Reviews in computational chemistry. Volume 31

Content: List of Contributors ix Preface xi Contributors to Previous Volumes xv 1 Lattice-Boltzmann Modeling of Multicomponent Systems: An Introduction 1Ulf D. Schiller and Olga Kuksenok Introduction 1 The Lattice Boltzmann Equation: A Modern Introduction 4 A Brief History of the LBM 5 The Lattice Boltzmann Equation 7 The Fluctuating Lattice Boltzmann Equation 23 Boundary Conditions 25 Fluid-Particle Coupling 30 LBM for Multiphase Fluids 37 Governing Continuum Equations 37 Lattice Boltzmann Algorithm for Binary Fluid: Free-Energy Approach 42 Minimizing Spurious Velocities 47 Conclusions 50 References 51 2 Mapping Energy Transport Networks in Proteins 63David M. Leitner and Takahisa Yamato Introduction 63 Thermal and Energy Flow in Macromolecules 65 Normal Modes of Proteins 65 Simulating Energy Transport in Terms of Normal Modes 69 Energy Diffusion in Terms of Normal Modes 70 Energy Transport from Time Correlation Functions 73 Energy Transport in Proteins is Inherently Anisotropic 75 Locating Energy Transport Networks 77 Communication Maps 77 CURrent calculations for Proteins (CURP) 80 Applications 83 Communication Maps: Illustrative Examples 83 CURP: Illustrative Examples 89 Future Directions 98 Summary 99 Acknowledgments 100 References 100 3 Uncertainty Quantification for Molecular Dynamics 115Paul N. Patrone and Andrew Dienstfrey Introduction 115 From Dynamical to Random: An Overview of MD 118 System Specification 119 Interatomic Potentials 121 Hamilton\'s Equations 123 Thermodynamic Ensembles 128 Where Does This Leave Us? 131 Uncertainty Quantification 131 What is UQ? 132 Tools for UQ 136 UQ of MD 143 Tutorial: Trajectory Analysis 143 Tutorial: Ensemble Verification 148 Tutorial: UQ of Data Analysis for the Glass-Transition Temperature 151 Concluding Thoughts 161 References 162 4 The Role of Computations in Catalysis 171Horia Metiu, Vishal Agarwal, and Henrik H. Kristoffersen Introduction 171 Screening 172 Sabatier Principle 173 Scaling Relations 175 BEP Relationship 176 Volcano Plots 180 Some Rules for Oxide Catalysts 189 Let Us Examine Some Industrial Catalysts 191 Sometimes Selectivity is More Important than Rate 191 Sometimes We Want a Smaller Rate! 191 Sometimes Product Separation is More Important than the Reaction Rate 193 Some Reactions are Equilibrium-limited 193 The Cost of Making the Catalyst is Important 194 The Catalyst Should Contain Abundant Elements 194 A Good Catalyst Should not be Easily Poisoned 195 Summary 195 References 196 5 The Construction of Ab Initio-Based Potential Energy Surfaces 199Richard Dawes and Ernesto Quintas-Sanchez Introduction and Overview 199 What is a PES? 199 Significance and Range of Applications of PESs 204 Challenges for Theory 207 Terminology and Concepts 209 The Schroedinger Equation 209 The BO Approximation 210 Mathematical Foundations of (Linear) Fitting 215 Quantum Chemistry Methods 221 General Considerations 221 Single Reference Methods 223 Multireference Methods 225 Compound Methods or Protocols 227 Fitting Methods 229 General Considerations and Desirable Attributes of a PES 229 Non-Interpolative Fitting Methods 231 Interpolative Fitting Methods 239 Applications 242 The Automated Construction of PESs 242 Concluding Remarks 248 Acknowledgements 250 Acronyms/Abbreviations 250 References 251 6 Modeling Mechanochemistry from First Principles 265Heather J. Kulik Introduction and Scope 265 Potential Energy Surfaces and Reaction Coordinates 266 Theoretical Models of Mechanochemical Bond Cleavage 268 Linear Model (Kauzmann, Eyring, and Bell) 268 Tilted Potential Energy Profile Model 270 First-Principles Models for Mechanochemical Bond Cleavage 271 Constrained Geometries Simulate External Force (COGEF) 271 Force-Modified Potential Energy Surfaces 273 Covalent Mechanochemistry 278 Overview of Characterization Methods 278 Representative Mechanophores 280 Representative Mechanochemistry Case Studies 281 Benzocyclobutene 281 gem-Difluorocyclopropane 285 PPA: Heterolytic Bond Cleavage 288 Mechanical Force for Sampling: Application to Lignin 292 Best Practices for Mechanochemical Simulation 296 Conclusions 298 Acknowledgments 299 References 300 Index 313