Structure and Function

Structure and Function

Jan C.A. Boeyens – A Holistic Scientist

Root

Preface

Contents

Contributors

1 Molecular Associations Determined from Free Energy Calculations

1.1 Introduction

1.2 Statistical Mechanics of Molecular Association

1.3 Condensed Phase Molecular Dynamics Simulations

1.4 Free Energies from Adaptive Reaction Coordinate Forces

1.5 Associative Solvents

1.5.1 Water

1.5.2 Methanol

1.6 Ions in Associative Solvents

1.7 Reactions in Associative Solvents

References

2 Molecular Modelling for Systems Containing Transition Metal Centres

2.1 Introduction

2.2 Molecular Mechanics

2.2.1 Shortcomings of MM for TM Systems

2.2.2 Ligand Field Molecular Mechanics

2.3 Applications of LFMM

2.3.1 Simple Coordination Complexes: Cu(II) Amines

2.3.2 [MCl4]2- Complexes

2.3.3 Cu(II) Bis-oxazoline Complexes

2.3.4 Jahn–Teller Effects in Six-Coordinate Cu(II) Complexes

2.3.4.1 The Mexican Hat Potential Energy Surface

2.3.4.2 The Warped Mexican Hat

2.3.4.3 Theoretical Treatment of the Jahn–Teller Effect in Cu(II) Species

2.3.4.4 Barriers Between Successive Elongations

2.3.4.5 Truly Compressed Complexes

2.3.5 Spin-State Effects

2.3.6 Type 1 Copper Enzymes

2.3.7 Dinuclear Copper Centres

2.4 Conclusions

References

3 Magnetic Anisotropy in Cyanide Complexes of First Row Transition Metal Ions

3.1 Introduction

3.2 Jahn–Teller Coupling Versus Spin-Orbit Coupling in the Ground State of [Fe(CN)6]3-

3.3 Modeling of the Magnetic Anisotropy in Ni-NC-FeIII Pairs

3.3.1 Theory

3.3.2 Regular (C4v) Versus Distorted (Cs) [Fe(CN)63-] and Its Influence on the Magnetic Anisotropy of the Fe-Ni Pair

3.3.3 Effect of Combined Spin-Orbit Coupling and Strain at the FeIII Subunit

3.4 Magnetic Anisotropy in Linear Trinuclear Cu-NC-Fe-CN-Cu complexes

3.5 Computation of the Magnetic Anisotropy in Oligonuclear Complexes with Nearly Degenerate Ground States

3.5.1 Theory

3.5.2 Applications to Various Cyanide-Bridged MnFem Complexes (M = CuII, NiIII)

3.6 Conclusions

References

4 Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations

4.1 Introduction

4.2 The MM Method

4.3 Handling Metal Ions

4.4 Extending the Force Field

4.5 Applications of the Corrin Force Field: Structure and Function of B12 Derivatives

4.6 Applications of the Corrin Force Field: The Structure of the Cobalt Corrins in Solution

4.7 Applications of the Porphyrin Force Field: The Solution Structures of the Complexes Formed Between Ferriprotoporphyrin IX and Arylmethanol Antimalarials

References

5 Artificial Photosynthetic Reaction Center

5.1 Introduction

5.2 Electron Donor–Acceptor Ensembles with Covalent Bonding

5.2.1 Multi-step Electron Transfer

5.2.2 Nanocarbon Materials Linked with Multiple Porphyrins

5.2.3 Simple Electron Donor–Acceptor Dyads with Long CS Lifetimes

5.3 Electron Donor–Acceptor Ensembles with Non-covalent Bonding

5.3.1 – Interaction

5.3.2 Porphyrin Nanochannels

5.3.3 Supramolecular Electron Donor–Acceptor Complexes of Phthalocyanines

5.4 Summary

References

6 Multifrequency EPR Spectroscopy: A Toolkitfor the Characterization of Mono- and Di-nuclear MetalIon Centers in Complex Biological Systems

6.1 Introduction

6.2 Multifrequency EPR Toolkit

6.2.1 g-Value Resolution and Orientation Selection

6.2.2 Magnitude of the Microwave Frequency

6.2.3 State Mixing

6.2.4 Angular Anomalies

6.2.5 Distribution of Spin Hamiltonian Parameters

6.2.6 Numerical Differentiation and Fourier Filtering

6.2.7 High Resolution EPR Techniques

6.2.8 Geometric and Electronic Structure Determination

6.2.8.1 Computer Simulation

6.2.8.2 Computational Chemistry

6.2.8.3 Molecular Sophe – An Integrated Approach

6.3 Application of Multifrequency EPR to the Structural Characterization of Complex Biological Systems

6.3.1 EPR Studies of MoV Complexes and Their Relevance to Mononuclear Molybdenum Enzymes

6.3.2 EPR Studies of Copper(II) Cyclic Peptide Complexes

6.3.2.1 Copper(II) Complexes with Marine Cyclic Peptides

6.3.2.2 Copper(II) Complexes with Westiellamide and Synthetic Analogues

6.3.3 Purple Acid Phosphatases

6.4 Conclusions

References

7 On Stacking

7.1 Introduction

7.2 Intra- and Inter-Strand Base Stacking

7.3 Parallel and Perpendicular Intercalating Agents

7.3.1 Cofacial Versus Edge-On Stacking

7.4 Base-Backbone Inclination and Sugar-Base Stacking

7.4.1 Amino Acid-Nucleobase Stacking

7.5 Stacked Dipoles: The C-Rich i-Motif

7.6 Cation– Interactions

7.7 Lone Pair– and Anion– Interactions

7.8 Unique Properties of the TATA-Motif Major Groove

7.9 Conclusion

References

8 Structurally Complex Intermetallic Thermoelectrics – Examples from Modulated Rock-Salt structuresand the System Zn-Sb

8.1 Introduction

8.1.1 Incommensurate Structure Analysis

8.1.2 Modulated Rock-Salt Like Compounds

8.1.3 The Remarkable System Sb-Zn

8.2 Conclusion

References

9 Solid State Transformations in Crystalline Salts

9.1 Introduction

9.2 Solid State Transformation in Some Metal-Organic Salts

9.3 Sublimation and Dissociation in Simple Salts of an Organic Compound

9.3.1 Crystal Structures and Isostructurality

9.3.2 Thermal Analysis

9.3.3 Comparison of 3H+.Cl- and 3H+.NO3-

References

10 Influence of Size and Shape on Inclusion Propertiesof Transition Metal-Based Wheel-and-Axle Diols

10.1 Shape and Packing

10.2 Metallo-organic Frameworks: Transition Metal-Based Wheel-and-Axle Diols

10.2.1 Structural Analysis of Trans-palladium(II) Complexes of Triarylcarbinol Ligands: A Class of Transition Metal-Based Wheel-and-Axle Diol

10.2.1.1 Identification of the ``Bistable Framework'

10.2.1.2 Inclusion Sites and Guest Migration

10.2.2 Robustness of the Pattern with Increasing Shape Complexity

10.2.3 Validation of the Wheel-and-Axle Shape

References

Index