Reviews in Computational Chemistry, Volume 32 de A Parrill

Reviews in Computational Chemistry, Volume 32: Reviews in Computational Chemistry

A Parrill

REVIEWS IN COMPUTATIONAL CHEMISTRY THE LATEST VOLUME IN THE REVIEWS IN COMPUTATIONAL CHEMISTRY SERIES, THE INVALUABLE REFERENCE TO METHODS AND TECHNIQUES IN COMPUTATIONAL CHEMISTRY Reviews in Computational Chemistry reference texts assist researchers in selecting and applying new computational chemistry methods to their own research. Bringing together writings from leading experts in various fields of computational chemistry, Volume 32 covers topics including global structure optimization, time-dependent density functional tight binding calculations, non-equilibrium self-assembly, cluster prediction, and molecular simulations of microphase formers and deep eutectic solvents. In keeping with previous books in the series, Volume 32 uses a non-mathematical style and tutorial-based approach that provides students and researchers with easy access to computational methods outside their area of expertise. The chapters comprising Volume 32 are connected by two themes: methods that can be broadly applied to a variety of systems, and special considerations required when modeling specific system types. Each in-depth chapter contains background and theory, strategies for using the methods correctly, mini-tutorials and best practices, and critical literature reviews highlighting advanced applications. Essential reading for both newcomers and experts in the area of molecular modeling, this state-of-the-art resource: * Covers topics such as non-deterministic global optimization (NDGO) approaches and excited-state dynamics calculations * Contains a detailed overview of deep eutectic solvents (DESs) and simulation methods * Presents methodologies for investigating chemical systems that form microphases with periodic morphologies such as lamellae and cylinders * Features step-by-step tutorials on applying techniques to probe and understand the chemical dynamics exhibited in a system * Includes detailed subject indices on each volume in the series and up-to-date compendiums of molecular modeling software, services, programs, suppliers, and other useful information Reviews in Computational Chemistry, Volume 32 is a must-have guide for computational chemists, theoretical chemists, pharmaceutical chemists, biological chemists, chemical engineers, researchers in academia and industry, and graduate students involved in molecular modeling.

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Notă biografică

ABBY L. PARRILL, PhD, is Professor of Chemistry in the Department of Chemistry and Dean of the College of Arts and Sciences at the University of Memphis. Her research interests are in bioorganic chemistry, protein modeling, NMR Spectroscopy, and rational ligand design and synthesis. She has given more than 100 presentations and authored numerous papers and books. KENNY B. LIPKOWITZ, PhD, was one of the founding co-editors of Reviews in Computational Chemistry. He spent 28 years as an academician and then moved to the Office of Naval Research, where he is currently a Program Manager in Computer-Aided Materials Design.

Cuprins

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. Belén 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