Spring Semester 2017

Table of Contents:

Course Description

Lecture Notes

Paper Project Listing




Links to the Scientific Literature

Literature References

Additional Resources

Course Description:


Professor James E. Jackson
Phone:  517-353-0504 (but e-mail is vastly preferred)
Office:  Room 534 Chemistry Building
Office Hours: W 10:00-12:00 or by appointment

Lectures: TTh 12:30-1:50, Room 183 Chemistry Building; Note: this is 10 minutes earlier than the official scheduled time

Problem Discussion Sessions: Monday evenings, 5-7, Room 581East, Chemistry Building

Primary Text ("A&D"): Modern Physical Organic Chemistry by E. V. Anslyn & D. A. Dougherty (I know it's expensive, but you should own this valuable reference)

Other Useful Texts: (Strategies to make these available on reserve still TBA):

Advanced Organic Chemistry, Part A, Structure and Mechanisms (2007 Part A) (2002 Part B)

F. A. Carey and R. J. Sundberg

Structure and Mechanism in Organic Chemistry

F. A. Carroll

Mechanism and Theory in Organic Chemistry, 3rd Edition 

T. S. Lowry and K. S. Richardson

Advanced Organic Chemistry, 4th Edition (2001, 5th ed.)  (2013, 7th ed.)

J. March and M. B. Smith

Frontier Orbitals and Organic Chemical Reactions

I. Fleming

Determination of Organic Reaction Mechanisms

B. K. Carpenter

Reactive Molecules

C. Wentrup

Introduction to Stereochemistry (2002)

K. Mislow

Organic Chemistry, 2nd Edition

J. C. Stowell

Organic Chemist's Book of Orbitals

W. Jorgensen

Basic Organic Stereochemistry

E. L. Eliel, S. H. Wilen & M. P. Doyle

Advanced Organic Chemistry (2010)

R. Bruckner

Homework: Weekly problem sets will be assigned on Tuesday. Problems may come from A&D or other sources. Their answers will be presented and discussed by class members chosen at random at the problem discussion sessions. You should have complete answers for every assigned problem written-out using ChemDraw and ready for display using Powerpoint or Keynote. We will have a laptop and projector at these meetings, and when you are selected to answer a problem, you should have a USB flashdrive (or a CD) with your answers ready to load up and display. Clarity and conciseness in your answers will be critiqued. Your answer presentations will be evaluated on a 10-point scale; your semester cumulative performance will serve as the problem set component of the course grade. So be sure you (a) have written up the answers and (b) are ready to explain them to your colleagues. Alternatively, the whole class may be asked to write up answers to one or more of the problem set questions at the meeting. This is effectively an easy "pop quiz" where you've already seen the questions. We will make every effort to have keys posted on the CEM 851 website shortly after the discussion period.

Research paper + presentation: Drafts due Monday, 27 March (first, to which I provide feedback) and Monday, 10 April (final); presentations (20 minutes) are to be prepared the following week and given the next. We will also have smaller writing exercises along the way.

Exams: One midterm, Tuesday, 14 March (just after break). Final exam is officially Monday, May 1, 12:45-2:45 PM, but we will reschedule at a mutually acceptable afternoon/evening time for greater time flexibility. Last year's individual oral exam scheme was quite effective and we will use this mode again in 2017.


Problem Sets (weekly)


Midterm Exam


Paper + presentation


Final exam (comprehensive)


Course Content: This course will attempt to cover roughly 1/2 of A&D, in what they describe as a very fast-moving semester. Topics will often use material from other sources (literature, other books, etc.)-we will develop the precise sequence as we go along. Needless to say, we'll spend more time on some parts of this very thick book than others. Readings will be put on the web or handed out in lecture, depending on length and class size. The schedule of topics will follow the book's sequence, though a given topic may get more or less time, depending on the class's response and the instructors' enthusiasm. We will also use discussion sessions for computational labs, problems, and Q&A.

Preliminary Outline:

* Electrons, Orbitals, Bonds, & Shapes of molecules

* Molecular Modeling: Intro to Spartan

* Stereochemistry

* Conformational, Strain, Steric, & Stereoelectronic Effects

* Basic Tools of Physical Organic Chemistry
        Thermochemistry, Kinetics, and Correlations (Linear Free Energy Relations)
        Structural Probes: Stereochemical and Isotopic labeling
        Kinetic Probes: Solvent and Isotope Effects
        Acid/base catalysis

* Nucleophilic Substitution

* Addition and Elimination Reactions

* Hydrocarbon Acidity, Carbanions & other C Nucleophiles

* Carbenes

* Carbonyl Compounds

* Aromaticity and Aromatic Substitution Reactions

* Radical Chemistry

* Pericyclic Reactions & Orbital Symmetry Rules

* Photochemistry

Note to the Class:

For most of you, this is your first term of graduate level physical organic chemistry. It can be a hard subject, but it is also full of interesting detective work and elegantly designed experiments. From experience with previous classes and in my own education, I want to point out several common stumbling blocks and misconceptions which you may experience in this course. For some, these suggestions are irrelevant, but for many, a little careful thought now may enrich the 851 experience and save considerable future pain.

First of all, PLAN AHEAD! It seems obvious, but this subject matter takes time and repeated review to sink in to the point where it becomes useful. To be honest, I develop a new appreciation of this stuff each time I go through it. Read the assignments early and carefully, and give yourself time to digest the ideas. Similarly, start problem sets early. They are powerful teaching tools which cement your understanding by forcing you to use the course material in new ways. They are also a good part of your grade; if you view each problem set as a take-home test, for which there's no reason not to get 100%, then the concepts and tools taught here will become your friends.

Secondly, COMMUNICATE! If you're having trouble with a difficult or poorly explained concept, it's likely your neighbor is too. In class, you should tactfully stop me and ask that critical clarifying question right away--I don't want to waste anyone's time talking to lost faces. If a particular point gets out of hand, of course, I reserve the right to postpone that discussion until after the lecture. Outside class, find me, preferably during my scheduled office hours. Failing that, ask a classmate or more advanced student in your lab. Not only is it OK to study together, I encourage it. Putting new concepts into your own words in the process of discussing them with your colleagues always helps you to hammer out an understanding. Obviously, problem sets and take-home tests must be your own work, but even there, talking the problems over can help you to understand the chemistry.

Third, VISUALIZE! There is no substitute for the ability to mentally see the three-dimensional nature of molecules and the processes they undergo. An overwhelming amount of what we know about the subtleties of organic reactions comes from tracking stereochemistry, a fundamentally three-dimensional property of molecules. Yet we learn mostly from flat, two-dimensional representations-images from books, blackboards, slides, etc. Such pictures, even more than "methyl, ethyl, propyl, butyl..," are the language of organic chemistry, and it is essential early on to develop a "mind's eye" that can see the three-dimensional molecule that a two-dimensional drawing represents. As we mentally translate meaning (thoughts) into sounds (spoken words) without even noticing that we are doing so, so we need to train our hands to draw flat pictures even as we are thinking of three-dimensional objects. So build a model, look at it from all angles, noting symmetry, connectivity, stereochemical centers, etc. Then, without the model, envision the structure, the geometric relationships of its various parts, and practice (practice, practice) drawing it.

Fourth, LEARN TO COUNT! This may sound like an insult; it is not. It is simply essential that you know how many electrons there are around an atom in a given setting, and that you keep track of hydrogens and how many bonds are formed to a given center. This sounds trivial, yet simply obeying the rules of valence and conservation of charge and mass (i.e. atoms and electrons appearing/disappearing) would raise the average organic exam score by a substantial margin. Part of the difficulty arises from the convention of leaving out hydrogens in drawing organic structures, unless they are needed to indicate stereochemistry or participate in a reaction step. H atoms are then often forgotten completely and extra bonds sprout from a given carbon atom.... Don't laugh--we've all drawn these erroneous structures. The key is learning to check drawings reflexively to protect against such obscene blunders.

Finally, WELCOME TO CEM 851! I look forward to getting to know you all this spring.

Lecture Notes: TBA

Paper Project Listing: TBA


    Wenthold et al. "Transition State Spectroscopy of Cyclooctatetraene"

    Hoffmann and Hopf "Learning from Molecules in Distress"

    Factors affecting orbital interactions

    Remarks on symmetry and the Dn point groups

    BDEs and Heats of formation

    Measures of Aromaticity

    Pericyclic Reaction Glossary

    Pictures of MOs (HF/6-31G* level, computed with GAMESS and drawn with MacMolPlt
         H2O (linear)
         H2O (bent)
         1CH2 (bent)
         CH4 (square planar)
         CH4 (square pyramidal)

Homeworks: TBA

Exams: TBA

Links to the Scientific Literature

    Web of Science

    Scifinder Scholar (Chem. Abstracts)


    MSU Science Library (BPS) Chemistry E-resources

    MSU Science E-Journals by topic

Literature References:

    BDEs of Organic Molecules (Ellison, G. B.; Blanksby, S. J. Acc. Chem. Res. 2003, 36, 225-263.)

    Bent Bonds in Organic Compounds (Wiberg, K. B. Acc. Chem. Res. 1996, 29, 229-234.)

    Selected papers of K. B. Wiberg

Additional Resources:

    Organic Study Topic Summaries

    Interactive Study Problems

    IUPAC Symposium

    IUPAC Glossary of Physical Organic Chemistry terms

    NIST Webbook (thermochemical data)

    CCCBDB (Computational Chemistry Comparison and Benchmark DataBase)

    RFW Bader's Theory of Atoms in Molecules

    Integrated Spectral Data Base System for Organic Compounds

    UCLA WebSpectra: NMR and IR problems

    Chemistry 556, (Theoretical Chemistry), Prof. Ray Fort (U. of Maine)