This course will examine the tools - both theoretical and experimental - that the modern organic chemist has at his or her disposal for elucidating mechanisms.


Strongly Recommended Text:

Anslyn, E. V.; Dougherty, D. A. Modern Physical Organic Chemistry. University Science Books, 2006.


Additional Useful References, Not Required:

• Grossman, R. B. The Art of Writing Reasonable Organic Reaction Mechanisms, Springer, 2002 (hardback) and 2010 (paperback).

• Fleming, I. Molecular Orbitals and Organic Chemical Reactions. Wiley, 2010 (both a reference edition and student edition are available)

• Alabugin, I. Stereoelectronic Effects: A Bridge Between Structure and Reactivity. Wiley, 2016.

• Sundberg, R. J.; Carey, F. A. Advanced Organic Chemistry, Part A: Structure and Mechanism, 4th Edition. Kluwer/Plenum Press, 2000.

• Gómez-Gallego, M.; Sierra, M. A. Organic Reaction Mechanisms–40 Solved Cases. Springer, 2004.

• Isaacs, N. Physical Organic Chemistry, 2nd Edition, Addison-Wesley-Longman, 1995

• Fleming, I. Frontier Orbitals and Organic Chemical Reactions. Wiley, 1996.

• Carpenter, B. K. Determination of Organic Reaction Mechanisms. Wiley, 1994.

• Smith, M. B.; March, J. March’s Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 6th Edition. Wiley, 2007.

• Lowry, T. H.; Richardson, K. S. Mechanism and Theory in Organic Chemistry, 3rd Edition. Harper Collins, 1987.

• Quinkert, G.; Egert, E.; Griesinger, C. Aspects of Organic Chemistry: Structure. VCH, 1996.

• Moss, R. A.; Platz, M. S.; Jones, M. Reactive Intermediate Chemistry. Wiley, 2004.

• Eliel, E. L.; Wilen, S. H. Stereochemistry of Organic Compounds. Wiley, 1994.

• Young, D. Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems.Wiley, 2001.


A Great Source of Practice Problems:


The IUPAC Glossary of Terms Used in Physical Organic Chemistry:


My Expectations:

A working knowledge of undergraduate Organic Chemistry is expected.

This class is not about memorization. It is about developing analytical thinking and problem solving skills.

By the end of the quarter, I expect the following:

When given an experimental observation on a particular reaction, you should be able to:

(1) write down a reasonable arrow-pushing mechanism for the reaction

(2) decide whether existing theories can explain the observed reactivity

(3) design experiments to test your proposed mechanism/explanation

(4) evaluate the validity/plausibility of others' explanations


Outline (subject to change):



1. Introduction to arrows

2. Lightning fast survey of organic reactivity (10.1)

• carbanions
• carbocations
• carbenes
• radicals

3. Strategies and “rules” for arrow-pushing



1. Energy

• types: E, H, G, S

2. What do you mean by stability?

• kinetic v. thermodynamic
• isodesmic equations

3. Potential energy surfaces

• what the axes mean
• problems with “rate-determining” and “selectivity-determining”
• Curtin-Hammett principle
• Hammond postulate and Bell-Evans/Polanyi principle
• concertedness and synchronicity; Moore-O’Ferral/Jencks plots

4. Transition state theory

5. Dynamic effects

• dynamic matching
• rate enhancement; A --> B
• selectivity control; A --> B --> C or D
• post-transition state bifurcations: A --> C or D

6. Multiple possible reasonable mechanistic proposals

• norbornyl cation dimethylcyclopentenyl cation



1. Point Group Symmetry

• symmetry elements and operations, point groups
• chirality and topicity
• symmetry as a mechanistic tool
• musings on symmetry and efficiency

2. Introduction to chemical kinetics

3. Solvent effects

4. Kinetic isotope effects

• primary
• secondary normal and inverse
• tunneling

5. Linear Free Energy Relationships (Hammett plots)



1. What does the Schrodinger equation mean?

2. Simple Huckel theory, i.e., doing quantum mechanics by hand

3. Frontier MO theory, i.e., donor-acceptor interactions

4. Aromaticity

5. Pericyclic reactions