Molecular Modeling of Inorganic Compounds

Transcription

1 Peter Comba, Trevor W. Hambley and Bodo Martin Molecular Modeling of Inorganic Compounds Third Completely Revised and Enlarged Edition WILEY- VCH WILEY-VCH Verlag GmbH & Co. KGaA

2 v Contents Preface to the Third Edition XIII Preface to the Second Edition XV Preface to the First Edition XVII I Theory 1 1 Introduction Molecular Modeling Historical Background 6 2 Molecular Modeling Methods in Brief Molecular Mechanics Quantum Mechanics Hartree Fock Calculations Semi-Empirical Approaches Density Functional Theory Methods and Basis Sets Other Methods Conformational Searching Stochastic Methods Molecular Dynamics Database Searching Cluster Analysis Free Energy Perturbation QSAR 17 3 Parameterization, Approximations and Limitations of Molecular Mechanics Concepts 19 Molecular Modeling of Inorganic Compounds. Third Edition. Peter Comba, Trevor W. Hambley and Bodo Martin Copyright 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN:

3 VI Contents 3.2 Potential Energy Functions Bond Length Deformation Valence Angle Deformation Torsion Angle Deformation Cross-Terms van der Waals Interactions Electrostatic Interactions Hydrogen Bonding Interactions Out-of-Plane Deformation Force-Field Parameters Bond Length Deformation Valence Angle Deformation Torsion Angle Deformation Out-of-Plane Deformation Non-Bonded Interactions Electrostatic Interactions Hydrogen-Bonding Interactions Spectroscopic Force Fields Model and Reality Electronic Effects The Environment Entropy Effects Summary 58 4 Computation Input and Output Energy Minimization The Simplex Method Gradient Methods Conjugate-Gradient Methods The Newton Raphson Method Least-Squares Methods Constraints and Restraints 67 5 The Multiple Minima Problem Deterministic Methods Stochastic Methods Molecular Dynamics Practical Considerations Malring Use of Experimental Data 73 6 Conclusions 75

4 Contents I VII II Applications 77 7 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 88 8 Stereoselectivities Conformational Analysis Enantioselectivities Racemate Separation Stereoselective Synthesis Prediction of Enantioinduction Structure Evaluation Mechanistic Information Metal Ion Selectivity Chelate Ring Size Macrocycle Hole Size Preorganization Quantitative Correlations Between Strain and Stability Differences Condusions Spectroscopy Vibrational Spectroscopy Electronic Spectroscopy EPR Spectroscopy NMR Spectroscopy QM-Based Methods Electron Transfer Redox Potentials Electron-Transfer Rates Electronic Effects d-orbital Directionality 160

5 VIII I Contents 12.2 The frans Influence Jahn Teller Distortions Bioinorganic Chemistry Complexes of Amino Acids and Peptides Metalloproteins Metalloporphyrins Metal Nucleotide and Metal DNA Interactions Other Systems Condusions 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 Crown Ethers Cryptands Spherands Biologically Relevant Ligands Main Group Elements Lanthanoids and Actinoids Condusions 201 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 Motivation and Rationale The Program Setup and Philosophy Building a Simple Metal Complex Theory 220

6 Practice Optimizing the Structure Theory Practice Building a Set of Conformers Theory Practice Building [Co(en) 3] Changing Conformations Exercise Calculating the Strain Energies and Isomer Distribution of a Set of Conformers Theory Practice Exercise Constructing and Optimizing a Set of Isomers Automatically Theory Practice Exercise Building More Difficult Metal Complexes Theory Practice Importring Structures from Other Sources Building Fragments Exercise Analyzing Structures Theory Practice Exercise Potential Energy Functions I: Bond Length, Valence Angle, Torsion Angle, Twist Angle, and Out-of-Plane Deformation Functions Theory Practice Bond Length Deformation Valence Angle Deformation Out-of-Plane Deviations Torsion Angle or Dihedral Angle Functions Exercise Potential Energy Functions II: Non-Bonded Interactions Theory van der Waals Interactions Practice Theory Hydrogen Bonds Practice 249 Contents I IX

7 Contents Theory 249 Electrostatic Interactions 249 Practice 250 Exercise 251 Force-Field Parameters I: Developing a Force Field for Cobalt(III) Hexaamines Normal Bond Distances 251 Theory 251 Practice 254 Exercise 255 Force-Field Parameters II: Refining the New Force Field Very Short Bond Distances 256 Theory 256 Practice 257 Exercise 258 Force-Field Parameters III: Refining the New Force Field Very Long Bond Distances 259 Theory 259 Practice 259 Exercise 261 Exercise 261 Force-Field Parameters IV: Comparison of Isomer Distributions Using Various Cobalt(III) Amine Force Fields 262 Theory 262 Practice 263 Exercise 266 Force-Field Parameters V: Parameterizing a New Potential The Tetrahedral Twist of Four-Coordinate Compounds 266 Theory 266 Practice 268 Exercise 269 Using Constraints to Compute Energy Barriers 269 Theory 269 Practice 270 Exercise 272 Using Constraints to Compute Macrocyclic Ligand Hole Sizes 272 Theory 272 Practice 275 Exercise 279 Cavity Sizes of Unsymmetrical Ligands 280 Theory 280 Practice 281 Exercise 282 Using Strain Energies to Compute Reduction Potentials of Coordination Compounds 282 Theory 282

8 Contents IXI Practice Exercise Using Force-Field Calculations with NMR Data Theory Practice Exercise Optimizing Structures with Rigid Groups Theory Practice Exercise 292 Appendix 1: Glossary 293 Appendix 2: Fundamental Constants, Units, and Conversion Factors 297 A2.1 Constants 297 A2.2 Basic SI Units 297 A2.3 Derived Units and Conversion Factors 298 A2.4 Energy Units in Molecular Mechanics Calculations 298 Appendix 3: Software and Force Fields 299 Appendix 4: Books on Molecular Modeling and Reviews on Inorganic Molecular Modeling 301 A4.1 List of Books an Molecular Modeling 301 A4.2 List of Reviews in the Field of Inorganic Molecular Modeling 302 A4.3 List of Publications an the Momec Force Field 304 References 305 Index 323