tool
Label an atom using a HotKey
Draw a double bond (solid, dashed, bold only)
Draw a triple bond (solid only)
Reduce bond order using Eraser tool
Change double bond alignment
Change double bond type
Move an atom
Change bond type
Change bond layering using bond tool
Draw a ring
Create a spiro-linkage
Create a fused ring
Change size of non-bond object
WWW www.camsoft.com/support/
EMAIL support@camsoft.com
CS ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corp. © 2000 CambridgeSoft.
IME 05812 0001
= command
= option
Here’s how … a = shift
a + select items not currently selected
a + select items currently selected
+ drag Selection Rectangle
a + drag Selection Rectangle
a+ + drag Selection Rectangle
CTRL + + TAB
Drag Resize handle of Selection Rectangle
+ drag Resize handle of Selection Rectangle
Drag Rotation handle of Selection Rectangle
+ drag Rotation handle of Selection Rectangle
a + drag Resize handle of Selection Rectangle
Double-click Resize handle or Rotation handle
Drag to draw the bond
Click an atom or drag from an atom
Double-click an atom (triple-click to repeat last label)
Click an atom (double-click to repeat last label)
Point at an atom and press a HotKey (e.g., “c”)
Select bond type from Shortcut menu
Select bond type from Shortcut menu
Select bond type from Shortcut menu
Click center of double bond using any bond tool
Click center of double bond using different bond tool
a + drag an atom using a bond or selection tool
Click center of bond using different bond tool
Double-click center of bond you want forward
Click or drag using a Ring tool
Click or drag from an atom using a Ring tool
Click or drag from a bond using a Ring tool
a + drag starting point of object (e.g., arrowhead)
CambridgeSoft
TEL 617 588–9300 MAIL 100 CambridgePark Drive
FAX 617 588–9360 Cambridge, MA 02140 U S A
 CS ChemOffice ®

Drawing, Modeling and Information

ChemOffice Ultra includes

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for a seamlessly integrated suite that fulfills
the day-to day needs of chemists. Predict 1H
and 13C-NMR spectra, use Name=Struct, and
visualize 3D molecular surfaces and orbitals. Use
the ChemDraw and Chem3D Plugins to publish
your work or to query databases on the web.
ChemOffice WebServer provides e-commerce,
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solutions integrated with chemical databases like ChemACX
and with Oracle. Serve your chemical database over your
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