Chemical Reactivity in Confined Systems

Pratim Kumar Chattaraj is an Institute Chair Professor, Department of Chemistry, Indian Institute of Technology Kharagpur, India and a J.C. Bose National Fellow. His research focuses on density functional theory, ab-initio calculations, nonlinear dynamics and aromaticity in metal clusters. Debdutta Chakraborty is a Research Associate in the Department of Chemistry at Katholieke Universiteit Leuven, Belgium. His research focus is on computational quantum chemistry, direct dynamics simulations, atmospheric chemistry and quantum trajectories.

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