Molecular modeling theory: applications in the geosciences / ed. by R.T.Cygan, J.D.Kubick. - Washington: Mineralogical society of America, 2001. - xii, 531 p.: ill. - (Reviews in mineralogy and geochemistry; vol.42). - Bibliogr. at the end of the art. - ISBN 0-939950-54-5; ISSN 1529-6466  Место хранения:   018 | Институт нефтегазовой геологии и геофизики им. А.А.Трофимука | Новосибирск | Библиотека

Оглавление / Contents

1 Molecular Modeling in Mineralogy and Geochemistry Randall T. Cygan INTRODUCTION .................................................... 1 Historical perspective ....................................... 2 Molecular modeling tools ..................................... 3 POTENTIAL ENERGY ................................................ 6 Energy terms ................................................. 7 Atomic charges .............................................. 10 Practical concerns .......................................... 11 MOLECULAR MODELING TECHNIQUES .................................. 11 Conformational analysis ..................................... 11 Energy minimization ......................................... 13 Energy minimization and classical-based equilibrium structures .................................................. 14 Quantum chemistry methods ................................... 15 Energy minimization and quantum-based equilibrium structures .................................................. 18 Monte Carlo methods ......................................... 20 Molecular dynamics methods .................................. 23 Quantum dynamics ............................................ 25 FORSTERITE: THE VERY MODEL OF A MODERN MAJOR MINERAL ........... 26 Static calculations and energy minimization studies ......... 27 Lattice dynamics studies .................................... 27 Quantum studies ............................................. 27 THE FUTURE ..................................................... 28 ACKNOWLEDGMENTS ................................................ 28 GLOSSARY OF TERMS .............................................. 29 REFERENCES ..................................................... 30 2 Simulating the Crystal Structures and Properties of Ionic Materials From Interatomic Potentials Julian D. Gale INTRODUCTION ................................................... 37 INTERATOMIC POTENTIAL MODELS FOR IONIC MATERIALS ............... 37 Long-range interactions ..................................... 39 Short-range interactions .................................... 40 Energy minimization ......................................... 41 CRYSTAL PROPERTIES FROM STATIC CALCULATION ..................... 44 Elastic constants ........................................... 44 Dielectric constants ........................................ 44 Piezoelectric constants ..................................... 45 Phonons ..................................................... 45 DERIVATION OF POTENTIAL PARAMETERS ............................. 47 Simultaneous fitting ........................................ 47 Relaxed fitting ............................................. 49 SIMULATING THE EFFECT OF TEMPERATURE AND PRESSURE ON CRYSTAL STRUCTURES ..................................................... 50 FUTURE DIRECTIONS IN INTERATOMIC POTENTIAL MODELLING OF IONIC MATERIALS ...................................................... 56 Structure solution and prediction ........................... 58 ACKNOWLEDGMENTS ................................................ 59 REFERENCES ..................................................... 59 3 Application of Lattice Dynamics and Molecular Dynamics Techniques to Minerals and Their Surfaces Steve C. Parker, Nora H. de Leeuw, Ekatarina Bourova, David J. Cooke INTRODUCTION ................................................... 63 METHODOLOGY .................................................... 63 LATTICE DYNAMICS ............................................... 64 MOLECULAR DYNAMICS ............................................. 67 SIMULATION OF MINERAL-WATER INTERFACES ......................... 74 CONCLUSIONS .................................................... 80 REFERENCES ..................................................... 81 4 Molecular Simulations of Liquid and Supercritical Water: Thermodynamics, Structure, and Hydrogen Bonding Audrey G. Kalinichev INTRODUCTION ................................................... 83 CLASSICAL METHODS OF MOLECULAR SIMULATIONS ..................... 86 Molecular dynamics .......................................... 86 Monte Carlo methods ......................................... 87 Boundary conditions, long-range corrections, and statistical errors .......................................... 89 Interaction potentials for aqueous simulations .............. 90 THERMODYNAMICS OF SUPERCRITICAL AQUEOUS SYSTEMS ................ 95 Macroscopic thermodynamic properties of simulated supercritical water ......................................... 96 Micro-thermodynamic properties .............................. 97 STRUCTURE OF SUPERCRITICAL WATER .............................. 101 HYDROGEN BONDING IN LIQUID AND SUPERCRITICAL WATER ............ 104 MOLECULAR CLUSTERIZATION IN SUPERCRITICAL WATER ............... 109 DYNAMICS OF MOLECULAR TRANSLATIONS, LIBRATIONS, AND VIBRATIONS IN SUPERCRITICAL WATER ............................. 113 CONCLUSIONS AND OUTLOOK ....................................... 120 ACKNOWLEDGMENTS ............................................... 121 REFERENCES .................................................... 121 5 Molecular Dynamics Simulations of Silicate Glasses and Glass Surfaces Stephen H. Garofalini INTRODUCTION .................................................. 131 MOLECULAR DYNAMICS COMPUTER SIMULATION TECHNIQUE .............. 131 Interatomic potentials ..................................... 135 Periodic boundary conditions ............................... 137 MD SIMULATIONS OF OXIDE GLASSES ............................... 140 Bulk glasses ............................................... 140 Bulk SiO2 .................................................. 141 Multicomponent silicate glasses ............................ 145 MD SIMULATIONS OF OXIDE GLASS SURFACES ........................ 147 SiO2 ....................................................... 147 Multicomponent silicate surfaces ........................... 162 SUMMARY ....................................................... 162 ACKNOWLEDGMENTS ............................................... 164 REFERENCES .................................................... 164 6 Molecular Models of Surface Relaxation, Hydroxylation, and Surface Charging at Oxide-Water Interfaces James R. Rustad INTRODUCTION .................................................. 169 SCOPE ......................................................... 170 THE STILLINGER-DAV1D WATER MODEL .............................. 172 IRON-WATER AND SILICON-WATER POTENTIALS AND THE BEHAVIOR OF FE3+ AND SI4+ IN THE GAS PHASE AND IN AQUEOUS SOLUTION ..... 174 CRYSTAL STRUCTURES ............................................ 177 VACUUM-TERMINATED SURFACES .................................... 179 HYDRATED AND HYDROXYLATED SURFACES ............................ 183 Neutral surfaces ........................................... 183 Surface charging ........................................... 188 SOLVATED INTERFACES ........................................... 191 REMARKS ....................................................... 193 ACKNOWLEDGMENTS ............................................... 193 REFERENCES .................................................... 194 7 Structure and Reactivity of Semiconducting Mineral Surfaces: Convergence of Molecular Modeling and Experiment Kevin M. Rosso INTRODUCTION .................................................. 199 BACKGROUND CONCEPTS ........................................... 200 Experimental approaches .................................... 200 Semiconductors and their surfaces .......................... 201 THEORETICAL METHODS ........................................... 212 Theory-Hartree-Fock versus density functional theory ....... 213 Basis sets-Gaussian orbital versus plane waves ............. 216 Surface model-Cluster versus periodic ...................... 221 Codes-Crystal vs. CASTEP ................................... 223 APPLICATIONS .................................................. 226 Sulfides ................................................... 226 Oxides ..................................................... 248 CONCLUDING REMARKS AND OUTLOOK ................................ 260 ACKNOWLEDGMENTS ............................................... 262 REFERENCES .................................................... 262 8 Quantum Chemistry and Classical Simulations of Metal Complexes in Aqueous Solutions David M. Sherman INTRODUCTION .................................................. 273 Experimental methods ....................................... 273 Continuum models ........................................... 274 Atomistic computational methods ............................ 274 QUANTUM CHEMISTRY OF METAL COMPLEXES: THEORETICAL BACKGROUND AND METHODOLOGY ............................................... 275 Quantum mechanics of many-electron systems ................. 275 Bonding in molecules and complexes ......................... 280 Calculating thermodynamic quantities from first principles ................................................. 283 Simulations of solvent effects ............................. 284 APPLICATIONS OF QUANTUM CHEMISTRY TO METAL COMPLEXES IN AQUEOUS SOLUTIONS ............................................. 285 Group IIB cations Zn, Cd and Hg ............................ 285 Group IB cations Cu, Ag, and Au ............................ 292 Iron and manganese ......................................... 296 Alkali earth and alkali metal cations ...................... 299 Post-transition metals ..................................... 299 CLASSICAL ATOMISTIC SIMULATIONS OF METAL COMPLEXES IN AQUEOUS SOLUTIONS ............................................. 301 Background ................................................. 301 Interatomic potentials ..................................... 302 Molecular dynamics ......................................... 304 Metropolis Monte Carlo simulations ......................... 305 Applications ............................................... 305 THE NEXT ERA: AB INITIO MOLECULAR DYNAMICS .................... 310 Application to copper(I) chloride solutions ................ 311 SUMMARY AND FUTURE DIRECTIONS ................................. 311 ACKNOWLEDGMENTS ............................................... 312 REFERENCES .................................................... 312 9 First Principles Theory of Mantle and Core Phases Lars Stixrude INTRODUCTION .................................................. 319 THEORY ........................................................ 321 Overview ................................................... 321 Total energy, forces, and stresses ......................... 324 Statistical mechanics ...................................... 326 SELECTED APPLICATIONS ......................................... 332 Overview ................................................... 332 Phase transformations in silicates ......................... 332 High temperature properties of transition metals ........... 336 CONCLUSIONS AND OUTLOOK ....................................... 339 Scale ...................................................... 339 Duration ................................................... 339 Materials .................................................. 340 ACKNOWLEDGMENTS ............................................... 340 REFERENCES .................................................... 340 10 A Computational Quantum Chemical Study of the Bonded Interactions in Earth Materials and Structurally and Chemically Related Molecules G.V. Gibbs, Monte B. Boisen, Jr., Lesa L. Beverly, Kevin M. Rosso INTRODUCTION .................................................. 345 BOND LENGTH AND BOND STRENGTH CONNECTIONS FOR OXIDE, FLUORIDE, NITRIDE, AND SULFIDE MOLECULAR AND CRYSTALLINE MATERIALS ..................................................... 345 Bond lengths and crystal radii ............................. 345 Bonded interactions ........................................ 346 Pauling bond strength and bond length variations ........... 347 Brown and Shannon bond strength and bond length variations ................................................. 348 Bond strength p and bond length variations ................. 348 Bond number and bond length variations ..................... 350 Nitride, fluoride and sulfide bond strength and bond length variations .......................................... 351 Bond strength and crystal radii ............................ 352 FORCE CONSTANTS, COMPRESSIBILITIES OF COORDINATED POLYHEDRA, AND POTENTIAL ENERGY MODELS ................................... 353 Force constants and bond length variations ................. 353 Force constants and polyhedral compressibilities ........... 354 Force fields and bond length and angle variations .......... 355 Generation of new and viable structure types for silica .... 357 CALCULATED ELECTRON DENSITY DISTRIBUTIONS FOR EARTH MATERIALS AND RELATED MOLECULES ............................... 358 Bond critical point properties and electron density distributions .............................................. 358 Bond critical point properties calculated for molecules .... 359 Bond critical point properties calculated for earth materials .................................................. 361 Variable radius of the oxide anion ......................... 362 BOND STRENGTH, ELECTRON DENSITY, AND BOND TYPE CONNECTIONS .... 365 SITES OF POTENTIAL ELECTROPHILIC ATTACK IN EARTH MATERIALS .... 367 Bonded and nonbonded electron pairs ........................ 367 Bonded and nonbonded electron lone pairs for a silicate molecule ................................................... 369 Localization of the electron density for the silica polymorphs ................................................. 370 Nonbonded lone pair electrons for low albite ............... 372 CONCLUDING REMARKS ............................................ 373 ACKNOWLEDGMENTS ............................................... 375 REFERENCES .................................................... 376 11 Modeling the Kinetics and Mechanisms of Petroleum and Natural Gas Generation: A First Principles Approach Yitian Xiao INTRODUCTION .................................................. 383 AB INITIO METHOD .............................................. 385 KEROGEN DECOMPOSITION AND OIL AND GAS GENERATION .............. 390 Introduction ............................................... 390 The kinetics and mechanisms of hydrocarbon thermal cracking ................................................... 394 Computational methods ...................................... 396 Initiation reaction (homolytic scission) ................... 397 Hydrogen transfer reaction ................................. 400 Radical decomposition (P scission) ......................... 403 Elementary reactions versus overall hydrocarbon cracking ... 406 Summary .................................................... 407 ISOTOPIC FRACTIONATION AND NATURAL GAS GENERATION ............. 408 Introduction ............................................... 408 Transition state theory and gas isotopic fractionation ..... 409 Natural gas plot ........................................... 410 Carbon kinetic isotope effect: homolytic scission verses β scission ................................................. 411 Biogenic gas versus thermogenic gas ........................ 415 Summary .................................................... 416 POSSIBLES ROLES OF MINERALS AND TRANSITION METALS IN OIL AND GAS GENERATION ................................................ 416 Introduction ............................................... 416 Acid catalyzed isomerization of C7 alkanes and light HC origin ..................................................... 417 Transition metal catalysis and natural gas generation ...... 420 WATER-ORGANIC INTERACTIONS AND THEIR IMPLICATIONS ON PETROLEUM FORMATION ........................................... 423 Introduction ............................................... 423 Why don't oil and water mix? ............................... 424 The kinetics and mechanisms of water-organic (kerogen) interaction ................................................ 425 Hydrolysis of ether linkages ............................... 425 Hydrolysis of ester linkages ............................... 427 Water-hydrocarbon radical interactions ..................... 428 Hydrolytic disproportionate and kerogen oxidation .......... 430 CONCLUSIONS ................................................... 431 ACKNOWLEDGMENTS ............................................... 431 REFERENCES .................................................... 431 12 Calculating the NMR Properties of Minerals, Glasses, and Aqueous Species John D. Tossell INTRODUCTION .................................................. 437 BASIC THEORY OF NMR SHIELDING ................................. 437 A BRIEF HISTORY OF NMR CALCULATIONS ON MOLECULES .............. 439 PRESENT STATUS OF NMR CALCULATIONS ON MOLECULES ............... 439 CALCULATION OF SI NMR SHIELDINGS IN ALUMINOSILICATES .......... 443 CALCULATIONS OF SHIELDINGS FOR OTHER ELECTROPOSITIVE ELEMENTS: B, P, SE, NA AND RB ................................. 446 CALCULATION OF ELECTRIC FIELD GRADIENTS AT О IN ALUMINOSILICATES .............................................. 448 CALCULATION OF NMR SHIELDING OF О IN OXIDES ................... 449 CALCULATION OF NMR SHIELDINGS FOR TRANSITION METAL COMPOUNDS AND HEAVY MAIN-GROUP METAL COMPOUNDS .......................... 450 CALCULATIONS OF С NMR SHIELDINGS IN ORGANIC GEOCHEMISTRY ...... 450 APPLICATIONS OF NMR SHIELDING CALCULATIONS IN GEOCHEMISTRY AND MINERALOGY ................................................ 451 A FINAL WORD ON INTERPRETATION OF CALCULATED NMR SHIELDINGS ... 453 CONCLUSION .................................................... 454 ACKNOWLEDGMENTS ............................................... 454 REFERENCES .................................................... 454 13 Interpretation of Vibrational Spectra Using Molecular Orbital Theory Calculations James D. Kubicki INTRODUCTION .................................................. 459 ENERGY MINIMIZATIONS .......................................... 460 CALCULATION OF SPECTRA ........................................ 461 CALCULATION OF FREQUENCIES .................................... 462 CALCULATION OF IR AND RAMAN INTENSITIES ....................... 463 Infrared intensities ....................................... 463 Raman intensities .......................................... 465 VIBRATIONAL BANDWIDTHS ........................................ 466 EXAMPLES AND COMPARISON TO EXPERIMENT ......................... 467 Gas-phase .................................................. 467 Aqueous-phase .............................................. 469 Mineral surfaces ........................................... 473 Minerals ................................................... 475 Glasses .................................................... 475 CONCLUSIONS AND FUTURE DIRECTIONS ............................. 478 ACKNOWLEDGMENTS ............................................... 478 REFERENCES .................................................... 479 14 Molecular Orbital Modeling and Transition State Theory in Geochemistry Mihali A. Felipe, Titian Xiao, James D. Kubicki INTRODUCTION .................................................. 485 TRANSITION STATE THEORY ....................................... 486 Conventional transition state theory ....................... 486 Potential energy surfaces and MO calculations .............. 490 Other rate theories ........................................ 494 DETERMINATION OF ELEMENTARY STEPS AND REACTION MECHANISMS ..... 496 Stationary-point searching schemes ......................... 496 Transition state initial guesses ........................... 498 Optimization to stationary points .......................... 501 MO-TST STUDIES IN THE GEOSCIENCES ............................. 504 Introduction and definitions ............................... 504 Reaction pathways of mineral-water interaction ............. 505 Atmospheric reactions of global significance ............... 511 ACCURACY ISSUES ............................................... 517 Basis sets ................................................. 517 Basis set superposition error .............................. 518 Methods .................................................... 518 Long-range interactions .................................... 519 Activation energies and zero point energies ................ 519 Quantum tunneling .......................................... 520 CONCLUSIONS AND FUTURE DIRECTIONS ............................. 521 ACKNOWLEDGMENTS ............................................... 522 LIST OF SYMBOLS ............................................... 522 REFERENCES .................................................... 524