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Spin States in Biochemistry and Inorganic Chemistry: Influence on Structure and Reactivity

ISBN: 978-1-118-89831-4
472 pages
December 2015
Spin States in Biochemistry and Inorganic Chemistry: Influence on Structure and Reactivity (1118898311) cover image

Description

It has long been recognized that metal spin states play a central role in the reactivity of important biomolecules, in industrial catalysis and in spin crossover compounds. As the fields of inorganic chemistry and catalysis move towards the use of cheap, non-toxic first row transition metals, it is essential to understand the important role of spin states in  influencing molecular structure, bonding and reactivity.

Spin States in Biochemistry and Inorganic Chemistry provides a complete picture on the importance of spin states for reactivity in biochemistry and inorganic chemistry, presenting both theoretical and experimental perspectives. The successes and pitfalls of theoretical methods such as DFT, ligand-field theory and coupled cluster theory are discussed, and these methods are applied in studies throughout the book. Important spectroscopic techniques to determine spin states in transition metal complexes and proteins are explained, and the use of NMR for the analysis of spin densities is described.

Topics covered include:

  • DFT and ab initio wavefunction approaches to spin states
  • Experimental techniques for determining spin states
  • Molecular discovery in spin crossover
  • Multiple spin state scenarios in organometallic reactivity and gas phase reactions
  • Transition-metal complexes involving redox non-innocent ligands
  • Polynuclear iron sulfur clusters
  • Molecular magnetism
  • NMR analysis of spin densities

This book is a valuable reference for researchers working in bioinorganic and inorganic chemistry, computational chemistry, organometallic chemistry, catalysis, spin-crossover materials, materials science, biophysics and pharmaceutical chemistry.

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Table of Contents

About the Editors xv

List of Contributors xvii

Foreword xxi

Acknowledgments xxiii

1 General Introduction to Spin States 1
Marcel Swart and Miquel Costas

1.1 Introduction 1

1.2 Experimental Chemistry: Reactivity, Synthesis and Spectroscopy 2

1.3 Computational Chemistry: Quantum Chemistry and Basis Sets 4

2 Application of Density Functional and Density Functional Based Ligand Field Theory to Spin States 7
Claude Daul, Matija Zlatar, Maja Gruden-Pavlovic and Marcel Swart

2.1 Introduction 7

2.2 What Is the Problem with Theory? 9

2.2.1 Density Functional Theory 9

2.2.2 LF Theory: Bridging the Gap Between Experimental and Computational Coordination Chemistry 11

2.3 Validation and Application Studies 15

2.3.1 Use of OPBE, SSB-D and S12g Density Functionals for Spin-State Splittings 17

2.3.2 Application of LF-DFT 21

2.4 Concluding Remarks 25

3 Ab Initio Wavefunction Approaches to Spin States 35
Carmen Sousa and Coen de Graaf

3.1 Introduction and Scope 35

3.2 Wavefunction-Based Methods for Spin States 35

3.2.1 Single Reference Methods 36

3.2.2 Multireference Methods 37

3.2.3 MR Perturbation Theory 39

3.2.4 Variational Approaches 40

3.2.5 Density Matrix Renormalization Group Theory 40

3.3 Spin Crossover 41

3.3.1 Choice of Active Space and Basis Set 41

3.3.2 The HS–LS Energy Difference 43

3.3.3 Light-Induced Excited Spin State Trapping (LIESST) 45

3.3.4 Spin Crossover in Other Metals 47

3.4 Magnetic Coupling 47

3.5 Spin States in Biochemical and Biomimetic Systems 50

3.6 Two-State Reactivity 52

3.7 Concluding Remarks 52

4 Experimental Techniques for Determining Spin States 59
Carole Duboc and Marcello Gennari

4.1 Introduction 59

4.2 Magnetic Measurements 61

4.2.1 g-Anisotropy and Zero-Field Splitting (zfs) 64

4.2.2 Unquenched Orbital Moment in the Ground State 64

4.2.3 Exchange Interactions 64

4.2.4 Spin Transitions and Spin Crossover 66

4.3 EPR Spectroscopy 66

4.4 Mössbauer Spectroscopy 70

4.5 X-ray Spectroscopic Techniques 74

4.6 NMR Spectroscopy 77

4.7 Other Techniques 80

4.A Appendix 81

4.A.1 Theoretical Background 81

4.A.2 List of Symbols 82

5 Molecular Discovery in Spin Crossover 85
Robert J. Deeth

5.1 Introduction 85

5.2 Theoretical Background 85

5.2.1 Spin Transition Curves 88

5.2.2 Light-Induced Excited Spin State Trapping 89

5.3 Thermal SCO Systems: Fe(II) 90

5.4 SCO in Non-d6 Systems 93

5.5 Computational Methods 95

5.6 Outlook 98

6 Multiple Spin-State Scenarios in Organometallic Reactivity 103
Wojciech I. Dzik, Wesley Böhmer and Bas de Bruin

6.1 Introduction 103

6.2 "Spin-Forbidden" Reactions and Two-State Reactivity 104

6.3 Spin-State Changes in Transition Metal Complexes 107

6.3.1 Influence of the Spin State on the Kinetics of Ligand Exchange 108

6.3.2 Stoichiometric Bond Making and Breaking Reactions 109

6.3.3 Spin-State Situations Involving Redox-Active Ligands 115

6.4 Spin-State Changes in Catalysis 119

6.4.1 Catalytic (Cyclo)oligomerizations 119

6.4.2 Phillips Cr(II)/SiO2 Catalyst 121

6.4.3 SNS–CrCl3 Catalyst 123

6.5 Concluding Remarks 125

7 Principles and Prospects of Spin-States Reactivity in Chemistry and Bioinorganic Chemistry 131
Dandamudi Usharani, Binju Wang, Dina A. Sharon and Sason Shaik

7.1 Introduction 131

7.2 Spin-States Reactivity 132

7.2.1 Two-State and Multi-State Reactivity 133

7.2.2 Origins of Spin-Selective Reactivity: Exchange-Enhanced Reactivity and Orbital Selection Rules 137

7.2.3 Considerations of Exchange-Enhanced Reactivity versus Orbital-Controlled Reactivity 140

7.2.4 Consideration of Spin-State Selectivity in H-Abstraction: The Power of EER 142

7.2.5 The Origins of Mechanistic Selection – Why Are C–H Hydroxylations Stepwise Processes? 146

7.3 Prospects of Two-State Reactivity and Multi-State Reactivity 148

7.3.1 Probing Spin-State Reactivity 148

7.3.2 Are Spin Inversion Probabilities Useful for Analyzing TSR? 150

7.4 Concluding Remarks 151

8 Multiple Spin-State Scenarios in Gas-Phase Reactions 157
Jana Roithová

8.1 Introduction 157

8.2 Experimental Methods for the Investigation of Metal-Ion Reactions 158

8.3 Multiple State Reactivity: Reactions of Metal Cations with Methane 160

8.4 Effect of the Oxidation State: Reactions of Metal Hydride Cations with Methane 163

8.5 Two-State Reactivity: Reactions of Metal Oxide Cations 164

8.6 Effect of Ligands 171

8.7 Effect of Noninnocent Ligands 174

8.8 Concluding Remarks 177

9 Catalytic Function and Mechanism of Heme and Nonheme Iron(IV)–Oxo Complexes in Nature 185
Matthew G. Quesne, Abayomi S. Faponle, David P. Goldberg and Sam P. de Visser

9.1 Introduction 185

9.2 Cytochrome P450 Enzymes 186

9.2.1 Importance of Cytochrome P450 Enzymes 187

9.2.2 P450 Activation of Long-Chain Fatty Acids 188

9.2.3 Heme Monooxygenases and Peroxygenases 188

9.2.4 Catalytic Cycle of Cytochrome P450 Enzymes 188

9.3 Nonheme Iron Dioxygenases 190

9.3.1 Cysteine Dioxygenase 191

9.3.2 AlkB Repair Enzymes 192

9.3.3 Nonheme Iron Halogenases 194

9.4 Conclusions 197

9.5 Acknowledgments 197

10 Terminal Metal–Oxo Species with Unusual Spin States 203
Sarah A. Cook, David C. Lacy and Andy S. Borovik

10.1 Introduction 203

10.2 Bonding 204

10.2.1 Bonding Considerations: Tetragonal Symmetry 204

10.2.2 Bonding Considerations: Trigonal Symmetry 205

10.2.3 Methods of Characterization 206

10.3 Case Studies 206

10.3.1 Iron–Oxo Chemistry 206

10.3.2 Manganese–Oxo Chemistry 212

10.3.3 Cautionary Tales: Late Transition Metal Oxido Complexes 217

10.3.4 Effects of Redox Inactive Metal Ions 217

10.3.5 Metal–Oxyl Complexes 218

10.4 Reactivity 218

10.4.1 General Concepts: Proton versus Electron Transfer 218

10.4.2 Spin State and Reactivity 220

10.5 Summary 220

11 Multiple Spin Scenarios in Transition-Metal Complexes Involving Redox Non-Innocent Ligands 229
Florian Heims and Kallol Ray

11.1 Introduction 229

11.2 Survey of Non-Innocent Ligands 231

11.3 Identification of Non-Innocent Ligands 232

11.3.1 X-ray Crystallography 232

11.3.2 EPR Spectroscopy 234

11.3.3 Mössbauer Spectroscopy 235

11.3.4 XAS Spectroscopy 236

11.4 Selected Examples of Biological and Chemical Systems Involving Non-Innocent Ligands 237

11.4.1 Copper–Radical Interaction 237

11.4.2 Iron–Radical Interaction 246

11.5 Concluding Remarks 252

12 Molecular Magnetism 263
Guillem Aromí, Patrick Gamez and Olivier Roubeau

12.1 Introduction 263

12.2 Molecular Magnetism: Motivations, Early Achievements and Foundations 264

12.3 Molecular Nanomagnets (MNM) 265

12.3.1 Single-Molecule Magnets 266

12.3.2 Single-Chain Magnets (SCM) 268

12.3.3 Single-Ion Magnets (SIM) 271

12.4 Switchable Systems 273

12.4.1 Spin Crossover (SCO) 273

12.4.2 Valence Tautomerism (VT) 273

12.4.3 Charge Transfer (CT) 275

12.4.4 Light-Driven Ligand-Induced Spin Change (LD-LISC) 276

12.4.5 Photoswitching (PS) Through Intermetallic CT 277

12.5 Molecular-Based Magnetic Refrigerants 278

12.5.1 The Magneto-Caloric Effect, Its Experimental Determination and Key Parameters 278

12.5.2 Molecular to Extended Framework Coolers Towards Applications 280

12.6 Quantum Manipulation of the Electronic Spin for Quantum Computing 282

12.6.1 Organic Radicals 283

12.6.2 Transition Metal Clusters 284

12.6.3 Lanthanides as Realization of Qubits 285

12.6.4 Engineering of Molecular Quantum Gates with Lanthanide Qubits 285

12.7 Perspectives Toward Applications and Concluding Remarks 287

13 Electronic Structure, Bonding, Spin Coupling, and Energetics of Polynuclear Iron–Sulfur Clusters – A Broken Symmetry Density Functional Theory Perspective 297
Kathrin H. Hopmann, Vladimir Pelmenschikov, Wen-Ge Han Du and Louis Noodleman

13.1 Introduction 297

13.2 Iron–Sulfur Coordination: Geometric and Electronic Structure 298

13.3 Spin Polarization Splitting and the Inverted Level Scheme 300

13.4 Spin Coupling and the Broken Symmetry Method 300

13.5 Electron Localization and Delocalization 301

13.6 Polynuclear Systems – Competing Heisenberg Interactions and Spin-Dependent Delocalization 303

13.7 Preamble to Three Major Topics: Iron–Sulfur–Nitrosyls, Adenosine-5'-Phosphosulfate Reductase, and the Proximal Cluster of Membrane-Bound [NiFe]-Hydrogenase 303

13.7.1 Nonheme Iron Nitrosyl Complexes 303

13.7.2 Adenosine-5'-Phosphosulfate Reductase 310

13.7.3 Proximal Cluster of O2-Tolerant Membrane-Bound [NiFe]-Hydrogenase in Three Redox States 315

13.8 Concluding Remarks 318

13.9 Acknowledgments 319

14 Environment Effects on Spin States, Properties, and Dynamics from Multi-level QM/MM Studies 327
Alexander Petrenko and Matthias Stein

14.1 Introduction 327

14.1.1 Environmental Effects 328

14.1.2 Hybrid QM/MM Embedding Schemes 329

14.2 The Quantum Spin Hamiltonian – Linking Theory and Experiment 332

14.3 The Solvent as an Environment 335

14.3.1 Fourier Transform Infrared Spectroscopy 336

14.3.2 Nuclear Magnetic Resonance 336

14.3.3 Electron Paramagnetic Resonance 336

14.4 Effect of Different Levels of QM and MM Treatment 338

14.4.1 Convergence and Caveats at the QM Level 338

14.4.2 Accuracy of the MM Part 341

14.4.3 QM versus QM/MM Methods 341

14.5 Illustrative Bioinorganic Examples 343

14.5.1 Cytochrome P450 343

14.5.2 Hydrogenase Enzymes 349

14.5.3 Photosystem II and the Effect of QM Size 354

14.6 From Static Spin-State Properties to Dynamics and Kinetics of Electron Transfer 357

14.7 Final Remarks and Conclusions 359

14.8 Acknowledgments 362

15 High-Spin and Low-Spin States in {FeNO}7, FeIV=O, and FeIII–OOH Complexes and Their Correlations to Reactivity 369
Edward I. Solomon, Kyle D. Sutherlin and Martin Srnec

15.1 Introduction 369

15.2 High- and Low-Spin {FeNO}7 Complexes: Correlations to O2 Activation 372

15.2.1 Spectroscopic Definition of the Electronic Structure of High-Spin {FeNO}7 372

15.2.2 Computational Studies of S = 3/2 {FeNO}7 Complexes and Related {FeO2}8 Complexes 375

15.2.3 Extension to IPNS and HPPD: Implications for Reactivity 377

15.2.4 Correlation to {FeNO}7 S = 1/2 385

15.3 Low-Spin (S = 1) and High-Spin (S = 2) FeIV=O Complexes 386

15.3.1 FeIV=O S = 1 Complexes: π* FMO 386

15.3.2 FeIV=O S = 2 Sites: π* and σ* FMOs 390

15.3.3 Contributions of FMOs to Reactivity 392

15.4 Low-Spin (S = 1/2) and High-Spin (S = 5/2) FeIII–OOH Complexes 396

15.4.1 Spin State Dependence of O–O Bond Homolysis 396

15.4.2 FeIII–OOH S = 1/2 Reactivity: ABLM 398

15.4.3 FeIII–OOH Spin State-Dependent Reactivity: FMOs 399

15.5 Concluding Remarks 401

15.6 Acknowledgments 402

16 NMR Analysis of Spin Densities 409
Kara L. Bren

16.1 Introduction and Scope 409

16.2 Spin Density Distribution in Transition Metal Complexes 410

16.3 NMR of Paramagnetic Molecules 412

16.3.1 Chemical Shifts 413

16.3.2 Relaxation Rates 414

16.4 Analysis of Spin Densities by NMR 416

16.4.1 Factoring Contributions to Hyperfine Shifts 416

16.4.2 Relaxation Properties and Spin Density 418

16.4.3 DFT Approaches to Analyzing Hyperfine Shifts 419

16.4.4 Natural Bond Orbital Analysis 420

16.4.5 Application and Practicalities 421

16.5 Probing Spin Densities in Paramagnetic Metalloproteins 422

16.5.1 Heme Proteins 422

16.5.2 Iron-Sulfur Proteins 425

16.5.3 Copper Proteins 427

16.6 Conclusions and Outlook 429

17 Summary and Outlook 435
Miquel Costas and Marcel Swart

17.1 Summary 435

17.2 Outlook 436

Index 439

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Author Information

Prof. Dr. Marcel Swart, Universitat de Girona, Spain
Marcel Swart is ICREA Research Professor in the Institute of Computational Chemistry Catalysis at the Universitat de Girona, Spain. He is a computational/theoretical chemist working in the field of (bio)chemistry and biomedicine. He has published >100 papers in peer-reviewed scientific journals and has an h-index of 26. He was awarded the Young Scientist 2005 award by ICCMSE (International Conference of Computational Methods in Sciences and Engineering), and was selected as one of the promising young inorganic chemists of "The next generation" that were invited to contribute to a special issue of Inorganica Chimica Acta in 2007, and to a special issue of Polyhedron in 2010.
In 2012, he was awarded the MGMS Silver Jubilee Prize "for his development of new computational chemistry programs, design of new research tools and application to (bio)chemical systems that are highly relevant for society and science." In September 2012 he organized a CECAM/ESF Workshop on "Spin states in biochemistry and inorganic chemistry", highlighted in Nature Chem. 2013, 5, 7-9.

Prof. Dr. Miquel Costas, Universitat de Girona, Spain
Miquel Costas became Professor Titular at the University of Girona in 2003. He has published over 70 papers in international journals that have received over 3470 citations. His research interests involve the study of transition metal complexes involved in challenging oxidative transformations, including functionalization of C-H bonds and water oxidation. These systems commonly operate in multistate reactivity scenarios, implicating multiple spin states.

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Reviews

"Spin States in Biochemistry and Inorganic Chemistry: Influence on Structure and Reactivity, edited by Marcel Swart and Miquel Costas is impressive testimony to the advances in theory, computations, and experiment, especially regarding transition metals in recent years, and a revealing look at how much remains to be developed....The authors provide detailed comparison of various computational methods with each other and with experimental data in many cases. Each chapter is an extensively referenced focused review article.  Chapters 1-3 emphasize computational methods....No single monograph can encompass a topic as broad as the title of this book, which is almost the entire chemistry of the periodic table.  However, for the selected topics, the volume provides a very valuable concise snapshot of the field.Computational chemistry for compounds of CHNO have advanced to the point that many experimentalists can routinely apply standard methods in Gaussian and other such programs with confidence, guided only by the state of the art described in other publications.  This book shows that in spite of enormous effort related to transition metal energy states and spin states, even the expert computational chemists need to proceed with caution and compare many functionals"- (Gareth Eaton- December 2016)
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