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.

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


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.

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

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 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):

I. Point Group Symmetry

symmetry elements, operations, and point groups

chirality and topicity

symmetry as mechanistic tool

symmetry and efficiency

II. Intro to Arrow-Pushing

conventions, drawing

arrow-pushing strategies

typical reactivity patterns for various reactive intermediates

III. Kinetics and Thermodynamics

types of energy

potential energy surfaces

intro to chemical kinetics

rate theory

kinetic vs. thermodynamic control

dynamics and tunneling

Hammond postulate and Curtin-Hammett principle

linear free energy relationships

isotope effects

solvent effects

IV. Molecular Orbital Theory

what does the Schrodinger equation mean?

simple Huckel theory: doing quantum mechanics by hand!

frontier orbital concepts (FMO)

computational chemistry


pericyclic reactions

V. Noncovalent Interactions and Supramolecular Chemistry

types of noncovalent interactions

"supramolecular chemistry" as an independent field

preorganization and templating

incarceration and mechanical forces

devices, sensors and machines

interactions in transition states: catalysis

VI. Conformational Analysis

sterics, strain, electronics, noncovalent interactions

orbital (e.g. anomeric) effects

polar effects (H-bonding, solvent effects)

transition state effects - models for selectivity in organic reactions

VII. Reactive Intermediates and Reactivity Redux

acidity, basicity, philicity

mechanistic probes

carbanions, carbocations, carbenes and other diradicals, radicals, radical ions

other weird wild stuff