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A Computational Toolkit to Understand Orbital Overlap And A COMPUTATIONAL TOOLKIT TO UNDERSTAND ORBITAL OVERLAP AND CHEMICAL REACTIVITY by ARSHAD MEHMOOD M.Sc. Chemistry, 2009 The Islamia University of Bahawalpur, Pakistan M.Phil. Physical Chemistry, 2011 The Islamia University of Bahawalpur, Pakistan Submitted to the Graduate Faculty of the College of Science and Engineering Texas Christian University in partial fulfillment of the requirements for the degree of Doctor of Philosophy December 2020 Acknowledgments I am grateful to my advisor, Dr. Benjamin G. Janesko, for his support, motivation, and guidance throughout the years of my Ph.D. Your help in my professional development, personal life, and career planning is exemplary. I am deeply indebted to you for your support in official matters, encouraging me to be independent and supporting me in expanding my skills. I have grown greatly as a researcher and person under your guidance. Thank you for being my mentor and a role model for my future life. I am thankful to the members of my committee, Prof. Jeffery L. Coffer, Prof. Sergei V. Dzyuba, and Prof. Jing Kong (Middle Tennessee State University), for their guidance at each step of my Ph.D. I am also thankful to Prof. Eric E. Simanek and Prof. Kayla N. Green for their help and collaborations. I am grateful to Prof. Onofrio Annunziata and Dr. Yulia V. Sevryugina, for their support and encouragement. Many thanks to my colleague, collaborator, and outrageously talented close friend, Dr. Stephanie I. Jones, who helped me and supported me to succeed during the years of my graduate study at TCU. I am thankful to my friends Dr. Alan E. Enciso, Dr. Vishal Sharma, Dr. Akop Yepremyan, and Dr. Adam Montoya. Thank you, Page Kimbrell, for your appreciated help in administrative matters and for being so cheerful about it. I want to thank the TCU College of Science and Engineering for their funding, travel grants, and financial support. I am also thankful to GC University Lahore, Pakistan, for granting me the study leave to complete my Ph.D. I must express my very profound gratitude to my parents, my sisters, and especially to my brother Maqsood Ahmed. He has always been a significant support to me and encouraged me in all my endeavors. Finally, a big thanks to my wife, Aisha, for listening to my complaints, excitements, and for her patience. Thank you for completing my life, supporting me through every desperation and every triumph, and going through the journey of Ph.D. together. ii Contents Acknowledgments ii List of Figures vi List of Tables xii List of Abbreviations xiii Chapter 1 Introduction 1 1.1 Interpreting Quantum Chemistry Calculations ...................................................... 1 1.2 Orbitals ................................................................................................................... 5 1.3 Our Interpretive Tools ............................................................................................ 6 1.4 The Chemistry of the Orbital Overlap ................................................................. 11 1.5 Specific Objectives and Organization ................................................................... 13 Chapter 2 Electron Delocalization in Stretched Bonds 15 2.1 Background ........................................................................................................... 15 2.2 Ground-state Singlet H2 ........................................................................................ 16 2.3 van der Waals Interaction: He2 ............................................................................. 21 2.4 Polar Covalent Bond: HF ..................................................................................... 24 2.5 Charge-shift Bond: F2 ........................................................................................... 27 2.6 Ionic Interaction: LiH ........................................................................................... 30 2.7 Concluding Remarks ............................................................................................. 33 2.8 Computational Details .......................................................................................... 34 Chapter 3 Quantifying the Reactivity of Atoms in Molecules 35 3.1 Background ........................................................................................................... 35 3.2 The Relation Between QA and DA ........................................................................ 37 3.3 Quantifying the Effects of Substituents ................................................................ 39 3.4 DA and Aromaticity .............................................................................................. 43 3.5 Quantifying the Reactivity of Isomers .................................................................. 45 3.6 Quantifying the Site-dependent Reactivity .......................................................... 48 3.7 Quantifying the Angle Strain Effects ................................................................... 50 iii 3.8 Concluding Remarks ............................................................................................. 51 3.9 Computational Details .......................................................................................... 51 Chapter 4 Quantifying Protein-ligand Interactions 52 4.1 Background ........................................................................................................... 52 4.2 Combination of ESP and Overlap Distance – An Illustration ............................. 54 4.3 Visualizing Protein-ligand Interactions ................................................................ 55 4.3.1 Avidin-Biotin Binding ............................................................................... 55 4.3.2 Thyroxine-Globulin Binding ..................................................................... 58 4.4 Quantifying Protein-metal Interactions ................................................................ 61 4.4.1 Gold–GolB Binding ................................................................................... 61 4.4.2 Selective Binding in Formylglycine-Generating Enzyme .......................... 63 4.5 Applications for Structure-based Drug Design ..................................................... 66 4.5.1 Promiscuous Binding ................................................................................ 66 4.5.2 Designing of CENP-E Inhibitor ................................................................ 67 4.6 Concluding Remarks ............................................................................................. 70 4.7 Computational Details .......................................................................................... 70 4.7.1 Preparation of Systems for MD Simulations ............................................. 70 4.7.2 Initial Energy Minimization ...................................................................... 72 4.7.3 MD Simulations ........................................................................................ 73 4.7.4 Molecular Orbital Calculations and Analysis............................................ 74 Chapter 5 Quantifying Solvent Softness 75 5.1 Background ........................................................................................................... 75 5.2 Empirical Solvent Softness Scales ......................................................................... 76 5.3 Quantifying Softness Using Electronic Structure ................................................. 77 5.4 Predicting Marcus Softness Scale Using Overlap Distance .................................. 78 5.5 Extension to Other Solvent Softness Scales.......................................................... 82 5.6 Development of Solvent Versatility Scale ............................................................. 83 5.7 Applications to Ionic Liquids ................................................................................ 84 5.8 Applications to Ionic Liquids/co-solvents ............................................................. 88 5.9 Concluding Remarks ............................................................................................. 89 5.10 Computational Details .......................................................................................... 89 Chapter 6 Quantifying the Reactivity of Graphene Defects 91 6.1 Background ........................................................................................................... 91 6.2 Quantifying the Reactivity of Intrinsic Defects .................................................... 93 6.3 Quantifying the Reactivity of Extrinsic Defects ................................................... 97 6.4 Quantifying the Adsorption of Metal Atoms ........................................................ 99 6.5 Concluding Remarks ........................................................................................... 102 iv 6.6 Computational Details ........................................................................................ 102 Chapter 7 Visualizing the σ-hole Using Orbital Overlap Distance 104 7.1 Background ......................................................................................................... 104 7.2 σ-holes on p-Block Elements .............................................................................. 108 7.3 σ-holes on Transition Metal Nanoclusters .......................................................... 113 7.4 Quantifying σ-holes Interactions .......................................................................
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