880 J. Chem. Inf. Comput. Sci., Vol. 40, No.

3, 2000 BOOK REVIEWS

BOOK REVIEWS

Comparative QSAR. Edited by James Devillers. Taylor & appreciably the fragrance. High-throughput molecular modeling tech-
Francis, Washington, D.C. 1998. ix + 371 pp. ISBN 1-56032- niques used in pharmacology are yet to be applied in this area.
716-2. $135.00. K. N. Reddy, F. E. Dayan, and S. O. Duke present in their chapter
a QSAR analysis of protoporphyrinogen oxidase (protox) inhibitors.
The eight chapters are written by experts in their fields, and the These are among the most potent herbicides of the past decade. The
editor states in his preface that no attempt has been made to enforce a protox enzyme converts protoporphyrinogen IX into protoporphyrin
consensus view. Nonetheless, the reader will find that there is, however, IX, which is a precursor both for heme and for chlorophyll, and whose
a consensus, namely, that the field of quantiative structure-activity
accumulation in the plasma membrane induces the formation of the
relationships (QSAR) has reached a maturity enabling it to address
lethal singlet oxygen. An intriguing variety of 10 chemical classes of
both the billion-dollar drug design industry and the molecular mech-
anisms governing chemical and biological interactions. structures able to inhibit protox is reviewed accordingly, but since the
enzyme structure is not yet known, unifying properties derived from
The first two chapters deal with QSAR involving aquatic organisms.
QSAR analysis have yet to be discovered. The authors agree with
J. Devillers, D. Domine, S. Bintein, and W. Karcher present in their
Hansch and Leo that QSAR is useful for lead optimization, but not for
chapter (Comparison between Fish Bioconcentration Models) extensive
generating new leads.
tables for hundreds of compounds on bioconcentration factors in fish,
discussing in depth modeling based on lipophilicity and comparing nine The bactericidal activity of sulfa drugs is known to be due to their
equations in terms of log P (five linear and four nonlinear dependences). similarity to p-aminobenzoic acid involved in the synthesis of folic
The results are of interest both as scientific results and in terms of acid, which is a vitamin for humans. Tetrahydrofolic acid mediates
forthcoming possible regulations of the European Union in the aquatic one-carbon transport. Methotrexate owes its anticancer activity to its
environment. T. W. Schultz, G. D. Sinks, and A. P. Bearden then present similarity with folic acid. The inhibitors of dihydrofolate reductase
a mechanism of action (MOA) approach concerning aquatic toxicity (DHFR) are reviewed by C. D. Selasssie and T. E. Klein. QSAR in
to a gram-negative prokariotic bacterium, a ciliate single-celled this area is of long date, and although molecular graphics analysis can
eukariotic protozoan (in both cases static tests were performed), and a be successfully used in this case when the enzyme structure is known,
fish species under a flow-through system (fathead minnow). Again, differences between DHFR isolated from various bacterial or animal
comprehensive tabulated data are presented, and the molecular descrip- species can also be understood on the basis of the corresponding
tors are limited to hydrophobicity and the calculated super-delocaliz- dependency on electrostatic or hydrophobic parameters in QSAR.
ability. Whereas some corrrelations are excellent, this chapter also The most extensive, and, in the reviewer’s opinion, the most
includes numerical and graphical data for regression analyses (e.g. for fascinating of all chapters, is authored by Corwin Hansch, the “father”
nitrobenzene derivatives) which show no correlation and could have of QSAR since his 1962 study, and his co-workers, H. Gao and D.
been dispensed with in words rather than figures. The conclusion of Hoekman. This chapter should become a citation classic, since it opens
the authors is that there is some similarity between the protozoan and many “doors of perception” and has many paragraphs and data worthy
fish species, but extrapolation of ecotoxicity data from in Vitro studies of being quoted. In brief, the authors describe how their database of
with simpler organisms to vertebrates is risky, unless the toxicity about 10 000 QSAR data (of which one-third are for biological systems)
mechanism is perfectly understood. can be put to use in understanding the chemistry of living cells and
R. L. Compadre, C. Byrd, and C. M. Compadre describe in their thus in devising better drugs or pesticides. Together with the reviews
chapter (Comparative QSAR and 3D-QSAR Analysis of Mutagenicity published by Hansch in Chem. ReV., this chapter can become a gold
of Nitroaromatic Compounds) an approach which involves on one hand mine for medicinal chemists and pharmacologists, if they know how
“classic” description by means of steric, electronic, and hydrophobic to read it and how to use the database.
parameters contrasted on the other hand with the comparative molecular A few quotes from this last chapter are in order: “(T)he advent of
field analysis (CoMFA) which describes better the steric factors. ... ‘sexy’ 3-D pictures of ligands bound to enzymes of established
Whereas it is well-established that the mechanism involves reduction structure captured researchers’s attention the way that the Lorelei of
of nitro compounds to nucleophilic species which attack the polynucle- old entranced the sailors on the Rhein. Mechanism based on physical
otides, the Ames test does not identify which enzymes and chemical organic chemistry was forgotten.... Can SAR problems be solved de
species (nitro anion-radical, hydroxylamine radical, or superoxide noVo with 3-D pictures? Our belief is that mechanistic physical organic
radical) are responsible for the mutagenic action. A table with about chemistry is on the verge of an exciting new venture in helping to
260 nitro derivatives and the corresponding equations indicates general elucidate chemico-biological interactions that will do vastly more than
agreement between the two approaches, separately or combined, with simply justify its existence to make only incremental advances in our
more detail provided by the elaborate CoMFA calculations. study of the chemistry of life.”
The following four chapters deal with separate, non-overlapping What the authors of this chaper do is first let the reader know how
topics. Thus, P. S. Magee presents some novel approaches to modeling to mine the rich database for relevant, meaningful, and manageable
transdermal penetration and reactivity with epidermal proteins. Allergic information. Then they show by example what one can learn from such
contact dermatitis and the skin permeation rate are mechanistically data. By grouping together QSAR equations in trems of electronic and/
determined by lipophilicity (log P, which can be partitioned between or lipophilicy parameters, it becomes possible to gain insight into
lipophilic and hydrophilic factors) and by molecular size, modeled by mechanisms of enzymatic reactions. Thus, the signs and Values of the
the molar refraction. Data for about 400 compounds are presented with slopes and intercepts in such equations are powerful indicators about
the various approaches for QSAR. The author then hypothesizes on similarity or dissimilarity between complicated biochemical reactions
the thermodynamic properties of haptens and ends by declaring that and simple reactions that are well-understood mechanistically. Because
he would welcome cooperative efforts to fill in the many blanks in the biological QSARs are more difficult and expensive, and frequently less
field of hapten-protein reactivity. precise and with smaller numbers of data, than physical-organic
An interesting discussion about structure-odor relationships for musk QSARs, “lateral” support by the latter ones can add confidence in the
fragrance is presented by D. Zakarya and M. Chastrette. The authors results of the former studies. Bridges must be built between these two
offer a concise presentation of the various hypotheses, empirical rules, strictly compartmentalized areas of research. Numerous examples are
and QSAR studies concerning structure-musk odor relationships. The presented and discussed, connecting this last chapter with several
most comprehensive study, mentioned in the bibliography of the chapter, previous ones. On this basis, several suggestions for plausible mech-
involved 230 musks and 132 non-musks with structures related to anisms and for promising classes of new drugs are made in this chapter.
musks. The three main classes of synthetic musks are monocyclic It is fitting to conclude this book review with a few other quotations
benzenoid nitromusks, indanes, and tetralins. Subtle steric factors change from this chapter: “The rather abstract, ‘boring’, multivariate equations
BOOK REVIEWS J. Chem. Inf. Comput. Sci., Vol. 40, No. 3, 2000 881

have left many who stopped to think of the enormous complexity of book describes recent developments in automated gene characterization.
the problem of formulating QSAR from a set of chemicals perturbing It does not address mature, well-documented technology such as
a cell or a mouse with the feeling that they were watching a con game.... fluorescence-based sequencing or flow cytometry, but focuses on newer
The 3-D graphics distracted many from trying to relate biological QSAR evolving technologies. The areas covered are quite diverse, including,
to the much better understood mechanistic studies from the fields of for example, atomic force microscopy, miniaturized systems, robotics
physical organic and biochemistry. But the enormous driving force to and robotics software, electronic notebooks, data handling, and data
understand how chemicals react with the various forms of life (and its analysis.
constituent parts) and the economic prospects in terms of designing The book is divided into four sections. The first four chapters cover
the billion-dollar drug as well as understanding toxicology, have been laboratory automation: robotics, software, modular equipment, and
relentless encouragement for more and more researchers to attempt what machine vision. The second section discusses control systems which
some still regard as impossible.... Because there are virtually an un- can integrate and coordinate the operation of different components.
limited number of organic chemicals and a huge number of biological This is followed by a series of chapters describing new technologies
systems (DNA, enzymes, organelles, cells, and whole organisms) with for DNA and RNA sequencing. The final section describes ways to
which they can intercact, we must develop generalizations, limited as acquire, analyze, and manage the mountains of data which are generated
they may be, to be used in the planning stage of synthesis of the myriad by large-scale genome projects.
chemicals we seem to need to facilitate our existence.... Our present The editor has assembled an interesting discussion of the problems
system is a small start on the problem of the design and construction posed by the Human Genome Project and other large-scale sequencing
of a computerized means of keeping account of what has been done efforts. He has illustrated clearly the broad range of-disciplines which
and how it can be used, but we are confident that it will grow rapidly.” must work together to generate and use genomic information. This book
This book will be useful and inspiring for chemists, biochemists, will likely be more interesting to those involved in generating the data
medicinal chemists, and pharmacologists, in addition to the “hard-core” than to the end-users of the data, but the end-users might be interested
professionals involved in drug design, such as computational chemists to see the many different tools which are involved in wrestling the
who devise high-throughput synthesis and screening of combinatorial data from a string of nucleic acids.
libraries. D. Eric Walters
Alexandru T. Balaban Finch UniVersity of Health Sciences/
Polytechnic UniVersity Bucharest, Romania The Chicago Medical School
CI000342O
CI0003404 10.1021/ci000342o
10.1021/ci0003404
The Physics of Laser-Atom Interactions. By Dieter Suter.
Named Organic Reactions. By Thomas Laue and Andreas Cambridge Studies in Modern Optics. Cambridge University
Plagens. John Wiley & Sons: Chichester, U.K., 1998. 288 pp. Press: Cambridge, U.K. 1997. 457 pp. ISBN 0-521-46239-8.
ISBN 0-471-97142-1. $69.95. $100.00
Organic students and chemists know the importance of named This book is joined by several other titles in the series “Cambridge
reactions to their field, and Named Organic Reactions aims to fill an Studies in Modern Optics”, with P. L. Knight and A. Miller serving as
information gap in this area. The authors assert that the book is “suitable series editors. This is an international series which contains books on
for easy reading and learning, as well as for revision [sic] for an exam all aspects of theoretical and applied modem optics at levels ranging
in organic chemistry.” However, the text is dense and includes a level from advanced textbooks to monographs. The book under review
of detail that may prove difficult for some beginning organic students. provides a thorough introduction to the interaction of atoms and atomic
Laue and Plagens describe over 100 reactions judged to be the most ions with optical and magnetic fields. Particular emphasis is placed on
important in preparative organic chemistry and organic classes. They multilevel effects, where more than two atomic states participate in
do not include reactions whose mechanisms are straightforward enough the interaction. Atomic vapors can exhibit anisotropic behavior under
to be deduced easily. Ample references include citations to the original these conditions, giving rise to a wide range of interesting phenomena.
literature, review articles, and recent works. The book is divided into 11 chapters. The Introductory chapter is
As compared to Organic Syntheses Based on Name Reactions and followed by those on Two-Level Atoms, Three-Level Effects, Internal
Unnamed Reactions (Pergamon, 1994), Named Organic Reactions Degrees of Freedom, Optical Pumping, Optically Anisotropic Vapors,
provides a more in-depth description for each reaction, although its Coherent Raman Processes, Sublevel Dynamics, Two-Dimensional
coverage is only 30% of reactions in the older title. The Laue and Spectroscopy, Nonlinear Dynamics, and Mechanical Effects of Light.
Plagens book has only a subject index. Organic Syntheses, on the other With a full and theoretical coverage, and over 250 illustrations, the
hand, provides four indexes including the named reactions, reagents, book will be of great interest to graduate students of laser spectroscopy,
types of reactions, and synthesis of functional groups. quantum electronics, and quantum optics and to researchers in these
This book would be a good supplemental reference; however, it is fields. The book has an extensive list of references and a well-structured
not recommended to be the sole source for named reactions. index.
Sarah George Venkat K. Raman
Indiana UniVersity Chemical Abstracts SerVice
CI000341W CI0003451

10.1021/ci000341w 10.1021/ci0003451

Automation Technologies for Genome Characterization. Data Compression in Digital Systems. By Roy Hoffman.
Edited by Tony J. Beugelsdijk. Wiley-Interscience: New York. Digital Multimedia Standards Series. International Thomson
1997. 306 pp. ISBN 0-471-12806-6. $69.95. Publishing/Chapman & Hall: New York. 1996. 415 pp. ISBN
0-412-08551-8. $64.95.
Once, not long ago, genes were discovered one at a time, with a
great deal of manual effort. Now, the Human Genome Project (and Data compression is a very dynamic field, with applications for
genome projects for other organisms) has turned genomics into a highly compression of speech, audio, image, and video data. As part of the
automated process. This process has, at the same time, become much Digital Multimedia Standards Series, the book is about compressing
more multidisciplinary because automation has brought in robotics and data to make digital systems work more efficiently. The exciting
has created a need for data handling on an unprecedented scale. This technology and its importance for current and future digital systems
882 J. Chem. Inf. Comput. Sci., Vol. 40, No. 3, 2000 BOOK REVIEWS

are explained in easy-to-understand terms. With a well-written overview, Diagrams and illustrations are great. There are hundreds of worked-
the material is organized in four parts: Marketplace, Algorithms, out problems. You could not go wrong selecting this textbook.
Applications, and Digital Systems. Marketplace explores the user But my favorite part of the book comes before chapter 1. There is
requirements for data compression and the marketplace constraints and a letter from Ralph Burns to the chemistry student which explains
rules that effect its application. The chapter on algorithms provides exactly how to learn chemistry. I particularly like the way he addresses
the background needed to understand how the most important data that question which plagues every professor: “What should I memorize
compression algorithms operate; these include algorithms for diffuse for the exam?” Professor Burns, could I please copy those three para-
data and symbolic data. A comprehensive industry-by-industry guide graphs and distribute them to my biochemistry students?
to modern data compression applications is presented in the chapter
on applications. The final chapter on digital systems describes important
D. Eric Walters
decisions and techniques for incorporating data compression in current Finch UniVersity of Health Sciences/
and future digital information-handling systems. The Chicago Medical School
The book has a short list of abbreviations and acronyms and an
CI000346T
extensive list of references. This easy-to-read book is an invaluable
reference and presents a unique blend of introductory material on what 10.1021/ci000346t
data compression is and how it operates, combined with an in-depth
look at how the technology is used in real-world applications. The book
covers data available only at the time of writing (1996), lacking Process Design Principles: Synthesis, Analysis, and Eval-
information on more-recent developments in the fast-paced world of uation. By Warren D. Seider, J. D. Seader, and Daniel R.
consumer electronics. Lewin. Wiley: New York. 1999. 824 pp. ISBN 0-471-24312-
Venkat K. Raman 4. $99.95.
Chemical Abstracts SerVice The courseware for the design of chemical processes is addressed
CI000343G to senior undergraduates. It is a textbook accompanied by a multimedia
CD-ROM that contains more than 500 Mb using ASPEN PLUS,
10.1021/ci000343g HYSYS, and DYNAPLUS; other programs (CHEMCAD, PRO/II) are
to be added in the near future.
Handbook of Computational Quantum Chemistry. By The course is organized in five parts (15 chapters, 550 pages) plus
David B. Cook. Oxford University Press: New York. 1998. 12 appendices (263 pages), followed by author and subject indexes.
743 pp. ISBN 0-19-850114-5. $140.00. Part 1 (Process InventionsHeuristics and Analysis) has the following
four chapters: The Design Process, Process Creation, Simulation To
Quantum chemistry forms the basis of molecular modeling, a tool Assist in Process Creation, and Heuristics for Process Synthesis. Part
widely used to obtain important chemical information and visual images 2 (Detailed Process SynthesissAlgorithmic Methods) contains the
of molecular systems. Advances in computing have meant that there following three chapters: Synthesis of Separation Trains, Second Law
have been considerable developments in molecular modeling, and these Analysis, and Heat and Power Integration. Part 3 (Detailed Design,
developments have lead to significant achievements in the design and
Equipment Sizing, Economics, and Optimization) has four chapters:
synthesis of, for example, drugs and catalysts.
Heat Exchanger Design, Capital Cost Estimation, Profitability Analysis,
The modern and thorough text provides an accessible introduction
and Optimization of Process Flowsheets. Part 4 (Plantwide Control-
to the theory of the main streams of quantum chemical ideas.
lability Assessment) has three chapters: Interaction of Process Design
Throughout the book, the practical implementation of the main areas
and Process Control, Flowsheet Controllability Analysis, and Dynamic
of quantum chemistry accompanies the theoretical explanation. The
Simulation of Process Flowsheets. Part 5 (Design Report) is a single
author presents this in a straightforward and accessible manner, leading
chapter addressing written process design reports and oral presentation.
to the use of modem “Literate Programming” software tools (D. E.
The appendices describe software for process design (ASPEN PLUS,
Knuth’s WEB system).
HYSYS), for dynamic simulation (DYNAPLUS), or for algebraic
The book is divided into 34 well-written chapters, including
modeling systems (GAMS); phase equilibria and process unit models;
Mechanics and Molecules, the Hartree-Fock Method, The Matrix SCF
physical property estimation, solids handling, and electrolytes. Appendix
Equations, A Special Case: Closed Shells, Implementation of the
8 contains problem statements for 31 design projects, each prepared
Closed-shell Case, Tools and Methods, Molecular Integrals, Repulsion
by chemical engineers in Pennsylvania companies for design teams of
Integral Storage, Virtual Orbitals, Population Analysis, The General
three students; the design is to be completed during one semester, with
MO Functional, Molecular Symmetry, The Orthogonal VB model, etc.
advice from faculty and industrial consultants.
A separate chapter is devoted to a compilation of resource materials
A striking feature of this textbook is the continuous use of real-
for additional reading and materials available for downloading from
world problems, lavish use of illustrations, diagrams, tables, and sim-
the Internet; several of the URL’s have, however, already changed.
ulation flowsheets provided by computer programs, as well as numerous
The book provides an up-to-date account of a subject which has
exercises at the end of each chapter. The presentation of case studies
expanded enormously over the past decade both in theoretical methods
enhances the interest of students and provides a background for seminar
and areas of application. This informative text will be of interest to
discussions. A few leading bibliographic references are provided at the
graduate students, academic faculty, and industrial research and
beginning and at the end of most chapters.
development staff in the chemical and pharmaceutical fields.
Environmental protection, safety considerations, and engineering
Venkat K. Raman ethics are discussed in the first chapter, but these aspects are encountered
Chemical Abstracts SerVice throughout the course. Half of the problem statements in Appendix 8
CI0003449 involve environmental tasks. Economics analysis (gross profit) for
alternative reaction paths, along with technical/safety/environmental
10.1021/ci0003449 considerations, determines the ultimate feasibility of a project. Practical
use of computer-aided design tools gives confidence to students.
Fundamentals of Chemistry (3rd ed.). By Ralph A. Burns. In conclusion, this is an excellent and highly recommended course-
Prentice-Hall: Upper Saddle River, NJ. 1999. 744 pp. ISBN ware for undergraduate and postgraduate chemical engineering students.
0-13-918665-4. $77.75. Alexandru T. Balaban
First, the content: This is a sound, well-written textbook for Polytechnic UniVersity of Bucharest, Romania
introductory college chemistry. The material is organized logically and CI000347L
presented in a clear and engaging writing style. Principles are illustrated
with numerous real world examples to which students can relate. 10.1021/ci0003471
BOOK REVIEWS J. Chem. Inf. Comput. Sci., Vol. 40, No. 3, 2000 883

Contemporary Instrumental Analysis. By Kenneth A. Ru- and reliable as the restricted HF (RHF) methods for closed-shell
binson and Judith Faye Rubinson. Prentice-Hall: Upper Saddle molecules. Caveats in the use of DFT methods are discussed; it is
River, NJ. 2000. 840 pp. ISBN 0-13-790726-5. $110. believed that the B3LYP (Becke-Lee-Yang-Parr) ab initio method
is the method of choice. Examples are provided to warn the reader
Instrumental analysis using physical methods such as electrochemical that for open-shell molecules symmetry should never be taken for
methods, electronic absorption and emission spectra, vibrational spectra granted. For diradicals, three cases are discussed in detail: twisted
(infrared and Raman), nuclear magnetic resonance spectra, and mass ethene, square cyclobutadiene, and trimethylenemethane. Various
spectra have changed the paradigms of chemistry, particularly organic properties can be predicted by such calculations: rotation barriers and
chemistry. Coupled with various chromatographic and electrophoretic
other kinetic or thermodynamic parameters, vibrational and electronic
methods, both the identification of natural products and the organic
spectra, and ESR spectra. A glossary of acronyms completes this
synthesis are now based heavily on such post-WWII techniques.
The present textbook mirrors the analytical chemist’s interest and chapter.
approach, starting with sampling techniques and statistical treatment Chapter 2 by Kestner and Combariza, entitled “Basis Set Superposi-
of data, following with principles and intricacies of instruments, and tion Errors: Theory and Practice”, discusses the artifact caused by the
ending with applications of the various methods enumerated above. It lowering of energy of a molecule by the electron density of molecules
is a book of analytical chemists, by analytical chemists, and for in its neighborhood. The full counterpoise correction method is able
analytical chemists. to solve this problem. An appendix provides a sample input deck for
The 18 chapters are well-illustrated with clear figures and numerous counterpoise corrections using Gaussian 92 or 94.
tables, case studies, cross-references, suggestions for further reading, The third chapter by Anderson, entitled “Quantum Monte Carlo:
problems, and exercises. Several appendices, answers to exercises, and Atoms, Molecules, Clusters, Liquids, and Solids”, reviews techniquess
an index conclude the book. such as variational, diffusion, Green’s function, and path integralsapplied
The authors mentioned radioimmunoassay and neutron activation to the increasingly complex systems presented in the chapter’s title.
analysis but did not include some of the other radiochemical techniques, The chapter starts with a quotation from I. N. Levine’s book on quantum
such as Mössbauer spectra and radioisotope dilution analysis; however, chemistry: “If you learn enough abbreviations you can convince some
they did discuss isotope dilution analysis in the framework of mass people that you know quantum chemistry.” There are three main
spectrometry. X-ray diffraction analysis was also left out. Carbon-13 branches of the quantum chemistry’s family tree: density functional
NMR spectra are reported to require either highly concentrated samples, theory (DFT), quantum Monte Carlo (QMC), and Rayleigh-Ritz
13C-enriched samples, or long data collection times (days)sbut this is variational theory (RRV). Many additional branches follow, and they
no longer true with present-day high-field Fourier transform instruments. are illustrated in a diagram. Although the Monte Carlo computer
No 13C-NMR exercises are provided, only figures with 1H-NMR spectra programs are less user friendly than those based on the Hartree-Fock
are among the exercises. A list of available software for analytical approach, and although the Monte Carlo method has not been as widely
chemistry would have been welcome. used as other ways for solving the Schrödinger equation, the power of
This is, however, an excellent textbook, different from the books such calculations consists of their applicability to very large systems.
on physical methods familiar to organic chemists. It is highly However, even for systems with few electrons, QMC methods are
recommended both for analytical and for organic chemistry undergradu- sometimes superior to other approaches. A sampling of applications
ate and graduate students. concludes this chapter, starting with the potential energy surface for
the reaction of a hydrogen atom with a hydrogen molecule, and
Alexandru T. Balaban including metallic lithium or liquid water.
Polytechnic UniVersity Bucharest, Romania “Molecular Models of Water: Derivation and Description” is the
title of the next chapter by Wallqvist and Mountain. Aqueous solutions
have a tremendous importance in chemistry and life sciences; therefore,
CI000348D
many calculations on such systems have been published involving both
10.1021/ci000348d QMC and molecular dynamics computer simulations with a few
thousand water molecules at liquid density. The results reflect the
Reviews in Computational Chemistry, Volume 13. Edited accuracy of the potential functions. The intermolecular interactions
by Kenny B. Lipkowitz and Donald B. Boyd. Wiley-VCH: New between water molecules involve attractive electrostatic, polarization
York. 1999. 426 pp. ISBN 0-471-33135-X. $135. and dispersion forces as well as exchange repulsion. The authors provide
a guide for those who wish to use available computer programs. They
The latest volume in this series continues to provide excellent reviews indicate that the simple point charge (SPC/E) model is probably the
for theoretical and computational chemists. The preface by the two
model of choice, followed by the transferable intermolecular four-site
editors discusses (on the basis of data provided by the Institute of
potential model (TIP4P, with a CPU time load almost twice as high as
Scientific Information for the most cited chemists) the major contribu-
tions due to practitioners of computational chemistry: from the top 50 SPC/E).
authors, a quarter are computational chemists, and from the top 1000 Chapter 5 by Briggs and Antosiewicz is entitled “Simulation of pH-
authors, a tenth are in computational chemistry. Many of these most- Dependent Properties of Proteins Using Mesoscopic Models”. Steering
cited computational chemists have contributed a chapter to ReViews in substrates of enzymes toward the active site, protein stability and
Computational Chemistry. The preface also presents personal views folding, or binding of ligands are among the pH-dependent properties
on the contributions of Professors Norman L. Allinger and Michael J. of proteins. Molecular dynamics simulations, such as the finite
S. Dewar. difference Poisson-Boltzmann (FDPB) method reported by Bashford
The first chapter by Bally and Borden is entitled “Calculations on and Karplus in 1990, were followed by developments which included
Open-Shell Molecules: A Beginner’s Guide”; it provides, as the title the authors’ own calculations based on the Monte Carlo technique. A
says, a survey of methods for computing wave functions for radicals, computationally-efficient three-step algorithm is presented. Protonation
radical-ions, and diradicals. Such open-shell species have gained equilibria of proteins are discussed assuming that the solvent and the
importance after the discovery that many reactions previously believed solute can be treated as continuous dielectric media. Alternative
to involve movements of electron pairs actually occur by single- microscopic simulations based on the protein dipole-Langevin dipole
electron-transfer steps. The restricted open-shell Hartree-Fock (HF) (PDLD) model are extremely time intensive. The experimental and
method does not include spin polarization; hence, it is unable to predict theoretical approaches for determining pKa values and pH-dependent
spin densities, whereas the unrestricted Hartree-Fock wave functions properties of proteins are presented and are followed by sample
do not yield pure spin states because they introduce the artifact of spin applications such as the total charge of the bovine pancreas trypsin
contamination. A possible remedy is to use the CASSCF (complete inhibitor, the binding of inhibitors by HIV protease, and the dipole
active space self-consistent field) and other procedures. An attractive moments of proteins.
alternative is provided by density functional theory (DFT), which is The sixth and last chapter, entitled “Structure Diagram Generation”,
able to make calculations for most radicals and radical-ions as easy was written by Helson. Nowadays all chemical journals expect two-
884 J. Chem. Inf. Comput. Sci., Vol. 40, No. 3, 2000 BOOK REVIEWS

dimensional chemical structures to be provided using commercially Chapter 1 presents the concepts behind the molecular mechanics
available programs such as ChemDraw, ChemWindow, or ISIS/Draw. method, while Chapter 2 describes and compares the factors which
The effort to produce such software during the past 2 decades is determine the performance of the most commonly used force fields.
reviewed, without burdening the reader by specialist jargon (and a Both chapters end with a useful summary section. Chapter 3 describes
glossary plus list of acronyms assists the less initiated). One should be how various force fields were parametrized and concludes with a
aware that years of effort and tens of thousands of lines of code are practical guide on how to derive parameters for applications not covered
needed for such software; some of the programs are available free for by the chosen force field. Chapter 4 focuses on solvation. Discrete
the asking. solvent models are very briefly discussed. Continuum solvation models
All chapters are accompanied by many bibliographic references, and are evaluated, and suggestions are made for the appropriate application
the volume has an author and an extensive subject index, reflecting of each. Chapter 5 describes energy minimization techniques with the
the editors’ care to produce yet another high-quality review volume. goal of providing sufficient information to allow the nonspecialist user
Alexandru T. Balaban to select the appropriate technique for a particular application. Two
Polytechnic UniVersity of Bucharest, Romania cases are used as benchmarks for the various minimization routines:
minimization of a small protein and minimization of a molecular
CI0003496 complex. In addition, special attention is given to how to locate
transition states on a potential energy surface. Chapter 6 describes the
10.1021/ci0003496
various methods of conformational analysis and their application to
location of a global energy minimum, treatment of macrocyclic
Molecular Mechanics and Conformational Analysis in structures, and docking of a ligand in a protein. Chapter 7 describes
Drug Design. By Gyorgy Keseru and Istvan Kolossvary. various techniques for calculating binding free energy with particular
attention paid to the MINTA technique developed by one of the authors.
Blackwell Science Ltd.: Oxford, U.K. 1999. 168 pp. ISBN
Chapter 8 presents a case study in biomolecular modeling based on
0-632-05289-9. $120.
the example of ligand binding to cytochrome P-450.
The aim of this book is to introduce the basic concepts of molecular The book contains 18 color plates illustrating various molecular
mechanics and conformational analysis to the nonspecialist. Since structures, properties, and complexes. It is a very readable introduction
desktop modeling is becoming widespread in the workplace, compu- to the concepts and applications of molecular mechanics for the
tational chemistry tools are routinely used by many nonspecialists as specialist and nonspecialist alike.
an aid to their research. The present book provides a useful introduction Bruce Slutsky and Carol A. Venanzi
to the theory behind the computational algorithms. The material is
presented in sufficient detail to allow the nonspecialist to make informed
New Jersey Institute of Technology
decisions about force field parameters, solvation models, and complete- CI0003505
ness of a conformational search, for example, so that the modeling
software can be used as more than a calculational “black box”. 10.1021/ci003505