Inorganic Chemistry for Geochemistry and Environmental Sciences: Fundamentals and Applications

About the Author xvPreface xviiCompanion Website xix1. Inorganic Chemistry and the Environment 11.1 Introduction 11.1.1 Energetics of Processes 11.2 Neutron-Proton Conversion 31.3 Element Burning Reactions - Buildup of Larger Elements 41.4 Nuclear Stability and Binding Energy 51.4.1 The "r" and "s" Processes 61.5 Nuclear Stability (Radioactive Decay) 81.6 Atmospheric Synthesis of Elements 81.7 Abundance of the Elements 81.7.1 The Cosmos and the Earth's Lithosphere 81.7.2 Elemental Abundance (Atmosphere, Oceans, and Human Body) 101.8 Scope of Inorganic Chemistry in Geochemistry and the Environment 171.8.1 Elemental Distribution Based on Photosynthesis and Chemosynthesis 171.8.2 Stratified Waters and Sediments - the Degradation of Organic Matter by Alternate Electron Acceptors 191.9 Summary 211.9.1 Environmental Inorganic Chemistry 22References 222. Oxidation-Reduction Reactions (Redox) 242.1 Introduction 242.1.1 Energetics of Half Reactions 242.1.2 Standard Potential and the Stability of a Chemical Species of an Element 262.2 Variation of Standard Potential with pH (the Nernst Equation) 292.3 Thermodynamic Calculations and pH Dependence 292.4 Stability Field of Aqueous Chemical Species 312.5 Natural Environments 322.6 Calculations to Predict Favorable Chemical Reactions 322.6.1 Coupling Half-Reactions 342.6.2 One-Electron Oxygen Transformations with Fe2+ and Mn2+ to Form O2 . 352.7 Highly Oxidizing Conditions 382.7.1 Ozonolysis Reactions 382.7.2 Atmospheric Redox Reactions 39Appendix 2.1 Gibbs Free Energies of Formation 43References 433. Atomic Structure 453.1 History 453.2 The Bohr Atom 463.3 The Schrodinger Wave Equation 473.4 Components of the Wave Function 503.4.1 Radial Part of the Wave Function, R(r) 503.4.2 Angular Part of the Wavefunction Ylml( ) and Atomic Orbitals 543.5 The Four Quantum Numbers 563.6 The Polyelectronic Atoms and the Filling of Orbitals for the Atoms of the Elements 583.7 Aufbau Principle 613.8 Atomic Properties 623.8.1 Orbitals Energies and Shielding 623.8.2 Term Symbols: Coupling of Spin and Orbital Angular Momentum 633.8.3 Periodic Properties - Atomic Radius 673.8.4 Periodic Properties - Ionization Potential (IP) 673.8.5 Periodic Properties - Electron Affinity (EA) 713.8.6 Periodic Properties - Electronegativity ( ) 743.8.7 Periodic Properties - Hardness ( ) 75References 774. Symmetry 794.1 Introduction 794.2 Symmetry Concepts 794.2.1 Symmetry Operation 794.2.2 Symmetry Element 794.2.3 Symmetry Elements and Operations 804.3 Point Groups 844.3.1 Special Groups and Platonic Solids/Polyhedra 854.3.2 Examples of the Use of the Scheme for Determining Point Groups 884.4 Optical Isomerism and Symmetry 924.4.1 Dichloro-Allene Derivatives (C3H2Cl2) 924.4.2 Tartaric Acid 934.4.3 Cylindrical Helix Molecules 934.5 Fundamentals of Group Theory 934.5.1 C2v Point Group 954.5.2 Explanation of the Character Table 964.5.3 Generation of the Irreducible Representations (C2v Case) 974.5.4 Notation for Irreducible Representations 974.5.5 Some Important Properties of the Characters and their Irreducible Representations 984.5.6 Nonindependence of x and y Transformations (Higher Order Rotations) 984.6 Selected Applications of Group Theory 1014.6.1 Generation of a Reducible Representation to Describe a Molecule 1014.6.2 Determining the IR and Raman Activity of Vibrations in Molecules 1044.6.3 Determining the Vibrational Modes of Methane, CH4 1054.6.4 Determining the Irreducible Representations and Symmetry of the Central Atom's Atomic Orbitals that Form Bonds 1074.7 Symmetry Adapted Linear Combination (SALC) of Orbitals 1114.7.1 Sigma Bonding with Hydrogen as Terminal Atom 1114.7.2 Sigma and Pi Bonding with Atoms Other than Hydrogen as Terminal Atom 114Appendix 4.1 Some Additional useful Character Tables 120References 1225. Covalent Bonding 1235.1 Introduction 1235.1.1 Lewis Structures and the Octet Rule 1235.1.2 Valence Shell Electron Pair Repulsion Theory (VSEPR) 1265.2 Valence Bond Theory (VBT) 1275.2.1 H2 and Valence Bond Theory 1295.2.2 Ionic Contributions to Covalent Bonding 1305.2.3 Polyatomic Molecules and Valence Bond Theory 1315.3 Molecular Orbital Theory (MOT) 1325.3.1 H2 1325.3.2 Types of Orbital Overlap 1375.3.3 Writing Generalized Wave Functions 1385.3.4 Brief Comments on Computational Methods and Computer Modeling 1395.3.5 Homonuclear Diatomic Molecules (A2) 1405.3.6 Heteronuclear Diatomic Molecules and Ions (AB; HX) - Sigma Bonds Only 1445.3.7 Heteronuclear Diatomic Molecules and Ions (AB) - Sigma and Pi Bonds 1475.4 Understanding Reactions and Electron Transfer (Frontier Molecular Orbital Theory) 1505.4.1 Angular Overlap 1515.4.2 H+ +OH. 1515.4.3 H2 +D2 1525.4.4 H2 +F2 1535.4.5 H2 +C2 1545.4.6 H2 +N2 (also CO+H2) 1545.4.7 Dihalogens as Oxidants 1565.4.8 O2 as an Oxidant and its Reaction with H2S and HS. 1575.5 Polyatomic Molecules and Ions 1615.5.1 H3 + Molecular Cation 1615.5.2 BeH2 - Linear Molecule with Sigma Bonds Only 1635.5.3 H2O - Angular Molecule with Sigma Bonds Only 1655.6 Tetrahedral and Pyramidal Species with Sigma Bonds only (CH4, NH4 +, SO4 2.) 1685.6.1 CH4 1685.6.2 NH3 (C3v) 1705.6.3 BH3 and the Methyl Cation, CH3 + (D3h) 1725.7 Triatomic Compounds and Ions Involving Bonds (A3, AB2, and ABC) 1755.7.1 A3 Linear Species 1755.7.2 AB2 Linear Species CO2 (COS and N2O) 1785.7.3 O3, NO2 ., and SO2 (Angular Molecules) 1805.8 Planar Species (BF3, NO3 ., CO3 2., SO3) 182Appendix 5.1 Bond Energies for Selected Bonds 184Appendix 5.2 Energies of LUMOs and HOMOs 185References 1866. Bonding in Solids 1896.1 Introduction 1896.2 Covalent Bonding in Metals: Band Theory 1896.2.1 Atomic Orbital Combinations for Metals 1896.2.2 Metal Conductors 1916.2.3 Semiconductors and Insulators 1916.2.4 Fermi Level 1936.2.5 Density of States (DOS) 1946.2.6 Doping of Semiconductors 1956.2.7 Structures of Solids 1966.3 Ionic Solids 2006.3.1 Solids AX Stoichiometry 2006.3.2 Solids with Stoichiometry of AX2, AO2, A2O3, ABO3 (Perovskite), AB2O4 (Spinel) 2036.3.3 Crystal Radii 2056.3.4 Radius Ratio Rule 2056.3.5 Lattice Energy 2076.3.6 Born-Haber Cycle 2096.3.7 Thermal Stability of Ionic Solids 2106.3.8 Defect Crystal Structures 2126.4 Nanoparticles and Molecular Clusters 214References 2177. Acids and Bases 2197.1 Introduction 2197.2 Arrhenius and Bronsted-Lowry Definitions 2197.3 Hydrolysis of Metal-Water Complexes 2227.4 Hydration of Anhydrous Acidic and Basic Oxides 2237.4.1 Acidic Oxides 2237.4.2 Basic Oxides 2247.4.3 Amphoteric Oxides 2247.5 Solvent System Definition 2247.5.1 Leveling Effect 2257.6 Gas Phase Acid-Base Strength 2257.6.1 H3 + as a Reactant 2277.7 Lewis Definition 2277.7.1 MOT 2287.7.2 Molecular Iodine Adducts or Complexes as Examples 2287.7.3 Thermodynamics of Lewis Acid-Base Reactions 2297.7.4 Lewis Acid-Base Reactions of CO2 and I2 with Water and Hydroxide Ion 2307.7.5 Lewis Acid-Base Competitive Reactions 2327.8 Classification of Acids and Bases 2327.8.1 Irving-Williams Stability Relationship for the First Transition Metal Series 2327.8.2 Class "a" and "b" Acids and Bases 2337.8.3 Hard Soft Acid Base (HSAB) Theory 2337.9 Acid-Base Properties of Solids 235References 2358. Introduction to Transition Metals 2378.1 Introduction 2378.2 Coordination Geometries 2378.3 Nomenclature 2408.3.1 Complex Ion is Positive 2418.3.2 Complex Ion is Negative 2428.3.3 Complex Ion with Multiple Ligands 2428.3.4 Complex Ion with Ligand that can Bind with More Than One Atom (Ambidentate) 2438.3.5 Complex Ion with Multidentate Ligands 2438.3.6 Two Complex Ions with a Bridging Ligand 2438.4 Bonding and Isomers for Octahedral Geometry 2438.4.1 Ionization Isomerism 2448.4.2 Hydrate (Solvate) Isomers 2448.4.3 Coordination Isomerism 2458.4.4 Linkage Isomerism 2458.4.5 Geometrical Isomerism - Four Coordination 2468.4.6 Optical Isomerism in Octahedral Geometry 2488.5 Bonding Theories for Transition Metal Complexes 2508.5.1 Valence Bond Theory 2518.5.2 Crystal Field Theory 2528.6 Molecular Orbital Theory 2688.6.1 Case 1 - Octahedral Geometry (Sigma Bonding Only) 2688.6.2 Case 2 - Octahedral Geometry (Sigma Bonding Plus Ligand Donor) 2718.6.3 Case 3 - Octahedral Geometry (Sigma Bonding Plus Ligand Acceptor) 2728.7 Angular Overlap Model 2748.7.1 AOM and Ligand Donor Bonding 2778.7.2 AOM and Ligand Acceptor Bonding 2788.7.3 MOT, Electrochemistry, and the Occupancy of Electrons in d Orbitals in Oh 2788.7.4 AOM and Other Geometries 2798.8 More on Spectroscopy of Metal-Ligand Complexes 2818.8.1 Charge Transfer Electronic Transitions 2828.8.2 Electronic Spectra, Spectroscopic Terms, and the Energies of the Terms for d-->d Transitions 2838.8.3 Energy and Spatial Description of the Electron Transitions Between t2g and eg * Orbitals 2968.8.4 More Details on Correlation Diagrams 2978.8.5 Luminescence 2998.8.6 Magnetism and Spin Crossover in Octahedral Complexes and Natural Minerals 3018.8.7 Note about f Orbitals in Cubic Symmetry (Oh) 303References 3039. Reactivity of Transition Metal Complexes: Thermodynamics, Kinetics and Catalysis 3059.1 Thermodynamics Introduction 3059.1.1 Successive Stability Constants on Water Substitution 3059.1.2 The Chelate Effect 3079.2 Kinetics of Ligand Substitution Reactions 3089.2.1 Kinetics of Water Exchange for Aqua Complexes 3109.2.2 Intimate Mechanisms for Ligand Substitution Reactions 3109.2.3 Kinetic Model and Activation Parameters 3119.2.4 Dissociative Versus Associative Preference for Octahedral Ligand Substitution Reactions 3149.2.5 Stoichiometric Mechanisms 3159.2.6 Tests for Reaction Mechanisms 3209.3 Substitution in Octahedral Complexes 3219.3.1 Examples of Dissociative Activated Mechanisms 3219.3.2 Associative Activated Mechanisms 3229.4 Intimate Mechanisms Affected by Steric Factors (Dissociative Preference) 3249.4.1 Intimate Mechanisms Affected by Ligands in Cis versus Trans Positions (Dissociative Preference) 3249.4.2 Base Hydrolysis 3259.5 Intimate Versus Stoichiometric Mechanisms 3279.6 Substitution in Square Planar Complexes (Associative Activation Predominates) 3289.6.1 Effect of Leaving Group 3309.6.2 Effect of Charge 3309.6.3 Nature of the Intermediate - Electronic Factors 3309.6.4 Nature of the Intermediate - Steric Factors 3319.7 Metal Electron Transfer Reactions 3329.7.1 Outer Sphere Electron Transfer 3339.7.2 Cross Reactions 3379.7.3 Inner Sphere Electron Transfer 3399.8 Photochemistry 3419.8.1 Redox 3419.8.2 Photosubstitution Reactions d-->d 3419.8.3 LMCT and Photoreduction 3429.8.4 MLCT Simultaneous Substitution and Photo-Oxidation Redox 3429.9 Effective Atomic Number (EAN) Rule or the Rule of 18 3429.10 Thermodynamics and Kinetics of Organometallic Compounds 3449.11 Electron Transfer to Molecules during Transition Metal Catalysis 3459.12 Oxidation Addition (OXAD) and Reductive Elimination (Redel) Reactions 3469.13 Metal Catalysis 3479.13.1 OXO or Hydroformylation Process 3489.13.2 Heck Reaction 3509.13.3 Methyl Transferases 3509.13.4 Examples of Abiotic Organic Synthesis (Laboratory and Nature) 3519.13.5 The Haber Process Revisited 353References 35310. Transition Metals in Natural Systems 35610.1 Introduction 35610.2 Factors Governing Metal Speciation in the Environment and in Organisms 35610.3 Transition Metals Essential for Life 35810.4 Important Environmental Iron and Manganese Reactions 35910.4.1 Oxidation of Fe2+ and Mn2+ by O2 - Environmentally Important Metal Electron Transfer Reactions 36010.4.2 Redox Properties of Iron-Ligand Complexes 36310.4.3 Metal Ions Exhibiting Outer Sphere Electron Transfer 36410.5 Oxygen (O2) Storage and Transport 36410.5.1 Hemoglobin 36510.5.2 Hemocyanin and Hemerythrin 36810.6 Oxidation of CH4, Hydrocarbons, NH4 + 36810.6.1 Cytochrome P450: An Example of Cytochrome (Heme - O2) Redox Chemistry 36910.6.2 Conversion of NH4 + to NO3 . (Nitrification or Aerobic Ammonium Oxidation) 37110.7 Oxygen Production in Photosynthesis 372References 37411. Solid Phase Iron and Manganese Oxidants and Reductants 37711.1 Introduction 37711.2 Reduction of Solid MnO2 and Fe(OH)3 by Sulfide 37711.2.1 Fe(III) and Mn(IV) Electron Configurations 37811.2.2 MnO2 Reaction with Sulfide 37911.2.3 Fe(OH)3 Reaction with Sulfide 38211.3 Pyrite, FeS2, Oxidation 38411.3.1 Pyrite Reacting with O2 38411.3.2 Pyrite Reacting with Soluble Fe(III) 38511.3.3 Pyrite Reacting with Dihalogens and Cr2+ 387References 38812. Metal Sulfides in the Environment and in Bioinorganic Chemistry 39012.1 Introduction 39012.2 Idealized Molecular Reaction Schemes from Soluble Complexes to ZnS and CuS Solids 39112.3 Nanoparticle Size and Filtration 39412.4 Ostwald Ripening versus Oriented Attachment 39412.5 Metal Availability and Detoxification for MS Species 39612.6 Iron Sulfide Chemistry 39612.6.1 FeSmack (Mackinawite) 39612.6.2 FeSmack Conversion to Pyrite, FeS2 39712.6.3 FeS as a Catalyst in Organic Compound Formation 40012.6.4 FeS as an Electron Transfer Agent in Biochemistry 40012.7 More on the Nitrogen Cycle (Nitrate Reduction, Denitrification, and Anammox) 402Appendix 12.1 PbS Nanoparticle Model and Size Ranges of Natural Materials 404References 40413. Kinetics and Thermodynamics of Metal Uptake by Organisms 40613.1 Introduction 40613.1.1 Conditional Metal-Ligand Stability Constants 40713.1.2 Thermodynamic Metal-Ligand Stability Constants 40913.2 Metal Uptake Pathways 41013.2.1 Ion Channels for Potassium 41113.2.2 Metal Uptake by Cells via Ligands on Membranes 41313.2.3 Evaluation of kf, kd, and KcondM'L' from Laboratory and Natural Samples 418References 420Index 421