Computational materials, chemistry, and biochemistry : from bold initiatives to the last mile : in honor of William A. Goddard's contributions to science and engineering

This book provides a broad and nuanced overview of the achievements and legacy of Professor William (“Bill”) Goddard in the field of computational materials and molecular science. Leading researchers from around the globe discuss Goddard’s work and its lasting impacts, which can be seen in today’s cutting-edge chemistry, materials science, and biology techniques. Each section of the book closes with an outline of the prospects for future developments. In the course of a career spanning more than 50 years, Goddard’s seminal work has led to dramatic advances in a diverse range of science and engineering fields. Presenting scientific essays and reflections by students, postdoctoral associates, collaborators and colleagues, the book describes the contributions of one of the world’s greatest materials and molecular scientists in the context of theory, experimentation, and applications, and examines his legacy in each area, from conceptualization (the first mile) to developments and extensions aimed at applications, and lastly to de novo design (the last mile). Goddard’s passion for science, his insights, and his ability to actively engage with his collaborators in bold initiatives is a model for us all. As he enters his second half-century of scientific research and education, this book inspires future generations of students and researchers to employ and extend these powerful techniques and insights to tackle today’s critical problems in biology, chemistry, and materials. Examples highlighted in the book include new materials for photocatalysts to convert water and CO2 into fuels, novel catalysts for the highly selective and active catalysis of alkanes to valuable organics, simulating the chemistry in film growth to develop two-dimensional functional films, and predicting ligand–protein binding and activation to enable the design of targeted drugs with minimal side effects. Preface and Overview Retrospective Perspectives from Bill Goddard Sec7 Contents Contributors 1 The Amazing Bill Goddard! 2 1% of Bill Goddard References 3 My Early Collaboration with Bill Goddard References 4 Academic-Industrial Collaborations: Tale of Two Universities 4.1 Introduction 4.2 Common Ground and Competing Interests 4.3 The Communication Gap 4.4 The University Relations Officer 4.5 The Research Manager 4.6 The Center Liaison Officer 4.7 The Industry Collaboration Officer (ICO) 4.8 Best Practices 4.9 Industry Collaborations at Caltech 4.10 KAUST in a Nutshell 4.11 KAUST Research Centers 4.12 KAUST and Economic Development 4.13 Industry Collaborations at KAUST 4.14 Conclusions and Recommendations Appendix 1: Center Liaison Officer Position Summary Major Responsibilities Competencies Qualifications Appendix 2: Industry Collaboration Officer Position Summary Major Responsibilities Competencies Qualifications Appendix 3: KRISP: Informatics Tool for Industry Collaborations Summary Overview Appendix 4: Company Profile Example Company: Dow Chemical (2015) Appendix 5: Example of Research Symposium Agenda for Industry Collaborations References Part IMethods 5 Beyond Molecular Orbital Theory: The Impact of Generalized Valence Bond Theory in Molecular Science 5.1 Introduction 5.2 GVB-Based Approaches to Molecular Electronic Structure 5.2.1 GVB and GVB(PP/SO) Methods 5.2.2 GVB-CI Methods 5.3 Insights from GVB Theory 5.3.1 Studies with the GI/SOGI Method in the 1960s and 1970s 5.3.2 Studies with the GVB(PP/SO) Method in the 1970s and 1980s 5.3.3 Studies with the Full GVB Method in the 2000s and 2010s 5.4 Conclusions References 6 A Robust and Automated Approach for the Calculation of Absolute Entropy from the Two-Phase Thermodynamic Model with Gaussian Memory Function 6.1 Introduction 6.2 Theory 6.2.1 The Two-Phase Thermodynamic (2PT) Model 6.2.2 The Memory Function Approach 6.2.3 A New Approach for Determining Fluidicity Using Gaussian Kernel 6.3 Simulation Details 6.4 Results and Discussion 6.5 Conclusion Appendix A Appendix B Appendix C References 7 Quantum Mechanical Simulation of Electron Dynamics on Surfaces of Materials 7.1 Introduction 7.2 Methodology 7.2.1 Existence of a Rigorous TDDFT for Open Systems 7.2.2 TDDFT Methods for Practical Calculations 7.3 Results and Discussions 7.3.1 Real-Time Electron Transport in Quasi-One-Dimensional Atomic Chains 7.4 Conclusion References 8 Accelerated Molecular Dynamics Methods for Long-Time Simulations in Materials 8.1 Introduction 8.2 Parallel Replica Dynamics 8.3 Hyperdynamics 8.4 Temperature Accelerated Dynamics 8.5 Example Applications 8.5.1 Void Evolution in FCC Metals 8.5.2 Stretching a Silver Nanowire 8.5.3 Radiation Damage Recovery in Spinel 8.6 Ongoing Challenge of Low Barriers 8.7 Conclusions References 9 Development and Applications of the ReaxFF Reactive Force Field for Biological Systems 9.1 Overview and Scope 9.2 Phosphodiester Bond Cleavage of RNA and DNA Dinucleotide 9.3 Imidazole and Zn-Ligand Complex 9.3.1 Determination of the Imidazole Protonation State 9.3.2 ReaxFF Force Field for Zn-Ligand Interactions 9.3.3 Formation of Zn(Im)n(H2O)m Complex at Neutral PH 9.4 Cu(II)-Assisted Hydrolysis of Peptide Bond 9.5 Serine Protease Reaction with a Catalytic Triad 9.6 Conclusions and Prospective References 10 Machine Learning Corrections for DFT Noncovalent Interactions 10.1 Introduction 10.2 Methods and Materials 10.2.1 DFT Calculations 10.2.2 Machine Learning Correction 10.3 Results and Discussions 10.3.1 Databases 10.3.2 NCI Calculations with DFT Methods 10.3.3 GRNN Correction Model 10.4 Conclusions Appendix References 11 Characterization of Phases and Orientations of Micro-structured Materials Using Computational Crystallography 11.1 Introduction 11.2 Mathematical Approach 11.2.1 Bravais Lattice and Grain Boundaries Determination 11.2.2 Interlocking Structures 11.2.3 Boundary Points 11.2.4 Crystals with Multiple Element Types 11.2.5 Crystals with Off-Lattice Atomic Positions 11.2.6 Crystal Imperfections and Numerical Tolerances 11.2.7 Algorithmic Efficiency and Stability 11.3 Results 11.4 Conclusions References 12 Pictures are Crucial: Intuition, Electronic Structure, and Reactions in Materials Chemistry References 13 Prediction of Heats of Formation of Polycyclic Saturated Hydrocarbons Using the XYG3 Double Hybrid Functionals 13.1 Introduction 13.2 Computational Details 13.3 Results and Discussion 13.4 Conclusion References 14 Integrated Molecular Modeling and Experimental Studies: Applications to Advanced Material Design and Process Optimization 14.1 Catalyzed Methane Conversion 14.1.1 Methane Conversion Through Ionic Liquid—Mediated C–H Activation 14.1.2 Development of Ternary Homogeneous Catalytic Systems 14.1.3 Chemical and Thermal Stability of N-Heterocyclic Ionic Liquids in Catalytic C–H Activation Reactions 14.1.4 IL-Mediated C–H Activation Mechanism Studies 14.1.5 High-Temperature Shilov-Like Methane Conversion 14.2 Robust Surfactant IFT Prediction Models for EOR Applications 14.2.1 Surfactant Flooding for IOR/EOR 14.2.2 Surfactants for IOR/EOR 14.2.3 Theoretical Methods for IFT Prediction 14.2.4 Effect of the Architecture of Alkyl Benzene Sulfonate Ionic Surfactants 14.2.5 Conclusion Marks 14.3 Catalyzed Decarboxylation Process for Acidic/Heavy Oil Upgrading 14.3.1 The Acidity of Crude Oil 14.3.2 Acid Removal for Heavy Oil Upgrading 14.3.3 In-depth Understanding of the Reaction Mechanism of MgO-Catalyzed Decarboxylation 14.3.4 Conclusion Marks References 15 Quantum-Based Molecular Dynamics Simulations with Applications to Industrial Problems 15.1 Introduction 15.2 Born–Oppenheimer Molecular Dynamics from Density-Functional Theory 15.3 Self-consistent Density-Functional Tight-Binding Theory 15.4 Extended Lagrangian Born–Oppenheimer Molecular Dynamics 15.5 Recursive Fermi-Operator Expansion 15.6 Congruence Transformation Using Iterative Refinement 15.7 Integration of the Suite of Techniques 15.8 Applications to Industrial Problems References 16 Rapid Screening of Chemical Sensing Materials Using Molecular Modeling Tools for the JPL Electronic Nose 16.1 Introduction 16.2 Understanding and Selection of Polymer-Carbon Sensing Arrays 16.3 Rapid Screening Using Quantum Mechanics 16.4 Results and Discussion 16.4.1 Screening and Validation of Organics for SO2 Detection 16.4.2 Screening and Validation of Organics for Elemental Hg Detection 16.5 Conclusions References 17 How Computational Chemistry Has Launched Me Hypersonically Towards Microgravity Research 17.1 Introduction 17.2 Polymer Clay Nanocomposites: The Clay Exfoliation Process 17.2.1 The Real-World Problem 17.2.2 Computational Chemistry Solution 17.3 Wax Formation and Inhibition: The Molecular Mechanisms of Nucleation 17.3.1 The Real-World Problem 17.3.2 Computational Chemistry Solution 17.4 Designing a Solid-State Nanopore for Optimized DNA Sequencing 17.4.1 The Real-World Problem 17.4.2 Computational Chemistry Solution 17.5 Hypersonic Reentry 17.5.1 The Real-World Problem 17.5.2 Gas-Surface Interactions in Hypersonic Flow 17.5.3 Thermal Decomposition of Charring Ablators 17.6 Microgravity Research 17.6.1 The Real-World Problem 17.6.2 Microgravity and Computational Chemistry 17.6.3 Closing Thoughts: The Value of Successful Commercialization to R&D Part IIBulk Materials, Surfaces, Interfaces, Nanomaterials 18 Advanced Electronic Structure Calculations for Nanoelectronics 18.1 Introduction 18.2 The Effective Mass Equations: Electronic Structure of Nanoelectronic Devices 18.3 Configuration Interaction in a Finite-Element Basis 18.4 Gaussian Basis Sets for the Electronic Structure Problem 18.4.1 Anisotropic Gaussian Basis Sets 18.5 One- and Two-Center Integrals with Anisotropic Gaussians 18.5.1 Efficient Evaluation of Two-Center Integrals 18.5.2 Screening Rules for Grid Basis Sets 18.5.3 Efficient Summation Techniques 18.5.4 Efficient Evaluation of the Fock Matrix 18.6 Explicit Example: Hooke's Atom 18.7 Conclusion 18.8 Appendix: Efficient Gaussian Approximation of the Coulomb Kernel References 19 Dendrimers: A Novel Nanomaterial 19.1 Introduction to Dendrimers 19.2 Bulk Properties of Dendrimers 19.2.1 Radius of Gyration (Rg) 19.2.2 Aspect Ratios and Asphericity 19.2.3 Density Distributions 19.2.4 Surface and Bound Water 19.2.5 Root-Mean-Square Fluctuations (RMSF) 19.2.6 Effect of Core Functionality 19.2.7 Comparison Between PETIM and PAMAM Dendrimers 19.3 Applications of Dendrimers 19.3.1 Dendrimers in Drug Delivery 19.3.2 Dendrimers in Gene Delivery 19.3.3 Dendrimers as Dispersing Agents 19.4 Conclusions References 20 Thermal Transport for Nanostructured Materials 20.1 Introduction 20.2 Theoretical Background and Methods 20.2.1 Equilibrium Molecular Dynamics 20.2.2 Non-equilibrium Molecular Dynamics 20.3 Applications to Low-Dimensional Nanostructured Materials 20.3.1 Thermal Conductivity in one- and two-Dimensional Nanostructures 20.3.2 Graphene and Nanoribbons: Influence of Defects and Edges 20.3.3 Phonon Confinement and Boundary Scattering Effects 20.3.4 Isotope Effects 20.4 Summary and Concluding Remarks References 21 DNA-Guided Self-assembly of Carbon Nanotube Electronics 21.1 Background 21.2 DNA-Guided Assembly of Nanoscale SWNT Patterns 21.2.1 DNA Origami Templated Assembly 21.2.2 DNA-Guided Surface Diffusion Assembly 21.3 DNA Guides Assembly and the Path Towards SWNT Processors 21.4 The Benefits of a Theory Centered World View in the Land of Experiments References 22 Silica Particles as Surfactant Nanocarriers for Enhanced Oil Recovery 22.1 Introduction 22.2 Materials and Methods 22.2.1 Materials 22.2.2 Procedure for Modification of Silica Nanoparticles with Adsorbed Surfactants in Aqueous Solution 22.2.3 Characterization of Modified Silica Nanoparticles 22.2.4 Surface and Interfacial Tension Measurements 22.3 Results and Discussion 22.3.1 Synergism in CTAB:NPE10 Mixtures at Reducing Surface (Air/Water) and Interfacial (Oil/Water) Tension 22.3.2 Preparation and Characterization of Surfactant-Coated Silica Nanoparticles 22.3.3 Desorption of Surfactants from Surfactant-Coated Silica Nanoparticles 22.4 Conclusions References 23 Simulation-Based Characterization of Electrolytes and Small Molecule Diffusion in Oriented Mesoporous Silica Thin Films 23.1 Introduction 23.1.1 Ion Transport in Mesoporous Films and the Impact of Defects 23.1.2 Techniques for Incorporating Microscopy Data into Nanoscale Simulations 23.1.3 Modeling Approaches for Ionic Transport in Mesoporous Media 23.1.4 Objectives 23.2 Methods 23.2.1 Matched Filter Unit Cell Determination from Segmentation of Bulk Mesocrystal and Defect EM Data 23.2.2 Mesh Generation from Matched Filter Unit Cells 23.2.3 Effective Transport Parameter Determination via Finite Element Solutions of the Poisson–Nernst–Plank Transport Model 23.2.4 Extrapolation of Effective Conductivity Estimates on EM-imaging Data 23.3 Results and Discussion 23.3.1 Automated Feature Detection and Mesh Generation for Oriented Porous Films 23.3.2 Electrokinetic Model of Transport in Oriented Mesoporous Films and Other Porous Media 23.3.3 Small Charged Molecule Permeation Properties of a Mesoporous Silica Film 23.4 Conclusions 23.5 Supplement 23.5.1 Supplemental Figures 23.5.2 Supplemental Results 23.5.3 KCl Conductance Using Navier–Stokes (Fluid Flow) and Poisson–Nernst–Planck Formalisms 23.5.4 Ionic Conductance of Electrolyte Solutions at Varying Wall Electric Potentials in Nanopore/Nanoslit References 24 Fundamentals of Capacitive Charge Storage in Carbon-Based Supercapacitors 24.1 Introduction 24.2 Theoretical Background 24.3 Computational Approaches 24.3.1 Electronic Structure and Quantum Capacitance 24.3.2 Double-Layer Microstructure and Capacitance 24.4 Graphene-Derived Materials 24.4.1 Chemical Modifications to Graphene 24.4.2 Structural Modifications to Graphene 24.5 Nanoporous Carbon Materials 24.5.1 Insights from Electrodes with Positive and Negative Curvature 24.5.2 Electrokinetic Insights from Ion Confinement in Nanopores 24.6 Summary and Perspective References 25 Direct Growth of Graphene/Graphene Oxide Heterostructures on Polar Oxide Substrates 25.1 Introduction 25.2 Experimental Methods 25.3 Results 25.3.1 Graphene Growth on Co3O4(111) 25.3.2 Graphene Growth on MgO(111) 25.3.3 Other Oxides 25.3.4 Implications for Novel Devices 25.4 Summary and Conclusions References 26 Damage-Free Atomic-Scale Etching and Surface Enhancements by Electron-Enhanced Reactions: Results and Simulations 26.1 Introduction and Differentiation of LE4 Technology 26.2 Illustrative Applications of LE4 Technology 26.2.1 Profile Control and Line Width Roughness (LWR) in Si 26.2.2 Ultrasmall Structures in Si 26.2.3 Atomically Smooth Etching of SiO2 26.2.4 Damage-Free Etching of Low K Dielectric Films 26.2.5 Key Results in Work Reported Previously 26.3 Summary of Applications 26.4 Mechanism of LE4 26.5 Outlook for LE4 Technology 26.5.1 Commercialization 26.5.2 Advanced Applications References 27 Multiscale Modeling and Applications of Bioinspired Materials with Gyroid Structures 27.1 Introduction 27.2 Lightweight Graphene Based Porous Materials 27.3 Bioinspired Gyroid Microstructure 27.4 Energy Absorption Capacity of 3D Graphene Assembly 27.5 Conclusion References 28 In Silico Prediction and Design of Dye-Sensitized Solar Cells 28.1 Introduction 28.2 Theoretical and Experimental Methods 28.2.1 Microscale Simulation 28.2.2 Mesoscale Simulation 28.2.3 Macroscale Simulation 28.2.4 Synthesis of Zinc-Porphyrin Dyes 28.2.5 Fabrication of DSSCs 28.3 Results and Discussion 28.3.1 Probe Molecules and Inheritance of Parameters 28.3.2 Microscale and Mesoscale Simulations 28.3.3 Macroscale Simulation and J-V Characteristics 28.3.4 Design Rules of DSSCs 28.3.5 Rational Design of Zinc-Porphyrin Dyes 28.4 Conclusion References 29 Characterizing the Morphology and Efficiency of Organic Solar Cells by Multiscale Simulations 29.1 Introduction 29.2 Simulation Methods 29.2.1 Dissipative Particle Dynamics Simulation 29.2.2 Graph Theory to Predict the Efficiency 29.2.3 Models and Parameters 29.3 Result and Discussion 29.3.1 The Effect of Molecular Weight on the Morphology and Efficiency of P3HT:PCBM Solar Cells 29.3.2 The Effect of Alkyl Chain Length of P3HT on the Morphology and Efficiency of P3HT:PCBM Solar Cells 29.3.3 The Effect of the Annealing Temperature on the Morphology and Efficiency 29.3.4 The Effect of the Additive on the Morphology and the Efficiency 29.4 Conclusions 29.5 Outlook References 30 Multiscale Quantum Mechanics/Electromagnetics Method for the Simulation of Photovoltaic Devices 30.1 Introduction 30.2 Methodology 30.3 Applications 30.4 Conclusions References Part IIIChemistry, Catalysis 31 An Integrated Methodology for Screening Hydrogen Evolution Reaction Catalysts: Pt/Mo2C as an Example 31.1 Introduction 31.2 Methods 31.3 Results 31.4 Conclusions References 32 Selective Oxidation Catalysis: An Organic Chemist’s View of Mechanism 32.1 Introduction 32.2 Surface Organic Intermediates Probes 32.3 Current Mechanistic Insights 32.4 Other Bismuth Molybdate-Catalyzed Allylic Oxidation Reactions 32.5 Summary and Conclusions References 33 Atomic and Molecular Unit Energy Conversion Catalysis of Carbon Dioxides in Value-Added Chemical Fuels 33.1 Introduction 33.1.1 Background and History 33.2 Objective 33.3 Challenges 33.3.1 Development of High Efficient Photocatalysts and Electrocatalysts for Conversion of CO2 into Hydrocarbon Fuels 33.3.2 Design and Fabrication of the Scale-up CO2 Conversion Reactors 33.4 Outlook References 34 Studies of C–H Activation and Functionalization: Combined Computational and Experimental Efforts to Elucidate Mechanisms, Principles, and Catalysts 34.1 Introduction 34.2 C–H Functionalization Using Iodine Oxides and Chloride 34.2.1 Hypervalent Iodine/Chloride Alkane Oxidation (HIAO) Process 34.2.2 Mechanistic Discussion 34.2.3 Computational Modeling 34.2.4 Experimental Study of the Reaction Mechanism 34.2.5 Conclusions 34.3 Development of Electrophilic Rhodium Complexes for C–H Activation 34.3.1 Rh Catalyzed H/D Exchange Between Arenes and Trifluoroacetic Acid 34.3.2 Computational Investigation of RhIII Complexes for Methane Partial Oxidation 34.3.3 RhIII Complexes Supported by “Capping Arene” Ligands 34.3.4 Conclusions 34.4 C–H Halogenation via Biomimetic Mn–X Rebound Catalysis 34.4.1 Manganese Porphyrin Catalysts: Nature of the Radical Rebound Process 34.4.2 Biomimetic Radical C–H Fluorination 34.4.3 Conclusion References 35 Revised Mechanism of Propylene Ammoxidation References Part IVBiological Materials, Devices, Polymers 36 Development of Biomarkers and Point-of-Care Tests for Cerebrovascular Pathology: A Marriage of Chemistry, Biology, and Medicine 36.1 Introduction 36.2 Importance of Biomarkers in Clinical Medicine and Research 36.3 Development of Biomarkers 36.3.1 Choice of Biosample 36.3.2 Standardizing Sample Collection, Handling, and Analysis 36.3.3 Biomarker Study Design 36.3.4 Point-of-Care Testing 36.4 Stroke 36.4.1 Biomarkers of Stroke 36.5 Subarachnoid Hemorrhage 36.5.1 Biomarkers of SAH 36.6 Conclusions and Perspectives References 37 Structural Variation and Odorant Binding for Olfactory Receptors Selected from the Six Major Subclasses of the OR Phylogenetic Tree 37.1 Introduction 37.2 Results and Discussion 37.2.1 Sequence Alignment and Phylogenetic Tree 37.2.2 Intermolecular Interactions in the Apo-Protein 37.2.3 Ensemble Docking 37.2.4 Molecular Dynamics (MD) 37.2.5 Discussion 37.3 Methods 37.3.1 Sequence Alignment and Phylogenetic Tree 37.3.2 7-Helix Packing Prediction 37.3.3 Ligand Binding Site Predictions 37.3.4 Molecular Dynamics 37.4 Conclusions Appendix References 38 Single Molecule Studies of a Biological Motor F1-ATPase: Interplay of Experiment, Analytic Theory and Computation References 39 Early Goddard Contributions Confirming the Dendritic State: Engineering PAMAM Dendrimer CNDPs to Generate CW-Terahertz Radiation Suitable for Molecular, Bio- and Diagnostics Imaging Spectroscopy 39.1 Introduction 39.1.1 Prolog 39.1.2 Historical 39.1.3 The Early 1990s: A Dendritic Epiphany 39.2 A Seminal Goddard Collaboration Leading to Confirmation of Discrete Dendrimer CNDPs, Nanoperiodic Property Patterns (i.e., Dendritic Effects), Superatom Mimicry and the Nanoperiodic Concept 39.3 Quantized Building Blocks (i.e., Hard/Soft Superatoms) and Their Critical Hierarchical Design Parameters (CHDPs) 39.4 Terahertz Radiation: One of the Last Electromagnetic Radiation Frontiers 39.5 Applying CNDP Engineering Principles to Dendrimer-Based Nonlinear Optical (NLO) Substrates for Generating Terahertz Radiation 39.6 Design and Implementation of a Dendrimer Dipole Excitation-Based Terahertz Spectrometer with a Practical Bio-Imaging Application Example 39.7 Bio-imaging with Terahertz Spectroscopy: Multispectral Reconstructive Imaging of Biological Specimen and Comparison of Human Skin in Healthy Versus Diseased State 39.8 Conclusions References 40 Stepwise as Opposed to Concerted Conformational Changes Optimize Signal Transmission in Allosteric Dimers 40.1 Introduction 40.2 Results 40.2.1 Coupled Energy Landscape Model of Allosteric Coupling 40.2.2 Diffusive Dynamics on an Energy Landscape 40.2.3 Relation Between Driven Dynamics and Undriven Fluctuations 40.2.4 Signal Transmission Is Optimized by an Intermediate Value of Coupling Energy Which Balances Switching Rate and Fidelity 40.3 Discussion 40.4 Methods 40.4.1 Computing Trajectories on an Energy Landscape 40.4.2 Evaluating Rate and Fidelity from Undriven Trajectories 40.4.3 Evaluating Signal and Noise from Driven Trajectories 40.4.4 Comparison of Transmission Coefficients Computed Numerically Versus with an Approximate Rate-Fidelity Expression 40.5 Appendix 1 40.5.1 Stationary Points of the Coupled Oscillator Potential 40.5.2 Analytic Expression for the Transmission Coefficient in the High Barrier Limit 40.6 Appendix 2 40.6.1 Signal-to-Noise Properties of a Single Stochastic Oscillator 40.6.2 Signal-to-noise Properties of a Coupled Pair of Stochastic Oscillators References Part VMethods 41 GVB Interpretations of Bonding and Reactions 41.1 Understanding the Chemical Bond in Terms of GVB Atomic-like Orbitals: H2 Dissociation, Sp2 and Sp3 Hybridization, the Bonding in Ozone 41.2 GVB View of O2, Reactions with O2 41.3 GVB View of Bonding in Oxy Myoglobin 41.4 GVB Rules for Reactions: The Orbital Phase Continuity Principle: The GVB Alternative to the Woodward Hoffman Rules 41.5 GVB View of Organometallics with a Single Transition Metal 41.6 GVB View of Bonding in Metallic Solids: the Interstitial Electron Model 41.7 Chemisorption of Organic Radicals on Group VIII Metals 41.8 The VB View of the Origin of the Chemical Bond 41.9 Full GVB Wavefunctions for Atoms and Molecules 41.10 Excited States of Molecules 41.11 Biradicals 41.12 Perfect Pairing-Based GVB Wavefunctions 41.13 GVB with Resonance Orbital Interpretations 41.14 Orbital Description of the Excited States of H2 from Re to Dissociation 41.15 Orbital Description of the Excited States of He2 from Re to Dissociation 41.16 GVB Orbital Description for Allyl Radical 41.17 The GVB Orbital Description for the Resonant and Antiresonant States of Cyclobutadiene 41.18 Aklylidenes and Carbenes 41.18.1 CH2 Singlet–Triplet Gap Controversy Theory Versus Experiment 41.18.2 Other Singlet and Triplet Aklylidene like Species 41.19 Hyperfine Interactions 41.20 Other Papers 42 Methods for GVB and Extended Wavefunctions and for DFT 42.1 General Formulation with Full Orbital and Spin Optimization, no Restrictions on Core Orbitals 42.2 Optimal Optimization of Optimal Orbitals 42.3 Perfect Pairing 42.4 GVB-RCI 42.5 Resonance 42.6 Developments in DFT Theory 42.6.1 Including London Dispersion 42.6.2 X3LYP Extended Density Functional 42.6.3 Extended DFT: PBE, OPTX 42.7 Applications of QM to Systems Involving Solvent 42.8 Grand Canonical QM 42.9 Reactive Force Field Embedded QM (ReQM) 42.10 Band Gaps 42.11 Improved Virtual Orbital for Excited Rydberg States 42.12 Periodic Boundary Conditions QM 42.13 Quantum Monte Carlo QM 42.14 Pseudospectral Methods, Collaboration with Rich Friesner 42.15 Miscellaneous 43 Ab Initio Pseudopotentials (Extending Ab Initio QM Throughout the Periodic Table) 44 Electron Dynamics and Electron Transfer 44.1 Large-Scale Electron Dynamics (EFF) 44.2 Simulation of Low Energy Electron-Enhanced Etching (LE4). Test of the Auger-Induced Etching Hypothesis 44.3 Exoelectron Emission in Fracturing of Si 44.4 Summary EFF 44.5 Studies of Electron Transfer 44.6 Dielectric Breakdown in SiO2 44.7 Predicting Electrical Resistivity 44.8 Electron Impact Spectroscopy 45 Classical Force Fields and Methods of Molecular Dynamics 45.1 First Principles Force Constants—Biased Hessian Method 45.1.1 Hessian-Biased References 45.1.2 Other FF Fitting to Experiment 45.2 Dreiding Generic Force Field 45.3 Extending MD Simulation to Far Larger Atomistic Systems—The UFF Generic Force Field 45.4 Nonbond Interactions and London Dispersion, from Experiment 45.5 The Next Generation Nonbond and London Dispersion Function from QM for the RexPoN Reactive FF 45.6 Coarse Grain Force Field for Malto-Oligosaccharides 45.7 Methods for Long-Range Summations: Fast Ewald, Cell Multipole Expansions 45.8 MD Simulation Talks 46 Charges and Polarization Without QM 46.1 QEq—Charge Equilibration 46.2 PQEq—Polarized Charge Equilibration 46.3 Implementations of QEq 47 Force Fields for Reactive Dynamics (ReaxFF, RexPoN) 47.1 ReaxFF Reactive Force Fields 47.2 ReaxFF Reactive Force Field for H2O the First Principles-Based FF for Proton-Water Systems 47.3 Recent Developments. the RexPoN Reactive Force Field Based on the Universal NB Functions from QM and PQEq 47.3.1 The MS-Q Reactive Force Field 47.4 Generalized Extended BO Dependent Force Field 48 Free Energy and Entropy from MD 48.1 Two-Phase Thermodynamics (2PT) Theory 48.2 Application of 2PT to Liquid H2O 48.3 Application of 2PT to the DNA Three-Way Junction 48.4 2PT References 48.5 Collaborations with Rick Flagan: Entropy and Free Energy of Clusters 48.6 Other Studies 49 Extracting Reaction Kinetics for Complex Reaction Systems 49.1 Predicting the Chapman–Jouguet Chemical Equilibrium State (CJ State) in a Detonation Wave 49.2 Accelerated Reaction Dynamics Using ReaxFF 49.3 Extracting Reaction Kinetics for Complex Reaction Systems 49.4 Reactions Mechanisms from ReaxFF Reactive Dynamics 49.5 Reactions Mechanisms from QM for Hypergolic Liquids 49.6 Reactions Mechanisms Involving Singlet Di-Oxygen 49.7 Reactions Mechanisms Involving Ozone 49.8 Dynamics of Surface Desorption 49.9 Other Reactions Mechanisms 50 Solvation Methods and Applications 50.1 Finite Systems Poisson–Boltzmann 50.2 Periodic Systems 50.3 COSMO and Cluster Methods 50.4 The Water–Air Interface 50.5 Surface Tension 50.6 Solvent Effects on Conformational Equilibria; Collaboration with Jack Roberts 50.7 Applications to Oil Field Technology 50.8 Other Solvent-Based Reactions Part VIBulk Materials, Surfaces, Interfaces, Nanomaterials 51 Surface Science 51.1 Introduction 51.2 Silicon Surfaces and Chemisorbed Species 51.3 GaAs Surfaces and Oxidation of Si and GaAs 51.4 Metal Surfaces and Chemisorbed Species 51.4.1 Nickel 51.4.2 Platinum 51.5 Interfaces 51.6 Kinetics of Desorption 51.7 Interpretation of STM and AFM 51.8 CVD Growth 51.9 Self-assembled Monolayers Alkanethiols on Au(111) 51.10 Ceramic Surfaces 51.11 Diffusion on Surfaces 52 Nanotechnology 52.1 Synthesis of Carbon Single-Wall Nanotubes 52.2 Fullerenes and Carbon Nanotubes 52.3 Contacts to Carbon Nanotubes, Graphene 52.4 STM Images 52.5 2D Electronics 52.5.1 Collaboration with Seiko-Epson 52.5.2 Negative Differential Resistance 52.5.3 Others 52.6 Plasmon-Electronic Coupling (Collaboration with Harry Atwater) 52.7 Topological Insulators 52.8 Additional Papers Nanotechnology 52.9 Molecular Machines 53 Metals 53.1 Amorphous Metals, Bulk Metallic Glasses 53.2 QM-Based Modeling Plasticity in Ta and Ni 53.3 Cavitation, Spallation 53.4 Tribology 53.4.1 Al2O3 and Metallic Aluminum (General Motors) 53.4.2 Friction for Diamond-like Carbon (Nissan) 53.4.3 Wear Inhibitors (Chevron, Oronite) Dithiophosphate and Dithiocarbamate 53.4.4 Corrosion Inhibitors (Chevron). Oleic Imidazolines 53.5 Nanoscale Mechanical Properties 53.6 Geochemistry 53.7 Viscosity 53.8 Talks 54 Ceramics–Boron Carbide-Ferroelectrics 54.1 Strength and Brittleness in Ceramics (B4C) 54.2 Boron Compounds Boron leads to some strange structures involving B12 icosahedra and also B28 shells 54.3 SiC, MgO, C3N4 54.4 Bulk Semiconductor Defects 54.5 Silica to describe silica glass with Na, Mg, etc. we developed the MsQ force field, which uses QEq to describe the electrostatics combined with cation-oxygen Morse term to provide the inner wall. This is a great way to describe oxides, but we did not publish a systematic study 54.6 Zeolites and Clays 54.7 Ferroelectrics and Sensors 54.8 Crack Propagation in Silicon Crystals 54.9 Miscellaneous 55 Mechanically Bonded Materials (Stoddart) 55.1 The Rotaxane-TTF Switch 55.2 Barrier Hopping 55.3 Design of a Three-Station Catenane, Voltage Tunable for Three-Color RGB Molecular Switch 55.4 Design of Mechanically Bonded Machines 55.5 Establishing the 1:1 Inclusion Complex Nature of CBPQT with TTF 55.6 Design of Multi-Radical Using Mechanical Bonding 55.7 Transport in Mechanical Bonded Systems 56 Solar Cells 56.1 Cu-In-Ga-Se Solar Cells (CIGS) 56.2 Dye-Sensitized Solar Cells 56.3 Photonics and Photo-Electrochemistry 56.4 Semiconductor Growth 56.5 Perovskite Solar Cells 57 Batteries 57.1 RexPoN Embedded QM (ReQM) Methodology for Atomistic Description of the SEI 57.2 Electrodes 57.3 Dendrite Growth 57.4 Superprotonic Acid Electrolytes 57.5 Electrode-Electrolyte Interface 57.6 Supercapacitor Electrodes 57.7 Electrolytes for Batteries 58 Thermoelectrics 58.1 ZT Thermoelectrics 58.2 Local Defects Thermoelectrics 58.3 Mechanical Strength Thermoelectrics 58.4 Thermal Conductivity Calculations 59 MOFs, COFs, and ZIFs Plus H2 and CH4 Storage 59.1 H2 Storage Materials, not Framework Systems 59.2 H2 Storage in MOFs, COFs, and ZIFs 59.3 CH4 Storage in MOFs, COFs, and ZIFs 59.4 MOF Large Negative Thermal Expansion (NTE) Behavior 60 Energetic Materials 60.1 QM Unimolecular Decomposition of RDX, HMX and ReaxFF Reactive Force Field 60.2 Shock Decomposition of Plastic Bonded Explosives (PBX) Formation of Hot Spots 60.3 Simulations of New Generation Energetic Materials, CJ Condition, Detonation Velocity 60.4 Origin and Computational Tests for Sensitivity 60.5 ReaxFF for Energetic Materials 60.6 Shock Decomposition of Other Materials 60.7 Predicting the Chapman–Jouguet Chemical Equilibrium State (CJ State) in a Detonation Wave 61 Superconductors: Cuprate High Tc and BEDT-TTF Organic Superconductors 61.1 Cuprates Round 1; the Magnon Pairing Theory 61.2 The tJ Model of Superconductivity 61.3 Cuprates Round 2; Chiral Plaquette Polaron Theory of Cuprate Superconductivity 61.4 The BEDT-TTF Organic Superconductors 61.5 Other Papers on Superconductivity Part VIIChemistry, Catalysis 62 Mechanisms for Homogeneous Catalysis 62.1 Papers in Collaboration with Roy Periana: CH4 Activation and Functionalization 62.2 Papers in Collaboration with Brent Gunnoe: Rh Based Homogeneous Catalysts and CH4 Activation 62.3 Papers in Collaboration with Jay Groves: Porphyrin-Oxo Systems 62.4 Papers in Collaboration with Alan Goldman: Ir Based Homogeneous Catalysts for Activation C–H Bonds 62.5 Papers in Collaboration with Harry Gray: HER 62.6 Papers in Collaboration with Andrei Vedernikov: Alkane Activation 62.7 Papers in Collaboration with Brian Stoltz: Enantioselective Reaction Mechanisms 62.8 Papers in Collaboration with Dow Corning: Olefin Hydrosilylation 62.9 Papers in Collaboration with Dow Chemical: Copolymerization of Ethylene with Polar Olefins 62.10 Papers in Collaboration with Bob Grubbs: Metathesis with Grubbs Ru Catalyst 62.11 Papers in Collaboration with Dave Evans: Oxy Anionic Cope Rearrangement 62.12 Activa