Erich Hums, Consulting Environmental Catalysis, Erlangen, Germany, reviews the book Computational Organic Chemistry by Steven M. Bachrach, Trinity University, TX, USA.
The Rising Importance of Computational Chemistry
The second edition of Computational Organic Chemistry is a strategically well-placed addition to the library of computational quantum chemistry books keeping pace with technological process.
It cannot be denied that mathematics-based theories are an increasingly integral part of modern chemistry. The complex causality of experimental parameters often has to be studied by use of operators to simplify calculation processes. Within these models, results show high mathematical accuracy but with the drawback of an incomplete description of areas outside of these models. Apart from the narrow scope of interpretation, another problem is that results mostly lose criteria of evaluation if spanned aspects are not known so far. It is an eminently helpful approach to bridge this gap in knowledge by quantum mechanics (QM) computational chemistry. In contrast to extensive mathematical accuracy, quantum mechanic models are based on more qualitative or approximately quantitative computational schemes to analyze chemical systems in a more complete view.
Interplay between Calculation and Experiment
S. Grimme is one of the preeminent computational chemists and outlined his individual expectations in this book when interviewed by S. Bachrach: “I want to have methods that are as black box as possible, as robust as possible, that can be used for large systems. Large chemical systems are always my focus. I am not always looking for high accuracy methods; a little bit of empiricism is ok. But this kind of empiricism must be physically well-founded”.
From this point of view, computational quantum chemistry not only gives useful insight into complex problems but also stimulates further experimental approaches, and the computationally proposed causality of parameters can be verified and studied in detail. Almost identically, S. Bachrach wrote in the preface “in close interplay with experiment, computational chemistry can draw out important insights, help interpret results, and propose critical experiments to be carried out next”. In light of past experiences, there will be an ongoing interplay between results of quantum mechanical models and experimental data.
New in the Second Edition
In the second updated edition, including two new chapters, the reader will find an extensive collection of cited papers as reference to each chapter. This allows to use the book as an introduction, directing the reader to important primary literature. It is also the objective of the author to include links to web sites and blogs, allowing the work to be perpetually updated and finally part of an increasingly large community interested in a dialog with others.
Quantum Mechanics for Organic Chemistry
In view of the fact that the Schrödinger equation generally cannot be solved exactly, Quantum Mechanics for Organic Chemistry (Chapter 1) brings the reader up to date on a number of approximations to make the mathematics tractable. The presented computational methods are focused on structures, properties, and reactions of organic molecules – highlighting successes but emphasizing the potential of pitfalls to the reader as well. The subchapters addressed to QM/MM (quantum mechanics/molecular mechanics) computations and the topology of potential energy surfaces demonstrate the chemical relevance. The functionals used within density functional theory (DFT) are extensively discussed, including the consequences of a chosen functional failing. The list of functionals that have been developed and utilized is extremely comprehensive and growing. Double hybrid functionals are introduced, which exhibit significantly lower deviations compared to standard DFT.
Computed Spectral Properties and Structure Identification (Chapter 2) consists of a number of case studies. The results of computed and experimental spectral properties are compared with a focus on NMR, IR and Raman spectra, examining physical characteristics.
Some Fundamentals of Organic Chemistry are discussed in Chapter 3 in terms of functional group transformations and reaction mechanisms to design complex syntheses. Bond dissociation enthalpy, acidity, and aromaticity are examined based on case studies. These studies also include some new examples, such as π-stacking of aromatic rings and discussing the ring strain energy of cyclic compounds. Special attention is given to the discussion about isomerism and difficulties in understanding organic structures when DFT is used.
Organic Reactions
Pericyclic Reactions (Chapter 4) highlights a few reactions to show that computational chemistry has served to broaden insights into pericyclic reactions, and includes some studies that show the limitations of computational methods currently in use. In this context, it is of interest to read the comments of W. Th. Borden interviewed by S. Bachrach: “Functionals that work well for most problems can unexpectedly fail. The same is, of course, also true for ab initio methods.” Although the concept of conservation of orbital symmetry as developed by Woodward and Hoffmann is not the focus of discussion, Borden mentioned “Roald’s early papers, which relied exclusively on Extended Hückel theory, taught me that critical interpretation of calculations is even more important than their numerical accuracy”.
Diradicals and Carbenes in Chapter 5 is one of the major additions to the book. It guides the reader to understand properties, structure, and chemistry of these intermediates and to participate in the debate resolving the controversies and discrepancies that arose in trying to understand these unusual species. Part of the chapter is concerned with the tunnelling phenomenon in carbenes. Understanding that tunnelling occurs in some carbenes was made possible by quantum computations and this led directly to the brand new concept of controlling tunnelling phenomena.
The chemistry of Organic Reactions of Anions is the topic of Chapter 6. This chapter is an updated version of the first edition incorporating new examples, such as proline and proline-related molecules, primarily in the area of organo-catalysis.
Chapter 7, entitled Solution-Phase Organic Chemistry, is updated and includes some new examples to discuss solvent effects on equilibria and kinetics. This chapter presents case studies of aqueous-phase chemistry analyzed using quantum mechanical computations. Microsolvation and the change in charge distribution manifested by solvent effects will be a challenging area to be studied in detail in the near future.
The revised and updated Chapter 8, Organic Reaction Dynamics, includes some new types of dynamic effects and discusses the roundabout pathway in SN2 reactions, as well as the roaming mechanism.
Enzymes
A small but interesting supplementation to the second edition is Chapter 9 devoted to Computational Approaches to Understanding Enzymes. This chapter extends the coverage of quantum chemistry towards biochemistry. Since computational biochemistry truly deserves its own entire book, this chapter presents a glimpse of computational quantum chemistry techniques applied to biochemical systems. It presents a few examples of QM/MM calculations on enzymes and enzyme catalysis.
This chapter also includes a discussion of the de-novo design of enzymes, which is a research area that is just becoming feasible and one that will surely continue to develop and excite a growing number of chemists involved in biochemical research.
Conclusion
The second edition of Computational Organic Chemistry is not only a useful extended compendium but also worth reading because the author presents the use of computational chemistry as tool to enrich technological process both in theoretical and experimental studies. It should be kept in mind that quantum mechanical calculations and the interpretation of laboratory experiments are both based on models.
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Computational Organic Chemistry, 2nd Edition, |
