Additional Information
Book Details
Abstract
Technological and computational advances in the past decade have meant a vast increase in the study of crystalline matter in both organic, inorganic and organometallic molecules. These studies revealed information about the conformation of molecules and their coordination geometry as well as the role of intermolecular interactions in molecular packing especially in the presence of different intermolecular interactions in solids. This resulting knowledge plays a significant role in the design of improved medicinal, mechanical, and electronic properties of single and multi-component solids in their crystalline state.
Understanding Intermolecular Interactions in the Solid State explores the different techniques used to investigate the interactions, including hydrogen and halogen bonds, lone pair–pi, and pi–pi interactions, and their role in crystal formation.
From experimental to computational approaches, the book covers the latest techniques in crystallography, ranging from high pressure and in situ crystallization to crystal structure prediction and charge density analysis. Thus this book provides a strong introductory platform to those new to this field and an overview for those already working in the area. A useful resource for higher level undergraduates, postgraduates and researchers across crystal engineering, crystallography, physical chemistry, solid-state chemistry, supramolecular chemistry and materials science.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover | Cover | ||
| Understanding Intermolecular Interactions in the Solid State: Approaches and Techniques | i | ||
| Foreword | v | ||
| Preface | vii | ||
| Acknowledgements | ix | ||
| Dedication | xi | ||
| Contents | xiii | ||
| Chapter 1 - Integrating Computed Crystal Energy Landscapes in Crystal Form Discovery and Characterisation | 1 | ||
| 1.1 Introduction | 1 | ||
| 1.2 Computational Methodology for Predicting Molecular Crystal Structures | 3 | ||
| 1.2.1 Overview | 3 | ||
| 1.2.2 Searching the Conformational Phase Space and Estimating the Total Crystal Lattice Energy | 6 | ||
| 1.2.3 Search Methods for Finding Hypothetical Crystal Structures | 9 | ||
| 1.3 Applications of Computed Crystal Energy Landscapes | 11 | ||
| 1.3.1 Polymorph Screening and Characterisation | 11 | ||
| 1.3.2 Multicomponent Crystal Form Discovery | 14 | ||
| 1.3.3 Structure Solution from Powder X-ray Diffraction Data | 18 | ||
| 1.4 CCDC Blind Tests: Assessing Progress in Crystal Structure Prediction Methods (1999–2016) | 21 | ||
| 1.5 Conclusion | 26 | ||
| Acknowledgements | 26 | ||
| References | 26 | ||
| Chapter 2 - High Pressure Crystallography: Elucidating the Role of Intermolecular Interactions in Crystals of Organic and Coordination Compounds | 32 | ||
| 2.1 Introduction | 32 | ||
| 2.2 High-pressure Experiments | 35 | ||
| 2.3 Continuous Anisotropic Compression | 38 | ||
| 2.4 Polymorphic Transitions | 44 | ||
| 2.5 Crystallization | 56 | ||
| 2.6 Multi-component Crystals | 59 | ||
| 2.7 Pressure-induced Reactions and Effect of Pressure on Photo- and Thermo-chemical Transformations | 64 | ||
| 2.8 Conclusions | 68 | ||
| Acknowledgements | 69 | ||
| References | 70 | ||
| Chapter 3 - Intermolecular Interactions in In situ Cryocrystallized Compounds | 98 | ||
| 3.1 Introduction | 98 | ||
| 3.2 Methodology, Equipment and Instrumentation | 99 | ||
| 3.2.1 OHCD (Optical Heating and Crystallization Device) | 101 | ||
| 3.2.2 Problems and Concerns During the OHCD Experiment | 103 | ||
| 3.3 Applications of In situ Cryocrystallization | 103 | ||
| 3.3.1 Investigation of Strong and Weak Hydrogen Bonds (HBs) in In situ Cryocrystallized Liquids | 104 | ||
| 3.3.2 In situ Cryocrystallization Study of Halogen Bonding | 106 | ||
| 3.3.3 Investigation of Other Weak Interactions in In situ Cryocrystallized Liquids | 111 | ||
| 3.3.4 Computational Analysis | 117 | ||
| 3.3.4.1 Determination of Intermolecular Interaction Energy Using the PIXEL Method | 118 | ||
| 3.3.4.2 Topological Analysis for Intermolecular Interactions Using QTAIM | 119 | ||
| 3.3.4.3 Non-covalent Interaction (NCI) Index and RDG Isosurface | 119 | ||
| 3.3.4.4 Analysis of Distributed Atomic Polarizability Tensor Using Polaber | 119 | ||
| 3.3.5 In situ Cryocrystallization Study in Fluorinated Benzoyl Chlorides | 120 | ||
| 3.3.6 In situ Cryocrystallization in Organometallic Liquids | 124 | ||
| 3.4 Overview | 125 | ||
| Acknowledgements | 126 | ||
| References | 126 | ||
| Chapter 4 - Experimental Electron Density Studies of Inorganic Solids | 130 | ||
| 4.1 Introduction | 130 | ||
| 4.2 Methods for Electron Density Studies | 131 | ||
| 4.3 Electron Density Studies of Inorganic Crystals | 135 | ||
| 4.3.1 Experimental Strategies and Challenges | 135 | ||
| 4.3.2 Challenges Related to Aspherical Modelling of Electron Densities in Inorganic Solids | 137 | ||
| 4.3.3 Analysis of Electron Densities in Inorganic Solids | 139 | ||
| 4.4 Few Reported Case Studies | 142 | ||
| 4.4.1 Electron Densities in Elemental Boron Allotropes | 142 | ||
| 4.4.2 Electron Density in Pyrope (Mg3Al2Si3O12) | 145 | ||
| 4.4.3 Electron Densities in Pyrite and Marcasite Polymorphs of FeS2 | 147 | ||
| 4.4.4 Electron Density in Caesium Uranyl Chloride (Cs2UO2Cl4) | 150 | ||
| 4.5 Conclusion | 153 | ||
| Acknowledgements | 155 | ||
| References | 155 | ||
| Chapter 5 - Experimental Charge Density Analysis in Organic Solids | 159 | ||
| 5.1 Introduction | 159 | ||
| 5.2 Experimental Requirements | 161 | ||
| 5.2.1 Good Quality Single Crystals and High-resolution X-Ray Data | 161 | ||
| 5.2.2 Multipolar Modeling of CD Data | 162 | ||
| 5.3 Evaluation of ED Features from the Experimental CD Model | 163 | ||
| 5.3.1 Quantum Theory of Atoms in Molecules (QTAIM) | 163 | ||
| 5.3.2 Source Function (SF) Analysis | 165 | ||
| 5.3.3 Non-covalent Interactions (NCIs) Descriptor | 165 | ||
| 5.3.4 Lattice and Interaction Energies from the CD Model | 167 | ||
| 5.3.5 Molecular Electrostatic Potentials | 168 | ||
| 5.4 Applications | 168 | ||
| 5.4.1 Evaluation of Intra- and Intermolecular Interactions | 168 | ||
| 5.4.2 Chemical Reactivity in Organic Solids | 171 | ||
| 5.4.3 Polymorphs and Cocrystals | 173 | ||
| 5.4.4 Halogen Bonding (XB) and Other σ-Hole Bonding | 176 | ||
| 5.4.5 Validating the Concept of Charge Shift Bonding (CSB) | 178 | ||
| 5.4.6 Phase Transitions in Organic Solids | 179 | ||
| 5.4.7 CD Studies Under High Pressure | 180 | ||
| 5.4.8 CD Databases | 181 | ||
| 5.5 Conclusions | 183 | ||
| Acknowledgements | 183 | ||
| References | 183 | ||
| Chapter 6 - Charge Density Studies and Topological Analysis of Hydrogen Bonds in Proteins | 189 | ||
| 6.1 Introduction | 189 | ||
| 6.2 Protein Charge Density Analysis | 193 | ||
| 6.2.1 Approach | 193 | ||
| 6.2.2 Basic Requirements | 193 | ||
| 6.2.3 Methodologies and Tools | 194 | ||
| 6.2.4 Multipolar Refinement | 195 | ||
| 6.3 Six Selected ECDA Studies | 196 | ||
| 6.4 Use of Neutron Diffraction Data | 199 | ||
| 6.5 Topological Analysis of Hydrogen Bonding | 200 | ||
| 6.5.1 Computation of Electrostatic Interaction and Dissociation Energies | 200 | ||
| 6.5.2 The Case of Human Aldose Reductase (hAR) | 201 | ||
| 6.6 Final Remarks | 205 | ||
| Acknowledgements | 207 | ||
| References | 207 | ||
| Chapter 7 - Towards a Generalized Database of Atomic Polarizabilities | 211 | ||
| 7.1 Introduction | 211 | ||
| 7.2 Theoretical Background | 215 | ||
| 7.2.1 Earlier Atomic Polarizability Databases and the Need for a New One | 215 | ||
| 7.2.2 Distributed Atomic Polarizabilities | 218 | ||
| 7.3 Constructing the Database | 220 | ||
| 7.3.1 Computational Details | 220 | ||
| 7.3.2 The Local Coordinate System | 221 | ||
| 7.3.3 Multivariate Data Analysis and Clustering | 223 | ||
| 7.3.4 Recognizing a Functional Group | 227 | ||
| 7.4 Results | 227 | ||
| 7.4.1 Clustering the CH2 Polarizabilities | 227 | ||
| 7.4.2 Clustering all Functional Groups | 229 | ||
| 7.4.3 Using the Database to Compute Polarizabilities | 229 | ||
| 7.5 Conclusions | 239 | ||
| Acknowledgements | 240 | ||
| References | 240 | ||
| Chapter 8 - Solid-state NMR in the Study of Intermolecular Interactions | 243 | ||
| 8.1 Introduction | 243 | ||
| 8.2 Essential Techniques and Parameters in Solid-state NMR | 244 | ||
| 8.2.1 Magic-angle Spinning, High-power Proton Decoupling and Cross Polarization | 244 | ||
| 8.2.2 Chemical Shift | 246 | ||
| 8.2.3 Dipolar Interaction | 248 | ||
| 8.2.4 Quadrupolar Interaction | 249 | ||
| 8.3 SSNMR and Hydrogen Bond | 250 | ||
| 8.3.1 Hydrogen Bond and Chemical Shift/Chemical Shift Anisotropy | 251 | ||
| 8.3.2 Hydrogen Bond and Dipolar Interaction | 259 | ||
| 8.3.3 Hydrogen Bond and Quadrupolar Interaction | 267 | ||
| 8.4 SSNMR and Halogen Bonds | 268 | ||
| 8.5 SSNMR and π–π Stacking | 275 | ||
| 8.6 Conclusion and Outlook | 276 | ||
| References | 277 | ||
| Chapter 9 - Quantitative Analysis of Weak Non-covalent σ-Hole and π-Hole Interactions | 285 | ||
| 9.1 Introduction and Historical Perspective | 285 | ||
| 9.2 Nature of σ-Hole and Π-Hole Interactions | 288 | ||
| 9.2.1 σ-Hole Interactions | 288 | ||
| 9.2.2 π-Hole Interactions | 290 | ||
| 9.3 Hirshfeld Surface Technique | 293 | ||
| 9.3.1 Crystal Engineering and Models to Describe Crystal Packing | 293 | ||
| 9.3.2 Theoretical Background for Hirshfeld Surface Calculation | 294 | ||
| 9.3.3 Various Surfaces and Associated Fingerprint Plots | 295 | ||
| 9.4 Computational Methods | 298 | ||
| 9.5 Exploration of σ-Hole Interactions | 298 | ||
| 9.5.1 Group VII Interactions (Halogen Bonding) | 298 | ||
| 9.5.2 Group VI Interactions (Chalcogen Bonding) | 303 | ||
| 9.5.3 Group V Interactions (Pnictogen Bonding) | 307 | ||
| 9.5.4 Group IV Interactions (Tetrel Bonding) | 311 | ||
| 9.6 Exploration of π-Hole Interactions | 315 | ||
| 9.6.1 Group III Interactions (Triel Bonding) | 315 | ||
| 9.6.2 Group V Interactions (Pnicogen Bonding) | 318 | ||
| 9.7 Conclusions | 321 | ||
| Acknowledgements | 322 | ||
| References | 322 | ||
| Subject Index | 334 |