Molecular Modeling of Inorganic Compounds, Second Edition

322 Pages·2001·16.513 MB·English

by  Prof. Dr. Peter Comba, Prof. Dr. Trevor W. Hambley(auth.)

Peter Comba, Trevor W. Hambley
Molecular Modeling of Inorganic Compounds
@WILEY-VCH
Further Reading from Wiley-VCH
and John Wiley & Sons
H.-D. Holtje I G. Folkers
Molecular Modeling. Basic Principles and Applications
1997.206 pages. Wiley-VCH.
ISBN 3-527-29384-1
F. Jensen
Introduction to Computational Chemistry
1998. 454 pages. Wiley.
ISBN 0-471-98425-6
W. Koch I M. C. Holthausen
A Chemist’s Guide to Density Functional Theory
2000.308 pages. Wiley-VCH.
ISBN 3-527-29918-1
K. B. Lipkowitz I D. B. Boyd (Eds.)
Reviews in Computational Chemistry, Vol. 13
1999. 384 pages. Wiley.
ISBN 0-471-33135-X
M. F. Schlecht
Molecular Modeling on the PC
1998. 763 pages. Wiley.
ISBN 0-47 1- 18467- 1
P. von Schleyer (Ed.)
Encyclopedia of Computational Chemistry
1998. 3580 pages. Wiley.
ISBN 0-471-96588-X
J. Zupan I J. Gasteiger
Neural Networks in Chemistry and Drug Design
1999.400 pages. Wiley-VCH.
ISBN 3-527-29779-0 (Softcover), 3-527-29778-2 (Hardcover)
Peter Comba, Trevor W. Hambley
Molecular Modeling
of Inorganic Compounds
Second, Completely Revised and Enlarged Edition
Includes CD-ROM
With Tutorial
@WILEY-VCH
- -
Weinheim New York Chichester
-
Brisbane Singapore Toronto
*
Prof. Dr. Peter Comba Prof. Dr. Trevor W. Hambley
Anorganisch-Chemisches Institut School of Chemistry
Im Neuenheimer Feld 270 University of Sydney
69120 Heidelberg Sydney, NSW 2006
Germany Australia
e-mail : e-mail: [email protected]
[email protected]
homepage: http://www.uni-heidelberg.de/ homepage: http://www.chem.usyd.edu.au/
institutelfak 1Z /AC/comba/ -hamble-t
This book was carefully produced. Nevertheless, editors, authors and publisher do not warrant the in-
formation contained therein to be free of errors. Readers are advised to keep in mind that statements,
data, illustrations, procedural details or other items may inadvertently be inaccurate.
Shown on the cover are the calculated structures and energetics of two conformations of a figure-of-
eight-shaped dicopper(1) compound, together with the observed 'H-NMR spectra (J.Chem.Soc., Dalton
Trans. (1999), 509; Eur.J.Inorg.Chem. (1999), 509).
Library of Congress Card No.: applied for
A catalogue record for this book is available from the British Library
Die Deutsche Bibliothek - CIP Cataloguing-in-Publication Data
A catalogue record for this publication is available from Die Deutsche Bibliothek
ISBN 3-527-29915-7
0 WILEY-VCH Verlag GmbH, D-69469 Weinheim (Federal Republic of Germany), 2001
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Preface
Over the past thirty years molecular-mechanical modeling of organic molecules
has developed to the point where comprehensive models are now available and
the structures and energetics of most simple molecules can be reliably calculated.
More recently there has been a rapid expansion in the application of molecular
mechanics and dynamics to biological macromolecules such as proteins and
DNA. Highly sophisticated commercial packages are available that combine mole-
cular mechanics with computer-graphical construction, manipulation and graphi-
cal output.
Proceeding in parallel with these developments has been the application of mo-
lecular mechanics to inorganic and coordination compounds. Initially, simple me-
tal complexes were modeled, but recently the field has been extended to include
organometallic compounds, catalysis and the interaction of metal ions with biolo-
gical macromolecules. The application of molecular mechanics to coordination
compounds is complicated by the number of different metals and the variety of
coordination numbers, coordination modes, geometries and electronic states they
can adopt. For this reason the existing models used for metal containing com-
pounds are more complex than those available for organic molecules, and only
few of the commercially available packages are able to reliably deal with even a
small subset of the possible metal-based systems. The difficulties encountered in
modeling inorganic and coordination compound systems have deterred many from
making use of the method.
The goals of this book are to provide an understanding of molecular mechanics,
to show that it can be applied successhlly to a wide variety of inorganic and coor-
dination compound based systems and to show how to undertake such a study.
This book should give the reader the ability to judge the reliability of published
data, to evaluate reported interpretations and to judge the scope and limitation of
the various models for her or his own studies.
The book is aimed at students and scientists who have a basic understanding of
inorganic chemistry. No prior knowledge of theoretical chemistry, sophisticated
mathematics or computing is assumed. The basic concepts of molecular me-
chanics are developed and discussed in Part I. Examples of applications and the
difficulties encountered are reviewed in Part 11. In Part a practical guide to un-
I11
dertaking a molecular modeling study of a new system is presented and the pro-
blems and pitfalls likely to be encountered are outlined. The three parts of the
book can be read and used separately.
VI Preface
We are gratefd for the help of Sigrid Rieth, Brigitte Sau1,Volker Licht and Dr
Norbert Okon in the preparation of the manuscript, to Dr Thomas Kellersohn for
a strain-free collaboration with VCH, to our coworkers for allowing us to report
unpublished data and for their helpful hints on scientific, didactic and linguistic
aspects. A special thank is due to Prof. Marc Zimmer for his invaluable help dur-
ing his sabbatical leave as a Humboldt Fellow in Heidelberg. Many interesting dis-
cussions with and suggestions by him have been of importance to this book.
Finally, we owe our families a huge debt for their love and patience.
Peter Comba Trevor W. Hambley
Preface to the Second Edition
The field of inorganic molecular modeling has developed in the past five years to
an extent that it has led us to add some chapters and rewrite others. The division
of the book into three parts; I Theory, 11 Applications and Ill Practice that can be
read and used separately is retained. Our emphasis is still on empirical force field
calculations. Quantum-mechanical calculations have undergone an enormous de-
velopment in recent years, and techniques such as DFT and combined quantum
mechanics/molecular mechanics (QWMM) are now routinely used by theoreti-
cians and experimentalists to predict and interpret structures, stabilities, electronic
properties and reactivities of metal-containing compounds. Where appropriate, we
have included results derived from such methods in this second edition of our
book, without going into detailed discussion of the theoretical background, since
this is given in many recent textbooks and review articles.
We have made only a few changes to Part I and most examples from Part I1
have remained unchanged, since our goal is to cover the types of application
rather than to provide a comprehensive review of inorganic molecular modeling.
New developments and some new examples have been added.
Part I11 has been rewritten completely. Important rules for molecular modeling
and for the interpretation of the results, possible pitfalls and guidelines for the
publication of molecular modeling studies are given in an introduction. This is
followed by a tutorial, based on software included in this book, where the reader
experiences in 20 lessons, how inorganic molecular modeling works in reality.
The appendices have been updated and lists of molecular modeling books and in-
organic molecular modeling reviews have been added (see Appendix Regularly
4).
updated lists and comments related to the field appear also on our homepages.
We are grateful for comments by colleagues on the first edition. We are also
gratehl for the help of Marlies von Schoenebeck-Schilli, Karin Stelzer and Bri-
gitte Saul in preparing the manuscript, to Dr Norbert Okon for the setup of MO-
MEClite and to Dr Roland Wengenmayr for an excellent collaboration with
Wiley-VCH. The continuing support of our families has allowed us to complete
this project and is greatly appreciated.
Peter Comba Trevor W. Hambley
Contents
Preface ................................................... V
Preface to the Second Edition ................................. VII
Part I: Theory ............................................. 1
1 Introduction ......................................... 3
1.1 Molecular Modeling .................................... 3
1.2 Historical Background .................................. 6
2 Molecular Modeling Methods in Brief ..................... 9
2.1 Molecular Mechanics ................................... 9
2.2 Quantum Mechanics .................................... 11
2.2.1 Hartree-Fock Calculations ............................... 12
2.2.2 Semi-Empirical Approaches .............................. 12
2.2.3 Density Functional Theory ............................... 13
2.3 Other Methods ........................................ 13
2.3.1 Conformational Searching ................................ 13
2.3.2 Database Searching .................................... 15
2.3.3 Cluster Analysis ....................................... 15
2.3.4 Free Energy Perturbation ................................ 15
2.3.5 QSAR .............................................. 16
3 Parameterization. Approximations and Limitations of Molecular
Mechanics ........................................... 17
3.1 Concepts ............................................ 17
3.2 Potential Energy Functions ............................... 21
3.2.1 Bond Length Deformation ............................... 23
3.2.2 Valence Angle Deformation .............................. 25
3.2.3 Torsion Angle Deformation ............................... 30
3.2.4 Cross-terms .......................................... 31
3.2.5 van der Waals Interactions ............................... 32
3.2.6 Electrostatic Interactions ................................. 34
3.2.7 Hydrogen Bonding Interactions ............................ 35
Contents
X
Out-of-plane Deformation ................................
3.2.8 36
Force Field Parameters ..................................
3.3 36
Bond Length Deformation ...............................
3.3.1 40
Valence Angle Deformation ..............................
3.3.2 41
Torsion Angle Deformation ...............................
3.3.3 43
3.3.4 Out-of-plane Deformation ................................ 45
3.3.5 Nonbonded Interactions ................................. 45
Electrostatic Interactions .................................
3.3.6 47
3.3.7 Hydrogen Bonding Interactions ............................ 48
3.4 Spectroscopic Force Fields ............................... 48
3.5 Model and Reality ..................................... 50
Electronic Effects ......................................
3.6 52
3.7 The Environment ...................................... 53
3.8 Entropy Effects ....................................... 55
3.9 Summary ............................................ 56
4 Computation ......................................... 59
4.1 Input and Output ...................................... 59
4.2 Energy Minimization ................................... 62
4.2.1 The Simplex Method ................................... 63
4.2.2 Gradient Methods ...................................... 64
4.2.3 Conjugate-Gradient Methods .............................. 64
4.2.4 The Newton-Raphson Method ............................. 65
4.2.5 Least-Squares Methods .................................. 66
4.3 Constraints and Restraints ................................ 66
5 The Multiple Minima Problem ........................... 69
5.1 Deterministic Methods .................................. 70
5.2 Stochastic Methods ..................................... 70
5.3 Molecular Dynamics .................................... 71
5.4 Practical Considerations ................................. 72
5.5 Making Use of Experimental Data ......................... 73
6 Conclusions .......................................... 75
Part 11: Applications ........................................ 77
7 Structural Aspects .................................... 79
7.1 Accuracy of Structure Prediction ........................... 79
7.2 Molecular Visualization ................................. 80
7.3 Isomer Analysis .......................................
82
7.4 Analysis of Structural Trends ............................. 83
7.5 Prediction of Complex Polymerization ....................... 84
7.6 Unraveling Crystallographic Disorder ....................... 85
7.7 Comparison with Solution Properties ........................ 87
Contents XI
8 Stereoselectivities ..................................... 89
8.1 Conformational Analysis ................................ 89
8.2 Enantioselectivities ..................................... 92
8.2.1 Racemate Separation ................................... 93
8.2.2 Stereoselective Synthesis ................................ 95
8.3 Structure Evaluation .................................... 97
8.4 Mechanistic Information ................................. 101
9 Metal Ion Selectivity ................................... 103
9.1 Chelate Ring Size ...................................... 104
9.2 Macrocycle Hole Size ................................... 107
9.3 Preorganization ....................................... 113
9.4 Quantitative Correlations Between Strain and Stability Differences . . 11 5
9.5 Conclusion ........................................... 117
10 Spectroscopy ......................................... 119
10.1 Vibrational Spectroscopy ................................ 120
10.2 Electronic Spectroscopy ................................. 121
10.3 EPR Spectroscopy ..................................... 133
10.4 NMR Spectroscopy ..................................... 139
11 Electron Transfer ..................................... 141
11.1 Redox Potentials ....................................... 143
11.2 Electron Transfer Rates .................................. 147
12 Electronic Effects ..................................... 149
12.1 d-Orbital Directionality .................................. 150
12.2 The trans lnfluence .................................... 153
12.3 Jahn-Teller Distortions .................................. 154
13 Bioinorganic Chemistry ................................ 161
13.1 Complexes of Amino Acids and Peptides ..................... 161
13.2 Metalloproteins ....................................... 162
13.3 Metalloporphyrins ..................................... 164
13.4 Metal-Nucleotide and Metal-DNA Interactions ................ 166
13.5 Other Systems ........................................ 168
13.6 Conclusions .......................................... 170
14 Organometallics ...................................... 171
14.1 Metallocenes ......................................... 172
14.2 Transition Metal-Ally1 Systems ............................ 175
14.3 Transition Metal Phosphine Compounds ..................... 177
14.4 Metal-Metal Bonding .................................. 179
14.5 Carbonyl Cluster Compounds ............................. 181