Cover Page......Page 1
Title Page......Page 4
ISBN 1402053711......Page 5
CONTENTS (with page links)......Page 6
PREFACE......Page 8
CHAPTER 1 THEORY OF INTERMOLECULAR FORCES: AN INTRODUCTORY ACCOUNT......Page 11
1. INTRODUCTION......Page 12
2. THE BORN-OPPENHEIMER APPROXIMATION......Page 15
2.1. Born-Huang Expansion of the Total Wave Function......Page 16
2.2. Adiabatic and Born-Oppenheimer Approximations......Page 18
2.4. Schrรถdinger Equation for the Nuclear Motions......Page 19
2.5. Failures of the Born-Oppenheimer Approximation and the Nonadiabatic Approach......Page 20
3. SUPERMOLECULAR APPROACH TO INTERMOLECULAR INTERACTIONS......Page 21
4.1. Rayleigh-Schrรถdinger Perturbation Theory......Page 24
4.2. Symmetry Adaptation......Page 28
5.1. Electrostatic Energy......Page 37
5.2. First-order Exchange (Heitler-London) Energy......Page 38
5.3. Induction Energy......Page 40
5.4. Exchange-induction Energy......Page 42
5.5. Dispersion Energy......Page 43
5.7. Third-order Polarization and Exchange Contributions......Page 44
6. MULTIPOLE EXPANSION OF THE INTERACTION ENERGY......Page 46
6.1. One-center Expansion......Page 47
6.2. Multicenter Expansions......Page 55
6.3. Bipolar Expansion of the Interaction Energy......Page 60
6.4. Importance of the Charge-overlap (Damping) Effects......Page 62
7. MANY-ELECTRON FORMULATION OF THE SRS THEORY......Page 63
8.1. Hartree-Fock Theory......Page 66
8.2. Mรธller-Plesset Theory......Page 68
8.3. Coupled Cluster Theory......Page 69
8.4. Selfconsistent Reaction Field Theory......Page 71
9.1. Morokuma Partitioning of the Hartree-Fock Interaction Energy......Page 74
9.2. Variation-Perturbation Approach......Page 77
9.3. Tang-Toennies Model......Page 78
9.4. Atom-Atom and Site-Site Potentials......Page 80
9.5. Empirical Force Fields......Page 81
10.1. Supermolecular Approach......Page 83
10.2. Perturbation Theory of Three-Body Interactions......Page 84
10.3. Physical Interpretation of the Polarization Effects......Page 86
10.4. Exchange Effects......Page 89
11. SYMMETRY-ADAPTED PERTURBATION THEORY OF THE INTERACTION-INDUCED PROPERTIES......Page 91
12.1. Collision-induced Raman Light Scattering in Atomic Gas......Page 94
12.2. Dielectric Second Virial Coefficients of Atomic Gases......Page 95
12.3. Refractive (Kerr) Second Virial Coefficients of Atomic Gases......Page 97
12.4. Rovibrational Spectra of Weakly Bound Complexes......Page 98
12.5. Scattering Cross Sections for Rotational Excitation......Page 102
12.6. Thermodynamic Second Virial Coefficients......Page 103
12.7. Simulations of Condensed Phases......Page 105
13.1. Pair Potentials and Modelling of Spectroscopic, Collisional, and Thermodynamic Properties of Binary Complexes......Page 106
13.2. Nonadditive Interactions, Spectroscopic Signatures of Molecular Clusters, and Simulations of Condensed Phases......Page 115
13.3. Solvation Processes in Small Water Clusters......Page 124
13.4. Collision-induced Properties and Modelling of Raman Spectra of Atomic Gases......Page 131
13.5. Modelling of Dielectric and Refractive Properties of Atomic Gases......Page 133
14. CONCLUSIONS AND OUTLOOK FOR THE FUTURE......Page 137
REFERENCES......Page 140
CHAPTER 2 HOHENBERG-KOHN-SHAM DENSITY FUNCTIONAL THEORY The formal basis for a family of succesful and still evolving computational methods for modelling interactions in complex chemical systems.......Page 163
1. INTRODUCTION......Page 164
2. THE KOHN-SHAM EQUATIONS......Page 167
3.1. The Starting Point: Local Density Approximation......Page 170
3.2. The First Breakthrough: Generalized Gradient Approximation......Page 172
3.3. Meta-GGA......Page 173
3.4. Hybrid Functionals......Page 174
3.5. Beyond Meta-GGA......Page 175
4.1. Electric Properties: Electric Moments......Page 176
4.2. Electric Properties: Polarizabilities......Page 178
4.3. Ionization Potentials and Electron Affinities......Page 181
4.4. Intermolecular Interactions......Page 184
5. ONGOING DEVELOPMENTS......Page 190
5.1. Optimized Effective Potential......Page 191
5.2. Weighted Density Approximation......Page 192
5.4. Van der Waals Density Functional of Langreth and Lundqvist......Page 193
5.5. Current-dependent Exchange-Correlation Functional......Page 194
5.7. Dispersion Interactions from the Analysis of the Dipole Moment of the Exchange Hole......Page 195
5.8. Subsystem Formulation of DFT......Page 196
6. CONCLUDING REMARKS......Page 197
APPENDIX......Page 200
REFERENCES......Page 201
CHAPTER 3 SELECTED MICROSCOPIC AND MEZOSCOPIC MODELLING TOOLS AND MODELS โ AN OVERVIEW......Page 213
1. INTRODUCTION......Page 214
2.1. Atomic Resolution of Molecular Models and Microscopic Potential Energy Functions......Page 215
2.2. Coarse-grained Models for Biomolecules......Page 218
3. SCC-DFTB METHOD AND CM3 CHARGES......Page 221
4. SOLVATION FREE ENERGY......Page 222
4.1. Potential of Mean Force and Landau Free Energy......Page 224
5. OUTLINE OF THE POISSON-BOLTZMANN (PB) MODEL......Page 226
6. OUTLINE OF THE GENERALIZED BORN (GB) MODEL......Page 227
7. NONPOLAR CONTRIBUTION TO THE FREE ENERGY OF SOLVATION......Page 228
ACKNOWLEDGEMENTS......Page 229
REFERENCES......Page 230
1. INTRODUCTION......Page 235
2.1. Born-Oppenheimer MD and Car-Parinello MD......Page 237
2.2. Forces in ab initio MD; Plane-wave-based Electronic Structure Methods......Page 239
2.3. Finite Temperature Simulations: Thermostats......Page 241
2.4. Practical Aspects of Car-Parinello MD Simulation......Page 242
3.1. Towards Overcoming High Energy Barriers......Page 247
3.2. Constrained Dynamics, Thermodynamic Integration, and Free-energy Barriers......Page 248
3.3. MD along Intrinsic Reaction Paths......Page 250
3.4. Illustrative Examples......Page 251
4.1. The Polar Copolymerization Process and its Mechanism......Page 263
4.2. DFT and MD Studies on the Monomer Binding and Insertion......Page 266
4.3. MD Studies on the Chelate Opening by Ethylene......Page 270
REFERENCES......Page 278
1. INTRODUCTION......Page 285
2. AIMS IN MODELLING ENZYME REACTIONS......Page 286
3. METHODS FOR MODELLING ENZYME-CATALYSED REACTION MECHANISMS......Page 287
3.1. Quantum Chemical Approaches to Modelling Enzyme Reactions: Cluster (or Supermolecule) Approaches......Page 290
3.2. Empirical Valence Bond Methods......Page 291
3.3. Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods......Page 292
4.1. Chorismate Mutase: Analysing Fundamental Principles of Enzyme Catalysis......Page 297
4.2. Cytochrome P450: Mechanism and StructureโReactivity Relationships......Page 300
4.3. Other Recent Modelling Studies of Enzyme-Catalysed Reactions......Page 302
ACKNOWLEDGEMENTS......Page 304
REFERENCES......Page 305
CHAPTER 6 COMPUTATIONAL DETERMINATION OF THE RELATIVE FREE ENERGY OF BINDING โ APPLICATION TO ALANINE SCANNING MUTAGENESIS......Page 315
1. INTRODUCTION......Page 316
2. COMPUTATIONAL CALCULATION OF THE RELATIVE BINDING ENERGY......Page 317
3. EMPIRICAL APPROACHES AND SIMPLE PHYSICAL MODELS......Page 319
3.1. Wallqvist Model......Page 320
3.3. Partitioning Approach......Page 321
4. LINEAR INTERACTION ENERGY (LIE)......Page 322
5. MM-PBSA......Page 323
5.1. Force Fields for Bimolecular Simulations......Page 324
5.2. Solvation......Page 325
5.3. The MM-PBSA approach fundamental theory......Page 328
6. FREE ENERGY PERTURBATION (FEP) AND THERMODYNAMIC INTEGRATION (TI)......Page 331
8. ฮ - DYNAMICS AND CHEMICAL MONTE CARLO/MOLECULAR DYNAMICS (CMC/MD)......Page 333
9. CONCLUSION......Page 334
REFERENCES......Page 335
1. INTRODUCTION......Page 351
2. BINDING CAN BE REFLECTED IN ISOTOPE EFFECTS......Page 352
3. ISOTOPE EFFECTS AND HYDROGEN BONDING......Page 353
4. PURINE NUCLEOSIDE PHOSPHORYLASE โ MULTIPLE KIEs STUDY AND TS ANALOGUES DESIGN......Page 360
4.1. What do KIEs Tell us about the TS Properties and its Interactions with Enzymes?......Page 362
REFERENCES......Page 369
1. INTRODUCTION......Page 375
2. COMPUTER AIDED INHIBITOR DESIGN......Page 377
2.1. Lead Generation......Page 378
2.2. Lead Optimization......Page 380
2.3. The Physical Nature of Ligand Binding......Page 382
3. LEUCINE AMINOPEPTIDASE INHIBITORS......Page 384
4. GLUTAMINE SYNTHETASE INHIBITORS......Page 391
5. L-PHENYLALANINE AMMONIA LYASE INHIBITORS......Page 395
REFERENCES......Page 402
1. INTRODUCTION......Page 409
2.1. Active Site of Dg......Page 412
2.2. Active Site of DvMF......Page 421
3. CONCLUSION......Page 435
REFERENCES......Page 436
INTRODUCTION......Page 443
2. HOW DOES PH INFLUENCE THE UNFOLDING PATHWAY OF W-BR......Page 447
3. UNFOLDING HELICES G AND F......Page 448
4. UNFOLDING HELICES E AND D......Page 450
6. UNFOLDING HELIX A......Page 452
8. TEMPERATURE DEPENDENCE OF UNFOLDING PROFILES OF W- BR......Page 454
CONCLUSION......Page 458
REFERENCES......Page 459
1. INTRODUCTION......Page 463
2. G PROTEIN-COUPLED RECEPTORS......Page 464
2.2. Rhodopsin as a Template......Page 465
3.1. Experimental evidence......Page 468
3.2. Modeling the Complexes of Oligomeric Rhodopsin......Page 469
4. CONCLUSIONS AND CHALLENGES......Page 473
REFERENCES......Page 475
1. INTRODUCTION......Page 479
2. COMPUTATIONAL METHODS......Page 481
3.1. H2 Distribution......Page 483
3.2. Heat of Adsorption......Page 485
3.3. Radial Distribution Functions......Page 486
3.4 H2 Vibrational Spectrum......Page 487
3.5 H2 Diffusion Coefficients in SWNT......Page 488
4 H2 ADSORPTION IN FINITE SWNT BUNDLES......Page 489
5. CONCLUSIONS......Page 492
ACKNOWLEDGEMENTS......Page 493
REFERENCES......Page 494
1. INTRODUCTION......Page 497
2.1. Electrostatic Potential......Page 499
2.2. Average Local Ionization Energy......Page 500
2.3. Computational Approach......Page 501
3.1. General......Page 502
3.2. Functionalized Open Carbon Model Nanotubes......Page 504
3.3. Closed Model Nanotubes......Page 507
3.4. Applications in Area of Nonlinear Optics......Page 508
4. SUMMARY AND FUTURE WORK......Page 509
REFERENCES......Page 510
1. INTRODUCTION......Page 515
2.1. The Si Surface......Page 516
2.2. Unsaturated Hydrocarbons......Page 518
2.3. Amines......Page 521
2.4. Phosphines......Page 522
2.5. Alcohols......Page 523
3.1. Motivation and Methodology......Page 525
3.2. The Physisorbed and Chemisorbed Configurations......Page 526
3.3. Energy Barriers......Page 529
3.4. Band Structure......Page 530
3.5. Dependence on the Level of Coverage......Page 533
3.6. Room Temperature Molecular Dynamics Calculations......Page 535
4. SUMMARY......Page 537
REFERENCES......Page 538
1. INTRODUCTION......Page 543
2. COMPUTATIONAL DETAILS......Page 545
3. FULLERENE ADSORPTION ON THE C(4ร4) RECONSTRUCTED GAAS(001) SURFACE......Page 547
3.1. Structure and Energetics of Fullerenes......Page 548
3.2. C28 Adsorption on the GaAs(001) c(4ร4) Surface......Page 549
3.3. Cn(n = 32, 36, 40, 44, 48, 60) Adsorption on the GaAs(001)-c(4ร4) Surface......Page 556
3.4. Bonding Analyses......Page 561
4. C60 ADSORPTION ON SI(001)-C(2ร1) SURFACE......Page 564
5. SUMMARY......Page 568
REFERENCES......Page 569
CHAPTER 16 A QUEST FOR EFFICIENT METHODS OF DISINTEGRATION OF ORGANOPHOSPHORUS COMPOUNDS: MODELING ADSORPTION AND DECOMPOSITION PROCESSES......Page 575
1.1. Importance of Catalytic Decomposition of Organophosphorus Compounds......Page 576
1.2. Organophosphorus Compounds, Transition Metals and Metal Oxides......Page 577
2. COMPUTATIONAL METHODS AND MODELS......Page 579
2.1. Quantum-chemical Approximations for the Modeling of Surface Reactivity......Page 580
2.2. Quantum-chemical Approximations for the Influence of the Solvent......Page 583
3. APPLICATIONS OF TRANSITION METALS AND METAL OXIDES AS CATALYSTS FOR ADSORPTION AND DECOMPOSITION OF ORGANOPHOSPHORUS COMPOUNDS......Page 585
4.1. Summary......Page 595
4.2. Future Research Area......Page 596
REFERENCES......Page 597
INDEX (with page links)......Page 603