Welcome to CHEM 2OA3 Summer 2010 Organic Chemistry I

Contact: Teri Gullon for EVERYTHING Lectures: BSB 147; T, Th: 6-9pm Office hours TBA ABB-301 x23548 gullontj@mcmaster.ca

EMAIL correspondence is preferred, dont call me unless urgent! Also in charge of Laboratories and Tutorials, incl: Scheduling and Conflict Resolution
2

The Course
Lectures (2 per week) Labs (every week) Tutorials (optional) every week

 Text book: Solomons and Fryhle; Organic Chemistry, 9th Edition (packaged with study guide/solutions manual/molecular models/WileyPlus online) The 8th edition is very similar and acceptable, but note that page numbers, problem sets, etc. refer to the 9th ed. There are excellent and free on-line learning aids available see syllabus. Molecular Models (required): we recommend Molecular Visions, from Bookstore; other models are also acceptable. Lab book, duplicate (required). This can be purchased from bookstore. WileyPlus on-line software comes bundled with the 9th edition, and is also available as stand-alone in bookstore (includes full online 4 textbook). This software is not required for this course.

Course Materials

Course web page:

http://elm.mcmaster.ca login: MUGSI userid and password All relevant course info will be posted on the Course web page There are 2 shells: 1- STRICTLY for lab grades check to make sure TAs input marks correctly 2- For everything else (lectures, assignments, marks etc)
5

Information on ELM
Lecture notes: feel free to print and bring to lectures, or use laptop. Annotated notes will be uploaded after each lecture. Lab manuals, lab locations Tutorials, locations, solutions (after tutorials are done) Assignments, and solutions Test info, and solutions Info on Tutors Chat room (No rude comments, please!) Any important announcements 6

Evaluation Chem 2OA3

Midterm Test (1): Written Assignments (2): Laboratories (5): Final Exam: Practice Assignments (Wiley): 25% 5% 20% 50% 0%

In order to pass the course:

ALL (5) labs must be completed with a passing grade An overall mark of 50% must be obtained

Midterm Test
Date: Thur May 27th, 6pm Location: TBA Contains both multiple choice (40%) and written parts (60%). Sample tests from previous years will be posted on ELM.
8

 You get the BEST mark of the weighted average of: a) Midterm (25%) + Final (50%), or b) Final Exam (75%) So, if you miss the midterm test, your final grade will automatically be re-calculated to compensate (Final Exam 75%) NO MAKE UP MIDTERM If you have a conflict with test writing on the specific date for religious or sports reasons, you will write your test earlier the same day.

Marks

Act Now for early writing!

1. You still have to get a note from your Associate Dean by May 12th 2. Students who write the early test without a valid Deans note will be given a mark of zero on that test

10

Assignments
There are 2 written Take-Home assignments. No late assignments will be accepted Written assignments MUST be handed-in in the drop boxes in ABB (around the corner from the CHEM office - ABB-156 - look for signs), in the correct slot.
Assignment Assignment #1 Assignment #2 Out May 13 June 3 Due May 20 June 10
11

Laboratory Check-in
Everyone checks into the labs next week !!!! Along with Exp 1 Be prepared to show up to the labs as early as Monday Lab Room: ABB-302 or 306 depending on your station # (will be posted outside 302 for the first lab) Checkin and Exp 1 will both happen next week (May 10-14). You will be given the checkin sheet at the start of the lab.
12

Experiment Dates
Exp. 1 + May 10 14 Checkin Exp. 2 Exp. 3 Exp. 4 Exp. 5 May 17-21 May 25-31* June 1-7 June 8-14 Thin Layer Chromatography (TLC) of Analgesic Drugs & Column Chromatography. Separation of Liquids by Distillation. Separation of Solids, Recrystallization & Melting Point Determination Nucleophilic Substitution, SN1 and SN2 Reactions. The Chemistry of Alkenes: Cis-Trans Isomerization, Addition and Oxidation Reactions.

YOU MUST complete ALL 5 labs to pass the course, if you know you have a conflict with a lab, email Teri ASAP to reschedule.
*Note the change of Mondays, now moved to the following week 13 due to Victoria Day

Lab Attendance
Students must attend correct lab period You must get a Deans note if you miss a lab and contact Teri Gullon to arrange an alternate lab day If you have a lab conflict, try to resolve the issue on Solar.
See Teri Gullon if you cannot resolve the issue with Solar BEFORE MAY 7th!! If a section is blocked, its full.

Remember: You must complete all 5 labs to pass the course!

14

Must have:

Lab Exemptions

Taken CHEM 2OA3 @ MAC Completed ALL 5 labs Have 75% or better lab mark

If you satisfy ALL of these criteria then email Teri (gullontj@mcmaster.ca) by May 7th Provide: You name std # year and term you took 2OA3 15

Lab Work
Some general information and techniques are currently posted on ELM, make sure to read this information! Experiments will be posted on ELM the week before YOU are responsible for reading and bringing a printed copy of the experiment to the lab EACH lab has a pre-lab to be completed before entering the lab, some take quite a bit of work, so don t leave them to the last minute!
Any questions? See Teri during her office hours!
16

Lab Notebooks
Duplicate Format only!!! Available in the bookstore Finish all results in the lab period TA signs both copies! TA keeps the duplicate Duplicate returned next lab period only! (No access to TA outside regular lab period).
17

Chemistry Lab Safety

Essential: NO contacts, no shoes that show ANY part of your foot (ie sandals, crocs, flats), SOCKS/tights do not make them any better!

YOU WILL NOT be permitted to do the lab Recommended: Sneakers

18

Chemistry Lab Safety

Essential: GOGGLES must be worn at all times! Not just safety glasses AGAIN: NO CONTACTS even with goggles! No gum No shorts/skirts above knee height! Long hair ALWAYS tied back! You will NOT be permitted to do the lab without the appropriate attire
We work with some nasty stuff!

ALWAYS wear GLOVES!!!! For your own safety! NEVER touch door handles with GLOVES! For everyones safety! MARKS WILL BE LOST! Recommended: Full length pants, long sleeve shirts and/or lab coat
19

Lab Breakdown
Prelab (2 marks) -Summary of experimental procedure (1/2-full page, 0.5 marks) include equations, chemicals used (quantity) how you PHYSCIALLY will perform the lab. Give lots of detail in your own words!! -Prelab questions (1.5 marks) Lab Performance (3 marks) - How prepared you are, follow safety procedures, know what you are doing Results (5) - Different for each exp, calculations, graphs, observations, melting points/IRs etc
20

Tutorials
Take place T and Th at 1:30-4:30 pm in ABB 102 TAs will go through the assigned tutorial questions Questions other than the official tutorial questions may be asked at the end of the tutorial, during Q&A/Help Center These tutorials are optional, but HIGHLY recommended. Answers will be posted the week after the tutorial is over
21

Wiley Plus
You will need a registration code to access WileyPLUS. Its your choice to buy it with or without the printed text: Use the online version of your text in WileyPLUS, go to: www.wileyplus.com/buy and save up to 50% off the price of the print text! Buy the new, printed text in the bookstore and a WileyPLUS access code will be included. DO NOT THROW THIS AWAY! Getting started: Once you purchase your WileyPLUS registration code, you will need to register for WileyPLUS: 1. GO TO: http://edugen.wiley.com/edugen/class/cls175544/ Class Section Name Summer 2OA3 2010 2. Check that the section matches your schedule before you register! 3. Click the REGISTER button to start. 4. Need help registering? http://www.wiley.com/college/twomin/stu/register.html
22

Checking Grades
Marks will be posted on ELM shortly after assignments, tests or labs have been returned to everyone It is YOUR responsibility to check the web site for accuracy Applications for mark changes will NOT be accepted after June 17th

23

Grade Corrections
Any changes to term marks must be requested in writing PRIOR to writing the final exam on June 17th Bring up any discrepancies to Teri during office hours. Bring you original lab or assignment

Note: Work done in pencil (midterm/assignments) will not be remarked

24

Academic Integrity / Academic Dishonesty

Academic Integrity is the standard Academic dishonesty consists of misrepresentation by deception or by other fraudulent means and can result in serious consequences. e.g. the grade of zero on an assignment, loss of credit with a notation on the transcript (notation reads: "Grade of F assigned for academic dishonesty"), and/or suspension or expulsion from the university. It is your responsibility to understand what constitutes academic integrity and academic dishonesty see the course website for a full description.

25

Examples of academic dishonesty

The following illustrates only four forms of academic dishonesty: Plagiarism, e.g. the submission of work that is not one's own or for which other credit has been obtained Improper collaboration in group work, e.g. copying other students' assignments Copying or using unauthorized aids in tests and examinations Ignoring time limits during a test or exam
26

Academic Dishonesty
All cases of suspected academic dishonesty will be followed up with the academic integrity officer All findings of academic dishonesty will result in a penalty of at least an F (i.e. a zero) for the work in question Please refer to McMasters policy regarding academic integrity (particularly appendix 3) See also the academic integrity statement on the 2OA3 web site http://www.mcmaster.ca/policy/StudentsAcademicStudies/AcademicIntegrity.pdf

27

Important!!
It is the students responsibility to ensure that medical slips (and other related documents) are filed with your (Associate) Deans Office You are also responsible for all information in this lecture (see website). Failure to follow procedures will result in lost marks!
28

Course Outline
Available on-line Describes the course content Review Year 1 Organic Chemistry. Pdf files and ppt versions of lecture notes will be posted about one week before we cover that chapter. Well largely follow Solomon and Whyle chapters 1 through 12, adding some practice questions and skipping some sub-chapters.
29

AND IT BEGINS

30

Chapter 1 Carbon Compounds and Chemical Bonds This chapter is largely review we will cover it quite rapidly

31

Our Objectives Learn Dont Memorize!!

Chap 1-3 is mainly Year 1 review Parts of Chap 4,5 are review of structure Chap 6-8, 11, 12 cover key chemical reactions Lab/spectroscopy section: Analysis of organic molecules by separation,
chromatography, IR, 13C NMR, 1H NMR, MS You will learn how to UNDERSTAND the following for organic chemistry:

STRUCTURE SYNTHESIS MECHANISM Organic Chemistry = Chemistry of Carbon (plus a little H, O, N, X)

32

1.4 Electronegativity
Electronegativity is the ability of an atom to attract electrons increases from left to right and from bottom to top (noble gases excluded) Fluorine (F) is the most electronegative atom and can stabilize excess electron density the best Potassium (K) is the most electropositive atom and can hold on to its single 4s electron only weakly, hence it is most easy to remove an electron from K

33

1.4B Covalent Bonds and the Octet Rule

Atoms achieve octet shells (8 valence electrons) by sharing their valence electrons this results in molecules held together by covalent bonds Covalent bonds are common between atoms of similar electronegativity Valence electrons can be indicated by dots (electron-dot formula or Lewis structures) or by a line (each line represents two electrons)

34

Electron Counting
To check the Formal Charge (of an atom): Total # of valence e-s the atom comes in with (number of e- in lone pairs) (number of bonds) To check the octet rule (of an atom): Count the # of electons around it (each lone pair = 2 electrons, and each bond = 2 electrons) Ex: What is the charge of the O in

O H

Does it obey the octet rule?

35

1.6 Limitations to the Octet Rule

The octet rule is obeyed by atoms in the second row of the periodic table (C, N, O, F), with valence electrons in the 2s and 2p orbitals Exception of the second row elements: Some molecules with fewer than 8 electrons in a shell can be stable, for example: BF3 (it is reactive, and easily converts into BF4-) +

In higher rows, other orbitals are accessible and more than 8 electrons around an atom are possible Example: PCl5 and SF6

36

Phosphorus pentachloride

Used as reagent in chlorinations of alcohols and carboxylic acids

37

1.7A A Summary of Formal Charges on Molecules

carboniom ions (or carbocation) ammonium ions oxonium ions Ex: bromonium

borane alkane alkene alkyne amine imine nitrile ether carbonyl alkyl halide

carbanion imide alkoxide halide anion

38

1.7 Examples of molecules having full formal Charges

Ammonium ion (NH4)+

Nitrate ion (NO3)-

O O N
+

+ is on N
39

Practice You need to know the fundamentals to do well in the course

How would you draw the following: CH2O2

HNO3

40

Three Dimensional Shape of Molecules

In 1874 vant Hoff and le Bel realized that the four bonds around carbon were not all in one plane (as in a cross) but rather in a (3D) tetrahedral arrangement. Almost all molecules have a 3-dimensional shape. We usually represent this using different types of 2D drawings. Why do they have 3D shapes?

Tetrahedron (greek) = four planes

41

1.10 Atomic Orbital region where the probability of finding an electron is large REALLY its all math, but shhhhh!
s orbitals (1s , 2s) can have one or 2 electrons in them The 1s orbital is a sphere. The 2s orbital has a core and an outer region with diferent phase signs, separated by a nodal surface. There are 3 degenerate (equal energy) perpendicular (orthogonal) 2p orbitals (px, py and pz) and each orbital can contain 2 electrons (up to 6 electrons total in the 2p orbitals) Each 2p orbital has two nearly touching lobes (blobs). One lobe has a positive phase sign, the other a negative phase sign; a nodal plane separates the lobes The 2p orbitals are higher in energy than the 1s or 2s

No nodal surfaces in 1s orbitals

42

Molecular Orbitals (MOs) A model of covalent bonding, using H

Region I: two isolated atoms no attraction Region II: nucleus of one atom starts attracting the electrons of the other energy of the system decreases the

Region III: at 0.74 separation, the attraction between electrons and nuclei balances the repulsion between the two nuclei this is the bond length of H2 Region IV: energy rises as the repulsion between the two nuclei predominates

I IV III Message for organic chemistry: II Internuclear distance sharing electrons is often better (lower energy of system) than unpaired, unshared electrons
43

2 Atomic Orbitals combine to give 2 Molecular Orbitals (MOs) AOs of the same phase sign overlap to form bonding Molecular Orbitals (molec) Constructive combination, the AO wave functions reinforce, and the values of (wave function) and of (electron probability density) 2 between the two nuclei increases. In this ground state, the two electrons shield the nuclei from each other, leading to attraction. Destructive combination results from overlap of AOs having opposite phase signs. The resulting anti-bonding MOs have a node (region of low electron density) between the nuclei, which causes repulsion. H

H2

H II H

44

Drawing MO Diagrams: The atomic orbitals go on the left and right with the molecular orbitals in the middle Assume the atomic orbitals combine to give the resulting molecular orbitals:
The # of atomic orbitals must always equal the # of molecular orbitals

The net energy of the atomic orbitals must always equal the net energy of the molecular orbitals

Fill the atomic orbitals with the valence electrons Fill the molecular orbitals with the valence electrons, always fill the lowest energy orbitals FIRST! (Aufbau principle)

MO diagram Of H2

In their ground state H2 electrons occupy the lower energy bonding orbital only.

45

MO of H2

H H2

Bond Order = (# of e-s in bonding orbitals # of e-s in antibonding orbitals) / 2

46

O O MO Diagram of O2

47

1.12 The Making of Methane in two steps: hybridization and bonding

Methane has: 4 (bonding) molecular orbitals, 4 * (antibonding) molecular orbitals, plus 4 bonds ( bonding MOs actually filled with two electrons each) 1. Hybridization of carbon to form 4 equivalent sp3 hybrid orbitals (see below) 2. Combination of these 4 AOs with 4 hydrogen AOs to form the 4 MOs (and 4 bonds) of methane

Methane,48 4 CH

An sp3 orbital looks like a p orbital with one lobe greatly extended.

The extended sp3 lobe can overlap well with the hydrogen 1s AO to form a strong covalent bond

This bond formed is called a sigma () bond because it is circularly symmetrical in cross section when viewed along the bond axis

49

One C-H sigma bond in methane Circular cross section

Bond Axis

calculated electron density surface

ball-and-stick model

typical 3D drawing

50

Hybridizations
The number of hybridized orbitals formed must always equal the number of atomic orbitals used An ATOM becomes hybridized to form bonds (MOs) sp3 = 1 s orbital + 3 p orbitals combine to give 4 sp3 orbtials (no leftover p orbitals) sp2 = 1 s orbital + 2 p orbitals combine to give 3 sp3 orbitals (1 leftover p orbital) sp = 1 s orbital + 1 p orbital combine to give 2 sp orbitals (2 leftover p orbitals)

51

1.13 The Structure of Ethene (Ethylene) : sp2 Hybridization

Ethene (C2H4) contains a carbon-carbon double bond and is in the class of organic compounds called alkenes. Another example of an alkene is propene

The geometry around each carbon in ethene is called trigonal planar (each carbon and its three substituents lie in one plane, the bonds of each carbon point towards the corners of a regular triangle, and the bond angles are approximately 120o)

52

Overlap of the sp2 orbitals in ethylene results in formation of a framework: One sp2 orbital on each carbon overlaps to form a carbon-carbon bond; the remaining sp2 orbitals form bonds to hydrogen The remaining p orbitals on each C overlap (bend towards each other) to form a bonding MO (aka bond) between the two carbons. This bond has a nodal plane going through all six atoms and between the two lobes of the molecular orbital p orbitals overlap

bonds bonds
bond
53

The bonding orbital results from overlap of p orbital lobes of the same phase An antibonding * orbital results from overlap of p lobes of opposite phase The antibonding orbital has a node in the molecular plane, and another node between the two carbons The bonding orbital is lower in energy than the antibonding orbital, and hence in the ground state two spin-paired electrons occupy the bonding orbital The antibonding *orbital can be occupied if an electron becomes promoted from a lower level ( e.g. by absorption of light) 2 AOs 2 MOs

Energy

Showing only the p orbital on the 2 Cs

54

The ground state electronic configuration of ethene (C-C and only)

The is lower in energy than the MO. The 4 AO electrons will sequentially populate first the MO, then the MO, leading to formation of a double bond, consisting of a bond and a bond.

Showing only the C-C and C-C orbitals (there will also be a orbital (filled) and * orbital (unfilled) for each C-H bond) Generally speaking we will only talk about MOs between 2 atoms at a time
55

56

Restricted Rotation and the Double Bond

There is a large barrier to rotation (about 264 kJ/mol) around the double bond, corresponding to the strength of the bond This rotational barrier results because the p orbitals must be well aligned for maximum overlap and formation of the bond. Rotating one p orbital 90o completely breaks the bond. In contrast, the rotational barrier of a C - C single bond is low: 13-26 kJ/mol

p orbitals cannot overlap in this geometry the molecule is much less stable. This rotation only happens under very energetic conditions, such as UV irradiation, or temperatures above ~ 300 C

57

1.14 Ethyne (acetylene, C2H2, HCCH) sigma bond framework

In ethyne one sp orbital from each of the two carbons overlap to form a bond The remaining sp orbitals overlap with hydrogen 1s orbitals The remaining four unhybridized p orbitals on each carbon overlap to form two bonds The triple bond consists of one and two bonds

bond bond

bond
58

Ethyne (acetylene, C2H2, HCCH) bonds

The electron density around its carbon-carbon bond has circular symmetry Even if rotation around the carbon-carbon bond occurred, a different compound would not result

59

Resonance Sharing Electrons through bonds

One resonance contributor is converted into another by the use of curved arrows which show the movement of electrons ONE curly arrow moves TWO electrons The use of these arrows serves as a bookkeeping device to assure all structures differ only in position of electrons NET CHARGE MUST ALWAYS REMAIN THE SAME

An electrostatic potential map of carbonate shows the electron density spread equally among the three oxygens. Red areas are more negatively charged; blue areas have less electron density. All three bonds have the same length. The energy of the actual molecule is lower than the energy of any single contributing form - this lowering of energy is called resonance stabilization
60

Resonance versus the MO view of life

Resonance is a way of viewing MOs that are spread over more than 2 atoms Resonance uses bonds and curly arrows (particle view of electrons); MOs treat electrons as waves Resonance structures easy to write; MOs explain chemical properties better E.g. Benzene (more in CHEM 2OB3): electrons are spread over 6 atomic p orbitals:

Benzene Hybrid Representation

61

ACTUALLY CHAPTER 2.2D MO theory explains the equal bond lengths of benzene by suggesting there is a continuous overlap of p orbitals around the entire ring All carbons in benzene are sp2 hybridized (form bonds to other Cs and to Hs) Each carbon also has a p orbital Each p orbital overlaps with the p orbitals on either side to give a continuous bonding molecular orbital that encompasses all 6 carbons All 6 electrons are therefore delocalized over the entire ring and this results in the equivalence of all of the carbon-carbon bonds

Schematic p orbitals in benzene

Calculated p orbitals shapes in benzene

Chapter 1

Calculated benzene MO resulting from overlap of p orbitals above and below the plane of the ring

62

1.8A Rules of Resonance

Resonance structures exist only on paper - they help us figure out reactivity of a molecule Drawing resonance you can only move lone pairs and double bonds (electrons) NEVER break a sigma bond All the resonance structures must be proper Lewis structures The energy of the actual molecule is lower than the individual energy of each resonance structure

63

1.8A Rules of Resonance cont

The more stable the resonance structure (on its own), the more it plays into the resonance hybrid (combined resonance structures)

-2/3 O

+ N O

-2/3

Resonance Hybrid
-2/3

Stability has to do with lots of things

64

What makes a GOOD resonance structure?

The more covalent bonds the better

More octets the better Keep opposite charges close together (if you have to have charges at all) Put negative charges on more electronegative atoms Make carbon happy as possible! TIP: ALWAYS check that the net charge hasnt changed between resonance structures, if it did, YOU MESSED UP!
65

Resonance Practice
H C OH O

+
66

How to Draw Organic Compounds

1.17 Condensed Structural Formulas

1.17C Bond-Line Formulas

Faster, but PRACTICE! Always count your carbons

1.17D Three-Dimensional Formulas

Only really necessary for showing stereochemistry (Ch 5)
67

Isomers are different molecules with the same molecular formula

Many types exist: Consider two compounds with molecular formula C2H6O cannot be distinguished based on molecular formula; however they have different structures: two compounds differ in the connectivity of their atoms Such constitutional isomers are just one type of isomer: They are different compounds that have the same molecular formula but different connectivity of atoms They typically differ in their physical properties (e.g. boiling point, melting point, density) and chemical properties

68

Geometric isomers, such as Cis-trans isomers

Cis-trans isomers are the result of restricted rotation about double bonds THE PROPER NAMES ARE Z (for cis) and E (for trans) These isomers have the same molecular formula and the same connectivity of atoms, and differ only in the arrangement of atoms in space This puts them in the broader class of stereoisomers (Chapter 5) The molecules below do not superpose on each other One molecule is designated cis, or Z (groups on same side) and the other is trans, or E (groups on opposite side) E Z

Z = Zusammen E = Entgegen
Cis-trans isomerism is not possible if one carbon of the double bond has two identical groups

69

(First Year) Assign E, Z

Z E

Look for the highest PRIORITY (based on atomic number) at each carbon center See if the highest priority substituent on each carbon is on the same or opposite side Trick for remembering: E (Opposite), Z (Same) Vowels Consonants
70