Time-dependent quantum mechanics shows how mixing orbitals of different energy causes electrons to vibrate. Mixing 1s with 2p causes a vibration that can absorb or generate light, while mixing 1s with 2s causes "breathing" that does not interact with light. Many natural organic chromophores involve mixing an unshared electron pair with a vacant pi orbital, whose conjugation determines color. Infrared spectra reveal atomic vibration frequencies, which are related by Hooke’s law to bond strengths and "reduced" masses. Infrared spectra are complicated by the coupling of local oscillators of similar frequency to give "normal" modes. Alkane chains possess characteristic stretching and bending modes, with descriptive names, that may, or may not, absorb infrared light.

1. Mechanism: How Energies and Kinetic Order Influence Reaction Rates
2. Peculiar Rate Laws, Bond Dissociation Energies, and Relative Reactivities
3. Rate and Selectivity in Radical-Chain Reactions
4. Electronegativity, Bond Strength, Electrostatics, and Non-Bonded Interactions
5. Solvation, H-Bonding, and Ionophores
6. Brønsted Acidity and the Generality of Nucleophilic Substitution
7. Nucleophilic Substitution Tools - Stereochemistry, Rate Law, Substrate, Nucleophile, Leaving Group
8. Solvent, Leaving Group, Bridgehead Substitution, and Pentavalent Carbon
9. Pentavalent Carbon? E2, SN1, E1
10. Cation Intermediates - Alkenes: Formation, Addition, and Stability
11. Carbocations and the Mechanism of Electrophilic Addition to Alkenes and Alkynes
12. Nucleophilic Participation During Electrophilic Addition to Alkenes: Halogen, Carbene, and Borane
13. Addition to Form Three-Membered Rings: Carbenoids and Epoxidation
14. Epoxide Opening, Dipolar Cycloaddition, and Ozonolysis
15. Metals and Catalysis in Alkene Oxidation, Hydrogenation, Metathesis, and Polymerization
16. Isoprenoids, Rubber, and Tuning Polymer Properties
17. Alkynes; Conjugation in Allylic Intermediates and Dienes
18. Linear and Cyclic Conjugation Theory; 4n+2 Aromaticity
19. Aromatic Transition States: Cycloaddition and Electrocyclic Reactions
20. Electronic and Vibrational Spectroscopy
21. Functional Groups and Fingerprints in IR Spectroscopy; Precession of Magnetic Nuclei
22. Medical MRI and Chemical NMR
23. Diamagnetic Anisotropy and Spin-Spin Splitting
24. Higher-Order Effects, Dynamics, and the NMR Time Scale
25. C-13 and 2D NMR - Electrophilic Aromatic Substitution
26. Aromatic Substitution in Synthesis: Friedel-Crafts and Moses Gomberg
27. Triphenylmethyl and an Introduction to Carbonyl Chemistry
28. Mechanism and Equilibrium of Carbonyl Reactions
29. Imines and Enamines; Oxidation and Reduction
30. Oxidation States and Mechanisms
31. Periodate Cleavage, Retrosynthesis, and Green Chemistry
32. Measuring Bond Energies: Guest Lecture by Prof. G. Barney Ellison
33. Green Chemistry; Acids and Acid Derivatives
34. Acids and Acid Derivatives
35. Acyl Insertions and a-Reactivity
36. α-Reactivity and Condensation Reactions
37. Proving the Configuration of Glucose and Synthesizing Two Unnatural Products
38. Review: Synthesis of Cortisone

This is a continuation of Freshman Organic Chemistry I (CHEM 125a), the introductory course on current theories of structure and mechanism in organic chemistry for students with excellent preparation in chemistry and physics. This semester treats simple and complex reaction mechanisms, spectroscopy, organic synthesis, and some molecules of nature.