Chemical Reactivity in Confined Systems

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 lambda 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 infinity 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 sigma-Hole and pi-Hole Interactions 118 7.6.2 Hydrogen Bonding: A sigma-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 Ex°Box¯4+ (CBPQT¯4+) 398 20.4 ExBox¯4+ and Ex²Box¯4+ 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