Molecular modelling for beginners / Alan Hinchliffe.

Format:

Book

Author/Creator:

Hinchliffe, Alan.

Language:

English

Subjects (All):

Molecules--Mathematical models.

Molecules.

Molecules--Computer simulation.

Computer simulation.

Physical Description:

xviii, 410 pages : illustrations ; 25 cm

Place of Publication:

Chichester, West Sussex, England ; Hoboken, NJ : Wiley, [2003]

Summary:

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.

Contents:

1.1 Chemical Drawing 1

1.2 Three-Dimensional Effects 2

1.3 Optical Activity 3

1.4 Computer Packages 4

1.5 Modelling 4

1.6 Molecular Structure Databases 6

1.7 File Formats 7

1.8 Three-Dimensional Displays 8

1.9 Proteins 10

2 Electric Charges and Their Properties 13

2.1 Point Charges 13

2.2 Coulomb's Law 15

2.3 Pairwise Additivity 16

2.4 The Electric Field 17

2.5 Work 18

2.6 Charge Distributions 20

2.7 The Mutual Potential Energy U 21

2.8 Relationship Between Force and Mutual Potential Energy 22

2.9 Electric Multipoles 23

2.10 The Electrostatic Potential 29

2.11 Polarization and Polarizability 30

2.12 Dipole Polarizability 31

2.13 Many-Body Forces 33

3 The Forces Between Molecules 35

3.1 The Pair Potential 35

3.2 The Multipole Expansion 37

3.3 The Charge-Dipole Interaction 37

3.4 The Dipole-Dipole Interaction 39

3.5 Taking Account of the Temperature 41

3.6 The Induction Energy 41

3.7 Dispersion Energy 43

3.8 Repulsive Contributions 44

3.9 Combination Rules 46

3.10 Comparison with Experiment 46

3.11 Improved Pair Potentials 47

3.12 Site-Site Potentials 48

4 Balls on Springs 51

4.1 Vibrational Motion 52

4.2 The Force Law 55

4.3 A Simple Diatomic 56

4.4 Three Problems 57

4.5 The Morse Potential 60

4.6 More Advanced Potentials 61

5 Molecular Mechanics 63

5.1 More About Balls on Springs 63

5.2 Larger Systems of Balls on Springs 65

5.3 Force Fields 67

5.4 Molecular Mechanics 67

5.5 Modelling the Solvent 72

5.6 Time-and-Money-Saving Tricks 72

5.7 Modern Force Fields 73

5.8 Some Commercial Force Fields 75

6 The Molecular Potential Energy Surface 79

6.1 Multiple Minima 79

6.2 Saddle Points 80

6.3 Characterization 82

6.4 Finding Minima 82

6.5 Multivariate Grid Search 83

6.6 Derivative Methods 84

6.7 First-Order Methods 85

6.8 Second-Order Methods 87

6.9 Choice of Method 91

6.10 The Z Matrix 92

6.11 Tricks of the Trade 94

6.12 The End of the Z Matrix 97

6.13 Redundant Internal Coordinates 99

7 A Molecular Mechanics Calculation 101

7.1 Geometry Optimization 101

7.2 Conformation Searches 102

7.3 QSARs 104

8 Quick Guide to Statistical Thermodynamics 113

8.1 The Ensemble 114

8.2 The Internal Energy U[subscript th] 116

8.3 The Helmholtz Energy A 117

8.4 The Entropy S 117

8.5 Equation of State and Pressure 117

8.6 Phase Space 118

8.7 The Configurational Integral 119

8.8 The Virial of Clausius 121

9 Molecular Dynamics 123

9.1 The Radial Distribution Function 124

9.2 Pair Correlation Functions 127

9.3 Molecular Dynamics Methodology 128

9.4 The Periodic Box 131

9.5 Algorithms for Time Dependence 133

9.6 Molten Salts 135

9.7 Liquid Water 136

9.8 Different Types of Molecular Dynamics 139

9.9 Uses in Conformational Studies 140

10 Monte Carlo 143

10.2 MC Simulation of Rigid Molecules 148

10.3 Flexible Molecules 150

11 Introduction to Quantum Modelling 151

11.1 The Schrodinger Equation 151

11.2 The Time-Independent Schrodinger Equation 153

11.3 Particles in Potential Wells 154

11.4 The Correspondence Principle 157

11.5 The Two-Dimensional Infinite Well 158

11.6 The Three-Dimensional Infinite Well 160

11.7 Two Non-Interacting Particles 161

11.8 The Finite Well 163

11.9 Unbound States 164

11.10 Free Particles 165

11.11 Vibrational Motion 166

12 Quantum Gases 171

12.1 Sharing Out the Energy 172

12.2 Rayleigh Counting 174

12.3 The Maxwell Boltzmann Distribution of Atomic Kinetic Energies 176

12.4 Black Body Radiation 177

12.5 Modelling Metals 180

12.6 The Boltzmann Probability 184

12.7 Indistinguishability 188

12.8 Spin 192

12.9 Fermions and Bosons 194

12.10 The Pauli Exclusion Principle 194

12.11 Boltzmann's Counting Rule 195

13 One-Electron Atoms 197

13.1 Atomic Spectra 197

13.2 The Correspondence Principle 200

13.3 The Infinite Nucleus Approximation 200

13.4 Hartree's Atomic Units 201

13.5 Schrodinger Treatment of the H Atom 202

13.6 The Radial Solutions 204

13.7 The Atomic Orbitals 206

13.8 The Stern-Gerlach Experiment 212

13.9 Electron Spin 215

13.10 Total Angular Momentum 216

13.11 Dirac Theory of the Electron 217

13.12 Measurement in the Quantum World 219

14 The Orbital Model 221

14.1 One- and Two-Electron Operators 221

14.2 The Many-Body Problem 222

14.3 The Orbital Model 223

14.4 Perturbation Theory 225

14.5 The Variation Method 227

14.6 The Linear Variation Method 230

14.7 Slater Determinants 233

14.8 The Slater-Condon-Shortley Rules 235

14.9 The Hartree Model 236

14.10 The Hartree-Fock Model 238

14.11 Atomic Shielding Constants 239

14.12 Koopmans' Theorem 242

15 Simple Molecules 245

15.1 The Hydrogen Molecule Ion H[subscript 2 superscript +] 246

15.2 The LCAO Model 248

15.3 Elliptic Orbitals 251

15.4 The Heitler-London Treatment of Dihydrogen 252

15.5 The Dihydrogen MO Treatment 254

15.6 The James and Coolidge Treatment 256

15.7 Population Analysis 256

16 The HF-LCAO Model 261

16.1 Roothaan's Landmark Paper 262

16.2 The J and K Operators 264

16.3 The HF-LCAO Equations 264

16.4 The Electronic Energy 268

16.5 Koopmans' Theorem 269

16.6 Open Shell Systems 269

16.7 The Unrestricted Hartree-Fock Model 271

16.8 Basis Sets 273

16.9 Gaussian Orbitals 276

17 HF-LCAO Examples 287

17.1 Output 289

17.2 Visualization 293

17.3 Properties 294

17.4 Geometry Optimization 297

17.5 Vibrational Analysis 300

17.6 Thermodynamic Properties 303

17.7 Back to L-phenylanine 308

17.8 Excited States 309

17.9 Consequences of the Brillouin Theorem 313

17.10 Electric Field Gradients 315

18 Semi-empirical Models 319

18.1 Huckel [pi]-Electron Theory 319

18.2 Extended Huckel Theory 322

18.3 Pariser, Parr and Pople 324

18.4 Zero Differential Overlap 325

18.5 Which Basis Functions Are They? 327

18.6 All Valence Electron ZDO Models 328

18.7 Complete Neglect of Differential Overlap 328

18.8 CNDO/2 329

18.9 CNDO/S 330

18.10 Intermediate Neglect of Differential Overlap 330

18.11 Neglect of Diatomic Differential Overlap 331

18.12 The Modified INDO Family 331

18.13 Modified Neglect of Overlap 333

18.14 Austin Model 1 333

18.15 PM3 333

18.16 SAM1 334

18.17 ZINDO/1 and ZINDO/S 334

18.18 Effective Core Potentials 334

19 Electron Correlation 337

19.1 Electron Density Functions 337

19.2 Configuration Interaction 339

19.3 The Coupled Cluster Method 340

19.4 Moller-Plesset Perturbation Theory 341

19.5 Multiconfiguration SCF 346

20 Density Functional Theory and the Kohn-Sham LCAO Equations 347

20.1 The Thomas-Fermi and X[alpha] Models 348

20.2 The Hohenberg-Kohn Theorems 350

20.3 The Kohn-Sham (KS-LCAO) Equations 352

20.4 Numerical Integration (Quadrature) 353

20.5 Practical Details 354

20.6 Custom and Hybrid Functionals 355

20.7 An Example 356

20.8 Applications 358

21 Miscellany 361

21.1 Modelling Polymers 361

21.2 The End-to-End Distance 363

21.3 Early Models of Polymer Structure 364

21.4 Accurate Thermodynamic Properties; The G1, G2 and G3 Models 367

21.5 Transition States 370

21.6 Dealing with the Solvent 372

21.7 Langevin Dynamics 373

21.8 The Solvent Box 375

21.9 ONIOM or Hybrid Models 376

Appendix A Mathematical Aide-Memoire 379

A.1 Scalars and Vectors 379

A.2 Vector Algebra 380

A.3 Scalar and Vector Fields 384

A.4 Vector Calculus 384

A.5 Determinants 389

A.6 Matrices 391

A.7 Angular Momentum 394

A.8 Linear Operators 396

A.9 Angular Momentum Operators 399.

Notes:

Includes bibliographical references (pages [403]-406) and index.

ISBN:

0470843098

0470843101

OCLC:

52766128

Online:

Publisher description