Chemistry 125
 
(the Registrar calls it Chem 124)

Freshman Organic Chemistry
Fall 2010

If you are viewing this page on Yale Classes*V2, you should point your browser to 
https://webspace.yale.edu/chem125

so you have more space. (We use ClassesV2 mostly for Wiki and Schedule.)

Chem 125 lecture videos, transcripts, and other material from Fall 2008 are available by clicking here (Open Yale Courses) 
The videos only are mirrored  here (YouTube)

Go to Spring Semester 2011

Material for First Quarter of the Fall Semester 2010 (lectures 1-9)

 Material for Second Quarter of the Fall Semester 2010 (lectures 10-18)

 Material for Third Quarter of the Fall Semester 2010 (lectures 18-28)

(Alternate 3rd Quarter Links)

Material for Fourth Quarter of the Fall Semester 2009 (lectures 29-37)

Syllabus and Course Mechanics

(Discussion Sections)  (Exams & Grading)

Click to go to Spring Semester 2010


Material from the first quarter of the Fall Semester 2010

Goals of Chem 125
Do read this

  Advice from Alumni
More evaluations are available through http://students.yale.edu/oci/
You may want to check fall term reports for Chem 125 (2006, 2007) as well as the new name Chem 124 (2008)

Lecture 1 (9/1/2010) Viewing Instructions
Lecture for 2010 pptx  2010
Audio (begins ~4 min in)  Annika movie for ppt
(2009 ppt) (2009 audio file mov) (2008 mov
(Course Mechanics ; The BIG Question ; The Royal Society ; Pepys as a model Chem 125 student)

We'll finish up Pepys on Friday.

Note:  the powerpoint file linked above is a timed file. You can run it without timing, so as to skip around by choosine "Manually" under Slide Show / Set up Show...; or you can run it in synchrony with the audio file by selecting "Browsed by an individual (window)" and "Use timings, if present".  If you want to include the video clip of Annika in the powerpoint, it must be downloaded into the same folder as the pptx file.

Samuel Pepys and Isaac Newton - How might they do in Chem 125?

Note the Problems   (Due Wednesday, 9/8/10)

You may work in groups of up to 6 to prepare a group hard copy or e-mail submission (with the names of all participants on it).


Lecture 2 (9/3/10)
2010 Timed Powerpoint pptx

2010 Audio (begins with frame 12, check 2009 audio for narration of missing slides)
 (2009 ppt) (2009 audio file wma) and/or (2008 mov)
( Force Laws and Springs; Chemical Force Law? ; Lewis's Electron Octet)

You can synchronize the audio and timed powerpoint yourself, if you wish, by playing them simultaneously and using the right and left arrow keys to make the powerpoint line up with the audio.

note Problems for Friday 9/10/10 on frame 44 (Lewis structure for H/C/N in that order, H/C/H/O in any order)

Newton's Chemistry & the Business of Experimental Philosophy

Two Coulomb Problems  (due Wednesday 9/8/10)


Lecture 3 (9/3/10) afternoon
2010 Timed Powerpoint pptx  2010 Audio
(2009 ppt folder zipped) (2009 Audio File WMA) and/or (2008 mov)
( Lewis Structures; equilibrium vs. resonance; acetic acid geometry & energy; Lore, O2/O3 4-D plotting; charge distribution; Earnshaw and Faraday's Lines of Force)

What's Wrong with Lewis Structures
What are Force Laws?
Earnshaw via Lines of Force
Shell Structure for Charged Balls in 2D

Dealing with Graphs - Lesson 1

Drill on multidimensional plotting
(you don't need to turn the problems in, but you should know how to do them)
answer key

Problem Set for Friday, 9-10-10(html) or (PDF) or (WORD)
(ignore that these documents are dated for previous years)

Functional Group Table

An organic chemistry course is supposed to have a lot of memorizing.  We try to keep this to a minimum, but the minimum isn't nothing. For the first hour exam you will be responsible for memorizing the names of 17 "functional groups" and how to recognize and draw simple "constitutional" structures for them.  These functional groups are identified in red in a table that includes 16 additional functional groups that we'll probably encounter this semester.  You can access the table in three formats:  as a web page ; as a pdf file ; as an downloadable Excel Spreadsheet.  I find that sorting a spreadsheet different ways and stepping through it is an effective tool for memorization (that's how I learn your names).  Good luck.    N.B. the amide functional group is -CONH2, not -COONH2, sorry for the typo.

There will be NO peer tutor session this Sunday afternoon, and no TA discussion section Monday evening.

At 10:30 Monday and Wednesday there will be small-group problem sessions with the TAs and Peer Tutors.  Come to the leture room, SCL 160,  at 10:30.  You will be divided into small groups (according to your residential-college-based problem solving association).  Two groups will stay in SCL 160, two others will meet in SCL 112, the fifth will meet downstairs in SCL 21.  On Wednesday you may go directly to your discussion room.

The Monday discussion will focus on the problems to be turned in on Wednesday and multidimensional graphing;
Statistics
Coulomb's Experiments
Multidimensional Graphing


The Wednesday discussion will focus on the 8 problems to be turned in on Friday:
Lewis Dot Structures and Resonance
to which a 9th problem should be added:  Compare several different Chemistry texts as to "Rules" for drawing Lewis structures and Resonance structures.

NOTE: Lecture 5 will be delivered on FRIDAY afternoon 3:30-4:30
(if you are unable to attend the live session, you may use the audio record and timed powerpoint)


Lecture 4 (9/10/2010)
2010 Timed Powerpoint (pptx)
2010 Audio
(2009 ppt) (2009 audio file wma) and/or (2008 mov)
(HCNO & Lewis structures; Plum Pudding Atoms; Was Coulomb Wrong? Clairvoyant "Science" ; Powers of 105 ;  Measuring the very small - Franklin; Feeling atoms SPM)

The first subject of the course is how we know about the existence of atoms, molecules, and bonds. It also teaches about the role of authority in science. To begin we will contrast two erroneous treatments of atomic and molecular structure a century ago. One of them is by two great scientists G. N. Lewis (Lewis dot structures) and J. J. Thomson (discoverer of the electron). The other is by "clairvoyant" frauds.

Seeing Atoms with Clairvoyance (relevant, but not assigned reading)
If you're skeptical that Crookes really believed in psychic pheomena, click here (also not assigned, just for the curious)

SPM web page
Also a humorous question related to the smallness of atoms

It will be VERY helpful to read ahead on the x-ray page

Lecture 5 (9/10/2010)
2010 Timed Powerpoint (pptx)

2010 Audio
(2009 ppt) (2009 audio file wma) and/or (2008 mov)
(types of SPM; seeing by wave interference, x-ray diffraction, molecular and lattice diffraction )

X-Ray Diffraction

Diffraction examples from laser demonstration

Notice the "What is the line spacing?" question within ppt frame 44. You should work out an answer, so you are confident of understanding. You need not hand it in.

Lecture 6 (9/13/10) 
2010 Powerpoint (ppt)

2010 Audio
(2009 ppt (2009 audio file wma) and/or (2008 mov)
(understanding molecular and lattice diffraction, Franklin's DNA photo; e-density maps, difference maps and bonding)

Leslie Leiserowitz on his Triene (Transcript 16K)
Leiserowitz Quicktime Movie (160 x 120, 5.6 Meg) or (240 x 180, 10.3 Meg)

Jack Dunitz on the C-F Difference Density (Transcript 12K)
Dunitz Quicktime Movie (160 x 120, 6.2 MB) or (240 x 180, 11.2 MB)

(You are not responsible for the page on anomalous dispersion.)

The Second Key Question

It will be VERY helpful to read ahead on the Quantum Mechanics page

Lecture 7 (9/15/10)
2010 timed Powerpoint zipped with Schrdinger sound (ppt) or (ppt only)
2010 Audio
(2009 ppt downloads zipped folder containing ppt and Schroedinger sound files) (2009 audio files wma 1 frames 1-18,  wma 2 frames 19-30 ) and/or (2008 mov)
(Pathological Bonding; Schroedinger's Invention; Weird Kinetic Energy; The Jeopardy Method, Goldilocks)

Quantum Mechanics (Sections I-V on 1st Exam)

Erwin Meets Goldilocks (problem set due Monday, Sept. 20 - PDF document)

It's a pretty safe bet that you have never worked on this kind of problem before, so you should get started as soon as possible. Although you should learn how to solve all of the problems in this important problem set, it is unrealistic to solve them all by yourself. You should form groups, parcel out the problems, and explain what you learn to one another. 

Jon will demonstrate the use of Erwin Meets Goldilocks at the Thursday discussion section.  This program will help you develop a quantum mechanical intuition. You will be doing the relevant problem set in self-selected groups. Be sure that at least one representative from your group (or someone else who is willing to help you) attends the demonstration session. Bring your laptop to the session.  It would help if you download the Applet ahead of time.

Goldilocks Yoonjoo Lee
      thanks to Yoonjoo Lee

Lecture 8 (9/17/10)
2010 Powerpoint (ppt)  
(I apologize that, by mistake, the link was not updated until long after the ppt itself was online. I try to update the ppt and make the audio available soon after the lecture.  Please do let me know in such a situation, and try changing the address manually in your browser to the current year.)
2010 Audio
(2009 ppt) and/or (2008 mov, see also a transcript) (no 2009 audio file because of operator malfunction - sorry)
(1D Quantum - Erwin meets Goldilocks; Nodes & Quantization; Ψ2 & Structure; Vibration, Double Minima)

Lecture 9 (9/20/10)
2010 Powerpoint (pptx)
2010 Audio
(2009  ppt) ( 2009 audio WMA) or (2008 mov, see also a transcript)
(Double Minima - bonding and tunneling; Chladni - nodes in 2D; H-like atom wave functions; ρ for r, orbital shapes)

Chladni Figure Short Movie (Quicktime - 3MB)

4 Chladni Figures (Quicktime - 9.5 MB)

Quantum Mechanics V: H-like Atoms & problem set

Problems for Wednesday, September 24 :

1) Why are there no Chladni Star Figures with an odd number of branches? (e.g. 3 or 5 radii)
2)Why are the first two cells [(0,0) (1,0)] in Chladni's tables vacant?
3) Compare 1s of H with 2s of C+5 in Energy
4) Do the six Atomic Orbital problems HERE (also for Atom-in-a-Box Download)
Clicking here links to a Java program that provides some of AiB functionality for a PC.

Note: AiB will not be covered on Friday's exam

The exam at class time on Friday, Sept. 22, will cover through Lecture 9 (Lecture 10 will be covered on the next exam)

60 minutes will be alloted for the exam, either 10:30-11:30 in SCL 160 (the normal lecture room) or 10:15-11:15 in SCL 111 down the hall.  That is, you can either stay 10 minutes late or come 10 minutes early.

Prof. McBride will lead a review session on Wednesday, Sept. 20, in room 119 WLH from 8 to 10 pm.  Come with questions.

Note incidentally that the Monday and Thursday discussion sections are held in WLH 204 (contrary to what the syllabus used to say - sorry for the mistake)


You may be wondering what kind of questions might appear on exams in this course. (Our first exam will occur on Friday, Sept. 24 The following PDF file contains a number of questions based on topics we have been discussing. Most of these would be fair game, but a few from earlier years refer to material we won't cover until shortly after the first test. It might be useful to look them over as we go along.

2001 First Exam (PDF)  Answer Key for 2001 First Exam (PDF)
First Hour Exam 2002 (PDF) Answer Key for First Hour Exam 2002 (PDF)

Answer Key for Exam 1 2003 (PDF)
First Hour Exam 2004 (PDF) First Hour Exam 2004 Answers (PDF)
First Hour Exam 2005 (PDF)

First Hour Exam 2005 Answers (PDF)

First Hour Exam 2006 (PDF)

First Hour Exam 2006 Answers (PDF)
First Hour Exam 2007 First Hour Exam 2007 Answer Key
First Hour Exam 2008 (pdf)     First Hour Exam 2008 Answer Key(pdf)
First Hour Exam 2009 (pdf)  First Hour Exam 2009 Answer Key(pdf)

Sample questions for first hour exam

Sample Quantum Mechanics Questions (PDF)

Sample questions on Early Topics (PDF) 

First Hour Exam 2010 (pdf)    First Hour Exam 2010 Answer Key(pdf)

Exam scores are available via Post'em.

The class average was very good (75.6) with 1/3 of the scores greater than 77 and 2/3 of the scores greater than 71.  Congratulations, you seem to be learning a lot! (although some show need for improvement in drawing resonance structures)

You can check your own points, both by question and total, using Post'em on ClassesV2.  If you have questions about the grading, consult the answer key (above) first, and then speak to  the grader of the relevant question (1-6, Miller; 7-10, McBride).

These scores are of course almost insignificant, because they represent such a small, preliminary portion of the grading for the semester. But the course content is cumulative, so it can be helpful to see where you stand thus far, and whether it is important to be sure you're not falling behind.

  There is plenty of help available from the teaching staff.  5/6 of the semester scoring is still to come, so it's way too early either to despair or to become self-satisfied.  The plot to the right from several years ago shows that the first exam score was not a great predictor of semester total. There is some correlation, but it is easy by working (or not) to move up (or down) by a letter grade.
exam correlation




Material for the second quarter of the Fall Semester 2010

Lecture 10 (9/22/10) 
2010 zipped timed Powerpoint (pptx) (folder includes juggling video)  (or pptx only)
2010 Audio
(2009 ppt - downloads zipped folder with ppt file)  ( 2009 audio WMA) and/or (2008 mov, also here is a transcript)
(Parts of 2p; Dauger's Atom-in-Box; r2 weighting; scaling size and energy; hybridization for orientation and shape; The Problem With Orbitals)

If you are have difficulty with why r2 is sometimes used to multiply Ψ2 in discussing electron distribution, 
you might try
these optional problems from a previous year and discuss them with friends or TAs.

Hybridization Animation


Lecture 11 (9/27/10)
2010 Powerpoint (ppt)
2010 Audio
(Lecture 11 ppt) (2009 Audio wma) or (2008 mov)
( 2-electrons,  Zeff,  SCF,  "Correlation Energy", Energy Magnitudes; Orbital Shapes; "Plum-Pudding" molecular orbitals)

Quantum Mechanics VI-VII
(orbitals for several electrons,  hybridization)
 

Energy Scales and Correlation Energy

Lecture 12 (9/29/10)
2010 Powerpoint (ppt)
2010 Audio
(Lecture 12 ppt) (2009 Audio wma) or (2008 mov)
(Pairwise LCAO-MO, Bonding in H2, C-C Overlap & Hybridization, Bond Strength and Electron Count)

Quantum Mechanics VIII-IX
(molecular orbitals; HOMOs and LUMOs for functional groups)

H-H Bonding

C-C Overlap and Hybridization

Lecture 13 (10/1/10)
2010 Powerpoint (ppt)

2010 Audio
(Lecture 13 ppt) (2009 Audio wma or (2008 mov) 
(Newton's Grail; Energy-Match, H2 vs. HF, hybridization & geometry; Reality; Predictions for Experimental Test with XH3)

Overlap / E-Match / Tunneling

XH3 (contact with reality)

Lecture 14 (10/4/10)
2010 Powerpoint (ppt)

2010 Audio
(Lecture 14 ppt) (2009 Audio wma 1st 25 min only, sorry) or (2008 mov) 
(XH3: IR, ESR, CF3; Goals; Pathological Bonds; BH3 and local bonds)

  BH3, an Example of an MO Computation & an Apology for Local Bonds
Note: the pictures on this page are fun to look at, but don't worry too much about the verbal content,
unless you can't sleep because we use local bond analysis instead of the MOs that computers find.


Lecture 15 (10/6/10)
2010 Powerpoint (ppt)

2010 Audio
(Lecture 15 ppt) (2009 Audio wma) or (2008 mov)
(BH3 and local bonds; Which mixings are important?; Acid-Base Theory; What makes HOMO high, LUMO low?)

HOMO-LUMO Reactivity:

MO Interactions, which ones count? (HOMO/LUMO)Functional Groups (high HOMO base / low LUMO acid)


Lecture 16 (10/7/10)
2010 Powerpoint (ppt)

2010 Audio
(Lecture 16 ppt) (2009 Audio wma) or (2008 mov & mov)

(What makes HOMO high, LUMO low? B2H6; HF LUMO; Acid-Base - SN2 - E2 LUMO Analogies; Make & Break)

Orbital Shapes of:
HF an acid (substitution at H)
CH3F substitution at C (an acid)
O=CH2 the carbonyl group (an acid)

LUMO Analogies (elimination from C2H5X)




Last year pairs of class members adopted a functional group to discuss in terms of pair-wise and atomic orbitals (and their interactions).  You should study their Wiki pages, decide whether you agree with their analyses, and be prepared to produce such a report on any of these functional groups, or on some unfamiliar functional group.

If you would like optional problems to help firm up your understanding of quantum mechanics before the exam a week from Monday (Oct. 18), you could look at the exams from previous years linked below.

Lecture 17 (10/8/10)
2010 Powerpoint (ppt)

2010 Audio
(Lecture 17 ppt) (2009 Audio wma) or (2008 mov & mov)
(
N2H4 Synthesis; Four Functional Groups: Carbonyl-Buergi-Dunitz Angle, Amide)

Note: the last half-hour of the 2009 wma recording (beginning at 57:30) contains the optional after-class demonstration of Spartan in which MOs of an enol were calculated and compared with class-member predictions.  After the END frame of the Lecture 17 ppt, there is a supplementary timed ppt showing some screen shots from the demonstration.  This is optional, not required reading/listening, but it may help to make the computer's contribution less vague.

Where should R2C=O be attacked? (Buergi-Dunitz Angle)

Intramolecular HOMO/LUMO mixing and "Resonance"
]

OMO-OMO Mixing Problem
 (not to turn in, but you may want to discuss it)



Lecture 18 (10/11/10)
2010 Powerpoint (ppt) link corrected to 2010
2010 Audio
(Lecture 18 ppt) (2009 Audio wma) or (2008 mov)
(
Functional Group Analysis: Amide cont., Carboxylic Acid, C-Metal bond and aggregation.  How Did They Know? Precursors of Modern Chemistry- Alchemy)

3-Center "Electron-Deficient" "Y" Bonds
[ B2H6 & (CH3Li)4 •4 OMe2

History (how humans actually learned about organic chemistry)

History Index

Why we study chemical history (DO READ THIS & the others)

Your Genealogy in Organic Structure Theory


Review Sessions for the Exam on
Monday, Oct. 18

Audio (.mov Quicktime file) of McBride review session Tuesday, Oct 12
(of limited utility without gestures and blackboard, but here it is)

The Peer Tutors and Graduate TAs will hold their regularly scheduled help sessions on Monday and Thursday evenings and Sunday afternoons.  In addition Jon will hold a help session on Friday morning, Oct 15, 10:30-11:20 in 160 SCL (the normal lecture time and place).  These are the opportunity for you to practice functional group analysis.

Note: the exam will focus on Lectures 10-18 but will not include the history material from the last 21 minutes of Lecture 18


Sample Problems for Oct. 18 Exam
2nd Hour Exam 2008 (pdf)  2nd Hour Exam 2008 Answers (pdf)
2nd Hour Exam 2007 (PDF) 2nd Hour Exam 2007 Answers (PDF)
2nd Hour Exam 2006 (PDF) 2nd Hour Exam 2006 Answers (PDF)
2nd Hour Exam 2005 (PDF) 2nd Hour Exam 2005 Answers
2nd Hour Exam 2004 (pdf)
2nd Hour Exam 2004 Answers (pdf)
2nd Hour Exam 2003 (pdf) 2nd Hour Exam 2003 Answer Key (pdf)
 2nd Hour Exam 2002 (Word)... (PDF) 2nd Exam 2002 Answers (Word)... (PDF)
2nd Hour Exam 2001 (PDF) ... (Word)

2nd Hour Exam 2000 (Word) Answers to 2000 2nd Exam
2nd Hour Exam 1999 (web page)  (answers at end)
2nd Hour Exam from 1998 (Word) Answers to 1998 2nd Exam
2nd Hour Exam 2009 (pdf) Answers to 2nd Exam 2009 (pdf)
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The exam will take place at 10:30 AM (normal lecture time) in SCL 160 (normal lecture room). It will be budgeted for 50 minutes, but 60 minutes will be allowed for writing exam papers. To accommodate students who must leave for the following class (or who just wish to get it over with), the exam may be taken early from 10:15-11:15 in SCL 111 (next to southeast corner of SCL - at other end of the hall from 160).

2nd Hour Exam 2010 (pdf)  
2nd Hour Exam 2010 Answer Key (pdf)


Material for 3rd Quarter of First Semester 2010

(Alternate source for 3rd Quarter Links)

Lecture 18 timed (ppt)  2010 Audio
The material after slide 14 (Audio 30 min) is for this 3rd quarter of the course
(Yale chemistry and equipment 100 years ago and its alchemical roots; the Doctrine of Sympathies; Scheele's Laboratory)

Lecture 19 (10/13/10)
2010 Powerpoint (ppt)
   2010 Audio (first 2.5 min. exclamations about Hg)
(Lecture 19 ppt)  
(2009 Audio wma) or (2008 mov) 
(
Scheele's Acids; Oxygen; Lavoisier's Revolution: Nomenclature, Trait, Analysis, Elements, Measuring Gases, Radicals & Language, Measuring Heat)

NOTE: This lecture will be covered on subsequent exams, not this exam.  Concentrate on quantum mechanics (and Lect 18).


Prerevolutionary contributions - Scheele

Lavoisier & the Chemical Revolution: Analysis

(14 Questions for Friday, Oct 22, indicated by * below (you may work in groups) 

Portrait (we discuss the problem re. Fig. 10 in class, you need not turn it in)
for no reason that I can understand the first link below works only when you click the first C

Combustion of Phosphorus and Carbon*4
Quantitative Chemical "Formulae" *4

1789 Preface
Elements & Oxidation *2
How to determine Gas Density
Calorimeter *4

Lecture 20 (10/20/10) 
2010 timed Powerpoint (ppt)  2010 Audio (wma)

(Lecture 20 ppt)
(2009 Audio wmv) or (2008 mov)
(Lavoisier
Analysis & Bookkeeping; Dalton: Atoms & Proportions; Berzelius: Symbols & Analysis; Gay-Lussac Volumes; Mitscherlich As/P ratio; )

Combustion Analysis Lavoisier/Prout/Liebig/Dumas (1788-1841)

Note: problems for Wednesday, October 27 (on web pages with red years 1828 and 1832 below)

Liebig's Kaliapparat and the etymology of K and Na (1831) 
Distillation and the "Liebig" Condenser (1771)

1828-1851 Isomerism
Radical (Dualistic) vs.
Type (Unitary, Substitution) Theory

 Woehler/Berzelius Letters about Urea (1828) 
Woehler's Urea Paper (1828) (analysis and isomerism preview)

Berzelius Coins the Term Isomeric (1830)

Woehler/Berzelius on Liebig, Isomerism, & Organic Chemistry (1830-35)

Woehler/Liebig Discovery of Benzoyl Radical (1832)
(by analysis)

Lecture 21 (10/22/10)
2010 timed Powerpoint (ppt)  2010 Audio (wma)

(Lecture 21 ppt 2009 downloads a zipped folder including movie of Liebig's Invention) (2009 Audio wmv) or (2008 mov)
(
Berzelius: Analysis, Electrolysis & Dualism; Woehler & Urea; Isomerism; Liebig Analysis)

Lecture 22 (10/25/09) 
2010
Powerpoint (ppt)
 2010 Audio (wma)
(Lecture 22 ppt) (2009 Audio wmv) or (2008 mov)
(
Radical Theory; Addition and Substitution Reaction Mechanisms; Type Theory; Valence: Couper) 

Dumas's Panegyric on the Radical Theory (1837)
Berzelius on Dumas Substitution Theory (1838)

Simple Alkane Etymology
Woehler's Spoof of the Type Theory (1840)

Competing Views of Organic Chemistry (~1851)


1858-1860s Constitution
"Nature and Sequence of Bonds"

Couper On a New Chemical Theory (1858)
Kirkintilloch Movie (11Mb)

Kekul on the Superiority of his Sausage Formulae (1865)
Other Molecular Diagrams and Models (mid 1860s)
Cannizzaro, the Cautious Revolutionary, on Models (1872)

Lecture 23 (10/27/10)
2010 Timed Powerpoint (ppt)  2010 Audio (wma)
(2009 Lecture 23 ppt ) (2009 Audio wmv) or (mov
(
Valence: Couper, Kekul; Notation, Models, Counting Isomers)

Note isomer counting Problem for Friday on Frame 48 (if we get that far, otherwise for Monday)

1869-1880 Configuration
"Arrangement of Atoms in Space"


Koerner Proves 6-fold Symmetry of Benzene (1869)
Patern's Tetrahedral Carbons (1869)

Lecture 24 (10/29/10)
2010 Timed
Powerpoint (ppt)
  2010 Audio (wma)
(Lecture 24
ppt ) (2009 Audio wmv) or (2008 mov) 
( Koerner's Benzene Proof, Paterno's tetrahedral carbon)

Lieben to Patern on Atoms in Space (1869)

Lecture 25 (11/1/10)
2010 Timed
Powerpoint (ppt)
  2010 Audio (wma)
(Lecture 25
ppt ) (2009 Audio wmv - sorry, only first 20 min) or (2008 mov) 
(Benzene Structure - van't Hoff vs. Ladenburg; Carvone/Tartaric Acid Isomerism; Pasteur, van't Hoff)

van't Hoff's Tetrahedral Carbon (configuration) (1875)
Kolbe's Criticism of van't Hoff (1877)
Your Teacher, a Later-Day Kolbe?


Lecture 26 (11/3/10)
2010 Timed
Powerpoint (ppt)  2010 Audio (wma)

(Lecture 26 ppt ) (2009 Audio wmv) (2008 mov)
(van't Hoff, Tetrahedral C; Coordinate Transformation; Alkenes & Allenes; Mirrors & Alice; Chirality; Stereochemistry; Notation; Fischer Counts Configurational Isomers)

Fischer on Models and the Fischer Projection (1891)


Lecture 27 (11/5/10)
2010 Timed Powerpoint (ppt)  2010 Audio (wma)

(Lecture 27 ppt
(2009 Audio wmv)  (2008 mov)
(Fischer's Ambiguous DL Nomenclature for Configuration.  Leiserowitz on Absolute Configuration and the Stereochemistry of Malaria)

Using Asymmetric Crystal Growth to Identify Molecular Configuration
Higher on this same webpage is an explaination of Bijvoet's anomalous dispersion technique for which you are NOT responsible.

Lecture 28 (11/8/10)
2010 Timed Powerpoint (ppt)   2010 Audio (wma)

(Nomenclature for constitution and configuration)

AUDIO OF THE LAST 2/3 OF THE MONDAY REVIEW SESSION (OF LIMITED INTEREST, CERTAINLY BETTER TO SPEND YOUR TIME ON THE LECTURES AND OLD EXAMS)

Sample Nomenclature Drill (Yale only) 



Old Third Exams for Practice :
Note - we are ahead of the pace for several previous years and very slightly ahead of last year,
so different material covered in some of the earlier exams will be relevant this year.


3rd Hour Exam 2003 (pdf) ...3rd Hour Exam 2003 Answer Key (pdf)

3rd Hour Exam 2004 (pdf)   3rd Hour Exam 2004 Answer Key (pdf)

3rd Hour Exam 2005 (pdf)     3rd Hour Exam 2005 Answer Key (pdf)

3rd Hour Exam 2006 (pdf)     3rd Hour Exam 2006 Answer Key (pdf)

3rd Hour Exam 2007 (pdf)     Sorry, no answer key
(even earlier exams available in the table below)
2002 questions (pdf)
2002 answers (pdf)
2001 questions (pdf) (Word)
2001 answers (pdf) (Word)
2000 questions (pdf) (Word)
2000 answers (pdf) (Word)
1999 questions (pdf) (Word)
sorry, answer key unavailable
1998 questions (pdf) (Word)
1998 answers (pdf) (Word)

The exam will be offered 10:15-11:15 in 111 SCL and 10:30-11:30 in 160 SCL

3rd Hour Exam 2008 (pdf)   3rd Hour Exam 2008 Answer Key (pdf)

3rd Hour Exam 2009 (pdf)  .3rd Hour Exam 2009 answer key (pdf)




Exam Score Statistics 2009 Mean 1/3 of scores > 2/3 of scores >
3rd Exam 84.2 88 82
Sum of 3 Exams 234.7
247 222

3rd Hour Exam 2010 (pdf)  Answer key not ready yet



Material from 4th Quarter of Fall Semester 2010

Lecture 29 (11/12/10) Prof. K. B. Wiberg guest lecture
2010 Timed Powerpoint (ppt)    2010 Audio (wma)
(2009 mov or mp4)  (2009 audio wma) (2008 Laurence D. Barron on Optical Rotation mov)

(Wiberg describes some of his contributions to classical configuration correlation and the calculation of optical rotatory strength)

Stereochemical Nomenclature: Cahn-Ingold-Prelog
Chirality in the 8th Century  (note Problem for Monday)

Problem for Monday Nov 15 (based on frames 17-18 of Lecture 27)
In 1927 P. A. Levene et al. used reaction with HI to convert butane-1,3-diol into 4-iodobutane-2-ol and thus related their stereochemical configurations.  In 1952 young K. B. Wiberg worried that an alternative mechanism for this conversion might invalidate Levene's conclusion.  Use HOMO-LUMO analysis for possible reactions to see what worried Wiberg.  At each reaction step consider alternative possibilities for reaction.  (You may work in groups on this problem.)

Lecture 30 (11/15/10)
2010 Timed Powerpoint (ppt) 2010 Audio (wma)

( Optical Rotation, Resolution; Aldol Reaction; Enantiospecificity)

Lecture 31 (11/17/10)
2010 Timed Powerpoint (ppt)  2010 Audio (wmv)

 (2008 Dr. Dianne Duffey presentation on clinician perspective)
(Stereo Viewing; Who Cares  Drugs; Esomeprazole: name, chirality, mode of action, Chiral Switch, Clinician Perspective,)

(Stereo Viewing this is optional, ask if you're interested)

Thalidomide/Ritalin Chiral Switch

Lecture 32 (11/19/09)
2010 Timed Powerpoint (ppt) 2010 Audio (wmv)

(2009 ppt
(2009 audio wma) (2008 mov and mov)
(Litigation; Resolution & Chiral Synthesis, Sharpless Allylic Oxidation; Omeprazole Mechanism; Conformation & Energy; Newman Projection)

Lecture 33 (11/29/10)
2010 Timed Powerpoint (ppt) 2010 Audio (wmv)

(2009 ppt
(2009 audio wma) (2008 mov )
(Rotational Barrier from Heat Capacity; Source of Barrier; Stereotopicity and Toponomy; Baeyer Strain Theory)

Topicity: Prochirality and Dehydrogenase

1885- Conformation & "Strain"

Baeyer Proposes Strain Theory (1885)

Sachse Identifies Conformational Isomers; Baeyer objects (1890-93)

Lecture 34 (12/1/10)
2010 Timed Powerpoint (ppt) 2010 Audio (wmv)

(2009 ppt
(2009 audio wma) (2008 mov and end of mov)
(Sachse's Rhetoric; Mohr's Drawings; Drawing Cyclohexane; Barton's Conformational Analysis; Ring Flips; Rotational Barriers; Strain Energy and Molecular Mechanics)

Mohr Vindicates Sachse (1918)

Drawing Perspective Views of Cyclohexane

Lecture 35 (12/3/10)
2010 Timed Powerpoint (ppt) 2010 Audio (wmv)
(2009 ppt
(2009 audio MP3 N.B. this is an MP3 file because I had difficulty editing the wma. Tell me if you have trouble with it.) (2008 mov )
(Axial vs. Equatorial Energy; Ring Relaxation; MM vs. Quantum)

Strain Energy in Butane

Non-Spherical Bromine

Lecture 36 (12/6/10)
2010 Timed Powerpoint (ppt) 2010 Audio (wmv)
(2009 ppt (2009 audio wma) (2008 mov )
(Generic Geometries and CSD; Energy Models; Heat of Formation; Average Bond Energies; deltaHatomCarbon, "effects" in ketone-enol equilibrium; Statistics and Equilibrium)
Energy
Energies: Choice of Zero and Chupka's Heat of Atomization of Carbon

Lecture 37 (12/8/10)
2010 Powerpoint (ppt) 2010 Audio (wmv)

(2009 ppt
 (2009 audio wma) (2008 mov )
(Statistics and Equilibrium; Reaction on the Potential Energy Surface; why we studied The Chemical Bond)

Relevant websites:
Boltzmann Distribution
Distributions - Maxwell to Bush (powerpoint)  (marginal relevance)
Entropy & Disorder Riddle

REVIEW SESSIONS:

Thursday, Dec 9, 7-9 pm, WLH 204, Miller

Friday, Dec10 10:30-11:30 am, 160 SCL, McBride
Audio Recording (wmv)
The beginning of this session concerned exam struture (0:00-1:30), then an excursion through recent topics (5:00-14:00) 
and some thermodynamics/statistics (H 14:00-22:30; S 22:30-32:00)
Much of the conversation turned on understanding how heat capacity and entropy could relate to the rotational barrier in ethane (Lecture 33 slides 4-7)
(33:30-55:30 1:05:00-1:16:30, 1:17:50-1:29:00) We have now spent more than enough time on this topic.
Other topics:  numbers worth memorizing (59:30-1:00:10); configurational nomenclature (1:00:10-1:04-50); utility of models (1:16-30-1:17:14)

Sunday, Dec 12, 3-5 pm, WLH 117, Peer Tutors

Monday, Dec 13, 7-10 pm,  WLH 204,  Miller

Wednesday, Dec. 15,  8-10 pm, WLH 208,  McBride
Audio Recording (wmv)  (Note that it may be more useful to spend time reviewing the organized lectures than this stream-of-consciousness session)
Topics covered included: Stereochemistry-Resolution (00:28-8:00), tartaric acid (8:00-16:30), nomenclature, history of the 4Cs (16:30-29:00);

Thermodynamics, Statistics, Transition State (29:00-44:30); Chiral Catalysis (44:30-52:00); Reaction Mechanisms (52:00-1:06:00); 
Fischer Projection (1:06:00-1:10:00); Seeing Molecules, SPM, X-ray (1:10:00-1:18:00); 
Quantum Mechanics (1:18:00-1:23:00), Psi(x) to V(x) (1:23:00-1:30:30), Floppiness vs. number of quantum states (1:30:30-1:34:15); 
Reaction Coordinate, Potential Energy Surface, Transition State Theory (1:34:15-1:39:20); Topicity,  Conformation, and Configuration (1:39:20-1:52:00)

Thursday, Dec. 16, 7-9 pm, WLH 204, Lichtor & Miller

First Semester Final Exam

9 AM - 12 Noon Friday, December 17

SPL 59

The exam will be budgeted for 150 minutes, but you will have 180 minutes to complete it. Roughly half of the questions will be focussed on material since the third hour exam. (If half of the final covers the last quarter of the course, and the final counts for half of the semester points, the last quarter of the course counts for 1/4 of the semester total.)

Previous Fall Final Examinations:

Note: Some previous exams covered a few more topics that we did not cover this year.  You are responsible only for what was presented in lecture this year and for assigned reading and problems.

1999 First Semester Final Exam (pdf 128kB) and Answer Key (pdf 68kB)

2000 First Semester Final Exam (pdf 180kB) and Answer Key (pdf 48kB)

2001 First Semester Final Exam (pdf 180kB) and Answer Key (pdf 220kB)
Supplemental information for above:
Resonance Structures            ProtonatedMeOHLUMO

2002 First Semester Final Exam (pdf 164kB) Answer Key (pdf 192kB)

2003 First Semester Final Exam (pdf 380kB)      (sorry no answer key)

2004 First Semester Final Exam      Answer Key

2005 First Semester Final Exam (sorry no answer key)

2006 First Semester Final Exam        Answer Key

2007 First Semester Final Exam  Answer Key

2008 First Semester Final Exam   Answer Key

2009 First Semester Final Exam  Answer Key
Question 12 ribosome movie



Material for First Quarter of the Fall Semester 2009

Material for Second Quarter of the Fall Semester 2009

Material for Third Quarter of the Fall Semester 2009

Material for Fourth Quarter of the Fall Semester 2009


Comments? j.mcbride@yale.edu

copyright 2008 J. M. McBride