In this and the next post I discuss some of the new materials in the Second Edition of my book Computational Organic Chemistry. Every chapter has been updated, meaning that the topics from the First Edition that remain in this Second Edition (and that’s most of them) have been updated with any new relevant work that have appeared since 2007, when the First Edition was published. What I present in this and the next post are those sections or chapters that are entirely new. This post covers chapters 1-4 and the next post covers chapters 5-9.
Chapter 1: Quantum Mechanics for Organic Chemistry
The section on Density Functional Theory has been expanded and updated to include
- a presentation of Jacob’s ladder, Perdew’s organizational model of the hierarchy of density
- a discussion of dispersion corrections, principally Grimme’s “-D” and “-D3” corrections
- a discussion of Grimme’s double hybrid functions and Martin’s DSD-DFT method (dispersion corrected, spin-component scaled double hybrid)
- and a brief discussion of functional selection
The discussion of basis set superposition error (BSSE) is expanded and includes intramolecular BSSE. A new section has been added to discuss QM/MM methods including ONIOM. The discussion of potential energy surfaces is expanded, including presentation of more complicated surfaces that including valley-ridge inflection (VRI) points. Lastly, the chapter concludes with an interview of Prof. Stefan Grimme.
Chapter 2. Computed Spectral Properties and Structure Identification
This is essentially a brand new chapter dealing with how computed spectral properties have been used in structural identification. The chapter begins with a presentation of computed structural features (bond lengths and angles) and how they compare with experiment. Next, I present some studies of computer IR spectra and their use in structure identification. The bulk of this chapter deals with NMR. I present methods for computing NMR with scaling techniques. The statistical methods of Goodman (CP1 and DP4) are described in the context of discriminating stereoisomers. The section ends with five case studies where computed NMR spectra were used to identify chemical structure. Next, computed optical activity including ORD and ECD and VCD used for structure determination are described through 6 case studies. This chapter ends with an interview of Prof. Jonathan Goodman.
Chapter 3. Fundamentals of Organic Chemistry
The main addition to this chapter is an extensive discussion of alkane isomerism, and the surprising failure of many standard density functionals (including B3LYP) to properly account for isomer energies. The work in this area led to the recognition of the importance of dispersion and medium-range correlation, and the development of new functionals and dispersion corrections. Other new sections include a case study of the acidity of amino acids (especially cysteine and tyrosine where the most acidic proton in the gas phase is not the carboxylic acid proton), and two added studies of aromaticity: (a) the competition between aromaticity and strain and (b) π-π stacking.
Chapter 4. Pericyclic Reactions
The chapter is updated from the first addition with two major additions. First, a section on bispericyclic reactions is added. This type of reaction is important in the context of a number of reactions that display dynamic effects (see Chapter 8). Second, the notion of transition state distortion energy as guiding reaction selectivity is described.
The highlights of the new materials in Chapters 5-9 will appear in the next blog post.