ALBERT

Note: Chapter 1. Molecular Modeling in Mineralogy and Geochemistry by Randall T. Cygan, p. 1 - 36 Chapter 2. Simulating the Crystal Structures and Properties of Ionic Materials From Interatomic Potentials by Julian D. Gale, p. 37 - 62 Chapter 3. Application of Lattice Dynamics and Molecular Dynamics Techniques to Minerals and Their Surfaces by Steve C. Parker, Nora H. de Leeuw, Ekatarina Bourova, and David J. Cooke, p. 63 - 82 Chapter 4. Molecular Simulations of Liquid and Supercritical Water: Thermodynamics, Structure, and Hydrogen Bonding by Andrey G. Kalinichev, p. 83 - 130 Chapter 5. Molecular Dynamics Simulations of Silicate Glasses and Glass Surfaces by Stephen H. Garofalini, p. 131 - 168 Chapter 6. Molecular Models of Surface Relaxation, Hydroxylation, and Surface Charging at Oxide-Water Interfaces by James R. Rustad, p. 169 - 198 Chapter 7. Structure and Reactivity of Semiconducting Mineral Surfaces: Convergence of Molecular Modeling and Experiment by Kevin M. Rosso, p. 199 - 272 Chapter 8. Quantum Chemistry and Classical Simulations of Metal Complexes in Aqueous Solutions by David M. Sherman, p. 273 - 318 Chapter 9. First Principles Theory of Mantle and Core Phases by Lars Stixrude, p. 319 - 344 Chapter 10. A Computational Quantum Chemical Study of the Bonded Interactions in Earth Materials and Structurally and Chemically Related Molecules by G. V. Gibbs, Monte B. Boisen, Jr., Lesa L. Beverly, and Kevin M. Rosso, p. 345 - 382 Chapter 11. Modeling the Kinetics and Mechanisms of Petroleum and Natural Gas Generation: A First Principles Approach by Yitian Xiao, p. 383 - 436 Chapter 12. Calculating the NMR Properties of Minerals, Glasses, and Aqueous Species by John D. Tossell, p. 437 - 458 Chapter 13. Interpretation of Vibrational Spectra Using Molecular Orbital Theory Calculations by James D. Kubicki, p. 459 - 484 Chapter 14. Molecular Orbital Modeling and Transition State Theory in Geochemistry by Mihali A. Felipe, Yitian Xiao, and James D. Kubicki, p. 485 - 531

Note: Table of Contents: 1 The Solid Phase of Marine Sediments / DIETER K. FÜTTERER 1.1 Introduction 1.2 Sources and Components of Marine Sediments 1.2.1 Lithogenous Sediments 1.2.2 Biogenous Sediments 1.2.3 Hydrogenous Sediments 1.3 Classification of Marine Sediments 1.3.1 Terrigenous Sediments 1.3.2 Deep-Sea Sediments 1.4 Global Patterns of Sediment Distribution 1.4.1 Distribution Patterns of Shelf Sediments 1.4.2 Distribution Patterns of Deep-Sea Sediments 1.4.3 Distribution Patterns of Glay Minerals 1.4.4 Sedimentation Rates 2 Geophysical Perspectives in Marine Sediments 2.1 Physical Properties of Marine Sediments / MONIKA BREITZKE 2.1.1 Introduction 2.1.2 Porosity and Wet Bulk Density 2.1.2.1 Analysis by Weight and Volume 2.1.2.2 Gamma Ray Attenuation 2.1.2.3 Electrical Resistivity (Galvanic Method) 2.1.2.4 Electrical Resistivity (Inductive Method) 2.1.3 Permeability 2.1.4 Acoustic and Elastic Properties 2.1.4.1 Biot-Stoll Model 2.1.4.2 Full Waveform Ultrasonic Gore Logging 2.1.5 Sediment Classification 2.1.5.1 Full Waveform Gore Logs as Acoustic Images 2.1.5.2 P-and S-Wave Velocity, Attenuation, Elastic Moduli and Permeability 2.1.6 Sediment Echosounding 2.1.6.1 Synthetic Seismograms 2.1.6.2 Narrow-Beam Parasound Echosounder Recordings 2.2 Sedimentary Magnetism / ULRICH BLEIL 2.2.1 Introduction 2.2.2 Biogenie Magnetic Minerals in Marine Sediments 2.2.3 Reduction Diagenesis of Magnetic Minerals in Marine Environments 3 Quantification of Early Diagenesis: Dissolved Constituents in Marine Pore Water / HORST D. SCHULZ 3.1 Introduction: How to Read Pore Water Concentration Profiles 3.2 Calculation of Diffusive Fluxes and Diagenetic Reaction Rates 3.2.1 Steady State and Non-Steady State Situations 3.2.2 The Steady State Situation and Fick's First Law of Diffusion 3.2.3 Quantitative Evaluation of Steady State Concentration Profiles 3.2.4 The Non-Steady State Situation and Fick's Second Law of Diffusion 3.2.5 The Primary Redox-Reactions: Degradation of Organic Matter 3.3 Sampling of Pore Water for Ex-Situ Measurements 3.3.1 Obtaining Sampies of Sediment for the Analysis of Pore Water 3.3.2 Pore Water Extraction from the Sediment 3.3.3 Storage, Transport and Preservation of Pore Water 3.4 Analyzing Constituents in Pore Water, Typical Profiles 3.5 In-Situ Measurements 3.6 Influence of Bioturbation, Bioirrigation, and Advection 4 Organic Matter: The Driving Force for Early Diagenesis / JÜRGEN RULLKÖTTER 4.1 The Organic Carbon Cycle 4.2 Organic Matter Accumulation in Sediments 4.2.1 Productivity Versus Preservation 4.2.2 Primary Production of Organic Matter and Export to the Ocean Bottom 4.2.3 Transport of Organic Matter through the Water Column 4.2.4 The Influence of Sedimentation Rate on Organic Matter Burial 4.2.5 Allochthonous Organic Matter in Marine Sediments 4.3 Early Diagenesis 4.3.1 The Organic Carbon Content of Marine Sediments 4.3.2 Chemical Composition of Biomass 4.3.3 The Principle of Selective Preservation 4.3.4 The Formation of Fossil Organic Matter and its Bulk Composition 4.3.5 Early Diagenesis at the Molecular Level 4.3.6 Biological Markers (Molecular Fossils) 4.4 Organic Geochemical Proxies 4.4.1 Total Organic Carbon and Sulfur 4.4.2 Marine Versus Terrigenous Organic Matter 4.4.3 Molecular Paleo-Seawater Temperature and Climate Indicators 4.5 Analytical Techniques 4.5.1 Sam pie Requirements 4.5.2 Elemental and Bulk Isotope Analysis 4.5.3 Rock-Eval Pyrolysis and Pyrolysis Gas Chromatography 4.5.4 Organic Petrography 4.5.5 Bitumen Analysis 4.6 The Future of Marine Geochemistry of Organic Matter 5 Bacteria and Marine Biogeochemistry / Bo BARKER JORGENSEN 5.1 Role of Microorganisms 5.1.1 From Geochemistry to Microbiology - and back 5.1.2 Approaches in Marine Biogeochemistry 5.2 Life and Environments at Small Scale 5.2.1 Hydrodynamics of Low Reynolds Numbers 5.2.2 Diffusion at Small Scale 5.2.3 Diffusive Boundary Layers 5.3 Regulation and Limits of Microbial Processes 5.3.1 Substrate Uptake by Microorganisms 5.3.2 Temperature as a Regulating Factor 5.3.3 Other Regulating Factors 5.4 Energy Metabolism of Prokaryotes 5.4.1 Free Energy 5.4.2 Reduction-Oxidation Processes 5.4.3 Relations to Oxygen 5.4.4 Definitions of Energy Metabolism 5.4.5 Energy Metabolism of Microorganisms 5.4.6 Chemolithotrophs 5.4.7 Respiration and Fermentation 5.5 Pathways of Organic Matter Degradation 5.5.1 Depolymerization of Macromolecules 5.5.2 Aerobic and Anaerobic Mineralization 5.5.3 Depth Zonation of Oxidants 5.6 Methods in Biogeochemistry 5.6.1 Incubation Experiments 5.6.2 Radioactive Tracers 5.6.3 Example: Sulfate Reduction 5.6.4 Specific Inhibitors 5.6.5 Other Methods 6 Early Diagenesis at the Benthic Boundary Layer: Oxygen and Nitrate in Marine Sediments / CHRISTIAN HENSEN AND MATTHIAS ZABEL 6.1 Introduction 6.2 Oxygen and Nitrate Distribution in Seawater 6.3 The Role of Oxygen and Nitrate in Marine Sediments 6.3.1 Respiration and Redox Processes 6.3.1.1 Nitrification and Denitrification 6.3.1.2 Coupling of Oxygen and Nitrate to other Redox Pathways 6.3.2 Determination of Consumption Rates and Senthic Fluxes 6.3.2.1 Fluxes and Concentration Profiles Determined by In-Situ Devices 6.3.2.2 Ex-Situ Pore Water Data from Deep-Sea Sediments 6.3.2.3 Determination of Denitrification Rates 6.3.3 Oxic Respiration, Nitrification and Denitrification in Different Marine Environments 6.3.3.1 Quantification of Rates and Fluxes 6.3.3.2 Variation in Different Marine Environments: Case Studies 6.4 Summary 7 The Reactivity of Iron / RALF R. HAESE 7.1 Introduction 7.2 Pathways of Iron Input to Marine Sediments 7.2.1 Fluvial Input 7.2.2 Aeolian Input 7.3 Iron as a Limiting Nutrient for Primary Productivity 7.4 The Early Diagenesis of Iron in Sediments 7.4.1 Dissimilatary Iran Reductian 7.4.2 Solid Phase Ferric Iron and its Bioavailability 7.4.2.1 Properties of Iron Oxides 7.4.2.2 Bioavailability of Iron Oxides 7.4.2.3 Bioavailability of Sheet Silicate Sound Ferric lron 7.4.3 Iron and Manganese Redax Cycles 7.4.4 Iron Reactivity towards S, O2, Mn, NO3, P, HCO3, and Si-AI 7.4.4.1 lron Reduction by HS and Ligands 7.4.4.2 Iron Oxidation by O2, NO3, and Mn4+ 7.4.4.3 Iron-Sound Phosphorus 7.4.4.4 The Formation of Siderite 7.4.4.5 The Formation of lron Searing Aluminosilicates 7.4.5 Discussion: The Importance of Fe-and Mn-Reactivity in Various Enyironments 7.5 The Assay for Ferric and Ferrous Iron 8 Sulfate Reduction in Marine Sediments / SABINE KASTEN AND BO BARKER JØRGENSEN 8.1 Introduction 8.2 Sulfate Reduction and the Degradation of Organic Matter 8.3 Biotic and Abiotic Processes Coupled to Sulfate Reduction 8.3.1 Pyrite Formation 8.3.2 Effects of Sulfate Reduction on Sedimentary Solid Phases 8.4 Determination of Sulfate Reduction Rates 9 Marine Carbonates: Their Formation and Destruction / RALPH R. SCHNEIDER, HORST D. SCHULZ AND CHRISTIAN HENSEN 9.1 Introduction 9.2 Marine Environments of Carbonate Production and Accumulation 9.2.1 Shallow-Water Carbonates 9.2.2 Pelagic Calcareous Sediments 9.3 The Calcite-Carbonate-Equilibrium in Marine Aquatic Systems 9.3.1 Primary Reactions of the Calcite-Carbonate-Equilibrium with Atmospheric Contact in Infinitely Diluted Solutions 9.3.2 Primary Reactions of the Calcite-Carbonate-Equilibrium without Atmospheric Contact 9.3.3 Secondary Reactions of the Calcite-Carbonate-Equilibrium in Seawater 9.3.4 Examples for Calculation of the Calcite-Carbonate-Equilibrium in Ocean Waters 9.4 Carbonate Reservoir Sizes and Fluxes between Particulate and Dissolved Reservoirs 9.4.1 Production Versus Dissolution of Pelagic Carbonates 9.4.2 Inorganic and Organic Carbon Release trom Deep-Sea Sediments 10 Influences of Geochemical Processes on Stable Isotope Distribution in Marine Sediments / TORSTEN SICKERT 10.1 Introduction 10.2 Fundamentals 10.2.1 Principles of Isotopic Fractionation 10.2.2 Analytical Procedures 10.3 Geochemicallnfluences on 18O/16O Ratios 10.3.1 δ18O of Seawater 10.3.2 δ18O in Marine Carbonates 10.4 Geochemical Influences on 13C/12C Ratios 10.4.1