Reviews in Computational Chemistry, Volume 28

Herausgegeben von Parrill, Abby L.; Lipkowitz, Kenny B.

• Gebundenes Buch

Produktbeschreibung

The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include:
* Free-energy Calculations with Metadynamics
* Polarizable Force Fields for Biomolecular Modeling
* Modeling Protein Folding Pathways
* Assessing Structural Predictions of Protein-Protein Recognition
* Kinetic Monte Carlo Simulation of Electrochemical Systems
* Reactivity and Dynamics at Liquid Interfaces

Produktdetails

• Reviews in Computational Chemistry .28
• Verlag: Wiley & Sons
• 1. Auflage
• Seitenzahl: 560
• Erscheinungstermin: 4. Mai 2015
• Englisch
• Abmessung: 212mm x 212mm x 4mm
• Gewicht: 4011g
• ISBN-13: 9781118407776
• ISBN-10: 1118407776
• Artikelnr.: 39380792

Autorenporträt

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.

Inhaltsangabe

Preface xi List of Contributors xv Contributors to Previous Volumes xvii 1.
Free-Energy Calculations with Metadynamics: Theory and Practice 1 Giovanni
Bussi and Davide Branduardi Introduction 1 Molecular Dynamics and
Free-Energy Estimation 3 Molecular Dynamics 3 Free-Energy Landscapes 4 A
Toy Model: Alanine Dipeptide 6 Biased Sampling 8 Adaptive Biasing with
Metadynamics 9 Reweighting 12 Well-Tempered Metadynamics 12 Reweighting 14
Metadynamics How-To 14 The Choice of the CV(s) 15 The Width of the
Deposited Gaussian Potential 17 The Deposition Rate of the Gaussian
Potential 18 A First Test Run Using Gyration Radius 19 A Better Collective
Variable: Phi Dihedral Angle 23 Well-Tempered Metadynamics Using Gyration
Radius 24 Well-Tempered Metadynamics Using Dihedral Angle Phi 27 Advanced
Collective Variables 28 Path-Based Collective Variables 30 Collective
Variables Based on Dimensional Reduction Methods 32 Template-Based
Collective Variables 34 Potential Energy as a Collective Variable 35
Improved Variants 36 Multiple Walkers Metadynamics 36 Replica Exchange
Metadynamics 37 Bias Exchange Metadynamics 38 Adaptive Gaussians 39
Conclusion 41 Acknowledgments 42 Appendix A: Metadynamics Input Files with
PLUMED 42 References 44 2. Polarizable Force Fields for Biomolecular
Modeling 51 Yue Shi, Pengyu Ren, Michael Schnieders, and Jean-Philip
Piquemal Introduction 51 Modeling Polarization Effects 52 Induced Dipole
Models 52 Classic Drude Oscillators 54 Fluctuating Charges 54 Recent
Developments 55 AMOEBA 55 SIBFA 57 NEMO 58 CHARMM-Drude 58 CHARMM-FQ 59
X-Pol 60 PFF 60 Applications 61 Water Simulations 61 Ion Solvation 62 Small
Molecules 63 Proteins 64 Lipids 66 Continuum Solvents for Polarizable
Biomolecular Solutes 66 Macromolecular X-ray Crystallography Refinement 67
Prediction of Organic Crystal Structure, Thermodynamics, and Solubility 70
Summary 71 Acknowledgment 71 References 72 3. Modeling Protein Folding
Pathways 87 Clare-Louise Towse and Valerie Daggett Introduction 87 Outline
of this Chapter 90 Protein Simulation Methodology 90 Force Fields, Models
and Solvation Approaches 90 Unfolding: The Reverse of Folding 97 Elevated
Temperature Unfolding Simulations 100 Biological Relevance of Forced
Unfolding 103 Biased or Restrained MD 108 Characterizing Different States
111 Protein Folding and Refolding 115 Folding in Families 118 Conclusions
and Outlook 121 Acknowledgment 122 References 122 4. Assessing Structural
Predictions of Protein-Protein Recognition: The CAPRI Experiment 137 Joël
Janin, Shoshana J. Wodak, Marc F. Lensink, and Sameer Velankar Introduction
137 Protein-Protein Docking 138 A Short History of Protein-Protein Docking
138 Major Current Algorithms 141 The CAPRI Experiment 144 Why Do Blind
Predictions? 144 Organizing CAPRI 145 The CAPRI Targets 146 Creating a
Community 149 Assessing Docking Predictions 150 The CAPRI Evaluation
Procedure 150 A Survey of the Results of 12 Years of Blind Predictions on
45 Targets 154 Recent Developments in Modeling Protein-Protein Interaction
160 Modeling Multicomponent Assemblies. The Multiscale Approach 160
Genome-Wide Modeling of Protein-Protein Interaction 161 Engineering
Interactions and Predicting Affinity 162 Conclusion 164 Acknowledgments 165
References 165 5. Kinetic Monte Carlo Simulation of Electrochemical Systems
175 C. Heath Turner, Zhongtao Zhang, Lev D. Gelb, and Brett I. Dunlap
Background 175 Introduction to Kinetic Monte Carlo 176 Electrochemical
Relationships 180 Applications 184 Transport in Li-ion Batteries 184 Solid
Electrolyte Interphase (SEI) Passive Layer Formation 187 Analysis of
Impedance Spectra 189 Electrochemical Dealloying 189 Electrochemical Cells
190 Solid Oxide Fuel Cells 193 Other Electrochemical Systems 197
Conclusions and Future Outlook 198 Acknowledgments 199 References 199 6.
Reactivity and Dynamics at Liquid Interfaces 205 Ilan Benjamin Introduction
205 Simulation Methodology for Liquid Interfaces 207 Force Fields for
Molecular Simulations of Liquid Interfaces 207 Boundary Conditions and the
Treatment of Long-Range Forces 210 Statistical Ensembles for Simulating
Liquid Interfaces 213 Comments About Monte Carlo Simulations 214 The Neat
Interface 214 Density, Fluctuations, and Intrinsic Structure 215 Surface
Tension 221 Molecular Structure 223 Dynamics 230 Solutes at Interfaces:
Structure and Thermodynamics 235 Solute Density 236 Solute-Solvent
Correlations 240 Solute Molecular Orientation 242 Solutes at Interfaces:
Electronic Spectroscopy 243 A Brief General Background on Electronic
Spectroscopy in the Condensed Phase 243 Experimental Electronic
Spectroscopy at Liquid Interfaces 245 Computer Simulations of Electronic
Transitions at Interfaces 249 Solutes at Interfaces: Dynamics 253 Solute
Vibrational Relaxation at Liquid Interfaces 253 Solute Rotational
Relaxation at Liquid Interfaces 258 Solvation Dynamics 263 Summary 269
Reactivity at Liquid Interfaces 270 Introduction 270 Electron Transfer
Reactions at Liquid/Liquid Interfaces 271 Nucleophilic Substitution
Reactions and Phase Transfer Catalysis (PTC) 277 Conclusions 283
Acknowledgments 284 References 284 7. Computational Techniques in the Study
of the Properties of Clathrate Hydrates 315 John S. Tse Historical
Perspective 315 Structures 317 The van der Waals-Platteeuw Solid Solution
Theory 318 Computational Advancements 322 Thermodynamic Modelling 322
Atomistic Simulations 327 Thermodynamic Stability 344 Hydrate Nucleation
and Growth 355 Guest Diffusion Through Hydrate Cages 368 Ab Initio Methods
371 Outlook 381 References 382 8. The Quantum Chemistry of Loosely-Bound
Electrons 391 John M. Herbert Introduction and Overview 391 What Is a
Loosely-Bound Electron? 391 Scope of This Review 392 Chemical Significance
of Loosely-Bound Electrons 394 Challenges for Theory 400 Terminology and
Fundamental Concepts 402 Bound Anions 402 Metastable (Resonance) Anions 415
Quantum Chemistry for Weakly-Bound Anions 425 Gaussian Basis Sets 425 Wave
Function Electronic Structure Methods 439 Density Functional Theory 456
Quantum Chemistry for Metastable Anions 471 Maximum Overlap Method 474
Complex Coordinate Rotation 477 Stabilization Methods 483 Concluding
Remarks 495 Acknowledgments 495 Appendix A: List of Acronyms 496 References
497 Index 519