Cover -- Title Page -- Contents -- Preface -- Acknowledgments -- Chapter 1 Quantum Mechanics for Organic Chemistry -- 1.1 Approximations to the Schrodinger Equation---The Hartree--Fock Method -- 1.1.1 Nonrelativistic Mechanics -- 1.1.2 The Born--Oppenheimer Approximation -- 1.1.3 The One-Electron Wavefunction and the Hartree--Fock Method -- 1.1.4 Linear Combination of Atomic Orbitals (LCAO) Approximation -- 1.1.5 Hartree--Fock--Roothaan Procedure -- 1.1.6 Restricted Versus Unrestricted Wavefunctions -- 1.1.7 The Variational Principle -- 1.1.8 Basis Sets -- 1.1.8.1 Basis Set Superposition Error -- 1.2 Electron Correlation---Post-Hartree--Fock Methods -- 1.2.1 Configuration Interaction (CI) -- 1.2.2 Size Consistency -- 1.2.3 Perturbation Theory -- 1.2.4 Coupled-Cluster Theory -- 1.2.5 Multiconfiguration SCF (MCSCF) Theory and Complete Active Space SCF (CASSCF) Theory -- 1.2.6 Composite Energy Methods -- 1.3 Density Functional Theory (DFT) -- 1.3.1 The Exchange-Correlation Functionals: Climbing Jacob's Ladder -- 1.3.1.1 Double Hybrid Functionals -- 1.3.2 Dispersion-Corrected DFT -- 1.3.3 Functional Selection -- 1.4 Computational Approaches to Solvation -- 1.4.1 Microsolvation -- 1.4.2 Implicit Solvent Models -- 1.4.3 Hybrid Solvation Models -- 1.5 Hybrid QM/MM Methods -- 1.5.1 Molecular Mechanics -- 1.5.2 QM/MM Theory -- 1.5.3 ONIOM -- 1.6 Potential Energy Surfaces -- 1.6.1 Geometry Optimization -- 1.7 Population Analysis -- 1.7.1 Orbital-Based Population Methods -- 1.7.2 Topological Electron Density Analysis -- 1.8 Interview: Stefan Grimme -- References -- Chapter 2 Computed Spectral Properties and Structure Identification -- 2.1 Computed Bond Lengths and Angles -- 2.2 IR Spectroscopy -- 2.3 Nuclear Magnetic Resonance -- 2.3.1 General Considerations -- 2.3.2 Scaling Chemical Shift Values.

2.3.3 Customized Density Functionals and Basis Sets -- 2.3.4 Methods for Structure Prediction -- 2.3.5 Statistical Approaches to Computed Chemical Shifts -- 2.3.6 Computed Coupling Constants -- 2.3.7 Case Studies -- 2.3.7.1 Hexacyclinol -- 2.3.7.2 Maitotoxin -- 2.3.7.3 Vannusal B -- 2.3.7.4 Conicasterol F -- 2.3.7.5 1-Adamantyl Cation -- 2.4 Optical Rotation, Optical Rotatory Dispersion, Electronic Circular Dichroism, and Vibrational Circular Dichroism -- 2.4.1 Case Studies -- 2.4.1.1 Solvent Effect -- 2.4.1.2 Chiral Solvent Imprinting -- 2.4.1.3 Plumericin and Prismatomerin -- 2.4.1.4 2,3-Hexadiene -- 2.4.1.5 Multilayered Paracyclophane -- 2.4.1.6 Optical Activity of an Octaphyrin -- 2.5 Interview: Jonathan Goodman -- References -- Chapter 3 Fundamentals of Organic Chemistry -- 3.1 Bond Dissociation Enthalpy -- 3.1.1 Case Study of BDE: Trends in the R--X BDE -- 3.2 Acidity -- 3.2.1 Case Studies of Acidity -- 3.2.1.1 Carbon Acidity of Strained Hydrocarbons -- 3.2.1.2 Origin of the Acidity of Carboxylic Acids -- 3.2.1.3 Acidity of the Amino Acids -- 3.3 Isomerism and Problems With DFT -- 3.3.1 Conformational Isomerism -- 3.3.2 Conformations of Amino Acids -- 3.3.3 Alkane Isomerism and DFT Errors -- 3.3.3.1 Chemical Consequences of Dispersion -- 3.4 Ring Strain Energy -- 3.4.1 RSE of Cyclopropane (28) and Cylcobutane (29) -- 3.5 Aromaticity -- 3.5.1 Aromatic Stabilization Energy (ASE) -- 3.5.2 Nucleus-Independent Chemical Shift (NICS) -- 3.5.3 Case Studies of Aromatic Compounds -- 3.5.3.1 [n]Annulenes -- 3.5.3.2 The Mills--Nixon Effect -- 3.5.3.3 Aromaticity Versus Strain -- 3.5.4 π--π Stacking -- 3.6 Interview: Professor Paul Von Rague Schleyer -- References -- Chapter 4 Pericyclic Reactions -- 4.1 The Diels--Alder Reaction -- 4.1.1 The Concerted Reaction of 1,3-Butadiene with Ethylene.

4.1.2 The Nonconcerted Reaction of 1,3-Butadiene with Ethylene -- 4.1.3 Kinetic Isotope Effects and the Nature of the Diels--Alder Transition State -- 4.1.4 Transition State Distortion Energy -- 4.2 The Cope Rearrangement -- 4.2.1 Theoretical Considerations -- 4.2.2 Computational Results -- 4.2.3 Chameleons and Centaurs -- 4.3 The Bergman Cyclization -- 4.3.1 Theoretical Considerations -- 4.3.2 Activation and Reaction Energies of the Parent Bergman Cyclization -- 4.3.3 The cd Criteria and Cyclic Enediynes -- 4.3.4 Myers--Saito and Schmittel Cyclization -- 4.4 Bispericyclic Reactions -- 4.5 Pseudopericyclic Reactions -- 4.6 Torquoselectivity -- 4.7 Interview: Professor Weston Thatcher Borden -- References -- Chapter 5 Diradicals and Carbenes -- 5.1 Methylene -- 5.1.1 Theoretical Considerations of Methylene -- 5.1.2 The H--C--H Angle in Triplet Methylene -- 5.1.3 The Methylene and Dichloromethylene Singlet--Triplet Energy Gap -- 5.2 Phenylnitrene and Phenylcarbene -- 5.2.1 The Low Lying States of Phenylnitrene and Phenylcarbene -- 5.2.2 Ring Expansion of Phenylnitrene and Phenylcarbene -- 5.2.3 Substituent Effects on the Rearrangement of Phenylnitrene -- 5.3 Tetramethyleneethane -- 5.3.1 Theoretical Considerations of Tetramethyleneethane -- 5.3.2 Is TME a Ground-State Singlet or Triplet? -- 5.4 Oxyallyl Diradical -- 5.5 Benzynes -- 5.5.1 Theoretical Considerations of Benzyne -- 5.5.2 Relative Energies of the Benzynes -- 5.5.3 Structure of m-Benzyne -- 5.5.4 The Singlet--Triplet Gap and Reactivity of the Benzynes -- 5.6 Tunneling of Carbenes -- 5.6.1 Tunneling control -- 5.7 Interview: Professor Henry ``Fritz'' Schaefer -- 5.8 Interview: Professor Peter R. Schreiner -- References -- Chapter 6 Organic Reactions of Anions -- 6.1 Substitution Reactions -- 6.1.1 The Gas Phase SN2 Reaction.

6.1.2 Effects of Solvent on SN2 Reactions -- 6.2 Asymmetric Induction Via 1,2-Addition to Carbonyl Compounds -- 6.3 Asymmetric Organocatalysis of Aldol Reactions -- 6.3.1 Mechanism of Amine-Catalyzed Intermolecular Aldol Reactions -- 6.3.2 Mechanism of Proline-Catalyzed Intramolecular Aldol Reactions -- 6.3.3 Comparison with the Mannich Reaction -- 6.3.4 Catalysis of the Aldol Reaction in Water -- 6.3.5 Another Organocatalysis Example---The Claisen Rearrangement -- 6.4 Interview: Professor Kendall N. Houk -- References -- Chapter 7 Solution-Phase Organic Chemistry -- 7.1 Aqueous Diels--Alder Reactions -- 7.2 Glucose -- 7.2.1 Models Compounds: Ethylene Glycol and Glycerol -- 7.2.1.1 Ethylene Glycol -- 7.2.1.2 Glycerol -- 7.2.2 Solvation Studies of Glucose -- 7.3 Nucleic Acids -- 7.3.1 Nucleic Acid Bases -- 7.3.1.1 Cytosine -- 7.3.1.2 Guanine -- 7.3.1.3 Adenine -- 7.3.1.4 Uracil and Thymine -- 7.3.2 Base Pairs -- 7.4 Amino Acids -- 7.5 Interview: Professor Christopher J. Cramer -- References -- Chapter 8 Organic Reaction Dynamics -- 8.1 A Brief Introduction To Molecular Dynamics Trajectory Computations -- 8.1.1 Integrating the Equations of Motion -- 8.1.2 Selecting the PES -- 8.1.3 Initial Conditions -- 8.2 Statistical Kinetic Theories -- 8.3 Examples of Organic Reactions With Non-Statistical Dynamics -- 8.3.1 [1,3]-Sigmatropic Rearrangement of Bicyclo[3.2.0]hex-2-ene -- 8.3.2 Life in the Caldera: Concerted versus Diradical Mechanisms -- 8.3.2.1 Rearrangement of Vinylcyclopropane to Cyclopentene -- 8.3.2.2 Bicyclo[3.1.0]hex-2-ene 20 -- 8.3.2.3 Cyclopropane Stereomutation -- 8.3.3 Entrance into Intermediates from Above -- 8.3.3.1 Deazetization of 2,3-Diazabicyclo[2.2.1]hept-2-ene 31 -- 8.3.4 Avoiding Local Minima -- 8.3.4.1 Methyl Loss from Acetone Radical Cation.

8.3.4.2 Cope Rearrangement of 1,2,6-Heptatriene -- 8.3.4.3 The SN2 Reaction: HO-+CH3F -- 8.3.4.4 Reaction of Fluoride with Methyl Hydroperoxide -- 8.3.5 Bifurcating Surfaces: One TS, Two Products -- 8.3.5.1 C2--C6 Enyne Allene Cyclization -- 8.3.5.2 Cycloadditions Involving Ketenes -- 8.3.5.3 Diels--Alder Reactions: Steps toward Predicting Dynamic Effects on Bifurcating Surfaces -- 8.3.6 Stepwise Reaction on a Concerted Surface -- 8.3.6.1 Rearrangement of Protonated Pinacolyl Alcohol -- 8.3.7 Roaming Mechanism -- 8.3.8 A Roundabout SN2 reaction -- 8.3.9 Hydroboration: Dynamical or Statistical? -- 8.3.10 A Look at the Wolff Rearrangement -- 8.4 Conclusions -- 8.5 Interview: Professor Daniel Singleton -- References -- Chapter 9 Computational Approaches to Understanding Enzymes -- 9.1 Models for Enzymatic Activity -- 9.2 Strategy for Computational Enzymology -- 9.2.1 High Level QM/MM Computations of Enzymes -- 9.2.2 Chorismate Mutase -- 9.2.3 Catechol-O-Methyltransferase (COMT) -- 9.3 De Novo Design of Enzymes -- References -- Index -- Supplemental Images.