Combined Quantum Mechanical and Molecular Mechanical Methods

by Jiali Gao, Mark A. Thompson

Overview

Combined quantum mechanical and molecular mechanical methods (QM/MM) are one of the most promising approaches for quantum mechanical calculations of chemical processes in solution and in enzymes. In such a method a relatively small part of the system (e.g., the solute) is analyzed through quantum mechanics and the remainder (e.g., the solvent) is represented through molecular mechanics, thus combining the accuracy of one method with the efficiency of the other. This book provides an in-depth survey of the methods and their applications in chemistry and biochemistry.

Product Details

ISBN-13:	9780841235908
Publisher:	American Chemical Society
Publication date:	01/28/1999
Series:	ACS Symposium Series , #712
Pages:	320
Product dimensions:	6.20(w) x 9.10(h) x 0.80(d)

About the Author

State University of New York, Buffalo

Table of Contents

Preface
Model Development
1. Quantum Mechanical-Molecular Mechanical Coupled Potentials, Kenneth M. Merz, Jr.
2. Quantum Mechanical-Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solutions, Jörg Bentzien et al.
3. The Geometry of Water in Liquid Water from Hybrid Ab Initio-Monte Carlo and Density Functional-Molecular Dynamics Simulations, Cristobal Alhambra, Kyoungrim Byun, and Jiali Gao
4. On the Treatment of Link Atoms in Hybrid Methods, Iris Antes and Walter Thiel
5. A Method of Hybrid Quantum-Classical Calculations for Large Organometallic-Metallobiochemical Systems: Applications to Iron Picket-Fence Porphyrin and Vitamin B[1[2, Isaac B. Bersuker et al.
6. A Methodology for Quantum Molecular Modeling of Structure and Reactivity at Solid-Liquid Interfaces, Eugene V. Stefanovich and Thanh N. Truong
Ab Initio Dynamics
7. Dual-Level Methods for Electronic Structure Calculations of Potential Energy Functions that Use Quantum Mechanics as the Lower Level, José C. Corchado and Donald G. Truhlar
8. A Combined Car-Parrinello Quantum Mechanical-Molecular Mechanical Implementation of Ab Initio Molecular Dynamics Simulations of Extended Systems, Tom K. Woo et al.
9. The Molecular Mechanics Valence Bond Method: Electronic Structure and Semiclassical Dynamics: Applications to Problems in Photochemistry, Michael J. Bearpark et al.
10. Density Functional Theory Ab Initio Molecular Dynamics and Combined Density Functional Theory and Molecular Dynamics Simulations, Dongqing Wei and Dennis R. Salahub
Solvation
11. Generalized Molecular Mechanics Including Quantum Electronic Structure Variation of Polar Solvents: An Overview, Hyung J. Kim et al.
12. RISM-SCF Study of Solvent Effect on Electronic Structure and Chemical Reaction in Solution: Temperature Dependence of pKw, Fumio Hirata et al.
13. Universal Solvation Models, Gregory D. Hawkins et al.
14. Quantum Mechanical-Molecular Mechanical Calculations of (Hyper-)Polarizabilities with the Direct Reaction Field Approach, Piet Th. van Duijnen, Marcel Swart, and Ferdinand Grozema
Biochemical Applications
15. The Local Self-Consistent Field Principles and Applications to Combined Quantum Mechanical-Molecular Mechanical Computations on Biomacromolecular Systems, Xavier Assfeld, Nicolas Ferré, and Jean-Louis Rivail
16. Investigating Enzyme Reaction Mechanisms with Quantum Mechanical-Molecular Mechanical Plus Molecular Dynamics Calculations, Peter L. Cummins and Jill E. Gready
17. Ab Initio and Hybrid Molecular Dynamics Simulations of the Active Site of Human Carbonic Anhydrase II: A Test Case Study, Ursula Röthlisberger
18. Application of Linear-Scaling Electronic Structure Methods to the Study of Polarization of Proteins and DNA in Solution, Darrin M. York
19. Exciting Green Fluorescent Protein, Volkhard Helms et al.
Indexes
Author Index
Subject Index

Editorial Reviews

"The November 1997 symposium drew scientists from several industrialized countries to Las Vegas to describe how they can tremendously simplify the study of chemical structures and reactions in solution and in enzymes by subjecting the smaller solute part of the system to quantum mechanics and the remainder solvent to classical force field. They discuss such aspects as treating link atoms in hybrid methods, dual-level methods for electronic structure calculations of potential energy functions that use quantum mechanics as the lower level, generalized molecular mechanics including quantum electronic structure variations of polar solvents, applying linear- scaling electronic structure methods to the study of the polarization of proteins and DNA in solutions, and exciting green fluorescent protein. The text is reproduced from typescripts, some of which are double-spaced."—SciTech Book News

From the Publisher

The November 1997 symposium drew scientists from several industrialized countries to Las Vegas to describe how they can tremendously simplify the study of chemical structures and reactions in solution and in enzymes by subjecting the smaller solute part of the system to quantum mechanics and the remainder solvent to classical force field. They discuss such aspects as treating link atoms in hybrid methods, dual-level methods for electronic structure calculations of potential energy functions that use quantum mechanics as the lower level, generalized molecular mechanics including quantum electronic structure variations of polar solvents, applying linear- scaling electronic structure methods to the study of the polarization of proteins and DNA in solutions, and exciting green fluorescent protein. The text is reproduced from typescripts, some of which are double-spaced. Distributed in the US by Oxford University Press. Annotation c. Book News, Inc., Portland, OR (booknews.com)

Booknews