Essentials of Computational Chemistry : Theories and Models (2ND)

Essentials of Computational Chemistry : Theories and Models (2ND)

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  • 製本 Hardcover:ハードカバー版/ページ数 596 p.
  • 言語 ENG
  • 商品コード 9780470091814
  • DDC分類 541.0285

Table of Contents

Preface to the First Edition                       xv
Preface to the Second Edition xix
Acknowledgments xxi
What are Theory, Computation, and Modeling? 1 (16)
Definition of Terms 1 (3)
Quantum Mechanics 4 (1)
Computable Quantities 5 (6)
Structure 5 (1)
Potential Energy Surfaces 6 (4)
Chemical Properties 10 (1)
Cost and Efficiency 11 (4)
Intrinsic Value 11 (1)
Hardware and Software 12 (2)
Algorithms 14 (1)
Note on Units 15 (2)
Bibliography and Suggested Additional 15 (1)
Reading
References 16 (1)
Molecular Mechanics 17 (52)
History and Fundamental Assumptions 17 (2)
Potential Energy Functional Forms 19 (20)
Bond Stretching 19 (2)
Valence Angle Bending 21 (1)
Torsions 22 (5)
van der Waals Interactions 27 (3)
Electrostatic Interactions 30 (4)
Cross Terms and Additional Non-bonded 34 (2)
Terms
Parameterization Strategies 36 (3)
Force-field Energies and Thermodynamics 39 (1)
Geometry Optimization 40 (10)
Optimization Algorithms 41 (5)
Optimization Aspects Specific to Force 46 (4)
Fields
Menagerie of Modern Force Fields 50 (12)
Available Force Fields 50 (9)
Validation 59 (3)
Force Fields and Docking 62 (2)
Case Study: 64 (5)
(2R*,4S*)-1-Hydroxy-2,4-dimethylhex-5-ene
Bibliography and Suggested Additional 66 (1)
Reading
References 67 (2)
Simulations of Molecular Ensembles 69 (36)
Relationship Between MM Optima and Real 69 (1)
Systems
Phase Space and Trajectories 70 (2)
Properties as Ensemble Averages 70 (1)
Properties as Time Averages of 71 (1)
Trajectories
Molecular Dynamics 72 (8)
Harmonic Oscillator Trajectories 72 (2)
Non-analytical Systems 74 (3)
Practical Issues in Propagation 77 (2)
Stochastic Dynamics 79 (1)
Monte Carlo 80 (2)
Manipulation of Phase-space Integrals 80 (1)
Metropolis Sampling 81 (1)
Ensemble and Dynamical Property Examples 82 (6)
Key Details in Formalism 88 (10)
Cutoffs and Boundary Conditions 88 (2)
Polarization 90 (1)
Control of System Variables 91 (2)
Simulation Convergence 93 (3)
The Multiple Minima Problem 96 (2)
Force Field Performance in Simulations 98 (1)
Case Study: Silica Sodalite 99 (6)
Bibliography and Suggested Additional 101(1)
Reading
References 102(3)
Foundations of Molecular Orbital Theory 105(26)
Quantum Mechanics and the Wave Function 105(1)
The Hamiltonian Operator 106(5)
General Features 106(2)
The Variational Principle 108(2)
The Born-Oppenheimer Approximation 110(1)
Construction of Trial Wave Functions 111(4)
The LCAO Basis Set Approach 111(2)
The Secular Equation 113(2)
Huckel Theory 115(4)
Fundamental Principles 115(1)
Application to the Allyl System 116(3)
Many-electron Wave Functions 119(12)
Hartree-product Wave Functions 120(1)
The Hartree Hamiltonian 121(1)
Electron Spin and Antisymmetry 122(2)
Slater Determinants 124(2)
The Hartree-Fock Self-consistent Field 126(3)
Method
Bibliography and Suggested Additional 129(1)
Reading
References 130(1)
Semiempirical Implementations of Molecular 131(34)
Orbital Theory
Semiempirical Philosophy 131(3)
Chemically Virtuous Approximations 131(2)
Analytic Derivatives 133(1)
Extended Huckel Theory 134(2)
CNDO Formalism 136(3)
INDO Formalism 139(4)
INDO and INDO/S 139(2)
MINDO/3 and SINDO1 141(2)
Basic NDDO Formalism 143(4)
MNDO 143(2)
AM1 145(1)
PM3 146(1)
General Performance Overview of Basic 147(5)
NDDO Models
Energetics 147(3)
Geometries 150(1)
Charge Distributions 151(1)
Ongoing Developments in Semiempirical MO 152(7)
Theory
Use of Semiempirical Properties in SAR 152(1)
d Orbitals in NDDO Models 153(2)
SRP Models 155(2)
Linear Scaling 157(1)
Other Changes in Functional Form 157(2)
Case Study: Asymmetric Alkylation of 159(6)
Benzaldehyde
Bibliography and Suggested Additional 162(1)
Reading
References 163(2)
Ab Initio Implementations of Hartree-Fock 165(38)
Molecular Orbital Theory
Ab Initio Philosophy 165(1)
Basis Sets 166(14)
Functional Forms 167(1)
Contracted Gaussian Functions 168(2)
Single-ζ, Multiple-ζ, and 170(3)
Split-Valence
Polarization Functions 173(3)
Diffuse Functions 176(1)
The HF Limit 176(2)
Effective Core Potentials 178(2)
Sources 180(1)
Key Technical and Practical Points of 180(12)
Hartree-Fock Theory
SCF Convergence 181(1)
Symmetry 182(6)
Open-shell Systems 188(2)
Efficiency of Implementation and Use 190(2)
General Performance Overview of Ab Initio 192(7)
HF Theory
Energetics 192(4)
Geometries 196(2)
Charge Distributions 198(1)
Case Study: Polymerization of 199(4)
4-Substituted Aromatic Enynes
Bibliography and Suggested Additional 201(1)
Reading
References 201(2)
Including Electron Correlation in Molecular 203(46)
Orbital Theory
Dynamical vs. Non-dynamical Electron 203(2)
Correlation
Multiconfiguration Self-Consistent Field 205(6)
Theory
Conceptual Basis 205(2)
Active Space Specification 207(4)
Full Configuration Interaction 211(1)
Configuration Interaction 211(5)
Single-determinant Reference 211(5)
Multireference 216(1)
Perturbation Theory 216(8)
General Principles 216(3)
Single-reference 219(4)
Multireference 223(1)
First-order Perturbation Theory for 223(1)
Some Relativistic Effects
Coupled-cluster Theory 224(3)
Practical Issues in Application 227(10)
Basis Set Convergence 227(3)
Sensitivity to Reference Wave Function 230(5)
Price/Performance Summary 235(2)
Parameterized Methods 237(7)
Scaling Correlation Energies 238(1)
Extrapolation 239(1)
Multilevel Methods 239(5)
Case Study: Ethylenedione Radical Anion 244(5)
Bibliography and Suggested Additional 246(1)
Reading
References 247(2)
Density Functional Theory 249(56)
Theoretical Motivation 249(3)
Philosophy 249(1)
Early Approximations 250(2)
Rigorous Foundation 252(3)
The Hohenberg-Kohn Existence Theorem 252(2)
The Hohenberg-Kohn Variational Theorem 254(1)
Kohn-Sham Self-consistent Field 255(2)
Methodology
Exchange-correlation Functionals 257(14)
Local Density Approximation 258(5)
Density Gradient and Kinetic Energy 263(1)
Density Corrections
Adiabatic Connection Methods 264(4)
Semiempirical DFT 268(3)
Advantages and Disadvantages of DFT 271(9)
Compared to MO Theory
Densities vs. Wave Functions 271(2)
Computational Efficiency 273(1)
Limitations of the KS Formalism 274(4)
Systematic Improvability 278(1)
Worst-case Scenarios 278(2)
General Performance Overview of DFT 280(19)
Energetics 280(11)
Geometries 291(3)
Charge Distributions 294(5)
Case Study: Transition-Metal Catalyzed 299(6)
Carbonylation of Methanol
Bibliography and Suggested Additional 300(1)
Reading
References 301(4)
Charge Distribution and Spectroscopic 305(50)
Properties
Properties Related to Charge Distribution 305(25)
Electric Multipole Moments 305(3)
Molecular Electrostatic Potential 308(1)
Partial Atomic Charges 309(15)
Total Spin 324(1)
Polarizability and Hyperpolarizability 325(2)
ESR Hyperfine Coupling Constants 327(3)
Ionization Potentials and Electron 330(1)
Affinities
Spectroscopy of Nuclear Motion 331(13)
Rotational 332(2)
Vibrational 334(10)
NMR Spectral Properties 344(5)
Technical Issues 344(1)
Chemical Shifts and Spin--spin Coupling 345(4)
Constants
Case Study: Matrix Isolation of 349(6)
Perfluorinated p-Benzyne
Bibliography and Suggested Additional 351(1)
Reading
References 351(4)
Thermodynamic Properties 355(30)
Microscopic-macroscopic Connection 355(1)
Zero-point Vibrational Energy 356(1)
Ensemble Properties and Basic Statistical 357(9)
Mechanics
Ideal Gas Assumption 358(1)
Separability of Energy Components 359(1)
Molecular Electronic Partition Function 360(1)
Molecular Translational Partition 361(1)
Function
Molecular Rotational Partition Function 362(2)
Molecular Vibrational Partition Function 364(2)
Standard-state Heats and Free Energies of 366(9)
Formation and Reaction
Direct Computation 367(3)
Parametric Improvement 370(2)
Isodesmic Equations 372(3)
Technical Caveats 375(6)
Semiempirical Heats of Formation 375(1)
Low-frequency Motions 375(2)
Equilibrium Populations over Multiple 377(1)
Minima
Standard-state Conversions 378(1)
Standard-state Free Energies, 379(2)
Equilibrium Constants, and
Concentrations
Case Study: Heat of Formation of H2NOH 381(4)
Bibliography and Suggested Additional 383(1)
Reading
References 383(2)
Implicit Models for Condensed Phases 385(44)
Condensed-phase Effects on Structure and 385(8)
Reactivity
Free Energy of Transfer and Its 386(3)
Physical Components
Solvation as It Affects Potential 389(4)
Energy Surfaces
Electrostatic Interactions with a 393(13)
Continuum
The Poisson Equation 394(8)
Generalized Born 402(2)
Conductor-like Screening Model 404(2)
Continuum Models for Non-electrostatic 406(4)
Interactions
Specific Component Models 406(1)
Atomic Surface Tensions 407(3)
Strengths and Weaknesses of Continuum 410(12)
Solvation Models
General Performance for Solvation Free 410(6)
Energies
Partitioning 416(1)
Non-isotropic Media 416(3)
Potentials of Mean Force and Solvent 419(1)
Structure
Molecular Dynamics with Implicit Solvent 420(1)
Equilibrium vs. Non-equilibrium 421(1)
Solvation
Case Study: Aqueous Reductive 422(7)
Dechlorination of Hexachloroethane
Bibliography and Suggested Additional 424(1)
Reading
References 425(4)
Explicit Models for Condensed Phases 429(28)
Motivation 429(1)
Computing Free-energy Differences 429(15)
Raw Differences 430(2)
Free-energy Perturbation 432(3)
Slow Growth and Thermodynamic 435(2)
Integration
Free-energy Cycles 437(2)
Potentials of Mean Force 439(4)
Technical Issues and Error Analysis 443(1)
Other Thermodynamic Properties 444(1)
Solvent Models 445(3)
Classical Models 445(2)
Quantal Models 447(1)
Relative Merits of Explicit and Implicit 448(4)
Solvent Models
Analysis of Solvation Shell Structure 448(2)
and Energetics
Speed/Efficiency 450(1)
Non-equilibrium Solvation 450(1)
Mixed Explicit/Implicit Models 451(1)
Case Study: Binding of Biotin Analogs to 452(5)
Avidin
Bibliography and Suggested Additional 454(1)
Reading
References 455(2)
Hybrid Quantal/Classical Models 457(30)
Motivation 457(1)
Boundaries Through Space 458(9)
Unpolarized Interactions 459(2)
Polarized QM/Unpolarized MM 461(5)
Fully Polarized Interactions 466(1)
Boundaries Through Bonds 467(10)
Linear Combinations of Model Compounds 467(6)
Link Atoms 473(2)
Frozen Orbitals 475(2)
Empirical Valence Bond Methods 477(5)
Potential Energy Surfaces 478(2)
Following Reaction Paths 480(1)
Generalization to QM/MM 481(1)
Case Study: Catalytic Mechanism of Yeast 482(5)
Enolase
Bibliography and Suggested Additional 484(1)
Reading
References 485(2)
Excited Electronic States 487(32)
Determinantal/Configurational 487(5)
Representation of Excited States
Singly Excited States 492(7)
SCF Applicability 493(3)
CI Singles 496(2)
Rydberg States 498(1)
General Excited State Methods 499(5)
Higher Roots in MCSCF and CI 499(2)
Calculations
Propagator Methods and Time-dependent 501(3)
DFT
Sum and Projection Methods 504(3)
Transition Probabilities 507(4)
Solvatochromism 511(2)
Case Study: Organic Light Emitting Diode 513(6)
Alq3
Bibliography and Suggested Additional 515(1)
Reading
References 516(3)
Adiabatic Reaction Dynamics 519(30)
Reaction Kinetics and Rate Constants 519(3)
Unimolecular Reactions 520(1)
Bimolecular Reactions 521(1)
Reaction Paths and Transition States 522(2)
Transition-state Theory 524(14)
Canonical Equation 524(7)
Variational Transition-state Theory 531(2)
Quantum Effects on the Rate Constant 533(5)
Condensed-phase Dynamics 538(1)
Non-adiabatic Dynamics 539(5)
General Surface Crossings 539(2)
Marcus Theory 541(3)
Case Study: Isomerization of Propylene 544(5)
Oxide
Bibliography and Suggested Additional 546(1)
Reading
References 546(3)
Appendix A Acronym Glossary 549(8)
Appendix B Symmetry and Group Theory 557(8)
Symmetry Elements 557(2)
Molecular Point Groups and Irreducible 559(2)
Representations
Assigning Electronic State Symmetries 561(1)
Symmetry in the Evaluation of Integrals 562(3)
and Partition Functions
Appendix C Spin Algebra 565(10)
Spin Operators 565(1)
Pure- and Mixed-spin Wave Functions 566(5)
UHF Wave Functions 571(1)
Spin Projection/Annihilation 571(4)
Reference 574(1)
Appendix D Orbital Localization 575(6)
Orbitals as Empirical Constructs 575(3)
Natural Bond Orbital Analysis 578(3)
References 579(2)
Index 581