Computational chemistry workbook: learning through examples
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| Main Authors: | , , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Weinheim
Wiley-VCH
2009
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| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Item Description: | Hier auch später erschienene, unveränderte Drucke |
| Physical Description: | XVII, 232 S. graph. Darst. 1 CD-ROM (12 cm) |
| ISBN: | 9783527324422 |
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MARC
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Titel: Computational chemistry workbook
Autor: Heine, Thomas
Jahr: 2009
Contents
Foreword VII
Acknowledgments IX
1 Introduction 1
1.1 Basics of Computational Chemistry 1
1.2 Aim of This Book 2
1.3 How to Use This Book 3
1.4 Structure of This Book 4
1.5 The Chapters 5
1.6 The Software 9
2 Molecular Coordinates and Symmetry 11
2.1 Aim II
2.2 Theoretical Background 11
2.2.1 Cartesian and Internal Coordinates 11
2.2.2 The Z-Matrix 12
2.2.3 The Dihedral Angle 13
2.2.4 Symmetry 35
2.2.5 Symmetry Elements and Operations 16
2.2.6 Point Groups 17
2.3 Demonstration 19
2.3.1 Constructing a Z-Matrix 39
2.3.2 Determining Molecular Point Groups 20
2.4 Problems 22
2.5 Technical Details 23
2.6 Review and Summary 23
References 23
XII Contents
3 Vibrations of Diatomic Molecules: The Harmonic
Approximation 25
3.1 Aim 25
3.2 Theoretical Background 25
3.2.1 The Harmonic Approximation 25
3.2.2 The Reduced Mass 27
3.2.3 The Vibrational Frequencies 28
3.3 Demonstration 30
3.4 Problems 32
3.5 Technical Details 33
3.6 Review and Summary 34
References 34
4 Vibrations of Diatomic Molecules: The Schrodinger
Equation 35
4.1 Aim 35
4.2 Theoretical Background 35
4.2.1 Classical Versus Quantum Mechanics 35
4.2.2 The Stationary Schrodinger Equation 37
4.2.3 Solutions to the Schrodinger Equation 39
4.3 Demonstration 43
4.4 Problems 44
4.5 Technical Details 45
4.6 Review and Summary 45
References 45
5 Atomic Orbitals 47
5.1 Aim 47
5.2 Theoretical Background 47
5.2.1 The Schrodinger Equation of the Atom 47
5.2.2 Atomic Orbitals 49
5.3 Demonstration 51
5.4 Problems 53
5.5 Technical Details 54
5.6 Review and Summary 54
References 55
6 lonization Potentials and Electron Affinities of Atoms 57
6.1 Aim 57
6.2 Theoretical Background 57
6.2.1 lonization Potential and Electron Affinity 57
6.2.2 Slater Rules: Wavefunction and Binding Energies of
Electrons in Atoms and Ions 59
6.2.3 Calculation of lonization Potentials and Electron
Affinities 61
Contents XIII
6.3 Demonstration 62
6.4 Problems 64
6.5 Technical Details 65
6.6 Review and Summary 66
References 66
7 Huckel Molecular Orbital Theory:
Stability of Conjugated Carbon it Systems 67
7.1 Aim 67
7.2 Theoretical Background 67
7.2.1 Molecular Orbital Theory 68
7.2.2 The Huckel Postulates 70
7.2.3 Topology Matrices 71
7.2.4 Values for a and (3 73
7.2.5 The Trap of Defining x 73
7.2.6 7t Electron Binding Energy 74
7.2.7 7i Electron Molecular Orbitals and Probability Density 74
7.3 Demonstration 75
7.3.1 Huckel Calculation of the Cyclopropenyl Cation 75
7.4 Problems 78
7.5 Technical Details 79
7.6 Review and Summary 80
References 81
8 Huckel Molecular Orbital Theory:
Bond Order, Charge Order, and Molecular Orbitals 83
8.1 Aim 83
8.2 Theoretical Background 83
8.2.1 Bond Order 83
8.2.2 Charge Order 84
8.3 Demonstration 85
8.3.1 Huckel Calculation of the Butadiene Molecule 85
8.4 Problems 88
8.5 Review and Summary 89
References 90
9 Geometry Optimization of a Diatomic Molecule 91
9.1 Aim 91
9.2 Theoretical Background 91
9.2.1 The Potential Energy Surface 91
9.2.2 Forces in a Diatomic Molecule 93
9.2.3 The Steepest Descent Method 94
9.2.4 Hessian-Based Optimizers and the Newton-Raphson
Method 95
9.2.5 Application to the Morse Potential 97
XIV Contents
9.2.6 Global Versus Local Geometry Optimization 97
9.3 Demonstration 98
9.3.1 Optimizing CO With the Steepest Descent
Method 98
9.3.2 Optimizing CO Using a Hessian-Based Newton-Raphson
Optimizer 100
9.4 Problems 103
9.5 Technical Details 103
9.6 Review and Summary 104
References 105
10 The Electron Spin 107
10.1 Aim 107
10.2 Theoretical Background 107
10.2.1 The Electron Spin 107
10.2.2 The Multiplicity 108
10.2.3 The Jahn-Teller Effect 108
10.3 Demonstration 109
10.4 Problems 110
10.5 Technical Details 111
10.6 Review and Summary 112
References 112
11 Vibrational Spectroscopy 113
11.1 Aim 113
11.2 Theoretical Background 113
11.2.1 Analysis of Classical Vibrations Within the Harmonic
Approximation 114
11.2.2 The Harmonic Oscillator Revisited 115
11.2.3 The Vibrational Modes 117
11.2.4 Intensities 119
11.3 Demonstration 120
11.3.1 The Vibrational Modes of a Linear Molecule 120
11.4 Problems 124
11.5 Technical Details 125
11.6 Review and Summary 126
References 126
12 Vibrational Spectroscopy and Character Tables -
Advanced Topics 127
12.1 Aim 127
12.2 Theoretical Background 127
12.2.1 The Hessian Matrix 127
12.2.2 Normal Modes 129
12.2.3 Symmetry in Normal Modes 130
Contents XV
12.2.4 Selection Rules 133
12.3 Demonstration 136
12.4 Problems 138
12.5 Review and Summary 240
References 141
13 lonization Potential and Electron Affinities
of Molecules 143
13.1 Aim 143
13.2 Theoretical Background 143
13.2.1 Field of Application 143
13.2.2 Influence of Geometry 144
13.3 Demonstration 146
13.4 Problems 147
13.4.1 Technical Details 148
13.5 Review and Summary 148
References 149
14 Thermochemistry 151
14.1 Aim 151
14.2 Theoretical Background 153
14.2.1 Calculating Thermodynamic Functions Using the Partition
Function 352
14.2.2 Thermochemistry Within the Ideal-Gas
Approximation 354
14.2.3 The Molecular Partition Function q 156
14.2.4 Calculating the Relative Abundance of Isomers in the
Gas Phase 360
14.3 Demonstration 363
14.4 Problems 164
14.5 Review and Summary 365
References 3 65
15 Molecular Dynamics - Basic Concepts 167
15.1 Aim 167
15.2 Theoretical Background 367
15.2.1 Computer Simulations in Chemistry 367
15.2.2 The Bom-Oppenheimer Approximation 369
15.2.3 The Trajectory: Startup Conditions and Propagation of
Atoms in Time 369
15.2.4 The Verlet Algorithm 370
15.2.5 The Velocity Verlet Algorithm 171
15.2.6 Conservation of Fundamental Physical Quantities:
Energy, Momentum, and Angular Momentum 172
15.2.7 Numerical Considerations 173
XVI Contents
15.2.8 Heat Bath: Thermostats 174
15.3 Demonstration 174
15.3.1 Classical Molecular Dynamics in a Spreadsheet 174
15.4 Problems 178
15.5 Review and Summary 178
References 179
16 Molecular Dynamics and Basic Thermodynamics 181
16.1 Aim 181
16.2 Theoretical Background 181
16.2.1 Basic Thermodynamics: Ensembles 182
16.2.2 The Temperature and the Ergodic Theorem 183
16.2.3 The Connection to Real Macroscopic Systems 185
16.2.4 External Heat Baths - Thermostats 186
16.2.4.1 A Simple Scaling Thermostat 186
16.2.4.2 The Berendsen Thermostat 186
16.2.4.3 The Andersen Thermostat 187
16.2.4.4 The Nose-Hoover Thermostat 187
16.2.5 Averages 188
16.3 Demonstration 188
16.4 Problems 194
16.5 Review and Summary 195
References 196
17 Molecular Dynamics - Simulated Annealing 197
17.1 Aim 197
17.2 Theoretical Background 197
17.2.1 The Potential Energy Surface 199
17.2.2 Simulated Annealing 200
17.3 Demonstration 201
17.3.1 Inspecting Stationary Points With Simulated
Annealing 201
17.3.2 Finding the Global Minimum of Al42' Using Simulated
Annealing 203
17.4 Problems 205
17.5 Review and Summary 206
References 207
Appendix
The Computational Chemistry Software Delivered
with This Book 209
A.I Getting Started 220
A.1.1 Booting Directly the Live System 210
A.1.2 Booting as Virtual Machine 210
A.1.3 Running From a Pen Drive (USB Stick) 211
Contents XVII
A. 1.4 Configure Your Environment 213
A.2 A Brief Introduction to Linux 214
A. 3 Character Tables for Chemically Important Point
Groups 218
A.4 Computational Chemistry Software Delivered With
This Book 219
A.4.1 Molden 219
A.4.2 deMon 219
A.4.3 CaGe 220
A.4.4 hueckel 222
A.4.5 THERMO Scripts 222
A.4.6 Xmgrace 223
A.4.7 GNUplot 223
Index 225 |
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| discipline | Chemie / Pharmazie Physik Chemie |
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| spelling | Heine, Thomas 1970- Verfasser (DE-588)142518573 aut Computational chemistry workbook learning through examples Thomas Heine ; Jan-Ole Joswig ; Achim Gelessus Weinheim Wiley-VCH 2009 XVII, 232 S. graph. Darst. 1 CD-ROM (12 cm) txt rdacontent n rdamedia nc rdacarrier Hier auch später erschienene, unveränderte Drucke Computational chemistry - Beispielsammlung Chemie Datenverarbeitung Mathematik Chemistry Computer simulation Chemistry Data processing Chemistry Mathematics Computational chemistry (DE-588)4290091-8 gnd rswk-swf (DE-588)4144384-6 Beispielsammlung gnd-content Computational chemistry (DE-588)4290091-8 s DE-604 Joswig, Jan-Ole Verfasser aut Geleßus, Achim 1966- Verfasser (DE-588)121483495 aut text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3227448&prov=M&dok_var=1&dok_ext=htm Inhaltstext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017557365&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Heine, Thomas 1970- Joswig, Jan-Ole Geleßus, Achim 1966- Computational chemistry workbook learning through examples Computational chemistry - Beispielsammlung Chemie Datenverarbeitung Mathematik Chemistry Computer simulation Chemistry Data processing Chemistry Mathematics Computational chemistry (DE-588)4290091-8 gnd |
| subject_GND | (DE-588)4290091-8 (DE-588)4144384-6 |
| title | Computational chemistry workbook learning through examples |
| title_auth | Computational chemistry workbook learning through examples |
| title_exact_search | Computational chemistry workbook learning through examples |
| title_full | Computational chemistry workbook learning through examples Thomas Heine ; Jan-Ole Joswig ; Achim Gelessus |
| title_fullStr | Computational chemistry workbook learning through examples Thomas Heine ; Jan-Ole Joswig ; Achim Gelessus |
| title_full_unstemmed | Computational chemistry workbook learning through examples Thomas Heine ; Jan-Ole Joswig ; Achim Gelessus |
| title_short | Computational chemistry workbook |
| title_sort | computational chemistry workbook learning through examples |
| title_sub | learning through examples |
| topic | Computational chemistry - Beispielsammlung Chemie Datenverarbeitung Mathematik Chemistry Computer simulation Chemistry Data processing Chemistry Mathematics Computational chemistry (DE-588)4290091-8 gnd |
| topic_facet | Computational chemistry - Beispielsammlung Chemie Datenverarbeitung Mathematik Chemistry Computer simulation Chemistry Data processing Chemistry Mathematics Computational chemistry Beispielsammlung |
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