Reviews in Computational Chemistry, Volume 32

Reviews in Computational Chemistry, Volume 32

Parrill, Abby L.; Lipkowitz, Kenny B.

John Wiley & Sons Inc






15 a 20 dias


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List of Contributors ix

Preface xi

Contributors to Previous Volumes xv

1 Non-Deterministic Global Structure Optimization: An Introductory Tutorial 1
Bernd Hartke

List of abbreviations 1

Introduction 2

The Need for Structural Optimization 2

Search Space is Vast 3

Deterministic vs Non-Deterministic Search 5

Fundamental Take-Home Lessons 8

A Closer Look at Some NDGO Background Details 8

Too Inspired by Nature 8

No Free Lunch 11

NDGO Algorithm Comparisons 14

Barrier Crossing 15

Old vs New Machine Learning 19

Take-Home Lessons for NDGO Background Details 20

General Guidelines for NDGO Applications 21

Brief Summary of Some Fundamental NDGO Algorithm Ideas 21

NDGO Method Design Choices 22

NDGO Tips for Absolute Beginners 28

Things to Do, and Pitfalls to Avoid 31

Recent Highlights 32

References 34

2 Density Functional Tight Binding Calculations for Probing Electronic-Excited States of Large Systems 45
Sharma S.R.K.C. Yamijala, Ma. Belen Oviedo, and Bryan M. Wong

Introduction 45

Real-Time Time-Dependent DFTB (RT-TDDFTB) 46

Theory and Methodology 46

Tutorial on RT-TDDFTB Electron Dynamics for a Naphthalene Molecule 49

Absorption Spectrum for Naphthalene 49

Electron Dynamics of Naphthalene with a Laser-Type Perturbation 51

RT-TDDFTB Electron Dynamics of a Realistic Large Systems 51

DFTB-Based Nonadiabatic Electron Dynamics 59

Adiabatic vs Nonadiabatic Dynamics 59

Equations Governing Nonadiabatic Electron Dynamics 61

The Classical Path Approximation 62

Surface Hopping and Fewest Switches Criterion 63

Implementation Details of CPA-FSSH-DFTB 65

Post-processing Tools 67

Computational Details 67

An Example on Charge Transfer Dynamics in Organic Photovoltaics 68

Conclusion and Outlook 72

Acknowledgments 72

References 73

3 Advances in the Molecular Simulation of Microphase Formers 81
Patrick Charbonneau and Kai Zhang

Introduction 81

Block Copolymers 83

Surfactants and Microemulsions 84

Lattice Spin Systems 87

Colloidal Suspensions 87

Other Examples 90

Field Theory of Microphase Formation 90

Molecular Simulations and Challenges 91

Simulating Periodic Microphases 93

Expanded Thermodynamics 94

Thermodynamic Integration for Microphases 95

Ghost Particle/Cluster Switching Method 100

Cluster Volume Moves 103

Determining Phase Transitions 105

Simulations of Disordered Microphases 106

Wolff-Like Cluster Algorithms 106

Virtual Cluster Moves 107

Aggregation Volume Biased (AVB) Moves 109

Morphological Crossovers in the Disordered Regime 110

Microphase Formers Solved by Molecular Simulations 112

One-Dimensional Models 112

Lattice Spin Models 113

Colloidal Models 117

Conclusion 118

Free Energy of an Ideal Gas in a Field 119

Constant pressure Simulations of Particles in A Field 120

Virial Coefficients of Particles in a Field 120

Acknowledgments 122

References 122

4 Molecular Simulations of Deep Eutectic Solvents: A Perspective on Structure, Dynamics, and Physical Properties 135
Shalini J. Rukmani, Brian W. Doherty, Orlando Acevedo, and Coray M. Colina

Introduction 135

Deep Eutectic Solvents 137

Definition of Deep Eutectic Solvents 137

DES as Ionic Liquid Analogues 137

Molecular Structure of DESs and Type of Interactions 140

Types of DES 142

Molecular Simulation Methods 143

An Overview of Ab Initio Methods 145

Classical Molecular Dynamics at the Atomic Level 149

Nonpolarizable Force Fields used for DES Simulations 153

Physical Properties 159

Liquid Density 159

Volume Expansivity 162

Surface Tension 162

Thermodynamic Properties 164

Heat Capacity 164

Heats of Vaporization 168

Isothermal Compressibility 169

Transport Properties 170

Viscosity 170

Diffusion Coefficients 178

Deep Eutectic Solvent Structure 183

Radial Distribution Functions 183

Hydrogen Bond Analysis 189

Spatial Distribution Functions 196

Application of DES Through Simulation 196

Gas Sorption Studies on DES 196

DES Interactions at Metal Surfaces 198

Proteins in DES 199

Summary 200

Acknowledgments 201

References 201

Index 217
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