Description
Annual Reports in Computational Chemistry, Volume 13 provides timely and critical reviews of important topics in computational chemistry. Topics in this new release include chapters on the Quantum Chemical Model for Molecular Properties and Processes at the Extreme High Pressure, a section on Interpreting Bonding and Spectra with Correlated, One-Electron Concepts from Electron Propagator Theory, Benchmark databases of intermolecular interaction energies: design, construction, and significance, Gaussian Accelerated Molecular Dynamics: Theory, Implementation and Applications, and Dissociation in Binary Acid/Base Clusters: An Examination of Inconsistencies Introduced into the Many-Body Expansion by Naive Fragmentation Schemes.
Topics covered in this series include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists.
- Includes timely discussions on quantum chemistry and molecular mechanics
- Covers force fields, chemical education and more
- Presents the latest in chemical education and applications in both academic and industrial settings
Chapter
Section A: Quantum Chemistry - Weak and Non-Bonded Interactions
Chapter One: Benchmark Databases of Intermolecular Interaction Energies: Design, Construction, and Significance
2. Computing Accurate Interaction Energies
2.1. Leading Term: Frozen-Core CCSD(T)
2.1.3. Explicitly Correlated CCSD(T)
2.1.4. CCSD(T) Benchmarks for Large Systems
2.2. Coupled-Cluster Terms Beyond CCSD(T)
2.3.1. 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
Chapter Two: Dissociation in Binary Acid/Base Clusters: An Examination of Inconsistencies Introduced Into the Many-Body E ...
1.2. A Simple Illustration With the Hydrogen Fluoride Tetramer
3. Results and Discussion
3.3. Hydrated Hydrochloric Acid
3.4. Hydrated Sulfuric Acid
4. Summary and Conclusions
Chapter Three: The Quantum Chemical Study of Chemical Reactions at Extreme High Pressure by Means of the Extreme-Pressure ...
2.1. The Effective PES of a Reactive Molecular Systems at Extreme High Pressure
2.2. The Free Energy Functional Ger
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
4.1. 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
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
3.3. Super-Operator Theory and the Dyson Equation
3.4. Diagonalization of Ĥ
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
4.7. 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
6.5. Positronic Complexes
6.7. Photoionization Cross Sections
Section C: Quantum Chemistry - Periodic Simulations
Chapter Five: Plane-Wave DFT Methods for Chemistry
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
4. Recent Implementation of AIMD in NWChem for Many-Core Architectures
4.2. Lagrange Multipliers and Nonlocal Pseudopotentials on 1D and 2D Processor Grids
4.3. Timings for NWChem AIMD on KNL
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
Section D: Biochemical Simulations - Molecular Dynamics
Chapter Six: Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications
2.1. Gaussian Accelerated Molecular Dynamics (GaMD)
2.2. Energetic Reweighting of GaMD for Free Energy Calculations
3.1. Implementation of GaMD in AMBER
3.2. Implementation of GaMD in NAMD
3.3. "PyReweighting" Toolkit for Energetic Reweighting
4.1.1. Simulation Protocol
4.1.2. Simulation Results
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
Annual Reports in Computational Chemistry
( Volume 13 )
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