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E-raamat: Understanding Intermolecular Interactions in the Solid State: Approaches and Techniques

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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 pairpi, and pipi 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.
Chapter 1 Integrating Computed Crystal Energy Landscapes in Crystal Form Discovery and Characterisation
1(31)
S. Mohamed
1.1 Introduction
1(2)
1.2 Computational Methodology for Predicting Molecular Crystal Structures
3(8)
1.2.1 Overview
3(3)
1.2.2 Searching the Conformational Phase Space and Estimating the Total Crystal Lattice Energy
6(3)
1.2.3 Search Methods for Finding Hypothetical Crystal Structures
9(2)
1.3 Applications of Computed Crystal Energy Landscapes
11(10)
1.3.1 Polymorph Screening and Characterisation
11(3)
1.3.2 Multicomponent Crystal Form Discovery
14(4)
1.3.3 Structure Solution from Powder X-ray Diffraction Data
18(3)
1.4 CCDC Blind Tests: Assessing Progress in Crystal Structure Prediction Methods (1999--2016)
21(5)
1.5 Conclusion
26(6)
Acknowledgements
26(1)
References
26(6)
Chapter 2 High Pressure Crystallography: Elucidating the Role of Intermolecular Interactions in Crystals of Organic and Coordination Compounds
32(66)
E. V. Boldyreva
2.1 Introduction
32(3)
2.2 High-pressure Experiments
35(3)
2.3 Continuous Anisotropic Compression
38(6)
2.4 Polymorphic Transitions
44(12)
2.5 Crystallization
56(3)
2.6 Multi-component Crystals
59(5)
2.7 Pressure-induced Reactions and Effect of Pressure on Photo- and Thermo-chemical Transformations
64(4)
2.8 Conclusions
68(30)
Acknowledgements
69(1)
References
70(28)
Chapter 3 Intermolecular Interactions in In situ Cryocrystallized Compounds
98(32)
Dhananjay Dey
Susanta K. Nayak
Deepak Chopra
3.1 Introduction
98(1)
3.2 Methodology, Equipment and Instrumentation
99(4)
3.2.1 OHCD (Optical Heating and Crystallization Device)
101(2)
3.2.2 Problems and Concerns During the OHCD Experiment
103(1)
3.3 Applications of In Cryocrystallization
103(22)
3.3.1 Investigation of Strong and Weak Hydrogen Bonds (HBs) in In situ Cryocrystallized Liquids
104(2)
3.3.2 In situ Cryocrystallization Study of Halogen Bonding
106(5)
3.3.3 Investigation of Other Weak Interactions in In situ Cryocrystallized Liquids
111(6)
3.3.4 Computational Analysis
117(3)
3.3.5 In situ Cryocrystallization Study in Fluorinated Benzoyl Chlorides
120(4)
3.3.6 In situ Cryocrystallization in Organometallic Liquids
124(1)
3.4 Overview
125(5)
Acknowledgements
126(1)
References
126(4)
Chapter 4 Experimental Electron Density Studies of Inorganic Solids
130(29)
Swastik Mondal
4.1 Introduction
130(1)
4.2 Methods for Electron Density Studies
131(4)
4.3 Electron Density Studies of Inorganic Crystals
135(7)
4.3.1 Experimental Strategies and Challenges
135(2)
4.3.2 Challenges Related to Aspherical Modelling of Electron Densities in Inorganic Solids
137(2)
4.3.3 Analysis of Electron Densities in Inorganic Solids
139(3)
4.4 Few Reported Case Studies
142(11)
4.4.1 Electron Densities in Elemental Boron Allotropes
142(3)
4.4.2 Electron Density in Pyrope (Mg3Al2Si3012)
145(2)
4.4.3 Electron Densities in Pyrite and Marcasite Polymorphs of FeS2
147(3)
4.4.4 Electron Density in Caesium Uranyl Chloride (Cs2UO2Cl4)
150(3)
4.5 Conclusion
153(6)
Acknowledgements
155(1)
References
155(4)
Chapter 5 Experimental Charge Density Analysis in Organic Solids
159(30)
Venkatesha R. Hathwar
5.1 Introduction
159(2)
5.2 Experimental Requirements
161(2)
5.2.1 Good Quality Single Crystals and High-resolution X-Ray Data
161(1)
5.2.2 Multipolar Modeling of CD Data
162(1)
5.3 Evaluation of ED Features from the Experimental CD Model
163(5)
5.3.1 Quantum Theory of Atoms in Molecules (QTAIM)
163(2)
5.3.2 Source Function (SF) Analysis
165(1)
5.3.3 Non-covalent Interactions (NCIs) Descriptor
165(2)
5.3.4 Lattice and Interaction Energies from the CD Model
167(1)
5.3.5 Molecular Electrostatic Potentials
168(1)
5.4 Applications
168(15)
5.4.1 Evaluation of Intra- and Intermolecular Interactions
168(3)
5.4.2 Chemical Reactivity in Organic Solids
171(2)
5.4.3 Polymorphs and Cocrystals
173(3)
5.4.4 Halogen Bonding (XB) and Other a-Hole Bonding
176(2)
5.4.5 Validating the Concept of Charge Shift Bonding (CSB)
178(1)
5.4.6 Phase Transitions in Organic Solids
179(1)
5.4.7 CD Studies Under High Pressure
180(1)
5.4.8 CD Databases
181(2)
5.5 Conclusions
183(6)
Acknowledgements
183(1)
References
183(6)
Chapter 6 Charge Density Studies and Topological Analysis of Hydrogen Bonds in Proteins
189(22)
Suman Kumar Mandal
Parthapratim Munshi
6.1 Introduction
189(4)
6.2 Protein Charge Density Analysis
193(3)
6.2.1 Approach
193(1)
6.2.2 Basic Requirements
193(1)
6.2.3 Methodologies and Tools
194(1)
6.2.4 Multipolar Refinement
195(1)
6.3 Six Selected ECDA Studies
196(3)
6.4 Use of Neutron Diffraction Data
199(1)
6.5 Topological Analysis of Hydrogen Bonding
200(5)
6.5.1 Computation of Electrostatic Interaction and Dissociation Energies
200(1)
6.5.2 The Case of Human Aldose Reductase (hAR)
201(4)
6.6 Final Remarks
205(6)
Acknowledgements
207(1)
References
207(4)
Chapter 7 Towards a Generalized Database of Atomic Polarizabilities
211(32)
Michelle Ernst
Leonardo H. R. Dos Santos
Anna Krawczuk
Piero Macchi
7.1 Introduction
211(4)
7.2 Theoretical Background
215(5)
7.2.1 Earlier Atomic Polarizability Databases and the Need for a New One
215(3)
7.2.2 Distributed Atomic Polarizabilities
218(2)
7.3 Constructing the Database
220(7)
7.3.1 Computational Details
220(1)
7.3.2 The Local Coordinate System
221(2)
7.3.3 Multivariate Data Analysis and Clustering
223(4)
7.3.4 Recognizing a Functional Group
227(1)
7.4 Results
227(12)
7.4.1 Clustering the CH2 Polarizabilities
227(2)
7.4.2 Clustering all Functional Groups
229(1)
7.4.3 Using the Database to Compute Polarizabilities
229(10)
7.5 Conclusions
239(4)
Acknowledgements
240(1)
References
240(3)
Chapter 8 Solid-state NMR in the Study of Intermolecular Interactions
243(42)
F. Rossi
P. Cerreia Vioglio
M. R. Chierotti
R. Gobetto
8.1 Introduction
243(1)
8.2 Essential Techniques and Parameters in Solid-state NMR
244(6)
8.2.1 Magic-angle Spinning, High-power Proton Decoupling and Cross Polarization
244(2)
8.2.2 Chemical Shift
246(2)
8.2.3 Dipolar Interaction
248(1)
8.2.4 Quadrupolar Interaction
249(1)
8.3 SSNMR and Hydrogen Bond
250(18)
8.3.1 Hydrogen Bond and Chemical Shift/Chemical Shift Anisotropy
251(8)
8.3.2 Hydrogen Bond and Dipolar Interaction
259(8)
8.3.3 Hydrogen Bond and Quadrupolar Interaction
267(1)
8.4 SSNMR and Halogen Bonds
268(7)
8.5 SSNMR and π--π Stacking
275(1)
8.6 Conclusion and Outlook
276(9)
References
277(8)
Chapter 9 Quantitative Analysis of Weak Non-covalent σ-Hole and π-Hole Interactions
285(49)
Saikat Kumar Seth
Antonio Bauza
Antonio Frontera
9.1 Introduction and Historical Perspective
285(3)
9.2 Nature of σ-Hole and Π-Hole Interactions
288(5)
9.2.1 σ-Hole Interactions
288(2)
9.2.2 π-Hole Interactions
290(3)
9.3 Hirshfeld Surface Technique
293(5)
9.3.1 Crystal Engineering and Models to Describe Crystal Packing
293(1)
9.3.2 Theoretical Background for Hirshfeld Surface Calculation
294(1)
9.3.3 Various Surfaces and Associated Fingerprint Plots
295(3)
9.4 Computational Methods
298(1)
9.5 Exploration of a-Hole Interactions
298(17)
9.5.1 Group VII Interactions (Halogen Bonding)
298(5)
9.5.2 Group VI Interactions (Chalcogen Bonding)
303(4)
9.5.3 Group V Interactions (Pnictogen Bonding)
307(4)
9.5.4 Group IV Interactions (Tetrel Bonding)
311(4)
9.6 Exploration of π-Hole Interactions
315(6)
9.6.1 Group III Interactions (Triel Bonding)
315(3)
9.6.2 Group V Interactions (Pnicogen Bonding)
318(3)
9.7 Conclusions
321(13)
Acknowledgements
322(1)
References
322(12)
Subject Index 334