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  Home > JCE Print > Journal of Chemical Education > Issues > 2004  > November  >
Chemical Education Today
Book and Media Reviews
Molecular Modelling for Beginners (Alan Hinchliffe)
Wiley, Chichester, West Sussex, England, 2003. 428 pp. ISBN 0470843098 (cloth), $90; ISBN 0470843101 (paper), $35

reviewed by Frank L. Somer, Jr.
Columbia College, Columbia, MO 65216

Cover
November 2004
Vol. 81 No. 11
p. 1573

Full Text
Based on its title, and on the back-cover synopsis, I opened this book for the first time expecting an easy, applications-oriented introduction to molecular mechanics and statistical modeling (molecular dynamics and Monte Carlo) using classical force fields. One aspect of this misconception was revealed on reading the table of contents and realizing that more than half the text is devoted to quantum-mechanical topics. Another was suggested in the preface, where the author resorts to a dictionary definition of “beginner” to justify its use in the title, and confirmed through the rest of the book: this is not an elementary text, nor was it intended to be. The author’s stated intent is to bridge the gap between elementary texts that can give the reader a quick start in the field (and perhaps a somewhat inflated confidence level) and high-level texts that can provide deep understanding but can seem all but unreadable to non-specialists.

Somewhat ironically for an intermediate-level text, the author takes great pains to ensure that the treatment is largely self-contained—the only strict prerequisite seems to be a good grasp of basic calculus. (More advanced mathematical techniques used in the text are summarized in an extensive appendix.) Given the eclectic nature of molecular modeling, this necessitates inclusion of a great deal of background material, and at least half the text is devoted to basic molecular physics, rather than modeling, per se. For example, after an initial chapter on chemical drawing and nomenclature, and leading into the discussion of molecular mechanics, are chapters on electrostatics, intermolecular forces, and systems of masses interconnected by harmonic springs. These foundational chapters start essentially from scratch (e.g., by defining point charges and the sign convention for electrostatic charges) and provide adequate coverage for understanding how they form the basis for molecular modeling. They are necessarily very terse, however, and so are better suited as “refresher courses” than as true introductions. In any case, it is helpful to have all that background material at one’s fingertips when reading the text.

The coverage of molecular mechanics begins with a discussion of normal and internal coordinates, the various types of interactions present in molecules, and how these collectively constitute a force field. The author then gives a general “template” form for a force field and introduces several of the more widely used commercial examples by showing how they differ from the template. The empirical nature of force-field parametrizations is emphasized, and the scope of calibration for each force field is discussed, providing the reader guidance in choosing a force field for a particular problem. In introducing the OPLS force field, the author employs an interesting device, quoting at length from the abstract of the initial publication of the method. This is a recurring theme throughout the rest of text (sometimes entire abstracts are presented) and works well in a couple of ways. First, it reminds students that what they might think of primarily as a set of computer programs is firmly rooted in the primary literature. Second, reading an author’s summary, written before the work proved to be of great importance, gives a sense of drama usually lacking in such technical books.

After a fairly detailed treatment of molecular potential-energy surfaces—gradients, Hessians, stationary points and methods for finding them—is a chapter on the nuts-and-bolts application of molecular mechanics. Accompanying the discussion of geometry optimization, conformational searching, and calculation of various QSAR properties are explicit calculations, using standard commercial software and complete with screen shots. Then comes a brief but still fairly detailed introduction to statistical thermodynamics, followed by chapters on molecular dynamics and Monte Carlo simulations, touching on such topics as periodic boundaries, integration algorithms, and intermolecular potentials for water.

The second half of the book is devoted to quantum mechanics and its modeling applications. It is similar in construction to the first half, beginning with 90-plus pages of introductory quantum theory at a level that varies between that of undergraduate physical chemistry and a first graduate course in quantum chemistry. The development is clear and fairly easy to follow, provided that the reader has some facility with matrices. Traditional ab initio (HF–LCAO) calculations are then described in detail, and the development of basis sets followed from an historical perspective, explaining how shortcomings of early basis sets led to subsequent modifications. Then follows a chapter on HF-LCAO applications, complete with input and output of several sample calculations, including geometry optimization and calculation of thermodynamic properties. A couple of comparisons are made among results obtained using different basis sets, but it would be nice if there were more of these.

Semi-empirical methods are introduced starting with Hückel’s π-electron model, to show how costly integrals can be “traded in” for empirical parameters. The evolution of this approach is then traced up through the methods typically available in commercial modeling packages. Oddly, no sample semi-empirical calculations are shown, but the discussion is sufficiently detailed to give a sense of the strengths and weaknesses of the various methods. After a chapter on electron correlation, the coverage of quantum modeling finishes with density–functional theory. The author shows a sample DFT calculation, highlights the similarities and differences between DFT and the HF–LCAO method, and explains why both methods will continue to be important for the foreseeable future. A final chapter covers miscellaneous topics, such as polymers, transition states, and hybrid (classical/quantum) methods for treating solvated molecules, that didn’t fit neatly elsewhere.

This is clearly a well written and authoritative book, and I think it will nicely fill its intended niche—that of preparing highly motivated “beginners” for the sort of advanced study required to attain real expertise in molecular modeling. On the other hand, those who simply want to become more skilled users of modeling software, but whose primary interest is not modeling per se, might find it a bit heavy on fundamental theory and light on practical advice as to choice of basis set, expected errors for various methods, etc. The level is probably a little high for the average chemistry undergraduate, but this could certainly be an appropriate textbook for an advanced honors course or beginning graduate course in molecular modeling. It should also prove very useful as a self-study guide and desk reference for students and other practitioners seeking the deep understanding of the theoretical framework of molecular modeling necessary to contribute to the development of this ubiquitous and fast-moving field.

More Information
*  Citation
Somer, Frank L., Jr. J. Chem. Educ. 2004 81 1573.
*  Keywords
*  History
Created:
Last Updated:
September 27, 2004
October 5, 2004
  Home > JCE Print > Journal of Chemical Education > Issues > 2004  > November  > Page 1573


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