Note: Intro -- Computational Inorganic and Bioinorganic Chemistry -- Contents -- List of Contributors -- Series Preface -- Volume Preface -- PART 1: METHODS -- Calculation of Bonding Properties -- 1 Introduction -- 2 EDA Method -- 3 Diatomic Molecules H2, N2, CO, BF -- 4 Acetylene and Heavier Group-14 Homologs HEEH (E = C-Pb) -- 5 Bonding in Transition-Metal Carbonyl ComplexesTM(CO)6q (TMq = Hf2−, Ta−, W, Re+, Os2+,Ir3+) -- 6 Bonding in [Mo(ZnR)12] -- 7 Conclusion -- 8 Abbreviations and Acronyms -- 9 References -- Determining Transition States in Bioinorganic Reactions -- 1 Introduction -- 2 Methods to Locate Transition States -- 3 Connecting to Experiment -- 4 Is the Protein Effect Critical for Hydrogen Peroxide Reduction by Glutathione Peroxidase (GPX)? -- 5 Transition States in QM:MM Models of Isopenicillin N Synthase -- 6 Co-C Bond Cleavage and Hydrogen Transfer in B12-Dependent Methylmalonyl-CoA Mutase. Stepwise or Concerted? -- 7 Summary -- 8 Glossary -- 9 Acknowledgments -- 10 Related Articles -- 11 Abbreviations and Acronyms -- 12 References -- Quantum Mechanical/Molecular Mechanical (QM/MM) Methods and Applications in Bioinorganic Chemistry -- 1 Introduction -- 2 Methods -- 3 Structures -- 4 Energies -- 5 Applications -- 6 Practical Recommendations -- 7 Conclusions -- 8 Acknowledgments -- 9 Abbreviations and Acronyms -- 10 References -- Ab initio and Semiempirical Methods -- 1 Introduction -- 2 Correlated Ab initio Methods -- 3 Semiempirical SCF Methods -- 4 Acknowledgments -- 5 Abbreviations and Acronyms -- 6 References -- Spectroscopic Properties of Protein-Bound Cofactors: Calculation by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Approaches -- 1 Introduction -- 2 Combined Quantum Mechanics and Molecular Mechanics Methods -- 3 Use of QM/MM Methods in Computational Chemistry -- 4 Concluding Remarks -- 5 Acknowledgments. , 6 Abbreviations and Acronyms -- 7 References -- Spectroscopic Properties Obtained from Time-Dependent Density Functional Theory (TD-DFT) -- 1 Introduction -- 2 TD-DFT and Spectroscopic Properties -- 3 Benchmark Data and Some Case Studies -- 4 Concluding Remarks -- 5 Acknowledgments -- 6 End Notes -- 7 Abbreviations and Acronyms -- 8 References -- Nuclear Magnetic Resonance (NMR) Parameters of Transition Metal Complexes: Methods and Applications -- 1 Introduction -- 2 Methodological Aspects -- 3 NMR Parameters of Transition-Metal Nuclei -- 4 Ligand NMR Parameters -- 5 Ligand NMR Shifts for Paramagnetic Complexes -- 6 Concluding Remarks -- 7 End Notes -- 8 Related Articles -- 9 Abbreviations and Acronyms -- 10 References -- Calculation of Reduction Potential and pKa -- 1 Introduction -- 2 QM/MM/PCM Method -- 3 QM/PCM Method for pKa Calculations -- 4 QM/PCM Method: Reduction Potential -- 5 Empirical Method: PROPKA -- 6 Conclusion -- 7 Glossary -- 8 Acknowledgments -- 9 Abbreviations and Acronyms -- 10 References -- Quantum-Chemistry-Centered Normal Coordinate Analysis (QCC-NCA): Application of NCA for the Simulation of the Vibrational Spectra of Large Molecules -- 1 Vibrational Spectroscopy and Analysis -- 2 The Age of Density Functional Theory -- 3 The Best of Both Worlds: Combing DFT and NCA Using the QCC-NCA Approach -- 4 Application of the QCC-NCA Method to Simulate Nuclear Resonance Vibrational Data of Ferrous-Heme Nitrosyls -- 5 Outlook: Pushing the Limits -- 6 Acknowledgment -- 7 End Notes -- 8 Abbreviations and Acronyms -- 9 Further Reading -- 10 References -- Molecular Mechanics in Bioinorganic Chemistry -- 1 Introduction -- 2 Molecular Mechanics -- 3 Applications Involving s-Block Ions -- 4 Applications Involving Transition Metal Centers -- 5 Conclusions -- 6 Related Articles -- 7 Abbreviations and Acronyms -- 8 References. , Multiconfigurational Quantum Mechanics (QM) for Heavy Element Compounds -- 1 Introduction -- 2 The Complete Active Space Self-Consistent Field (CASSCF) Method -- 3 Second-Order Perturbation Theory (CASPT2) -- 4 Relativistic Effects -- 5 Applications -- 6 Summary and Conclusions -- 7 Acknowledgments -- 8 Abbreviations and Acronyms -- 9 References -- Approximate Density Functionals: Which Should I Choose? -- 1 Introduction -- 2 Functional Taxonomy -- 3 Hard Realities of Computation -- 4 Which System Do I Have? -- 5 Various Directions in DFT Development -- 6 Concluding Remarks -- 7 Acknowledgments -- 8 Abbreviations and Acronyms -- 9 Further Reading -- 10 References -- Spin Contamination in Inorganic Chemistry Calculations -- 1 Introduction -- 2 Hartree-Fock -- 3 Spin Operators -- 4 Projection Operators -- 5 Projected Methods -- 6 Applications -- 7 Conclusion -- 8 Acknowledgments -- 9 Related Articles -- 10 Abbreviations and Acronyms -- 11 References -- Gaussian Basis Sets for Quantum Mechanical (QM) Calculations -- 1 Introduction -- 2 General Considerations -- 3 Systematically Convergent Basis Sets -- 4 Basis Set Recommendations -- 5 Future Directions-Explicitly Correlated Approaches -- 6 Conclusions -- 7 Glossary -- 8 Abbreviations and Acronyms -- 9 References -- PART 2: CASE STUDIES - BIOINORGANIC -- Modeling Metalloenzymes with Density Functional and Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations: Progress and Challenges -- 1 Introduction -- 2 Overview of Computational Methods and Example Metalloenzyme Systems -- 3 Discussion -- 4 Conclusion -- 5 Acknowledgments -- 6 Abbreviations and Acronyms -- 7 Further Reading -- 8 References -- Broken Symmetry States of Iron-Sulfur Clusters -- 1 Introduction -- 2 Broken Symmetry and Spin States of Spin-Coupled Complexes -- 3 Quantum Cluster Interaction Energies With Protein and Solvent. , 4 4Fe4S Clusters -- 5 Nitrogenase Overview -- 6 Concluding Remarks -- 7 Glossary -- 8 Acknowledgments -- 9 Related Articles -- 10 Abbreviations and Acronyms -- 11 References -- Water Oxidation by the Manganese Cluster in Photosynthesis -- 1 Introduction -- 2 Methods and Models -- 3 S-State Transitions and O-O Bond Formation -- 4 Conclusions -- 5 Abbreviations and Acronyms -- 6 References -- Nature of the Catecholate-Fe(III) Bond: High Affinity Binding and Substrate Activation in Bioinorganic Chemistry -- 1 Introduction -- 2 Metal L-Edge Spectroscopy: Differential Orbital Covalency (DOC) -- 3 The Siderophores: High Affinity Binding -- 4 The Intradiol Dioxygenases: Activation for Catalysis -- 5 Concluding Comments -- 6 Acknowledgments -- 7 Abbreviations and Acronyms -- 8 References -- Computational Studies: B12 Cofactors and Their Interaction with Enzyme Active Sites -- 1 Introduction -- 2 Brief Overview of Computational Methods Used In B12 Research -- 3 The Free B12 Cofactors -- 4 Enzyme-Bound B12 Cofactors -- 5 Conclusions -- 6 Acknowledgments -- 7 Abbreviations and Acronyms -- 8 Further Reading -- 9 References -- Reaction Coordinate of Pyranopterin Molybdenum Enzymes -- 1 Introduction -- 2 Sulfite Oxidase -- 3 Xanthine Oxidase -- 4 Acknowledgments -- 5 Abbreviations and Acronyms -- 6 References -- Electronic Structure Calculations: Dinitrogen Reduction in Nitrogenase and Synthetic Model Systems -- 1 Introduction -- 2 DFT Treatments of N2 Reduction in Model Systems -- 3 DFT Calculations on The FeMoco and Its Reactivity With N2 -- 4 Summary and Conclusions -- 5 Acknowledgments -- 6 End Notes -- 7 Abbreviations and Acronyms -- 8 References -- Hydrogenases: Theoretical Investigations Towards Bioinspired H2 Production and Activation -- 1 Introduction -- 2 Characterization of Key [NiFe]-Hydrogenase Forms. , 3 Characterization of Key [FeFe]-Hydrogenases Forms -- 4 Computation of Reaction Barriers to Discriminate Among Plausible Catalytic Mechanisms -- 5 Contributions to the Design and Characterization of Structural and Functional Synthetic Models of The Hydrogenase Active Sites -- 6 Outlook and Concluding Remarks -- 7 Appendix: Computation of IR Frequencies -- 8 Abbreviations and Acronyms -- 9 References -- Computational Studies: Cisplatin -- 1 Introduction -- 2 Mode of Action of Cisplatin -- 3 Structural/Cellular Responses to Cisplatin DNA Binding -- 4 Modeling Cisplatin-DNA Complexes -- 5 Small Models -- 6 Large Models -- 7 Related Studies -- 8 Concluding Remarks -- 9 Abbreviations and Acronyms -- 10 References -- Computational Methods: Modeling of Reactivity in Zn-Containing Enzymes -- 1 Introduction -- 2 Computational Techniques -- 3 Reactivity: Zn-Enzyme Catalysis -- 4 Conclusions -- 5 Abbreviations and Acronyms -- 6 References -- Combined Density Functional Theory (DFT) and Electrostatics Study of the Proton Pumping Mechanism in Cytochrome c Oxidase -- 1 Introduction -- 2 Methods and Models -- 3 Results and Discussion -- 4 Conclusion -- 5 Acknowledgments -- 6 Abbreviations and Acronyms -- 7 References -- Computational Studies: Proton/Water Coupling to Metals in Biological Reaction Mechanisms -- 1 Introduction -- 2 Cytochrome c Oxidase -- 3 Yeast Cytosine Deaminase -- 4 Oniom-MD -- 5 Calcium Pump -- 6 Concluding Remarks -- 7 Acknowledgments -- 8 Abbreviations and Acronyms -- 9 References -- Computational Studies: Chemical Evolution of Metal Sites -- 1 Introduction -- 2 Methodology -- 3 Molecular Evolution of Vitamin B12 -- 4 Molecular Evolution of Heme -- 5 Coevolution of Metals and Ligands -- 6 Molecular Evolution of Iron-Sulfur Clusters -- 7 Perspectives and Conclusions -- 8 Glossary -- 9 Acknowledgments -- 10 Related Articles. , 11 Abbreviations and Acronyms.

Note: Cover Page -- Title Page -- Copyright Page -- Foreword -- Advisory Board -- Contents -- Preface -- RECENT ADVANCES IN GROUND-STATE METHODS -- Chapter 1 Structure Determination by Combination of CW and Pulsed '2-D' Orientation-Selective 1,2H Q-Band Electron-Nuclear Double Resonance -- Chapter 2 Combining Mössbauer Spectroscopy and Magnetometry -- Chapter 3 Advances in Single- and Multidimensional NMR Spectroscopy of Paramagnetic Metal Complexes -- Chapter 4 Metalloprotein Crystallography -- Chapter 5 Recent Advances in Electronic Absorption Spectroscopy -- Chapter 6 Recent Advances in Magnetic Circular DichroismSpectroscopy -- Chapter 7 Recent Advances in Resonance Raman Spectroscopy -- Chapter 8 Soft X-ray Absorption Spectroscopy:Applications to Bioinorganic Chemistry -- Chapter 9 Electronic Structure Calculations: Density Functional Methods for Spin Polarization, Charge Transfer, and Solvent Effects in Transition Metal Complexes -- Chapter 10 Spectroscopic Studies of Ferrocytochrome c Folding -- Chapter 11 Photoreduction-Triggered Folding of Cytochrome c: UV and Visible Resonance Raman Markers of Structure -- Chapter 12 A Probe of Metal-Ligand Interactions in Cupredoxin by Active Site Redesign and Resonance Raman Spectroscopy -- Chapter 13 XAS Studies on the CuA Centers of Heme-Copper Oxidases and Loop-Directed Mutants of Azurin: Implications for Redox Reactivity -- Chapter 14 Antiferromagnetic Exchange, Biquadratic Exchange, and Metal-Metal Bond in Metal Clusters: Application to the Multielectron versus Successive Monoelectron Steps Dilemma -- Chapter 15 Progress in Characterization of the Photosystem II Oxygen Evolving Complex Using Advanced EPR Methods -- Chapter 16 Valence-Delocalized [Fe2S2]+ Clusters -- Chapter 17 NMR of FeS Proteins. , Chapter 18 The Electronic Structure of Linear Thiophenolate-Bridged Heterotrinuclear Complexes: Localizedversus Delocalized Models -- Chapter 19 Amino Acid Side Chain Movements in the Active Site of the Hydroxylase Enzyme from Soluble Methane Monooxygenase -- Chapter 20 Applications of X-ray Absorption Spectroscopy to Characterization of the Mn Cluster in the Photosynthetic Oxygen Evolving Complex -- Chapter 21 EPR and MCD Studies of Oxomolybdenum Centers in Sulfite Oxidase and Related Model Compounds -- Chapter 22 Spectroscopic Signatures of the Fe2O2 Diamond Core -- Chapter 23 Intermediates in Non-Heme Iron Intradiol Dioxygenase Catalysis -- Chapter 24 Reaction Intermediates in Oxygen Activation Reactions by Enzymes Containing Carboxylate-Bridged Binuclear Iron Clusters -- Chapter 25 Spectroscopic Studies of O2 Intermediates in Copper Proteins: Electronic Structure Contributions to Function in Bioinorganic Chemistry -- Author Index -- Subject Index.