1204 J. Chem. Inf. Comput. Sci., Vol. 37, No. 6, 1997
BOOK REVIEWS
BOOK REVIEWS Computational Chemistry: Reviews of Current Trends. Edited by Jerzy Leszczynski. Volume 1. World Scientific: Singapore. 1996. 271pp. ISBN 981-02-2572-5. $48.00. This volume contains seven chapters, with topics ranging from progress made in computational techniques to application using computational tools. The main emphasis is on ab initio techniques. Each chapter treats the subject in-depth providing sufficient background information to enable a nonpractitioner to comprehend the contents. The chapters are also supported by an extensive list of references. Specific topics include survey of current techniques to compute atomic and molecular structures using relativistic quantum mechanics, techniques to speed the construction of Coulomb matrices, generating ab initio quality density matrices for the system involving more than 1000 atoms, discussion on the physical basis for the polarizable continuum model (PCM) to compute solute-solvent interactions along with the principles of computational methods based on PCM, exploring techniques to stuff fullerenes, interaction of DNA bases including base stacking and hydrogen bonding, and finally a chapter on designing drugs with minimal side effects. I highly recommend this book for researchers in the field of computational chemistry though most of the chapters can be understood by nonpractitioners. I look forward to additional volumes, which I hope might include applications in the area of material science.
P. S. Subramanian Texaco Inc. CI9604347
From Chemical Topology to Three-Dimensional Geometry. Edited by Alexandru T. Balaban. Plenum Press: New York. 1997. xvii + 420 pp. $125.00. ISBN 0-30645462-9. The title of this volume captures its contents very well. Here is a book about current work in extending the methods of chemical topology, which has traditionally dealt with two-dimensional approximations, to useful three-dimensional descriptions of molecules. Not only are theoretical advances covered but also experimental problems to which these advances might be applied in the foreseeable future. In a compilation of contributions by many authors, it is expected that some sections will be notably better than others. It was therefore a great pleasure to encounter the present volume, in which every chapter is of unimpeachable quality. The editor provides an introductory chapter of relevant historical material as well as an overview of current work in the field. As is the case throughout the book, the discussions are illustrated with many examples of molecules that have been analyzed by the methods discussed. Each chapter presents a great deal of information in a small space. This is not casual reading, but it rewards the attention it demands. The authors of the subsequent nine chapters are not merely scientists who are active in areas relevant to the subject, as the editor promises, but are leaders in their respective areas. Mezey presents quantitative shape descriptors. Especially intriguing are his claim that he has produced fragment-building results that are virtually indistinguishable from whole-molecule SCF 6-31G** calculations and his discussion of new, computationally accessible methods of geometry optimization. Veith and Mekenyan review real-world methods for obtaining accurate 3D molecular structures from 2D projections and conclude that searching for molecules that can assume a specific conformation may be a more important problem than determining the geometry of the most stable 3D conformers. Basak et al. discuss quantitative structureactivity relationships (QSAR) from a risk-assessment perspective and make the well-taken point that QSAR is now a necessity because the catalog of new substances is growing at a rate that wildly exceeds any imaginable increase in resources available for experimental toxicity
testing. They then examine means of selecting descriptors for quantifying molecular similarity. Trinajstic´ et al. consider the problems inherent in determining tertiary protein structures from amino acid sequences, with particular attention to membrane proteins. They conclude that neither theoretical methods nor experimental results alone give the most accurate pictures, but for these problems the two must be used in combination. Randic´ and Razinger examine (with 293 references) the characterization of 3D molecular structure, which they distinguish from the representation of structure by molecular codes, and demonstrate many examples and applications. Fowler takes a step farther away from synthetically realized structures with a chapter on the chemical graph theory of fullerenes, in which he summarizes both historical and current results. Anyone familiar with Fowler’s An Atlas of Fullerenes will appreciate his qualifications in this area. Even more theoretical are Kirby’s chapter on toroidal and other exotic fullerenes and Klein and Zhu’s general chapter on all-conjugated carbon species. All three chapters on fullerenes and related structures are more heavily mathematical than the previous ones, but the authors do an admirable job of writing for chemists who are not mathematicians. Once again, the authors’ publication records in these areas speak for themselves. After three chapters of essentially all-carbon structures, King, in the final chapter, explores applications of topology and graph theory to inorganic species, specifically boranes, transition metal clusters, and polyoxometalates. No brief review can provide an adequate description of the wealth of information packed into this volume. The editor specifies that the book is “addressed to graduate students and research scientists... who are interested in molecular modeling, in fullerene research, in drug design, and in modern mathematical chemistry”. Indeed, these people, of whom this reviewer is one, will find an abundance of state-of-theart information and up-to-date references. I can give From Chemical Topology to Three-Dimensional Geometry nothing less than a wholehearted recommendation. This review was written by Gordon Cash in his private capacity. No official support or endorsement by the Environmental Protection Agency is intended or should be inferred.
Gordon G. Cash United States EnVironmental Protection Agency CI970395E S0095-2338(97)00395-8
Genetic Algorithms in Molecular Modeling. Edited by James Devillers. Principles of QSAR and Drug Design, Vol. 1. Academic Press, Harcourt Brace & Company: New York. 1996. 327 pp. ISBN 0-12-213810-4. $55.00. Genetic Algorithms in Molecular Modeling is the first volume of a series “Principles of QSAR and Drug Design.” The authors describe the application of genetic methods (genetic algorithms, evolutionary strategies, evolutionary programming, and their variants) to the analysis, validation, and prediction of biological activity of chemical compounds. The content of the book is well organized. It begins with an introduction to the theory behind genetic algorithms, defines their uses and limitations, and gives many examples of their applications. A reader with a reasonable background in mathematics, chemistry, and biology can quickly grasp the implications of using genetic algorithms to model and predict structure-activity relationships. Applications of genetic algorithms described in this work include the following: validating quantitative structure-activity relationships (QSAR), analyzing quantitative structure-property relationships (QSPR), searching for pharmacophores in a database of structures, planning synthesis routes, and performing conformational searches and docking simulations. The use of these methods in basic research is well documented by the contributing chapters. The implications of this research to the pharmaceutical industry to reduce R&D costs by modeling and predicting the biological activity of drugs using their topological and/
BOOK REVIEWS
J. Chem. Inf. Comput. Sci., Vol. 37, No. 6, 1997 1205
or physicochemical descriptors is obvious. A less obvious but intriguing example utilizes genetic algorithms to validate the biodegradability of 49 chemicals. Of the 49 chemicals, 45 were classified correctly (91.8%) from the tested set. The implications are that these genetic methods have great promise in bioremediation research. The methods described can also be used to design materials possessing the chemical, physical, and biological properties desired and may have implications in green manufacturing. Genetic algorithms operate on a simple cycle: first an encoding mechanism must be devised, and a population created, followed by application of a fitness function and manipulation of genetic information by mating or mutation operators. The cycle generates offspring that increase the fitness of the population. Care must be exercised to prevent dominant characteristics from focusing on suboptimal solutions. Genetic methods can be used with other strategies as well to either produce alternative solutions or new insights. The authors have provided comprehensive bibliographies for each chapter, a keyword list for searching for similar information, a detailed list of software for all platforms, and an extensive list of genetic algorithms with descriptions of their strengths and weaknesses. The book has been thoroughly reviewed contributed chapters were presented and discussed at the Second International Workshop on Neural Networks and Genetic Algorithms Applied to QSAR and Drug Design held in Lyon, France and were reviewed by an expert in molecular modeling and an expert in chemometrics.
Paddy O’Hara-Mays Lock HaVen UniVersity CI970394M S0095-2338(97)00394-6
The production values are of the highest quality: acid-free paper, clear and well documented graphics, fairly dense text, an excellent index, a detailed (and easy to find) list of acronyms. The style varies from the traditional (this is not a complaint) in its method of referencing. There is an extensive and consistent list of references found at the end of the monograph, as opposed to each chapter, as well as having some references embedded in the text. It is not difficult to follow: in fact, it is very clear to the reader. The readership level is geared to a specialty group, namely radiologists. There is an assumption that the reader has some understanding of basic principles of radiology, although the terminology and fundamentals are sufficiently explained so that scientists from other digital imaging fields can grasp the concepts. The actual audience is, in fact, far larger than the targeted group of radiologists. Obviously, students and researchers of radiology are the primary audience and, as such, should consider this as a personal acquisition. However, the material is applicable to a much larger group, including any scientist researching or working with dense graphic and textual data. Any scientific team who needs to consult and communicate using these “voluminous pictures” should consider reading this book, e.g., electrooptical specialists, nuclear medicine scientists, magnetic resonance imaging researchers, computer/communication scientists involved in image compression, and the like, although its price may prevent it from being a personal acquisition. The comprehensiveness of subject matter makes it a good selection item primarily for Health Sciences Libraries and as supporting material in the Physical and Engineering Science libraries. Laboratories doing research in the area of digital-based operations in a hospital environment should consider buying this monograph as well.
Veronica Calderhead John Cotton Dana Library CI970398R
PACS: Picture Archiving and Communication Systems in Biomedical Imaging. By H. K. Huang. VCH Publishers, Inc.: New York. 1996. 489 pp. ISBN 1-56081-685-6. $150.00. PACS is the large scale digital technology application to the science of radiology. As the book notes, the most interesting advances in the area of digital radiology imaging have been furthered by the scientists most directly involved in radiology and computer/digital communication science. The author, Dr. H. K. Huang of the University of California, San Francisco, is one of the leaders in this joint area of research. He is one of the “new breed” of scientists who is uniquely qualified to understand digital technology and its applications in radiology. In addition to reviewing all the recent advances in PACS, the monograph is also an excellent textbook for those interested in radiological imaging. The book is organized like a textbook, providing the historical through the current trends and future direction of research. Though an edited series of chapters and articles may well have provided similar information, the cohesiveness and integrity of a single author’s work make it ideally suited to teaching, even though any single chapter could be used in isolation. There are very few single-authored monographs dealing with PACS and radiological imaging. In addition to this book being a good textbook, the subject comprehensiveness, systematic organization, strong scholarship, and excellent production values make it ideally suited for most academic library collections. Like any comprehensive information system, be it geographic, bibliographic, management, etc., the understanding of the totality of the PACS requires discussion of the input and output. This book does this over several chapters; it provides thorough detail on the five major PACS components: image acquisition, communications, databases, display, and information retrieval. Most important for the practitioners is the explanation of PACS in the hospital environment and finally for the physician’s desk top retrieval. The concluding chapters deal with the exciting advances in PACS, namely the integration of multimedia medical data, teleradiology (i.e., connecting geographically separated systems), intensive care unit applications, and appending a threedimensional rendering node, among other developments. There is an interesting introductory section that provides a selective global summary of operational PACS and the research facility in which the PACS is in use and the level of operation.
S0095-2338(97)00398-3
Chemical Group Theory: Techniques and Applications. Mathematical and Chemical Series, Vol. 4. Edited by Danail Bonchev and Dennis H. Rouvray. Gordon and Breach Publishers: U.S.A. 1995. xiv + 243 pp. ISBN 2-88449-034-5. ISSN 1049-801. $120.00 (Hard bound). This book is the fourth in a series of monographs entitled the Mathematical Chemistry Series. The first and the third volumes dealt with the introduction and fundamentals, respectively, of Chemical Graph Theory and Chemical Group Theory. Reactivity and Kinetic aspects were handled in volume 2. Group-theoretical principles have been extensively exploited in chemistry for the study of atomic and molecular systems, the interpretation of electronic and vibrational spectra, the enumeration of a host of differing chemical species, and the analysis of many thermodynamic systems and chemical reactions as well as for a broad variety of chemical combinatorial problems. Chapter 1 of this volume examines the meaning of the concept of group representation and then goes on to explore the varied theoretical frameworks that have been evolved in the application of group theory in the physical sciences. Chapter 2 takes a detailed look at applications of combinatorial techniques in the study of spectroscopy; all of these techniques derive from, or are built around, the Enumeration Theorem of Polya. Chapter 3 focuses on methods that have been developed to obtain the eigenvalue spectra of a wide variety of chemically significant molecular graphs. Chapter 4 addresses the group-theoretical treatment of molecular species not possessing rigid molecular skeleton. The two final chapters both relate to potential energy surfaces. In Chapter 5, the topic under discussion is molecular shape, and the ways in which this notion may be characterized by the use of potential energy surfaces. Chapter 6 examines the potential energy surface itself, and it is shown that group theory can be used to minimize the computational effort required to construct such surfaces. Group theory also has the advantage of making it possible to ensure that these surfaces will always correctly simulate those physical quantities that are dynamically conserved. The volume is very nicely produced, with many clearly drawn figures, many pertinent references, and an agreeable letter type. Each chapter is written by expert(s) internationally recognized within his/
1206 J. Chem. Inf. Comput. Sci., Vol. 37, No. 6, 1997 her respective fields. The contributors not only emphasize the methodology and its critical evaluation but also present instructive applications of their specialties. The Series provides a stimulating and an essential guide to current research in mathematical chemistry.
Venkat Raman Chemical Abstracts SerVice CI970400E S0095-2338(97)00400-9
Internet Tools of the Profession: A Guide for Information Professionals. Edited Hope N. Tillman. 2nd ed. Special Libraries Association: Washington, DC. 1997. 249 pp. ISBN 0-87111-467-4. Two years after the first edition, Internet Tools of the Profession once again provides a select list of tools relevant to Special Library Association (SLA) members. The number of subject chapters has been expanded, and so has the number of selected listings in each chapter. The work is in essence a review source for Internet resources with some introductory explanatory material. The chapters on “Searching on the Internet”, “SLA E-Mail Lists, Websites, and Other Internet Resources”, “Chemistry”, and “Information Technology” will be of most interest to chemical information specialists, but there are others of related value such as “Metals/Materials” and “Pharmaceutical”. One chapter for which I looked in vain was on the related subject of physics. This is surprising given the active nature of the Physics-Astronomy-Math division of SLA. I was impressed by the care taken by all of the chapter authors to whittle down the enormous numbers of available sites into a selected list of quality links. For each site, most of the following information is given: Source, Cost, Type of resource, Contact person, Purpose, and Value. The organization of each chapter is alphabetical by resource name or alphabetical within subdivisions of the subject as organized by the chapter author. I found the latter arrangement much more useful in trying to identify tools that I might want to use. This organization is successfully employed by Gary Wiggins and his co-authors in the chapter on “Chemistry” which they subdivide into Comprehensive Lists, Teaching, Directories of Chemists, and Directories of Software, among others. The Introduction states that there will be links on the SLA home page to web pages highlighted in this work, and this is viewed as a possible “precursor to an electronic version”. I applaud this move, since two years is much too long to wait for new information in our networked world.
Kimberly J. Parker Yale UniVersity CI970403R S0095-2338(97)00403-4
Recent Developments and Applications of Modern Density Functional Theory. Theoretical and Computational Chemistry; Vol. 4. Edited by J. M. Seminario. Elsevier: Amsterdam, 1996, xxiv + 838 pp. List price $409.50. ISBN 0-444-82404-9. This is the fourth book in the new series Theoretical and Computational Chemistry, edited by J. M Seminario (the series editors are P. Politzer and Z. B. Maksic). The book consists of 22 chapters written by leading researchers in the field and has been divided into four main parts: (i) Basics (5 chapters); (ii) Functionals and Their Problems (5 chapters); (iii) Approaches and Methods (4 chapters); and (iV) Applications (8 chapters). The second volume of this series, Modern Density Functional Theory: A Tool for Chemistry, was devoted to the development of density functional theory (DFT). The publication of a fourth volume just a few years after the publication of the second
BOOK REVIEWS volume in this series reflects the role of DFT in modern quantum chemistry as a promising alternative to conventional ab initio methods. Recent years have witnessed new results in the development of DFT and the growing number of its applications to various chemical problems. Some of the chapters of the book are interesting to specialists working in this area, while others can be useful to chemists who want to understand how to apply DFT methods in their research and the level of accuracy that can be achieved in such applications. Basic theoretical aspects of DFT are discussed in the first five chapters (Part I). The next five chapters (Part II) deal with a problem lying at the heart of the practice of DFT applications: development of density functionals and assessment of their performance. The first chapter in this part is a review by J. P. Perdew et al. in which the PW-91 functional, a widely used nonempirical functional, is analyzed. An interesting review of problems arising in DFT calculations of species with degenerate electronic states, and possible approaches to overcoming such problems, is presented by A. Savin (Chapter 9). In Part III, a particularly interesting article by B. G. Johnson et al. (Chapter 12) discusses linear scaling techniques that are implemented within the Q-Chem program. Relativistic DFT and its applications to metal clusters (gold, alkali-gold, and sodium-lead clusters) and metal complexes are discussed by N. Ro¨sch et al. (Chapter 14). To demonstrate the role of relativistic effects in catalysis by heavy metals, the authors have presented results of DFT calculations on nitrogen activation by molybdenum amide complex and alkene epoxidations with metal oxo complexes. Applications of DFT to various chemical problems are discussed in Part IV. An evaluation of the performance of DFT calculations for prototypical organic reactions (proton abstraction and addition reactions; cycloaddition reactions; pericyclic reactions; elimination reactions; isomerization reactions; and multiple proton transfer reactions) can be found in a review by B. S. Jursic (Chapter 19). Applications of various (26) functionals are considered and some recommendations have been made. The following chapter by M. Belcastro et al. (Chapter 20) can be seen as an extension of the studies by Jursic to larger molecules of biological interest. DFT calculations on relative stabilities of uracil tautomers, conformers of acetylcholine, proton affinities of glycine and cytosine, and peptide bond cleavage by carboxypeptidase are among examples given in this chapter. The molecular charge distributions obtained from DFT calculations are considered by P. Geerlings et al. A systematic study of model chemistries based on DFT methods and their comparison to one another and to those based on conventional ab initio methods is presented by M. J. Frisch et al. (Chapter 18). An assessment of the performance of the B3P86 functional in calculations of heats of reactions is given by P. Politzer et al. (Chapter 22). Almost every chapter is preceded by a short abstract, and all of them end with extensive references to the literature which is covered up to 1996. The subject index is generally satisfactory although the readers should keep in mind that it is not complete. For example, CH2 is indexed only to p 369, whereas a set of computational data on methylene is given on p 813. While the main audience of this book is expected to consist of experienced computational chemists, chemists who want to use DFT calculations as an addition to their experimental studies can find useful reviews in Part V. The price of the book, $409.50, is rather high, and any potential buyer will feel that it would be reasonable to review the book prior to purchasing it in order to see how many chapters will be of interest to him or her.
Mikhail Glukhovtsev UniVersity of Delaware CI970402Z S0095-2338(97)00402-2
Computer Modelling in Inorganic Crystallography. Edited by C. R. A. Catlow. Academic Press: San Diego. 1997. 340 pp. $65. ISBN 0-12-164135-X. This work surveys a variety of atomistic computer modeling techniques as applied principally to crystalline inorganic materials. It
BOOK REVIEWS is intended to show how such techniques are applicable to real, complex problems of importance in contemporary experimental studies. The text consists of a succinct introduction and overview by the editor, seven chapters describing different methodologies, and four chapters of “case studies”. Individual chapters focus on bond valence methods, lattice energy and free energy minimization, molecular dynamics, simulated annealing, reverse Monte Carlo, ab initio methods, and various techniques applicable to defects, surfaces, and interfaces. Some of the specific topics discussed are the following: modeling and predicting known and unknown structures, interatomic potentials for use with various modeling techniques, calculation of thermodynamic properties of a crystal, calculation of phase diagrams in oxide systems, calculation of coherent and incoherent neutron scattering, modeling and prediction of defect sites, prediction of possible structural polymorphs, and modeling of the defect structure and electronic structure of defective materials. Whole-chapter case studies are devoted to the applications of modeling techniques to microporous materials, high Tc superconductors, molecular crystals, and amorphous materials. Chapters are wellreferenced, with citations into 1996 in most cases and well over 650 references altogether. There is an eight-page subject index. This book is an excellent choice as an introduction to its title field. The crystallographer or chemist interested but inexperienced in computer modeling will find it useful in evaluating the capabilities and limitations of the techniques currently available for the study of
J. Chem. Inf. Comput. Sci., Vol. 37, No. 6, 1997 1207 inorganic solids. The level of theoretical background given and the discussion and examples of each methodology are appropriate for review articles, so the worker interested in utilizing any of the techniques discussed will want to refer to the cited literature for more detailed accounts. The book does a good job of conveying the flavor of current modeling techniques, and the directions in which they are being developed. It is not, and does not claim to be, an authoritative compendium; the rapidly expanding field would soon leave such a work dated anyway. Nevertheless, many of the new methodologies will have their foundations among those principles and techniques discussed in this book, so it will continue to serve as a useful introduction to the field for some years. Although some sections of this book may be suitable for advanced undergraduates, overall this book is inappropriate for most students below the graduate level. In addition, this work does not go sufficiently in depth about any particular methodology to be suitable as the primary text for any but a survey course.
John C. Bollinger Indiana UniVersity CI9704017 S0095-2338(97)00401-0
