Reviews in Computational Chemistry, Volume 30

ABBY L. PARRILL, Ph.D., is Professor of Chemistry in the Department of Chemistry at the University of Memphis, TN. Her research interests are in bioorganic chemistry, protein modeling and NMR Spectroscopy and rational ligand design and synthesis. In 2011, she was awarded the Distinguished Research Award by University of Memphis Alumni Association. She has given more than 100 presentations, and published more than 100 papers and books. KENNY B. LIPKOWITZ, Ph.D., was one of the founding Co-editors of Reviews in Computational Chemistry. He spent 28 years as an academician and then moved to Office of Naval Research, a Program Manager in Computer-Aided Materials Design.

• List of Contributors xiPreface xiiiContributors to Previous Volumes xvii1 Chemical Bonding at High Pressure 1Andreas HermannHigh-Pressure Science 1Motivation 1Pressure in Industrial Processes 2High-Pressure Experiments 2Pressure Effects in Materials 5Close Packing and Metallicity—or Not 6Hydrogen and Hydrogen-Rich Compounds 7Molecular Crystals 8Closed-Shell Reactivity 9Unusual Chemistry 9New Electronic States 10Electronic Structure Calculations on Materials Under Pressure 10Density and Wave Function–Based Approaches 11Basis Sets and Pseudopotentials 13Identifying High-Pressure Crystal Structures 14Stability of High-Pressure Phases 16Properties of Materials Under Pressure 20Mechanical Properties 21Electronic Properties 23Spectroscopic Properties 28Conclusions 29Acknowledgments 31References 312 Molecular Dynamics Simulations of Shock Loading of Materials: A Review and Tutorial 43Mitchell A. Wood, Mathew J. Cherukara, Edwin Antillon, and Alejandro StrachanIntroduction 43Shock Loading of Solids 101 44Chapter Organization 46Molecular Simulations of Shockwaves in Solids 46Molecular Dynamics and Coarse Grain Dynamics 46Direct Shock Simulations 48Indirect Shock Simulations: Achieving Longer Timescales 49Shock-Induced Plasticity and Failure 51Plastic Deformation 51Preexisting Defects: Voids and Vacancies 54Preexisting Defects: Polycrystalline Materials 56Granular Materials 56Dynamical Failure 57Critical Phenomena in Spallation and Cluster Formation 60Ejecta Formation and the Richtmyer–Meshkov Instability 61Shock-Induced Phase Transformation and Materials Synthesis 62Phase Transformations 63Shock-Induced and Shock-Assisted Chemical Reactions 69Reactive Composites 70Energetic Materials and Detonation 73Model Explosives: Shock to Detonation 74Reactive MD Simulations of Explosives 75Electronic Structure-Based Modeling 79Coarse-Grained Descriptions of Shock-Induced Chemistry 80Summary and Outlook 83Acknowledgments 84Appendix 84References 853 Basis Sets in Quantum Chemistry 93Balazs Nagy, and Frank JensenIntroduction 93The Basis Set Approximation 94Basis Set Desiderata 96Types of Basis Functions 98Slater and Gaussian Type Functions 98Plane-Wave Functions 101Real-Space Functions 103Other Functions 104Structure and Classification of Gaussian Type Basis Sets 105Contracted Basis Functions 108Optimization of Basis Set Parameters 111Basis Set Augmentation 113Diffuse Functions 113Tight Functions 114Fitting Functions 115Nonatom-Centered Basis Sets 115Examples of Basis Sets 116Segmented Contracted Basis Sets 116General Contracted Basis Sets 117Property Basis Sets 119Electric Properties 121Magnetic Properties 126Mixed Properties 128Relativistic Basis Sets 129Pseudopotentials 130Basis Set Convergence 131Convergence of Electronic Structure Methods with Gaussian Type Basis Sets 132Composite Extrapolation Methods 133Basis Set Incompleteness and Superposition Errors 134Aspects of Choosing A Suitable Basis Set 136Availability of Basis Sets 139Acknowledgment 139References 1394 The Quantum Chemistry of Open-Shell Species 151Anna I. KrylovIntroduction and Overview 151Quantum Chemistry Methods for Open- and Closed-Shell Species 155Some Aspects of Electronic Structure of Open-Shell Species 159Spin Contamination of Approximate Open-Shell Wave Functions 159Jahn–Teller Effect 160Vibronic Interactions and Pseudo-Jahn–Teller Effect 162High-Spin Open-Shell States 165Open-Shell States with Multiconfigurational Character 167EOM-IP and EOM-EA Methods for Open-Shell Systems 167Examples 169Diradicals, Triradicals, and Beyond 174Excited States of Open-Shell Species 181Metastable Radicals 186Bonding in Open-Shell Species 187Dyson Orbitals 188Density-Based Wave Function Analysis 189Insight into Bonding from Physical Observables 192Properties and Spectroscopy 193Vibrational Spectroscopy 194Electronic and Photoelectron Spectroscopy 194Electronic Transitions 200Outlook 207Acknowledgments 208Appendix: List of Acronyms 209References 2105 Machine Learning, Quantum Chemistry, and Chemical Space 225Raghunathan Ramakrishnan, and O. Anatole von LilienfeldIntroduction 225Paradigm 228Kernel Ridge Regression 230Representation 232Data 234Kernel 236Electrons 239Δ-Machine Learning 241Atoms in Molecules 245Crystals 247Conclusions and Outlook 248Acknowledgments 250References 2506 The Master Equation Approach to Problems in Chemical and Biological Physics 257Dmitrii E. MakarovIntroduction 257The General Form of A Master Equation and its Solution 260Microscopic Reversibility, Detailed Balance, and Their Consequences 262The Kinetic Monte Carlo (KMC) Method 265Quantum Master Equations 270The Reduced Density Matrix as a Description of a Molecule Interacting with Its Surroundings 270Diagonal and Off-Diagonal Elements of the Density Matrix and Significance of Dephasing 273Relaxation 275Kinetic Monte Carlo for Quantum Master Equations 277Physical Significance of The Quantum Kinetic Monte Carlo Scheme 282Concluding Remarks 283Acknowledgments 284References 2847 Continuous Symmetry Measures: A New Tool in Quantum Chemistry 289Pere Alemany, David Casanova, Santiago Alvarez, Chaim Dryzun, and David AvnirIntroduction 289Symmetry as a Fundamental Concept in Quantum Chemistry 289Symmetry, Pseudosymmetry, and Quasisymmetry 292Continuous Symmetry Measures 295General Definition of CSMs 295CSMs in Molecular Quantum Chemistry 299CSM for the Nuclear Framework 300CSMs for Matrices and Operators 303CSM for Functions: Electron Density, Wave Functions, and Molecular Orbitals 304CSMs for Irreducible Representations of a Group 307Pseudosymmetry Analysis of Molecular Orbitals 313Applications 315The Nature of the Chemical Bond from the Point of View of CSMs 315CSM Analysis of the Electronic Structure of Conjugated Hydrocarbons and Related Compounds 321Pseudosymmetry Analysis of the d-Block Molecular Orbitals of “Octahedral” ML6 Transition Metal Compounds 328Symmetry, Pseudosymmetry and Walsh Diagrams for ML 4 Compounds along the Planarization Path 334Conclusions 343Acknowledgment 344References 344Index 353