Combined Quantum Mechanical and Molecular Mechanical Methods

by Gao, Jiali; Thompson, Mark A.

• ISBN13: 9780841235908
• ISBN10: 0841235902
• Format: Hardcover
• Copyright: 1999-01-28
• Publisher: American Chemical Society

Summary

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.

Table of Contents

Preface	ix
Model Development	2	(104)
1. Quantum Mechanical-Molecular Mechanical Coupled Potentials	2	(14)
Kenneth M. Merz, Jr.
2. Quantum Mechanical-Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solution	16	(19)
Jorg Bentzien
Jan Florian
Timothy M. Glennon
Arieh Warshel
3. The Geometry of Water in Liquid Water from Hybrid Ab Initio-Monte Carlo and Density Functional-Molecular Dynamics Simulations	35	(15)
Cristobal Alhambra
Kyoungrim Byun
Jiali Gao
4. On the Treatment of Link Atoms in Hybrid Methods	50	(16)
Iris Antes
Walter Thiel
5. A Method of Hybrid Quantum-Classical Calculations for Large Organometallic-Metallobiochemical Systems: Applications to Iron Picket-Fence Porphyrin and Vitamin B(12)	66	(26)
Isaac B. Bersuker
Max K. Leong
James E. Boggs
Robert S. Pearlman
6. A Methodology for Quantum Molecular Modeling of Structure and Reactivity at Solid-Liquid Interfaces	92	(14)
Eugene V. Stefanovich
Thanh N. Truong
Ab Initio Dynamics	106	(66)
7. Dual-Level Methods for Electronic Structure Calculations of Potential Energy Functions That Use Quantum Mechanics as the Lower Level	106	(22)
Jose C. Corchado
Donald G. Truhlar
8. A Combined Car-Parrinello Quantum Mechanical-Molecular Mechanical Implementation for Ab Initio Molecular Dynamics Simulations of Extended Systems	128	(20)
Tom K. Woo
Peter M. Margl
Liqun Deng
Tom Ziegler
9. The Molecular Mechanics Valence Bond Method: Electronic Structure and Semiclassical Dynamics: Applications to Problems in Photochemistry	148	(11)
Michael J. Bearpark
Barry R. Smith
Fernando Bernardi
Massimo Olivucci
Michael A. Robb
10. Density Functional Theory Ab Initio Molecular Dynamics and Combined Density Functional Theory and Molecular Dynamics Simulations	159	(13)
Dongqing Wei
Dennis R. Salahub
Solvation	172	(62)
11. Generalized Molecular Mechanics Including Quantum Electronic Structure Variation of Polar Solvents: An Overview	172	(16)
Hyung J. Kim
Badry D. Bursulaya
Jonggu Jeon
Dominic A. Zichi
12. RISM-SCF Study of Solvent Effect on Electronic Structure and Chemical Reaction in Solution: Temperature Dependence of pKw	188	(13)
Fumio Hirata
Hirofumi Sato
Seiichiro Ten-no
Shigeki Kato
13. Universal Solvation Models	201	(19)
Gregory D. Hawkins
Tianhai Zhu
Jiabo Li
Candee C. Chambers
David J. Giesen
Daniel A. Liotard
Christopher J. Cramer
Donald G. Truhlar
14. Quantum Mechanical-Molecular Mechanical Calculations of (Hyper-) Polarizabilities with the Direct Reaction Field Approach	220	(14)
Piet Th. van Duijnen
Marcel Swart
Ferdinand Grozema
Biochemical Applications	234	(63)
15. The Local Self-Consistent Field Principles and Applications to Combined Quantum Mechanical-Molecular Mechanical Computations on Biomacromolecular Systems	234	(16)
Xavier Assfeld
Nicolas Ferre
Jean-Louis Rivail
16. Investigating Enzyme Reaction Mechanisms with Quantum Mechanical-Molecular Mechanical Plus Molecular Dynamics Calculations	250	(14)
Peter L. Cummins
Jill E. Gready
17. Ab Initio and Hybrid Molecular Dynamics Simulations of the Active Site of Human Carbonic Anhydrase II: A Test Case Study	264	(11)
Ursula Rothlisberger
18. Application of Linear-Scaling Electronic Structure Methods to the Study of Polarization of Proteins and DNA in Solution	275	(13)
Darrin M. York
19. Exciting Green Flourescent Protein	288	(9)
Volkhard Helms
Erik F.Y. Hom
T. P. Straatsma
J. Andrew McCammon
Peter Langhoff
Indexes	297
Author Index	297	(1)
Subject Index	298