Structure and Function (eBook)

Structure and Function 1
Jan C.A. Boeyens – A Holistic Scientist 4
Root 8
Preface 10
Contents 12
Contributors 14
1 Molecular Associations Determined from Free Energy Calculations 16
1.1 Introduction 16
1.2 Statistical Mechanics of Molecular Association 18
1.3 Condensed Phase Molecular Dynamics Simulations 20
1.4 Free Energies from Adaptive Reaction Coordinate Forces 20
1.5 Associative Solvents 22
1.5.1 Water 23
1.5.2 Methanol 25
1.6 Ions in Associative Solvents 29
1.7 Reactions in Associative Solvents 32
References 34
2 Molecular Modelling for Systems Containing Transition Metal Centres 36
2.1 Introduction 36
2.2 Molecular Mechanics 39
2.2.1 Shortcomings of MM for TM Systems 41
2.2.2 Ligand Field Molecular Mechanics 42
2.3 Applications of LFMM 44
2.3.1 Simple Coordination Complexes: Cu(II) Amines 45
2.3.2 [MCl4]2- Complexes 46
2.3.3 Cu(II) Bis-oxazoline Complexes 48
2.3.4 Jahn–Teller Effects in Six-Coordinate Cu(II) Complexes 49
2.3.4.1 The Mexican Hat Potential Energy Surface 49
2.3.4.2 The Warped Mexican Hat 50
2.3.4.3 Theoretical Treatment of the Jahn–Teller Effect in Cu(II) Species 52
2.3.4.4 Barriers Between Successive Elongations 54
2.3.4.5 Truly Compressed Complexes 56
2.3.5 Spin-State Effects 56
2.3.6 Type 1 Copper Enzymes 57
2.3.7 Dinuclear Copper Centres 60
2.4 Conclusions 64
References 65
3 Magnetic Anisotropy in Cyanide Complexes of First Row Transition Metal Ions 67
3.1 Introduction 67
3.2 Jahn–Teller Coupling Versus Spin-Orbit Coupling in the Ground State of [Fe(CN)6]3- 69
3.3 Modeling of the Magnetic Anisotropy in Ni-NC-FeIII Pairs 77
3.3.1 Theory 77
3.3.2 Regular (C4v) Versus Distorted (Cs) [Fe(CN)63-] and Its Influence on the Magnetic Anisotropy of the Fe-Ni Pair 79
3.3.3 Effect of Combined Spin-Orbit Coupling and Strain at the FeIII Subunit 82
3.4 Magnetic Anisotropy in Linear Trinuclear Cu-NC-Fe-CN-Cu complexes 85
3.5 Computation of the Magnetic Anisotropy in Oligonuclear Complexes with Nearly Degenerate Ground States 88
3.5.1 Theory 88
3.5.2 Applications to Various Cyanide-Bridged MnFem Complexes (M = CuII, NiIII) 93
3.6 Conclusions 96
References 97
4 Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations 100
4.1 Introduction 100
4.2 The MM Method 101
4.3 Handling Metal Ions 102
4.4 Extending the Force Field 103
4.5 Applications of the Corrin Force Field: Structure and Function of B12 Derivatives 106
4.6 Applications of the Corrin Force Field: The Structure of the Cobalt Corrins in Solution 107
4.7 Applications of the Porphyrin Force Field: The Solution Structures of the Complexes Formed Between Ferriprotoporphyrin IX and Arylmethanol Antimalarials 109
References 118
5 Artificial Photosynthetic Reaction Center 123
5.1 Introduction 123
5.2 Electron Donor–Acceptor Ensembles with Covalent Bonding 125
5.2.1 Multi-step Electron Transfer 125
5.2.2 Nanocarbon Materials Linked with Multiple Porphyrins 128
5.2.3 Simple Electron Donor–Acceptor Dyads with Long CS Lifetimes 130
5.3 Electron Donor–Acceptor Ensembles with Non-covalent Bonding 133
5.3.1 – Interaction 133
5.3.2 Porphyrin Nanochannels 136
5.3.3 Supramolecular Electron Donor–Acceptor Complexes of Phthalocyanines 139
5.4 Summary 142
References 142
6 Multifrequency EPR Spectroscopy: A Toolkitfor the Characterization of Mono- and Di-nuclear MetalIon Centers in Complex Biological Systems 145
6.1 Introduction 145
6.2 Multifrequency EPR Toolkit 146
6.2.1 g-Value Resolution and Orientation Selection 148
6.2.2 Magnitude of the Microwave Frequency 150
6.2.3 State Mixing 150
6.2.4 Angular Anomalies 150
6.2.5 Distribution of Spin Hamiltonian Parameters 151
6.2.6 Numerical Differentiation and Fourier Filtering 153
6.2.7 High Resolution EPR Techniques 154
6.2.8 Geometric and Electronic Structure Determination 154
6.2.8.1 Computer Simulation 155
6.2.8.2 Computational Chemistry 156
6.2.8.3 Molecular Sophe – An Integrated Approach 157
6.3 Application of Multifrequency EPR to the Structural Characterization of Complex Biological Systems 161
6.3.1 EPR Studies of MoV Complexes and Their Relevance to Mononuclear Molybdenum Enzymes 161
6.3.2 EPR Studies of Copper(II) Cyclic Peptide Complexes 168
6.3.2.1 Copper(II) Complexes with Marine Cyclic Peptides 168
6.3.2.2 Copper(II) Complexes with Westiellamide and Synthetic Analogues 172
6.3.3 Purple Acid Phosphatases 176
6.4 Conclusions 183
References 183
7 On Stacking 188
7.1 Introduction 188
7.2 Intra- and Inter-Strand Base Stacking 190
7.3 Parallel and Perpendicular Intercalating Agents 191
7.3.1 Cofacial Versus Edge-On Stacking 193
7.4 Base-Backbone Inclination and Sugar-Base Stacking 194
7.4.1 Amino Acid-Nucleobase Stacking 196
7.5 Stacked Dipoles: The C-Rich i-Motif 197
7.6 Cation– Interactions 199
7.7 Lone Pair– and Anion– Interactions 200
7.8 Unique Properties of the TATA-Motif Major Groove 202
7.9 Conclusion 204
References 204
8 Structurally Complex Intermetallic Thermoelectrics – Examples from Modulated Rock-Salt structuresand the System Zn-Sb 208
8.1 Introduction 208
8.1.1 Incommensurate Structure Analysis 210
8.1.2 Modulated Rock-Salt Like Compounds 212
8.1.3 The Remarkable System Sb-Zn 217
8.2 Conclusion 226
References 227
9 Solid State Transformations in Crystalline Salts 229
9.1 Introduction 229
9.2 Solid State Transformation in Some Metal-Organic Salts 230
9.3 Sublimation and Dissociation in Simple Salts of an Organic Compound 234
9.3.1 Crystal Structures and Isostructurality 234
9.3.2 Thermal Analysis 235
9.3.3 Comparison of 3H+.Cl- and 3H+.NO3- 240
References 242
10 Influence of Size and Shape on Inclusion Propertiesof Transition Metal-Based Wheel-and-Axle Diols 244
10.1 Shape and Packing 244
10.2 Metallo-organic Frameworks: Transition Metal-Based Wheel-and-Axle Diols 246
10.2.1 Structural Analysis of Trans-palladium(II) Complexes of Triarylcarbinol Ligands: A Class of Transition Metal-Based Wheel-and-Axle Diol 249
10.2.1.1 Identification of the ``Bistable Framework' 249
10.2.1.2 Inclusion Sites and Guest Migration 251
10.2.2 Robustness of the Pattern with Increasing Shape Complexity 253
10.2.3 Validation of the Wheel-and-Axle Shape 259
References 261
Index 263