Essentials of Computational Chemistry: Theories and Models, 2nd Edition,9780470091814

Essentials of Computational Chemistry: Theories and Models, 2nd Edition

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Edition: 2nd
ISBN13: 9780470091814
ISBN10: 0470091819
Format: Hardcover
Pub. Date: 2004-11-01
Publisher(s): WILEY
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Summary

Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject.  Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas.  The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.

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 Reading
15(1)
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 Terms
34(2)
Parameterization Strategies
36(3)
Force-field Energies and Thermodynamics
39(1)
Geometry Optimization
40(10)
Optimization Algorithms
41(5)
Optimization Aspects Specific to Force Fields
46(4)
Menagerie of Modern Force Fields
50(12)
Available Force Fields
50(9)
Validation
59(3)
Force Fields and Docking
62(2)
Case Study: (2R*,4S*)-1-Hydroxy-2,4-dimethylhex-5-ene
64(5)
Bibliography and Suggested Additional Reading
66(1)
References
67(2)
Simulations of Molecular Ensembles
69(36)
Relationship Between MM Optima and Real Systems
69(1)
Phase Space and Trajectories
70(2)
Properties as Ensemble Averages
70(1)
Properties as Time Averages of Trajectories
71(1)
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 Reading
101(1)
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 Method
126(3)
Bibliography and Suggested Additional Reading
129(1)
References
130(1)
Semiempirical Implementations of Molecular Orbital Theory
131(34)
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 NDDO Models
147(5)
Energetics
147(3)
Geometries
150(1)
Charge Distributions
151(1)
Ongoing Developments in Semiempirical MO Theory
152(7)
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 Benzaldehyde
159(6)
Bibliography and Suggested Additional Reading
162(1)
References
163(2)
Ab Initio Implementations of Hartree-Fock Molecular Orbital Theory
165(38)
Ab Initio Philosophy
165(1)
Basis Sets
166(14)
Functional Forms
167(1)
Contracted Gaussian Functions
168(2)
Single-ζ, Multiple-ζ, and Split-Valence
170(3)
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 Hartree-Fock Theory
180(12)
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 HF Theory
192(7)
Energetics
192(4)
Geometries
196(2)
Charge Distributions
198(1)
Case Study: Polymerization of 4-Substituted Aromatic Enynes
199(4)
Bibliography and Suggested Additional Reading
201(1)
References
201(2)
Including Electron Correlation in Molecular Orbital Theory
203(46)
Dynamical vs. Non-dynamical Electron Correlation
203(2)
Multiconfiguration Self-Consistent Field Theory
205(6)
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 Some Relativistic Effects
223(1)
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 Reading
246(1)
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 Methodology
255(2)
Exchange-correlation Functionals
257(14)
Local Density Approximation
258(5)
Density Gradient and Kinetic Energy Density Corrections
263(1)
Adiabatic Connection Methods
264(4)
Semiempirical DFT
268(3)
Advantages and Disadvantages of DFT Compared to MO Theory
271(9)
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 Carbonylation of Methanol
299(6)
Bibliography and Suggested Additional Reading
300(1)
References
301(4)
Charge Distribution and Spectroscopic Properties
305(50)
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 Affinities
330(1)
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 Constants
345(4)
Case Study: Matrix Isolation of Perfluorinated p-Benzyne
349(6)
Bibliography and Suggested Additional Reading
351(1)
References
351(4)
Thermodynamic Properties
355(30)
Microscopic-macroscopic Connection
355(1)
Zero-point Vibrational Energy
356(1)
Ensemble Properties and Basic Statistical Mechanics
357(9)
Ideal Gas Assumption
358(1)
Separability of Energy Components
359(1)
Molecular Electronic Partition Function
360(1)
Molecular Translational Partition Function
361(1)
Molecular Rotational Partition Function
362(2)
Molecular Vibrational Partition Function
364(2)
Standard-state Heats and Free Energies of Formation and Reaction
366(9)
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 Minima
377(1)
Standard-state Conversions
378(1)
Standard-state Free Energies, Equilibrium Constants, and Concentrations
379(2)
Case Study: Heat of Formation of H2NOH
381(4)
Bibliography and Suggested Additional Reading
383(1)
References
383(2)
Implicit Models for Condensed Phases
385(44)
Condensed-phase Effects on Structure and Reactivity
385(8)
Free Energy of Transfer and Its Physical Components
386(3)
Solvation as It Affects Potential Energy Surfaces
389(4)
Electrostatic Interactions with a Continuum
393(13)
The Poisson Equation
394(8)
Generalized Born
402(2)
Conductor-like Screening Model
404(2)
Continuum Models for Non-electrostatic Interactions
406(4)
Specific Component Models
406(1)
Atomic Surface Tensions
407(3)
Strengths and Weaknesses of Continuum Solvation Models
410(12)
General Performance for Solvation Free Energies
410(6)
Partitioning
416(1)
Non-isotropic Media
416(3)
Potentials of Mean Force and Solvent Structure
419(1)
Molecular Dynamics with Implicit Solvent
420(1)
Equilibrium vs. Non-equilibrium Solvation
421(1)
Case Study: Aqueous Reductive Dechlorination of Hexachloroethane
422(7)
Bibliography and Suggested Additional Reading
424(1)
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 Integration
435(2)
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 Solvent Models
448(4)
Analysis of Solvation Shell Structure and Energetics
448(2)
Speed/Efficiency
450(1)
Non-equilibrium Solvation
450(1)
Mixed Explicit/Implicit Models
451(1)
Case Study: Binding of Biotin Analogs to Avidin
452(5)
Bibliography and Suggested Additional Reading
454(1)
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 Enolase
482(5)
Bibliography and Suggested Additional Reading
484(1)
References
485(2)
Excited Electronic States
487(32)
Determinantal/Configurational Representation of Excited States
487(5)
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 Calculations
499(2)
Propagator Methods and Time-dependent DFT
501(3)
Sum and Projection Methods
504(3)
Transition Probabilities
507(4)
Solvatochromism
511(2)
Case Study: Organic Light Emitting Diode Alq3
513(6)
Bibliography and Suggested Additional Reading
515(1)
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 Oxide
544(5)
Bibliography and Suggested Additional Reading
546(1)
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 Representations
559(2)
Assigning Electronic State Symmetries
561(1)
Symmetry in the Evaluation of Integrals and Partition Functions
562(3)
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

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