An insightful analysis of confined chemical systems for theoretical and experimental scientists
Chemical Reactivity in Confined Systems: Theory and Applications presents a theoretical basis for the molecular phenomena observed in confined spaces. The book highlights state-of-the-art theoretical and computational approaches, with a focus on obtaining physically relevant clarification of the subject to enable the reader to build an appreciation of underlying chemical principles.
The book includes real-world examples of confined systems that highlight how the reactivity of atoms and molecules change upon encapsulation. Chapters include discussions on recent developments related to several host-guest systems, including cucurbit[n]uril, ExBox+4, clathrate hydrates, octa acid cavitand, metal organic frameworks (MOFs), covalent organic frameworks (COFs), zeolites, fullerenes, and carbon nanotubes. Readers will learn how to carry out new calculations to understand the physicochemical behavior of confined quantum systems.
Topics covered include:
- A thorough introduction to global reactivity descriptors, including electronegativity, hardness, and electrophilicity
- An exploration of the Fukui function, as well as dual descriptors, higher order derivatives, and reactivity through information theory
- A practical discussion of spin dependent reactivity and temperature dependent reactivity
- Concise treatments of population analysis, reaction force, electron localization functions, and the solvent effect on reactivity
Perfect for academic researchers and graduate students in theoretical and computational chemistry and confined chemical systems, Chemical Reactivity in Confined Systems: Theory and Applications will also earn a place in the libraries of professionals working in the areas of catalysis, supramolecular chemistry, and porous materials.
Table of Contents
Preface xiii
1 Effect of Confinement on the Translation-Rotation Motion of Molecules: The inelastic neutron scattering selection rule 1
1.1 Introduction 1
1.2 Diatomics in C60: entanglement, TR coupling, symmetry, basis representation, and energy level structure 4
1.2.1 Entanglement Induced Selection Rules 4
1.2.2 H@C60 5
1.2.3 H2@C60 7
1.2.3.1 Symmetry 7
1.2.3.2 Spherical basis and eigenstates 7
1.2.3.3 Energy level ordering with respect to 𝜆 8
1.2.4 HX@C60 10
1.3 INS selection rule for spherical (Kh) symmetry 11
1.3.1 Inelastic Neutron Scattering 11
1.3.2 Group Theory Derivation of the INS Selection Rule 12
1.3.2.1 Group-theory-based INS selection rule for cylindrical (C∞𝑣) environments 12
1.3.2.2 Group-theory-based INS selection rule for spherical (Kh) environments 12
1.3.3 Specific Systems, Quantum Numbers, and Basis Sets 13
1.3.3.1 H@sphere 14
1.3.3.2 H2@sphere 14
1.3.3.3 HX@sphere 15
1.3.4 Beyond Diatomic Molecules 15
1.3.4.1 H2O@sphere 15
1.3.4.2 CH4@sphere 17
1.3.4.3 Any guest molecule in any spherical (Kh) environment 18
1.4 INS selection rules for non-spherical structures 18
1.5 Summary and conclusions 20
Acknowledgments 22
References 22
2 Pressure-induced phase transitions 25
2.1 Pressure, a property of all flavours, and its importance for the Universe and life 25
2.2 Pressure: isotropic and anisotropic, positive and negative 26
2.3 Changes of the state of matter 27
2.4 Compression of solids 30
2.4.1 Isotropic or anisotropic compressibility 30
2.4.2 Negative linear compressibility 30
2.4.3 Negative area compressibility 31
2.4.4 Anomalous compressibility changes at high pressure 31
2.5 Structural solid-solid transitions 32
2.5.1 Structural phase transitions accompanied by volume collapse 32
2.5.2 Effects of volume collapse on free energy 33
2.5.3 Structure-influencing factors at compression 34
2.5.4 Changes in the nature of chemical bonding upon compression and upon phase transitions 35
2.6 Selected classes of magnetic and electronic transitions 36
2.6.1 High Spin-Low Spin transitions 36
2.6.2 Electronic com- vs disproportionation 37
2.6.3 Metal-to-metal charge transfer 37
2.6.4 Neutral-to-Ionic transitions 37
2.6.5 Metallization of insulators (and resisting it) 38
2.6.6 Turning metals into insulators 39
2.6.7 Superconductivity of elements and compounds 39
2.6.8 Topological phase transitions 41
2.7 Modelling and predicting HP phase transitions 41
Acknowledgements 42
References 42
3 Conceptual DFT and Confinement 49
3.1 Introduction and Reading Guide 49
3.2 Conceptual DFT 50
3.3 Confinement and Conceptual DFT 52
3.3.1 Atoms: global descriptors 52
3.3.2 Molecules: global and local descriptors 56
3.3.2.1 Electron Affinities 57
3.3.2.2 Hardness and electronic Fukui function 59
3.3.2.3 Inclusion of pressure in the E = E [N,v] functional 63
3.4 Conclusions 65
Acknowledgements 65
References 66
4 Electronic structure of systems confined by several spatial restrictions 69
4.1 Introduction 69
4.2 Confinement imposed by impenetrable walls 69
4.3 Confinement imposed by soft walls 72
4.4 Beyond confinement models 74
4.5 Conclusions 77
References 77
5 Unveiling the Mysterious Mechanisms of Chemical Reactions 81
5.1 Introduction 81
5.1.1 Context 81
5.1.2 Ideas and methods 82
5.1.3 Application 82
5.2 Energy and reaction force 83
5.2.1 The reaction force analysis (RFA) 83
5.2.2 RFA-based energy decomposition 84
5.2.3 Marcus potential energy function 85
5.2.4 Marcus RFA 86
5.3 Electronic activity along a reaction coordinate 87
5.3.1 Chemical potential, hardness, and electrophilicity index 87
5.3.2 The reaction electronic flux (REF) 88
5.3.2.1 Physical decomposition of REF 88
5.3.2.2 Chemical decomposition of REF 89
5.4 An application: the formation of aminoacetonitrile 90
5.4.1 Energetic analysis 91
5.4.2 Reaction mechanisms 91
5.5 Conclusions 94
Acknowledgments 95
References 95
6 A Perspective on the So-called Dual Descriptor 99
6.1 Introduction: conceptual DFT 99
6.2 The Dual Descriptor: fundamental aspects 99
6.2.1 Initial formulation 99
6.2.2 Alternative formulations 100
6.2.2.1 Derivative formulations 100
6.2.2.2 Link with Frontier Molecular Orbital theory 101
6.2.2.3 State-specific development 101
6.2.2.4 MO degeneracy 102
6.2.2.5 Quasi degeneracy 102
6.2.2.6 Spin polarization 103
6.2.2.7 Grand canonical ensemble derivation 105
6.2.3 Real-space partitioning 105
6.2.4 Dual descriptor and chemical principles 106
6.2.4.1 Principle of Maximum Hardness 106
6.2.4.2 Local hardness descriptors 106
6.2.4.3 Local electrophilicity and nucleophilicity 106
6.2.4.4 Local chemical potential and excited states reactivity 107
6.3 Illustrations 108
6.3.1 Woodward Hoffmann rules in Diels-Alder reactions 108
6.3.2 Perturbational MO Theory and Dual descriptor 109
6.3.3 Markovnikov rule 109
6.4 Conclusions 110
References 111
7 Molecular Electrostatic Potentials: Significance and Applications 113
7.1 A Quick Review of Some Classical Physics 113
7.2 Molecular Electrostatic Potentials 113
7.3 The Electronic Density and the Electrostatic Potential 114
7.4 Characterization of Molecular Electrostatic Potentials 115
7.5 Molecular Reactivity 116
7.6 Some Applications of Electrostatic Potentials to Molecular Reactivity 118
7.6.1 σ-Hole and π-Hole Interactions 118
7.6.2 Hydrogen Bonding: A σ-Hole Interaction 119
7.6.3 Interaction Energies 120
7.6.4 Close Contacts and Interaction Sites 121
7.6.5 Biological Recognition Interactions 124
7.6.6 Statistical Properties of Molecular Surface Electrostatic Potentials 125
7.7 Electrostatic Potentials at Nuclei 126
7.8 Discussion and Summary 127
References 127
8 Chemical Reactivity Within the Spin-Polarized Framework of Density Functional Theory 135
8.1 Introduction 135
8.2 The spin-polarized density functional theory as a suitable framework to describe both charge and spin transfer processes 137
8.3 Practical applications of SP-DFT indicators 141
8.4 Concluding remarks and perspectives 145
Acknowledgements 147
References 147
9 Chemical Binding and Reactivity Parameters: A Unified Coarse Grained Density Functional View 167
9.1 Introduction 167
9.2 Theory 169
9.2.1 Concept of electronegativity, chemical hardness, and chemical binding 169
9.2.1.1 Electronegativity and hardness 169
9.2.1.2 Interatomic charge transfer in molecular systems 169
9.2.1.3 Concept of chemical potential and hardness for the bond region 170
9.2.1.4 Spin-polarized generalization of chemical potential and hardness 171
9.2.1.5 Charge equilibriation methods: Split charge models and models with correct dissociation limits 172
9.2.1.6 Density functional perturbation approach: A coarse graining procedure 173
9.2.1.7 Atomic charge dipole model for interatomic perturbation and response properties 174
9.2.1.8 Force field generation in molecular dynamics simulation 174
9.3 Perspective on model building for chemical binding and reactivity 175
9.4 Concluding remarks 175
Acknowledgements 175
References 175
10 Softness kernel and nonlinear electronic responses 179
10.1 Introduction 179
10.2 Linear and nonlinear electronic responses 181
10.2.1 Linear response theory 181
10.2.1.1 Ground-state 181
10.2.1.2 Linear responses [1] 181
10.2.2 Nonlinear responses and the softness kernel 182
10.2.3 Eigenmodes of reactivity 184
10.3 One-dimensional confined quantum gas: analytical results from a model functional 185
10.4 Conclusion 188
References 188
11 Conceptual density functional theory in the grand canonical ensemble 191
11.1 Introduction 191
11.2 Fundamental equations for chemical reactivity 192
11.3 Temperature-dependent response functions 195
11.4 Local counterpart of a global descriptor and non-local counterpart of a local descriptor 200
11.5 Concluding remarks 203
Acknowledgements 204
References 204
12 Effect of confinement on the optical response properties of molecules 213
12.1 Introduction 213
12.2 Electronic contributions to longitudinal electric-dipole properties of atomic and molecular systems embedded in harmonic oscillator potential 215
12.3 Vibrational contributions to longitudinal electric-dipole properties of spatially confined molecular systems 218
12.4 Two-photon absorption in spatial confinement 219
12.5 Conclusions 220
References 221
13 A Density Functional Theory Study of Confined Noble Gas Dimers in Fullerene Molecules 225
13.1 Introduction 225
13.2 Computational details 226
13.3 Results and discussion 227
13.3.1 Changes in structure 227
13.3.2 Changes in interaction energy 227
13.3.3 Changes in bonding energy 228
13.3.4 Changes in energy components 228
13.3.5 Changes in noncovalent interactions 229
13.3.6 Changes in information-theoretic quantities 231
13.3.7 Changes in spectroscopy 232
13.3.8 Changes in reactivity 233
13.4 Conclusions 236
Acknowledgments 236
References 236
14 Confinement Induced Chemical Bonding: Case of Noble Gases 239
14.1 Introduction 239
14.2 Computational details and theoretical background 241
14.3 The bonding in He@C10H16: A debate 243
14.4 Confinement inducing chemical bond between two Ngs 244
14.5 XNgY insertion molecule: Confinement in one direction 251
14.6 Conclusions 254
Acknowledgements 255
References 255
15 Effect of both Structural and Electronic Confinements on Interaction, Chemical Reactivity and Properties 263
15.1 Introduction 263
15.2 Geometrical changes in small molecules under spherical and cylindrical confinement 264
15.3 Hydrogen bonding interaction of small molecules in the spherical and cylindrical confinement 265
15.4 Spherical and cylindrical confinement and chemical reactivity 267
15.5 Concluding remarks 268
References 270
16 Effect of confinement on gas storage potential and catalytic activity 273
16.1 Introduction 273
16.2 Endohedral gas adsorption inside clathrate hydrates 274
16.3 Hydrogen hydrates 276
16.4 Methane hydrates 278
16.5 Noble gas hydrates 279
16.6 Confinement induced catalysis of some chemical reactions 280
16.7 Outlook 285
Acknowledgements 285
References 285
17 Engineering the Confined Space of MOFs for Heterogeneous Catalysis of Organic Transformations 293
17.1 Introduction 293
17.2 Catalysis at the open metal sites 293
17.2.1 MOFs endowed with open metal site(s) 294
17.2.2 Removal of volatile molecules from metal nodes to perform catalysis 297
17.2.3 Catalysis at the metal node post transmetalation 299
17.3 Functionalization in the MOF to furnish catalytic site 301
17.3.1 Attaching the catalytically active moieties to the metal nodes (SBU) 301
17.3.2 Preconceived catalytic site into the linker 301
17.3.3 Post synthetic modification of the linker 304
17.3.4 MOFs with linkers having coordinated metal ions (metalloligands) 306
17.4 MOFs as bifunctional catalyst 310
17.5 Impregnation/encapsulation of nanoparticles in the MOF cavity for catalysis 317
17.6 Engineering homochiral MOFs for enantioselective catalysis 320
17.7 Conclusion 325
Acknowledgements 326
References 326
18 Controlling Excited State Chemistry of Organic Molecules in Water Through Incarceration 335
18.1 Introduction 335
18.2 Complexation properties of OA 337
18.3 Properties of OA capsule 339
18.4 Dynamics of encapsulated guests 340
18.5 Dynamics of host-guest complex 346
18.6 Room temperature phosphorescence of encapsulated organic molecules 353
18.7 Consequence of confinement on the photophysics of anthracene 356
18.8 Selective photo-oxidation of cycloalkenes 358
18.9 Remote activation of encapsulated guests: Electron transfer across an organic wall 360
18.10 Summary 362
Acknowledgements 363
References 363
19 Effect of Confinement on the Physicochemical Properties of Chromophoric Dyes/Drugs with Cucurbit[n]uril: Prospective Applications 371
19.1 Introduction 371
19.1.1 Confinement of dyes/drugs in macrocyclic hosts 372
19.1.1.1 Cyclodextrins 372
19.1.1.2 Calixarenes 373
19.1.1.3 Cucurbiturils 373
19.2 Confinement in cucurbituril hosts: effects on the physicochemical properties of guest molecules - advantages for various technological applications 374
19.2.1 Enhanced photostability and solubility of rhodamine dyes 375
19.2.1.1 Water-based dye laser 376
19.2.2 Enhanced luminescence and photostability of CH3NH3PbBr3 perovskite nanoparticles 377
19.2.3 Enhanced antibacterial activity and extended shelf-life of fluoroquinolone drugs with cucurbit[7]uril 377
19.2.4 Effect of confinement on the prototropic equilibrium 379
19.2.4.1 Salt-induced pKa tuning and guest relocation 379
19.2.5 Confinement in cucurbit[7]uril-mediated BSA: stimuli-responsive uptake and release of doxorubicin 380
19.2.6 Effect of confinement on the fluorescence behavior of chromophoric dyes with cucurbiturils 380
19.2.6.1 Fluorescence behavior of chromophoric dyes with cucurbit[7]uril 381
19.2.6.2 Fluorescence behavior of chromophoric dyes with cucurbit[8]uril 383
19.2.7 Effect of confinement on the catalytic performance within cucurbiturils 386
19.3 Conclusion 388
Acknowledgement 389
References 389
20 Box-Shaped Hosts: Evaluation of the Interaction Nature and Host Characteristics of ExBox Derivatives in Host-Guest Complexes from Computational Methods 395
20.1 Introduction 395
20.2 Noncovalent interactions through energy decomposition analysis 396
20.3 Ex0Box4+ (CBPQT4+) 398
20.4 ExBox4+ and Ex2Box4+ 399
20.5 Larger boxes 406
20.6 NMR features 408
20.7 All carbon counterpart 409
20.8 Conclusions 409
Acknowledgments 410
References 411
Index 417
