Syllabus
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 Text:
Anslyn, E. V.; Dougherty, D. A. Modern Physical Organic Chemistry. University Science Books, 2006.
Additional Useful References, Not Required:
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.
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:
http://evans.harvard.edu/problems/
The IUPAC Glossary of Terms Used in Physical Organic Chemistry:
http://www.chem.qmw.ac.uk/iupac/gtpoc/
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
aromaticity
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
