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


Required Texts:

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

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


Additional Useful References, Not Required:

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

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

Smith, M. B.; March, J. March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th Edition. Wiley, 2000.

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:


My Expectations:

A working knowledge of undergraduate Organic Chemistry is expected.

This class is not about memorization. It is about developing analytical thinking.

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):



I. Point Group Symmetry

symmetry elements, operations, and point groups


symmetry as mechanistic tool

symmetry and efficiency

II. Intro to Arrow-Pushing

intro to reactive intermediates

arrow-pushing strategies

III. Kinetics and Thermodynamics

types of energy

potential energy surfaces

kinetic equations

rate theory

kinetic vs. thermodynamic control


linear free energy relationships

isotope effects


IV. Molecular Orbital Theory

what does the Schrodinger equation mean?

simple Huckel theory

frontier orbital concepts (FMO)

computational chemistry

geometric effects


pericyclic reactions

V. Noncovalent Interactions and Supramolecular Chemistry

types of interaction

interactions in transition states

"supramolecular chemistry" as an independent field

preorganization and templating for synthesis


incarceration and mechanical forces

devices and machines


VI. Conformational Analysis

sterics, electronics, noncovalent interactions


orbital (anomeric) effects

polar effects (H-bonding, solvent effects)

typical rotational isomerization barriers

transition state effects - models for selectivity in organic reactions

VII. Catalysis


specific oriented noncovalent interactions

covalent catalysis

organometallics and surfaces

VIII. Reactive Intermediates: Structures and Reactivity

acidity and basicity

overview of types of reactive intermediates

techniques for generation and characterization



carbenes and other diradicals


radical ions

other weird wild stuff