{"product_id":"reviews-in-computational-chemistry-volume-28-isbn-9781118407776","title":"Reviews in Computational Chemistry, Volume 28","description":"\u003cp\u003eThe 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:\u003cbr\u003e\u003cbr\u003e\u003c\/p\u003e \u003cul\u003e \u003cli\u003eFree-energy Calculations with Metadynamics\u003c\/li\u003e \u003cli\u003ePolarizable Force Fields for Biomolecular Modeling\u003c\/li\u003e \u003cli\u003eModeling Protein Folding Pathways\u003c\/li\u003e \u003cli\u003eAssessing Structural Predictions of Protein-Protein Recognition\u003c\/li\u003e \u003cli\u003eKinetic Monte Carlo Simulation of Electrochemical Systems\u003c\/li\u003e \u003cli\u003eReactivity and Dynamics at Liquid Interfaces\u003c\/li\u003e \u003c\/ul\u003e \u003cp\u003ePreface xi\u003c\/p\u003e \u003cp\u003eList of Contributors xv\u003c\/p\u003e \u003cp\u003eContributors to Previous Volumes xvii\u003c\/p\u003e \u003cp\u003e\u003cb\u003e1. Free-Energy Calculations with Metadynamics: Theory and Practice 1\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eGiovanni Bussi and Davide Branduardi\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 1\u003c\/p\u003e \u003cp\u003eMolecular Dynamics and Free-Energy Estimation 3\u003c\/p\u003e \u003cp\u003eMolecular Dynamics 3\u003c\/p\u003e \u003cp\u003eFree-Energy Landscapes 4\u003c\/p\u003e \u003cp\u003eA Toy Model: Alanine Dipeptide 6\u003c\/p\u003e \u003cp\u003eBiased Sampling 8\u003c\/p\u003e \u003cp\u003eAdaptive Biasing with Metadynamics 9\u003c\/p\u003e \u003cp\u003eReweighting 12\u003c\/p\u003e \u003cp\u003eWell-Tempered Metadynamics 12\u003c\/p\u003e \u003cp\u003eReweighting 14\u003c\/p\u003e \u003cp\u003eMetadynamics How-To 14\u003c\/p\u003e \u003cp\u003eThe Choice of the CV(s) 15\u003c\/p\u003e \u003cp\u003eThe Width of the Deposited Gaussian Potential 17\u003c\/p\u003e \u003cp\u003eThe Deposition Rate of the Gaussian Potential 18\u003c\/p\u003e \u003cp\u003eA First Test Run Using Gyration Radius 19\u003c\/p\u003e \u003cp\u003eA Better Collective Variable: Φ Dihedral Angle 23\u003c\/p\u003e \u003cp\u003eWell-Tempered Metadynamics Using Gyration Radius 24\u003c\/p\u003e \u003cp\u003eWell-Tempered Metadynamics Using Dihedral Angle Φ 27\u003c\/p\u003e \u003cp\u003eAdvanced Collective Variables 28\u003c\/p\u003e \u003cp\u003ePath-Based Collective Variables 30\u003c\/p\u003e \u003cp\u003eCollective Variables Based on Dimensional Reduction Methods 32\u003c\/p\u003e \u003cp\u003eTemplate-Based Collective Variables 34\u003c\/p\u003e \u003cp\u003ePotential Energy as a Collective Variable 35\u003c\/p\u003e \u003cp\u003eImproved Variants 36\u003c\/p\u003e \u003cp\u003eMultiple Walkers Metadynamics 36\u003c\/p\u003e \u003cp\u003eReplica Exchange Metadynamics 37\u003c\/p\u003e \u003cp\u003eBias Exchange Metadynamics 38\u003c\/p\u003e \u003cp\u003eAdaptive Gaussians 39\u003c\/p\u003e \u003cp\u003eConclusion 41\u003c\/p\u003e \u003cp\u003eAcknowledgments 42\u003c\/p\u003e \u003cp\u003eAppendix A: Metadynamics Input Files with PLUMED 42\u003c\/p\u003e \u003cp\u003eReferences 44\u003c\/p\u003e \u003cp\u003e\u003cb\u003e2. Polarizable Force Fields for Biomolecular Modeling 51\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eYue Shi, Pengyu Ren, Michael Schnieders, and Jean-Philip\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003ePiquemal\u003c\/p\u003e \u003cp\u003eIntroduction 51\u003c\/p\u003e \u003cp\u003eModeling Polarization Effects 52\u003c\/p\u003e \u003cp\u003eInduced Dipole Models 52\u003c\/p\u003e \u003cp\u003eClassic Drude Oscillators 54\u003c\/p\u003e \u003cp\u003eFluctuating Charges 54\u003c\/p\u003e \u003cp\u003eRecent Developments 55\u003c\/p\u003e \u003cp\u003eAMOEBA 55\u003c\/p\u003e \u003cp\u003eSIBFA 57\u003c\/p\u003e \u003cp\u003eNEMO 58\u003c\/p\u003e \u003cp\u003eCHARMM-Drude 58\u003c\/p\u003e \u003cp\u003eCHARMM-FQ 59\u003c\/p\u003e \u003cp\u003eX-Pol 60\u003c\/p\u003e \u003cp\u003ePFF 60\u003c\/p\u003e \u003cp\u003eApplications 61\u003c\/p\u003e \u003cp\u003eWater Simulations 61\u003c\/p\u003e \u003cp\u003eIon Solvation 62\u003c\/p\u003e \u003cp\u003eSmall Molecules 63\u003c\/p\u003e \u003cp\u003eProteins 64\u003c\/p\u003e \u003cp\u003eLipids 66\u003c\/p\u003e \u003cp\u003eContinuum Solvents for Polarizable Biomolecular Solutes 66\u003c\/p\u003e \u003cp\u003eMacromolecular X-ray Crystallography Refinement 67\u003c\/p\u003e \u003cp\u003ePrediction of Organic Crystal Structure, Thermodynamics, and Solubility 70\u003c\/p\u003e \u003cp\u003eSummary 71\u003c\/p\u003e \u003cp\u003eAcknowledgment 71\u003c\/p\u003e \u003cp\u003eReferences 72\u003c\/p\u003e \u003cp\u003e\u003cb\u003e3. Modeling Protein Folding Pathways 87\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eClare-Louise Towse and Valerie Daggett\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 87\u003c\/p\u003e \u003cp\u003eOutline of this Chapter 90\u003c\/p\u003e \u003cp\u003eProtein Simulation Methodology 90\u003c\/p\u003e \u003cp\u003eForce Fields, Models and Solvation Approaches 90\u003c\/p\u003e \u003cp\u003eUnfolding: The Reverse of Folding 97\u003c\/p\u003e \u003cp\u003eElevated Temperature Unfolding Simulations 100\u003c\/p\u003e \u003cp\u003eBiological Relevance of Forced Unfolding 103\u003c\/p\u003e \u003cp\u003eBiased or Restrained MD 108\u003c\/p\u003e \u003cp\u003eCharacterizing Different States 111\u003c\/p\u003e \u003cp\u003eProtein Folding and Refolding 115\u003c\/p\u003e \u003cp\u003eFolding in Families 118\u003c\/p\u003e \u003cp\u003eConclusions and Outlook 121\u003c\/p\u003e \u003cp\u003eAcknowledgment 122\u003c\/p\u003e \u003cp\u003eReferences 122\u003c\/p\u003e \u003cp\u003e\u003cb\u003e4. Assessing Structural Predictions of Protein–Protein Recognition: The CAPRI Experiment 137\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eJoël Janin, Shoshana J. Wodak, Marc F. Lensink, and Sameer Velankar\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 137\u003c\/p\u003e \u003cp\u003eProtein–Protein Docking 138\u003c\/p\u003e \u003cp\u003eA Short History of Protein–Protein Docking 138\u003c\/p\u003e \u003cp\u003eMajor Current Algorithms 141\u003c\/p\u003e \u003cp\u003eThe CAPRI Experiment 144\u003c\/p\u003e \u003cp\u003eWhy Do Blind Predictions? 144\u003c\/p\u003e \u003cp\u003eOrganizing CAPRI 145\u003c\/p\u003e \u003cp\u003eThe CAPRI Targets 146\u003c\/p\u003e \u003cp\u003eCreating a Community 149\u003c\/p\u003e \u003cp\u003eAssessing Docking Predictions 150\u003c\/p\u003e \u003cp\u003eThe CAPRI Evaluation Procedure 150\u003c\/p\u003e \u003cp\u003eA Survey of the Results of 12 Years of Blind Predictions on 45 Targets 154\u003c\/p\u003e \u003cp\u003eRecent Developments in Modeling Protein–Protein Interaction 160\u003c\/p\u003e \u003cp\u003eModeling Multicomponent Assemblies. The Multiscale Approach 160\u003c\/p\u003e \u003cp\u003eGenome-Wide Modeling of Protein–Protein Interaction 161\u003c\/p\u003e \u003cp\u003eEngineering Interactions and Predicting Affinity 162\u003c\/p\u003e \u003cp\u003eConclusion 164\u003c\/p\u003e \u003cp\u003eAcknowledgments 165\u003c\/p\u003e \u003cp\u003eReferences 165\u003c\/p\u003e \u003cp\u003e\u003cb\u003e5. Kinetic Monte Carlo Simulation of Electrochemical Systems 175\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eC. Heath Turner, Zhongtao Zhang, Lev D. Gelb, and Brett I. Dunlap\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eBackground 175\u003c\/p\u003e \u003cp\u003eIntroduction to Kinetic Monte Carlo 176\u003c\/p\u003e \u003cp\u003eElectrochemical Relationships 180\u003c\/p\u003e \u003cp\u003eApplications 184\u003c\/p\u003e \u003cp\u003eTransport in Li-ion Batteries 184\u003c\/p\u003e \u003cp\u003eSolid Electrolyte Interphase (SEI) Passive Layer Formation 187\u003c\/p\u003e \u003cp\u003eAnalysis of Impedance Spectra 189\u003c\/p\u003e \u003cp\u003eElectrochemical Dealloying 189\u003c\/p\u003e \u003cp\u003eElectrochemical Cells 190\u003c\/p\u003e \u003cp\u003eSolid Oxide Fuel Cells 193\u003c\/p\u003e \u003cp\u003eOther Electrochemical Systems 197\u003c\/p\u003e \u003cp\u003eConclusions and Future Outlook 198\u003c\/p\u003e \u003cp\u003eAcknowledgments 199\u003c\/p\u003e \u003cp\u003eReferences 199\u003c\/p\u003e \u003cp\u003e\u003cb\u003e6. Reactivity and Dynamics at Liquid Interfaces 205\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eIlan Benjamin\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 205\u003c\/p\u003e \u003cp\u003eSimulation Methodology for Liquid Interfaces 207\u003c\/p\u003e \u003cp\u003eForce Fields for Molecular Simulations of Liquid Interfaces 207\u003c\/p\u003e \u003cp\u003eBoundary Conditions and the Treatment of Long-Range Forces 210\u003c\/p\u003e \u003cp\u003eStatistical Ensembles for Simulating Liquid Interfaces 213\u003c\/p\u003e \u003cp\u003eComments About Monte Carlo Simulations 214\u003c\/p\u003e \u003cp\u003eThe Neat Interface 214\u003c\/p\u003e \u003cp\u003eDensity, Fluctuations, and Intrinsic Structure 215\u003c\/p\u003e \u003cp\u003eSurface Tension 221\u003c\/p\u003e \u003cp\u003eMolecular Structure 223\u003c\/p\u003e \u003cp\u003eDynamics 230\u003c\/p\u003e \u003cp\u003eSolutes at Interfaces: Structure and Thermodynamics 235\u003c\/p\u003e \u003cp\u003eSolute Density 236\u003c\/p\u003e \u003cp\u003eSolute–Solvent Correlations 240\u003c\/p\u003e \u003cp\u003eSolute Molecular Orientation 242\u003c\/p\u003e \u003cp\u003eSolutes at Interfaces: Electronic Spectroscopy 243\u003c\/p\u003e \u003cp\u003eA Brief General Background on Electronic Spectroscopy in the Condensed Phase 243\u003c\/p\u003e \u003cp\u003eExperimental Electronic Spectroscopy at Liquid Interfaces 245\u003c\/p\u003e \u003cp\u003eComputer Simulations of Electronic Transitions at Interfaces 249\u003c\/p\u003e \u003cp\u003eSolutes at Interfaces: Dynamics 253\u003c\/p\u003e \u003cp\u003eSolute Vibrational Relaxation at Liquid Interfaces 253\u003c\/p\u003e \u003cp\u003eSolute Rotational Relaxation at Liquid Interfaces 258\u003c\/p\u003e \u003cp\u003eSolvation Dynamics 263\u003c\/p\u003e \u003cp\u003eSummary 269\u003c\/p\u003e \u003cp\u003eReactivity at Liquid Interfaces 270\u003c\/p\u003e \u003cp\u003eIntroduction 270\u003c\/p\u003e \u003cp\u003eElectron Transfer Reactions at Liquid\/Liquid Interfaces 271\u003c\/p\u003e \u003cp\u003eNucleophilic Substitution Reactions and Phase Transfer\u003c\/p\u003e \u003cp\u003eCatalysis (PTC) 277\u003c\/p\u003e \u003cp\u003eConclusions 283\u003c\/p\u003e \u003cp\u003eAcknowledgments 284\u003c\/p\u003e \u003cp\u003eReferences 284\u003c\/p\u003e \u003cp\u003e\u003cb\u003e7. Computational Techniques in the Study of the Properties of Clathrate Hydrates 315\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eJohn S. Tse\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eHistorical Perspective 315\u003c\/p\u003e \u003cp\u003eStructures 317\u003c\/p\u003e \u003cp\u003eThe van der Waals–Platteeuw Solid Solution Theory 318\u003c\/p\u003e \u003cp\u003eComputational Advancements 322\u003c\/p\u003e \u003cp\u003eThermodynamic Modelling 322\u003c\/p\u003e \u003cp\u003eAtomistic Simulations 327\u003c\/p\u003e \u003cp\u003eThermodynamic Stability 344\u003c\/p\u003e \u003cp\u003eHydrate Nucleation and Growth 355\u003c\/p\u003e \u003cp\u003eGuest Diffusion Through Hydrate Cages 368\u003c\/p\u003e \u003cp\u003eAb Initio Methods 371\u003c\/p\u003e \u003cp\u003eOutlook 381\u003c\/p\u003e \u003cp\u003eReferences 382\u003c\/p\u003e \u003cp\u003e\u003cb\u003e8. The Quantum Chemistry of Loosely-Bound Electrons 391\u003cbr\u003e\u003c\/b\u003e\u003ci\u003eJohn M. Herbert\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003eIntroduction and Overview 391\u003c\/p\u003e \u003cp\u003eWhat Is a Loosely-Bound Electron? 391\u003c\/p\u003e \u003cp\u003eScope of This Review 392\u003c\/p\u003e \u003cp\u003eChemical Significance of Loosely-Bound Electrons 394\u003c\/p\u003e \u003cp\u003eChallenges for Theory 400\u003c\/p\u003e \u003cp\u003eTerminology and Fundamental Concepts 402\u003c\/p\u003e \u003cp\u003eBound Anions 402\u003c\/p\u003e \u003cp\u003eMetastable (Resonance) Anions 415\u003c\/p\u003e \u003cp\u003eQuantum Chemistry for Weakly-Bound Anions 425\u003c\/p\u003e \u003cp\u003eGaussian Basis Sets 425\u003c\/p\u003e \u003cp\u003eWave Function Electronic Structure Methods 439\u003c\/p\u003e \u003cp\u003eDensity Functional Theory 456\u003c\/p\u003e \u003cp\u003eQuantum Chemistry for Metastable Anions 471\u003c\/p\u003e \u003cp\u003eMaximum Overlap Method 474\u003c\/p\u003e \u003cp\u003eComplex Coordinate Rotation 477\u003c\/p\u003e \u003cp\u003eStabilization Methods 483\u003c\/p\u003e \u003cp\u003eConcluding Remarks 495\u003c\/p\u003e \u003cp\u003eAcknowledgments 495\u003c\/p\u003e \u003cp\u003eAppendix A: List of Acronyms 496\u003c\/p\u003e \u003cp\u003eReferences 497\u003c\/p\u003e \u003cp\u003eIndex 519\u003c\/p\u003e \u003cp\u003e\u003cb\u003eAbby L. Parrill\u003c\/b\u003e, 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.\u003c\/p\u003e \u003cp\u003e\u003cb\u003eKenny B. Lipkowitz\u003c\/b\u003e, PhD, is a recently retired Professor of Chemistry from North Dakota State University.\u003c\/p\u003e  \u003cp\u003eREVIEWS IN COMPUTATIONAL CHEMISTRY\u003cbr\u003e \u003cbr\u003e The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered on 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:\u003cbr\u003e \u003cbr\u003e \u003c\/p\u003e \u003cul\u003e \u003cli\u003eFree-energy Calculations with Metadynamics\u003c\/li\u003e \u003cli\u003ePolarizable Force Fields for Biomolecular Modeling\u003c\/li\u003e \u003cli\u003eModeling Protein Folding Pathways\u003c\/li\u003e \u003cli\u003eAssessing Structural Predictions of Protein-Protein Recognition\u003c\/li\u003e \u003cli\u003eKinetic Monte Carlo Simulation of Electrochemical Systems\u003c\/li\u003e \u003cli\u003eReactivity and Dynamics at Liquid InterfacesFrom Reviews Of The Series\u003c\/li\u003e \u003c\/ul\u003e \u003cbr\u003e FROM REVIEWS OF THE SERIES\u003cbr\u003e \u003cbr\u003e \"Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry.\"—JOURNAL OF MOLECULAR GRAPHICS AND MODELLING\u003cbr\u003e \u003cbr\u003e \"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general).\"—JOURNAL OF THE AMERICAN CHEMICAL SOCIETY\u003cbr\u003e \u003cp\u003e \u003c\/p\u003e","brand":"Wiley","offers":[{"title":"Default Title","offer_id":47989960442085,"sku":"NP9781118407776","price":225.95,"currency_code":"USD","in_stock":false}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/1842\/7735\/files\/9781118407776.jpg?v=1761786037","url":"https:\/\/k12savings.com\/es\/products\/reviews-in-computational-chemistry-volume-28-isbn-9781118407776","provider":"K12savings","version":"1.0","type":"link"}