This blog serves as the companion to my book Computational Organic Chemistry published by John Wiley.

The book provides a survey of examples where computational chemistry served to explicate problems in organic chemistry. The Table of Contents is:

• Chapter 1. Quantum Mechanics for Organic Chemistry
  • 1.1 Approximations to the Schrödinger Equation – the Hartree Fock Method
    • 1.1.1 Non-Relativistic 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 vs. Unrestricted Wavefunctions
    • 1.1.7 The Variational Principle
    • 1.1.8 Basis Sets
  • 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 Multi-Configuration 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
  • 1.4 Geometry Optimization
  • 1.5 Population Analysis
    • 1.5.1 Orbital-based Population Methods
    • 1.5.2 Topological Electron Density Analysis
  • 1.6 Computed Spectral Properties
    • 1.6.1 IR spectroscopy
    • 1.6.2 Nuclear Magnetic Resonance
    • 1.6.3 Optical Rotation and Optical Rotatory Dispersion
  • 1.7 References
• Chapter 2. Fundamentals of Organic Chemistry
  • 2.1 Bond Dissociation Enthalpy
    • 2.1.1 Case Studies of BDE
  • 2.2 Acidity
    • 2.2.1 Case Studies of Acidity
  • 2.3 Ring Strain Energy
    • 2.3.1 RSE of Cyclopropane and Cylcobutane
  • 2.4 Aromaticity
    • 2.4.1 Aromatic Stabilization Energy (ASE)
    • 2.4.2 Nucleus-Independent Chemical Shift (NICS)
    • 2.4.3 Case Studies of Aromatic Compounds
  • 2.5 Interview: Professor Paul von Ragué Schleyer
  • 2.6 References
• Chapter 3. Pericyclic Reactions
  • 3.1 The Diels-Alder Reaction
    • 3.1.1 The Concerted Reaction of 1,3-Butadiene with Ethylene
    • 3.1.2 The Non-Concerted Reaction of 1,3-Butadiene with Ethylene
    • 3.1.3 Kinetic Isotope Effects and the Nature of the Diels-Alder Transition State
  • 3.2 The Cope Rearrangement
    • 3.2.1 Theoretical Considerations
    • 3.2.2 Computational Results
    • 3.2.3 Chameleons and Centaurs
  • 3.3 The Bergman Cyclization
    • 3.3.1 Theoretical Considerations
    • 3.3.2 Activation and Reaction Energies of the Parent Bergman Cyclization
    • 3.3.3 The cd Criteria and Cyclic Enediynes
    • 3.3.4 Mayers-Saito and Schmittel Cyclization
  • 3.4 Pseudopericyclic Reactions
  • 3.5 Torquoselectivity
  • 3.6 Interview: Professor Weston Thatcher Borden
  • 3.7 References
• Chapter 4. Diradicals and Carbenes
  • 4.1 Methylene
    • 4.1.1 Theoretical Considerations of Methylene
    • 4.1.2 The H-C-H Angle in Triplet Methylene
    • 4.1.3 The Methylene Singlet-Triplet Energy Gap
  • 4.2 Phenylnitrene and Phenylcarbene
    • 4.2.1 The Low-Lying States of Phenylnitrene and Phenylcarbene
    • 4.2.2 Ring Expansion of Phenylnitrene and Phenylcarbene
    • 4.2.3 Substituent Effects on the Rearrangement of Phenylnitrene
  • 4.3 Tetramethyleneethane
    • 4.3.1 Theoretical Considerations of Tetramethyleneethane
    • 4.3.2 Is TME a Ground-State Singlet or Triplet?
  • 4.4 Benzynes
    • 4.4.1 Theoretical Considerations of Benzyne
    • 4.4.2 Relative Energies of the Benzynes
    • 4.4.3 Structure of m-Benzyne
    • 4.4.4 The Singlet-Triplet Gap and Reactivity of the Benzynes
  • 4.5 Intramolecular Addition of Radicals to C-C Double Bonds
    • 4.5.1 Cyclization of Acyl-substituted Hexenyl Radicals
    • 4.5.2 Cyclization of 1,3-Hexadiene-5-yn 1-yl Radical
  • 4.6 Interview: Professor Henry “Fritz” Schaefer
  • 4.7 References
• Chapter 5. Organic Reactions of Anions
  • 5.1 Substitution Reactions
    • 5.1.1 The Gas Phase S_N2 Reaction
    • 5.1.2 Nucleophilic Substitution at Heteroatoms
    • 5.1.3 Solvent Effects on S_N2 Reactions
  • 5.2 Asymmetric Induction via 1,2-Addition to Carbonyl Compounds
  • 5.3 Asymmetric Organocatalysis of Aldol Reactions
    • 5.3.1 Mechanism of Amine-Catalyzed Intermolecular Aldol Reactions
    • 5.3.2 Mechanism of Proline-Catalyzed Intramolecular Aldol Reactions
    • 5.3.3 Comparison with the Mannich Reaction
    • 5.3.4 Catalysis of the Aldol Reaction in Water
  • 5.4 Interview – Professor Kendall N. Houk
  • 5.5 References
• Chapter 6. Solution-Phase Organic Chemistry
  • 6.1 Computational Approaches to Solvation
    • 6.1.1 Microsolvation
    • 6.1.2 Implicit Solvent Models
    • 6.1.3 Hybrid Solvation Models
  • 6.2 Aqueous Diels-Alder Reactions
  • 6.3 Glucose
    • 6.3.1 Models Compounds: Ethylene Glycol and Glycerol
    • 6.3.2 Solvation Studies of Glucose
  • 6.4 Nucleic Acids
    • 6.4.1 Nucleic Acid Bases
    • 6.4.2 Base Pairs
  • 6.5 Interview: Professor Christopher J. Cramer
  • 6.6 References
• Chapter 7. Organic Reaction Dynamics
  • 7.1 A Brief Introduction to Molecular Dynamics Trajectory Computations
    • 7.1.1 Integrating the Equations of Motion
    • 7.1.2 Selecting the PES
    • 7.1.3 Initial Conditions
  • 7.2 Statistical Kinetic Theories
  • 7.3 Examples of Organic Reactions with Non-statistical Dynamics
    • 7.3.1 [1,3]-Sigmatropic rearrangement of bicyclo[3.2.0]hex-2-ene
    • 7.3.2 Life in the Caldera: Concerted vs. Diradical Mechanisms
    • 7.3.3 Entrance into Intermediates from Above
    • 7.3.4 Avoiding Local Minima
    • 7.3.5 Crossing Ridges: One TS, Two Products
    • 7.3.6 Stepwise Reaction on a Concerted Surface
  • 7.4 Conclusions
  • 7.5 Interview: Professor Daniel Singleton
  • 7.6 References

Any book that hopes to capture the status of a dynamic field like computational chemistry is destined to become out-of-date. Even between the time the manuscript was completed and when the book was printed and distributed, research continued on, and the book is by definition incomplete. This blog serves as a mechanism to update the book, providing brief posts commenting on recent articles that touch on or expand upon the subjects discussed in the printed book.

The book’s auxiliary web site and this blog extend the printed version into Web 2.0 space. On the auxiliary site, I have included all of the citations with links (using the DOI) to the cited articles, where electronic versions of those articles exist. Please keep in mind that most of these articles are not open-access and it is up to the reader to secure proper access rights to these articles. Also, all figures of 3-D molecules are reproduced in color along with their 3-D coordinates (as xyz files). These coordinates can be downloaded into your favorite molecular visualization tool for maniupluation and re-use.

I have included the InChI (unofficial InChI FAQ) for all of the molecules discussed in the blog. A special feature of the blog is the ability to view 3-D molecules directly within the blog page itself. All figures of 3-D molecules that have a border are actually links to the 3-D coordinates that will automatically load up into a Jmol applet, allowing you to manipulate the structure on-screen, in real time, within the blog window. Simply click on the figure to get this to work! (My thanks to Dan at the OpenScience Project for instructions on embedding Jmol into WordPress.)

In addition, the blog provides an avenue for feedback from the readers. I welcome readers to comment on the book and the blog posts. I am particularly interested in correcting any errors that may be present in the book (or the blog).

Note added 5/21/2009 regarding the relocation of the site: I decided to move the location of the blog and auxiliary web site off of the Trinity University campus. This actually gives me more flexibility in designing and maintaing the site. It also allows for a greater continuity of purpose into the future. Some have wondered about the decision to move to a “.com” site. I have no plans to commercialize the site, but since the site is both promoting the book (a commercial product) and a framework to keep the book updated, I thought it would be consistent to have the site within the “.com” domain space. The other issue that may now be more of a concern is the status of comments in the blog. I consider the comments to be under the same license as the blog, which is the Creative Commons Attribution-No Derivative Works 3.0 Unported License.

Steven Bachrach
Trinity University