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 xiii1 Effect of Confinement on the Translation-Rotation Motion of Molecules: The inelastic neutron scattering selection rule 11.1 Introduction 11.2 Diatomics in C60: entanglement, TR coupling, symmetry, basis representation, and energy level structure 41.2.1 Entanglement Induced Selection Rules 41.2.2 H@C60 51.2.3 H2@C60 71.2.3.1 Symmetry 71.2.3.2 Spherical basis and eigenstates 71.2.3.3 Energy level ordering with respect to 𝜆 81.2.4 HX@C60 101.3 INS selection rule for spherical (Kh) symmetry 111.3.1 Inelastic Neutron Scattering 111.3.2 Group Theory Derivation of the INS Selection Rule 121.3.2.1 Group-theory-based INS selection rule for cylindrical (C∞𝑣) environments 121.3.2.2 Group-theory-based INS selection rule for spherical (Kh) environments 121.3.3 Specific Systems, Quantum Numbers, and Basis Sets 131.3.3.1 H@sphere 141.3.3.2 H2@sphere 141.3.3.3 HX@sphere 151.3.4 Beyond Diatomic Molecules 151.3.4.1 H2O@sphere 151.3.4.2 CH4@sphere 171.3.4.3 Any guest molecule in any spherical (Kh) environment 181.4 INS selection rules for non-spherical structures 181.5 Summary and conclusions 20Acknowledgments 22References 222 Pressure-induced phase transitions 252.1 Pressure, a property of all flavours, and its importance for the Universe and life 252.2 Pressure: isotropic and anisotropic, positive and negative 262.3 Changes of the state of matter 272.4 Compression of solids 302.4.1 Isotropic or anisotropic compressibility 302.4.2 Negative linear compressibility 302.4.3 Negative area compressibility 312.4.4 Anomalous compressibility changes at high pressure 312.5 Structural solid-solid transitions 322.5.1 Structural phase transitions accompanied by volume collapse 322.5.2 Effects of volume collapse on free energy 332.5.3 Structure-influencing factors at compression 342.5.4 Changes in the nature of chemical bonding upon compression and upon phase transitions 352.6 Selected classes of magnetic and electronic transitions 362.6.1 High Spin–Low Spin transitions 362.6.2 Electronic com- vs disproportionation 372.6.3 Metal-to-metal charge transfer 372.6.4 Neutral-to-Ionic transitions 372.6.5 Metallization of insulators (and resisting it) 382.6.6 Turning metals into insulators 392.6.7 Superconductivity of elements and compounds 392.6.8 Topological phase transitions 412.7 Modelling and predicting HP phase transitions 41Acknowledgements 42References 423 Conceptual DFT and Confinement 493.1 Introduction and Reading Guide 493.2 Conceptual DFT 503.3 Confinement and Conceptual DFT 523.3.1 Atoms: global descriptors 523.3.2 Molecules: global and local descriptors 563.3.2.1 Electron Affinities 573.3.2.2 Hardness and electronic Fukui function 593.3.2.3 Inclusion of pressure in the E = E [N,v] functional 633.4 Conclusions 65Acknowledgements 65References 664 Electronic structure of systems confined by several spatial restrictions 694.1 Introduction 694.2 Confinement imposed by impenetrable walls 694.3 Confinement imposed by soft walls 724.4 Beyond confinement models 744.5 Conclusions 77References 775 Unveiling the Mysterious Mechanisms of Chemical Reactions 815.1 Introduction 815.1.1 Context 815.1.2 Ideas and methods 825.1.3 Application 825.2 Energy and reaction force 835.2.1 The reaction force analysis (RFA) 835.2.2 RFA-based energy decomposition 845.2.3 Marcus potential energy function 855.2.4 Marcus RFA 865.3 Electronic activity along a reaction coordinate 875.3.1 Chemical potential, hardness, and electrophilicity index 875.3.2 The reaction electronic flux (REF) 885.3.2.1 Physical decomposition of REF 885.3.2.2 Chemical decomposition of REF 895.4 An application: the formation of aminoacetonitrile 905.4.1 Energetic analysis 915.4.2 Reaction mechanisms 915.5 Conclusions 94Acknowledgments 95References 956 A Perspective on the So-called Dual Descriptor 996.1 Introduction: conceptual DFT 996.2 The Dual Descriptor: fundamental aspects 996.2.1 Initial formulation 996.2.2 Alternative formulations 1006.2.2.1 Derivative formulations 1006.2.2.2 Link with Frontier Molecular Orbital theory 1016.2.2.3 State-specific development 1016.2.2.4 MO degeneracy 1026.2.2.5 Quasi degeneracy 1026.2.2.6 Spin polarization 1036.2.2.7 Grand canonical ensemble derivation 1056.2.3 Real-space partitioning 1056.2.4 Dual descriptor and chemical principles 1066.2.4.1 Principle of Maximum Hardness 1066.2.4.2 Local hardness descriptors 1066.2.4.3 Local electrophilicity and nucleophilicity 1066.2.4.4 Local chemical potential and excited states reactivity 1076.3 Illustrations 1086.3.1 Woodward Hoffmann rules in Diels-Alder reactions 1086.3.2 Perturbational MO Theory and Dual descriptor 1096.3.3 Markovnikov rule 1096.4 Conclusions 110References 1117 Molecular Electrostatic Potentials: Significance and Applications 1137.1 A Quick Review of Some Classical Physics 1137.2 Molecular Electrostatic Potentials 1137.3 The Electronic Density and the Electrostatic Potential 1147.4 Characterization of Molecular Electrostatic Potentials 1157.5 Molecular Reactivity 1167.6 Some Applications of Electrostatic Potentials to Molecular Reactivity 1187.6.1 σ-Hole and π-Hole Interactions 1187.6.2 Hydrogen Bonding: A σ-Hole Interaction 1197.6.3 Interaction Energies 1207.6.4 Close Contacts and Interaction Sites 1217.6.5 Biological Recognition Interactions 1247.6.6 Statistical Properties of Molecular Surface Electrostatic Potentials 1257.7 Electrostatic Potentials at Nuclei 1267.8 Discussion and Summary 127References 1278 Chemical Reactivity Within the Spin-Polarized Framework of Density Functional Theory 1358.1 Introduction 1358.2 The spin-polarized density functional theory as a suitable framework to describe both charge and spin transfer processes 1378.3 Practical applications of SP-DFT indicators 1418.4 Concluding remarks and perspectives 145Acknowledgements 147References 1479 Chemical Binding and Reactivity Parameters: A Unified Coarse Grained Density Functional View 1679.1 Introduction 1679.2 Theory 1699.2.1 Concept of electronegativity, chemical hardness, and chemical binding 1699.2.1.1 Electronegativity and hardness 1699.2.1.2 Interatomic charge transfer in molecular systems 1699.2.1.3 Concept of chemical potential and hardness for the bond region 1709.2.1.4 Spin-polarized generalization of chemical potential and hardness 1719.2.1.5 Charge equilibriation methods: Split charge models and models with correct dissociation limits 1729.2.1.6 Density functional perturbation approach: A coarse graining procedure 1739.2.1.7 Atomic charge dipole model for interatomic perturbation and response properties 1749.2.1.8 Force field generation in molecular dynamics simulation 1749.3 Perspective on model building for chemical binding and reactivity 1759.4 Concluding remarks 175Acknowledgements 175References 17510 Softness kernel and nonlinear electronic responses 17910.1 Introduction 17910.2 Linear and nonlinear electronic responses 18110.2.1 Linear response theory 18110.2.1.1 Ground-state 18110.2.1.2 Linear responses [1] 18110.2.2 Nonlinear responses and the softness kernel 18210.2.3 Eigenmodes of reactivity 18410.3 One-dimensional confined quantum gas: analytical results from a model functional 18510.4 Conclusion 188References 18811 Conceptual density functional theory in the grand canonical ensemble 19111.1 Introduction 19111.2 Fundamental equations for chemical reactivity 19211.3 Temperature-dependent response functions 19511.4 Local counterpart of a global descriptor and non-local counterpart of a local descriptor 20011.5 Concluding remarks 203Acknowledgements 204References 20412 Effect of confinement on the optical response properties of molecules 21312.1 Introduction 21312.2 Electronic contributions to longitudinal electric-dipole properties of atomic and molecular systems embedded in harmonic oscillator potential 21512.3 Vibrational contributions to longitudinal electric-dipole properties of spatially confined molecular systems 21812.4 Two-photon absorption in spatial confinement 21912.5 Conclusions 220References 22113 A Density Functional Theory Study of Confined Noble Gas Dimers in Fullerene Molecules 22513.1 Introduction 22513.2 Computational details 22613.3 Results and discussion 22713.3.1 Changes in structure 22713.3.2 Changes in interaction energy 22713.3.3 Changes in bonding energy 22813.3.4 Changes in energy components 22813.3.5 Changes in noncovalent interactions 22913.3.6 Changes in information-theoretic quantities 23113.3.7 Changes in spectroscopy 23213.3.8 Changes in reactivity 23313.4 Conclusions 236Acknowledgments 236References 23614 Confinement Induced Chemical Bonding: Case of Noble Gases 23914.1 Introduction 23914.2 Computational details and theoretical background 24114.3 The bonding in He@C10H16: A debate 24314.4 Confinement inducing chemical bond between two Ngs 24414.5 XNgY insertion molecule: Confinement in one direction 25114.6 Conclusions 254Acknowledgements 255References 25515 Effect of both Structural and Electronic Confinements on Interaction, Chemical Reactivity and Properties 26315.1 Introduction 26315.2 Geometrical changes in small molecules under spherical and cylindrical confinement 26415.3 Hydrogen bonding interaction of small molecules in the spherical and cylindrical confinement 26515.4 Spherical and cylindrical confinement and chemical reactivity 26715.5 Concluding remarks 268References 27016 Effect of confinement on gas storage potential and catalytic activity 27316.1 Introduction 27316.2 Endohedral gas adsorption inside clathrate hydrates 27416.3 Hydrogen hydrates 27616.4 Methane hydrates 27816.5 Noble gas hydrates 27916.6 Confinement induced catalysis of some chemical reactions 28016.7 Outlook 285Acknowledgements 285References 28517 Engineering the Confined Space of MOFs for Heterogeneous Catalysis of Organic Transformations 29317.1 Introduction 29317.2 Catalysis at the open metal sites 29317.2.1 MOFs endowed with open metal site(s) 29417.2.2 Removal of volatile molecules from metal nodes to perform catalysis 29717.2.3 Catalysis at the metal node post transmetalation 29917.3 Functionalization in the MOF to furnish catalytic site 30117.3.1 Attaching the catalytically active moieties to the metal nodes (SBU) 30117.3.2 Preconceived catalytic site into the linker 30117.3.3 Post synthetic modification of the linker 30417.3.4 MOFs with linkers having coordinated metal ions (metalloligands) 30617.4 MOFs as bifunctional catalyst 31017.5 Impregnation/encapsulation of nanoparticles in the MOF cavity for catalysis 31717.6 Engineering homochiral MOFs for enantioselective catalysis 32017.7 Conclusion 325Acknowledgements 326References 32618 Controlling Excited State Chemistry of Organic Molecules in Water Through Incarceration 33518.1 Introduction 33518.2 Complexation properties of OA 33718.3 Properties of OA capsule 33918.4 Dynamics of encapsulated guests 34018.5 Dynamics of host-guest complex 34618.6 Room temperature phosphorescence of encapsulated organic molecules 35318.7 Consequence of confinement on the photophysics of anthracene 35618.8 Selective photo-oxidation of cycloalkenes 35818.9 Remote activation of encapsulated guests: Electron transfer across an organic wall 36018.10 Summary 362Acknowledgements 363References 36319 Effect of Confinement on the Physicochemical Properties of Chromophoric Dyes/Drugs with Cucurbit[n]uril: Prospective Applications 37119.1 Introduction 37119.1.1 Confinement of dyes/drugs in macrocyclic hosts 37219.1.1.1 Cyclodextrins 37219.1.1.2 Calixarenes 37319.1.1.3 Cucurbiturils 37319.2 Confinement in cucurbituril hosts: effects on the physicochemical properties of guest molecules – advantages for various technological applications 37419.2.1 Enhanced photostability and solubility of rhodamine dyes 37519.2.1.1 Water-based dye laser 37619.2.2 Enhanced luminescence and photostability of CH3NH3PbBr3 perovskite nanoparticles 37719.2.3 Enhanced antibacterial activity and extended shelf-life of fluoroquinolone drugs with cucurbit[7]uril 37719.2.4 Effect of confinement on the prototropic equilibrium 37919.2.4.1 Salt-induced pKa tuning and guest relocation 37919.2.5 Confinement in cucurbit[7]uril-mediated BSA: stimuli-responsive uptake and release of doxorubicin 38019.2.6 Effect of confinement on the fluorescence behavior of chromophoric dyes with cucurbiturils 38019.2.6.1 Fluorescence behavior of chromophoric dyes with cucurbit[7]uril 38119.2.6.2 Fluorescence behavior of chromophoric dyes with cucurbit[8]uril 38319.2.7 Effect of confinement on the catalytic performance within cucurbiturils 38619.3 Conclusion 388Acknowledgement 389References 38920 Box-Shaped Hosts: Evaluation of the Interaction Nature and Host Characteristics of ExBox Derivatives in Host-Guest Complexes from Computational Methods 39520.1 Introduction 39520.2 Noncovalent interactions through energy decomposition analysis 39620.3 Ex0Box4+ (CBPQT4+) 39820.4 ExBox4+ and Ex2Box4+ 39920.5 Larger boxes 40620.6 NMR features 40820.7 All carbon counterpart 40920.8 Conclusions 409Acknowledgments 410References 411Index 417