Reviews in Computational Chemistry, Volume 28 E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Reviews in Computational Chemistry
• Sprache: Englisch

Seitenzahl: 1153

Veröffentlichungsjahr: 2015

Beschreibung

The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include: * Free-energy Calculations with Metadynamics * Polarizable Force Fields for Biomolecular Modeling * Modeling Protein Folding Pathways * Assessing Structural Predictions of Protein-Protein Recognition * Kinetic Monte Carlo Simulation of Electrochemical Systems * Reactivity and Dynamics at Liquid Interfaces

Leseprobe

Contents

Cover

Title Page

Preface

List of Contributors

Contributors to Previous Volumes

Chapter 1: Free-Energy Calculations with Metadynamics

Introduction

Molecular Dynamics and Free-Energy Estimation

A Toy Model: Alanine Dipeptide

Biased Sampling

Adaptive Biasing with Metadynamics

Well-Tempered Metadynamics

Metadynamics How-To

Advanced Collective Variables

Improved Variants

Conclusion

Acknowledgments

Appendix A: Metadynamics Input Files with PLUMED

References

Chapter 2: Polarizable Force Fields for Biomolecular Modeling

Introduction

Modeling Polarization Effects

Recent Developments

Applications

Summary

Acknowledgment

References

Chapter 3: Modeling Protein Folding Pathways

Introduction

Protein Simulation Methodology

Unfolding: The Reverse of Folding

Elevated Temperature Unfolding Simulations

Biological Relevance of Forced Unfolding

Biased or Restrained MD

Characterizing Different States

Protein Folding and Refolding

Folding in Families

Conclusions and Outlook

Acknowledgment

References

Chapter 4: Assessing Structural Predictions of Protein-Protein Recognition

Introduction

Protein-Protein Docking

The CAPRI Experiment

Assessing Docking Predictions

Recent Developments in Modeling Protein-Protein Interaction

Conclusion

Acknowledgments

References

Chapter 5: Kinetic Monte Carlo Simulation of Electrochemical Systems

Background

Introduction to Kinetic Monte Carlo

Electrochemical Relationships

Applications

Conclusions and Future Outlook

Acknowledgments

References

Chapter 6: Reactivity and Dynamics at Liquid Interfaces

Introduction

Simulation Methodology for Liquid Interfaces

The Neat Interface

Solutes at Interfaces: Structure and Thermodynamics

Solutes at Interfaces: Electronic Spectroscopy

Solutes at Interfaces: Dynamics

Summary

Reactivity at Liquid Interfaces

Conclusions

Acknowledgments

References

Chapter 7: Computational Techniques in the Study of the Properties

Historical Perspective

Structures

The van der Waals-Platteeuw Solid Solution Theory

Computational Advancements

Outlook

References

Chapter 8: The Quantum Chemistry of Loosely-Bound Electrons

Introduction and Overview

Terminology and Fundamental Concepts

Quantum Chemistry for Metastable Anions

Quantum Chemistry for Weakly-Bound Anions

Concluding Remarks

Acknowledgments

Appendix A: List of Acronyms

References

Index

End User License Agreement

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Guide

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Table of Contents

Preface

Begin Reading

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List of Tables

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Reviews in Computational Chemistry 28

Edited by

Abby L. Parrill

Kenny B. Lipkowitz

Abby L. Parrill,

Department of Chemistry

The University of Memphis Memphis, TN 38152, U.S.A.

[email protected]

Kenny B. Lipkowitz,

Office of Naval Research

875 North Randolph Street

Arlington, VA 22203-1995, U.S.A.

[email protected]

Copyright © 2015 by John Wiley & Sons, Inc. All rights reserved

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Library of Congress Cataloging-in-Publication Data:

ISBN: 978-1118-40777-6 ISSN: 1069-3599

Preface

As Reviews in Computational Chemistry begins its 24th year with this 28th volume, it is interesting to reflect on how it has integrated with and influenced my own career over this time period, now that I have joined Kenny as a new series editor. The pedagogically driven reviews focused on computational chemistry were a tremendous resource to me during my graduate studies in the mid-1990s. The series was such an asset in so many ways that none of the volumes could ever be found in the university library, but were always on loan to one of the members of my research group and could be found right in our lab on someone’s desk. I have continued to use the series as a first resource when moving into new areas of computational chemistry, as well as a first place to refer my own graduate students when they begin learning how to function as computational chemists. I hope you have enjoyed and utilized this series in these and other ways throughout your own computational chemistry career.

This volume of Reviews in Computational Chemistry begins with a tutorial on the theory and practice of metadynamics for free-energy calculations. Metadynamics is one of the growing number of methodologies to improve sampling of rare events in order to study chemical processes that occur at timescales outside the scope of unbiased molecular dynamics simulations. As with many biased sampling methods, the choices of the user have tremendous influence on the quality of results. Giovanni Bussi and Davide Branduardi discuss results of different types of metadynamics simulations on the alanine dipeptide with different choices of collective variables to illustrate practical usage of the theories they describe. Users interested in learning how to perform metadynamics calculations will appreciate the sample input files provided in Appendix A.

Chapter 2 addresses a different modeling challenge, namely improving the accuracy of force fields with regard to their treatment of the environmental dependence of charge polarization in molecular systems. Traditional molecular mechanics force fields have relied upon fixed charges that can only represent averaged polarization. This leads to inaccuracies that prevent fixed-charge force fields from correctly modeling the phase transitions of molecules as small as water or accurately computing the barrier height to ion permeation across lipid membranes. Yue Shi, Pengyu Ren, Michael Schnieders, and Jean-Philip Piquemal provide a historical reflection on the development of polarizable force fields and a thorough review of recent developments. Specific applications of polarizable force fields from water simulations to crystal structure prediction demonstrate the current capabilities of polarizable force fields.

In Chapter 3, Clare-Louise Towse and Valerie Daggett demonstrate how the simple principle of microscopic reversibility can be utilized to simplify investigations of protein folding. In particular, a variety of methods to accelerate the unfolding process are described in order to address two of the major challenges faced when simulating protein folding by molecular dynamics. First, the protein unfolding pathway can be initiated from a well-defined structure for any protein that has been characterized by X-ray crystallography. This is not the case for the protein folding pathway, for which starting structures are not known. Second, the timescale of protein folding can be as long as minutes, a timescale that is not tractable with unbiased and unaccelerated simulations. Applications of protein unfolding simulations and the insights they provide regarding protein folding demonstrate the value of this approach.

Assessment is an integral part of demonstrating the value of any new computational method or application area. Chapter 4 illustrates one of the ongoing ‘big science’ assessment initiatives, CAPRI (Critical Assessment of Predicted Interactions). CAPRI competitions over a 12-year period have been possible through the cooperation of structural biologists, who delayed publication of crystallographic structures of the protein assemblies that served as the basis for blind predictions of the assembled complex using crystallographic structures of individual members of the assembly as input. Joël Janin, Shoshana J. Wodak, Marc F. Lensink, and Sameer Velankar describe the assessment metrics, results and impacts of the CAPRI experiment on the field of protein-protein interaction prediction.

Chapter 5 draws attention to kinetic Monte Carlo simulations of electrochemical systems, systems with substantial commercial significance due to the relevance of such systems to our future energy needs. Kinetic Monte Carlo simulations are suitable for timescales and length scales between those typically modeled using molecular dynamics and those typically modeled using mesoscale modeling. Given a set of states and transition rates between those states, kinetic Monte Carlo simulations can predict both the system time evolution behavior and thermodynamic averages of the system at equilibrium. Applications of kinetic Monte Carlo to understand problems ranging from passive layer formation at the solid electrolyte interphase to electrochemical dealloying demonstrate the value of simulations in the design of next-generation materials and operational advances to improve device performance.

Chapter 6 focuses on liquid interfaces, at which reactivity and dynamics play a role in applications ranging from solar cell operation to ion channel function. Throughout this chapter, Ilan Benjamin balances the theoretical underpinnings and practical aspects of simulating the reactivity and dynamics of liquid interfaces with a review of the experimental data used to assess the accuracy of the simulated behaviors.

Chapter 7is tightly focused on clathrate hydrates. As in the previous two chapters, commercial significance is linked with energy due to the role of clathrate hydrates in natural gas pipeline obstructions and safety concerns as well as the untapped potential of naturally occurring methane hydrates to serve as a valuable energy source capable of fueling current energy consumption rates for several hundred years. Advances are described that allow computation of clathrate hydrate features from thermodynamic stability to hydrate nucleation and growth.

The volume concludes with a chapter by John Herbert defining the challenges inherent in modeling systems containing loosely-bound electrons (such as solvated electrons) and methods to meet those challenges. Studies on systems involving loosely-bound electrons have the potential to expand our understanding of low-energy electron-induced reactions, that exhibit highly selective cleavage of specific bonds, which are often not the thermodynamically weakest bonds in the molecule. Quantum calculations must accommodate the highly diffuse nature of the weakly-bound electron through the use of an “ultra-diffuse” one-particle basis set. More specialized techniques are required in the case of metastable and formally unbound anions.

Reviews in Computational Chemistry continues to be a valuable resource to the scientific community entirely due to the contributions of the authors whom we have contacted to provide the pedagogically driven reviews that have made this ongoing book series so popular. We are grateful for their contributions.

The most recent volumes of Reviews in Computational Chemistry are available in an online form through Wiley InterScience. Please consult the Web (http://www.interscience.wiley.com/onlinebooks) or contact [email protected] for the latest information.

We thank the authors of this and previous volumes for their excellent chapters.

Abby L. ParrillMemphis

Kenny B. Lipkowitz Washington January 2015

List of Contributors

Ilan Benjamin, Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA

Davide Branduardi, Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Frankfurt am Main, D-60438, Germany

Giovanni Bussi, Statistical and Molecular Biophysics Group, International School for Advanced Studies (SISSA), Trieste, IT-34136, Italy

Valerie Daggett, Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA

Brett I. Dunlap, Chemistry Division, US Naval Research Laboratory, Washington, DC, 20375-5342, USA

Lev D. Gelb, Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, TX, 75080, USA

John M. Herbert, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA

Joël Janin, IBBMC, Université Paris-Sud, Orsay 91405, France

Marc F. Lensink, UGSF, CNRS UMR8576, University Lille North of France, Villeneuve d’Ascq, 59658, France

Jean-Philip Piquemal, Laboratoire de Chimie Théorique (UMR 7616), UPMC, Sorbonne Universités, Paris, Cedex 05 75252, France

Pengyu Ren, Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA

Michael Schnieders, Department of Biomedical Engineering, College of Engineering, Department of Biochemistry, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA

Yue Shi, Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA

Clare-Louise Towse, Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, United States

John S. Tse, Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B2, Canada

C. Heath Turner, Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487-0203, USA

Sameer Velankar, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK

Shoshana J. Wodak, VIB Structural Biology Research Center, VUB Building E Pleinlaan 2 1050, Brussel, Belgium

Zhongtao Zhang, Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487-0203, USA

Contributors to Previous Volumes

Volume 1 (1990)

David Fellerand Ernest R. Davidson, Basis Sets for Ab Initio Molecular Orbital Calculations and Intermolecular Interactions.

James J. P. Stewart, Semiempirical Molecular Orbital Methods.

Clifford E. Dykstra, Joseph D. Augspurger, Bernard Kirtman, and David J. Malik, Properties of Molecules by Direct Calculation.

Ernest L. Plummer, The Application of Quantitative Design Strategies in Pesticide Design.

Peter C. Jurs, Chemometrics and Multivariate Analysis in Analytical Chemistry.

Yvonne C. Martin, Mark G. Bures, and Peter Willett, Searching Databases of Three-Dimensional Structures.

Paul G. Mezey, Molecular Surfaces.

Terry P. Lybrand, Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods.

Donald B. Boyd, Aspects of Molecular Modeling.

Donald B. Boyd, Successes of Computer-Assisted Molecular Design.

Ernest R. Davidson, Perspectives on Ab Initio Calculations.

Volume 2 (1991)

Andrew R. Leach, A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules.

John M. Troyer and Fred E. Cohen, Simplified Models for Understanding and Predicting Protein Structure.

J. Phillip Bowen and Norman L. Allinger, Molecular Mechanics: The Art and Science of Parameterization.

Uri Dinur and Arnold T. Hagler, New Approaches to Empirical Force Fields.

Steve Scheiner, Calculating the Properties of Hydrogen Bonds by Ab Initio Methods.

Donald E. Williams, Net Atomic Charge and Multipole Models for the Ab Initio Molecular Electric Potential.

Peter Politzer and Jane S. Murray, Molecular Electrostatic Potentials and Chemical Reactivity.

Michael C. Zerner, Semiempirical Molecular Orbital Methods.

Lowell H. Hall and Lemont B. Kier, The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modeling.

I. B. Bersuker and A. S. Dimoglo, The Electron-Topological Approach to the QSAR Problem.

Donald B. Boyd, The Computational Chemistry Literature.

Volume 3 (1992)

Tamar Schlick, Optimization Methods in Computational Chemistry.

Harold A. Scheraga, Predicting Three-Dimensional Structures of Oligopeptides.

Andrew E. Torda and Wilfred F. van Gunsteren, Molecular Modeling Using NMR Data.

David F. V. Lewis, Computer-Assisted Methods in the Evaluation of Chemical Toxicity.

Volume 4 (1993)

Jerzy Cioslowski, Ab Initio Calculations on Large Molecules: Methodology and Applications.

Michael L. McKee and Michael Page, Computing Reaction Pathways on Molecular Potential Energy Surfaces.

Robert M. Whitnell and Kent R. Wilson, Computational Molecular Dynamics of Chemical Reactions in Solution.

Roger L. DeKock, Jeffry D. Madura, Frank Rioux, and Joseph Casanova, Computational Chemistry in the Undergraduate Curriculum.

Volume 5 (1994)

John D. Bolcer and Robert B. Hermann, The Development of Computational Chemistry in the United States.

Rodney J. Bartlett and John F. Stanton, Applications of Post-Hartree-Fock Methods: A Tutorial.

Steven M. Bachrach, Population Analysis and Electron Densities from Quantum Mechanics.

Jeffry D. Madura, Malcolm E. Davis, Michael K. Gilson, Rebecca C. Wade, Brock A. Luty, and J. Andrew McCammon, Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations.

K. V. Damodaran and Kenneth M. Merz Jr., Computer Simulation of Lipid Systems.

Jeffrey M. Blaney and J. Scott Dixon, Distance Geometry in Molecular Modeling.

Lisa M. Balbes, S. Wayne Mascarella, and Donald B. Boyd, A Perspective of Modern Methods in Computer-Aided Drug Design.

Volume 6 (1995)

Christopher J. Cramer and Donald G. Truhlar, Continuum Solvation Models: Classical and Quantum Mechanical Implementations.

Clark R. Landis, Daniel M. Root, and Thomas Cleveland, Molecular Mechanics Force Fields for Modeling Inorganic and Organometallic Compounds.

Vassilios Galiatsatos, Computational Methods for Modeling Polymers: An Introduction.

Rick A. Kendall, Robert J. Harrison, Rik J. Littlefield, and Martyn F. Guest, High Performance Computing in Computational Chemistry: Methods and Machines.

Donald B. Boyd, Molecular Modeling Software in Use: Publication Trends.

Eiji Ōsawa and Kenny B. Lipkowitz, Appendix: Published Force Field Parameters.

Volume 7 (1996)

Geoffrey M. Downs and Peter Willett, Similarity Searching in Databases of Chemical Structures.

Andrew C. Good and Jonathan S. Mason, Three-Dimensional Structure Database Searches.

Jiali Gao, Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials.

Libero J. Bartolotti and Ken Flurchick, An Introduction to Density Functional Theory.

Alain St-Amant, Density Functional Methods in Biomolecular Modeling.

Danya Yang and Arvi Rauk, The A Priori Calculation of Vibrational Circular Dichroism Intensities.

Donald B. Boyd, Appendix: Compendium of Software for Molecular Modeling.

Volume 8 (1996)

Zdenek Slanina, Shyi-Long Lee, and Chin-hui Yu, Computations in Treating Fullerenes and Carbon Aggregates.

Gernot Frenking, Iris Antes, Marlis Böhme, Stefan Dapprich, Andreas W. Ehlers, Volker Jonas, Arndt Neuhaus, Michael Otto, Ralf Stegmann, Achim Veldkamp, and Sergei F. Vyboishchikov, Pseudopotential Calculations of Transition Metal Compounds: Scope and Limitations.

Thomas R. Cundari, Michael T. Benson, M. Leigh Lutz, and Shaun O. Sommerer, Effective Core Potential Approaches to the Chemistry of the Heavier Elements.

Jan Almlöf and Odd Gropen, Relativistic Effects in Chemistry.

Donald B. Chesnut, The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding.

Volume 9 (1996)

James R. Damewood, Jr., Peptide Mimetic Design with the Aid of Computational Chemistry.

T. P. Straatsma, Free Energy by Molecular Simulation.

Robert J. Woods, The Application of Molecular Modeling Techniques to the Determination of Oligosaccharide Solution Conformations.

Ingrid Pettersson and Tommy Liljefors, Molecular Mechanics Calculated Conformational Energies of Organic Molecules: A Comparison of Force Fields.

Gustavo A. Arteca, Molecular Shape Descriptors.

Volume 10 (1997)

Richard Judson, Genetic Algorithms and Their Use in Chemistry.

Eric C. Martin, David C. Spellmeyer, Roger E. Critchlow Jr., and Jeffrey M. Blaney, Does Combinatorial Chemistry Obviate Computer-Aided Drug Design?

Robert Q. Topper, Visualizing Molecular Phase Space: Nonstatistical Effects in Reaction Dynamics.

Raima Larter and Kenneth Showalter, Computational Studies in Nonlinear Dynamics.

Stephen J. Smith and Brian T. Sutcliffe, The Development of Computational Chemistry in the United Kingdom.

Volume 11 (1997)

Mark A. Murcko, Recent Advances in Ligand Design Methods.

David E. Clark, Christopher W. Murray, and Jin Li, Current Issues in De Novo Molecular Design.

Tudor I. Oprea and Chris L. Waller, Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure-Activity Relationships.

Giovanni Greco, Ettore Novellino, and Yvonne Connolly Martin, Approaches to Three-Dimensional Quantitative Structure-Activity Relationships.

Pierre-Alain Carrupt, Bernard Testa, and Patrick Gaillard, Computational Approaches to Lipophilicity: Methods and Applications.

Ganesan Ravishanker, Pascal Auffinger, David R. Langley, Bhyravabhotla Jayaram, Matthew A. Young, and David L. Beveridge, Treatment of Counterions in Computer Simulations of DNA.

Donald B. Boyd, Appendix: Compendium of Software and Internet Tools for Computational Chemistry.

Volume 12 (1998)

Hagai Meirovitch, Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation.

Ramzi Kutteh and T. P. Straatsma, Molecular Dynamics with General Holonomic Constraints and Application to Internal Coordinate Constraints.

John C. Shelley and Daniel R. Bérard, Computer Simulation of Water Physisorption at Metal-Water Interfaces.

Donald W. Brenner, Olga A. Shenderova, and Denis A. Areshkin, Quantum-Based Analytic Interatomic Forces and Materials Simulation.

Henry A. Kurtz and Douglas S. Dudis, Quantum Mechanical Methods for Predicting Nonlinear Optical Properties.

Chung F. Wong, Tom Thacher, and Herschel Rabitz, Sensitivity Analysis in Biomolecular Simulation.

Paul Verwer and Frank J. J. Leusen, Computer Simulation to Predict Possible Crystal Polymorphs.

Jean-Louis Rivail and Bernard Maigret, Computational Chemistry in France: A Historical Survey.

Volume 13 (1999)

Thomas Bally and Weston Thatcher Borden, Calculations on Open-Shell Molecules: A Beginner’s Guide.

Neil R. Kestner and Jaime E. Combariza, Basis Set Superposition Errors: Theory and Practice.

James B. Anderson, Quantum Monte Carlo: Atoms, Molecules, Clusters, Liquids, and Solids.

Anders Wallqvist and Raymond D. Mountain, Molecular Models of Water: Derivation and Description.

James M. Briggs and Jan Antosiewicz, Simulation of pH-dependent Properties of Proteins Using Mesoscopic Models.

Harold E. Helson, Structure Diagram Generation.

Volume 14 (2000)

Michelle Miller Francl and Lisa Emily Chirlian, The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials.

T. Daniel Crawford and Henry F. Schaefer III, An Introduction to Coupled Cluster Theory for Computational Chemists.

Bastiaan van de Graaf, Swie Lan Njo, and Konstantin S. Smirnov, Introduction to Zeolite Modeling.

Sarah L. Price, Toward More Accurate Model Intermolecular Potentials For Organic Molecules.

Christopher J. Mundy, Sundaram Balasubramanian, Ken Bagchi, Mark E. Tuckerman, Glenn J. Martyna, and Michael L. Klein, Nonequilibrium Molecular Dynamics.

Donald B. Boyd and Kenny B. Lipkowitz, History of the Gordon Research Conferences on Computational Chemistry.

Mehran Jalaie and Kenny B. Lipkowitz, Appendix: Published Force Field Parameters for Molecular Mechanics, Molecular Dynamics, and Monte Carlo Simulations.

Volume 15 (2000)

F. Matthias Bickelhaupt and Evert Jan Baerends, Kohn-Sham Density Functional Theory: Predicting and Understanding Chemistry.

Michael A. Robb, Marco Garavelli, Massimo Olivucci, and Fernando Bernardi, A Computational Strategy for Organic Photochemistry.

Larry A. Curtiss, Paul C. Redfern, and David J. Frurip, Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds.

Russell J. Boyd, The Development of Computational Chemistry in Canada.

Volume 16 (2000)

Richard A. Lewis, Stephen D. Pickett, and David E. Clark, Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design.

Keith L. Peterson, Artificial Neural Networks and Their Use in Chemistry.

Jörg-Rüdiger Hill, Clive M. Freeman, and Lalitha Subramanian, Use of Force Fields in Materials Modeling.

M. Rami Reddy, Mark D. Erion, and Atul Agarwal, Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities.

Volume 17 (2001)

Ingo Muegge and Matthias Rarey, Small Molecule Docking and Scoring.

Lutz P. Ehrlich and Rebecca C. Wade, Protein-Protein Docking.

Christel M. Marian, Spin-Orbit Coupling in Molecules.

Lemont B. Kier, Chao-Kun Cheng, and Paul G. Seybold, Cellular Automata Models of Aqueous Solution Systems.

Kenny B. Lipkowitz and Donald B. Boyd, Appendix: Books Published on the Topics of Computational Chemistry.

Volume 18 (2002)

Geoff M. Downs and John M. Barnard, Clustering Methods and Their Uses in Computational Chemistry.

Hans-Joachim Böhm and Martin Stahl, The Use of Scoring Functions in Drug Discovery Applications.

Steven W. Rick and Steven J. Stuart, Potentials and Algorithms for Incorporating Polarizability in Computer Simulations.

Dmitry V. Matyushov and Gregory A. Voth, New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases.

George R. Famini and Leland Y. Wilson, Linear Free Energy Relationships Using Quantum Mechanical Descriptors.

Sigrid D. Peyerimhoff, The Development of Computational Chemistry in Germany.

Donald B. Boyd and Kenny B. Lipkowitz, Appendix: Examination of the Employment Environment for Computational Chemistry.

Volume 19 (2003)

Robert Q. Topper, David, L. Freeman, Denise Bergin and Keirnan R. LaMarche, Computational Techniques and Strategies for Monte Carlo Thermodynamic Calculations, with Applications to Nanoclusters.

David E. Smith and Anthony D. J. Haymet, Computing Hydrophobicity.

Lipeng Sun and William L. Hase, Born-Oppenheimer Direct Dynamics Classical Trajectory Simulations.

Gene Lamm, The Poisson-Boltzmann Equation.

Volume 20 (2004)

Sason Shaik and Philippe C. Hiberty, Valence Bond Theory: Its History, Fundamentals and Applications. A Primer.

Nikita Matsunaga and Shiro Koseki, Modeling of Spin Forbidden Reactions.

Stefan Grimme, Calculation of the Electronic Spectra of Large Molecules.

Raymond Kapral, Simulating Chemical Waves and Patterns.

Costel Sârbu and Horia Pop, Fuzzy Soft-Computing Methods and Their Applications in Chemistry.

Sean Ekins and Peter Swaan, Development of Computational Models for Enzymes, Transporters, Channels and Receptors Relevant to ADME/Tox.

Volume 21 (2005)

Roberto Dovesi, Bartolomeo Civalleri, Roberto Orlando, Carla Roetti and Victor R. Saunders, Ab Initio Quantum Simulation in Solid State Chemistry.

Patrick Bultinck, Xavier Gironés and Ramon Carbó-Dorca, Molecular Quantum Similarity: Theory and Applications.

Jean-Loup Faulon, Donald P. Visco, Jr. and Diana Roe, Enumerating Molecules.

David J. Livingstone and David W. Salt, Variable Selection- Spoilt for Choice.

Nathan A. Baker, Biomolecular Applications of Poisson-Boltzmann Methods.

Baltazar Aguda, Georghe Craciun and Rengul Cetin-Atalay, Data Sources and Computational Approaches for Generating Models of Gene Regulatory Networks.

Volume 22 (2006)

Patrice Koehl, Protein Structure Classification.

Emilio Esposito, Dror Tobi and Jeffry Madura, Comparative Protein Modeling.

Joan-Emma Shea, Miriam Friedel, and Andrij Baumketner, Simulations of Protein Folding.

Marco Saraniti, Shela Aboud, and Robert Eisenberg, The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods.

C. Matthew Sundling, Nagamani Sukumar, Hongmei Zhang, Curt Breneman, and Mark Embrechts, Wavelets in Chemistry and Chemoinformatics.

Volume 23 (2007)

Christian Ochsenfeld, Jörg Kussmann, and Daniel Lambrecht, Linear Scaling in Quantum Chemistry.

Spiridoula Matsika, Conical Intersections in Molecular Systems.

Antonio Fernandez-Ramos, Benjamin Ellingson, Bruce Garrett, and Donald Truhlar, Variational Transition State Theory with Multidimensional Tunneling.

Roland Faller, Coarse Grain Modeling of Polymers.

Jeffrey Godden and Jürgen Bajorath, Analysis of Chemical Information Content using Shannon Entropy.

Ovidiu Ivanciuc, Applications of Support Vector Machines in Chemistry.

Donald Boyd, How Computational Chemistry Became Important in the Pharmaceutical Industry.

Volume 24 (2007)

Martin Schoen, and Sabine H. L. Klapp, Nanoconfined Fluids. Soft Matter Between Two and Three Dimensions.

Volume 25 (2007)

Wolfgang Paul, Determining the Glass Transition in Polymer Melts.

Nicholas J. Mosey and Martin H. Müser, Atomistic Modeling of Friction.

Jeetain Mittal, William P. Krekelberg, Jeffrey R. Errington, and Thomas M. Truskett, Computing Free Volume, Structured Order, and Entropy of Liquids and Glasses.

Laurence E. Fried, The Reactivity of Energetic Materials at Extreme Conditions.

Julio A. Alonso, Magnetic Properties of Atomic Clusters of the Transition Elements.

Laura Gagliardi, Transition Metal- and Actinide-Containing Systems Studied with Multiconfigurational Quantum Chemical Methods.

Hua Guo, Recursive Solutions to Large Eigenproblems in Molecular Spectroscopy and Reaction Dynamics.

Hugh Cartwright, Development and Uses of Artificial Intelligence in Chemistry.

Volume 26 (2009)

C. David Sherrill, Computations of Noncovalent π Interactions.

Gregory S. Tschumper, Reliable Electronic Structure Computations for Weak Noncovalent Interactions in Clusters.

Peter Elliott, Filip Furche and Kieron Burke, Excited States from Time- Dependent Density Functional Theory.

Thomas Vojta, Computing Quantum Phase Transitions.

Thomas L. Beck, Real-Space Multigrid Methods in Computational Chemistry.

Francesca Tavazza, Lyle E. Levine and Anne M. Chaka, Hybrid Methods for Atomic-Level Simulations Spanning Multi-Length Scales in the Solid State.

Alfredo E. Cárdenas and Eric Bath, Extending the Time Scale in Atomically Detailed Simulations.

Edward J. Maginn, Atomistic Simulation of Ionic Liquids.

Volume 27 (2011)

Stefano Giordano, Allessandro Mattoni, Luciano Colombo, Brittle Fracture: From Elasticity Theory to Atomistic Simulations.

Igor V. Pivkin, Bruce Caswell, George Em Karniadakis, Dissipative Particle Dynamics.

Peter G. Bolhuis and Christoph Dellago, Trajectory-Based Rare Event Simulation.

Douglas L. Irving, Understanding Metal/Metal Electrical Contact Conductance from the Atomic to Continuum Scales.

Max L. Berkowitz and James Kindt, Molecular Detailed Simulations of Lipid Bilayers.

Sophya Garaschuk, Vitaly Rassolov, Oleg Prezhdo, Semiclassical Bohmian Dynamics.

Donald B. Boyd, Employment Opportunities in Computational Chemistry. Kenny B. Lipkowitz, Appendix: List of Computational Molecular Scientists.