Organic Geochemistry

I • Introduction.- 1 • Biogeochemical Cycles: A Review of Fundamental Aspects of Organic Matter Formation, Preservation, and Composition.- 1. Introduction.- 2. Organic Matter as an Information Source.- 3. Classification of Living Organisms; the Importance and Diversity of Microbes.- 4. Biogeochemical Cycles and Inventories of Major Bioactive Elements.- 5. Biochemistry and Isotopic Consequences of Incorporation of Bioelements into Biomass; Diagnostic Isotopic Fossils.- 6. Diagnostic Molecular Structures Encoded in Fossil Organic Matter.- 7. Geological History of the Biogeochemical Cycles.- 8. Future Research Directions.- References.- 2 A Review of Macromolecular Organic Compounds That Comprise Living Organisms and Their Role in Kerogen, Coal, and Petroleum Formation.- 1. Introduction.- 2. Inventory of Macromolecular Substances, Their Ocurrence in Organisms, and Their Potential for Survival in Recent Sediments.- 3. Structural Relationships between Kerogen/Coal and Selectively Preserved Resistant Biopolymers.- 4. Consequences for Formation of Oil, Coal, and Gas.- References.- 3 • Isotope Fractionation during Primary Production.- 1. Introduction.- 2. Definition of Isotope Terms.- 3. Carbon Isotopes.- 4. Nitrogen Isotopes.- 5. Oxygen Isotopes.- 6. Hydrogen Isotopes.- 7. Sulfur Isotopes: Fractionation during Photosynthesis.- 8. Implications for Organic Geochemistry.- References.- II • Early Diagenesis of Organic Matter.- 4 • Early Diagenesis of Organic Matter: The Dynamics (Rates) of Cycling of Organic Compounds.- 1. Introduction.- 2. Methods of Measuring Decomposition and Transformation Rates during Early Diagenesis.- 3. Key Processes and Rates.- 4. Accuracy of Rate Measurements.- 5. Patterns of Variation in Rates of Early Diagenesis.- 6. Goals for the Future.- 7. Conclusions.- References.- 5 • The Early Diagenesis of Organic Matter: Bacterial Activity.- 1. Introduction to Bacteria as Primary Agents.- 2. Current Conceptual Models and Experimental Approaches.- 3. Bacterial Abundance and Global Distribution in Sediments.- 4. Constraints on Bacterial Activities in Sediments.- 5. Unique Catalytic Properties and Microbial Consortia.- 6. Concluding Remarks.- References.- 6 • Production, Transport, and Alteration of Particulate Organic Matter in the Marine Water Column.- 1. Introduction.- 2. Vertical Flux of Organic Matter Sinking through the Water Column.- 3. Influences on the Quality of Particulate Organic Matter Sinking through the Water Column.- 4. Concluding Remarks.- References.- 7 • Organic Matter at the Sediment-Water Interface.- 1. Introduction.- 2. Organic Material at the Mineral-Water Interface.- 3. Organic Matter at the Sediment-Water Interface.- 4. Synthesis and Future Directions.- References.- 8 • The Early Diagenesis of Organic Matter in Lacustrine Sediments.- 1. Sources and Sedimentation of Organic Matter in Lakes.- 2. Indicators of Early Diagenesis of Organic Matter in Lacustrine Sediments.- 3. Molecular Indicators of Early Diagenesis of Organic Matter.- 4. Summary and Conclusion.- References.- 9 • Early Diagenesis of Organic Matter in Sediments: Assessment of Mechanisms and Preservation by the Use of Isotopic Molecular Approaches.- 1. Introduction.- 2. Amino Acid Nitrogen in Sediments.- 3. Bulk Characterization of Sediments: C/N.- 4. Isotopes and Diagenetic Fractionation.- 5. Molecular-Level Isotope Analyses.- References.- 10 • Marine Invertebrate Feeding and the Sedimentary Lipid Record.- 1. Introduction.- 2. Fatty Acids.- 3. Phytol and Fatty Alcohols.- 4. Sterols.- 5. Hydrocarbons and Long-Chain Lipids.- 6. Conclusions.- References.- 11 • Early Diagenesis: Consequences for Applications of Molecular Biomarkers.- 1. Introduction.- 2. The Nature of Early Diagenesis.- 3. Compositional Trends in Degrading Organic Matter—a Simple Model.- 4. Effects of Early Diagenesis on Different Biomarker Applications.- 5. Conclusions.- References.- 12 • The Early Diagenesis of Organic Matter: Reaction at the Air-Sea Interface.- 1. Introduction.- 2. The Air-Sea Interface: Description and Composition.- 3. Transformation of Dissolved to Particulate Carbon in Surface Microlayers.- 4. Transformation from Low to High Molecular Weight.- 5. Photochemical Alterations.- 6. Summary and a Special Case.- References.- III • Kerogen and Related Materials.- 13 • Determination of Structural Components of Kerogens by the Use of Analytical Pyrolysis Methods.- 1. Introduction.- 2. Elucidation of Kerogen Composition by Pyrolysis.- 3. Pyrolysis as a Structural Tool.- 4. Analytical Pyrolysis and Implications for Kerogen Formation and Petroleum Generation.- 5. Summary.- References.- 14 • Chemical Methods for Assessing Kerogen and Protokerogen Types and Maturity.- 1. Introduction and Scope.- 2. Definitions and Isolation Procedures.- 3. Kerogen Type.- 4. Principal Kerogen Maturation Techniques Now in Use.- 5. Spectral Methods of Determining Kerogen Type and Maturation.- 6. Other Miscellaneous Methods of Kerogen Typing and Maturation.- References.- 15 • Organic Petrographic Approach to Kerogen Characterization.- 1. Introduction.- 2. Optical Methods of Kerogen Characterization.- 3. Optical Methods to Evaluate Thermal Maturity.- 4. Conclusions.- References.- IV • Thermal Alteration of Organic Matter and the Formation of Fossil Fuels.- 16 • The Thermal Alteration of Kerogen and the Formation of Oil.- 1. Introduction.- 2. Thermal Alteration of Kerogen.- 3. Quantitation of Hydrocarbon Generation.- 4. Composition of Crude Oils.- 5. Timing of Oil Generation.- 6. Conclusions.- References.- 17 • Hydrothermal Alteration of Organic Matter in Marine and Terrestrial Systems.- 1. Introduction.- 2. Geological Locales with Hydrothermal Petroleum.- 3. Interactions of Hydrothermal Activity with Organic Matter.- 4. Hydrothermal Petroleum Generation and Migration.- 5. Summary.- References.- 18 • Laboratory Simulation of Petroleum Formation: Hydrous Pyrolysis.- 1. Introduction.- 2. Definition of Hydrous Pyrolysis.- 3. Significance of Expelled Oil.- 4. Comparison of Pyrolysate Yields.- 5. Utility of Rock Samples.- 6. Effects of Reactor Wall Composition.- 7. Consideration of Experimental Artifacts.- 8. Conclusions.- References.- V • Applications of Organic Geochemical Research for Hydrocarbon Exploration.- 19 • Oil-Oil and Oil-Source Rock Correlations: Techniques.- 1. Introduction.- 2. Gas Chromatography and Mass Spectrometry.- 3. Direct Insertion Probe MS/MS (DIP-MS/MS).- 4. Pyrolysis.- 5. High-Pressure Liquid Chromatography and Mass Spectrometry.- 6. Supercritical Fluid Chromatography and Mass Spectrometry.- 7. Gas Chromatography and Carbon Deuterium and Isotopic Compositions.- 8. Summary.- References.- 20 • Organic Geochemistry of Estancia Vieja Oils, Rio Negro Norte Block: Correlation with Other Neuquen Basin, Argentina, Oils.- 1. Introduction.- 2. Results and Discussion.- 3. Conclusions.- References.- 21 • Oil to Source Rock Correlation: Concepts and Case Studies.- 1. Introduction.- 2. Oil-Source Rock Correlations—A Conceptual Framework.- 3. Case Studies.- 4. Future Directions.- References.- 22 • The Kinetics of Biomarker Reactions: Implications for the Assessment of the Thermal Maturity of Organic Matter in Sedimentary Basins.- 1. Introduction.- 2. Chemical Kinetics.- 3. Elucidation of the Activation Energy and Pre-Exponential Constant.- 4. Case Studies.- 5. The Effect of Mineral Matrix.- 6. Conclusions.- References.- 23 • Effect of Biodegradation and Water Washing on Crude Oil Composition.- 1. Introduction.- 2. Geologic Constraints and Physicochemical Conditions for Biodegradation and Water Washing.- 3. Effects of Biodegradation and Water Washing on Crude Oil Composition.- 4. Examples of Occurrences of Biodegradation and Water Washing.- 5. Summary.- References.- 24 • The Origin and Distribution of Gas Hydrates in Marine Sediments.- 1. Introduction.- 2. Structure and Stability.- 3. Bottom-Simulating Reflector.- 4. Geochemical Evidence and Hydrate Occurrence.- 5. The Significance of Gas Hydrates.- References.- VI • Organic Matter and Metalliferous Deposits.- 25 • The Role of Organic Matter in Ore Transport Processes.- 1. Introduction.- 2. Metals in Petroleum Liquids.- 3. Metals in Oil Field and Formation Waters.- 4. Discussion.- 5. Behavior of Metals in a Composite Petroleum-Brine System.- References.- 26 • Aspects of the Organic Geochemistry and Petrology of Metalliferous Ores.- 1. Introduction.- 2. Low-Temperature Deposits.- 3. High-Temperature Deposits: Optical Anisotropy.- 4. Hydrocarbon Phases.- 5. Thucholite.- 6. Petroleum Inclusions.- 7. Geological Controls.- 8. Conclusion.- References.- 27 • Metals in Black Shales.- 1. Introduction.- 2. Organic Matter in Shales.- 3. Metals in Shales.- 4. Metal Sources.- 5. Geochemistry of Metalliferous Black Shales.- 6. Carbon and Sulfur Relationships.- 7. Degree of Pyritization.- 8. Resources and Raw Materials.- 9. Summary.- References.- 28 • Trace and Minor Elements in Coal.- 1. Introduction.- 2. Source and Variation of Inorganic Constituents.- 3. Modes of Occurrence.- 4. Organic-Inorganic Interactions.- 5. Why Concern Ourselves with the Elements in Coal?.- 6. Conclusions.- References.- VII • The Precambrian.- 29 • Evolution of the Earth’s Atmosphere and Hydrosphere: Hadean to Recent.- 1. Formation of the Atmosphere and Ocean.- 2. Early Atmospheric Composition and Climate.- 3. Sulfur Gases and Ultraviolet Radiation.- 4. Ocean Composition and pH.- 5. The Faint Young Sun Problem and the Decline in Atmospheric CO2.- 6. The Rise of Oxygen and Ozone.- 7. Other Trace Gases.- 8. Summary.- References.- 30 • The Prebiotic Synthesis of Organic Compounds on the Early Earth.- 1. The Composition of the Primitive Atmosphere.- 2. Energy Sources.- 3. Prebiotic Synthesis of Amino Acids.- 4. Mildly Reducing and Nonreducing Atmospheres.- 5. Purine and Pyrimidine Synthesis.- 6. Sugars.- 7. Other Prebiotic Compounds.- 8. Compounds That Have Not Been Synthesized Prebiotically.- 9. Organic Compounds in Carbonaceous Chondrites.- 10. Interstellar Molecules.- 11. Production Rates and Concentrations of Hydrogen Cyanide, Formaldehyde, and Amino Acids in the Primitive Ocean.- 12. The Concentration of Amino Acids in the Primitive Ocean.- References.- 31 • The Initiation of Biological Processes on Earth: Summary of Empirical Evidence.- 1. Introduction.- 2. Origins of Life on Earth: Evidence and Constraints from the Geological Record.- 3. Summary and Conclusions.- References.- 32 • Organic Geochemistry of Precambrian Sedimentary Rocks.- 1. Introduction.- 2. The Precambrian: Geological and Paleontological Aspects.- 3. Organic Carbon.- 4. Kerogen Studies.- 5. Extract and Oil Studies.- 6. Economic Geology.- 7. Summary and Conclusions.- References.- 33 • The Organic Geochemistry of Carbonaceous Meteorites: Amino Acids and Stable Isotopes.- 1. Introduction.- 2. Distribution of Amino Acids in the Murchison Meteorite.- 3. Amino Acid Stereochemistry.- 4. Stable Isotopes.- 5. Implications for the Origin of Life on Earth.- 6. Conclusions.- References.- VIII • Applications of Organic Geochemistry for Quaternary Research.- 34 • Applications of Biomarkers for Delineating Marine Paleoclimatic Fluctuations during the Pleistocene.- 1. Introduction.- 2. Climatic Changes during the Pleistocene.- 3. Biomarkers as Climatic Indicators.- 4. Future Potential and Scope for Biomarkers in Paleoclimatic Assessment.- References.- 35 • The Diagenesis of Proteins and Amino Acids in Fossil Shells.- 1. Introduction.- 2. Diagenesis of Proteins and Amino Acids in Fossil Shells.- 3. Hydrolysis of Proteins and Peptides in Fossil Shells.- 4. Stereochemistry and Racemization of Amino Acids.- 5. Amino Acid Racemization in Fossil Shells.- 6. Rate and Extent of Isoleucine Epimerization in Peptides.- 7. A Model for Isoleucine Epimerization in Proteins.- 8. Summary.- References.- 36 • Applications of Organic Geochemistry for Quaternary Research: Aminostratigraphy and Aminochronology.- 1. Introduction.- 2. Foraminiferal Aminostratigraphy and Aminochronology: Examples of the Relationships among Enantiomeric Ratios, Statigraphic Position, and Taxonomy.- 3. Molluscan Aminostratigraphy: General Depositional Framework Models.- 4. Molluscan Aminostratigraphy: Examples of the Relationship between Enantiomeric Ratios, Stratigraphic Position, and Taxonomy.- 5. Molluscan Aminochronology: Examples of Calibrated Racemization Kinetics in Sequences of Coastal Deposits.- 6. Correlation.- 7. Geochemical Techniques for the Recognition of Anomalous Results.- 8. Summary and Conclusions.- References.- 37 • Sources and Cycling of Organic Matter within Modern and Prehistoric Food Webs.- 1. Introduction.- 2. Isotopic Variation among Primary Producers.- 3. Isotopic Composition of Consumers.- 4. Quantitative Analysis through Mixing Equations.- 5. Isotopic Compositions of Individual Compounds.- 6. Prehistoric Dietary Reconstruction.- 7. Conclusions.- References.- 38 • Macromolecules from Living and Fossil Biominerals: Implications for the Establishment of Molecular Phylogenies.- 1. Introduction.- 2. Fossil Proteins.- 3. Future Directions.- References.- 39 • Immunospecificity of Fossil Proteins: Implications for the Establishment of Evolutionary Trends.- 1. Introduction.- 2. Radioimmunoassay.- 3. Applications of RIA to Fossils.- 4. RIA Phylogenies, Biogeography, and Molecular Clocks.- 5. Future Prospects.- 6. Summary.- References.- IX • Summary.- 40 • Postscript.