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Format: 1 online resource (438 p.)

Edition: First edition.

ISBN: 0-444-63682-X , 0-444-63710-9

Series Statement: Annual Reports in Computational Chemistry ; v.11

Note: Description based upon print version of record. , Front Cover -- Annual Reports in Computational Chemistry -- Copyright -- CONTENTS -- CONTRIBUTORS -- PREFACE -- A - Quantum Chemistry -- One - NMR Calculations for Paramagnetic Molecules and Metal Complexes -- 1. INTRODUCTION -- 2. THEORY -- 3. PNMR CHEMICAL SHIFTS: SELECTED CASE STUDIES AND OVERVIEW OF RECENTLY PUBLISHED COMPUTATIONAL STUDIES -- 4. SUMMARY AND OUTLOOK -- ACKNOWLEDGMENTS -- REFERENCES -- Two - The Nonlocal Correlation Density Functional VV10: A Successful Attempt to Accurately Capture Noncovalent Inte ... -- 1. INTRODUCTION -- 2. HISTORICAL DEVELOPMENT OF NONLOCAL DENSITY FUNCTIONAL CORRELATION KERNELS -- 3. THE NONLOCAL CORRELATION DENSITY FUNCTIONAL VV10: AN ELEGANT AND SEAMLESS APPROXIMATION -- 4. THE NONLOCAL CORRELATION DENSITY FUNCTIONAL VV10 COUPLED TO MODERN EXCHANGE-CORRELATION FUNCTIONALS -- 4.1 Accuracy of the Nonlocal VV10-Type Approximation: Benchmarks Against the S22 and S66 Training Sets -- 4.2 Accuracy of the Nonlocal Approximation in Large Molecular Aggregates -- 4.3 Additional Chemical Benchmarks of the Nonlocal Approximation -- 4.4 Molecular Crystal Properties -- 4.5 Layered Solids -- 4.6 Physisorption of Small Molecules -- 5. ROADMAP: FUTURE DIRECTIONS AND CHALLENGES -- 6. CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- Three - Modeling Laser-Induced Molecule Excitations Using Real-Time, Time-Dependent Density Functional Theory -- 1. INTRODUCTION -- 2. THEORETICAL BACKGROUND -- 2.1 Overview of RT-TDDFT -- 2.2 Time-Dependent Fock Matrix -- 2.3 Time Propagation Methods -- 2.4 The External Laser Field and Molecular Properties -- 2.5 Quantum Chemistry Codes -- 3. APPLICATIONS OF RT-TDDFT STUDIES -- 3.1 Electronic Absorption Spectra -- 3.2 Assignment of Excitations in Terms of Orbital Transitions -- 3.3 Excited Charge Dynamics -- 3.4 The Influence of the Laser Field Parameters -- 4. FINAL REMARKS -- ACKNOWLEDGMENTS. , REFERENCES -- Four - Chemical Bonding, Reactivity, and Viability of Large Boron Clusters -- 1. INTRODUCTION -- 2. CHEMICAL BONDING AND SYMMETRY OF B80 -- 2.1 Chemical Bonding Analysis -- 2.2 Symmetry of B80 and B80+ -- 2.2.1 Instability of the Icosahedral B80 -- 2.2.2 Instability of the Icosahedral B80+ -- 3. REACTIVITY AND AROMATICITY OF B80 -- 3.1 Reactivity of B80 -- 3.1.1 Fukui Function Indices -- 3.1.2 Molecular Electrostatic Potential -- 3.1.3 Frontier Molecular Orbital Theory and Natural Bond Orbitals -- 3.1.4 Exohedral and Endohedral B80 Complexes -- 3.2 Is B80 Nonaromatic as Is Its Homologous C60? -- 4. THE BORON CONUNDRUM -- 4.1 The Leapfrog Principle for Boron Fullerenes -- 4.1.1 Principle -- 4.1.2 Application of Leapfrog Principle to C28 -- 4.2 Which Principle Underlies the Formation of B80 Fullerenes? -- 4.2.1 All Pentagons Capped Structures (Volleyballs) -- 4.2.1.1 Symmetry Classification and Search for the Most Stable Isomer -- 4.2.1.2 Geometrical and Electronic Structures of Volleyball Type B80 Isomers -- 4.2.2 Partially Filled Pentagons Structures -- 5. CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- B - Scattering Theory -- Five - A Computational Perspective on Multichannel Scattering Theory with Applications to Physical and Nuclear Chem ... -- 1. INTRODUCTION -- 2. ELECTRON SPECTROSCOPIES -- 2.1 Electron Energy Loss Spectroscopy -- 2.2 Photoelectron Spectroscopy -- 2.3 Auger Emission -- 2.4 Near-Edge X-Ray Absorption Fine Structure -- 3. GENERAL THEORIES OF MULTICHANNEL SCATTERING AND DECAY PROCESSES -- 3.1 Time-Dependent versus Time-Independent Approach to Scattering -- 3.2 Time-Independent Scheme for Multichannel Scattering in Many-Body Systems -- 3.3 The T Matrix and the Lippmann-Schwinger Equation -- 3.4 The Scattering States and Cross Sections -- 3.4.1 The Time-Independent Fano's Approach to Resonant Multichannel Scattering. , 3.4.2 The Concept of Autoionization and Auger Effect as Resonant Multichannel Scattering -- 3.5 A Scattering View of Many-Body Perturbation Theory -- 3.6 Time-Dependent Quantum Mechanical Approach -- 3.6.1 Wave Packet Propagation in the Excited States -- 3.6.2 Path-Integral Formulation of Multichannel Resonant Scattering -- 3.6.3 The Feshbach Time-Dependent View of Resonant Scattering -- 4. CALCULATION OF THE SPECTRAL ENERGY IN ELECTRON SPECTROSCOPY -- 4.1 The HF Method -- 4.2 Post-HF Methods -- 4.2.1 Configuration Interaction Method -- 4.2.2 The Green's Function Method -- 4.2.3 Toward an Accurate Treatment of Correlation in Extended Systems: DFT, MBPT, TDDFT, DMRG -- 5. A UNIFIED METHOD FOR CALCULATING EXCITATION SPECTRA IN SOLIDS -- 5.1 Strategies for Calculating Excitation Spectra in Extended Systems -- 5.2 On the Use of the Projection Operator Formalism in Many-Body Scattering Theory -- 5.3 Evaluation of Spectroscopic Quantities -- 5.4 Cini-Sawatzky Theory for CVV Auger Transitions and Multisite Correlations -- 5.5 Ab Initio Calculation of Electron Spectra -- 5.5.1 Chemical Shifts in Photoemission -- 5.5.1.1 Propene -- 5.5.1.2 Graphene -- 5.5.2 NEXAFS Spectrum from Graphene and Hydrogenated Graphene -- 5.6 EEL Spectra for Quantitative Understanding of Electron Spectra -- 5.6.1 Electron-Atom Elastic Scattering -- 5.6.2 Electron-Electron Interaction -- 5.6.3 Electron-Phonon Interaction -- 5.6.4 Electron-Polaron Interaction -- 5.6.5 The MC Scheme -- 5.7 The Unified Method at Work: Auger Spectra from SiO2 Including the Energy Loss -- 5.8 Core-Level Spectroscopy of Folding Proteins -- 6. BEC-BCS CROSSOVER WITH CONTACT INTERACTION -- 6.1 Ab Initio Calculation of the Scattering Length of Alkali Metals: The Case of 6Li -- 6.2 Application of Scattering Theory to the Solution of the BdG Equations -- 6.2.1 The HF Term W. , 6.2.2 The Equation for the Pairing Function Δ -- 6.3 Calculation of the T-Matrix of the Pair-Potential -- 6.3.1 Nonuniversal Behavior in the Unitary Limit -- 6.4 Computational Flowchart of Our Multichannel Approach to Ultracold Fermi Gases -- 7. APPLICATIONS OF OUR AB INITIO APPROACH TO NUCLEAR PHYSICS AND STELLAR NUCLEOSYNTHESIS: THE CASE OF β-DECAY OF BE AND LA -- 8. CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- C - Theory of Liquids -- Six - Intermolecular Network Theory: A General Approach for Understanding the Structural and Dynamic Properties of ... -- 1. INTRODUCTION -- 2. DEFINITION OF THE INTERACTION, CREATION OF THE NETWORK, AND ESSENTIAL TERMINOLOGY -- 3. LOCAL STRUCTURE OF THE NETWORK -- 3.1 Edge-Based Properties -- 3.2 Two- and Three-Dimensional Pattern Recognition -- 3.2.1 Two-Dimensional (2D) Cycles -- 3.2.2 Direct Three-Dimensional (3D) Searches -- 3.2.3 PageRank -- 4. EXTENDED STRUCTURE IN A NETWORK -- 4.1 Network Neighborhood -- 4.2 Geodesic Analysis -- 4.2.1 Topological Indices -- 4.2.2 Chemical Clustering -- 4.3 Spectral Graph Theory -- 4.4 Clustering and Percolation Theory -- 5. DYNAMIC PROPERTIES OF THE NETWORK -- 5.1 Persistence of Network Patterns -- 5.2 Mechanisms of Pattern Dynamics -- 6. OPEN-SOURCE SOFTWARE -- 7. OUTLOOK -- ACKNOWLEDGMENTS -- REFERENCES -- SUBJECT INDEX -- A -- B -- C -- D -- E -- F -- G -- H -- I -- J -- K -- L -- M -- N -- O -- P -- Q -- R -- S -- T -- U -- V -- W -- X -- Z -- CUMULATIVE INDEX -- Symbols -- A -- B -- C -- D -- E -- F -- G -- H -- I -- J -- K -- L -- M -- N -- O -- P -- Q -- R -- S -- T -- U -- V -- X -- Y -- Z -- Back Cover.

Language: English

UID:

Format: 1 online resource (266 pages) : , illustrations, tables.

ISBN: 0-444-63741-9

Series Statement: Annual Reports in Computational Chemistry, Volume 12

Note: Front Cover -- ANNUAL REPORTS IN COMPUTATIONALCHEMISTRY -- ANNUAL REPORTS IN COMPUTATIONALCHEMISTRY -- Copyright -- Contents -- CONTRIBUTORS -- Preface -- Section A Quantum Chemistry -- One - Prediction of Thermochemical Properties Across the Periodic Table: A Review of the correlation consistent Com ... -- 1. INTRODUCTION TO THE CCCA METHODOLOGY -- 2. CCCA FUNDAMENTALS -- 3. CCCA VARIANTS -- 3.1 Extension of ccCA to 3d Transition Metal Systems: ccCA-TM -- 3.2 relativistic-pseudopotential Approach: rp-ccCA -- 3.3 Inclusion of Multireference Character: MR-ccCA and ccCA-CC(2,3) -- 3.4 Application to Larger Chemical Systems: ONIOM-ccCA -- 3.5 Methods to Decrease the Computational Cost: RI-ccCA and ccCA-F12 -- 3.6 Prediction of Solvation Effects: Solv-ccCA -- 3.7 Description of Heavy Element Chemistry in the f-Block -- 4. APPLICATION OF CCCA ACROSS THE PERIODIC TABLE -- 5. CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- Two - The Impact of Larger Basis Sets and Explicitly Correlated Coupled Cluster Theory on the Feller-Peterson-Dixon ... -- 1. INTRODUCTION -- 2. SUMMARY OF THE FPD APPROACH -- 3. RESULTS FROM STANDARD COUPLED CLUSTER METHODS WITH LARGER BASIS SETS -- 3.1 Atomization Energies -- 3.2 Adiabatic Electron Affinities -- 3.3 Adiabatic Ionization Energies -- 3.4 Miscellaneous Spectroscopic Properties -- 4. COMPARISONS WITH EXPLICITLY CORRELATED COUPLED CLUSTER METHODS -- 5. CONCLUSION -- ACKNOWLEDGMENTS -- REFERENCES -- Section B New Theories of Bonding -- Three - Recoupled Pair Bonding: Unifying the Theory of Valence for the Main Group Elements -- 1. INTRODUCTION -- 2. GENERALIZED VALENCE BOND THEORY -- 3. THE CFN AND SFN SERIES -- 3.1 Ground and First Excited States of the CF and SF Molecules -- 3.2 Ground and First Excited States of the CF2 and SF2 Molecules -- 3.3 Ground States of CF3 and SF3 -- 3.4 Ground States of CF4 and SF4. , 3.5 Beyond SF4 -- 3.6 Other Late Main Group Compounds -- 4. ADDITIONAL OCCURRENCES OF RECOUPLED PAIR BONDING -- 4.1 Edge Inversion in Heavily Fluorinated Phosphorus Compounds -- 4.2 Reactions of Organic Sulfur Species with Molecular Fluorine -- 4.3 Dimerization of SF2 -- 4.4 Differences in First and Second Row Valence Isoelectronic Species -- 5. SUMMARY -- ACKNOWLEDGMENTS -- REFERENCES -- Section C Geochemistry -- Four - Computational Isotope Geochemistry -- 1. INTRODUCTION -- 2. OVERVIEW OF ELECTRONIC STRUCTURE THEORY FOR IFF CALCULATIONS ESPECIALLY FOR GEOCHEMICAL APPLICATIONS -- 3. THE VIBRATIONAL EIGENVALUE PROBLEM -- 4. ISOTOPE EXCHANGE EQUILIBRIA -- 5. QUALITATIVE INSIGHTS -- 6. QUANTITATIVE ESTIMATES -- 7. CALCULATING THE 11B-10B ISOTOPE FRACTIONATION FACTOR FOR B(OH)3(AQ) AND B(OH)4-(AQ)-A SPECIFIC EXAMPLE -- 8. RELATIONSHIP TO EMPIRICAL ESTIMATES -- 9. BEYOND THE HARMONIC APPROXIMATION -- 10. KINETIC ISOTOPE EFFECTS -- REFERENCES -- Section D Nanoparticles -- Five - Computer Simulation and Modeling Techniques in the Study of Nanoparticle-Membrane Interactions -- 1. INTRODUCTION -- 1.1 Nanoparticles in Computational Studies -- 1.2 The Cellular Entry of Nanoparticles -- 2. FREQUENTLY EMPLOYED COMPUTATIONAL TECHNIQUES IN NANOPARTICLE-MEMBRANE STUDIES -- 2.1 All-Atom Molecular Dynamics -- 2.1.1 Theoretical Background -- 2.1.2 Model Construction and Parameterization -- 2.1.3 Example Applications -- 2.2 Coarse-Grained Molecular Dynamics -- 2.2.1 Martini Coarse-Grained Force Field -- 2.2.1.1 Theoretical Background -- 2.2.1.2 Model Construction and Parameterization -- 2.2.1.3 Example Applications -- 2.2.2 Implicit-Solvent Coarse-Grained Model of Membranes -- 2.2.2.1 Theoretical Background -- 2.2.2.2 Model Construction and Parameterization -- 2.2.2.3 Example Applications -- 2.3 Dissipative Particle Dynamics -- 2.3.1 Theoretical Background. , 2.3.2 Model Construction and Parameterization -- 2.3.3 Pure Lipid Bilayer -- 2.3.4 Nanoparticle-Bilayer -- 2.3.5 Example Applications -- 2.4 Continuum Modeling -- 2.4.1 Theoretical Background -- 2.4.2 Model Construction and Parameterization -- 2.4.3 Example Applications -- 3. SUMMARY -- ACKNOWLEDGMENT -- REFERENCES -- SUBJECT INDEX -- A -- B -- C -- D -- E -- F -- G -- H -- I -- L -- M -- N -- O -- P -- R -- S -- V -- Z -- CUMULATIVE INDEX -- Symbols -- A -- B -- C -- D -- E -- F -- G -- H -- I -- J -- K -- L -- M -- N -- O -- P -- Q -- R -- S -- T -- U -- V -- W -- X -- Y -- Z -- Back Cover.

Additional Edition: ISBN 0-444-63714-1

Language: English

UID:

Format: 1 online resource (294 pages) : , illustrations.

ISBN: 0-444-63944-6 , 0-444-63940-3

Series Statement: Annual Reports in Computational Chemistry ; Volume 13

Note: Front Cover -- Annual Reports in Computational Chemistry -- Copyright -- Contents -- Contributors -- Preface -- Section A: Quantum Chemistry - Weak and Non-Bonded Interactions -- Chapter One: Benchmark Databases of Intermolecular Interaction Energies: Design, Construction, and Significance -- 1. Introduction -- 2. Computing Accurate Interaction Energies -- 2.1. Leading Term: Frozen-Core CCSD(T) -- 2.1.1. CBS Extrapolation -- 2.1.2. Bond Functions -- 2.1.3. Explicitly Correlated CCSD(T) -- 2.1.4. CCSD(T) Benchmarks for Large Systems -- 2.2. Coupled-Cluster Terms Beyond CCSD(T) -- 2.3. Other Corrections -- 2.3.1. Core-Core and Core-Valence Correlation -- 2.3.2. Relativistic and QED Effects -- 2.3.3. Diagonal Born-Oppenheimer Correction -- 2.3.4. Molecular Clusters and Many-Body Interactions -- 2.3.5. Beyond Interaction Energies: Monomer Deformation and Zero-Point Energy -- 3. The Design of Benchmark Databases -- 3.1. Diversity of the Benchmark Set -- 3.2. Assessing Performance Over a Database: Statistical Measures -- 3.3. Interaction Energies of Dimers -- 3.4. Binding Energies of Clusters -- 4. Applications of Benchmark Noncovalent Databases -- 4.1. Assessing and Improving DFT-Based Approaches -- 4.2. Assessing and Improving Wavefunction-Based Approaches -- 4.3. Assessment and Development of Semiempirical and Empirical Approaches -- 5. Summary and Outlook -- Acknowledgments -- References -- Chapter Two: Dissociation in Binary Acid/Base Clusters: An Examination of Inconsistencies Introduced Into the Many-Body E ... -- 1. Introduction -- 1.1. Background -- 1.2. A Simple Illustration With the Hydrogen Fluoride Tetramer -- 1.3. Overview -- 2. Computational Details -- 3. Results and Discussion -- 3.1. (HF)4 -- 3.2. (HF)3(NH3) -- 3.3. Hydrated Hydrochloric Acid -- 3.4. Hydrated Sulfuric Acid -- 4. Summary and Conclusions -- Acknowledgments -- References. , Chapter Three: The Quantum Chemical Study of Chemical Reactions at Extreme High Pressure by Means of the Extreme-Pressure ... -- 1. Introduction -- 2. The XP-PCM Method -- 2.1. The Effective PES of a Reactive Molecular Systems at Extreme High Pressure -- 2.2. The Free Energy Functional Ger -- 2.3. The Pressure -- 2.4. The Cavitation Free Energy -- 3. The Computational Protocol for the Study of the PES of a Reaction at Extreme High Pressure -- 3.1. The Scaling of the Molecular Cavity for the Calculation of the Electronic Energy and of the Pressure -- 3.2. Dielectric Permittivity and Numeral Density of the External Medium -- 3.3. The PES Gtot(R) as a Function of the Pressure p -- 4. Numerical Results -- 4.1. Diels-Alder Reaction of the Endo Dimerization of Cyclopentadiene -- 4.2. Effect of Extreme High Pressure on the Reaction Energy Profile -- 4.3. The Calculation of the Activation and Reaction Volumes -- 5. Conclusion -- Acknowledgments -- References -- Section B: Quantum Chemistry - Novel Approaches for Understanding Bonding -- Chapter Four: Interpreting Bonding and Spectra With Correlated, One-Electron Concepts From Electron Propagator Theory -- 1. Insight Into Molecular Properties and the Electron Propagator -- 2. One-Electron Concepts in Electron Propagator Theory -- 2.1. Dyson Quasiparticle Equation: Electron Binding Energies and Dyson Orbitals -- 2.2. Reference-State Energies and Properties -- 2.3. Transition Probabilities and Final-State Properties -- 2.4. Approximations and Applications -- 3. Electron Propagator Foundations -- 3.1. Time and Energy Representations -- 3.2. Equation of Motion -- 3.3. Super-Operator Theory and the Dyson Equation -- 3.4. Diagonalization of Ĥ -- 3.5. Pole Strengths -- 3.6. Reference-State Properties -- 4. Approximations in the Fock and Self-Energy Matrices -- 4.1. Operator Manifolds and Reference States. , 4.2. Hermiticity and Orthogonality Considerations -- 4.3. Second-Order Approximations -- 4.4. Third-Order Approximations and Their Extensions -- 4.5. Non-Dyson Methods -- 4.6. GW Methods -- 4.7. Nondiagonal, Renormalized, Second-Order Theory -- 4.8. Partial Third-Order and Renormalized Partial Third-Order Methods -- 4.9. Renormalized Reference States -- 5. Numerical Characterization -- 5.1. Comparisons of F+Σ(E) Approximations -- 5.2. Estimation of Basis-Set Effects -- 6. Recent Applications and Extensions -- 6.1. Molecular Wires -- 6.2. Solvated Molecules -- 6.3. Gas-Phase Anions -- 6.4. Super-Halogens -- 6.5. Positronic Complexes -- 6.6. Anionic Resonances -- 6.7. Photoionization Cross Sections -- 7. Software Developments -- Acknowledgments -- References -- Section C: Quantum Chemistry - Periodic Simulations -- Chapter Five: Plane-Wave DFT Methods for Chemistry -- 1. Introduction -- 2. Plane-Wave Basis Set -- 2.1. Brillouin Zone -- 3. Pseudopotential Plane-Wave and Projector Augmented Wave Methods -- 3.1. Total Energy of the Pseudopotential Plane-Wave Method -- 3.2. Total Energy of the PAW method -- 3.3. Electronic Gradients and Atomic Forces -- 3.4. Charged Systems and Free-Space Boundary Conditions -- 3.5. Exact Exchange in Periodic Boundary Conditions -- 3.6. AIMD/MM -- 4. Recent Implementation of AIMD in NWChem for Many-Core Architectures -- 4.1. 3D FFTs -- 4.2. Lagrange Multipliers and Nonlocal Pseudopotentials on 1D and 2D Processor Grids -- 4.3. Timings for NWChem AIMD on KNL -- 5. Applications -- 5.1. AIMD Simulations in Geochemistry -- 5.2. AIMD/MM Simulations of the Hydrolysis of Nitroaromatic Compounds -- 5.2.1. Comparisons Between Gaussian DFT and PSPW DFT of Hydrolysis Reaction Energies -- 5.2.2. Potential of Mean Force Using AIMD/MM -- 6. Conclusion -- Acknowledgments -- References. , Section D: Biochemical Simulations - Molecular Dynamics -- Chapter Six: Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications -- 1. Introduction -- 2. Theory -- 2.1. Gaussian Accelerated Molecular Dynamics (GaMD) -- 2.2. Energetic Reweighting of GaMD for Free Energy Calculations -- 3. Implementation -- 3.1. Implementation of GaMD in AMBER -- 3.2. Implementation of GaMD in NAMD -- 3.3. "PyReweighting" Toolkit for Energetic Reweighting -- 4. Applications -- 4.1. Alanine Dipeptide -- 4.1.1. Simulation Protocol -- 4.1.2. Simulation Results -- 4.2. Protein Folding -- 4.2.1. Simulation Protocol -- 4.2.2. Simulation Results -- 4.3. Biomolecular Conformational Transitions: G Protein-Coupled Receptors (GPCRs) -- 4.3.1. Simulation Protocol -- 4.3.2. Simulation Results -- 4.4. Biomolecular Recognition: Ligand Binding of the T4 Lysozyme -- 4.4.1. Simulation Protocol -- 4.4.2. Simulation Results -- 4.5. Biomolecular Recognition: Ligand Binding of the M3 Muscarinic GPCR -- 4.5.1. Simulation Protocol -- 4.5.2. Simulation Results -- 4.6. Biomolecular Recognition: Ligand Dissociation and Binding of the M2 Muscarinic GPCR -- 4.6.1. Simulation Protocol -- 4.6.2. Simulation Results -- 5. Concluding Remarks -- Acknowledgments -- References -- Back Cover.

Language: English

UID:

Format: 1 online resource (438 pages) : , illustrations (some color)

Edition: First edition.

ISBN: 9780444636829 (e-book)

Language: English

Keywords: Electronic books.

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