دانلود کتاب Computational Materials, Chemistry, and Biochemistry: From Bold Initiatives to the Last Mile. In Honor of William A. Goddard’s Contributions to Science and Engineering

فهرست مطالب :

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 Activation of Molecular O2
62.13 Wacker-Type Oxidation
62.14 Papers in Collaboration with Dean Toste: Au(I)
62.15 Papers in Collaboration with Tobias Ritter: Pd(IV)
62.16 Papers in Collaboration with Paula Diaconescu: Group 3 Chemistry
62.17 Bio-Mimetic: Methane Mono-Oxygenase
62.18 Other Papers on Homogeneous Catalysis
62.19 Organic Light Emitting Diodes (OLED) Collaboration with Mark Thompson
63 Mechanisms for Heterogeneous Catalysis
63.1 Ammoxidation of Propene by BiMoOx
63.2 Butane  → Maleic Anhydride (C4O3H2) by Vanadium Pyrophosphate, (VPO)
63.3 Ammoxidation of Propane by MoVNbTeOx
63.4 Haber–Bosch Synthesis of NH3 Over Fe(111)
63.5 Fischer-Tropsch
63.6 Epoxidation of Ethylene Over Ag
63.7 Ziegler-Natta Catalysis
63.8 Oxidative Dehydrogenation
63.9 Acceleration of Catalytic Reactions Using Surface Acoustic Waves
63.10 Resolving Rietveld Structures in Terms of Whole Atoms
63.11 Other Papers on Catalysis
64 Fuel Cells Electrocatalysis with QM and FF
64.1 The Reaction Mechanism and Barriers for the Oxygen Reduction Reaction (ORR) at the Pt(111) Cathode from QM Metadynamics
64.2 The Reaction Mechanism for De-alloyed Ni Rich Pt Alloy Nanoparticles
64.3 The Reaction Mechanism for De-alloyed Ni Rich Pt Alloy Nanowires
64.4 Other ORR Studies
64.5 Solid Oxide Fuel Cells
64.6 Solid Acid Fuel Cells
64.7 Nafion Electrolyte from MD Simulations
64.7.1 Nanoscale Structure
64.7.2 Degradation
64.8 Methanol Fuel Cell
64.9 Other Membranes
65 Electrocatalytic Water Splitting (H2O → H2+½ O2)
65.1 Oxygen Evolution Reaction (OER)
65.2 Hydrogen Evolution Reaction (HER)
65.2.1 HER at MoS2 Edge Sites
65.2.2 Other HER
65.3 Photoinduced HER on Organic Perovskites
65.4 Other Papers on Water Splitting
66 Electrocatalytic CO2 Reduction
66.1 CO2 Reduction on Cu(100) Using Full Solvent DFT Metadynamics
66.2 CO Reduction to CH4 at PH = 0 on Cu(100) Using Full Solvent DFT Metadynamics
66.3 CO Reduction at PH = 7 on Cu(100) Using Full Solvent DFT Metadynamics
66.4 CO Reduction on Cu(111) Using Grand Canonical Constant Potential QM
66.5 Design of New Catalysts for CO2 Reduction
66.6 CO2 → Ethanol on 10 nm Cu Nanoparticles (ReaxFF CVD)
66.7 CO2 → CO on 10 nm Au Nanoparticles (ReaxFF CVD)
66.8 In Silico Optimization of Au NP
66.9 Other Recent Papers on CO2 Reduction
Part VIIIBiological Materials, Devices, Polymers
67 Polymers: Dendrimers-Network-Electrolye-NLO
67.1 Dendrimers
67.2 Predicting the Structures of Amorphous Polymers
67.2.1 Single Chain Studies: The Continuous Configurational Boltzmann Biased Direct Monte Carlo Method
67.2.2 Periodic Methods the Belmares Cohesive Energy Protocol
67.2.3 The Scaled Effective Solvent (SES) Method to Grow High Molecular Weight Polymers
67.3 Predicting the Structures of Crystalline Polymers
67.3.1 Polyethylene
67.3.2 Poly(Vinylidene Fluoride), PVDF
67.3.3 Nylon
67.4 Polymer Electrolytes
67.5 Hydrogels and Network Polymers
67.6 Asphaltenes and Humic Acids
67.7 Nonlinear Optical Properties, Hyperpolarizabilities and Dielectric Properties
67.8 Smart Polymers
67.9 Aqueous Pullulan Oligomers
67.10 Gas Diffusion Through Polymer Membranes
67.11 Hyperbranched Polyethyleneimines
67.12 Making Gases into Polymers
68 GPCR and Other Proteins: Predictions of Structures and Ligand Binding
68.1 Protein Folding
68.2 Methods for Protein Structure Predictions, Particularly G Protein-Coupled Receptors (GPCRs)
68.2.1 Predicted Structures for Olfactory Receptors and Their Ligand Binding Sites
68.2.2 The First Full Atom Structures for β2 Adrenergic Receptor and D2 Dopamine Receptor
68.2.3 The 2nd Generation Methods: BiHelix, SuperBiHelix, and GEnSeMBLE
68.2.4 Application to DP Prostaglandin Receptor and Ligand Optimization
68.3 Structure Predictions for GPCRs and Other Protein Structures
68.3.1 Adenosine GPCR
68.3.2 Adrenergic GPCR
68.3.3 CB1 Receptor GPCR
68.3.4 Chemokine GPCRs: CCR1 and CCR5
68.3.5 Dopamine GPCRs: D1 and D2
68.3.6 Histamine GPCRs: H3
68.3.7 Lipid Binding GPCRs
68.3.8 Mrg GPCRs: Mouse MrgC11 and Rat Mrg a
68.3.9 Muscarinic GPCRs: M1
68.3.10 Olfactory GPCRs
68.3.11 Opioid Receptors GPCRs: Kappa and Mu
68.3.12 Ion Channel GPCRs: P2X7
68.3.13 Prostaglandin GPCRs: DP
68.3.14 Serotonin GPCRs: 2abc
68.3.15 Somatostatin GPCRs: SST5
68.3.16 Urotensin GPCRs: II
68.3.17 Taste GPCRs: Tas2R38
68.3.18 Class B GPCRs: GLP1-R
68.3.19 Non Mammal GPCRs
68.3.20 Rhinovirus
68.3.21 Chitinases
68.3.22 Bioinorganic Proteins
68.4 G Protein Activation
68.5 Ligand Binding Predictions to GPCRs and Other Proteins
68.6 Collaborations with Linda Hsieh-Wilson on GAG Control of Nerve Growth
68.7 Collaborations with David Tirrell: Non-natural Amino Acids
68.8 Collaborations with Nemani Prasadarao of Children’s Hospital LA: Neo-Natal Meningitis
68.9 Collaborations with Jack Beauchamp: Membranes and Surfactants
68.10 Collaboration with Richard Lerner of Scripps: Singlet O2 and Ozone in Antibodies
68.11 Collaborations with Steve Pandol of Cedars-Sinai Hospital: Ligands Against Disease
68.12 Collaborations with Xin Wen CSULA: Freezing Point Depression
68.13 Collaboration with Jack Snively of City of Hope: Cancer Radioimmunotherapy
68.14 Rubredoxin
68.15 Porphyrin Based Systems
68.16 Secondary Structure
68.17 Bio Simulations
68.18 Phosphoglycerate Kinase
69 DNA-RNA
69.1 Ned Seeman’s DNA Crossover Structures
69.2 DNA Origami
69.3 Design of Proteins to Very Selectively Recognize Specific 16 bp DNA Binding Sites
69.4 DNA Repair Mechanisms
69.5 Other DNA Applications
Author Index