Molecular Modeling of Geochemical Reactions: An Introduction

Title Page......Page 5
Copyright......Page 6
Contents......Page 7
List of Contributors......Page 13
Preface......Page 15
 1.1 Introduction......Page 17
 1.2 Essentials of Quantum Mechanics......Page 18
  1.2.2 Fundamental Examples......Page 20
  1.3.1 The Hartree and Hartree–Fock Approximations......Page 23
  1.3.2 Density Functional Theory......Page 29
  1.4.1 The Born–Oppenheimer Approximation......Page 33
  1.4.2 Basis Sets and the Linear Combination of Atomic Orbital Approximation......Page 34
  1.4.3 Periodic Boundary Conditions......Page 36
  1.4.4 Nuclear Motions and Vibrational Modes......Page 37
 1.5 From Quantum Chemistry to Thermodynamics......Page 38
  1.5.1 Molecular Dynamics......Page 40
 1.6 Available Quantum Chemistry Codes and Their Applications......Page 43
 References......Page 44
 2.1 Introduction......Page 49
  2.2.1 The Non-bonded Interactions......Page 51
  2.2.3 Polarisation Effects......Page 53
  2.2.4 Reactivity......Page 55
  2.2.5 Fundamentals of Coarse Graining......Page 56
  2.3.1 Combining Rules Between Unlike Species......Page 58
  2.3.2 Optimisation Procedures for All-Atom Force Fields......Page 59
  2.3.3 Deriving CG Force Fields......Page 61
  2.3.4 Accuracy and Limitations of the Fitting......Page 63
  2.4.1 General Force Fields......Page 64
  2.4.2 Force Field Libraries for Organics: Biomolecules with Minerals......Page 65
  2.4.3 Potentials for the Aqueous Environment......Page 66
  2.4.4 Current CGFF Potentials......Page 67
  2.4.5 Multi-scale Methodologies......Page 69
  2.5.1 Calcium Carbonate......Page 70
  2.5.2 Clay Minerals......Page 72
  2.5.4 Silica and Silicates......Page 76
  2.5.5 Iron-Based Minerals......Page 77
 2.6 Concluding Remarks......Page 79
 References......Page 80
 3.1 Introduction......Page 93
  3.2.1 Translation Invariance and Periodic Boundary Conditions......Page 95
  3.2.2 HF and KS Methods......Page 96
  3.2.3 Bloch Functions and Local BS......Page 97
 3.3 Structural Properties......Page 98
  3.3.1 P–V Relation Through Analytical Stress Tensor......Page 99
  3.3.2 P–V Relation Through Equation of State......Page 101
  3.4.1 Evaluation of the Elastic Tensor......Page 102
  3.4.3 Directional Seismic Wave Velocities and Elastic Anisotropy......Page 105
 3.5 Vibrational and Thermodynamic Properties......Page 107
  3.5.1 Solid-State Thermodynamics......Page 109
 3.6 Modeling Solid Solutions......Page 111
 3.7 Future Challenges......Page 114
 References......Page 115
 4.1 Introduction......Page 123
 4.2 Overview of the Theoretical Methods and Approximations Needed to Perform AIMD Calculations......Page 125
  4.3.1 Bulk Structural Properties......Page 129
  4.3.2 Bulk Electronic Structure Properties......Page 134
  4.4.1 Surface Structural Properties......Page 139
  4.4.2 Electronic Structure in the Surface Region......Page 143
  4.4.3 Water Adsorption on Surface......Page 145
  4.5.1 CPMD Simulations of the Vibrational Structure of the Hematite (012)–Water Interface......Page 146
  4.5.2 CPMD Simulations of Fe2+ Species at the Mineral–Water Interface......Page 148
 Appendix......Page 150
  A.1 Short Introduction to Pseudopotentials......Page 151
   A.1.1 The Spin Penalty Pseudopotential......Page 153
  A.2 Hubbard-Like Coulomb and Exchange (DFT+U)......Page 154
  A.3 Overview of the PAW Method......Page 155
 References......Page 159
Chapter 5 Computational Isotope Geochemistry......Page 167
 5.1 A Brief Statement of Electronic Structure Theory and the Electronic Problem......Page 168
 5.2 The Vibrational Eigenvalue Problem......Page 170
 5.3 Isotope Exchange Equilibria......Page 172
 5.4 Qualitative Insights......Page 175
 5.5 Quantitative Estimates......Page 176
 5.6 Relationship to Empirical Estimates......Page 185
 5.7 Beyond the Harmonic Approximation......Page 187
 5.9 Summary and Prognosis......Page 188
 References......Page 189
 6.1 Introduction......Page 193
  6.1.1 Review Examples of Molecular Modeling Applications in Organic and Contaminant Geochemistry......Page 195
  6.2.1 Molecular Mechanics: Brief Summary......Page 200
  6.2.2 Quantum Mechanics: Overview......Page 203
  6.2.3 Molecular Modeling Techniques: Summary......Page 208
  6.2.4 Models: Clusters, Periodic Systems, and Environmental Effects......Page 211
 6.3 Applications......Page 212
  6.3.1 Modeling of Surface Complexes of Polar Phenoxyacetic Acid-Based Herbicides with Iron Oxyhydroxides and Clay Minerals......Page 213
  6.3.2 Modeling of Adsorption Processes of Polycyclic Aromatic Hydrocarbons on Iron Oxyhydroxides......Page 233
  6.3.3 Modeling of Interactions of Polar and Nonpolar Contaminants in Organic Geochemical Environment......Page 236
 6.4 Perspectives and Future Challenges......Page 243
 Glossary......Page 245
 References......Page 247
 7.1 Introduction: Petroleum Geochemistry and Basin Modeling......Page 261
  7.2.1 Thermal Maturity and Vitrinite Reflectance......Page 262
  7.2.2 Rock-Eval Pyrolysis......Page 263
  7.2.3 Kerogen Pyrolysis and Gas Chromatography Analysis......Page 264
  7.2.4 Kinetic Modeling of Kerogen Pyrolysis......Page 265
  7.3.1 Ab Initio Calculations of the Unimolecular C–C Bond Rapture......Page 269
  7.3.2 Quantum Mechanical Calculations on Natural Gas 13C Isotopic Fractionation......Page 272
  7.3.3 Deuterium Isotope Fractionations of Natural Gas......Page 274
  7.3.4 Molecular Modeling of the 13C and D Doubly Substituted Methane Isotope......Page 276
 References......Page 278
 8.1 Introduction......Page 287
  8.2.1 Ab Initio Molecular Dynamics and Density Functional Theory......Page 291
 8.3 Calculation of the Surface Acidity from Reversible Proton Insertion/Deletion......Page 296
 8.4 Theoretical Methodology for Vibrational Spectroscopy and Mode Assignments......Page 298
 8.5 Property Calculations from AIMD: Dipoles and Polarisabilities......Page 300
  8.6.1 Organisation of Water at Silica–Water Interfaces: (0001) α-Quartz Versus Amorphous Silica......Page 302
  8.6.2 Organisation of Water at Alumina–Water Interface: (0001) α-Alumina Versus (101) Boehmite......Page 307
  8.6.3 How Surface Acidities Dictate the Interfacial Water Structural Arrangement......Page 309
  8.6.4 Vibrational Spectroscopy at Oxide–Liquid Water Interfaces......Page 311
  8.6.5 Clay–Water Interface: Pyrophyllite and Calcium Silicate......Page 315
 8.7 Some Perspectives for Future Works......Page 318
 References......Page 320
 9.1 Introduction......Page 327
  9.1.2 Mineral–Organic Interactions......Page 329
  9.2.1 Biominerals: Structure, Nucleation, and Growth......Page 330
  9.2.2 Conformational Sampling in Modeling Biomineralization......Page 333
  9.2.3 Force Field Benchmarking......Page 340
  9.2.4 Ab Initio MD and Hybrid QM/MM Approaches......Page 341
 9.3 Case Studies......Page 342
  9.3.1 Apatite......Page 343
  9.3.2 Calcite......Page 347
 9.4 Concluding Remarks and Future Perspectives......Page 350
 References......Page 351
 10.1 Introduction......Page 357
 10.2 Theoretical Background and Methods......Page 358
  10.2.1 Calculation of Vibrational Frequencies......Page 360
  10.2.2 Splitting of the Longitudinal Optical (LO) and Transverse Optical (TO) Modes......Page 362
  10.2.3 Calculation of Infrared (IR) and Raman Peak Intensities and of the IR Dielectric Function......Page 363
  10.2.4 Estimation of the Anharmonic Constant for X–H Stretching Modes......Page 365
  10.2.5 Accuracy of Basis Set and Hamiltonian......Page 366
 10.3 Examples and Applications......Page 368
  10.3.1 Vibrational Properties of Calcium and Magnesium Carbonates......Page 369
  10.3.2 A Complex Mineral: The IR Spectra of Ortho-enstatite......Page 375
  10.3.3 Treatment of the OH Stretching Modes: The Vibrational Spectra of Brucite and Diaspore......Page 376
 10.4 Simulation of Vibrational Properties for Crystal Structure Determination......Page 379
  10.4.1 Proton Disorder in γ-AlOOH Boehmite......Page 380
 References......Page 384
 11.1 Introduction......Page 391
  11.2.1 Potential Energy Surfaces......Page 395
  11.2.2 Choice of Solvation Methods......Page 400
  11.2.3 Activation Energies and Volumes......Page 402
  11.2.4 Transition States and Imaginary Frequencies......Page 406
  11.2.5 Rate Constants......Page 407
  11.2.6 Types of Reaction Mechanisms......Page 409
  11.3.1 Diffusion......Page 410
  11.3.2 Ligand Exchange Aqueous Complexes......Page 411
  11.3.4 Dissolution......Page 412
  11.3.5 Nucleation......Page 414
  11.4.1 Femtosecond Spectroscopy......Page 415
  11.4.3 Roaming......Page 416
  11.4.5 Reactive Force Fields......Page 417
 References......Page 419
Index......Page 431
EULA......Page 439