Book and Media Review pubs.acs.org/jchemeduc
Review of Molecular Modeling Basics John H. Shibata* Department of Chemistry, The University of the South, Sewanee, Tennessee 37383, United States appreciation for the methods behind the calculations. The final two chapters of the book (Chapters 4 and 5) provide an extensive description of sample calculations, illustrating the concepts presented in the preceding pages. These two chapters are exceptional for their clarity, and fittingly come after the chapters on the underlying theory. The book begins with a discussion of potential energy surfaces that leads to the topic of energy minimization (geometry optimization). In view of the intended purpose of this book, topics are not oversimplified, but are characteristically discussed with brevity, relying on other books to provide the reader with a more comprehensive discussion of the concepts. Chapter 2, Calculating the Energy, is a very dense chapter primarily focusing on the ab initio theory of molecular orbitals. A brief discussion of molecular mechanics is followed by an introduction to quantum mechanics. The Schrödinger equation for one-electron systems quickly gives way to multielectron systems, introducing restricted Hartree−Fock, restricted open shell Hartree−Fock, and unrestricted Hartree−Fock methods. The different basis sets used in calculations are then presented, followed by a description of the self-consistent field procedure. Standard topics in computational chemistry books such as semiempirical methods, density functional theory, and correlation energy are described as well. Practical advice on performing calculations and interpreting results occur throughout this chapter. For example, comments on what to consider when energy calculations do not converge are presented. The treatment of molecules in solution by explicit and implicit solvent models in Chapter 3 (Molecular Properties and the Condensed Phase) is especially welcome in an introductory book whose audience may include biochemists. Periodic boundary conditions and the particle mesh Ewald summation in the explicit solvent model, and the generalized Born model in the implicit solvent model are described concisely. Chapter 4 (Illustrating the Concepts) and Chapter 5 (The Details of the Calculations) provide examples of calculations that are performed using GAMESS. For example, the B3LYP/631G(d) optimized molecular geometry and bonding in NH3 is described. The software used to visualize the results is MacMolPlt.6 Although specific software programs are used to carry out the calculations and display the results, the discussion of setting up a calculation and interpreting the results can easily be applied to other software. In addition to the standard calculation of molecular orbitals, we are also shown an example of how to modify the GAMESS input file for computing the Ruedenberg localized orbitals. This book is a useful guide to computational chemistry, serving as an introduction to molecular modeling theory that
Molecular Modeling Basics by Jan H. Jensen. CRC Press, Taylor and Francis Group, LLC: Boca Raton, Florida, 2010. xiii + 175 pp. ISBN: 978-1420075267 (softcover). $51.95. Molecular Modeling Basics by Jan H. Jensen is a slender book that is intended as a supplement to a textbook on computational chemistry. As described by the author, the book is based on his lecture notes for a course on molecular modeling, with each section corresponding to approximately one lecture. The author has also established a Web site1 where tutorials, animations, color figures, and general comments and information on computational chemistry are posted. There is an additional Web site for color versions of figures in the book.2
Cover image provided by CRC Press and reproduced with permission.
This book successfully brings together descriptions of the theoretical background behind determining equilibrium molecular geometries, molecular energies, and other properties, with the practical aspects of performing computations, such as tips on what to consider when a calculation ends in an error. Sample computational studies using the software program GAMESS3 are described in sufficient detail to be useful examples for self-practice or in the classroom. Introduction to Computational Chemistry by Frank Jensen4 and Essentials of Computational Chemistry by Christopher Cramer5 are mentioned by the author as books he has used in teaching computational chemistry courses, which were supplemented by his lectures (the basis of this book). Interspersed throughout the theory sections of the book (Chapters 1−3) are useful insights into the practical aspects of performing calculations. These observations are suitably placed in the text to appear near the discussion of pertinent background material. For example, comments on restricted Hartree−Fock calculations are presented immediately after introducing basis sets and the self-consistent field procedure. This proximity of theory and application gives the reader an © 2012 American Chemical Society and Division of Chemical Education, Inc.
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Journal of Chemical Education
Book and Media Review
does not oversimplify explanations or skip important topics. The examples described in the book allow this book to also function as a workbook. Readers can perform calculations and compare results, following the discussion in the text. An added bonus is the Web site that the author maintains to respond to comments, to post new material, and to expand the coverage of the book. In summary, this is a worthwhile book for those interested in learning and teaching computational chemistry.
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AUTHOR INFORMATION
Corresponding Author
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[email protected].
REFERENCES
(1) Jensen, J. H. Molecular Modeling Basics: The “How To” of Molecular Modeling in Education and Research. http:// molecularmodelingbasics.blogspot.com/ (accessed Oct 2012). (2) Jensen, J. H. MolModBasics’ Photostream. http://www.flickr.com/ photos/molmodbasics (accessed Oct 2012). (3) Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347−1363. (4) Jensen, F. Introduction to Computational Chemistry; J. Wiley: New York, 1999. (5) Cramer, C. J. Essentials of Computational Chemistry; J. Wiley: New York, 2002. (6) Bode, B. M.; Gordon, M. S. J. Mol. Graphics Modell. 1998, 16, 133−138.
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dx.doi.org/10.1021/ed3007204 | J. Chem. Educ. 2012, 89, 1489−1490
