Comprehensive Computational Chemistry

1. Introduction to “Advanced Electronic Structure Methods in Computational Quantum Chemistry” - p. iii 2. Modern Basis Sets Across the Periodic Table - p. iii 3. How Coupled-Cluster Theory is Solving the Electron Correlation Problem - p. iii 4. Benchmark Accuracy in Thermochemistry, Kinetics, and Noncovalent Interactions - p. iii 5. Modern Density Functionals Derived From First Principles - p. iii 6. Benchmarking Modern Density Functionals for Broad Applications in Chemistry - p. iii 7. Coupled Cluster Accuracy at DFT Cost: Generalized Isodesmic Schemes in Quantum Chemistry and Illustrative Applications - p. iii 8. Projection-Based Molecular Quantum Embedding via Singular-Value-Informed Orbital Partitioning - p. iii 9. Computational Techniques for Strong Electron Correlation: Matrix Product State Ansatz and its Optimization - p. iii 10. Generalized Energy-Based Fragmentation Approach for Structures and Properties of Periodic Condensed Phase Systems - p. iii 11. Computational Spectroscopy of Large Molecules by Fragmentation Methods - p. iii 12. The Effective Fragment Potential: An Ab Initio Force Field - p. iii 13. Advanced Quantum Chemical Methods for Open-Shell Systems - p. iii 14. Abstract - p. iii 15. 1 Introduction - p. iii 16. 2 Fundamental Concept of Quantum Chemistry - p. iii 17. 3 Unrestricted Hartree-Fock Method - p. iii 18. 4 Restricted Open-Shell Hartree-Fock Method - p. iii 19. 5 Relation Between UHF and ROHF Methods - p. iii 20. 6 Spin Symmetry - p. iii 21. 7 Electron Correlation - p. iii 22. 8 Unrestricted Møller-Plesset Perturbation Theory - p. iii 23. 9 Concluding Remarks - p. iii 24. References - p. iii 25. Quantum Chemistry of d- and f-Block Elements - p. iii 26. Quantum Chemical and Informatics-Based Approaches for Probing Biomolecular Systems Toxicology - p. iii 27. Quantum Chemical Investigations on Functional Materials - p. iii 28. Quantum Algorithms for the Study of Electronic Structure and Molecular Dynamics: Novel Computational Protocols - p. iii 29. The Valence Bond and Alternative Viewpoints - p. iii 30. Introduction to the Valence Bond Section of the Mrw Project - p. iii 31. Understanding Valence Bond Theory - p. iii 32. A Tutorial on XMVB - p. iii 33. The Breathing-Orbital Valence Bond Method: A VB Method That Includes Dynamic Electron Correlation - p. iii 34. The Valence-Bond Quantum Monte Carlo Method - p. iii 35. Spin-Coupled Generalized Valence Bond Theory: An Appealing Orbital Theory of the Electronic Structure of Atoms and Molecules - p. iii 36. Abstract - p. iii 37. Glossary - p. iii 38. 1 Introduction - p. iii 39. 2 Basic Elements of SCGVB Theory - p. iii 40. 3 SCGVB Description of the Electronic Structure of Molecules - p. iii 41. 4 Beyond SCGVB Theory - p. iii 42. 5 Conclusion - p. iii 43. Acknowledgments - p. iii 44. References - p. iii 45. Valence Bond Methods for Molecules in Solution - p. iii 46. Variational Subspace Valence Bond - p. iii 47. VSVB: A Tutorial on VALENCE - p. iii 48. Orthogonal Valence Bond as a Bridge Between the Valence Bond and Molecular Orbital Representations of the Wave Function - p. iii 49. The Block-Localized Wavefunction (BLW) Method and Its Applications - p. iii 50. Non-Orthogonal Configuration Interaction for Fragments - p. iii 51. Tutorial for Non-Orthogonal Configuration Interaction Fragment Studies Using GronOR - p. iii 52. Valence Bond Description of Halogen Bonding - p. iii 53. The Chemical Bond as a Manifestation of Quantum Mechanical Interference: Theory and Applications of the Interference Energy Analysis Using SCGVB Wave Functions - p. iii 54. The Quantum Interference Energy Analysis: A Tutorial Introduction - p. iii 55. Local Description with Lewis Structures at the Hückel Level - p. iii 56. Tutorial on HuLiS: The Two Methods Implemented in HuLiS (HL-CI and HL-P) and Their Behavior for a Few Cases - p. iii 57. A Bridge Between MO And VB: The VB Description Of Functional Groups Inside Molecules By Means Of Poly-Electron Population Analysis - p. iii 58. Bridging MO and VB in Practice: A Computer Program for Poly-Electron Population Analysis - p. iii 59. Valence Bond Motifs from Wave Function Tesselation - p. iii 60. Unified Understanding of Structure, Reactivity and Spectroscopy Within General Valence Bond Scenarios, Obtained by Transferring Techniques Developed Within Electron-Transfer Theory - p. iii 61. Valence Bond Diagrams and Chemical Reactivity - p. iii 62. The Analysis of Chemical Bonding and the Interpretation of Wave Functions - p. iii 63. Section Introduction: The Analysis of Chemical Bonding and the Interpretation of Wave Functions‘Are we there yet?’ - p. iii 64. What is the Number of Electrons in a Spatial Domain? - p. iii 65. Electron Number Distribution Functions - p. iii 66. Abstract - p. iii 67. 1 Introduction - p. iii 68. 2 Where do Electrons Lie? - p. iii 69. 3 Atoms Persist in Molecules - p. iii 70. 4 Atoms in Molecules are Open Quantum Systems - p. iii 71. 5 Electron Number Distribution Functions - p. iii 72. 6 Non-Independent Particles - p. iii 73. 7 EDFs for Fuzzy or Orbital-Based Partitions of Space - p. iii 74. 8 Approximate Calculation of EDFs - p. iii 75. 9 From EDFs to Chemical Bonding - p. iii 76. 10 Fitting EDFs: The N-Electron EDF From Independent Bonds - p. iii 77. 11 Future Work - p. iii 78. 12 Summary and Conclusions - p. iii 79. Acknowledgment - p. iii 80. References - p. iii 81. Interacting Quantum Atoms - p. iii 82. The Conceptual and Mathematical Foundations of the MC-QTAIM - p. iii 83. Electron Localization-Delocalization Matrices (LDMs) - p. iii 84. The Source Function Concept in Chemistry - p. iii 85. Topological analysis of Electron Localization Function (ELF) as a Tool for Understanding Electronic Structure - p. iii 86. Electronic Density Changes for Non-Equilibrium Molecular Geometries: A Charge – Charge Transfer – Dipolar Polarization Model - p. iii 87. Topology of the Electronic Current Density Induced by a Static Magnetic Field in Lithium Hydride, Water, Ammonia and Methane Molecules - p. iii 88. Aromaticity: Types, Rules, and Quantification - p. iii 89. New Developments in the Non Covalent Interaction (NCI) Index - p. iii 90. Correlating Chemical Bonding With the Potential Energy Acting on One Electron in a Molecule - p. iii 91. Visualization Analysis of Weak Interactions in Chemical Systems - p. iii 92. Roby-Gould Bond Indices - p. iii 93. Conceptual Density Functional Theory - p. iii 94. Energy Decomposition Analysis of the Chemical Bond: Scope and Limitation - p. iii 95. Density-Derived Electrostatic and Chemical Methods - p. iii 96. Abstract - p. iii 97. 1 Introduction - p. iii 98. 2 Charge Partitioning - p. iii 99. 3 Reference Ion and Core Density Libraries - p. iii 100. 4 Spin Partitioning - p. iii 101. 5 Bond Order Analysis - p. iii 102. 6 Atom-in-Material Polarizabilities, Dispersion Coefficients, and Quantum Drude Oscillator Parameters - p. iii 103. 7 Scientific Testing - p. iii 104. 8 Outlook - p. iii 105. References - p. iii 106. Relevant Websites - p. iii 107. Natural Bond Orbital Analysis of Chemical Structure, Spectroscopy, and Reactivity: How it Works - p. iii 108. Clusters and Nanostructures - p. iii 109. Section Introduction: Clusters and Nanostructures Bridge Atomic and Molecular World, and the Bulk - p. iii 110. Geometry-Based Electronic Models for Aromaticity of Atomic Clusters - p. iii 111. Diversity of Chemical Bonding in Zintl Clusters - p. iii 112. Structure, Stability, Bonding and Aromaticity in All-metal and Nonmetal Clusters - p. iii 113. Electrostatic Potential and Tailoring Approach for Exploring Molecular Clusters - p. iii 114. Modeling Microsolvation Features Involving Clusters - p. iii 115. Small Gold Clusters: Structure, Energetics and Biomedical Applications - p. iii 116. Exploiting the Mechanical Behavior and Potentials of Graphyne Based Clusters via Atomistic Simulations - p. iii 117. Graphene Catalysis Made Easy - p. iii 118. Machine Learning-Based Approaches in Nanoparticle Catalysis - p. iii 119. Relativistic Effects and the Chemistry of Heavy Elements - p. iii 120. Introduction to Relativistic Effects and the Chemistry of Heavy Elements - p. iii 121. Basis Sets for Relativistic Calculations - p. iii 122. Relativistic Pseudopotentials - p. iii 123. Relativistic Effects From Coupled-Cluster Theory - p. iii 124. Relativistic Fock-Space Coupled Cluster Method: Theory and Recent Applications - p. iii 125. Quantum Electrodynamics Effects in Atoms and Molecules - p. iii 126. Abstract - p. iii 127. 1 Introduction - p. iii 128. 2 Basic QED Formalism - p. iii 129. 3 Bound-State QED Methods - p. iii 130. 4 Ab Initio QED Calculations - p. iii 131. 5 Calculations of QED Effects With Model Operators - p. iii 132. 6 Conclusion - p. iii 133. Acknowledgments - p. iii 134. References - p. iii 135. Modeling Environment Effects on Heavy-Element Compounds - p. iii 136. Relativistic Effects on Molecular Properties - p. iii 137. Relativistic Propagators: Theory and Applications - p. iii 138. Abstract - p. iii 139. 1 Introduction - p. iii 140. 2 Propagators and Green Functions - p. iii 141. 3 Relativistic Quantum Chemistry - p. iii 142. 4 Relativistic Polarization Propagators - p. iii 143. 5 Propagators and the Path Integral Formalism - p. iii 144. 6 Response Properties - p. iii 145. 7 Conclusion - p. iii 146. Acknowledgments - p. iii 147. References - p. iii 148. Relativistic Real-Time Methods - p. iii 149. Abstract - p. iii 150. 1 Introduction - p. iii 151. 2 Relativistic Particle–Field Interaction Hamiltonians - p. iii 152. 3 Equations-of-Motion for Exact-State Wave Function - p. iii 153. 4 Equations-of-Motion for Approximate-State Wave Functions - p. iii 154. 5 Real-Time Propagation - p. iii 155. 6 Signal Processing - p. iii 156. 7 Calculation of Molecular Properties Using Real-Time Methods - p. iii 157. 8 Conclusion and Perspectives - p. iii 158. References - p. iii 159. Real-Time Time-Dependent Density Functional Theories With Large Time Step and Short Simulation Time - p. iii 160. Abstract - p. iii 161. 1 Introduction - p. iii 162. 2 Real-Time TDDFT - p. iii 163. 3 Propagators and Predictor-Correctors - p. iii 164. 4 Time Step - p. iii 165. 5 Spectral Analysis of Time Signals - p. iii 166. 6 Illustrations - p. iii 167. 7 Conclusion - p. iii 168. Data Availability Statement - p. iii 169. Acknowledgment - p. iii 170. References - p. iii 171. Relativistic Effects on Photodynamical Processes - p. iii 172. Relativistic Theory of EPR and (p)NMR - p. iii 173. Abstract - p. iii 174. 1 Notation and List of Acronyms - p. iii 175. 2 Introduction - p. iii 176. 3 The Dirac–Coulomb–Breit Hamiltonian - p. iii 177. 4 A Balanced Basis for the Small Component of the Wavefunction - p. iii 178. 5 Evaluation of the Two-Electron Contribution to the Hartree-Fock Matrix - p. iii 179. 6 Noncollinear DFT Approaches - p. iii 180. 7 Time-Reversal Symmetry - p. iii 181. 8 Exact-State Theory for Calculation of Second-Order Properties at Finite Temperature - p. iii 182. 9 Paramagnetic NMR Theory Within the Exact-State Formalism - p. iii 183. 10 Mapping of the Paramagnetic NMR Theory to Parameters of the EPR Effective Spin Hamiltonian - p. iii 184. 11 Four-Component DFT Method for the Calculation of Orbital NMR Tensors - p. iii 185. 12 Exact-State Theory for the Calculation of EPR Parameters - p. iii 186. 13 Relativistic DFT Methods for the Calculation of g- and A-tensors - p. iii 187. 14 Relativistic DFT Methods for the Calculation of ZFS Parameters - p. iii 188. 15 Conclusion - p. iii 189. Acknowledgments - p. iii 190. References - p. iii 191. Molecular Dynamics Simulations and Reaction Rates - p. iii 192. Section Introduction: Molecular Dynamics Simulations and Reaction Rates - p. iii 193. Discrete Molecular Dynamics - p. iii 194. Mechanical Constraints in Molecular Dynamics Simulation - p. iii 195. Abstract - p. iii 196. 1 Introduction - p. iii 197. 2 Equations of Motion for Systems with Holonomic Constraints - p. iii 198. 3 Statistical Mechanics for Systems with Holonomic Constraints - p. iii 199. 4 Numerical Integration of the Equations of Motion with Holonomic Constraints - p. iii 200. 5 Rare Event Sampling and Constraints - p. iii 201. 6 Mass-Zero Constraints - p. iii 202. 7 Conclusion - p. iii 203. References - p. iii 204. Recent advances in Accelerated Molecular Dynamics Methods: Theory and Applications - p. iii 205. Equilibrium and Nonequilibrium Methods for Free-Energy Calculations With Molecular Dynamics - p. iii 206. Molecular Dynamics With Milestoning: Byways to Compute Kinetics - p. iii 207. Abstract - p. iii 208. 0 Introduction - p. iii 209. 1 Classical Kinetics and the Mean First Passage Time - p. iii 210. 2 Statistical Mechanics of Configurations and Trajectories - p. iii 211. 3 Stochastic Trajectory Weights and Averages - p. iii 212. 4 The Reaction Coordinate - p. iii 213. 5 Formula for and Exploitations of Rate Coefficients - p. iii 214. 6 The Basic Equations of Milestoning - p. iii 215. 7 Laplace Transform and Milestoning - p. iii 216. 8 Milestoning and the Generalized Master Equation - p. iii 217. 9 Milestoning Simulation Protocol - p. iii 218. 10 An Example: A Milestoning Calculation of a Conformational Transition in Alanine Dipeptide - p. iii 219. 11 Concluding Remarks - p. iii 220. Acknowledgments - p. iii 221. References - p. iii 222. Relevant Websites - p. iii 223. Interactive Molecular Dynamics - p. iii 224. Machine Learning in Molecular Dynamics Simulations of Biomolecular Systems - p. iii 225. Ab Initio Molecular Dynamics: A Guide to Applications - p. iii 226. NWChem and NWChemEx Plane-Wave Methods - p. iii 227. Abstract - p. iii 228. 1 Introduction - p. iii 229. 2 Plane-Wave Basis Set - p. iii 230. 3 Pseudopotential Plane-Wave (PSPW) and Projector Augmented Wave (PAW) Methods - p. iii 231. 4 Ongoing Developments of Hybrid Parallel Algorithms for Architectures With Many-Core CPUs and Multi-GPUs - p. iii 232. 5 Recent Applications - p. iii 233. 6 Conclusions - p. iii 234. Acknowledgments - p. iii 235. References - p. iii 236. Relevant Websites - p. iii 237. Enzyme Reaction Dynamics From Adaptive Reaction Coordinate Forces - p. iii 238. Chemical Processes at Aqueous Interfaces - p. iii 239. ESPResSo, a Versatile Open-Source Software Package for Simulating Soft Matter Systems - p. iii 240. Coarse Grained MD Simulations of Soft Matter - p. iii 241. Hierarchical Multiscale Modeling Through Inverse Problem Solving - p. iii 242. Hybrid Particle-Field Molecular Dynamics: A Primer - p. iii 243. Coarse Grained Models: The Martini Force Field - p. iii 244. The Development of Hierarchical Ion Models and Multiscale Modeling of Tetraalkylphosphonium and Imidazolium Ionic Liquids - p. iii 245. Reducing Uncertainties in and Analysis of Ionic Liquid Trajectories - p. iii 246. Molecular Dynamics Simulations of Ionic Liquid Crystals - p. iii 247. Nonequilibrium Molecular Dynamics Simulation of Liquid Crystals and Variational Principle for Nonequilibrium Steady States - p. iii 248. Classical Molecular Dynamics Simulation of Molecular Crystals and Materials: Old Lessons and New Perspectives - p. iii 249. Molecular Dynamics Simulations of Thermal Transport in Solid State Systems - p. iii 250. Molecular Dynamics Simulations and Vibrational Spectroscopy - p. iii 251. MD Simulations and X-Ray Scattering - p. iii 252. Theoretical analysis of X-Ray Free-Electron-Laser Experimental Data Using Monte-Carlo and Molecular-Dynamics Based Computational Tools - p. iii 253. Molecular Dynamics Simulations as a Tool to Understand Drug Solubilization in Pharmaceutical Systems - p. iii 254. Modeling and Simulating RNA: Combining Structural, Dynamic, and Evolutionary Perspectives for Coronavirus Applications - p. iii 255. Molecular Dynamics and QM/MM to Understand Genome Organization and Reproduction in Emerging RNA Viruses - p. iii 256. The Emerging Role of Molecular Dynamics Simulations in Cancer Research - p. iii 257. Computational Simulations of Glycan Recognition by Lectins and Other Carbohydrate Binding Proteins - p. iii 258. Constant-pH Simulation Methods for Biomolecular Systems - p. iii 259. Optimization of Non-Polarizable and Polarizable Force Fields and Their Application to Model Compounds - p. iii 260. Molecular Dynamics Simulations up to Earth: Modeling of Soil Organic Matter - p. iii 261. Excited States and Photodynamic Simulations from Photobiology to Photomaterials - p. iii 262. Introduction to the Section Excited States and Photodynamics Simulations From Photobiology to Photomaterials - p. iii 263. Basic Concepts of Electronic Excited States - p. iii 264. Mechanistic Photochemistry and Conical Intersections - p. iii 265. Classification and Analysis of Molecular Excited States - p. iii 266. Time-Dependent Density Functional Theory and Green’s Functions Methods with the Bethe–Salpeter Equation - p. iii 267. Abstract - p. iii 268. 1 Introduction - p. iii 269. 2 Density-Functional Theory - p. iii 270. 3 Time-Dependent Density-Functional Theory - p. iii 271. 4 Many-Body Green׳s Functions Methods for Electronically Excited States - p. iii 272. 5 Discussion and Practical Considerations - p. iii 273. 6 Conclusion and Outlook - p. iii 274. References - p. iii 275. Coupled-Cluster Theories for Excited States - p. iii 276. Abstract - p. iii 277. 1 Introduction - p. iii 278. 2 The Similarity-Transformed Hamiltonian - p. iii 279. 3 Equation-of-Motion Theory - p. iii 280. 4 Coupled-Cluster Linear Response Theory - p. iii 281. 5 Analytic Geometric Gradients - p. iii 282. 6 Approximations - p. iii 283. 7 Benchmarks - p. iii 284. 8 Methods for Large Systems - p. iii 285. 9 Open-Shell and Multireference Cases - p. iii 286. 10 Basis Set Limit - p. iii 287. 11 Availability - p. iii 288. 12 Conclusions - p. iii 289. References - p. iii 290. Multiconfigurational Methods Including XMCQDPT2 Theory for Excited States of Light-Sensitive Biosystems - p. iii 291. Hybrid QM/MM Approach for the Calculation of Excited States in Complex Environments - p. iii 292. Exact Factorization of the Electron-Nuclear Wavefunction: Fundamentals and Algorithms - p. iii 293. Gaussian Wave Packet and Coherent State Based Methods in Chemical Quantum Dynamics - p. iii 294. Fundamentals of Trajectory-Based Methods for Nonadiabatic Dynamics - p. iii 295. Abstract - p. iii 296. 1 Introduction - p. iii 297. 2 Basic Foundations - p. iii 298. 3 Components of the TSH Methods - p. iii 299. 4 Summary and Outlook - p. iii 300. References - p. iii 301. The Quantum Decoherence Problem in Nonadiabatic Trajectory Methods - p. iii 302. Quantum Dynamics Methods Based on the Real-Time Path Integral - p. iii 303. Excited States Reactivity of Natural and Unnatural DNA Nucleobases - p. iii 304. Photophysics and Photochemistry of Transition Metal Complexes: Complex Emissive and Photoreactivity Scenarios - p. iii 305. Photochemistry of Biological Systems: Excited-State Electronic Structure Calculations and Nonadiabatic Dynamics Simulations with QM/MM Methods - p. iii 306. Quantum Dynamics of Photoactive Transition Metal Complexes. A Case Study of Model Reduction - p. iii 307. Non-Adiabatic Dynamics in Condensed Matter and Nanoscale Systems - p. iii 308. Photodynamics With Neural Networks and Kernel Ridge Regression - p. iii 309. Machine Learning Accelerated Nonadiabatic Dynamics at Metal Surfaces - p. iii 310. Molecular Interactions and Catalysis - p. iii 311. Molecular Interactions and Catalysis - p. iii 312. Automated Mechanism Discovery - p. iii 313. Heuristics and Uncertainty Quantification in Rational and Inverse Compound and Catalyst Design - p. iii 314. Transition Structures, Reaction Paths, and Kinetics: Methods and Applications in Catalysis - p. iii 315. Computational Catalyst Design with Data–Driven Tools – General Approaches and Applications - p. iii 316. Evolutionary Algorithms and Workflows for De Novo Catalyst Design - p. iii 317. Density Functional Theory for Transition Metal Catalysis - p. iii 318. An Introductory Primer for Modeling Atomically Dispersed Catalysts using Density Functional Theory - p. iii 319. Computational Modeling of 4d and 5d Transition Metal Catalysts - p. iii 320. Chemical Bonding in Homogenous Catalysis – Seen Through the Eyes of Vibrational Spectroscopy - p. iii 321. Dynamics in Heterogeneous and Single-Site Catalysis - p. iii 322. Computational Chemistry for Photochemical Reactions - p. iii 323. Water/Solid Interface in Thermal- and Electrocatalysis for Wetting and Non-Wetting Surfaces: Interactions and Models - p. iii 324. Quantum Tunneling in Computational Catalysis and Kinetics: Is it Really Important? - p. iii 325. Short Hydrogen Bonds in Proteins - p. iii 326. Electric Fields in Enzyme Catalysis - p. iii 327. Modeling Metal Ions in Enzyme Catalysis - p. iii 328. Subject Index - p. iii 329. Authors - p. iii