Physical Organic Chemistry

Chemistry 641 is a one-semester course on physical-organic chemistry. Professor Zimmerman will cover the first half and Professor Steven F. Nelsen will cover the second half.

Textbook: "Perspectives on Structure and Mechanism in Organic Chemistry," Felix A. Carroll  (Brooks/Cole publisher)             

Recommended Texts for Reference
   1. J. March `Advanced Organic Chemistry`, 3rd Edition, Wiley
   2. H. E. Zimmerman `Quantum Mechanics for Organic Chemists`, Academic Press
   3. K. Wiberg, `Physical Organic Chemistry`, Wiley
   4. A. Frost and R. Pearson `Kinetics and Mechanism`, Wiley
   5. J. Hine `Physical Organic Chemistry`, McGraw-Hill
   6. B. Carpenter `Determination of Organic Reaction Mechanisms`, Wiley
   7. T. Lowry and K. Richardson, `Mechanism and Theory in Organic Chemistry, 3rd Ed, Harper and Row
   8. "Exploring Chemistry with Electronic Structure Methods", J. B. Foresman and A. Frisch.

A. Molecular Structure and Reactivity - The Basis of Organic Behavior, Chapters 1 and 4.
      1. Lewis Structures
      2. Basis Orbitals and MOs (Atomic orbital, hybrids)
      3. Hybridization and Interorbital Angles
      4. Correct form for hybrids
      5. NMR C13-H coupling and hybridization
      6. Streitwieser determination of C_H acidity & NMR correlation & thus with hybridization.
      7. Sigma and Pi Molecular Orbitals
      8. Equivalent Orbital Formulation (note identity of sigma-pi & bent bond Formalism (compare with pg 51 of text). i.e. p+sp² = two sp⁵'s
      9. Examples of ethylene, cyclopropane. "Banana bonds" from sp² hybridization; Walsh and Coulson models.
     10. The Thorpe-Ingold Effect. An example of a real effect but faulty evidence. Valence bond A-B controlled quantitatively by Bond C-D at carbon.
     11. Valence bond and MO wavefunctions compared. Antisymmetrization. Slater Determinant functions.
     12. LCAO MO Assumption LCAO MO's for basic organic molecules. The Frost-Musulin and the corresponding Wisconsin Mnemonics.
     13. Topological MO's and Energies. Methods of getting 1-electron MO's.
             a. Secular determinants and the use of molecular symmetry (informal group theory.
             b. LCAO MO coefficients.
             c. Alternants, Non-Alternants and properties.
             d. The special case of NBMOs & the Dewar,Longuet-Higgis,Coulson ideas
             e. Extended H\Uckel computations of Hofmann.
     14. Diradicals - Singlet, Triplet.
     15. Concept of Aromaticity
     16. Molecular Mechanics Generation of Approximate Geometries
     17. Semi-empirical and Ab Initio Methods (MNDO, AM1, Gamess, Gaussian; RHF, UHF, ROHF, SCF-CI, CASSCF (MCSCF).

B. Pericyclic Reactions.; Chapter 11.
        1. The Emmanuel Vogel Cyclobutene stereochemical observation.
        2. 1,6-, and 1,8-Disubstituted cyclooctatrienes.
        3. Electrocyclic Transformations in general and Woodward-Hoffmann's rules.
        4. Torquoselectivity (Baldwin, Houk).
        5. Homo, Lumo rationale; the Non-Crossing Rule and Symmetry Control
        6. MO Correlation Diagrams: Woodward-Hofmann & Longuet-Higgins,
        7. State correlations. Adiabatic and Non-adiabatic transformations.
        8. Sigmatropic reactions.
        9. The Möbius-Hückel Concept and simplification of the above.
       10. Concepts of Electron Pushing and MO Following.

C. Some Fundamental Concepts in Physical-Organic Chemistry.` Chapters 2, 3
        1. Some topics in Stereochemistry. Stereochemical terminology.
        2. Conformational Analysis.
        3. Molecular Mechanics.
        4. Free Energy
        5. Linear Free Energy Relationships; the Hammett Equation
        6. Sigma, Rho versus Structure and Mechanism; Prediction of Rho Constants
        7. Linear Free Energy Ideas Applied to Aliphatic systems
        8. The Isokinetic Temperature
        9. Bond Energies, Bond Dissociation Energies, Koopmans Theorum
       10. Strain in Organic Systems. I-strain, A(1,3) Strain, Etc.
       11. Van der Waals Effects
       12. Kinetic Versus Thermodynamic Control of Reactions
       13. Kinetics in Determining Mechanism. Some kinetic expressions
       14. The Arrhenius Equation (Energy & Preexponential A vs Free Energy and the Eyring Counterpart)
       15. Determination of Activation Energies
       16. Kinetic Order in Determining Mechanism. Zero order, 1st Order, 2nd Order Reactions. Pre-equilibria.
       17. The Steady-State (Stationary State) Approximation
       18. Diffusion Controlled Reactions
       19. State Hypersurfaces, Zero-point energies, Reaction Coordinates
       20. The Hammond Postulate
       21. Isotope Effects (Primary and Secondary)
       22. Determination of Excited State Rates
       23. Kinetic Protonation of Delocalized Carbanions and Enolates

D. Organic Reactions, Reaction Mechanisms and Molecular Rearrangements. Chapter 6.
        1. Techniques for determining mechanisms.
             a. Identification of products and consideration of alternative routes.
             b. Identification of intermediates
             c. Classical crossover experiments
             d. Crossover with labeled additives
             e. Isotopic labeling and determination of isotope location in product
             f. The effect of substituents (e.g. Hammett sigma-rho)
             g. Stereochemical tests
             h. Isotope effects - Primary and Secondary
             h. Selectivity - isotope tests
             i. Kinetics
             j. Determination of activation energies
   2. Rearrangments.
             a. 1,2 Migrations in Cations, Phenonium Ions, MO Control
             b. 1,2 Migrations in Radicals, Counterpart Phenyl-bridged Intermediates
             c. Carbanions, Phenanions, MO forbiddeness for Alkyls
             d. 1,2-Migrations in Excited States - Singlets, Triplets
             e. Substituent Effects in Rearrangements
             f. Memory Effects & Trajectory Analysis
             g. Cyclopropylcarbinyl, Cyclobutyl, Allylcarbinyl Cations -
             h. 7-Norbornyl and I-Steroid Rearrangements
             i. Norbornyl and the "Windshield Wiper Mechanism"
             j. Migrations to Carbonyl groups
             k. Migration to Electron Deficient Oxygen and Nitrogen
             l. Baeyer-Villiger, Beckmann, Second Order Beckmann, Curtius
             m. Carbene Rearrangements
             n. The Wittig Rearrangement as a Carbanion Process

E. Excited State Reactions and Reactivity (Chapter 12)
         1. Excited State Descriptions
         2. Prediction of Excited State Reactivity
         3. Photophysical Phenomena
         4. Meta Transmission in Excited States
         5. The "Type A" Rearrangement of Cyclohexadienones as Santonin
         6. The "Type B" Rearrangement of Cyclohexenones, Migratory Aptitudes
         7. The "Type B" Rearrangement of Bicyclo[3.1.0]hexenones
         7. The Norrish Type I and the Norrish Type II Reactions
         8. Photochemistry Without Light

Homework Problems: Problem Sets will be assigned and due as announced. Approximately 10% of the course grade will be based on Problem Set Performance.

Exams: Two exams will be given in this half of the semester. The exams will be scheduled on Thursdays on dates selected to minimize conflicts with TA duties and Cumulative Exams.