Reviews in Computational Chemistry, Volume 28

Abby L. Parrill, PhD, 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, more than 100 papers and books.Kenny B. Lipkowitz, PhD, is a recently retired Professor of Chemistry from North Dakota State University.

• Preface xiList of Contributors xvContributors to Previous Volumes xvii1. Free-Energy Calculations with Metadynamics: Theory and Practice 1Giovanni Bussi and Davide BranduardiIntroduction 1Molecular Dynamics and Free-Energy Estimation 3Molecular Dynamics 3Free-Energy Landscapes 4A Toy Model: Alanine Dipeptide 6Biased Sampling 8Adaptive Biasing with Metadynamics 9Reweighting 12Well-Tempered Metadynamics 12Reweighting 14Metadynamics How-To 14The Choice of the CV(s) 15The Width of the Deposited Gaussian Potential 17The Deposition Rate of the Gaussian Potential 18A First Test Run Using Gyration Radius 19A Better Collective Variable: Φ Dihedral Angle 23Well-Tempered Metadynamics Using Gyration Radius 24Well-Tempered Metadynamics Using Dihedral Angle Φ 27Advanced Collective Variables 28Path-Based Collective Variables 30Collective Variables Based on Dimensional Reduction Methods 32Template-Based Collective Variables 34Potential Energy as a Collective Variable 35Improved Variants 36Multiple Walkers Metadynamics 36Replica Exchange Metadynamics 37Bias Exchange Metadynamics 38Adaptive Gaussians 39Conclusion 41Acknowledgments 42Appendix A: Metadynamics Input Files with PLUMED 42References 442. Polarizable Force Fields for Biomolecular Modeling 51Yue Shi, Pengyu Ren, Michael Schnieders, and Jean-PhilipPiquemalIntroduction 51Modeling Polarization Effects 52Induced Dipole Models 52Classic Drude Oscillators 54Fluctuating Charges 54Recent Developments 55AMOEBA 55SIBFA 57NEMO 58CHARMM-Drude 58CHARMM-FQ 59X-Pol 60PFF 60Applications 61Water Simulations 61Ion Solvation 62Small Molecules 63Proteins 64Lipids 66Continuum Solvents for Polarizable Biomolecular Solutes 66Macromolecular X-ray Crystallography Refinement 67Prediction of Organic Crystal Structure, Thermodynamics, and Solubility 70Summary 71Acknowledgment 71References 723. Modeling Protein Folding Pathways 87Clare-Louise Towse and Valerie DaggettIntroduction 87Outline of this Chapter 90Protein Simulation Methodology 90Force Fields, Models and Solvation Approaches 90Unfolding: The Reverse of Folding 97Elevated Temperature Unfolding Simulations 100Biological Relevance of Forced Unfolding 103Biased or Restrained MD 108Characterizing Different States 111Protein Folding and Refolding 115Folding in Families 118Conclusions and Outlook 121Acknowledgment 122References 1224. Assessing Structural Predictions of Protein–Protein Recognition: The CAPRI Experiment 137Joël Janin, Shoshana J. Wodak, Marc F. Lensink, and Sameer VelankarIntroduction 137Protein–Protein Docking 138A Short History of Protein–Protein Docking 138Major Current Algorithms 141The CAPRI Experiment 144Why Do Blind Predictions? 144Organizing CAPRI 145The CAPRI Targets 146Creating a Community 149Assessing Docking Predictions 150The CAPRI Evaluation Procedure 150A Survey of the Results of 12 Years of Blind Predictions on 45 Targets 154Recent Developments in Modeling Protein–Protein Interaction 160Modeling Multicomponent Assemblies. The Multiscale Approach 160Genome-Wide Modeling of Protein–Protein Interaction 161Engineering Interactions and Predicting Affinity 162Conclusion 164Acknowledgments 165References 1655. Kinetic Monte Carlo Simulation of Electrochemical Systems 175C. Heath Turner, Zhongtao Zhang, Lev D. Gelb, and Brett I. DunlapBackground 175Introduction to Kinetic Monte Carlo 176Electrochemical Relationships 180Applications 184Transport in Li-ion Batteries 184Solid Electrolyte Interphase (SEI) Passive Layer Formation 187Analysis of Impedance Spectra 189Electrochemical Dealloying 189Electrochemical Cells 190Solid Oxide Fuel Cells 193Other Electrochemical Systems 197Conclusions and Future Outlook 198Acknowledgments 199References 1996. Reactivity and Dynamics at Liquid Interfaces 205Ilan BenjaminIntroduction 205Simulation Methodology for Liquid Interfaces 207Force Fields for Molecular Simulations of Liquid Interfaces 207Boundary Conditions and the Treatment of Long-Range Forces 210Statistical Ensembles for Simulating Liquid Interfaces 213Comments About Monte Carlo Simulations 214The Neat Interface 214Density, Fluctuations, and Intrinsic Structure 215Surface Tension 221Molecular Structure 223Dynamics 230Solutes at Interfaces: Structure and Thermodynamics 235Solute Density 236Solute–Solvent Correlations 240Solute Molecular Orientation 242Solutes at Interfaces: Electronic Spectroscopy 243A Brief General Background on Electronic Spectroscopy in the Condensed Phase 243Experimental Electronic Spectroscopy at Liquid Interfaces 245Computer Simulations of Electronic Transitions at Interfaces 249Solutes at Interfaces: Dynamics 253Solute Vibrational Relaxation at Liquid Interfaces 253Solute Rotational Relaxation at Liquid Interfaces 258Solvation Dynamics 263Summary 269Reactivity at Liquid Interfaces 270Introduction 270Electron Transfer Reactions at Liquid/Liquid Interfaces 271Nucleophilic Substitution Reactions and Phase TransferCatalysis (PTC) 277Conclusions 283Acknowledgments 284References 2847. Computational Techniques in the Study of the Properties of Clathrate Hydrates 315John S. TseHistorical Perspective 315Structures 317The van der Waals–Platteeuw Solid Solution Theory 318Computational Advancements 322Thermodynamic Modelling 322Atomistic Simulations 327Thermodynamic Stability 344Hydrate Nucleation and Growth 355Guest Diffusion Through Hydrate Cages 368Ab Initio Methods 371Outlook 381References 3828. The Quantum Chemistry of Loosely-Bound Electrons 391John M. HerbertIntroduction and Overview 391What Is a Loosely-Bound Electron? 391Scope of This Review 392Chemical Significance of Loosely-Bound Electrons 394Challenges for Theory 400Terminology and Fundamental Concepts 402Bound Anions 402Metastable (Resonance) Anions 415Quantum Chemistry for Weakly-Bound Anions 425Gaussian Basis Sets 425Wave Function Electronic Structure Methods 439Density Functional Theory 456Quantum Chemistry for Metastable Anions 471Maximum Overlap Method 474Complex Coordinate Rotation 477Stabilization Methods 483Concluding Remarks 495Acknowledgments 495Appendix A: List of Acronyms 496References 497Index 519