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 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:
http://evans.harvard.edu/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):
Intro
mechanisms
I. Point Group Symmetry
symmetry elements, operations, and point groups
chirality
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
dynamics
linear free energy relationships
isotope effects
tunneling
IV. Molecular Orbital Theory
what does the Schrodinger equation mean?
simple Huckel theory
frontier orbital concepts (FMO)
computational chemistry
geometric effects
aromaticity
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
sensors
incarceration and mechanical forces
devices and machines
zeolites
VI. Conformational Analysis
sterics, electronics, noncovalent interactions
strain
orbital (anomeric) effects
polar effects (H-bonding, solvent effects)
typical rotational isomerization barriers
transition state effects - models for selectivity in organic reactions
VII. Catalysis
kinetics
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
carbanions
carbocations
carbenes and other diradicals
radicals
radical ions
other weird wild stuff
