Molecular Modelling for Beginners / Edition 2

Molecular Modelling for Beginners / Edition 2

by Alan Hinchliffe
     
 

ISBN-10: 0470513136

ISBN-13: 9780470513132

Pub. Date: 11/25/2008

Publisher: Wiley

  • A concise, basic introduction to modelling and computational chemistry which focuses on the essentials, including MM, MC, and MD, along with a chapter devoted to QSAR and Discovery Chemistry.
  • Includes supporting website featuring background information, full colour illustrations, questions and answers tied into the text,Visual Basic packages

…  See more details below

Overview

  • A concise, basic introduction to modelling and computational chemistry which focuses on the essentials, including MM, MC, and MD, along with a chapter devoted to QSAR and Discovery Chemistry.
  • Includes supporting website featuring background information, full colour illustrations, questions and answers tied into the text,Visual Basic packages and many realistic examples with solutions
  • Takes a hands-on approach, using state of the art software packages G03/W and/or Hyperchem, Gaussian .gjf files and sample outputs.
  • Revised with changes in emphasis and presentation to appeal to the modern student.

Product Details

ISBN-13:
9780470513132
Publisher:
Wiley
Publication date:
11/25/2008
Pages:
432
Product dimensions:
6.80(w) x 9.80(h) x 1.10(d)

Table of Contents

Prefacexiii
List of Symbolsxvii
1Introduction1
1.1Chemical Drawing1
1.2Three-Dimensional Effects2
1.3Optical Activity3
1.4Computer Packages4
1.5Modelling4
1.6Molecular Structure Databases6
1.7File Formats7
1.8Three-Dimensional Displays8
1.9Proteins10
2Electric Charges and Their Properties13
2.1Point Charges13
2.2Coulomb's Law15
2.3Pairwise Additivity16
2.4The Electric Field17
2.5Work18
2.6Charge Distributions20
2.7The Mutual Potential Energy U21
2.8Relationship Between Force and Mutual Potential Energy22
2.9Electric Multipoles23
2.10The Electrostatic Potential29
2.11Polarization and Polarizability30
2.12Dipole Polarizability31
2.13Many-Body Forces33
3The Forces Between Molecules35
3.1The Pair Potential35
3.2The Multipole Expansion37
3.3The Charge-Dipole Interaction37
3.4The Dipole-Dipole Interaction39
3.5Taking Account of the Temperature41
3.6The Induction Energy41
3.7Dispersion Energy43
3.8Repulsive Contributions44
3.9Combination Rules46
3.10Comparison with Experiment46
3.11Improved Pair Potentials47
3.12Site-Site Potentials48
4Balls on Springs51
4.1Vibrational Motion52
4.2The Force Law55
4.3A Simple Diatomic56
4.4Three Problems57
4.5The Morse Potential60
4.6More Advanced Potentials61
5Molecular Mechanics63
5.1More About Balls on Springs63
5.2Larger Systems of Balls on Springs65
5.3Force Fields67
5.4Molecular Mechanics67
5.5Modelling the Solvent72
5.6Time-and-Money-Saving Tricks72
5.7Modern Force Fields73
5.8Some Commercial Force Fields75
6The Molecular Potential Energy Surface79
6.1Multiple Minima79
6.2Saddle Points80
6.3Characterization82
6.4Finding Minima82
6.5Multivariate Grid Search83
6.6Derivative Methods84
6.7First-Order Methods85
6.8Second-Order Methods87
6.9Choice of Method91
6.10The Z Matrix92
6.11Tricks of the Trade94
6.12The End of the Z Matrix97
6.13Redundant Internal Coordinates99
7A Molecular Mechanics Calculation101
7.1Geometry Optimization101
7.2Conformation Searches102
7.3QSARs104
8Quick Guide to Statistical Thermodynamics113
8.1The Ensemble114
8.2The Internal Energy U[subscript th]116
8.3The Helmholtz Energy A117
8.4The Entropy S117
8.5Equation of State and Pressure117
8.6Phase Space118
8.7The Configurational Integral119
8.8The Virial of Clausius121
9Molecular Dynamics123
9.1The Radial Distribution Function124
9.2Pair Correlation Functions127
9.3Molecular Dynamics Methodology128
9.4The Periodic Box131
9.5Algorithms for Time Dependence133
9.6Molten Salts135
9.7Liquid Water136
9.8Different Types of Molecular Dynamics139
9.9Uses in Conformational Studies140
10Monte Carlo143
10.1Introduction143
10.2MC Simulation of Rigid Molecules148
10.3Flexible Molecules150
11Introduction to Quantum Modelling151
11.1The Schrodinger Equation151
11.2The Time-Independent Schrodinger Equation153
11.3Particles in Potential Wells154
11.4The Correspondence Principle157
11.5The Two-Dimensional Infinite Well158
11.6The Three-Dimensional Infinite Well160
11.7Two Non-Interacting Particles161
11.8The Finite Well163
11.9Unbound States164
11.10Free Particles165
11.11Vibrational Motion166
12Quantum Gases171
12.1Sharing Out the Energy172
12.2Rayleigh Counting174
12.3The Maxwell Boltzmann Distribution of Atomic Kinetic Energies176
12.4Black Body Radiation177
12.5Modelling Metals180
12.6The Boltzmann Probability184
12.7Indistinguishability188
12.8Spin192
12.9Fermions and Bosons194
12.10The Pauli Exclusion Principle194
12.11Boltzmann's Counting Rule195
13One-Electron Atoms197
13.1Atomic Spectra197
13.2The Correspondence Principle200
13.3The Infinite Nucleus Approximation200
13.4Hartree's Atomic Units201
13.5Schrodinger Treatment of the H Atom202
13.6The Radial Solutions204
13.7The Atomic Orbitals206
13.8The Stern-Gerlach Experiment212
13.9Electron Spin215
13.10Total Angular Momentum216
13.11Dirac Theory of the Electron217
13.12Measurement in the Quantum World219
14The Orbital Model221
14.1One- and Two-Electron Operators221
14.2The Many-Body Problem222
14.3The Orbital Model223
14.4Perturbation Theory225
14.5The Variation Method227
14.6The Linear Variation Method230
14.7Slater Determinants233
14.8The Slater-Condon-Shortley Rules235
14.9The Hartree Model236
14.10The Hartree-Fock Model238
14.11Atomic Shielding Constants239
14.12Koopmans' Theorem242
15Simple Molecules245
15.1The Hydrogen Molecule Ion H[subscript 2 superscript +]246
15.2The LCAO Model248
15.3Elliptic Orbitals251
15.4The Heitler-London Treatment of Dihydrogen252
15.5The Dihydrogen MO Treatment254
15.6The James and Coolidge Treatment256
15.7Population Analysis256
16The HF-LCAO Model261
16.1Roothaan's Landmark Paper262
16.2The J and K Operators264
16.3The HF-LCAO Equations264
16.4The Electronic Energy268
16.5Koopmans' Theorem269
16.6Open Shell Systems269
16.7The Unrestricted Hartree-Fock Model271
16.8Basis Sets273
16.9Gaussian Orbitals276
17HF-LCAO Examples287
17.1Output289
17.2Visualization293
17.3Properties294
17.4Geometry Optimization297
17.5Vibrational Analysis300
17.6Thermodynamic Properties303
17.7Back to L-phenylanine308
17.8Excited States309
17.9Consequences of the Brillouin Theorem313
17.10Electric Field Gradients315
18Semi-empirical Models319
18.1Huckel [pi]-Electron Theory319
18.2Extended Huckel Theory322
18.3Pariser, Parr and Pople324
18.4Zero Differential Overlap325
18.5Which Basis Functions Are They?327
18.6All Valence Electron ZDO Models328
18.7Complete Neglect of Differential Overlap328
18.8CNDO/2329
18.9CNDO/S330
18.10Intermediate Neglect of Differential Overlap330
18.11Neglect of Diatomic Differential Overlap331
18.12The Modified INDO Family331
18.13Modified Neglect of Overlap333
18.14Austin Model 1333
18.15PM3333
18.16SAM1334
18.17ZINDO/1 and ZINDO/S334
18.18Effective Core Potentials334
19Electron Correlation337
19.1Electron Density Functions337
19.2Configuration Interaction339
19.3The Coupled Cluster Method340
19.4Moller-Plesset Perturbation Theory341
19.5Multiconfiguration SCF346
20Density Functional Theory and the Kohn-Sham LCAO Equations347
20.1The Thomas-Fermi and X[alpha] Models348
20.2The Hohenberg-Kohn Theorems350
20.3The Kohn-Sham (KS-LCAO) Equations352
20.4Numerical Integration (Quadrature)353
20.5Practical Details354
20.6Custom and Hybrid Functionals355
20.7An Example356
20.8Applications358
21Miscellany361
21.1Modelling Polymers361
21.2The End-to-End Distance363
21.3Early Models of Polymer Structure364
21.4Accurate Thermodynamic Properties; The G1, G2 and G3 Models367
21.5Transition States370
21.6Dealing with the Solvent372
21.7Langevin Dynamics373
21.8The Solvent Box375
21.9ONIOM or Hybrid Models376
AppendixA Mathematical Aide-Memoire379
A.1Scalars and Vectors379
A.2Vector Algebra380
A.3Scalar and Vector Fields384
A.4Vector Calculus384
A.5Determinants389
A.6Matrices391
A.7Angular Momentum394
A.8Linear Operators396
A.9Angular Momentum Operators399
References403
Index407

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