{"product_id":"molecular-modeling-of-geochemical-reactions-9781118845080","title":"Molecular Modeling of Geochemical Reactions","description":"\u003cb\u003eBook Synopsis\u003c\/b\u003e\u003cbr\u003eMolecular processes in nature affect human health, the availability of resources and the Earth   s climate. Molecular modelling is a powerful and versatile toolbox that complements experimental data and provides insights where direct observation is not currently possible.\u003cbr\u003e\u003cbr\u003e\u003cb\u003eTable of Contents\u003c\/b\u003e\u003cbr\u003e\u003cp\u003eList of Contributors xi\u003c\/p\u003e \u003cp\u003ePreface xiii\u003c\/p\u003e \u003cp\u003e\u003cb\u003e1 Introduction to the Theory and Methods of Computational Chemistry 1\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eDavid M. Sherman\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e1.1 Introduction 1\u003c\/p\u003e \u003cp\u003e1.2 Essentials of Quantum Mechanics 2\u003c\/p\u003e \u003cp\u003e1.2.1 The Schrödinger Equation 4\u003c\/p\u003e \u003cp\u003e1.2.2 Fundamental Examples 4\u003c\/p\u003e \u003cp\u003e1.3 Multielectronic Atoms 7\u003c\/p\u003e \u003cp\u003e1.3.1 The Hartree and Hartree–Fock Approximations 7\u003c\/p\u003e \u003cp\u003e1.3.2 Density Functional Theory 13\u003c\/p\u003e \u003cp\u003e1.4 Bonding in Molecules and Solids 17\u003c\/p\u003e \u003cp\u003e1.4.1 The Born–Oppenheimer Approximation 17\u003c\/p\u003e \u003cp\u003e1.4.2 Basis Sets and the Linear Combination of Atomic Orbital Approximation 18\u003c\/p\u003e \u003cp\u003e1.4.3 Periodic Boundary Conditions 20\u003c\/p\u003e \u003cp\u003e1.4.4 Nuclear Motions and Vibrational Modes 21\u003c\/p\u003e \u003cp\u003e1.5 From Quantum Chemistry to Thermodynamics 22\u003c\/p\u003e \u003cp\u003e1.5.1 Molecular Dynamics 24\u003c\/p\u003e \u003cp\u003e1.6 Available Quantum Chemistry Codes and Their Applications 27\u003c\/p\u003e \u003cp\u003eReferences 28\u003c\/p\u003e \u003cp\u003e\u003cb\u003e2 Force Field Application and Development 33\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eMarco Molinari, Andrey V. Brukhno, Stephen C. Parker, and Dino Spagnoli\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e2.1 Introduction 33\u003c\/p\u003e \u003cp\u003e2.2 Potential Forms 35\u003c\/p\u003e \u003cp\u003e2.2.1 The Non-bonded Interactions 35\u003c\/p\u003e \u003cp\u003e2.2.2 The Bonded Interactions 37\u003c\/p\u003e \u003cp\u003e2.2.3 Polarisation Effects 37\u003c\/p\u003e \u003cp\u003e2.2.4 Reactivity 39\u003c\/p\u003e \u003cp\u003e2.2.5 Fundamentals of Coarse Graining 40\u003c\/p\u003e \u003cp\u003e2.3 Fitting Procedure 42\u003c\/p\u003e \u003cp\u003e2.3.1 Combining Rules Between Unlike Species 42\u003c\/p\u003e \u003cp\u003e2.3.2 Optimisation Procedures for All-Atom Force Fields 43\u003c\/p\u003e \u003cp\u003e2.3.3 Deriving CG Force Fields 45\u003c\/p\u003e \u003cp\u003e2.3.4 Accuracy and Limitations of the Fitting 47\u003c\/p\u003e \u003cp\u003e2.3.5 Transferability 48\u003c\/p\u003e \u003cp\u003e2.4 Force Field Libraries 48\u003c\/p\u003e \u003cp\u003e2.4.1 General Force Fields 48\u003c\/p\u003e \u003cp\u003e2.4.2 Force Field Libraries for Organics: Biomolecules with Minerals 49\u003c\/p\u003e \u003cp\u003e2.4.3 Potentials for the Aqueous Environment 50\u003c\/p\u003e \u003cp\u003e2.4.4 Current CGFF Potentials 51\u003c\/p\u003e \u003cp\u003e2.4.5 Multi-scale Methodologies 53\u003c\/p\u003e \u003cp\u003e2.5 Evolution of Force Fields for Selected Classes of Minerals 54\u003c\/p\u003e \u003cp\u003e2.5.1 Calcium Carbonate 54\u003c\/p\u003e \u003cp\u003e2.5.2 Clay Minerals 56\u003c\/p\u003e \u003cp\u003e2.5.3 Hydroxides and Hydrates 60\u003c\/p\u003e \u003cp\u003e2.5.4 Silica and Silicates 60\u003c\/p\u003e \u003cp\u003e2.5.5 Iron-Based Minerals 61\u003c\/p\u003e \u003cp\u003e2.6 Concluding Remarks 63\u003c\/p\u003e \u003cp\u003eReferences 64\u003c\/p\u003e \u003cp\u003e\u003cb\u003e3 Quantum-Mechanical Modeling of Minerals 77\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eAlessandro Erba and Roberto Dovesi\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e3.1 Introduction 77\u003c\/p\u003e \u003cp\u003e3.2 Theoretical Framework 79\u003c\/p\u003e \u003cp\u003e3.2.1 Translation Invariance and Periodic Boundary Conditions 79\u003c\/p\u003e \u003cp\u003e3.2.2 HF and KS Methods 80\u003c\/p\u003e \u003cp\u003e3.2.3 Bloch Functions and Local BS 81\u003c\/p\u003e \u003cp\u003e3.3 Structural Properties 82\u003c\/p\u003e \u003cp\u003e3.3.1 P–V Relation Through Analytical Stress Tensor 83\u003c\/p\u003e \u003cp\u003e3.3.2 P–V Relation Through Equation of State 85\u003c\/p\u003e \u003cp\u003e3.4 Elastic Properties 86\u003c\/p\u003e \u003cp\u003e3.4.1 Evaluation of the Elastic Tensor 86\u003c\/p\u003e \u003cp\u003e3.4.2 Elastic Tensor-Related Properties 89\u003c\/p\u003e \u003cp\u003e3.4.3 Directional Seismic Wave Velocities and Elastic Anisotropy 89\u003c\/p\u003e \u003cp\u003e3.5 Vibrational and Thermodynamic Properties 91\u003c\/p\u003e \u003cp\u003e3.5.1 Solid-State Thermodynamics 93\u003c\/p\u003e \u003cp\u003e3.6 Modeling Solid Solutions 95\u003c\/p\u003e \u003cp\u003e3.7 Future Challenges 98\u003c\/p\u003e \u003cp\u003eReferences 99\u003c\/p\u003e \u003cp\u003e\u003cb\u003e4 First Principles Estimation of Geochemically Important Transition Metal Oxide Properties: Structure and Dynamics of the Bulk, Surface, and Mineral\/Aqueous Fluid Interface 107\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eYing Chen, Eric Bylaska, and John Weare\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e4.1 Introduction 107\u003c\/p\u003e \u003cp\u003e4.2 Overview of the Theoretical Methods and Approximations Needed to Perform AIMD Calculations 109\u003c\/p\u003e \u003cp\u003e4.3 Accuracy of Calculations for Observable Bulk Properties 113\u003c\/p\u003e \u003cp\u003e4.3.1 Bulk Structural Properties 113\u003c\/p\u003e \u003cp\u003e4.3.2 Bulk Electronic Structure Properties 118\u003c\/p\u003e \u003cp\u003e4.4 Calculation of Surface Properties 123\u003c\/p\u003e \u003cp\u003e4.4.1 Surface Structural Properties 123\u003c\/p\u003e \u003cp\u003e4.4.2 Electronic Structure in the Surface Region 127\u003c\/p\u003e \u003cp\u003e4.4.3 Water Adsorption on Surface 129\u003c\/p\u003e \u003cp\u003e4.5 Simulations of the Mineral–Water Interface 130\u003c\/p\u003e \u003cp\u003e4.5.1 CPMD Simulations of the Vibrational Structure of the Hematite (012)–Water Interface 130\u003c\/p\u003e \u003cp\u003e4.5.2 CPMD Simulations of Fe2+ Species at the Mineral–Water Interface 132\u003c\/p\u003e \u003cp\u003e4.6 Future Perspectives 134\u003c\/p\u003e \u003cp\u003eAcknowledgments 134\u003c\/p\u003e \u003cp\u003e\u003cb\u003eAppendix 134\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eA.1 Short Introduction to Pseudopotentials 135\u003c\/p\u003e \u003cp\u003eA.1.1 The Spin Penalty Pseudopotential 137\u003c\/p\u003e \u003cp\u003eA.1.2 Projected Density of States from Pseudo-Atomic Orbitals 138\u003c\/p\u003e \u003cp\u003eA.2 Hubbard-Like Coulomb and Exchange (DFT+U) 138\u003c\/p\u003e \u003cp\u003eA.3 Overview of the PAW Method 139\u003c\/p\u003e \u003cp\u003eReferences 143\u003c\/p\u003e \u003cp\u003e\u003cb\u003e5 Computational Isotope Geochemistry 151\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eJames R. Rustad\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e5.1 A Brief Statement of Electronic Structure Theory and the Electronic Problem 152\u003c\/p\u003e \u003cp\u003e5.2 The Vibrational Eigenvalue Problem 154\u003c\/p\u003e \u003cp\u003e5.3 Isotope Exchange Equilibria 156\u003c\/p\u003e \u003cp\u003e5.4 Qualitative Insights 159\u003c\/p\u003e \u003cp\u003e5.5 Quantitative Estimates 160\u003c\/p\u003e \u003cp\u003e5.6 Relationship to Empirical Estimates 169\u003c\/p\u003e \u003cp\u003e5.7 Beyond the Harmonic Approximation 171\u003c\/p\u003e \u003cp\u003e5.8 Kinetic Isotope Effects 172\u003c\/p\u003e \u003cp\u003e5.9 Summary and Prognosis 172\u003c\/p\u003e \u003cp\u003eAcknowledgments 173\u003c\/p\u003e \u003cp\u003eReferences 173\u003c\/p\u003e \u003cp\u003e\u003cb\u003e6 Organic and Contaminant Geochemistry 177\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eDaniel Tunega, Martin H. Gerzabek, Georg Haberhauer, Hans Lischka, and Adelia J. A. Aquino\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e6.1 Introduction 177\u003c\/p\u003e \u003cp\u003e6.1.1 Review Examples of Molecular Modeling Applications in Organic and Contaminant Geochemistry 179\u003c\/p\u003e \u003cp\u003e6.2 Molecular Modeling Methods 184\u003c\/p\u003e \u003cp\u003e6.2.1 Molecular Mechanics: Brief Summary 184\u003c\/p\u003e \u003cp\u003e6.2.2 Quantum Mechanics: Overview 187\u003c\/p\u003e \u003cp\u003e6.2.3 Molecular Modeling Techniques: Summary 192\u003c\/p\u003e \u003cp\u003e6.2.4 Models: Clusters, Periodic Systems, and Environmental Effects 195\u003c\/p\u003e \u003cp\u003e6.3 Applications 196\u003c\/p\u003e \u003cp\u003e6.3.1 Modeling of Surface Complexes of Polar Phenoxyacetic Acid-Based Herbicides with Iron Oxyhydroxides and Clay Minerals 197\u003c\/p\u003e \u003cp\u003e6.3.2 Modeling of Adsorption Processes of Polycyclic Aromatic Hydrocarbons on Iron Oxyhydroxides 217\u003c\/p\u003e \u003cp\u003e6.3.3 Modeling of Interactions of Polar and Nonpolar Contaminants in Organic Geochemical Environment 220\u003c\/p\u003e \u003cp\u003e6.4 Perspectives and Future Challenges 227\u003c\/p\u003e \u003cp\u003eGlossary 229\u003c\/p\u003e \u003cp\u003eReferences 231\u003c\/p\u003e \u003cp\u003e\u003cb\u003e7 Petroleum Geochemistry 245\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eQisheng Ma and Yongchun Tang\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e7.1 Introduction: Petroleum Geochemistry and Basin Modeling 245\u003c\/p\u003e \u003cp\u003e7.2 Technology Development of the Petroleum Geochemistry 246\u003c\/p\u003e \u003cp\u003e7.2.1 Thermal Maturity and Vitrinite Reflectance 246\u003c\/p\u003e \u003cp\u003e7.2.2 Rock-Eval Pyrolysis 247\u003c\/p\u003e \u003cp\u003e7.2.3 Kerogen Pyrolysis and Gas Chromatography Analysis 248\u003c\/p\u003e \u003cp\u003e7.2.4 Kinetic Modeling of Kerogen Pyrolysis 249\u003c\/p\u003e \u003cp\u003e7.2.5 Natural Gases and C\/H Isotopes 253\u003c\/p\u003e \u003cp\u003e7.3 Computational Simulations in Petroleum Geochemistry 253\u003c\/p\u003e \u003cp\u003e7.3.1 Ab Initio Calculations of the Unimolecular C–C Bond Rapture 253\u003c\/p\u003e \u003cp\u003e7.3.2 Quantum Mechanical Calculations on Natural Gas 13C Isotopic Fractionation 256\u003c\/p\u003e \u003cp\u003e7.3.3 Deuterium Isotope Fractionations of Natural Gas 258\u003c\/p\u003e \u003cp\u003e7.3.4 Molecular Modeling of the 13C and D Doubly Substituted Methane Isotope 260\u003c\/p\u003e \u003cp\u003e7.4 Summary 262\u003c\/p\u003e \u003cp\u003eReferences 262\u003c\/p\u003e \u003cp\u003e\u003cb\u003e\u003ci\u003e8 Mineral–Water Interaction 271\u003cbr\u003e \u003c\/i\u003e\u003c\/b\u003e\u003ci\u003eMarie-Pierre Gaigeot and Marialore Sulpizi\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e8.1 Introduction 271\u003c\/p\u003e \u003cp\u003e8.2 Brief Review of AIMD Simulation Method 275\u003c\/p\u003e \u003cp\u003e8.2.1 Ab Initio Molecular Dynamics and Density Functional Theory 275\u003c\/p\u003e \u003cp\u003e8.3 Calculation of the Surface Acidity from Reversible Proton Insertion\/Deletion 280\u003c\/p\u003e \u003cp\u003e8.4 Theoretical Methodology for Vibrational Spectroscopy and Mode Assignments 282\u003c\/p\u003e \u003cp\u003e8.5 Property Calculations from AIMD: Dipoles and Polarisabilities 284\u003c\/p\u003e \u003cp\u003e8.6 Illustrations from Our Recent Works 286\u003c\/p\u003e \u003cp\u003e8.6.1 Organisation of Water at Silica–Water Interfaces: (0001) α-Quartz Versus Amorphous Silica 286\u003c\/p\u003e \u003cp\u003e8.6.2 Organisation of Water at Alumina–Water Interface: (0001) α-Alumina Versus (101) Boehmite 291\u003c\/p\u003e \u003cp\u003e8.6.3 How Surface Acidities Dictate the Interfacial Water Structural Arrangement 293\u003c\/p\u003e \u003cp\u003e8.6.4 Vibrational Spectroscopy at Oxide–Liquid Water Interfaces 295\u003c\/p\u003e \u003cp\u003e8.6.5 Clay–Water Interface: Pyrophyllite and Calcium Silicate 299\u003c\/p\u003e \u003cp\u003e8.7 Some Perspectives for Future Works 302\u003c\/p\u003e \u003cp\u003eReferences 304\u003c\/p\u003e \u003cp\u003e\u003cb\u003e9 Biogeochemistry 311\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eWeilong Zhao, Zhijun Xu, and Nita Sahai\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e9.1 Introduction 311\u003c\/p\u003e \u003cp\u003e9.1.1 Mineral–Water Interactions 313\u003c\/p\u003e \u003cp\u003e9.1.2 Mineral–Organic Interactions 313\u003c\/p\u003e \u003cp\u003e9.2 Challenges and Approaches to Computational Modeling of Biomineralization 314\u003c\/p\u003e \u003cp\u003e9.2.1 Biominerals: Structure, Nucleation, and Growth 314\u003c\/p\u003e \u003cp\u003e9.2.2 Conformational Sampling in Modeling Biomineralization 317\u003c\/p\u003e \u003cp\u003e9.2.3 Force Field Benchmarking 324\u003c\/p\u003e \u003cp\u003e9.2.4 Ab Initio MD and Hybrid QM\/MM Approaches 325\u003c\/p\u003e \u003cp\u003e9.3 Case Studies 326\u003c\/p\u003e \u003cp\u003e9.3.1 Apatite 327\u003c\/p\u003e \u003cp\u003e9.3.2 Calcite 331\u003c\/p\u003e \u003cp\u003e9.4 Concluding Remarks and Future Perspectives 334\u003c\/p\u003e \u003cp\u003eAcknowledgments 335\u003c\/p\u003e \u003cp\u003eReferences 335\u003c\/p\u003e \u003cp\u003e\u003cb\u003e10 Vibrational Spectroscopy of Minerals Through Ab Initio Methods 341\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eMarco De La Pierre, Raffaella Demichelis, and Roberto Dovesi\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e10.1 Introduction 341\u003c\/p\u003e \u003cp\u003e10.2 Theoretical Background and Methods 342\u003c\/p\u003e \u003cp\u003e10.2.1 Calculation of Vibrational Frequencies 344\u003c\/p\u003e \u003cp\u003e10.2.2 Splitting of the Longitudinal Optical (LO) and Transverse Optical (TO) Modes 346\u003c\/p\u003e \u003cp\u003e10.2.3 Calculation of Infrared (IR) and Raman Peak Intensities and of the IR Dielectric Function 347\u003c\/p\u003e \u003cp\u003e10.2.4 Estimation of the Anharmonic Constant for X–H Stretching Modes 349\u003c\/p\u003e \u003cp\u003e10.2.5 Accuracy of Basis Set and Hamiltonian 350\u003c\/p\u003e \u003cp\u003e10.3 Examples and Applications 352\u003c\/p\u003e \u003cp\u003e10.3.1 Vibrational Properties of Calcium and Magnesium Carbonates 353\u003c\/p\u003e \u003cp\u003e10.3.2 A Complex Mineral: The IR Spectra of Ortho-enstatite 359\u003c\/p\u003e \u003cp\u003e10.3.3 Treatment of the O─H Stretching Modes: The Vibrational Spectra of Brucite and Diaspore 360\u003c\/p\u003e \u003cp\u003e10.4 Simulation of Vibrational Properties for Crystal Structure Determination 363\u003c\/p\u003e \u003cp\u003e10.4.1 Proton Disorder in γ-AlOOH Boehmite 364\u003c\/p\u003e \u003cp\u003e10.5 Future Challenges 368\u003c\/p\u003e \u003cp\u003eAcknowledgements 368\u003c\/p\u003e \u003cp\u003eReferences 368\u003c\/p\u003e \u003cp\u003e\u003cb\u003e11 Geochemical Kinetics via Computational Chemistry 375\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eJames D. Kubicki and Kevin M. Rosso\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e11.1 Introduction 375\u003c\/p\u003e \u003cp\u003e11.2 Methods 379\u003c\/p\u003e \u003cp\u003e11.2.1 Potential Energy Surfaces 379\u003c\/p\u003e \u003cp\u003e11.2.2 Choice of Solvation Methods 384\u003c\/p\u003e \u003cp\u003e11.2.3 Activation Energies and Volumes 386\u003c\/p\u003e \u003cp\u003e11.2.4 Transition States and Imaginary Frequencies 390\u003c\/p\u003e \u003cp\u003e11.2.5 Rate Constants 391\u003c\/p\u003e \u003cp\u003e11.2.6 Types of Reaction Mechanisms 393\u003c\/p\u003e \u003cp\u003e11.3 Applications 394\u003c\/p\u003e \u003cp\u003e11.3.1 Diffusion 394\u003c\/p\u003e \u003cp\u003e11.3.2 Ligand Exchange Aqueous Complexes 395\u003c\/p\u003e \u003cp\u003e11.3.3 Adsorption 396\u003c\/p\u003e \u003cp\u003e11.3.4 Dissolution 396\u003c\/p\u003e \u003cp\u003e11.3.5 Nucleation 398\u003c\/p\u003e \u003cp\u003e11.4 Future Challenges 399\u003c\/p\u003e \u003cp\u003e11.4.1 Femtosecond Spectroscopy 399\u003c\/p\u003e \u003cp\u003e11.4.2 H-Bonding 400\u003c\/p\u003e \u003cp\u003e11.4.3 Roaming 400\u003c\/p\u003e \u003cp\u003e11.4.4 Large-Scale Quantum Molecular Dynamics 401\u003c\/p\u003e \u003cp\u003e11.4.5 Reactive Force Fields 401\u003c\/p\u003e \u003cp\u003eReferences 403\u003c\/p\u003e \u003cp\u003eIndex 415\u003c\/p\u003e","brand":"John Wiley \u0026 Sons Inc","offers":[{"title":"Default Title","offer_id":49528838783319,"sku":"9781118845080","price":91.15,"currency_code":"GBP","in_stock":true}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/0817\/1739\/5799\/files\/9781118845080.jpg?v=1731873223","url":"https:\/\/bookcurl.com\/products\/molecular-modeling-of-geochemical-reactions-9781118845080","provider":"Book Curl","version":"1.0","type":"link"}