Essentials of computational chemistry: theories and models
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| Format: | Buch |
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| Veröffentlicht: |
Chichester [u.a.]
Wiley
2009
|
| Ausgabe: | 2. ed., repr. with corr. |
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| ISBN: | 9780470091821 9780470091814 0470091819 0470091827 |
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| 100 | 1 | |a Cramer, Christopher J. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Essentials of computational chemistry |b theories and models |c Christopher J. Cramer |
| 250 | |a 2. ed., repr. with corr. | ||
| 264 | 1 | |a Chichester [u.a.] |b Wiley |c 2009 | |
| 300 | |a XX, 596 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Hier auch später erschienene, unveränderte Nachdrucke | ||
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| 856 | 4 | 2 | |m Digitalisierung UB Regensburg |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020541894&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |3 Klappentext |
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Datensatz im Suchindex
| _version_ | 1804143232547815424 |
|---|---|
| adam_text | Contents
Preface
to the First Edition
xv
Preface to the Second Edition
xix
Acknowledgments
xxi
1
What are Theory, Computation, and Modeling?
1
1.1
Definition of Terms
1
1.2
Quantum Mechanics
4
1.3
Computable Quantities
5
1.3.1
Structure
5
1.3.2
Potential Energy Surfaces
6
1.3.3
Chemical Properties
10
1.4
Cost and Efficiency
11
1.4.1
Intrinsic Value
11
1.4.2
Hardware and Software
12
1.4.3
Algorithms
14
1.5
Note on Units
15
Bibliography and Suggested Additional Reading
15
References
16
17
17
19
19
21
22
27
30
34
36
39
40
41
46
Molecular
Mechanics
2.1
History
and Fundamental Assumptions
2.2
Potential Energy Functional Forms
2.2.1
Bond Stretching
2.2.2
Valence Angle Bending
2.2.3
Torsions
2.2.4
van
der Waals
Interactions
2.2.5
Electrostatic Interactions
2.2.6
Cross Terms and Additional Non-bonded Terms
2.2.7
Parameterization Strategies
2.3
Force-field Energies and Thermodynamics
2.4
Geometry Optimization
2.4.1
Optimization Algorithms
2.4.2
Optimization Aspects Specific to Force Fields
viii CONTENTS
2.5 Menagerie
of
Modern Force
Fields
50
2.5.1
Available Force Fields
50
2.5.2
Validation
59
2.6
Force Fields and Docking
62
2.7
Case Study: (2i?*,45*)-l-Hydroxy-2,4-dimethy]hex-5-ene
64
Bibliography and Suggested Additional Reading
66
References
67
3
Simulations of Molecular Ensembles
69
3.1
Relationship Between MM Optima and Real Systems
69
3.2
Phase Space and Trajectories
70
3.2.1
Properties as Ensemble Averages
70
3.2.2
Properties as Time Averages of Trajectories
71
3.3
Molecular Dynamics
72
3.3.1
Harmonic Oscillator Trajectories
72
3.3.2
Non-analytical Systems
74
3.3.3
Practical Issues in Propagation
77
3.3.4
Stochastic Dynamics
79
3.4
Monte Carlo
80
3.4.1
Manipulation of Phase-space Integrals
80
3.4.2
Metropolis Sampling
81
3.5
Ensemble and Dynamical Property Examples
82
3.6
Key Details in Formalism
88
3.6.1
Cutoffs and Boundary Conditions
88
3.6.2
Polarization
90
3.6.3
Control of System Variables
91
3.6.4
Simulation Convergence
93
3.6.5
The Multiple Minima Problem
96
3.7
Force Field Performance in Simulations
98
3.8
Case Study: Silica Sodalite
99
Bibliography and Suggested Additional Reading
101
References
102
4
Foundations of Molecular Orbital Theory
105
4.1
Quantum Mechanics and the Wave Function
105
4.2
The Hamiltonian Operator
106
4.2.1
General Features
106
4.2.2
The Variational Principle
108
4.2.3
The Born-Oppenheimer Approximation
110
4.3
Construction of Trial Wave Functions 111
4.3.1
The LCAO Basis Set Approach
111
4.3.2
The Secular Equation
113
4.4
Hiickel Theory
П5
4.4.1
Fundamental Principles
115
4.4.2
Application to the Allyl System
116
4.5
Many-electron Wave Functions
119
4.5.1
Hartree-product
Wave Functions
120
4.5.2
The
Hartree
Hamiltonian
121
4.5.3
Electron Spin and Antisymmetry
122
4.5.4
Slater Determinants
124
4.5.5
The Hartree-Fock Self-consistent Field Method
126
Bibliography and Suggested Additional Reading
129
References
130
CONTENTS ix
Semiempirical
Implementations of Molecular Orbital Theory
131
5.1
Semiempirical Philosophy
131
5.1.1
Chemically Virtuous Approximations
131
5.1.2
Analytic Derivatives
133
5.2
Extended Hiickel Theory
134
5.3
CNDO Formalism
136
5.4
INDO
Formalism
139
5.4.1
INDO
and INDO/S
139
5.4.2
MINDO/3 and SINDO1
141
5.5
Basic NDDO Formalism
143
5.5.1
MNDO
143
5.5.2
AMI
145
5.5.3
PM3
146
5.6
General Performance Overview of Basic NDDO Models
147
5.6.1
Energetics
147
5.6.2
Geometries
150
5.6.3
Charge Distributions
151
5.7
Ongoing Developments in Semiempirical MO Theory
152
5.7.1
Use of Semiempirical Properties in
SAR 152
5.7.2
d
Orbitals
in NDDO Models
153
5.7.3
SRP
Models
155
5.7.4
Linear Scaling
157
5.7.5
Other Changes in Functional Form
157
5.8
Case Study: Asymmetric Alkylation of
Benzaldehyde 159
Bibliography and Suggested Additional Reading
162
References
163
Ab Initio
Implementations of Hartree-Fock Molecular Orbital
Theory
165
6.1 Ab
Initio Philosophy
165
6.2
Basis Sets
166
6.2.1
Functional Forms
167
6.2.2
Contracted Gaussian Functions
168
6.2.3
Single-Ç, Multiple-Ç,
and Split-Valence
170
6.2.4
Polarization Functions
173
6.2.5
Diffuse Functions
176
6.2.6
The HF Limit
176
6.2.7
Effective Core Potentials
178
6.2.8
Sources
180
6.3
Key Technical and Practical Points of Hartree-Fock Theory
180
6.3.1
SCF Convergence
181
6.3.2
Symmetry
182
6.3.3
Open-shell Systems
188
6.3.4
Efficiency of Implementation and Use
190
6.4
General Performance Overview of
Ab
Initio HF Theory
192
6.4.1
Energetics
192
6.4.2
Geometries
196
6.4.3
Charge Distributions
198
6.5
Case Study: Polymerization of 4-Substituted Aromatic Enynes
199
Bibliography and Suggested Additional Reading
201
References
201
CONTENTS
Including
Electron
Correlation in Molecular
Orbital
Theory
203
7.1
Dynamical vs. Non-dynamical Electron Correlation
203
7.2
Multiconfiguration Self-Consistent Field Theory
205
7.2.1
Conceptual Basis
205
7.2.2
Active Space Specification
207
7.2.3
Full Configuration Interaction
211
7.3
Configuration Interaction
211
7.3.1
Single-determinant Reference
211
7.3.2
Multireference
216
7.4
Perturbation Theory
216
7.4.1
General Principles
216
7.4.2
Single-reference
219
7.4.3
Multireference
223
7.4.4
First-order Perturbation Theory for Some Relativistic Effects
223
7.5
Coupled-cluster Theory
224
7.6
Practical Issues in Application
227
7.6.1
Basis Set Convergence
227
7.6.2
Sensitivity to Reference Wave Function
230
7.6.3
Price/Performance Summary
235
7.7
Parameterized Methods
237
7.7.1
Scaling Correlation Energies
238
7.7.2
Extrapolation
239
7.7.3
Multilevel Methods
239
7.8
Case Study: Ethylenedione Radical
Anion
244
Bibliography and Suggested Additional Reading
246
References
247
Density Functional Theory
249
8.1
Theoretical Motivation
249
8.1.1
Philosophy
249
8.1.2
Early Approximations
250
8.2
Rigorous Foundation
252
8.2.1
The Hohenberg-Kohn Existence Theorem
252
8.2.2
The Hohenberg-Kohn Variational Theorem
254
8.3
Kohn-Sham Self-consistent Field Methodology
255
8.4
Exchange-correlation Functionals
257
8.4.1
Local Density Approximation
258
8.4.2
Density Gradient and Kinetic Energy Density Corrections
263
8.4.3
Adiabatic Connection Methods
264
8.4.4
Semiempirical DFT
268
8.5
Advantages and Disadvantages of DFT Compared to MO Theory
271
8.5.1
Densities vs. Wave Functions
271
8.5.2
Computational Efficiency
273
8.5.3
Limitations of the KS Formalism
274
8.5.4
Systematic Improvability
278
8.5.5
Worst-case Scenarios
278
8.6
General Performance Overview of DFT
280
8.6.1
Energetics
280
8.6.2
Geometries
291
8.6.3
Charge Distributions
294
8.7
Case Study: Transition-Metal Catalyzed Carbonylation of
Methanol 299
Bibliography and Suggested Additional Reading
300
References
oni
CONTENTS xi
9 Charge Distribution
and Spectroscopie
Properties
305
9.1
Properties Related to Charge Distribution
305
9.1.1
Electric Multipole Moments
305
9.1.2
Molecular Electrostatic Potential
308
9.1.3
Partial Atomic Charges
309
9.1.4
Total Spin
324
9.1.5
Polarizability and Hyperpolarizability
325
9.1.6
ESR Hyperflne Coupling Constants
327
9.2
Ionization Potentials and Electron Affinities
330
9.3
Spectroscopy of Nuclear Motion
331
9.3.1
Rotational
332
9.3.2
Vibrational
334
9.4
NMR Spectral Properties
344
9.4.1
Technical Issues
344
9.4.2
Chemical Shifts and Spin-spin Coupling Constants
345
9.5
Case Study: Matrix Isolation of Perfluorinated p-Benzyne
349
Bibliography and Suggested Additional Reading
351
References
351
10
Thermodynamic Properties
355
10.1
Microscopic-macroscopic Connection
355
10.2
Zero-point Vibrational Energy
356
10.3
Ensemble Properties and Basic Statistical Mechanics
357
10.3.1
Ideal Gas Assumption
358
10.3.2
Separability of Energy Components
359
10.3.3
Molecular Electronic Partition Function
360
10.3.4
Molecular Translational Partition Function
361
10.3.5
Molecular Rotational Partition Function
362
10.3.6
Molecular Vibrational Partition Function
364
10.4
Standard-state Heats and Free Energies of Formation and Reaction
366
10.4.1
Direct Computation
367
10.4.2
Parametric Improvement
370
10.4.3
Isodesmic Equations
372
10.5
Technical Caveats
375
10.5.1
Semiempirical Heats of Formation
375
10.5.2
Low-frequency Motions
375
10.5.3
Equilibrium Populations over Multiple Minima
377
10.5.4
Standard-state Conversions
378
10.5.5
Standard-state Free Energies, Equilibrium Constants, and Concentrations
379
10.6
Case Study: Heat of Formation of H2NOH
381
Bibliography and Suggested Additional Reading
383
References
383
11
Implicit Models for Condensed Phases
385
11.1
Condensed-phase Effects on Structure and Reactivity
385
11.1.1
Free Energy of Transfer and Its Physical Components
386
11.1.2
Solvation as It Affects Potential Energy Surfaces
389
11.2
Electrostatic Interactions with a Continuum
393
11.2.1
The
Poisson
Equation
394
11.2.2
Generalized Born
402
11.2.3
Conductor-like Screening Model
404
11.3
Continuum Models for Non-electrostatic Interactions
406
11.3.1
Specific Component Models
406
11.3.2
Atomic Surface Tensions
407
xii CONTENTS
11.4
Strengths and Weaknesses of Continuum
Solvation Models 410
11.4.1
General Performance for Solvation Free Energies
410
11.4.2
Partitioning
416
11.4.3
Non-isotropic Media
416
11.4.4
Potentials of Mean Force and Solvent Structure
419
11.4.5
Molecular Dynamics with Implicit Solvent
420
11.4.6
Equilibrium vs. Non-equilibrium Solvation
421
11.5
Case Study: Aqueous Reductive Dechlorination of Hexachloroethane
422
Bibliography and Suggested Additional Reading
424
References
425
12
Explicit Models for Condensed Phases
429
12.1
Motivation
429
12.2
Computing Free-energy Differences
429
12.2.1
Raw Differences
430
12.2.2
Free-energy Perturbation
432
12.2.3
Slow Growth and Thermodynamic Integration
435
12.2.4
Free-energy Cycles
437
12.2.5
Potentials of Mean Force
439
12.2.6
Technical Issues and Error Analysis
443
12.3
Other Thermodynamic Properties
444
12.4
Solvent Models
445
12.4.1
Classical Models
445
12.4.2
Quantal Models
447
12.5
Relative Merits of Explicit and Implicit Solvent Models
448
12.5.1
Analysis of Solvation Shell Structure and Energetics
448
12.5.2
Speed/Efficiency
450
12.5.3
Non-equilibrium Solvation
450
12.5.4
Mixed Explicit/Implicit Models
451
12.6
Case Study: Binding of Biotin Analogs to Avidin
452
Bibliography and Suggested Additional Reading
454
References
455
13
Hybrid Quantal/Classical Models
457
13.1
Motivation
457
13.2
Boundaries Through Space
458
13.2.1
Unpolarized Interactions
459
13.2.2
Polarized QM/Unpolarized MM
461
13.2.3
Fully Polarized Interactions
466
13.3
Boundaries Through Bonds
467
13.3.1
Linear Combinations of Model Compounds
467
13.3.2
Link Atoms
473
13.3.3
Frozen
Orbitals 475
13.4
Empirical Valence Bond Methods
477
13.4.1
Potential Energy Surfaces
47g
13.4.2
Following Reaction Paths
480
13.4.3
Generalization to QM/MM
4g
ţ
13.5
Case Study: Catalytic Mechanism of Yeast Enolase
482
Bibliography and Suggested Additional Reading
484
References 4g5
14
Excited Electronic States
437
14.1
Detenninantal/Configurational Representation of Excited States
487
CONTENTS
хш
14.2
Singly Excited States
492
14.2.1
SCF Applicability
493
14.2.2
CI
Singles
496
14.2.3
Rydberg
States
498
14.3
General Excited State Methods
499
14.3.1
Higher Roots in MCSCF and
CI
Calculations
499
14.3.2
Propagator Methods and Time-dependent DFT
501
14.4
Sum and Projection Methods
504
14.5
Transition Probabilities
507
14.6
Solvatochromism
511
14.7
Case Study: Organic Light Emitting Diode Alq3
513
Bibliography and Suggested Additional Reading
515
References
516
15
Adiabatic Reaction Dynamics
519
15.1
Reaction Kinetics and Rate Constants
519
15.1.1
Unimolecular Reactions
520
15.1.2
Bimolecular Reactions
521
15.2
Reaction Paths and Transition States
522
15.3
Transition-state Theory
524
15.3.1
Canonical Equation
524
15.3.2
Variational Transition-state Theory
531
15.3.3
Quantum Effects on the Rate Constant
533
15.4
Condensed-phase Dynamics
538
15.5
Non-adiabatic Dynamics
539
15.5.1
General Surface Crossings
539
15.5.2
Marcus Theory
541
15.6
Case Study: Isomerization of Propylene Oxide
544
Bibliography and Suggested Additional Reading
546
References
546
Appendix A Acronym Glossary
549
Appendix
В
Symmetry and Group Theory
557
B.I Symmetry Elements
557
B.2 Molecular Point Groups and Irreducible Representations
559
B.3 Assigning Electronic State Symmetries
561
B.4 Symmetry in the Evaluation of Integrals and Partition Functions
562
Appendix
С
Spin Algebra
565
C.I Spin Operators
565
C.2 Pure- and Mixed-spin Wave Functions
566
C.3
UHF
Wave Functions
571
C.4 Spin Projection/Annihilation
571
Reference
574
Appendix
D
Orbital Localization
575
D.I
Orbitals
as Empirical Constructs
575
D.2 Natural Bond Orbital Analysis
578
References
579
Index
581
Essentials of
Computational
Chemistry
Theories and Models second
Chistopher J. Cramer
Essentials of Computational Chemistry, Theories and Models, Second Edftion provides an accessible
introduction to this fast developing subject. Extensively revised and updated, the Second Edition has been
carefully developed to encourage student understanding and to establish seamless connections with the
primary literature for the advanced reader. The book opens with a presentation of classical models, gradually
moving on to increasingly more complex quantum mechanical and dynamical theories. Coverage and
examples are drawn from inorganic, organic and biological chemistry.
■
evolving topics like density functional theory, continuum sotvation models, and computational
thermochemistry brought firmly up-to-date.
■
carefully guides the reader through key equations, providing background information and
placing each in context.
■
numerous examples and applications with selected case studies designed as a basis for
classroom discussion.
■
supplementary website with exercises, problems and updates pdtux.cnem.umn.edu/8O21
Invaluable to all students taking a first course in computational chemistry, molecular modelling,
computational quantum chemistry or electronic structure theory. This book will also be of interest to
postgraduates, researchers and professionals needing an up-to-date, accessible introduction to this subject.
Reviews of the First Edftion
.....
this book has a lot to recommend to
,_.. . „ , . , .
undergraduate students as a way of getting them
This ,s an excellent text for graduates or advanced
¡nvo|ved ¡n
com
^јопа|
chemistry^Professor
undergraduates in any field of chemistry, the text Qamer has done a
љ
.
ь
md de$erves
provides an excellent introduction to the field for conaratulatina
students and researchers in any area of chemistry
„ _, ,_. _
л „лл„
The Alchemist,
2003
Theoretical Chemistry Accounts,
2003
Essentials is a useful tool not only for teaching and
learning but also as a quick reference, and thus will
most probably become one of the standard text
books for computational chemistry
Journal of Chemical Information and Computer
Science,
2003
|
| any_adam_object | 1 |
| author | Cramer, Christopher J. |
| author_facet | Cramer, Christopher J. |
| author_role | aut |
| author_sort | Cramer, Christopher J. |
| author_variant | c j c cj cjc |
| building | Verbundindex |
| bvnumber | BV036621883 |
| classification_rvk | VC 6100 |
| classification_tum | CHE 020f CHE 150f |
| ctrlnum | (OCoLC)552170072 (DE-599)BVBBV036621883 |
| dewey-full | 541.0285 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 541 - Physical chemistry |
| dewey-raw | 541.0285 |
| dewey-search | 541.0285 |
| dewey-sort | 3541.0285 |
| dewey-tens | 540 - Chemistry and allied sciences |
| discipline | Chemie / Pharmazie Physik Chemie |
| edition | 2. ed., repr. with corr. |
| format | Book |
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| id | DE-604.BV036621883 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:44:23Z |
| institution | BVB |
| isbn | 9780470091821 9780470091814 0470091819 0470091827 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-020541894 |
| oclc_num | 552170072 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-19 DE-BY-UBM |
| owner_facet | DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-19 DE-BY-UBM |
| physical | XX, 596 S. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Wiley |
| record_format | marc |
| spelling | Cramer, Christopher J. Verfasser aut Essentials of computational chemistry theories and models Christopher J. Cramer 2. ed., repr. with corr. Chichester [u.a.] Wiley 2009 XX, 596 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Hier auch später erschienene, unveränderte Nachdrucke Computational chemistry (DE-588)4290091-8 gnd rswk-swf Computational chemistry (DE-588)4290091-8 s DE-604 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020541894&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020541894&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext |
| spellingShingle | Cramer, Christopher J. Essentials of computational chemistry theories and models Computational chemistry (DE-588)4290091-8 gnd |
| subject_GND | (DE-588)4290091-8 |
| title | Essentials of computational chemistry theories and models |
| title_auth | Essentials of computational chemistry theories and models |
| title_exact_search | Essentials of computational chemistry theories and models |
| title_full | Essentials of computational chemistry theories and models Christopher J. Cramer |
| title_fullStr | Essentials of computational chemistry theories and models Christopher J. Cramer |
| title_full_unstemmed | Essentials of computational chemistry theories and models Christopher J. Cramer |
| title_short | Essentials of computational chemistry |
| title_sort | essentials of computational chemistry theories and models |
| title_sub | theories and models |
| topic | Computational chemistry (DE-588)4290091-8 gnd |
| topic_facet | Computational chemistry |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020541894&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020541894&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
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