Molecular Modeling of Geochemical Reactions

Professor James David Kubicki, Department of Geosciences, The Pennsylvania State University, USADr Kubicki has 25 years of experience in computational geochemistry across a variety of sub-disciplines. He has published on melts and glasses, high-pressure mineral physics, aqueous geochemistry, organic geochemistry, environmental geochemistry, biogeochemistry and isotopic geochemistry. He has been an editor of three books, two on computational geochemistry and one on geochemical kinetics. Dr Kubicki has been a professor at The Pennsylvania State University for 15 years and has taught about computational geochemistry in all of his graduate courses. In addition, he has participated in numerous multi-disciplinary research projects and mentored graduate and undergraduate students on computational geochemistry research methods. He has organized two workshops on methods and applications in computational geochemistry.

• List of Contributors xiPreface xiii1 Introduction to the Theory and Methods of Computational Chemistry 1David M. Sherman1.1 Introduction 11.2 Essentials of Quantum Mechanics 21.2.1 The Schrödinger Equation 41.2.2 Fundamental Examples 41.3 Multielectronic Atoms 71.3.1 The Hartree and Hartree–Fock Approximations 71.3.2 Density Functional Theory 131.4 Bonding in Molecules and Solids 171.4.1 The Born–Oppenheimer Approximation 171.4.2 Basis Sets and the Linear Combination of Atomic Orbital Approximation 181.4.3 Periodic Boundary Conditions 201.4.4 Nuclear Motions and Vibrational Modes 211.5 From Quantum Chemistry to Thermodynamics 221.5.1 Molecular Dynamics 241.6 Available Quantum Chemistry Codes and Their Applications 27References 282 Force Field Application and Development 33Marco Molinari, Andrey V. Brukhno, Stephen C. Parker, and Dino Spagnoli2.1 Introduction 332.2 Potential Forms 352.2.1 The Non-bonded Interactions 352.2.2 The Bonded Interactions 372.2.3 Polarisation Effects 372.2.4 Reactivity 392.2.5 Fundamentals of Coarse Graining 402.3 Fitting Procedure 422.3.1 Combining Rules Between Unlike Species 422.3.2 Optimisation Procedures for All-Atom Force Fields 432.3.3 Deriving CG Force Fields 452.3.4 Accuracy and Limitations of the Fitting 472.3.5 Transferability 482.4 Force Field Libraries 482.4.1 General Force Fields 482.4.2 Force Field Libraries for Organics: Biomolecules with Minerals 492.4.3 Potentials for the Aqueous Environment 502.4.4 Current CGFF Potentials 512.4.5 Multi-scale Methodologies 532.5 Evolution of Force Fields for Selected Classes of Minerals 542.5.1 Calcium Carbonate 542.5.2 Clay Minerals 562.5.3 Hydroxides and Hydrates 602.5.4 Silica and Silicates 602.5.5 Iron-Based Minerals 612.6 Concluding Remarks 63References 643 Quantum-Mechanical Modeling of Minerals 77Alessandro Erba and Roberto Dovesi3.1 Introduction 773.2 Theoretical Framework 793.2.1 Translation Invariance and Periodic Boundary Conditions 793.2.2 HF and KS Methods 803.2.3 Bloch Functions and Local BS 813.3 Structural Properties 823.3.1 P–V Relation Through Analytical Stress Tensor 833.3.2 P–V Relation Through Equation of State 853.4 Elastic Properties 863.4.1 Evaluation of the Elastic Tensor 863.4.2 Elastic Tensor-Related Properties 893.4.3 Directional Seismic Wave Velocities and Elastic Anisotropy 893.5 Vibrational and Thermodynamic Properties 913.5.1 Solid-State Thermodynamics 933.6 Modeling Solid Solutions 953.7 Future Challenges 98References 994 First Principles Estimation of Geochemically Important Transition Metal Oxide Properties: Structure and Dynamics of the Bulk, Surface, and Mineral/Aqueous Fluid Interface 107Ying Chen, Eric Bylaska, and John Weare4.1 Introduction 1074.2 Overview of the Theoretical Methods and Approximations Needed to Perform AIMD Calculations 1094.3 Accuracy of Calculations for Observable Bulk Properties 1134.3.1 Bulk Structural Properties 1134.3.2 Bulk Electronic Structure Properties 1184.4 Calculation of Surface Properties 1234.4.1 Surface Structural Properties 1234.4.2 Electronic Structure in the Surface Region 1274.4.3 Water Adsorption on Surface 1294.5 Simulations of the Mineral–Water Interface 1304.5.1 CPMD Simulations of the Vibrational Structure of the Hematite (012)–Water Interface 1304.5.2 CPMD Simulations of Fe2+ Species at the Mineral–Water Interface 1324.6 Future Perspectives 134Acknowledgments 134Appendix 134A.1 Short Introduction to Pseudopotentials 135A.1.1 The Spin Penalty Pseudopotential 137A.1.2 Projected Density of States from Pseudo-Atomic Orbitals 138A.2 Hubbard-Like Coulomb and Exchange (DFT+U) 138A.3 Overview of the PAW Method 139References 1435 Computational Isotope Geochemistry 151James R. Rustad5.1 A Brief Statement of Electronic Structure Theory and the Electronic Problem 1525.2 The Vibrational Eigenvalue Problem 1545.3 Isotope Exchange Equilibria 1565.4 Qualitative Insights 1595.5 Quantitative Estimates 1605.6 Relationship to Empirical Estimates 1695.7 Beyond the Harmonic Approximation 1715.8 Kinetic Isotope Effects 1725.9 Summary and Prognosis 172Acknowledgments 173References 1736 Organic and Contaminant Geochemistry 177Daniel Tunega, Martin H. Gerzabek, Georg Haberhauer, Hans Lischka, and Adelia J. A. Aquino6.1 Introduction 1776.1.1 Review Examples of Molecular Modeling Applications in Organic and Contaminant Geochemistry 1796.2 Molecular Modeling Methods 1846.2.1 Molecular Mechanics: Brief Summary 1846.2.2 Quantum Mechanics: Overview 1876.2.3 Molecular Modeling Techniques: Summary 1926.2.4 Models: Clusters, Periodic Systems, and Environmental Effects 1956.3 Applications 1966.3.1 Modeling of Surface Complexes of Polar Phenoxyacetic Acid-Based Herbicides with Iron Oxyhydroxides and Clay Minerals 1976.3.2 Modeling of Adsorption Processes of Polycyclic Aromatic Hydrocarbons on Iron Oxyhydroxides 2176.3.3 Modeling of Interactions of Polar and Nonpolar Contaminants in Organic Geochemical Environment 2206.4 Perspectives and Future Challenges 227Glossary 229References 2317 Petroleum Geochemistry 245Qisheng Ma and Yongchun Tang7.1 Introduction: Petroleum Geochemistry and Basin Modeling 2457.2 Technology Development of the Petroleum Geochemistry 2467.2.1 Thermal Maturity and Vitrinite Reflectance 2467.2.2 Rock-Eval Pyrolysis 2477.2.3 Kerogen Pyrolysis and Gas Chromatography Analysis 2487.2.4 Kinetic Modeling of Kerogen Pyrolysis 2497.2.5 Natural Gases and C/H Isotopes 2537.3 Computational Simulations in Petroleum Geochemistry 2537.3.1 Ab Initio Calculations of the Unimolecular C–C Bond Rapture 2537.3.2 Quantum Mechanical Calculations on Natural Gas 13C Isotopic Fractionation 2567.3.3 Deuterium Isotope Fractionations of Natural Gas 2587.3.4 Molecular Modeling of the 13C and D Doubly Substituted Methane Isotope 2607.4 Summary 262References 2628 Mineral–Water Interaction 271Marie-Pierre Gaigeot and Marialore Sulpizi8.1 Introduction 2718.2 Brief Review of AIMD Simulation Method 2758.2.1 Ab Initio Molecular Dynamics and Density Functional Theory 2758.3 Calculation of the Surface Acidity from Reversible Proton Insertion/Deletion 2808.4 Theoretical Methodology for Vibrational Spectroscopy and Mode Assignments 2828.5 Property Calculations from AIMD: Dipoles and Polarisabilities 2848.6 Illustrations from Our Recent Works 2868.6.1 Organisation of Water at Silica–Water Interfaces: (0001) α-Quartz Versus Amorphous Silica 2868.6.2 Organisation of Water at Alumina–Water Interface: (0001) α-Alumina Versus (101) Boehmite 2918.6.3 How Surface Acidities Dictate the Interfacial Water Structural Arrangement 2938.6.4 Vibrational Spectroscopy at Oxide–Liquid Water Interfaces 2958.6.5 Clay–Water Interface: Pyrophyllite and Calcium Silicate 2998.7 Some Perspectives for Future Works 302References 3049 Biogeochemistry 311Weilong Zhao, Zhijun Xu, and Nita Sahai9.1 Introduction 3119.1.1 Mineral–Water Interactions 3139.1.2 Mineral–Organic Interactions 3139.2 Challenges and Approaches to Computational Modeling of Biomineralization 3149.2.1 Biominerals: Structure, Nucleation, and Growth 3149.2.2 Conformational Sampling in Modeling Biomineralization 3179.2.3 Force Field Benchmarking 3249.2.4 Ab Initio MD and Hybrid QM/MM Approaches 3259.3 Case Studies 3269.3.1 Apatite 3279.3.2 Calcite 3319.4 Concluding Remarks and Future Perspectives 334Acknowledgments 335References 33510 Vibrational Spectroscopy of Minerals Through Ab Initio Methods 341Marco De La Pierre, Raffaella Demichelis, and Roberto Dovesi10.1 Introduction 34110.2 Theoretical Background and Methods 34210.2.1 Calculation of Vibrational Frequencies 34410.2.2 Splitting of the Longitudinal Optical (LO) and Transverse Optical (TO) Modes 34610.2.3 Calculation of Infrared (IR) and Raman Peak Intensities and of the IR Dielectric Function 34710.2.4 Estimation of the Anharmonic Constant for X–H Stretching Modes 34910.2.5 Accuracy of Basis Set and Hamiltonian 35010.3 Examples and Applications 35210.3.1 Vibrational Properties of Calcium and Magnesium Carbonates 35310.3.2 A Complex Mineral: The IR Spectra of Ortho-enstatite 35910.3.3 Treatment of the O─H Stretching Modes: The Vibrational Spectra of Brucite and Diaspore 36010.4 Simulation of Vibrational Properties for Crystal Structure Determination 36310.4.1 Proton Disorder in γ-AlOOH Boehmite 36410.5 Future Challenges 368Acknowledgements 368References 36811 Geochemical Kinetics via Computational Chemistry 375James D. Kubicki and Kevin M. Rosso11.1 Introduction 37511.2 Methods 37911.2.1 Potential Energy Surfaces 37911.2.2 Choice of Solvation Methods 38411.2.3 Activation Energies and Volumes 38611.2.4 Transition States and Imaginary Frequencies 39011.2.5 Rate Constants 39111.2.6 Types of Reaction Mechanisms 39311.3 Applications 39411.3.1 Diffusion 39411.3.2 Ligand Exchange Aqueous Complexes 39511.3.3 Adsorption 39611.3.4 Dissolution 39611.3.5 Nucleation 39811.4 Future Challenges 39911.4.1 Femtosecond Spectroscopy 39911.4.2 H-Bonding 40011.4.3 Roaming 40011.4.4 Large-Scale Quantum Molecular Dynamics 40111.4.5 Reactive Force Fields 401References 403Index 415