Comba Structure and Function

2010
ISBN: 978-90-481-2888-4
Verlag: Springer Netherlands
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 260 Seiten

The art of chemistry is to thoroughly understand the properties of molecular compounds and materials and to be able to prepare novel compounds with p- dicted and desirable properties. The basis for progress is to fully appreciate and fundamentally understand the intimate relation between structure and function. The thermodynamic properties (stability, selectivity, redox potential), reactivities (bond breaking and formation, catalysis, electron transfer) and electronic properties (spectroscopy, magnetism) depend on the structure of a compound. Nevertheless, the discovery of novel molecular compounds and materials with exciting prop- ties is often and to a large extent based on serendipity. For compounds with novel and exciting properties, a thorough analysis of experimental data - state-of-the-art spectroscopy, magnetism, thermodynamic properties and/or detailed mechanistic information - combined with sophisticated electronic structure calculations is p- formed to interpret the results and fully understand the structure, properties and their interrelation. From these analyses, new models and theories may emerge, and this has led to the development of ef cient models for the design and interpre- tion of new materials and important new experiments. The chapters in this book therefore describe various fundamental aspects of structures, dynamics and physics of molecules and materials. The approaches, data and models discussed include new theoretical developments, computational studies and experimental work from molecular chemistry to biology and materials science.

Autoren/Hrsg.

Comba, Peter

Inhaltsverzeichnis

1;Structure and Function;1
1.1;Jan C.A. Boeyens – A Holistic Scientist;4
1.1.1;Root;8
1.2;Preface;10
1.3;Contents;12
1.4;Contributors;14
1.5;1 Molecular Associations Determined from Free Energy Calculations;16
1.5.1;1.1 Introduction;16
1.5.2;1.2 Statistical Mechanics of Molecular Association;18
1.5.3;1.3 Condensed Phase Molecular Dynamics Simulations;20
1.5.4;1.4 Free Energies from Adaptive Reaction Coordinate Forces;20
1.5.5;1.5 Associative Solvents;22
1.5.5.1;1.5.1 Water;23
1.5.5.2;1.5.2 Methanol;25
1.5.6;1.6 Ions in Associative Solvents;29
1.5.7;1.7 Reactions in Associative Solvents;32
1.5.8;References;34
1.6;2 Molecular Modelling for Systems Containing Transition Metal Centres;36
1.6.1;2.1 Introduction;36
1.6.2;2.2 Molecular Mechanics;39
1.6.2.1;2.2.1 Shortcomings of MM for TM Systems;41
1.6.2.2;2.2.2 Ligand Field Molecular Mechanics;42
1.6.3;2.3 Applications of LFMM;44
1.6.3.1;2.3.1 Simple Coordination Complexes: Cu(II) Amines;45
1.6.3.2;2.3.2 [MCl4]2- Complexes;46
1.6.3.3;2.3.3 Cu(II) Bis-oxazoline Complexes;48
1.6.3.4;2.3.4 Jahn–Teller Effects in Six-Coordinate Cu(II) Complexes;49
1.6.3.4.1;2.3.4.1 The Mexican Hat Potential Energy Surface;49
1.6.3.4.2;2.3.4.2 The Warped Mexican Hat;50
1.6.3.4.3;2.3.4.3 Theoretical Treatment of the Jahn–Teller Effect in Cu(II) Species;52
1.6.3.4.4;2.3.4.4 Barriers Between Successive Elongations;54
1.6.3.4.5;2.3.4.5 Truly Compressed Complexes;56
1.6.3.5;2.3.5 Spin-State Effects;56
1.6.3.6;2.3.6 Type 1 Copper Enzymes;57
1.6.3.7;2.3.7 Dinuclear Copper Centres;60
1.6.4;2.4 Conclusions;64
1.6.5;References;65
1.7;3 Magnetic Anisotropy in Cyanide Complexes of First Row Transition Metal Ions;67
1.7.1;3.1 Introduction;67
1.7.2;3.2 Jahn–Teller Coupling Versus Spin-Orbit Coupling in the Ground State of [Fe(CN)6]3-;69
1.7.3;3.3 Modeling of the Magnetic Anisotropy in Ni-NC-FeIII Pairs;77
1.7.3.1;3.3.1 Theory;77
1.7.3.2;3.3.2 Regular (C4v) Versus Distorted (Cs) [Fe(CN)63-] and Its Influence on the Magnetic Anisotropy of the Fe-Ni Pair;79
1.7.3.3;3.3.3 Effect of Combined Spin-Orbit Coupling and Strain at the FeIII Subunit;82
1.7.4;3.4 Magnetic Anisotropy in Linear Trinuclear Cu-NC-Fe-CN-Cu complexes;85
1.7.5;3.5 Computation of the Magnetic Anisotropy in Oligonuclear Complexes with Nearly Degenerate Ground States;88
1.7.5.1;3.5.1 Theory;88
1.7.5.2;3.5.2 Applications to Various Cyanide-Bridged MnFem Complexes (M = CuII, NiIII);93
1.7.6;3.6 Conclusions;96
1.7.7;References;97
1.8;4 Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations;100
1.8.1;4.1 Introduction;100
1.8.2;4.2 The MM Method;101
1.8.3;4.3 Handling Metal Ions;102
1.8.4;4.4 Extending the Force Field;103
1.8.5;4.5 Applications of the Corrin Force Field: Structure and Function of B12 Derivatives;106
1.8.6;4.6 Applications of the Corrin Force Field: The Structure of the Cobalt Corrins in Solution;107
1.8.7;4.7 Applications of the Porphyrin Force Field: The Solution Structures of the Complexes Formed Between Ferriprotoporphyrin IX and Arylmethanol Antimalarials;109
1.8.8;References;118
1.9;5 Artificial Photosynthetic Reaction Center;123
1.9.1;5.1 Introduction;123
1.9.2;5.2 Electron Donor–Acceptor Ensembles with Covalent Bonding;125
1.9.2.1;5.2.1 Multi-step Electron Transfer;125
1.9.2.2;5.2.2 Nanocarbon Materials Linked with Multiple Porphyrins;128
1.9.2.3;5.2.3 Simple Electron Donor–Acceptor Dyads with Long CS Lifetimes;130
1.9.3;5.3 Electron Donor–Acceptor Ensembles with Non-covalent Bonding;133
1.9.3.1;5.3.1 – Interaction;133
1.9.3.2;5.3.2 Porphyrin Nanochannels;136
1.9.3.3;5.3.3 Supramolecular Electron Donor–Acceptor Complexes of Phthalocyanines;139
1.9.4;5.4 Summary;142
1.9.5;References;142
1.10;6 Multifrequency EPR Spectroscopy: A Toolkitfor the Characterization of Mono- and Di-nuclear MetalIon Centers in Complex Biological Systems;145
1.10.1;6.1 Introduction;145
1.10.2;6.2 Multifrequency EPR Toolkit;146
1.10.2.1;6.2.1 g-Value Resolution and Orientation Selection;148
1.10.2.2;6.2.2 Magnitude of the Microwave Frequency;150
1.10.2.3;6.2.3 State Mixing;150
1.10.2.4;6.2.4 Angular Anomalies;150
1.10.2.5;6.2.5 Distribution of Spin Hamiltonian Parameters;151
1.10.2.6;6.2.6 Numerical Differentiation and Fourier Filtering;153
1.10.2.7;6.2.7 High Resolution EPR Techniques;154
1.10.2.8;6.2.8 Geometric and Electronic Structure Determination;154
1.10.2.8.1;6.2.8.1 Computer Simulation;155
1.10.2.8.2;6.2.8.2 Computational Chemistry;156
1.10.2.8.3;6.2.8.3 Molecular Sophe – An Integrated Approach;157
1.10.3;6.3 Application of Multifrequency EPR to the Structural Characterization of Complex Biological Systems;161
1.10.3.1;6.3.1 EPR Studies of MoV Complexes and Their Relevance to Mononuclear Molybdenum Enzymes;161
1.10.3.2;6.3.2 EPR Studies of Copper(II) Cyclic Peptide Complexes;168
1.10.3.2.1;6.3.2.1 Copper(II) Complexes with Marine Cyclic Peptides;168
1.10.3.2.2;6.3.2.2 Copper(II) Complexes with Westiellamide and Synthetic Analogues;172
1.10.3.3;6.3.3 Purple Acid Phosphatases;176
1.10.4;6.4 Conclusions;183
1.10.5;References;183
1.11;7 On Stacking;188
1.11.1;7.1 Introduction;188
1.11.2;7.2 Intra- and Inter-Strand Base Stacking;190
1.11.3;7.3 Parallel and Perpendicular Intercalating Agents;191
1.11.3.1;7.3.1 Cofacial Versus Edge-On Stacking;193
1.11.4;7.4 Base-Backbone Inclination and Sugar-Base Stacking;194
1.11.4.1;7.4.1 Amino Acid-Nucleobase Stacking;196
1.11.5;7.5 Stacked Dipoles: The C-Rich i-Motif;197
1.11.6;7.6 Cation– Interactions;199
1.11.7;7.7 Lone Pair– and Anion– Interactions;200
1.11.8;7.8 Unique Properties of the TATA-Motif Major Groove;202
1.11.9;7.9 Conclusion;204
1.11.10;References;204
1.12;8 Structurally Complex Intermetallic Thermoelectrics – Examples from Modulated Rock-Salt structuresand the System Zn-Sb;208
1.12.1;8.1 Introduction;208
1.12.1.1;8.1.1 Incommensurate Structure Analysis;210
1.12.1.2;8.1.2 Modulated Rock-Salt Like Compounds;212
1.12.1.3;8.1.3 The Remarkable System Sb-Zn;217
1.12.2;8.2 Conclusion;226
1.12.3;References;227
1.13;9 Solid State Transformations in Crystalline Salts;229
1.13.1;9.1 Introduction;229
1.13.2;9.2 Solid State Transformation in Some Metal-Organic Salts;230
1.13.3;9.3 Sublimation and Dissociation in Simple Salts of an Organic Compound;234
1.13.3.1;9.3.1 Crystal Structures and Isostructurality;234
1.13.3.2;9.3.2 Thermal Analysis;235
1.13.3.3;9.3.3 Comparison of 3H+.Cl- and 3H+.NO3-;240
1.13.4;References;242
1.14;10 Influence of Size and Shape on Inclusion Propertiesof Transition Metal-Based Wheel-and-Axle Diols;244
1.14.1;10.1 Shape and Packing;244
1.14.2;10.2 Metallo-organic Frameworks: Transition Metal-Based Wheel-and-Axle Diols;246
1.14.2.1;10.2.1 Structural Analysis of Trans-palladium(II) Complexes of Triarylcarbinol Ligands: A Class of Transition Metal-Based Wheel-and-Axle Diol;249
1.14.2.1.1;10.2.1.1 Identification of the ``Bistable Framework';249
1.14.2.1.2;10.2.1.2 Inclusion Sites and Guest Migration;251
1.14.2.2;10.2.2 Robustness of the Pattern with Increasing Shape Complexity;253
1.14.2.3;10.2.3 Validation of the Wheel-and-Axle Shape;259
1.14.3;References;261
1.15;Index;263