Understanding Intermolecular Interactions in the Solid State: Approaches and Techniques / Edition 1

by Deepak Chopra

Overview

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.

Product Details

ISBN-13:	9781788010795
Publisher:	RSC
Publication date:	09/04/2018
Series:	Monographs in Supramolecular Chemistry , #26
Pages:	358
Product dimensions:	6.15(w) x 9.20(h) x (d)

About the Author

Hometown:

La Jolla, California

Date of Birth:

October 22, 1946

Place of Birth:

New Delhi, India

Education:

All India Institute of Medical Sciences

Table of Contents

Chapter 1 Integrating Computed Crystal Energy Landscapes in Crystal Form Discovery and Characterisation S. Mohamed 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 E. V. Boldyreva 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 Dhananjay Dey Susanta K. Nayak Deepak Chopra 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

3.3.5 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 Swastik Mondal 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 Venkatesha R. Hathwar 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 a-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 Suman Kumar Mandal Parthapratim Munshi 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 Michelle Ernst Leonardo H. R. Dos Santos Anna Krawczuk Piero Macchi 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 F. Rossi P. Cerreia Vioglio M. R. Chierotti R. Gobetto 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 Saikat Kumar Seth Antonio Bauzá Antonio Frontera 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