Volume 11 Reviews in Computational Chemistry Kenny B. Lipkowitz and Donald B. Boyd The Theme of this Eleventh Volume is Computer-Aided Ligand Design and Modeling of Biomolecules. A Stellar Group of Scientists from Around the World Join in this Volume to Provide Tutorials for Beginners and Experts. Chapters 1 and 2 Take A Detailed Look at De Novo Design Methodologies for Discovering New Ligands which May Become Pharmaceuticals. Chapters 3 and 4 Cover the Methods and Applications of Three-Dimensional Quantitative Structure-Activity Relationships (3D-QSAR) Currently Used in Drug Discovery. Ways to Compute the Correct Lipophilic/Hydrophilic Behavior of Molecules are Taught in Chapter 5. Chapter 6 is an Exposition of Realistically Simulating DNA in the Complex Milieu of Ions that Surround it. An Appendix to this Volume Gives A Compendium of Software and Internet Tools for Computational Chemistry. -From Reviews of the Series . This Well-Respected Series Continues the Fine Selection of Topics and Presentation Qualities Set Forth by the Previous Members. For Example, Each Chapter Contains Thorough Treatment of the Theory Behind the Topic Being Covered. Moreover, the Background Material is Followed by Ample Timely Examples Culled From Recent Literature. Journal of Medicinal Chemistry

Volume 5 Reviews in Computational Chemistry Kenny B. Lipkowitz and Donald B. Boyd A Valuable Resource for Novices and Practitioners Alike, This Series Features Detailed Treatments of the Latest Advances in Computational Methods for Organic, Pharmaceutical, Physical, and Biological Chemistry. Balancing Academic and Industrial Interests, Volume 5 Presents Tutorials on Post-Hartree-Fock Methods, Electron Population Analysis, Brownian Dynamics, Lipid Simulations, Distance Geometry in Molecular Modeling, and Computer-Aided Drug Design. A History Traces the Field's Growth and Relationship to Funding Agencies. An Enlarged Compendium of Software Serves As a Valuable Buyer's guide. -From Reviews of the Series Many of the Articles are Indeed Accessible to any Interested Nonspecialist, Even Without Theoretical Background. Journal of the American Chemical Society This Book Serves Beginners as Well as Experts Looking for New Perspectives in the Field and is Highly Recommended. Journal of Molecular Graphics

This volume in the series brings together reknowned experts in the field to present the reader with an account of the latest developments in quantum mechanics, molecular dynamics, and the teaching of computational chemistry.
There are so many developments in the field of computational chemistry that it is difficult to keep track of them. The series was established to review the high volume of developments in the field.
Rather than create a traditional article, each author approaches a topic to enable the reader to understand and solve problems and locate key references quickly. Each article has tutorial value.
An updated compendium of software for molecular modeling appears as an appendix as in previous volumes. To the editors' knowledge, this is the most complete listing of sources of software for computational chemistry anywhere.

This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Volume 19 is centered on the theme of macroscopic modeling, and discusses topics such as: Monte Carlo simulation techniques, computing hydrophobicity, classical trajectory simulations within the Born-Oppenheimer approximation, and the theory behind the widely used Poisson-Boltzmann equation.

FROM REVIEWS OF THE SERIES

"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."
–JOURNAL OF MOLECULAR GRAPHICS AND MODELLING

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
–JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Two chapters focus on molecular docking, one of which relates to drug discovery and cheminformatics and the other to proteomics. In addition, this volume contains tutorials on spin-orbit coupling and cellular automata modeling, as well as an extensive bibliography of computational chemistry books.

FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."—JOURNAL OF MOLECULAR GRAPHICS AND MODELLING

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."—JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Volume 16

Reviews In Computational Chemistry

Kenny B. Lipkowitz and Donald B. Boyd

The focus of this book is on methods useful in molecular design. Tutorials and reviews span (1) methods for designing compound libraries for combinatorial chemistry and high throughput screening, (2) the workings of artificial neural networks and their use in chemistry, (3) force field methods for modeling materials and designing new substances, and (4) free energy perturbation methods of practical usefulness in ligand design.

From Reviews of the Series

"This series spans all the subdisciplines in the field, from techniques to practical applications, and includes reviews from many of the acknowledged leaders in the field. the reviews cross many subdisciplines yet are both general enough to be of wide interest while including detailed information of use to workers in particular subdisciplines." –Journal of the American Chemical Society

Volume 10 Reviews in Computational Chemistry Kenny B. Lipkowitz and Donald B. Boyd In This Volume, Several Chapters Share the Theme of Chaos and Randomness. Chapter 1 Shows How Genetic Algorithms Work to Find Global Minima on Complex Response Surfaces; The Many Applications of This Increasingly Popular Tool are Reviewed. Chapter 2 Addresses the Question of Whether Computational Chemistry Can Survive in the New Era of Combinatorial Chemistry; Techniques for Optimal Design of Structure-Activity Relationships and Molecular Diversity are Explained. Chapter 3 Teaches about Phase Space and the Use of Nonlinear Dynamics to Solve Questions in Reaction Dynamics, While Chapter 4 is a Tutorial on Universal Phenomena in the Natural Sciences from the Perspective of Nonlinear Dynamics. Chapter 5 is a History of Pivotal Developments in the Growth of Computational Chemistry in the United Kingdom. -From Reviews of the Series ... An Excellent Source of Background Information as well as of Current Research Studies in Computational Chemistry. Journal of Medicinal Chemistry

Volume 9 Reviews in Computational Chemistry Kenny B. Lipkowitz and Donald B. Boyd A Select Group of Scientists from Around the World Join in this Volume to Create Unique Chapters Aimed at Both the Novice Molecular Modeler and the Expert Computational Chemist. Chapter 1 Shows how Molecular Modeling of Peptidomimetics Plays a Key Role in Drug Discovery. Specific Examples of Successful Computer-Aided Drug Design are Spelled Out. Chapter 2 is a Definitive Exposition on Thermodynamic Perturbation and Thermodynamic Integration Approaches in Molecular Dynamic Simulations. Three Chapters Elucidate Molecular Modeling of Carbohydrates, the Best Empirical Force Fields to Use in Molecular Mechanics, and Molecular Shape as a Useful Quantitative Descriptor. -From Reviews of the Series ...Very Capably Organized and Edited....Timely, Authoritative, and Well-Written....of Considerable Value to Anyone Pursuing Computational Methods. Journal of Medicinal Chemistry

Not only a major reference work for sale to the library market, this series is now receiving an increase in purchases by individuals. This increase is due to the explosive growth in the use of computational chemistry throughout many scientific disciplines As each volume does not follow a singular theme, the table of contents is a vital tool in the defining the areas examined by a volume The series contains updated and comprehensive compendiums of molecular modeling software that list hundreds of programs, services, suppliers, and other information that every chemist will find useful Detailed author and subject indices on each volume help the reader to quickly discover particular topics Uniting the most respected authors in their fields, the series is designed to help the reader stay abreast of the many new developments in computational techniques The chapters are approached in a tutorial manner and wirtten in a non-mathematical style allowing students and researches to access computational methods outside their immediate area of expertise

This is the seventh volume in the successful series designed to help the chemistry community keep current with the many new developments in computational techniques. The writing style is refreshingly pedagogical and non-mathematical, allowing students and researchers access to computational methods outside their immediate area of expertise. Each invited author approaches a topic with the aim of helping the reader understand the material, solve problems, and locate key references quickly.

From reviews of the series:
'Many of the articles are indeed accessible to any interested nonspecialist, even without theoretical background.'
Journal of the American Chemical Society
'...an invaluable resource for the serious molecular modeler.' Chemical Design Automation News

This second volume of the series 'Reviews in Computational Chemistry' explores new applications, new methodologies, and new perspectives. The topics covered include conformational analysis, protein folding, force field parameterizations, hydrogen bonding, charge distributions, electrostatic potentials, electronic spectroscopy, molecular property correlations, and the computational chemistry literature. Methodologies described include conformational search strategies, distance geometry, molecular mechanics, molecular dynamics, ab initio and semiempirical molecular orbital calculations, and quantitative structure-activity relationships (QSAR) using topological and electronic descriptors.
A compendium of molecular modeling software will help users select the computational tools they need. Each chapter in 'Reviews in Computational Chemistry' serves as a brief tutorial for organic, physical, pharmaceutical, and biological chemists new to the field. Practitioners will be interested in the recent advances.

This book is an account of current developments in computational chemistry, a new multidisciplinary area of research. Experts in computational chemistry, the editors use and develop techniques for computer-assisted molecular design. The core of the text itself deals with techniques for computer-assisted molecular design. The book is suitable for both beginners and experts.
In addition, protocols and software for molecular recognition and the relationship between structure and biological activity of drug molecules are discussed in detail. Each chapter includes a mini-tutorial, as well as discussion of advanced topics.
Special Feature: The appendix to this book contains an extensive list of available software for molecular modeling.

REVIEWS IN COMPUTATIONAL CHEMISTRY

Kenny B. Lipkowitz, Raima Larter, and Thomas R. Cundari

This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. TOPICS COVERED IN Volume 21 iNCLUDE AB INITIO QUANTUM SIMULATION IN SOLID STATE CHEMISTRY; MOLECULAR QUANTUM SIMILARITY; ENUMERATING MOLECULES; VARIABLE SELECTION; BIOMOLECULAR APPLICATIONS OF POISSON-BOLTZMANN METHODS; AND DATA SOURCES AND COMPUTATIONAL APPROACHES FOR GENERATING MODELS OF GENE REGULATORY NETWORKS.

FROM REVIEWS OF THE SERIES

"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."
--JOURNAL OF MOLECULAR GRAPHICS AND MODELLING

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
--JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

VOLUME 25

Reviews in Computational Chemistry

Kenny B. Lipkowitz and Thomas R. Cundari

This Volume, Like Those Prior To It, Features Pedagogically Driven Reviews By Experts In Various Fields Of Computational Chemistry. Volume 25 Contains: Eight Chapters Covering The Glass Transition In Polymer Melts, Atomistic Modeling Of Friction, The Computation Of Free Volume, Structural Order And Entropy Of Liquids And Glasses, The Reactivity Of Materials At Extreme Conditions, Magnetic Properties Of Transition Metal Clusters, Multiconfigurational Quantum Methods For The Treatment Of Heavy Metals, Recursive Solutions To Large Eigenvalue Problems, And The Development And Uses Of Artificial Intelligence In Chemistry.

From Reviews of the Series

"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."
--JOURNAL OF MOLECULAR GRAPHICS AND MODELLING

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
--JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reviews In Computational Chemistry

Martin Schoen and Sabine Klapp

Kenny B. Lipkowitz and Thomas Cundari, Series Editors

This volume, unlike those prior to it, consists of a single monograph covering the timely topic of confined fluids. Volume 24 features the thermodynamics of confined phases, elements of statistical thermodynamics, one-dimensional hard-rod fluids, mean-field theory, treatments of confined fluids with short-range and long-range interactions, and the statistical mechanics of disordered confined fluids. Six appendices are included, which cover the mathematical derivation of equations used throughout the book.

From Reviews Of The Series

"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."
--Journal Of Molecular Graphics And Modelling

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
--Journal Of The American Chemical Society

THIS VOLUME, WHICH IS DESIGNED FOR STAND-ALONE USE IN TEACHING AND RESEARCH, FOCUSES ON QUANTUM CHEMISTRY, AN AREA OF SCIENCE THAT MANY CONSIDER TO BE THE CENTRAL CORE OF COMPUTATIONAL CHEMISTRY. TUTORIALS AND REVIEWS COVER

1. HOW TO OBTAIN SIMPLE CHEMICAL INSIGHT AND CONCEPTS FROM DENSITY FUNCTIONAL THEORY CALCULATIONS,
2. HOW TO MODEL PHOTOCHEMICAL REACTIONS AND EXCITED STATES, AND
3. HOW TO COMPUTE ENTHALPIES OF FORMATION OF MOLECULES.

A FOURTH CHAPTER TRACES CANADIAN RESEARCH IN THE EVOLUTION OF COMPUTATIONAL CHEMISTRY. ALSO INCLUDED WITH THIS VOLUME IS A SPECIAL TRIBUTE TO QCPE.FROM REVIEWS OF THE SERIES

"Reviews in Computational Chemistry proves itself an invaluable resource to the computational chemist. This series has a place in every computational chemist’s library."—Journal of the American Chemical Society

THIS BOOK HAS SIX TUTORIALS AND REVIEWS WRITTEN BY INVITED EXPERTS. FIVE CHAPTERS TEACH TOPICS IN QUANTUM MECHANICS AND MOLECULAR SIMULATIONS. THE SIXTH CHAPTER EXPLAINS HOW PROGRAMS FOR CHEMICAL STRUCTURE DRAWING WORK. AN EDITORIAL DISCUSSES SOME OF THE MOST WELL-KNOWN PERSONAGES IN COMPUTATIONAL CHEMISTRY.
FROM REVIEWS OF THE SERIES "Anyone who is doing or intends to do computational research on molecular structure and design should seriously consider purchasing this book for his or her personal library."-JOURNAL OF COMPUTATIONAL CHEMISTRY.
"These reviews are becoming regarded as the standard reference among both specialists and novices in the expanding field of computational chemistry." -JOURNAL OF MOLECULAR GRAPHICS AND MODELLING.
"[This book is] written for newcomers learning about molecular modeling techniques as well as for seasoned professionals who need to acquire expertise in areas outside their own."-JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCE.

FROM REVIEWS OF THE SERIES
"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."
-JOURNAL OF MOLECULAR GRAPHICS AND MODELLING
"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
-JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

VOLUME 12: REVIEWS IN COMPUTATIONAL CHEMISTRY

Kenny B. Lipkowitz and Donald B. Boyd

HOW DOES ONE COMPUTE FREE ENERGY AND ENTROPY FROM MOLECULAR SIMULATIONS? WHAT HAPPENS WHEN SIMULATIONS ARE RUN WITH CONSTRAINTS? HOW SHOULD SIMULATIONS BE PERFORMED TO MODEL INTERFACIAL PHENOMENA? HOW IS DENSITY FUNCTIONAL THEORY USED TO SIMULATE MATERIALS? WHAT QUANTUM MECHANICAL METHODS SHOULD BE USED TO COMPUTE NONLINEAR OPTICAL PROPERTIES OF MATERIALS? WHICH PARAMETERS ARE MOST INFLUENTIAL IN A MOLECULAR SIMULATION? HOW CAN CRYSTAL STRUCTURES BE PREDICTED? TUTORIALS PROVIDING ANSWERS TO THESE QUESTIONS ARE THE FOCUS OF THIS BOOK.

FROM REVIEWS OF THE SERIES

"The series continues to be one of the most useful information sources."
--JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centred around molecular modelling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR).
The series contains updated and comprehensive compendiums of molecular modelling software that list hundreds of programs, services, suppliers and other information that every chemist will find useful.

THIS VOLUME, LIKE THOSE PRIOR TO IT, FEATURES CHAPTERS BY EXPERTS IN VARIOUS FIELDS OF COMPUTATIONAL CHEMISTRY. TOPICS COVERED IN VOLUME 20 INCLUDE VALENCE THEORY, ITS HISTORY, FUNDAMENTALS, AND APPLICATIONS; MODELING OF SPIN-FORBIDDEN REACTIONS; CALCULATION OF THE ELECTRONIC SPECTRA OF LARGE MOLECULES; SIMULATING CHEMICAL WAVES AND PATTERNS; FUZZY SOFT-COMPUTING METHODS AND THEIR APPLICATIONS IN CHEMISTRY; AND DEVELOPMENT OF COMPUTATIONAL MODELS FOR ENZYMES, TRANSPORTERS, CHANNELS, AND RECEPTORS RELEVANT TO ADME/TOX.

FROM REVIEWS OF THE SERIES

"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."
-JOURNAL OF MOLECULAR GRAPHICS AND MODELING

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
-JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics covered in volume 18 include molecular modeling, computer-assisted molecular design (camd), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (qsar).

FROM REVIEWS OF THE SERIES

"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."
–JOURNAL OF MOLECULAR GRAPHICS AND MODELLING

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
–JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

FROM REVIEWS OF THE SERIES Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry.-JOURNAL OF MOLECULAR GRAPHICS AND MODELLING One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general).-JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

THIS VOLUME, LIKE THOSE PRIOR TO IT, FEATURES CHAPTERS BY EXPERTS IN VARIOUS FIELDS OF COMPUTATIONAL CHEMISTRY. Volume 23 COVERS LINEAR SCALING METHODS FOR QUANTUM CHEMISTRY, VARIATIONAL TRANSITION STATE THEORY, COARSE GRAIN MODELING OF POLYMERS, SUPPORT VECTOR MACHINES, CONICAL INTERSECTIONS, ANALYSIS OF INFORMATION CONTENT USING SHANNON ENTROPY, AND HISTORICAL INSIGHTS INTO HOW COMPUTING EVOLVED IN THE PHARMACEUTICAL INDUSTRY.

FROM REVIEWS OF THE SERIES

""Reviews in Computational Chemistry" remains the most valuable reference to methods and techniques in computational chemistry."
--"JOURNAL OF MOLECULAR GRAPHICS AND MODELLING"

"One cannot generally do better than to try to find an appropriate article in the highly successful "Reviews in Computational Chemistry." The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."
--"JOURNAL OF THE AMERICAN CHEMICAL SOCIETY"