Reviews in Computational Chemistry, Volume 31

ABBY L. PARRILL, Ph.D., is a Professor in the Department of Chemistry at the University of Memphis, TN. Her research interests are in bioorganic chemistry, protein modeling, and rational ligand design and synthesis. 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 the Office of Naval Research where he is a Program Manager in Computer-Aided Materials Design.

• List of Contributors ixPreface xiContributors to Previous Volumes xv1 Lattice-Boltzmann Modeling of Multicomponent Systems: An Introduction 1Ulf D. Schiller and Olga KuksenokIntroduction 1The Lattice Boltzmann Equation: A Modern Introduction 4A Brief History of the LBM 5The Lattice Boltzmann Equation 7The Fluctuating Lattice Boltzmann Equation 23Boundary Conditions 25Fluid–Particle Coupling 30LBM for Multiphase Fluids 37Governing Continuum Equations 37Lattice Boltzmann Algorithm for Binary Fluid: Free-Energy Approach 42Minimizing Spurious Velocities 47Conclusions 50References 512 Mapping Energy Transport Networks in Proteins 63David M. Leitner and Takahisa YamatoIntroduction 63Thermal and Energy Flow in Macromolecules 65Normal Modes of Proteins 65Simulating Energy Transport in Terms of Normal Modes 69Energy Diffusion in Terms of Normal Modes 70Energy Transport from Time Correlation Functions 73Energy Transport in Proteins is Inherently Anisotropic 75Locating Energy Transport Networks 77Communication Maps 77CURrent calculations for Proteins (CURP) 80Applications 83Communication Maps: Illustrative Examples 83CURP: Illustrative Examples 89Future Directions 98Summary 99Acknowledgments 100References 1003 Uncertainty Quantification for Molecular Dynamics 115Paul N. Patrone and Andrew DienstfreyIntroduction 115From Dynamical to Random: An Overview of MD 118System Specification 119Interatomic Potentials 121Hamilton’s Equations 123Thermodynamic Ensembles 128Where Does This Leave Us? 131Uncertainty Quantification 131What is UQ? 132Tools for UQ 136UQ of MD 143Tutorial: Trajectory Analysis 143Tutorial: Ensemble Verification 148Tutorial: UQ of Data Analysis for the Glass-Transition Temperature 151Concluding Thoughts 161References 1624 The Role of Computations in Catalysis 171Horia Metiu, Vishal Agarwal, and Henrik H. KristoffersenIntroduction 171Screening 172Sabatier Principle 173Scaling Relations 175BEP Relationship 176Volcano Plots 180Some Rules for Oxide Catalysts 189Let Us Examine Some Industrial Catalysts 191Sometimes Selectivity is More Important than Rate 191Sometimes We Want a Smaller Rate! 191Sometimes Product Separation is More Important than the Reaction Rate 193Some Reactions are Equilibrium-limited 193The Cost of Making the Catalyst is Important 194The Catalyst Should Contain Abundant Elements 194A Good Catalyst Should not be Easily Poisoned 195Summary 195References 1965 The Construction of Ab Initio-Based Potential Energy Surfaces 199Richard Dawes and Ernesto Quintas-SánchezIntroduction and Overview 199What is a PES? 199Significance and Range of Applications of PESs 204Challenges for Theory 207Terminology and Concepts 209The Schrödinger Equation 209The BO Approximation 210Mathematical Foundations of (Linear) Fitting 215Quantum Chemistry Methods 221General Considerations 221Single Reference Methods 223Multireference Methods 225Compound Methods or Protocols 227Fitting Methods 229General Considerations and Desirable Attributes of a PES 229Non-Interpolative Fitting Methods 231Interpolative Fitting Methods 239Applications 242The Automated Construction of PESs 242Concluding Remarks 248Acknowledgements 250Acronyms/Abbreviations 250References 2516 Modeling Mechanochemistry from First Principles 265Heather J. KulikIntroduction and Scope 265Potential Energy Surfaces and Reaction Coordinates 266Theoretical Models of Mechanochemical Bond Cleavage 268Linear Model (Kauzmann, Eyring, and Bell) 268Tilted Potential Energy Profile Model 270First-Principles Models for Mechanochemical Bond Cleavage 271Constrained Geometries Simulate External Force (COGEF) 271Force-Modified Potential Energy Surfaces 273Covalent Mechanochemistry 278Overview of Characterization Methods 278Representative Mechanophores 280Representative Mechanochemistry Case Studies 281Benzocyclobutene 281gem-Difluorocyclopropane 285PPA: Heterolytic Bond Cleavage 288Mechanical Force for Sampling: Application to Lignin 292Best Practices for Mechanochemical Simulation 296Conclusions 298Acknowledgments 299References 300Index 313