Reviews in Computational Chemistry, Volume 19

TheReviews in Computational Chemistry series brings together leading authorities in the field. The chapters in this book series are written to teach the newcomer and update the expert. Topics include computational chemistry, molecular modeling, computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). Detailed author and subject indices on each volume help the reader to quickly discover particular topics. The chapters are approached in a tutorial manner and written in a non-mathematical style allowing students and researchers to access computational methods outside their immediate area of expertise.

Kenny B. Lipkowitz, PhD, is a retired Professor of Chemistry from North Dakota State University.

Raima Larter is Professors of Chemistry at Indiana University - Purdue University at Indianapolis.

Thomas R. Cundari is Professor of Chemistry at the University of Memphis.

Donald B. Boyd was apponted Research Professor of Chemistry at Indiana University - Purdue University Indianapolis in 1994. He has published over 100 refereed journal papers and book chapters.

1. Computational Techniques and Strategies for Monte Carlo Thermodynamic Calculations, with Applications to Nanoclusters

1

(42)

Robert Q. Topper, David L. Freeman, Denise Bergin, and Keirnan R. LaMarche

Introduction

1

(2)

Metropolis Monte Carlo

3

(15)

Random-Number Generation: A Few Notes

4

(1)

The Generalized Metropolis Monte Carlo Algorithm

5

(3)

Metropolis Monte Carlo: The "Classic" Algorithm

8

(3)

The Barker-Watts Algorithm for Molecular Rotations

11

(1)

Equilibration: Why Wait?

11

(2)

Error Estimation

13

(5)

Quasi-ergodicity: An Insidious Problem

18

(5)

Overcoming Quasi-ergodicity

23

(3)

Mag-Walking

23

(1)

Subspace Sampling

23

(1)

Jump-Between-Wells Method

24

(1)

Atom-Exchange Method

24

(1)

Histogram Methods

24

(1)

Umbrella Sampling

25

(1)

J-Walking, Parallel Tempering, and Related Methods

26

(8)

J-Walking

27

(3)

Parallel Tempering

30

(2)

Jumping to Tsallis Distributions

32

(1)

Applications to Microcanonical Simulations

33

(1)

Multicanonical Ensemble/Entropy Sampling

34

(2)

Conclusions

36

(1)

Acknowledgments

37

(1)

References

37

(6)

2. Computing Hydrophobicity

43

(36)

David E. Smith and Anthony D.J. Haymet

Introduction

43

(3)

Simulation Methods

46

(12)

Statistical Mechanics and Thermodynamics

47

(2)

Particle Insertion Methods

49

(3)

Perturbation Methods

52

(1)

Thermodynamic Integration

53

(2)

Free Energy and Structure

55

(1)

Entropy and Energy

55

(3)

Heat Capacity

58

(1)

Hydrophobic Hydration

58

(10)

Structure

59

(2)

Hydration Free Energy

61

(3)

Hydration Entropy and Energy

64

(2)

Hydration Heat Capacity

66

(1)

Water Mimics

67

(1)

Hydrophobic Interactions

68

(5)

Free Energy of Association

69

(1)

Entropy and Energy of Association

70

(2)

Heat Capacity of Association

72

(1)

Pressure Dependence of Hydrophobic Interactions

72

(1)

Outlook

73

(1)

Acknowledgments

73

(1)

References

73

(6)

3. Born-Oppenheimer Direct Dynamics Classical Trajectory Simulations

79

(68)

Lipeng Sun and William L. Hase

Introduction

79

(6)

Classical Trajectory Simulations

79

(1)

Traditional Approach: Analytic Potential Energy Surfaces

80

(4)

Direct Dynamics Simulations

84

(1)

Born-Oppenheimer Direct Dynamics

85

(9)

Semiempirical Electronic Structure Theory

86

(2)

Ab Initio Electronic Structure Theory

88

(3)

QM + MM and QM/MM Methods

91

(3)

Integrating the Classical Equations of Motion

94

(3)

Cartesian Coordinates

95

(1)

Instantaneous Normal-Mode Coordinates

96

(1)

Trajectory Initial Conditions

97

(17)

Unimolecular Reactions

97

(9)

Bimolecular Reactions

106

(3)

Exciting the Transition State

109

(3)

Gas-Surface Collisions

112

(2)

Importance of Quantum Effects

114

(4)

Bimolecular Reactions

114

(1)

Intramolecular Dynamics and Unimolecular Reactions

115

(1)

Summary

116

(2)

Applications of Born-Oppenheimer Direct Dynamics

118

(15)

Cyclopropane Stereomutation

118

(3)

Cl- + CH3Cl Central-Barrier Dynamics

121

(3)

OH- + CH3F Exit-Channel Dynamics

124

(4)

Protonated Glycine Surface-Induced Dissociation

128

(5)

Concluding Remarks

133

(2)

Acknowledgments

135

(1)

References

135

(12)

4. The Poisson-Boltzmann Equation

147

(220)

Gene Lamm

Introduction

147

(8)

State of the Field

147

(2)

Overview of the Chapter

149

(2)

A Brief History

151

(2)

The Poisson-Boltzmann Equation

153

(2)

Analytical Solutions to the Poisson-Boltzmann Equation

155

(135)

Planar Geometry: The Membrane Model

156

(44)

Curved Surfaces: Cylinders and Spheres

200

(26)

Cylindrical Geometry: The Polymer Model

226

(28)

Spherical Geometry: The Micelle Model

254

(34)

Mixed-Geometry Studies

288

(2)

Numerical Solutions to the Poisson-Boltzmann Equation

290

(26)

One-Dimensional Geometries

290

(1)

Finite-Difference/Finite-Element Algorithms

291

(10)

Alternative General-Purpose Methods

301

(1)

Large-Scale Applications

301

(15)

Beyond the Poisson-Boltzmann Equation

316

(14)

Assumptions of the Poisson-Boltzmann Equation

316

(7)

Common Approximations to the Poisson-Boltzmann Equation

323

(2)

Alternatives to the Poisson-Boltzmann Equation

325

(5)

Concluding Remarks

330

(3)

Acknowledgments

333

(1)

References

333

(34)

Author Index

367

(16)

Subject Index

383

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Reviews in Computational Chemistry, Volume 19

Summary

Author Biography

Table of Contents

Supplemental Materials