Computational Inorganic and Bioinorganic Chemistry E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: EIC Books
• Sprache: Englisch

Seitenzahl: 1935

Veröffentlichungsjahr: 2013

Beschreibung

Over the past several decades there have been major advances in our ability to computationally evaluate the electronic structure of inorganic molecules, particularly transition metal systems. This advancement is due to the Moore’s Law increase in computing power as well as the impact of density functional theory (DFT) and its implementation in commercial and freeware programs for quantum chemical calculations. Improved pure and hybrid density functionals are allowing DFT calculations with accuracy comparable to high-level Hartree-Fock treatments, and the results of these calculations can now be evaluated by experiment.

When calculations are correlated to, and supported by, experimental data they can provide fundamental insight into electronic structure and its contributions to physical properties and chemical reactivity. This interplay continues to expand and contributes to both improved value of experimental results and improved accuracy of computational predictions.

The purpose of this EIC Book is to provide state-of-the-art presentations of quantum mechanical and related methods and their applications, written by many of the leaders in the field. Part 1 of this volume focuses on methods, their background and implementation, and their use in describing bonding properties, energies, transition states and spectroscopic features. Part 2 focuses on applications in bioinorganic chemistry and Part 3 discusses inorganic chemistry, where electronic structure calculations have already had a major impact. This addition to the EIC Book series is of significant value to both experimentalists and theoreticians, and we anticipate that it will stimulate both further development of the methodology and its applications in the many interdisciplinary fields that comprise modern inorganic and bioinorganic chemistry.

This volume is also available as part of Encyclopedia of Inorganic Chemistry, 5 Volume Set.

This set combines all volumes published as EIC Books from 2007 to 2010, representing areas of key developments in the field of inorganic chemistry published in the Encyclopedia of Inorganic Chemistry.
Find out more at http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1119994284.html".

Leseprobe

EIC Books

Applications of Physical Methods to Inorganic and Bioinorganic Chemistry Edited by Robert A. Scott and Charles M. Lukehart ISBN 978-0-470-03217-6

Nanomaterials: Inorganic and Bioinorganic Perspectives Edited by Charles M. Lukehart and Robert A. Scott ISBN 978-0-470-51644-7

Computational Inorganic and Bioinorganic Chemistry Edited by Edward I. Solomon, Robert A. Scott and R. Bruce King ISBN 978-0-470-69997-3

Forthcoming

Radionuclides in the Environment Edited by David A. Atwood ISBN 978-0-470-71434-8

Energy Production and Storage—Inorganic Chemical Strategies for a Warming World Edited by Robert H. Crabtree ISBN 978-0-470-74986-9

Encyclopedia of Inorganic Chemistry

In 1994 John Wiley & Sons published the Encyclopedia of Inorganic Chemistry (EIC). This 8-volume work was well received by the community, and has become a standard publication in all libraries serving the inorganic, coordination chemistry, organometallic and bioinorganic communities. The 10-volume Second Edition of the Encyclopedia was published in print in 2005, and online in 2006, on the major reference platform Wiley InterScience:

http://www.mrw.interscience.wiley.com/eic/

This edition first published 2009© 2009 John Wiley & Sons Ltd

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Library of Congress Cataloging-in-Publication Data

Computational inorganic and bioinorganic chemistry / Edward I. Solomon, Robert A. Scott, R Bruce King, editors.

p. cm. -- (Eic books)

Includes bibliographical references and index.

ISBN 978-0-470-69997-3

1. Quantum biochemistry. 2. Quantum chemistry. 3. Bioinorganic chemistry--Data processing. 4. Chemistry, Inorganic--Data processing. I. Solomon, Edward I. II. Scott, Robert A., 1953- III. King, R. Bruce.

QP517.Q34C66 2009

541’.28--dc22

2009025915

A catalogue record for this book is available from the British Library.

ISBN-13: 978-0-470-69997-3

Set in 9½ / 11½ pt TimesNewRomanPS by Laserwords (Private) Limited, Chennai, India.Printed and bound in Singapore by Markono Print Media Pte Ltd.

Encyclopedia of Inorganic Chemistry

Editorial Board

Editor-in-Chief

Robert H. CrabtreeYale University, New Haven, CT, USA

Section Editors

David A. AtwoodUniversity of Kentucky, Lexington, KY, USA

R. Bruce KingUniversity of Georgia, Athens, GA, USA

Charles M. LukehartVanderbilt University, Nashville, TN, USA

Robert A. ScottUniversity of Georgia, Athens, GA, USA

International Advisory Board

Michael BruceAdelaide, Australia

Fausto CalderazzoPisa, Italy

Tristram ChiversCalgary, Canada

Odile EisensteinMontpellier, France

C. David GarnerNottingham, UK

Malcolm GreenOxford, UK

Wolfgang HerrmannMunich, Germany

Jean-Marie LehnStrasbourg, France

François MatheyUniversity of California Riverside, CA, USA

Akira NakamuraOsaka, Japan

Jan ReedijkLeiden, The Netherlands

Vivian YamHong Kong

Contents

Title

Copyright

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

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

12 REFERENCES

Electronic Structure Calculations: Transition Metal–NO Complexes

1 INTRODUCTION

2 HEME PARADIGMS

3 NONHEME NITROSY

4 CONCLUDING REMARKS

5 ABBREVIATIONS AND ACRONYMS

6 REFERENCES

Structural Origins of Noninnocent Coordination Chemistry

1 INTRODUCTION

2 CLASSICAL NONINNOCENT LIGANDS

3 NONCLASSICAL NONINNOCENT LIGANDS

4 CONCLUSIONS AND OUTLOOK

5 ACKNOWLEDGMENTS

6 ABBREVIATIONS AND ACRONYMS

7 REFERENCES

Electronic Structure of Metal–Metal Bonds

1 INTRODUCTION

2 TRANSITION METAL DIATOMICS

3 δ BONDING: QUADRUPLE AND QUINTUPLE BONDS

4 M-M σ BONDING

5 π-BONDING: DOUBLE AND TRIPLE BONDS

6 METAL-METAL BONDS BETWEEN f-BLOCK ELEMENTS

7 SUMMARY

8 ABBREVIATIONS AND ACRONYMS

9 REFERENCES

Computational Methods: Transition Metal Clusters

1 INTRODUCTION

2 BRIEF INTRODUCTION TO CLUSTER SHAPE DESCRIPTION AND ELECTRON COUNTING IN TRANSITION-METAL CLUSTERS AND MIXED TRANSITION-METAL/MAIN-GROUP CLUSTERS

3 COMPUTATIONAL TOOLS USED IN CALCULATIONS ON MOLECULAR AND SOLID-STATE TRANSITION-METAL CLUSTERS

4 APPLICATION TO A SELECTION OF EXAMPLES

5 RELATED ARTICLES

6 ABBREVIATIONS AND ACRONYMS

7 REFERENCES

Computational Methods: Heteropolyoxoanions

1 INTRODUCTION

2 STRUCTURE OF THE MOST REPRESENTATIVE HETEROPOLYOXOANIONS

3 COMPUTATIONAL METHODS

4 ELECTRONIC STRUCTURE

5 SOLVATED ANIONS

6 ELECTRON (DE)LOCALIZATION IN MIXED-VALENCE HPAs

7 ALTERNATING SHORT-LONG BOND DISTORTIONS

8 183W NMR CHEMICAL SHIFTS AND VIBRATIONAL SPECTRA

9 REACTIVITY OF POLYOXOANIONS

10 CONCLUDING REMARKS

11 ACKNOWLEDGMENTS

12 RELATED ARTICLES

13 ABBREVIATIONS AND ACRONYMS

Electronic Structure Calculations: Metal Carbonyls

1 INTRODUCTION

2 COMPUTATIONAL METHODS

3 CASE STUDIES

4 CONCLUDING REMARKS

5 GLOSSARY

6 RELATED ARTICLES

7 ABBREVIATIONS AND ACRONYMS

8 REFERENCES

Potential Energy Surfaces for Metal-Assisted Chemical Reactions

1 INTRODUCTION

2 METHOD

3 BOND ACTIVATION BY ATOMIC AND LIGATED METAL CATIONS

4 MODELING OF ENZYMATIC REACTIONS

5 ACKNOWLEDGMENTS

6 ABBREVIATIONS AND ACRONYMS

7 REFERENCES

Computational Methods: Lanthanides and Actinides

1 INTRODUCTION

2 METHODS

3 APPLICATIONS

4 CONCLUSIONS

5 RELATED ARTICLES

6 ABBREVIATIONS AND ACRONYMS

7 REFERENCES

Spin-Orbit Coupling: Effects in Heavy Element Chemistry

1 INTRODUCTION

2 APPLICATIONS OF Spin-orbit COUPLED TIME-DEPENDENT DENSITY FUNCTIONAL THEORY

3 APPLICATIONS OF THE Spin-orbit RESTRICTED ACTIVE SPACE STATE INTERACTION METHOD

4 CONCLUDING REMARKS

5 ABBREVIATIONS AND ACRONYMS

6 REFERENCES

Noble Gas Compounds: Reliable Computational Methods

1 INTRODUCTION

2 RARE GAS DIATOMICS

3 ACCURATE ELECTRONIC STRUCTURE FOR RARE GAS COMPOUNDS

4 XeFX COMPOUNDS

5 KrFX COMPOUNDS

6 NOBLE GAS PROTON AND METHYL CATION AFFINITIES

7 ACKNOWLEDGMENTS

8 ABBREVIATIONS AND ACRONYMS

9 REFERENCES

Computational Studies: Boranes

1 INTRODUCTION

2 COMPUTATIONAL STUDIES ON BORANES

3 MACROPOLYHEDRON-STRUCTURAL DEFINITION

4 THE ELECTRONIC REQUIREMENT FOR MACROPOLYHEDRAL BORANES

5 RELATIVE STABILITY OF THE MACROPOLYHEDRAL BORANES

6 ORBITAL COMPATIBILITY IN THE CONDENSATION OF POLYHEDRAL BORANES

7 MECHANISTIC STUDIES ON MACROPOLYHEDRAL BORANES

8 CONCLUSION

9 ABBREVIATIONS AND ACRONYMS

10 REFERENCES

Multiple Aromaticity, Multiple Antiaromaticity, and Conflicting Aromaticity in Inorganic Systems

1 INTRODUCTION

2 TETRAATOMIC AROMATIC INORGANIC SPECIES OF GROUP 15 AND 16 ELEMENTS

3 PENTAATOMIC AROMATIC SPECIES OF GROUP 14 AND 15 ELEMENTS

4 HEXAATOMIC AROMATIC SPECIES OF GROUP 14 ELEMENTS

5 AROMATIC ORGANOMETALLIC COMPOUNDS

6 ALL-METAL AROMATIC CLUSTERS

7 MULTIPLY AROMATIC Hg46– SPECIES IN THE Na3Hg2 AMALGAM

8 δ-AROMATICITY AND -AROMATICITY

9 CONCLUSIONS

10 ACKNOWLEDGMENTS

11 END NOTES

12 ABBREVIATIONS AND ACRONYMS

13 FURTHER READING

14 REFERENCES

Theoretical Aspects of Main Group Multiple Bonded Systems

1 INTRODUCTION

2 MULTIPLE BONDING BETWEEN GROUP 13 ELEMENTS

3 MULTIPLE BONDING BETWEEN GROUP 14 ELEMENTS

4 CONCLUSIONS

6 ACKNOWLEDGMENTS

5 RELATED ARTICLES

7 ABBREVIATIONS AND ACRONYMS

8 REFERENCES

Index

Contributors

Jochen Autschbach

State University of New York, Buffalo, NY, USA

• Spectroscopic Properties Obtained from Time-Dependent Density Functional Theory (TD-DFT)

Mu-Hyun Baik

Indiana University, Bloomington, IN, USA

• Computational Studies: Cisplatin

Luca Bertini

University of Milano-Bicocca, Milano, Italy

• Hydrogenases: Theoretical Investigations Towards Bioinspired H

2

Production and Activation

Alexander I. Boldyrev

Utah State University, Logan, UT, USA

• Multiple Aromaticity, Multiple Antiaromaticity, and Conflicting Aromaticity in Inorganic Systems

Thomas C. Brunold

University of Wisconsin-Madison, Madison, WI, USA

• Computational Studies: B

12

Cofactors and Their Interaction with Enzyme Active Sites

Maurizio Bruschi

University of Milano-Bicocca, Milano, Italy

• Hydrogenases: Theoretical Investigations Towards Bioinspired H

2

Production and Activation

Y. Bu

Shandong University, Jinan, China

• Computational Studies: Proton/Water Coupling to Metals in Biological Reaction Mechanisms

Michael Bühl

University of St. Andrews, Scotland, UK

• Nuclear Magnetic Resonance (NMR) Parameters of Transition Metal Complexes: Methods and Applications

Kieron Burke

University of California, Irvine, CA, USA

• Approximate Density Functionals: Which Should I Choose?

X. Cao

Universität zu Köln, Köln, Germany

• Computational Methods: Lanthanides and Actinides

David A. Case

Rutgers University, Piscataway, NJ, USA

• Broken Symmetry States of Iron–Sulfur Clusters

Jeanet Conradie

University of Tromsø, Tromsø, Norway and University of the Free State, Bloemfontein, South Africa

• Electronic Structure Calculations: Transition Metal–NO Complexes

Nathan R. M. Crawford

University of California, Irvine, CA, USA

• Approximate Density Functionals: Which Should I Choose?

R. I. Cukier

Michigan State University, East Lansing, MI, USA

• Computational Studies: Proton/Water Coupling to Metals in Biological Reaction Mechanisms

Chantal Daniel

CNRS/Université Louis Pasteur, Strasbourg, France

• Electronic Structure Calculations: Metal Carbonyls

Robert J. Deeth

University of Warwick, Coventry, UK

• Molecular Mechanics in Bioinorganic Chemistry

Luca De Gioia

University of Milano-Bicocca, Milano, Italy

• Hydrogenases: Theoretical Investigations Towards Bioinspired H

2

Production and Activation

David A. Dixon

University of Alabama, Tuscaloosa, AL, USA

• Noble Gas Compounds: Reliable Computational Methods

M. Dolg

Universität zu Köln, Köln, Germany

• Computational Methods: Lanthanides and Actinides

Piercarlo Fantucci

University of Milano-Bicocca, Milano, Italy

• Hydrogenases: Theoretical Investigations Towards Bioinspired H

2

Production and Activation

Gernot Frenking

Philipps-Universität Marburg, Marburg, Germany

• Calculation of Bonding Properties

Richard A. Friesner

Columbia University, New York, NY, USA

• Modeling Metalloenzymes with Density Functional and Mixed Quantum Mechanical/ Molecular Mechanical (QM/MM) Calculations: Progress and Challenges

Filipp Furche

University of California, Irvine, CA, USA

• Approximate Density Functionals: Which Should I Choose?

Régis Gautier

Ecole Nationale Supérieure de Chimie de Rennes, Rennes, France

• Computational Methods: Transition Metal Clusters

Abhik Ghosh

University of Tromsø, Tromsø, Norway

• Electronic Structure Calculations: Transition Metal–NO Complexes

Serge I. Gorelsky

University of Ottawa, Ottawa, Ontario, Canada

• Ab initio and Semiempirical Methods

Claudio Greco

University of Milano-Bicocca, Milano, Italy

• Hydrogenases: Theoretical Investigations Towards Bioinspired H

2

Production and Activation

Abebe Habtegabre

University of New Mexico, Albuquerque, NM, USA

• Reaction Coordinate of Pyranopterin Molybdenum Enzymes

Jean-François Halet

Ecole Nationale Supérieure de Chimie de Rennes, Rennes, France

• Computational Methods: Transition Metal Clusters

Jeremy N. Harvey

University of Bristol, Bristol, UK

• Computational Methods: Modeling of Reactivity in Zn-Containing Enzymes

Rosalie K. Hocking

Stanford University, Stanford, CA, USA and Monash University, Clayton, Australia

• Nature of the Catecholate–Fe(III) Bond: High Affinity Binding and Substrate Activation in Bioinorganic Chemistry

Kathrin H. Hopmann

University of Tromsø, Tromsø, Norway

• Electronic Structure Calculations: Transition Metal–NO Complexes

Hrant P. Hratchian

Gaussian Inc., Wallingford, CT, USA

• Spin Contamination in Inorganic Chemistry Calculations

Eluvathingal D. Jemmis

Indian Institute of Science Education and Research, Thiruvananthapuram, India

• Computational Studies: Boranes

Jan H. Jensen

University of Copenhagen, Copenhagen, Denmark

• Calculation of Reduction Potential and p

K

a

Kasper P. Jensen

Technical University of Denmark, Lyngby, Denmark

• Computational Studies: Chemical Evolution of Metal Sites

Nikolas Kaltsoyannis

University College London, London, UK

• Spin-Orbit Coupling: Effects in Heavy Element Chemistry

Martin Kaupp

University of Würzburg, Würzburg, Germany

• Nuclear Magnetic Resonance (NMR) Parameters of Transition Metal Complexes: Methods and Applications

R. Bruce King

University of Georgia, Athens, GA, USA

• Theoretical Aspects of Main Group Multiple Bonded Systems

Martin L. Kirk

University of New Mexico, Albuquerque, NM, USA

• Reaction Coordinate of Pyranopterin Molybdenum Enzymes

Sushilla Knottenbelt

University of New Mexico, Albuquerque, NM, USA

• Reaction Coordinate of Pyranopterin Molybdenum Enzymes

Nicolai Lehnert

University of Michigan, Ann Arbor, MI, USA

• Quantum-Chemistry-Centered Normal Coordinate Analysis (QCC-NCA): Application of NCA for the Simulation of the Vibrational Spectra of Large Molecules

Hui Li

University of Nebraska-Lincoln, Lincoln, NE, USA

• Calculation of Reduction Potential and p

K

a

Xavier López

Universitat Rovira i Virgili, Tarragona, Spain

• Computational Methods: Heteropolyoxoanions

Marcus Lundberg

Kyoto University, Kyoto, Japan

• Determining Transition States in Bioinorganic Reactions

Yogita Mantri

Indiana University, Bloomington, IN, USA

• Computational Studies: Cisplatin

Tiziana Marino

Università della Calabria, Rende, Italy

• Potential Energy Surfaces for Metal-Assisted Chemical Reactions

John E. McGrady

University of Glasgow, Glasgow, UK

• Electronic Structure of Metal–Metal Bonds

Maria del Carmen Michelini

Università della Calabria, Rende, Italy

• Potential Energy Surfaces for Metal-Assisted Chemical Reactions

Keiji Morokuma

Emory University, Atlanta, GA, USA and Kyoto University, Kyoto, Japan

• Determining Transition States in Bioinorganic Reactions

Jon I. Mujika

University of Bristol, Bristol, UK

• Computational Methods: Modeling of Reactivity in Zn-Containing Enzymes

Adrian J. Mulholland

University of Bristol, Bristol, UK

• Computational Methods: Modeling of Reactivity in Zn-Containing Enzymes

Frank Neese

University of Bonn, Bonn, Germany and Max-Planck Institute for Bioinorganic Chemistry, Mülheim, Germany

• Spectroscopic Properties of Protein-Bound Cofactors: Calculation by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Approaches

Gabriela Neme

Babe-Bolyai University, Cluj-Napoca, Romania

• Theoretical Aspects of Main Group Multiple Bonded Systems

Louis Noodleman

Scripps Research Institute, La Jolla, CA, USA

• Broken Symmetry States of Iron–Sulfur Clusters

Maylis Orio

University of Bonn, Bonn, Germany

• Spectroscopic Properties of Protein-Bound Cofactors: Calculation by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Approaches

Monita Y. M. Pau

Stanford University, Stanford, CA, USA

• Nature of the Catecholate–Fe(III) Bond: High Affinity Binding and Substrate Activation in Bioinorganic Chemistry

Kirk A. Peterson

Washington State University, Pullman, WA, USA

• Gaussian Basis Sets for Quantum Mechanical (QM) Calculations

Petronela Petrar

Babe-Bolyai University, Cluj-Napoca, Romania

• Theoretical Aspects of Main Group Multiple Bonded Systems

Josep M. Poblet

Universitat Rovira i Virgili, Tarragona, Spain

• Computational Methods: Heteropolyoxoanions

Dragan M. Popovi

University of California, Davis, CA, USA

• Combined Density Functional Theory (DFT) and Electrostatics Study of the Proton Pumping Mechanism in Cytochrome

c

Oxidase

Jason Quenneville

University of California, Davis, CA, USA

• Combined Density Functional Theory (DFT) and Electrostatics Study of the Proton Pumping Mechanism in Cytochrome

c

Oxidase

Dmitrij Rappoport

University of California, Irvine, CA, USA

• Approximate Density Functionals: Which Should I Choose?

Christoph Riplinger

University of Bonn, Bonn, Germany

• Spectroscopic Properties of Protein-Bound Cofactors: Calculation by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Approaches

Björn O. Roos

Chemical Center, Lund, Sweden

• Multiconfigurational Quantum Mechanics (QM) for Heavy Element Compounds

Nino Russo

Università della Calabria, Rende, Italy

• Potential Energy Surfaces for Metal-Assisted Chemical Reactions

Ulf Ryde

Lund University, Lund, Sweden

• Quantum Mechanical/Molecular Mechanical (QM/MM) Methods and Applications in Bioinorganic Chemistry

Jean-Yves Saillard

Ecole Nationale Supérieure de Chimie de Rennes, Rennes, France

• Computational Methods: Transition Metal Clusters

H. Bernhard Schlegel

Wayne State University, Detroit, MI, USA

• Spin Contamination in Inorganic Chemistry Calculations

Oottikkal Shameema

Indian Institute of Science, Bangalore, India

• Computational Studies: Boranes

Emilia Sicilia

Università della Calabria, Rende, Italy

• Potential Energy Surfaces for Metal-Assisted Chemical Reactions

Per E. M. Siegbahn

Stockholm University, Stockholm, Sweden

• Water Oxidation by the Manganese Cluster in Photosynthesis

Ioan Silaghi-Dumitrescu

Babe-Bolyai University, Cluj-Napoca, Romania

• Theoretical Aspects of Main Group Multiple Bonded Systems

Edward I. Solomon

Stanford University, Stanford, CA, USA

• Nature of the Catecholate–Fe(III) Bond: High Affinity Binding and Substrate Activation in Bioinorganic Chemistry

Jason L. Sonnenberg

Wayne State University, Detroit, MI, USA

• Spin Contamination in Inorganic Chemistry Calculations

Alexei A. Stuchebrukhov

University of California, Davis, CA, USA

• Combined Density Functional Theory (DFT) and Electrostatics Study of the Proton Pumping Mechanism in Cytochrome

c

Oxidase

Mahesh Sundararajan

University of Bonn, Bonn, Germany

• Spectroscopic Properties of Protein-Bound Cofactors: Calculation by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Approaches

Robert K. Szilagyi

Montana State University, Bozeman, MT, USA

• Structural Origins of Noninnocent Coordination Chemistry

Marirosa Toscano

Università della Calabria, Rende, Italy

• Potential Energy Surfaces for Metal-Assisted Chemical Reactions

Felix Tuczek

Christian-Albrechts-Universität Kiel, Kiel, Germany

• Electronic Structure Calculations: Dinitrogen Reduction in Nitrogenase and Synthetic Model Systems

Moritz von Hopffgarten

Philipps-Universität Marburg, Marburg, Germany

• Calculation of Bonding Properties

Frank Wennmohs

University of Bonn, Bonn, Germany

• Spectroscopic Properties of Protein-Bound Cofactors: Calculation by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Approaches

Giuseppe Zampella

University of Milano-Bicocca, Milano, Italy

• Hydrogenases: Theoretical Investigations Towards Bioinspired H

2

Production and Activation

Dmitry Yu. Zubarev

Utah State University, Logan, UT, USA

• Multiple Aromaticity, Multiple Antiaromaticity, and Conflicting Aromaticity in Inorganic Systems

Series Preface

The success of the Encyclopedia of Inorganic Chemistry (EIC) has been very gratifying to the Editors. We felt, however, that not everyone would necessarily need access to the full ten volumes of EIC. Some readers might prefer to have more concise thematic volumes targeted to their specific area of interest. This idea encouraged us to produce a series of EIC Books, focusing on topics of current interest. These books will continue to appear on a regular basis and will feature leading scholars in their fields. Like the Encyclopedia, we hope that EIC Books will give both the starting research student and the confirmed research worker a critical distillation of the leading concepts and provide a structured entry into the fields covered.

Computer literature searches have become so easy that one could be led into thinking that the problem of efficient access to chemical knowledge is now solved. In fact, these searches often produce such a vast mass of material that the reader is overwhelmed. As Henry Kissinger has remarked, the end result is often a shrinking of one’s perspective. From studying the volumes that comprise the EIC Books series, we hope that readers will find an expanding perspective to furnish ideas for research, and a solid, up-to-date digest of current knowledge to provide a basis for instructors and lecturers.

I take this opportunity of thanking Bruce King, who pioneered the Encyclopedia of Inorganic Chemistry, my fellow editors, as well as the Wiley personnel, and, most particularly, the authors of the articles for the tremendous effort required to produce such a series on time. I hope that EIC Books will allow readers to benefit in a more timely way from the insight of the authors and thus contribute to the advance of the field as a whole.

Robert H. CrabtreeYale UniversityDepartment of ChemistryJanuary 2009

Volume Preface

Over the past several decades there have been major advances in our ability to evaluate computationally the electronic structure of inorganic molecules, particularly transition metal systems. This is due to the Moore’s Law increase in computing power as well as the impact of density functional theory (DFT) and its implementation in commercial and freeware programs for quantum chemical calculations. Improved pure and hybrid density functionals are now allowing DFT calculations with accuracy comparable to high level Hartree–Fock (HF) treatments, and the results of these calculations can now be evaluated based on experiment. The latter is made possible through the development of modules for the calculation of spin-Hamiltonian parameters and other ground state properties (vibrational frequencies, g and A matrices, D tensor, etc.) and Δ SCF and time-dependent density functional theory (TDDFT) methods for correlation to electronic excited states. Developments in wave function methods have also extended their use to a wide range of transition metal systems.

The availability and ease in utility of electronic structure codes have led to their becoming a significant component of the experimental chemist’s toolbox. Indeed many papers on inorganic systems in the major chemical literature now contain electronic structure calculations as a complement to experimental results. Despite the significant advances in theory, the accuracy of computational methods is still limited when applied to transition metal systems, and different DFT functionals, levels of implementation of HF based methods (Moeller-Plesset perturbation theory (MP), complete active space (CAS), coupled cluster (CC), configurational interaction (CI)), and model designs can give different results. It is therefore of critical importance to calibrate calculations with experiments. However, when calculations are correlated to and supported by experimental data they can provide fundamental insight into electronic structure and its contributions to physical properties and chemical reactivity. This interplay will continue to expand and contribute to both improved value of experimental results and improved accuracy of computational predictions.

The purpose of this volume is to provide state-of-theart presentations of quantum mechanical and related methods and their applications by many of the leaders in the field. Part 1 of this volume focuses on methods, their background and implementation, and their use in describing bonding properties, energies, transition states and spectroscopic features. Then we focus on applications in bioinorganic chemistry (Part 2) and inorganic chemistry (Part 3) where electronic structure calculations have already had a major impact. We believe this volume will be of significant value to both experimentalists and theoreticians, and anticipate that it will stimulate both further development of the methodology and its applications in the many interdisciplinary fields that comprise modern inorganic chemistry.

Edward I. Solomon University of Stanford Department of Chemistry

Robert A. Scott University of Georgia Department of Chemistry

R. Bruce King University of Georgia Department of Chemistry

September 2009