Transition Metals in Coordination Environments (eBook)

Ewa Broclawik is a Professor Emeritus and former Full Professor at the Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences in Krakow, Poland. Her research interests focus on theoretical and applied quantum chemistry, in particular on the modeling of active sites in heterogeneous and enzymatic catalysis and on catalytic reaction mechanisms. Dr. Broclawik is the author of more than 180 publications, including 9 book chapters.   Tomasz Borowski is a Full Professor at the Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences. His research interests encompass computational chemistry, biochemistry, reaction mechanisms, metalloenzymes, and protein structure and dynamics. Dr. Borowski has published more than 60 research papers in refereed journals as well as 3 book chapters. Mariusz Radoń is an Assistant Professor at Jagiellonian University, Krakow, Poland. His primary research interest is in quantum chemistry, especially its applications to transition metal complexes and active sites of metalloproteins, with a focus on electronic structure, spin-state energetics, metal–ligand interactions and connections to catalytic activity. Dr. Radoń is the author of 30 publications, including 1 book chapter. 

Preface 6
Contents 12
Contributors 14
The Electronic Determinants of Spin Crossover Described by Density Functional Theory 17
1 Introduction 17
2 Fundamentals of Spin Crossover 19
2.1 The Dilemma and Choice Between LS and HS 19
2.2 The Spectrochemical Series 21
2.3 The Thermochemical Spin Series 21
2.4 The Oxidation State on the Central Metal Ion 22
2.5 Homoleptic SCO Complexes and the Case of Co3+(aq) 23
2.6 Geometry Preferences and Changes During SCO 25
2.7 The Nature of the SCO Transition 26
2.8 True Hysteresis and Intrinsic Hysteresis 27
3 Important Contributions to Single-Molecule SCO 28
3.1 Zero-Point Vibrational Energy 28
3.2 Dispersion Contributions to the Spin Crossover Equilibrium 29
3.3 Relativistic Stabilization of LS 30
3.4 Vibrational Entropy 32
4 Performance of DFT for Describing SCO 35
4.1 The Massive Role of HF Exchange Favoring HS 35
4.2 The Role of the Correlation Functional 37
4.3 The Use of Quantum-Chemical Benchmarks and the Post-HF Bias 38
4.4 Toward Spin-State-Balanced Density Functionals 39
5 Conclusions 41
References 41
Anisotropic Magnetic Spin Interactions of Transition Metal Complexes and Metalloenzymes from Spectroscopy and Quantum Chemistry 50
1 Introduction 50
2 Electron Spin Interactions with an External Magnetic Field 52
2.1 The Concept of an Effective Spin Hamiltonian 53
3 Quantum Chemical Calculations of EPR Parameters 57
4 Structural Information from the Anisotropy of Magnetic Interactions 60
4.1 EPR Studies on Single Crystals 60
4.2 Model Complexes 61
4.3 Transition Metal Containing Enzymes 66
5 Conclusion 74
References 75
Non-covalent Interactions in Selected Transition Metal Complexes 80
1 Introduction 81
2 Methods 82
2.1 ETS-NOCV Charge and Energy Decomposition Scheme 82
2.2 Non-covalent Index (NCI) 83
2.3 Quantum Theory of Atoms in Molecules (QTAIM) 83
2.4 Interacting Quantum Atoms (IQA) Energy Decomposition Scheme 84
2.5 Computational Details 84
3 Results and Discussion 85
4 Conclusions 101
References 102
Applications of the Density Matrix Renormalization Group to Exchange-Coupled Transition Metal Systems 105
1 Introduction 105
2 Theoretical Treatment of Exchange Coupling 107
3 The Density Matrix Renormalization Group Approach 110
4 Case Studies: Magnetic Coupling in Dinuclear Complexes 113
4.1 Fe2 and Cr2 Mono-?-Oxo Complexes 114
4.2 Mn2 Bis-?-Oxo/?-Acetato Complex 120
5 General Remarks 125
5.1 Active Space Composition 125
5.2 Orbital Optimization, State Selection and Convergence 126
5.3 Deviations from Heisenberg Behavior 128
5.4 Analysis of Exchange Coupling 129
6 Summary and Perspectives 130
References 131
New Strategies in Modeling Electronic Structures and Properties with Applications to Actinides 135
1 Introduction 136
2 A Brief Overview of Actinides and Their Complex Electronic Structure 136
3 Electronic Structure Methods in Quantum Chemistry 138
3.1 Introducing Relativistic Effects 139
3.2 Solving the Electronic Problem 142
4 Challenging Examples in Computational Actinide Chemistry 161
4.1 Symmetric Dissociation of UO22+ 161
4.2 Excitations of NUN 162
4.3 CUO Diluted in Noble Gas Matrices 164
4.4 Cation–cation Attraction in [NpO2]22+ 165
5 Summary 166
References 167
Computational Versus Experimental Spectroscopy for Transition Metals 175
1 Introduction 175
2 Structure of the FeMoco Cofactor of Nitrogenase in Comparison with the Oxygen-Evolving Complex of Photosystem II 176
3 Lewis-Acid Capped Iron-Oxygen and Copper-Nitrogen Species 179
4 Transient Species: The Case of Nickel(IV) Tris-?-Oxido 183
5 Magnetic Anisotropy in Transition-Metal Complexes 186
6 Concluding Remarks 192
7 Further Reading 193
References 193
Multiconfigurational Approach to X-ray Spectroscopy of Transition Metal Complexes 198
1 X-ray Spectroscopy for Transition Metals 199
2 Theoretical Simulations of X-ray Spectra 201
3 Multiconfigurational Approach to X-ray Processes 202
3.1 System Selection 203
3.2 Active-Space Selection 204
3.3 Generating Core-Hole States 205
3.4 Simulating Light-Matter Interaction 206
3.5 Number of States, Correlation Level and Basis Set 208
3.6 Relativistic Effects 211
3.7 Simulating X-ray Processes with Molcas 212
4 Electronic Structure from X-ray Spectra 213
4.1 Spin and Oxidation State 213
4.2 Molecular Orbitals in Metal–Ligand Binding 215
4.3 Transient Intermediates from Charge-Transfer Excitations 217
4.4 Multiconfigurational Description of Multiplet Splittings 218
4.5 Metal–Ligand Covalency from Multiplet Splittings 220
5 Extensions to Metal Dimers and Complex Systems 222
5.1 Intermolecular Coupling 222
5.2 Intramolecular Coupling 223
6 Conclusions and Outlook 224
References 225
Assessing Electronically Excited States of Cobalamins via Absorption Spectroscopy and Time-Dependent Density Functional Theory 231
1 Introduction 231
2 Electronic and Structural Properties of Cobalamins 234
3 Importance of Abs, CD, and MCD Spectroscopy 235
4 Transient Absorption Spectroscopy 238
5 Early Attempts to Analyze and Assign Electronically Excited States 238
6 Importance of Electronically Excited States: Relevance of DFT and TD-DFT in Electronic Structure Calculations 240
7 Co–C Bond Strength: Key to Theoretical Benchmarks 240
8 Benchmarks for Electronically Excited States 243
9 Absorption Features Across Specific Systems: Theory and Experiment 246
9.1 Free Base Corrin 246
9.2 Cyanocobalamin 250
9.3 Methylcobalamin 252
9.4 Adenosylcobalamin 256
9.5 Antivitamins B12 259
9.6 Non-alkyl Cobalamins 260
9.7 Reduced Cobalamins 262
10 Summary and Future Directions 264
References 266
Photodeactivation Channels of Transition Metal Complexes: A Computational Chemistry Perspective 271
1 General Overview 272
2 State-of-the-Art Theoretical and Computational Methods for the Study of the ES Deactivation Channels of TMCs 279
2.1 Quantum Chemical Methods for the ES 279
2.2 ES Decay Rate Theories 281
2.3 ES Reaction Dynamics Methods 283
3 Photodeactivation Channels of TMCs: Selected Recent Computational Works 285
3.1 ES Decay Rate Theory and ES Kinetic Modeling: Calculation of the Temperature-Dependent Photoluminescence Lifetimes and Efficiencies of Cyclometalated Ir(III) Complexes 285
3.2 ES Dynamics: TSH Dynamics Including ISC in [Ru(bpy)3]2+ 288
3.3 Anti-Kasha Emissions in Ru(II) Complexes: Kinetic Control of Photoluminescence or Solvent Effects? 290
4 Conclusion and Perspectives 294
References 294
Mechanism and Kinetics in Homogeneous Catalysis: A Computational Viewpoint 300
1 Introduction 300
2 Chemical Reaction Mechanisms 301
3 Reactivity Studies in Organic and Organometallic Chemistry 303
3.1 Sulfur Ylide Epoxidation 304
3.2 Ketone Hydrogenation by Ruthenium Hydrides 308
3.3 Mechanism Discovery: Cis–Trans Isomerization of Alkenes 311
3.4 Morita–Baylis–Hillman Reaction 314
4 Conclusions 321
References 323
Computational Modelling of Structure and Catalytic Properties of Silica-Supported Group VI Transition Metal Oxide Species 325
1 Introduction 325
2 Surface Modelling 326
3 CrOx/SiO2 System 328
3.1 Structure of Surface Chromium Oxide Species—Experimental Data 328
3.2 Structure of Surface Chromium Species—Computational Modelling 329
3.3 Catalytic Activity—Computational Studies 335
4 MoOx/SiO2 System 340
4.1 Structure of Surface Molybdenum Oxide Species—Experimental Data 340
4.2 Structure of Surface Molybdenum Species—Computational Modelling 341
4.3 Catalytic Activity—Computational Studies 343
5 WOx/SiO2 System 345
6 Concluding Remarks 347
References 348
Catalytic Properties of Selected Transition Metal Oxides—Computational Studies 355
1 Introduction 355
2 Methods 356
2.1 The DFT and Other Quantum-Chemical Methods 356
2.2 The Classical Mechanics—Force Fields 358
2.3 Other Issues 359
3 Systems: Oxides 361
3.1 Reducible and Non-reducible Oxides 361
4 Conclusions 397
References 397
Molecular Electrochemistry of Coordination Compounds—A Correlation Between Quantum Chemical Calculations and Experiment 419
1 Introduction 420
2 DFT Modelling of Redox Potentials 420
2.1 Problems with Calibration Based on Comparison with Experimental Data 422
2.2 Absolute Potential of Fc+/Fc 424
2.3 Molybdenum and Tungsten Scorpionates 427
2.4 Effect of Second Coordination Sphere and H-Bonding Changes on Reduction Potential 429
2.5 Further Relevant Reports 430
3 Electrochemical Communication Across Saturated Dioxoalkylene and Oxo Bridges in Dimolybdenum Scorpionates 431
4 Electrocatalytic Reductive Dehalogenation Driven by Non-covalent Interactions—Binding and Activation in Mo/W-Alkoxide System 436
5 Concluding Remarks 442
References 444
The Quest for Accurate Theoretical Models of Metalloenzymes: An Aid to Experiment 449
1 Introduction 449
2 Methodology 451
2.1 Cluster Models 451
2.2 Quantum Mechanics/Molecular Mechanics (QM/MM) 452
3 Developments in QM Cluster Calculations 454
3.1 Co-factor Free Dioxygenase Reaction Mechanism 454
3.2 Bioengineering of S-para-Hydroxymandalate Synthase into R-para-Hydroxymandalate Synthase 457
4 Developments in QM/MM Calculations 458
4.1 Explicit Solvent Effects Captured with QM/MM Models 459
4.2 QM/MM Techniques Are Often Essential for Replicating Minor Structural Anomalies that Lead to Large Changes in Reactivity 462
5 Conclusion 466
References 466
Applications of Computational Chemistry to Selected Problems of Transition-Metal Catalysis in Biological and Nonbiological Systems 473
1 Introduction 473
2 Computational Methods for Studying Catalysis in Various Systems 474
3 Studies of Transition-Metal Complexes for Homogeneous Catalysis 478
3.1 DFT Studies of Reaction Pathways in the Ground State 478
3.2 DFT Studies of Reaction Pathways in Excited States 479
3.3 QM/QM’ Studies of Reactions Catalyzed by Transition-Metal Catalysis Having Large Ligands 481
4 Studies of Metalloenzymes 483
4.1 Studies of Heme Enzymes 484
4.2 Studies of Nonheme Enzymes 484
5 Studies of MOFs 488
5.1 QM/MM Studies of MOFs 488
5.2 Force-Field Parameterization for MOF Simulations 490
6 Conclusions 493
References 494
How Metal Coordination in the Ca-, Ce-, and Eu-Containing Methanol Dehydrogenase Enzymes Can Influence the Catalysis: A Theoretical Point of View 497
1 Introduction 497
2 Computational Methods 499
2.1 Active Site Model 499
3 Results and Discussion 501
3.1 Ce-MDH PES 501
3.2 Michaelis–Menten Complex (ES) for Ce-MDH and Eu-MDH 503
4 Conclusions 508
References 508
Challenges in Modelling Metalloenzymes 512
1 Introduction 512
2 Checking the Structure Quality 514
3 Quantum Refinement 515
4 Homology Modelling 516
5 Modelling Loops 517
6 Prediction of pKa 518
7 Molecular Dynamics Simulations 522
8 Choosing MD Snapshots for QM or QM/MM Studies 524
9 QM Cluster Models for Metalloenzymes 527
10 Conclusions 531
References 531
Index 535