Molecular Modeling of Inorganic Compounds

PART I: Theory INTRODUCTION Molecular Modeling Historical Background MOLECULAR MOEDLING METHODS IN BRIEF Molecular Mechanics Quantum Mechanics Other Methods PARAMETERIZATION, APPROXIMATIONS AND LIMITATIONS OF MOLECULAR MECHANICS Concepts Potential Energy Functions Force-Field Parameters Spectroscopic Force Fields Model and Reality Electronic Effects The Environment Entropy Effects Summary COMPUTATION Input and Output Energy Minimization Constraints and Restraints THE MULTIPLE MINIMA PROBLEM Deterministic Methods Stochastic Methods Molecular Dynamics Practical Considerations Making Use of Experimental Data CONCLUSIONS PART II: Applications STRUCTURAL ASPECTS Accuracy of Structure Prediction Molecular Visualization Isomer Analysis Analysis of Structural Trends Prediction of Complex Polymerization Unraveling Crystallographic Disorder Enhanced Structure Determination Comparison with Solution Properties STEREOSELECTIVITIES Conformational Analysis Enantioselectivities Structure Evaluation Mechanistic Information METAL ION SELECTIVITY Chelate Ring Size Macrocycle Hole Size Preorganization Quantitative Correlations Between Strain and Stability Differences Conclusions SPECTROSCOPY Vibrational Spectroscopy Electronic Spectroscopy EPR Spectroscopy NMR Spectroscopy QM-Based Methods ELECTRON TRANSFER Redox Potentials Electron-Transfer Rates ELECTRONIC EFFECTS d-Orbital Directionality The trans Influence Jahn-Teller Distortions BIOINORGANIC CHEMISTRY Complexes of Amino Acids and Peptides Metalloproteins Metalloporphyrins Metal-Nucleotide and Metal-DNA Interactions Other Systems Conclusions ORGANOMETALLICS Metallocenes Transition Metal-Allyl Systems Transition Metal-Phosphine Compounds Metal-Metal Bonding Carbonyl Cluster Compounds COMPOUNDS WITH S-, P-, AND F-BLOCK ELEMENTS Alkali and Alkaline Earth Metals Main Group Elements Lanthanoids and Actinoids Conclusions PART III: Practice of Molecular Mechanics THE MODEL, THE RULES, AND THE PITFALLS Introduction The Starting Model The Force Field The Energy Minimization Procedure Local and Global Energy Minima Pitfalls, Interpretation, and Communication TUTORIAL Introduction to the Momec3 Program Building a Simple Metal Complex Optimizing the Structure Building a Set of Conformers Calculating the Strain Energies and Isomer Distribution of a Set of Conformers Constructing and Optimizing a Set of Isomers Automatically Building More Difficult Metal Complexes Analyzing Structures Potential Energy Functions I: Bond Length, Valence Angle, Torsion Angle, Twist Angle, and Out-of-Plane Deformation Functions Potential Energy Functions II: Non-Bonded Interactions Force-Field Parameters I: Developing a Force Field for Cobalt(III) Hexaamines - Normal Bond Distances Force-Field Parameters II: Refining the New Force Field - Very Short Bond Distances Force-Field Parameters III: Refining the New Force Field - Very Long Bond Distances Force-Field Parameters IV: Comparison of Isomer Distributions Using Various Cobalt(III) Amine Force Fields Force-Field Parameters V: Parameterizing a New Potential - The Tetrahedral Twist of Four-Coordinate Compounds Using Constraints to Compute Energy Barriers Using Constraints to Compute Macrocyclic Ligand Hole Sizes Cavity Sizes of Unsymmetrical Ligands Using Strain Energies to Compute Reduction Potentials of Coordination Compounds Using Force-Field Calculations with NMR Data Optimizing Structures with Rigid Groups APPENDIX 1: Glossary APPENDIX 2: Fundamental Constants, Units, and Conversion Factors Constants Basic SI Units Derived Units and Conversion Factors Energy Units in Molecular Mechanics Calculations APPENDIX 3: Software and Force Fields APPENDIX 4: Books on Molecular Modeling and Reviews on Inorganic Molecular Modeling List of Books on Molecular Modeling List of Reviews in the Field of Inorganic Molecular Modeling List of Publications on the Momec Force Field + CD with full software version and tutorial supplements