Molecular modelling for beginners

Library	Materyal Türü	Barkod	Yer Numarası	Durum
Searching... Pamukkale Merkez Kütüphanesi	Kitap	0039413	QD480.H58 2006	Searching... Unknown
Searching... Pamukkale Merkez Kütüphanesi	Kitap	0039721	QD480.H58 2006	Searching... Unknown

Presenting a concise, basic introduction to modelling and computational chemistry this text includes relevant introductory material to ensure greater accessibility to the subject. Provides a comprehensive introduction to this evolving and developing field Focuses on MM, MC, and MD with an entire chapter devoted to QSAR and Discovery Chemistry. Includes many real chemical applications combined with worked problems and solutions provided in each chapter Ensures that up-to-date treatment of a variety of chemical modeling techniques are introduced.

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Choice Review

This is an excellent book for chemists interested in performing molecular modeling calculations without the theoretical background of all the possible types of mathematical operations that can be performed. Hinchliffe (UMIST, Manchester, UK) presents fundamental theories based on classical mechanics, classical electrostatics, and statistical thermodynamics, and does a wonderful job in summarizing the different types of calculations and what they examine in terms of energy interactions, making it very easy to find the best applicability with a given molecular system. He also does a good job explaining the mathematical analysis of the different parameters. The inclusion of real-life chemical applications with associated software enables readers to better follow the author's ideas. For anyone interested in performing molecular calculations. ^BSumming Up: Highly recommended. Upper-division undergraduates through professionals. J. D. Pike Providence College

Preface	p. xiii
List of Symbols	p. xvii
1 Introduction	p. 1
1.1 Chemical Drawing	p. 1
1.2 Three-Dimensional Effects	p. 2
1.3 Optical Activity	p. 3
1.4 Computer Packages	p. 4
1.5 Modelling	p. 4
1.6 Molecular Structure Databases	p. 6
1.7 File Formats	p. 7
1.8 Three-Dimensional Displays	p. 8
1.9 Proteins	p. 10
2 Electric Charges and Their Properties	p. 13
2.1 Point Charges	p. 13
2.2 Coulomb's Law	p. 15
2.3 Pairwise Additivity	p. 16
2.4 The Electric Field	p. 17
2.5 Work	p. 18
2.6 Charge Distributions	p. 20
2.7 The Mutual Potential Energy U	p. 21
2.8 Relationship Between Force and Mutual Potential Energy	p. 22
2.9 Electric Multipoles	p. 23
2.10 The Electrostatic Potential	p. 29
2.11 Polarization and Polarizability	p. 30
2.12 Dipole Polarizability	p. 31
2.13 Many-Body Forces	p. 33
3 The Forces Between Molecules	p. 35
3.1 The Pair Potential	p. 35
3.2 The Multipole Expansion	p. 37
3.3 The Charge-Dipole Interaction	p. 37
3.4 The Dipole-Dipole Interaction	p. 39
3.5 Taking Account of the Temperature	p. 41
3.6 The Induction Energy	p. 41
3.7 Dispersion Energy	p. 43
3.8 Repulsive Contributions	p. 44
3.9 Combination Rules	p. 46
3.10 Comparison with Experiment	p. 46
3.11 Improved Pair Potentials	p. 47
3.12 Site-Site Potentials	p. 48
4 Balls on Springs	p. 51
4.1 Vibrational Motion	p. 52
4.2 The Force Law	p. 55
4.3 A Simple Diatomic	p. 56
4.4 Three Problems	p. 57
4.5 The Morse Potential	p. 60
4.6 More Advanced Potentials	p. 61
5 Molecular Mechanics	p. 63
5.1 More About Balls on Springs	p. 63
5.2 Larger Systems of Balls on Springs	p. 65
5.3 Force Fields	p. 67
5.4 Molecular Mechanics	p. 67
5.5 Modelling the Solvent	p. 72
5.6 Time-and-Money-Saving Tricks	p. 72
5.7 Modern Force Fields	p. 73
5.8 Some Commercial Force Fields	p. 75
6 The Molecular Potential Energy Surface	p. 79
6.1 Multiple Minima	p. 79
6.2 Saddle Points	p. 80
6.3 Characterization	p. 82
6.4 Finding Minima	p. 82
6.5 Multivariate Grid Search	p. 83
6.6 Derivative Methods	p. 84
6.7 First-Order Methods	p. 85
6.8 Second-Order Methods	p. 87
6.9 Choice of Method	p. 91
6.10 The Z Matrix	p. 92
6.11 Tricks of the Trade	p. 94
6.12 The End of the Z Matrix	p. 97
6.13 Redundant Internal Coordinates	p. 99
7 A Molecular Mechanics Calculation	p. 101
7.1 Geometry Optimization	p. 101
7.2 Conformation Searches	p. 102
7.3 QSARs	p. 104
8 Quick Guide to Statistical Thermodynamics	p. 113
8.1 The Ensemble	p. 114
8.2 The Internal Energy U[subscript th]	p. 116
8.3 The Helmholtz Energy A	p. 117
8.4 The Entropy S	p. 117
8.5 Equation of State and Pressure	p. 117
8.6 Phase Space	p. 118
8.7 The Configurational Integral	p. 119
8.8 The Virial of Clausius	p. 121
9 Molecular Dynamics	p. 123
9.1 The Radial Distribution Function	p. 124
9.2 Pair Correlation Functions	p. 127
9.3 Molecular Dynamics Methodology	p. 128
9.4 The Periodic Box	p. 131
9.5 Algorithms for Time Dependence	p. 133
9.6 Molten Salts	p. 135
9.7 Liquid Water	p. 136
9.8 Different Types of Molecular Dynamics	p. 139
9.9 Uses in Conformational Studies	p. 140
10 Monte Carlo	p. 143
10.1 Introduction	p. 143
10.2 MC Simulation of Rigid Molecules	p. 148
10.3 Flexible Molecules	p. 150
11 Introduction to Quantum Modelling	p. 151
11.1 The Schrodinger Equation	p. 151
11.2 The Time-Independent Schrodinger Equation	p. 153
11.3 Particles in Potential Wells	p. 154
11.4 The Correspondence Principle	p. 157
11.5 The Two-Dimensional Infinite Well	p. 158
11.6 The Three-Dimensional Infinite Well	p. 160
11.7 Two Non-Interacting Particles	p. 161
11.8 The Finite Well	p. 163
11.9 Unbound States	p. 164
11.10 Free Particles	p. 165
11.11 Vibrational Motion	p. 166
12 Quantum Gases	p. 171
12.1 Sharing Out the Energy	p. 172
12.2 Rayleigh Counting	p. 174
12.3 The Maxwell Boltzmann Distribution of Atomic Kinetic Energies	p. 176
12.4 Black Body Radiation	p. 177
12.5 Modelling Metals	p. 180
12.6 The Boltzmann Probability	p. 184
12.7 Indistinguishability	p. 188
12.8 Spin	p. 192
12.9 Fermions and Bosons	p. 194
12.10 The Pauli Exclusion Principle	p. 194
12.11 Boltzmann's Counting Rule	p. 195
13 One-Electron Atoms	p. 197
13.1 Atomic Spectra	p. 197
13.2 The Correspondence Principle	p. 200
13.3 The Infinite Nucleus Approximation	p. 200
13.4 Hartree's Atomic Units	p. 201
13.5 Schrodinger Treatment of the H Atom	p. 202
13.6 The Radial Solutions	p. 204
13.7 The Atomic Orbitals	p. 206
13.8 The Stern-Gerlach Experiment	p. 212
13.9 Electron Spin	p. 215
13.10 Total Angular Momentum	p. 216
13.11 Dirac Theory of the Electron	p. 217
13.12 Measurement in the Quantum World	p. 219
14 The Orbital Model	p. 221
14.1 One- and Two-Electron Operators	p. 221
14.2 The Many-Body Problem	p. 222
14.3 The Orbital Model	p. 223
14.4 Perturbation Theory	p. 225
14.5 The Variation Method	p. 227
14.6 The Linear Variation Method	p. 230
14.7 Slater Determinants	p. 233
14.8 The Slater-Condon-Shortley Rules	p. 235
14.9 The Hartree Model	p. 236
14.10 The Hartree-Fock Model	p. 238
14.11 Atomic Shielding Constants	p. 239
14.12 Koopmans' Theorem	p. 242
15 Simple Molecules	p. 245
15.1 The Hydrogen Molecule Ion H[subscript 2 superscript +]	p. 246
15.2 The LCAO Model	p. 248
15.3 Elliptic Orbitals	p. 251
15.4 The Heitler-London Treatment of Dihydrogen	p. 252
15.5 The Dihydrogen MO Treatment	p. 254
15.6 The James and Coolidge Treatment	p. 256
15.7 Population Analysis	p. 256
16 The HF-LCAO Model	p. 261
16.1 Roothaan's Landmark Paper	p. 262
16.2 The J and K Operators	p. 264
16.3 The HF-LCAO Equations	p. 264
16.4 The Electronic Energy	p. 268
16.5 Koopmans' Theorem	p. 269
16.6 Open Shell Systems	p. 269
16.7 The Unrestricted Hartree-Fock Model	p. 271
16.8 Basis Sets	p. 273
16.9 Gaussian Orbitals	p. 276
17 HF-LCAO Examples	p. 287
17.1 Output	p. 289
17.2 Visualization	p. 293
17.3 Properties	p. 294
17.4 Geometry Optimization	p. 297
17.5 Vibrational Analysis	p. 300
17.6 Thermodynamic Properties	p. 303
17.7 Back to L-phenylanine	p. 308
17.8 Excited States	p. 309
17.9 Consequences of the Brillouin Theorem	p. 313
17.10 Electric Field Gradients	p. 315
18 Semi-empirical Models	p. 319
18.1 Huckel [pi]-Electron Theory	p. 319
18.2 Extended Huckel Theory	p. 322
18.3 Pariser, Parr and Pople	p. 324
18.4 Zero Differential Overlap	p. 325
18.5 Which Basis Functions Are They?	p. 327
18.6 All Valence Electron ZDO Models	p. 328
18.7 Complete Neglect of Differential Overlap	p. 328
18.8 CNDO/2	p. 329
18.9 CNDO/S	p. 330
18.10 Intermediate Neglect of Differential Overlap	p. 330
18.11 Neglect of Diatomic Differential Overlap	p. 331
18.12 The Modified INDO Family	p. 331
18.13 Modified Neglect of Overlap	p. 333
18.14 Austin Model 1	p. 333
18.15 PM3	p. 333
18.16 SAM1	p. 334
18.17 ZINDO/1 and ZINDO/S	p. 334
18.18 Effective Core Potentials	p. 334
19 Electron Correlation	p. 337
19.1 Electron Density Functions	p. 337
19.2 Configuration Interaction	p. 339
19.3 The Coupled Cluster Method	p. 340
19.4 Moller-Plesset Perturbation Theory	p. 341
19.5 Multiconfiguration SCF	p. 346
20 Density Functional Theory and the Kohn-Sham LCAO Equations	p. 347
20.1 The Thomas-Fermi and X[alpha] Models	p. 348
20.2 The Hohenberg-Kohn Theorems	p. 350
20.3 The Kohn-Sham (KS-LCAO) Equations	p. 352
20.4 Numerical Integration (Quadrature)	p. 353
20.5 Practical Details	p. 354
20.6 Custom and Hybrid Functionals	p. 355
20.7 An Example	p. 356
20.8 Applications	p. 358
21 Miscellany	p. 361
21.1 Modelling Polymers	p. 361
21.2 The End-to-End Distance	p. 363
21.3 Early Models of Polymer Structure	p. 364
21.4 Accurate Thermodynamic Properties; The G1, G2 and G3 Models	p. 367
21.5 Transition States	p. 370
21.6 Dealing with the Solvent	p. 372
21.7 Langevin Dynamics	p. 373
21.8 The Solvent Box	p. 375
21.9 ONIOM or Hybrid Models	p. 376
Appendix A Mathematical Aide-Memoire	p. 379
A.1 Scalars and Vectors	p. 379
A.2 Vector Algebra	p. 380
A.3 Scalar and Vector Fields	p. 384
A.4 Vector Calculus	p. 384
A.5 Determinants	p. 389
A.6 Matrices	p. 391
A.7 Angular Momentum	p. 394
A.8 Linear Operators	p. 396
A.9 Angular Momentum Operators	p. 399
References	p. 403
Index	p. 407

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