Molecular Modeling of Inorganic Compounds / Edition 3

Molecular Modeling of Inorganic Compounds / Edition 3

by Peter Comba, Trevor W. Hambley, Bodo Martin
     
 

In many branches of chemistry, molecular modeling is a well-established and powerful tool for the investigation of complex structures. This book shows how the method has been and can be successfully applied to inorganic and coordination compounds.
In the first part a general introduction to molecular modeling is given which will be of use for chemists in all

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Overview

In many branches of chemistry, molecular modeling is a well-established and powerful tool for the investigation of complex structures. This book shows how the method has been and can be successfully applied to inorganic and coordination compounds.
In the first part a general introduction to molecular modeling is given which will be of use for chemists in all areas. The second part contains a discussion of many carefully selected examples, chosen to illustrate the wide range of applicability of molecular modeling to metal complexes and the approaches being taken to deal with some of the difficulties encountered. In the third part, the reader is shown how to apply molecular modeling to a new system and how to interpret the results. Using freely available software the reader can work through 20 tutorial lessons, based on examples from the literature and discussed elsewhere in the book.
The authors take special care to highlight the possible pitfalls and offer advice on how to avoid them. Therefore, this book will be invaluable to anyone working in or entering the field.

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Product Details

ISBN-13:
9783527317998
Publisher:
Wiley
Publication date:
10/19/2009
Edition description:
New Edition
Pages:
344
Product dimensions:
6.90(w) x 9.60(h) x 0.90(d)

Table of Contents

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

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