1720 J. Chem. Inf. Comput. Sci., Vol. 43, No. 5, 2003
BOOK REVIEWS
BOOK REVIEWS Essentials of Computational Chemistry, Theories and Models. By Christopher J. Cramer. Wiley: Chichester, England. 2002. 562 pp. ISBN 0-471-48551-9 (hardcover). $110. ISBN 0-471-48552-7 (paperback). $45. The fact that a new text book introducing the essentials of computational chemistry contains more than 500 pages shows impressively the grown and still growing size and importance of this field of chemistry. The author’s objectives of the book, using his own words, are “to provide a survey of computational chemistry - its underpinnings, its jargon, its strengths and weaknesses - that will be accessible to both the experimental and theoretical communities”. This design as a general introduction into computational chemistry makes it an alternative to Andrew R. Leach’s well-established “Molecular Modeling” (Prentice Hall) and Frank Jensen’s “Introduction to Computational Chemistry” (Wiley), although the latter focuses on the theory of electronic structure methods. Cramer’s “Essentials” covers force field and molecular orbital theory, Monte Carlo and Molecular Dynamics simulations, thermodynamic and electronic (spectroscopic) property calculation, condensed phase treatment and a few more topics. Moreover, the book contains thirteen selected case studiessexamples taken from the literaturesto illustrate the application of the just presented theoretical and computational models. This especially makes the text book well suited for both classroom discussion and self-study. Each chapter of “Essentials” covers a main topic of computational chemistry and will be briefly described here; all chapters are ended by a bibliography and suggested additional readings as well as the literature references cited in the text. In chapter 1 the author defines basic terms such as “theory”, “model”, and “computation”, introduces the concept of the potential energy surface and provides some general considerations about hardware and software. Interestingly, the first equation occurring in the text is not Schro¨dinger’s equation, as is the case for most computational chemistry introductions, but the famous Einstein relation. The second chapter deals with molecular mechanics. It explains the different potential energy contributions, introduces the field of structure optimization, and provides an overview of the variety of modern force fields. Chapter 3 covers the simulation of molecular ensembles. It defines phase space and trajectories and shows the formalism of, and problems and difference between, Monte Carlo and molecular dynamics. In chapter 4 the author introduces the foundations of molecular orbital theory. Basic concepts such as Hamilton operator, LCAO basis set approach, many-electron wave functions, etc. are explained. To illuminate the LCAO variational process, the Hu¨ckel theory is presented with an example. Chapter 5 deals with semiempirical molecular orbital (MO) theory. Besides the classical approaches (extended Hu¨ckel, CNDO, INDO, NDDO) and methods (e.g., MNDO, AM1, PM3) and their performance, examples are provided from the ongoing development in that still fascinating area. Ab initio MO theory is presented in chapter 6; the basis set concept is discussed in detail, and, after some considerations from an user’s point of view, the general performance of ab initio methods is explicated. The next chapter covers the problem of electron correlation and gives the most prominent solutions for its treatment: configuration interaction, theory of the multiconfiguration self-consistent field, perturbation, and coupled cluster. Practical issues are also discussed. Chapter 8’s topic is density functional theory (DFT). Its theoretical foundation, methodology, and some functionals as well as its pros and cons compared to MO theory are presented together with a general performance overview. The next two chapters deal with charge distribution, derived and spectroscopic properties (e.g., atomic charges, polarizability, rotational, vibrational, and NMR spectra), and thermodynamic properties (e.g., zero-point vibrational energy, free energy of formation, and reaction). The modeling of condensed phases is addressed in chapters 11 (implicit models) and 12 (explicit models), which closes with a comparison between the two approaches. Chapter 13 familiarizes the reader with hybrid quantum mechanical/molecular mechanical (QM/MM) models. Polarization as well as the problematic implications of unsaturated QM and MM components are discussed,
and empirical valence bond methods are also presented. The treatment of excited states is the topic of chapter 14; besides CI and MCSCF as computational methods, transition probabilities and solvatochromism are discussed. The last chapter deals with reaction dynamics, mostly adiabaticskinetics, rate constants, reaction paths, and transition state theory are section topics heresbut also nonadiabatic, introducing curve crossing and Marcus theory in brief. The appendix is divided into four parts: an acronym glossary (which is very helpful), an overview of symmetry and group theory, an introduction to spin algebra, and finally a section about orbital localization. A rather detailed index ends the book. The “Essentials” writing style fits the fascinating topic: one reads on and on and ssurprise!sanother chapter has been absorbed. The text is complemented by a large number of black and white figures and clear tables, mostly self-explanatory with descriptive captions. The use of equations and mathematical formulas in general is well-balanced, and the level of math should be understandable for every natural scientist with some basic knowledge of physics. There are only a few minor shortcomings: for example, a literature reference cited in the text (“Beck et al.”, p 142) is missing in the bibliography; “Kronecker” is mistyped with o¨; and the author completely forgot to reference Leach’s text book when referring to other computational chemistry introductions. However, the author has established a specific errata web page (http://pollux.chem.umn.edu/ ∼cramer/Errors.html) with all known errors. These will be corrected in the next printing or next revised edition, respectively. With its emphasis, on one hand, on the basic concepts and applications rather than pure theory and mathematics, and on the other hand, coverage of quantum mechanical and classical mechanical models including examples from inorganic, organic, and biological chemistry, “Essentials” is a useful tool not only for teaching and learning but also as a quick reference, and thus will most probably become one of the standard text books for computational chemistry.
Anselm H. C. Horn Friedrich-Alexander-UniVersita¨t Erlangen-Nu¨rnberg CI010445M 10.1021/ci010445m
QSPR/QSAR Studies by Molecular Descriptors. By Mircea V. Diudea. Nova Science Publishers: Huntington, NY. 2001. viii+438 pp. ISBN 1-5672-859-0. $97.00. This is a collection of articles, written by different authors, all devoted to various aspects of molecular descriptors and their applications by means of quantitative structure-property relations (QSPR) and quantitative structure-activity relations (QSAR). Research along these lines started around the middle of the last century (although some of its roots go much deeper in the past). Initially this research was a marginal branch of theoretical chemistry. As time passed, QSPR/QSAR became more and more popular because it proved to be useful, especially in pharmacology (drug design), medicinal chemistry, agrochemistry, environmental sciences, etc. The optimism and self-confidence of the present-day researchers may be illustrated by the words of Lionello Pogliani, who, speaking of the molecular connectivity theory (in Chapter 6), maintains that “this theory shows the characteristic of completeness. It is, in fact, possible to describe known properties or activities of molecules, and also, from desired properties or activities revert back to the corresponding molecule.” The increase of interest in QSPR/QSAR is paralleled by the publication of numerous books in this area. Of the most recent such
BOOK REVIEWS books, at least, “From Chemical Topology to Three-Dimensional Geometry” (edited by Balaban, 1997), “Topological Indices and Related Descriptors in QSAR and QSPR” (edited by Devillers and Balaban, 1999: reviewed in J. Chem. Inf. Comput. Sci. 2002, 42(6), 1507), and “Handbook of Molecular Descriptors” (by Todeschini and Consonni, 2000-2002) should be mentioned. Diudea’s “QSPR/QSAR Studies” is the newest in this series. The mentioned books necessarily overlap to some extent with each other, but each of them offers something new to the respective field of science. Those who can afford it should acquire all these books. Those who cannot will not lose much if they purchase only one or two titles. Diudea’s “QSPR/QSAR Studies” contains twelve chapters: 1. “A Personal View about Topological Indices for QSAR/QSPR” by Balaban 2. “Wiener-Type Graph Invariants” by Lukovits 3. “On Calculation of Molecular Descriptors Based on Various Graphical Bond Orders” by Plavsˇic´ and Graovac 4. “Modeling the Solubility of Aliphatic Alcohols in Water. Graph Connectivity Indices versus Line Graph Connectivity Indices” by Nikolic´ et al. 5. “QSPR/QSAR by Graph Theoretical Descriptors beyond the Frontiers” by Estrada and Molina 6. “The Concept of Graph Mass in Molecular Graph Theory. A Case in Data Reduction Analysis” by Pogliani 7. “Eigenvalues as Molecular Descriptors” by Randic´ et al. 8. “New Neural Networks for Structure-Property Models” by Ivanciuc 9. “3D QSAR Models” by Ivanciuc 10. “van der Waals Molecular Descriptors. Minimal Steric Difference” by Ciubotariu et al. 11. “TI-MTD Model. Applications in Molecular Design” by Minailiuc and Diudea 12. “ComPharm - Automated Comparative Analysis of Pharmacophoric Patterns and Derived QSAR Approaches. Novel Tools in High Throughput Drug Discovery. A Proof-of-Concept Study Applied to Farnesyl Protein Transferase Inhibitor Design” by Horvath The book gives a state-of-the-art profile of the research of molecular descriptors and their applications. Roughly speaking, the first half of the book is devoted to graph-based topological indices (including threedimensional indices, Chapter 9), the second half to applications (mainly in pharmacology). In this reviewer’s opinion two chapters are of especially high quality: Chapters 1 and 7. In Chapter 1, Alexandru T. Balaban, one of the founders of chemical graph theory (around 1970) and one of the most influential and prolific authors in this field, gives a concise but clear and rather informative “personal” account of the theory of topological indices, including their classification into four “generations”. This deserves to become obligatory reading for every graduate student of theoretical organic chemistry and every scholar intending to use topological indices in his or her research. In Chapter 7 (written by Milan Randic´ and two of his younger coauthors from Slovenia: Marjan Vracˇko and Marjana Novicˇ), in addition to a survey of graph-eigenvalue-based structure-descriptors, there are considerations of much wider importance. First of all, in the Introduction are stated and discussed Balaban’s “Six Commandments” and Randic´’s “Thirteen Commandments”snamely the 6 +13 conditions which a graph invariant is required to obey in order to be acceptable as a molecular structure-descriptor. Somewhere in the middle of this chapter we find a section “On the Interpretation of Molecular Descriptors” in which one of the most fundamental problems of the entire chemical graph theory is discussed. Therefore, Chapter 7 is recommended also to those who have no interest in matrix and graph eigenvalues. Space limitation does not allow us to survey all the interesting topics discussed in Diudea’s book. We, nevertheless, must mention the recently developed calculation schemes, directly applicable to real-world problems of chemistry and pharmacology, that are presented in detail in Chapters 5, 10, 11, and 12. In Chapter 5 the computer systems MODEST (acronym derived from MOecular DESign Tool) and TOSSMODE (from TOpological SubStructural MOlecular Design) are presented. Chapters 10 and 11 describe the MSD (“Minimal Steric Dif-
J. Chem. Inf. Comput. Sci., Vol. 43, No. 5, 2003 1721 ference”) method and its graph-based version, the TI-MTD (“Topological Index - Minimal Topological Difference”) model. In Chapter 12 we learn about CoMFA (“Comparative Molecular Field Analysis”) and ComPharm, which is a simplified version of the CoMFA approach suitable for pharmacological studies. In each of these chapters a large number of examples and applications is presented. Each chapter in the book has an extensive list of references. Over 1000 bibliographic units are quoted (of these 200 by Balaban and 180 by Randic´ et al.). In summary, “QSPR/QSAR Studies by Molecular Descriptors” is a valuable and comprehensive monograph and is recommended to all who do or intend to do research on, or by means of, QSPR/QSAR.
Ivan Gutman UniVersity of KragujeVac, Serbia and Montenegro CI0104432 10.1021/ci0104432
Library Handbook for Organic Chemists. By Andrew Poss. Chemical Publishing Co., Inc.: New York, NY. 2000. 356 pp. incl. index. ISBN 0-8206-0361-9 (paper). $64.95. Any book that starts with the frontispiece, “Two weeks in the laboratory will save you three hours in the library,” shows where the sympathies of the author lie, a refreshing attitude indeed. Aimed at organic chemists working in the laboratory, this book attempts to rationalize the needs of the researcher with the management, collection, and budgetary constraints of the research library. The Library Handbook (LHOC) is intended as a helpful guide to finding practical information for the performance of organic chemical research. The author’s intent is for this to be especially useful when dealing with incomplete series of reference sources in libraries. The primary emphasis is on printed library (or desktop) reference works, but information is given on other resources, including online and on the Internet. Tables of contents are provided for many series and collections of data and information especially of value to organic chemists. Location of the correct volume of a multivolume series is facilitated. The author is hopeful that even if the collection of a user’s library is incomplete, the correct volume could be located in another library. However, his anticipation of availability by interlibrary loan may be unrealistic: most research libraries do not have circulating copies of these valuable resources. LHOC is designed so that it need not be read in its entirety, and the user is guided to the appropriate section. Part A is a table of “FAQ” (frequently asked questions) with a listing of which descriptive sections are appropriate for searching. For example, for experimental or laboratory techniques, the user is directed to descriptive sections for Chemist’s Companion, Organic Synthesis, and Houben-Weyl. For chemical names, consult Aldrich, Beilstein, Chemical Abstracts, CRC Organic Compounds (HODOC), Dictionary of Organic Compounds (Heilbron), Lange’s, and Merck Index. Part B contains an alphabetical collection of descriptive chapters on the various resources, from Aldrich through Theilheimer. Tables of contents, indexes, Library of Congress call numbers, and information and tips on usage of the resource are provided. In addition, chapters are provided for more general resources including, dissertations, Internet resources, journals, literature sources (online databases and vendors), patents, purchasing chemicals, scientific dictionaries, and translations. Part C is a guide to finding reviews in organic chemistry plus an index to reviews in the journals Tetrahedron and Synthesis. The indexes to the large, multivolume resources are quite valuable. For example, pKa values for the Hammet and Taft equations appear in Section 3 of Lange’s Handbook; triazoles are found in vol. IVD of Rodd’s Chemistry of Carbon Compounds; epoxides appear in three
1722 J. Chem. Inf. Comput. Sci., Vol. 43, No. 5, 2003 volumes on ethers of Patai’s Chemistry of Functional Groups; and a dual table of the systematic classification of Theilheimer’s Synthetic Method of Organic Chemistry helps in finding specific reactions (including named reactions). Note that the emphasis is on traditional, printed resources. However, if the resource exists in multimedia or electronic formats, these are described. For example, the chapter on Merck Index describes the handbook, the online version, the CD-ROM version, and Internet access. The resource is described and an index to tables is provided. Description of the larger information sources is basic but good (extensive for Beilstein and Chemical Abstracts, more terse for the Science Citation Index). Here, although the nonprint media are referred to, the descriptions are primarily for the organization and content of the printed product and indexes. The lists of databases available on STN are titled misleadingly as “Chemical Abstracts Databases”, whereas CAS produces only about a half dozen (in basic form) of the STN databases. The chapters on patents and “literature sources” (online resources) are terse and consist mostly of references to other descriptive works. In addition, the sample search strategy in the patent chapter on finding all equivalent patents for those in a given CA file record is incomplete and obsolete. The chapter on Internet resources lists a few books and Web sites including, incorrectly, Damon Ridley’s book on online searching (which belongs in the literature sources chapter). The chapter on journals lists organic chemistry journals along with LC call numbers and Web sites with no-cost access to the tables of contents. There is a lot of information in this book, and many resources are covered, but in my opinion, the addition of indexes to the Landolt Bornstein physical properties series and the Katritzsky Advances in Chemistry series would be valuable. This book complements well other literature searching resources. However, at the price I hesitate to recommend that it be purchased either as a course text on chemical information or for the bookshelf of every laboratory organic chemist. However, I do recommend that it be available to all such researchers including availability in all libraries that support organic chemical research, either academic or industrial.
Robert E. Buntrock Buntrock Associates, Inc. CI010444U 10.1021/ci010444u
Applied Finite Group Actions. By Adalbert Kerber. SpringerVerlag: Berlin. 1999. 454 pp. (Algorithms and Combinatorics, Vol. 19). ISBN 35-4065-9412. $151.00. This book is a little unusual for review in a chemistry journal, in that the book is quite mathematicalsproviding a comprehensive treatment of the combinatorics associated with the classification, generation, and enumeration of a variety of discrete mathematical structures, with the classification mediated by a group action on the structures. But such structures notably include the following: molecular graphs; geometrical embedding classes of graphs; molecular reactions; quantum symmetry-adapted states; and a variety of other (chemical, physical, or mathematical) graphical and combinatorial species of interest. In such cases the structures are represented by a “code” and frequently entail a designation of substructures, e.g., by way of a set of positions in a molecule which may be substituted by different radicals or ligands. Some of the positions in a structure may be “equivalent” because of a symmetry in the underlying structural framework, so that a permutation of the “subcodes” for the different substituents leaves the overall molecular code the same (i.e., invariant). The application of one code-fixing permutation after another gives an overall result which is yet another code-fixing permutation, and the set of such codefixing permutations form a group acting on the set of codes. Thence
BOOK REVIEWS one anticipates the relevance of permutation groupssindeed such groups provide a precise elegant way of describing “equivalence” among different conceivable codes. Sometimes these permutation group actions are identifiable with molecular point-group symmetries (of the underlying skeleton on which the substitutions are to be made) but also they may be identifiable with nonrigid motions, such as may involve various internal rotations or internal inversions or internal pseudorotations. The idea of enumeration of structural (or constitutional) isomers is but one historically important aspect of the currently developed theory. Kerber’s development seeks to adhere to a maximum of generality within a framework of well-developed mathematical theory, and Kerber’s presentation unifies what are often otherwise viewed as rather different approaches to the same material. As characteristic of mathematics books, mathematical proofs occur throughout. Thence a formidable amount of mathematical nomenclature and notation is used, and much effort is required for a typical chemical reader. In this regard, chapter 11ssurveying some background materialsis useful, and inasmuch as symbols once defined are oft repeatedly used long afterward without redefinition, the (long) tabulation of symbols (following the table of contents) is very useful. But hopefully, if one perseveres, then new generality of chemical interest may be attained. Notably the text does pay explicit attention to chemistry, as one might suspect from the molecular structural formula for dioxin appearing on the back cover of the book. Chemical applications appear in several points in the text, including the following: some parts of section 2.1, all of section 3.4 (entitled “Chemical Applications”), some parts of section 7.1 (where combinatorial chemical libraries make a brief appearance), some parts of section 9.4, and a surprising amount of the section 12.1 (on the history of the subject of the book). Though the bulk of the book is quite mathematical, it offers a significant insight into an interesting interconnection between mathematical developments and chemical problems. Section 12.1, which is quite easy to read, provides a modicum of the history of chemicalenumeration methodology that is typically overlooked in standard histories of chemistry, perhaps because these developments, as by A. Cayley, or J. J. Sylvester, or G. Po´lya are viewed by many to be more important as developments in mathematics than in chemistry. And indeed, these three scientists are generally recognized as mathematicians, though their work noted in the present book was motivated largely by the chemical applications. Especially notable is Po´lya’s work which is often regarded as of a fundamental mathematical nature (so that this “Po´lya theory” often appears as a separate chapter or two in combinatorics texts without any mention of chemistry). Even with regard to the traditional chemical-history fare concerning the origin of the idea of chemical isomerism, the present text extends beyond much more extensive chemical histories which typically miss the early role of A. von Humboldt. Of course some mathematicians (such as Froebenius, Burnside, or Redfield; in the area of equivalences under group action) seem to have been entirely mathematically motivated (without even any evident awareness of possible chemical applications), while some mathematicians such as N. G. deBruijn and R. C. Read seem to have had chemistry as a sort of secondary motivation. In the last few decades, the theoretical chemist E. Ruch along with his students made fundamental contributions to the mathematical field, as is noted in Kerber’s book. The more recent work of Kerber and his several students in mathematics has been to a large degree motivated by chemical applications. There is contact with the work of S. Fujita on isomerenumeration, some of which has appeared in this journal during the past decade or so. To facilitate the use of the mathematics described in the text, a general software package has been developed by Kerber’s group over the last couple of decades. This package is available via the Internet at this URL (http://www.mathe2.uni-bayreuth.de/axel/symneu_engl.html) and takes advantage of the user shell of MAPLE. A chemically oriented article focusing on isomer enumeration and generation via such techniques is found in van Almsick et al. (J. Chem. Inf. Comput. Sci. 2000, 40(4), 956-966). A further collection of articles focusing on related chemical applications has appeared in volume 46 (2002) of Communications in Mathematical Chemistry (MatCh). The presently reviewed text, though of a general mathematical formality, seems to be promising for study (perhaps “concept mining”?)
BOOK REVIEWS by chemistssespecially by theoretical or mathematical chemists. Beyond classical isomer enumeration, the general focus on the various structures in terms of mappings offers different possibilities for extension: subclassifications perhaps with a requirement or exclusion of different substructures might be made; the variety of structures so generated might be efficiently and comprehensively generated; and various chemically meaningful graph-theoretic characteristics might be obtained, through some sort of combinatorial averaging procedure. With
J. Chem. Inf. Comput. Sci., Vol. 43, No. 5, 2003 1723 such combinatorial tools in hand the potential for use with virtual molecular libraries seems hopeful.
D. J. Klein Texas A&M UniVersity/GalVeston CI010446E 10.1021/ci010446e
