Handbook of Computational Chemistry

ISBN 9789400707108......Page 1
1 From Quantum Theory to Computational Chemistry. A Brief Account of Developments......Page 2
Introduction – Exceptional Status of Chemistry......Page 3
A Hypothetical Perfect Computer......Page 6
Does Predicting Mean Understanding?......Page 8
Orbital Model......Page 10
Conclusions......Page 11
References......Page 12
2 The Position of the Clamped Nuclei Electronic Hamiltonian in Quantum Mechanics......Page 14
The Clamped Nuclei Approximation......Page 15
The Separation of Translational Motion......Page 18
Choosing Electronic and Nuclear Variables in the Translationally InvariantHamiltonian......Page 20
Molecules......Page 22
Which Is the ``Correct\'\' Clamped Nuclei Hamiltonian?......Page 28
The Symmetries of the Clamped Nuclei Electronic Hamiltonian......Page 31
Permutational Symmetry......Page 33
Point Groups and Transformations......Page 37
Spin and Point Group Symmetry......Page 48
The Construction of Approximate Eigenfunctions of the Clamped NucleiHamiltonian......Page 49
Conclusions......Page 53
References......Page 54
3 Remarks on Wave Function Theory and Methods......Page 56
Introduction – What and Why?......Page 57
Quantum Mechanics for Dummies......Page 58
On the Way to Quantum Chemistry......Page 64
Perturbation Calculus – The Art of Estimation......Page 67
One-Electron Approximation – Describe One and Say Something About All......Page 71
Hartree–Fock Method – It Is Not that Sophisticated......Page 75
Møller–Plesset Perturbation Theory – HF Is Just the Beginning......Page 79
Beyond the HF Wave Function......Page 85
Coupled Cluster Approximation – The Operator Strikes Back......Page 89
Conclusions......Page 93
References......Page 94
4 Directions for Use of Density Functional Theory: A Short Instruction Manual for Chemists......Page 96
Introduction......Page 98
DFT: A Paradigm Shift in Theoretical Chemistry......Page 99
Holes and Electron Pairs......Page 103
First Rung: The Local Density Approximation......Page 105
Second Rung: The Generalized Gradient Approximation......Page 106
Fourth Rung: Hyper-Functionals......Page 107
Practical DFT and the Density Functional Zoo......Page 108
DFT: Computational Chemistry in Action......Page 110
Computational Performance......Page 111
Properties of Molecular and Electronic Structure......Page 112
Bond Lengths......Page 113
Bond Angles......Page 115
Vibrational Frequencies......Page 116
Electron Affinities and Ionization Potentials......Page 118
Heats of Formation......Page 119
Energy Barriers......Page 120
Bond Energies......Page 121
Hydrogen Bonding......Page 122
Weak Interactions......Page 123
Spin States......Page 124
Excited States......Page 125
Orbitals in DFT......Page 126
B3LYP Is No Synonym for DFT......Page 128
DFT Does Not Hold the Universal Answer to All Chemical Problems......Page 129
A Concise Guide to the Literature......Page 130
Conceptual Developments and Applications of DFT......Page 131
Practical Developments and Applications of DFT......Page 132
Reviews and Overviews of DFT......Page 133
Web Links......Page 134
5 Introduction to Response Theory......Page 136
Introduction......Page 137
Response Theory......Page 139
The Linear Response Function......Page 141
Quadratic and Higher-Order Response Functions......Page 146
Static Response Functions......Page 148
Gauge and Origin Invariance......Page 149
Effects of Nuclear Motion......Page 152
Acknowledgments......Page 156
References......Page 157
6 Intermolecular Interactions......Page 158
Introduction......Page 160
The Two-Body Interaction Energy......Page 161
Examples......Page 163
Supermolecular Methods......Page 165
Symmetry-Adapted Perturbation Theory......Page 166
Symmetry-Adapted Perturbation Theory Based on DFT......Page 167
Density-Fitting......Page 169
Higher-Order Contributions......Page 170
Basis Sets: Charge-Transfer......Page 171
Multipole Expansion for the Interaction Energy......Page 172
Many-Body Contributions to the Interaction Energy......Page 175
Distributed Multipoles......Page 177
Williams–Stone–Misquitta (WSM) Distribution......Page 178
Analyzing the Models......Page 180
Distributed Dispersion Coefficients......Page 181
Applications......Page 182
Polarization in Organic Crystals......Page 184
Outlook......Page 185
Annotated Bibliography......Page 187
References......Page 188
7 Molecular Dynamics Simulation: From ``Ab Initio\'\' to ``Coarse Grained\'\'......Page 196
Choosing the Right Method......Page 198
Born–Oppenheimer Approximation......Page 200
Ab Initio Molecular Dynamics......Page 201
Classical Molecular Dynamics......Page 202
Verlet Algorithm......Page 203
Velocity Verlet Algorithm......Page 204
Subtractive Scheme......Page 205
Bonds Across the QM/MM Boundary......Page 206
Frozen Localized Orbitals......Page 207
Coarse Grain Molecular Dynamics......Page 208
Classical Force Fields......Page 209
Nonbonded Interactions......Page 210
van der Waals Interactions......Page 211
Angle Bending Interactions......Page 213
First Principles Electronic Structure Methods......Page 214
Plane Wave Basis Set......Page 216
Normconserving Pseudopotentials......Page 217
Setting Up a Classical MD Simulation......Page 218
Building the System......Page 219
Steepest Descent......Page 220
Direct Inversion of the Iterative Subspace......Page 221
Controlling Temperature: Thermostats......Page 222
Berendsen Thermostat......Page 223
Controlling Pressure: Barostats......Page 224
Nosé–Hoover Barostat......Page 225
Born–Oppenheimer MD......Page 226
Car–Parrinello MD......Page 227
Spatial Distribution Functions......Page 228
Time Correlation Functions......Page 230
Visualization......Page 231
References......Page 232
8 Statistical Mechanics of Force-Induced Transitions of Biopolymers......Page 240
Introduction......Page 241
Continuum Models......Page 242
Lattice Models......Page 245
Polymer and Critical Phenomena......Page 246
Generating Function Technique......Page 247
Exact Enumeration Technique......Page 249
Monte Carlo Simulation......Page 250
Molecular Dynamics......Page 251
Applications......Page 255
Conclusions......Page 257
References......Page 258
9 Molecular Mechanics: Method and Applications......Page 260
Introduction......Page 261
General Expression and Terms of Molecular System Energy......Page 262
Intramolecular Contributions to Molecular System Energy......Page 263
Intermolecular and Non-bonded Intramolecular Interactions......Page 264
General Remarks on Molecular Mechanics, its Accuracy, and Applicability......Page 265
A Bit of History. The ``Precomputer\'\' and Early Computer-Aided MM Calculations......Page 266
First MM Applications to Three-Dimensional Structure and Thermodynamicsof Organic Molecules......Page 267
The Role of Molecular Crystal Study on the First Steps of Molecular Mechanics......Page 268
Molecular Mechanics on the First Steps of Molecular Biology. MolecularMechanics and Protein Physics......Page 270
Molecular Mechanics on the First Steps of the Biophysics of Nucleic Acids......Page 273
The Problems and Doubts of Further Development of the MM Approach......Page 276
Two Hypothetical Approaches to Choice of MM Formulae and Parameters......Page 277
Various Schemes of Water Molecules in MM Calculations......Page 278
Allinger\'s Force Fields and Programs......Page 279
Merck Molecular Force Field (MMFF94)......Page 280
The Force Fields and Programs Designed by Scheraga and Coauthors......Page 281
Force Fields and Programs Developed by Kollman and Coauthors......Page 282
Other Popular Force Fields and MM Software. CHARMM, OPLS, and GROMOS......Page 285
Conclusions......Page 287
References......Page 288
10 Molecular Structure and Vibrational Spectra......Page 294
Introduction......Page 295
He22+: An Illustrative Example......Page 296
The Newton–Raphson Step......Page 298
The Hessian Matrix and Hessian Updates......Page 300
Transition State Searches......Page 301
Choice of Coordinates......Page 303
The Modified Newton–Raphson Step......Page 304
GDIIS......Page 307
Performance for Minimization......Page 308
Minimization: An Example......Page 311
Transition State Searches: An Example......Page 319
Using Optimized Potential Scans in Transition State Searches......Page 325
Comparison of Experimental and Theoretical Geometries......Page 328
Geometry Optimization of Molecular Clusters......Page 330
Geometry Optimization in the Presence of External Forces......Page 331
Molecular Vibrations......Page 332
1,2-Dichloroethane: An Illustrative Example......Page 337
Scaled Quantum Mechanical Force Fields......Page 343
1,2-Dichloroethane: A Further Analysis......Page 344
Density Functional Theory and Weight Derivatives......Page 353
Conclusions......Page 356
References......Page 357
11 Molecular Electric, Magnetic, and Optical Properties......Page 362
Introduction......Page 364
The Molecular Hamiltonian......Page 365
The Molecular Breit–Pauli Hamiltonian......Page 366
Small Terms Due to the Scalar Potential in the Hamiltonian......Page 368
The Magnetic Vector Potential......Page 369
Small Terms Due to the Vector Potential in the Hamiltonian......Page 370
Molecular Response: Definitions, Symbols......Page 373
Expansions of Energy and Multipole Moments......Page 376
Electric Properties......Page 377
Electric Multipole Moments......Page 378
Dipole and Quadrupole Moments......Page 379
The Origin of the Frequency-Dependent Electric Dipole Polarizability andHyperpolarizabilities......Page 380
Dipole Polarizability......Page 382
First Dipole Hyperpolarizability......Page 384
Second Dipole Hyperpolarizability......Page 386
Cauchy Moments......Page 387
Long-Range Dispersion Interaction Coefficients......Page 388
Electric Field Gradient at the Nucleus, Nuclear Quadrupole Coupling Constant......Page 389
One-Photon Absorption, Excitation Energies, and Transition Moments......Page 390
Two-Photon Absorption......Page 393
Magnetizability......Page 394
Rotational g Tensor......Page 397
Birefringences and Dichroisms......Page 399
Optical Rotation......Page 402
Natural (Electronic) Circular Dichroism......Page 405
Two-Photon Circular Dichroism......Page 406
Faraday Effect......Page 407
Hypermagnetizabilities, Cotton–Mouton Effect......Page 408
Electric-Field-Gradient-Induced Birefringence......Page 410
Magnetic Circular Dichroism......Page 411
NMR Effective Spin Hamiltonian......Page 412
Nuclear Magnetic Shielding......Page 415
Shielding Derivatives......Page 419
Spin-Orbit Corrections to Nuclear Magnetic Shielding......Page 420
Nuclear Spin Rotation Constants......Page 421
NMR Indirect Spin–Spin Coupling......Page 422
Electron Spin–Related Properties......Page 425
Spin-Orbit Coupling Constants......Page 426
ESR Effective Spin Hamiltonian......Page 427
ESR Electronic g-Tensor......Page 429
Zero-Field Splitting......Page 430
ESR Hyperfine Coupling Tensors......Page 431
Conclusions......Page 433
References......Page 434
12 Weak Intermolecular Interactions: A Supermolecular Approach......Page 444
Introduction......Page 445
Hydrogen-Bonded Complexes......Page 446
Aromatic pi …pi  Stacking......Page 447
Other Interaction Types......Page 448
Methods......Page 449
Møller–Plesset Perturbation theory......Page 450
Spin Component Scaled MP2......Page 451
Density Functional Theory......Page 452
DFT-D......Page 453
Range Separated and Dispersion Functionals......Page 454
 SemiEmpirical Methods......Page 455
Basis Sets......Page 456
Benchmark Sets......Page 458
Performance Considerations......Page 460
Concluding Remarks and Recommendations......Page 462
References......Page 463
13 Chemical Reactions: Thermochemical Calculations......Page 468
Introduction......Page 469
Calculating the DeltaH, DeltaS, and DeltaG for a Chemical Reaction......Page 470
Preliminary Comments on Accuracy......Page 471
Case Study: 3H2(g) + N2(g) rightarrow  2NH3(g)......Page 472
Small Basis Set Study......Page 473
Study with Extended ``Pople-Type\'\' Basis Sets......Page 474
Effect of Geometry......Page 475
Results from Correlation-Consistent Basis sets......Page 476
Thermochemistry of Species with F–O Bonds......Page 478
Calculating the Heat of Formation of H2SO2......Page 480
References......Page 482
14 Calculation of Excited States: Molecular Photophysics and Photochemistry on Display......Page 484
Introduction......Page 486
Spectroscopy Overview......Page 487
General Overview......Page 494
Methods, Advantages, and Drawbacks......Page 497
Basis Sets......Page 503
Methods for Excited States......Page 505
How to Start: Selection of Goals, Methods, Geometries......Page 511
An Application Example: Psoralen......Page 513
Selection of Geometries......Page 517
Accuracy of the Excitation Energies and how to compare with experiment......Page 518
How to Obtain Intensities and Band Shapes: Vibrational Contributions......Page 519
Active Spaces for Multiconfigurational Methods......Page 520
An Application Example: Water......Page 521
How to Solve Valence-Rydberg Mixing......Page 524
An Application Example: p-benzosemiquinone Radical Anion......Page 525
Basis Sets and Spurious Solutions in Anions......Page 528
Negative Electron Affinities......Page 529
An Application Example: Thymine......Page 532
Reaction Paths: MEP Verses Other Approaches......Page 536
How to Compute Conical Intersections......Page 539
Setting the Path for Dynamics......Page 544
An Application Example of Reactivity: Cytosine Dimer......Page 545
An Application Example of Energy Transfer: Psoralen + O2......Page 549
The Basis Set Superposition Error (BSSE) for Excited States......Page 554
Computation of Electronic Couplings......Page 556
Conclusions......Page 557
References......Page 558
15 Solvent Effects in Quantum Chemistry......Page 562
The Supermolecule Model......Page 563
Continuum Models......Page 564
The Full Quantum Approaches of Liquids......Page 566
The Quantum Mechanical/Molecular Mechanical (QM/MM) Models......Page 567
Reference Interaction Site Model (RISM)......Page 568
References......Page 569
16 Auxiliary Density Functional Theory: From Molecules to Nanostructures......Page 574
Introduction......Page 576
Kohn–Sham Density Functional Theory......Page 577
The LCGTO Kohn–Sham Method......Page 579
Auxiliary Density Functional theory......Page 583
Auxiliary Density Perturbation theory......Page 585
Dynamics of Sodium Clusters......Page 587
Summary......Page 590
Structure of Zeolites......Page 591
Models and Methodology......Page 593
Previous Data for Extra-Framework Cations......Page 595
Analysis of the Properties of the Cationic Sites in Na-MOR1 and Na-MOR2......Page 596
Al Sites of H-MOR......Page 597
Stability of Giant Fullerenes......Page 599
Computational Details......Page 600
Results and Discussion......Page 601
Summary......Page 603
References......Page 604
17 Guide to Programs for Non-relativistic Quantum Chemistry Calculations......Page 612
Introduction......Page 613
GAMESS-US......Page 615
GAMESS-UK......Page 617
Dalton......Page 618
NWChem......Page 620
ORCA......Page 621
PSI3......Page 622
ACES II......Page 623
COLUMBUS......Page 624
Gaussian......Page 625
Ampac 9......Page 626
References......Page 627
18 Functional Nanostructures and Nanocomposites – Numerical Modeling Approach and Experiment......Page 632
Introduction......Page 633
General Features......Page 635
SiC-Based Nanomaterials and Nanocomposites......Page 636
Theoretical Background......Page 638
DFT and Semiempirical Codes......Page 639
Molecular Dynamics......Page 641
Numerical Simulations of IR and Raman Spectra......Page 642
Vibrational Density of States (VDOS) and Luminescence Features......Page 645
Experimental Results......Page 646
Photoluminescence Responses of SiC Nanoparticles......Page 649
Pockels Effects in Hybrid Nanocomposites......Page 655
Photoinduced SHG in Host–Guest SiC-Based Nanocomposites......Page 656
Molecular Dynamics Simulations......Page 657
Quantum Chemical Computations......Page 660
Conclusions......Page 663
References......Page 664
19 Fullerenes, Metallofullerenes,and Their Derivatives......Page 668
Introduction......Page 669
Definition of Fullerenes and Enumeration of Their Isomers......Page 671
The Isolated Pentagon Rule and Steric Strain......Page 672
The Isomers of IPR Fullerenes......Page 678
Metal-Cage Bonding in Endohedral Metallofullerenes......Page 685
IsomerisminEndohedralMetallofullerenes:StabilityoftheChargedCarbonCages......Page 688
Isomerism in Endohedral Metallofullerenes: The Cluster Size Factor......Page 693
Violation of the Isolated Pentagon Rule in Endohedral Metallofullerenes......Page 696
Addition of X2 to C60 – Isomers of C60X2 and General Considerations......Page 697
Addition of H and F to C60 – Contiguous Addition, Benzene Rings,and Failures of AM1......Page 699
Addition of Bulky Groups to C60: Bromination and Perfluoroalkylation......Page 702
Addition to C70 and Higher Fullerenes......Page 707
References......Page 711
20 Structures and Electric Properties of Semiconductor clusters......Page 724
Introduction......Page 725
The Ground-State Structure......Page 726
Structural Determination......Page 728
Selected Structural Studies......Page 730
The Si6 and Si36 Cases......Page 732
General Features......Page 735
Gallium Arsenide Clusters......Page 736
II–VI Semiconductor Clusters......Page 738
Definitions and Theory......Page 741
Cluster (Hyper)Polarizabilities: Computational Approach......Page 742
General Trends......Page 747
Polarizabilities......Page 749
Hyperpolarizabilities......Page 750
References......Page 752
21 Structures, Energetics, and Spectroscopic Fingerprints of Water Clusters n=2–24......Page 762
Introduction......Page 763
Models of Intermolecular Interactions......Page 764
Quantum Models from Electronic Structure Calculations......Page 765
The Basis Set Superposition Error Correction......Page 766
Global Minimum Structures of the n=2–10 Water Clusters......Page 768
The Global Minima of Medium-Sized Water Clusters in he Range 11 le n le \r16......Page 772
The Transition from ``All-Surface\'\' to ``Internally Solvated\'\' Clusters at n=17......Page 776
Validation from Electronic Structure Calculations......Page 777
Spectroscopic Signature......Page 778
The Family of Minima for (H2O)20......Page 779
Vibrational Spectra......Page 781
The Pentagonal Dodecahedron (D-cage) (H2O)20 Cluster......Page 783
The Tetrakaidecahedron (T-Cage) (H2O)24 Cluster......Page 786
Outlook......Page 787
Acknowledgments......Page 788
References......Page 789
22 Fundamental Structural, Electronic, and Chemical Properties of Carbon Nanostructures: Graphene, Fullerenes, Carbon Nanotubes, and Their Derivatives......Page 794
Introduction to Carbon Nanostructures......Page 796
Graphene......Page 798
Fullerenes......Page 801
Natural Abundance of Fullerenes......Page 805
Fullerene Nano-Capsules......Page 806
Isolated Pentagon Rule (IPR) in Fullerenes......Page 807
Common Defects in Fullerenes......Page 811
Discovery and Classification of CNTs......Page 812
Various Defects in Carbon Nanotubes......Page 816
Computational Approaches Used to Study CarbonNanostructures: An Overview......Page 818
Graphene......Page 821
Hydrogenation of Graphene with and Without Defects......Page 822
Computational Studies of Fullerene Isomers......Page 825
Giant Fullerenes......Page 828
Local Strain in Curved Polycyclic Systems: POAV and Pyramidalization Angle......Page 829
Computational Studies on Vacancy Defects in Fullerene C60......Page 832
Computational Studies of Single-Walled Carbon Nanotubes......Page 835
Covalent Functionalization of SWCNTs: H and F Atom Chemisorptions......Page 839
Stone–Wales Defect......Page 845
Topological Ring Defects......Page 847
Topological Ring Defects: Single- and Di-Vacancy......Page 848
Outlook of Potential Applications of Carbon Nanostructures......Page 852
Summary and Outlook......Page 853
References......Page 855
23 Optical Properties of Quantum Dot Nano-composite Materials Studied by Solid-State Theory Calculations......Page 870
Introduction......Page 871
Solid-State k.\rp Theory......Page 872
Excitons in Nanostructures......Page 876
Polarization and Optical Properties of Exciton-Polaritons......Page 879
Exciton-Polariton Photonic Crystals......Page 883
Photonic Dispersion of QD Dimer Systems......Page 884
Lossless Dielectric Constant of QD Dimer Systems......Page 888
Multiphoton Process......Page 890
Impact Ionization and Auger Recombination......Page 892
Summary......Page 897
References......Page 898
24 Modeling of Quasi-One-Dimensional Carbon Nanostructures with Density Functional Theory......Page 902
Density Functional Theory with Periodic Boundary Conditions......Page 904
Single-Walled Carbon Nanotubes......Page 906
Graphene Nanoribbons......Page 907
Single-Walled Carbon Nanotubes......Page 913
Graphene Nanoribbons......Page 916
Chemistry at the Edges of Graphene......Page 917
Quantum Confinement in Graphitic Systems......Page 919
Edge Effects in Graphitic Systems......Page 922
Carbon Nanotubes in NEMS Applications......Page 927
Graphene Nanoribbons in NEMS Applications......Page 931
References......Page 933
25 Variation of the Surface to Bulk Contribution to Cluster Properties......Page 940
Introduction......Page 941
Tight-Binding Molecular Dynamics Methodology......Page 943
Collinear Magnetic Effects......Page 944
Step 2: Inclusion of Spin-Orbit Interaction......Page 945
Evaluation of the TB representation of the SO-interaction......Page 946
Step 3: Inclusion of Temperature Effects......Page 947
Computational Approach......Page 948
Results and Discussion......Page 949
Conclusion......Page 953
References......Page 954
26 Theoretical Studies of Structural and Electronic Properties of Clusters......Page 956
Introduction......Page 957
Basics......Page 960
Methods......Page 962
Ni Clusters......Page 965
Bimetallic Clusters......Page 971
Clusters on Surfaces......Page 973
Methods......Page 975
Na and Au Clusters......Page 977
HAlO Clusters......Page 980
AB Semiconductor Clusters......Page 985
Metcars......Page 987
Conclusions......Page 990
References......Page 991
27 Modeling of Nanostructures......Page 996
0D Structures: Nanoparticles......Page 997
Global Optimization with Empirical Potentials......Page 1000
Local Optimization with Higher Accuracy Methods......Page 1002
1D Structures: Nanotubes, Nanowires, Nanorods......Page 1010
Elastic and Structural Properties......Page 1011
Structural Properties......Page 1014
Electronic, Magnetic and Optical Properties......Page 1015
2D Structures: Graphene and Derivatives......Page 1018
Graphene, Nanosheets, Nanoribbons, Nanobelts, Nanostrips......Page 1020
Electronic and Mechanical Properties......Page 1025
Magnetic and Optical Properties......Page 1033
Adsorption Phenomena......Page 1036
References......Page 1037
28 Quantum Cluster Theory for the Polarizable Continuum Model (PCM)......Page 1044
Introduction: Quantum Cluster Theory and Solvation......Page 1045
The Coupled-Cluster Theory for the Polarizable Continuum Model......Page 1049
PCM-CCSD Analytical Gradients......Page 1056
The Equation-of-Motion Coupled-Cluster Theory for the PolarizableContinuum Model......Page 1059
PCM-EOM-CCSD Analytical Gradients......Page 1062
Appendix A: The Solute-Solvent PCM Operator......Page 1064
References......Page 1065
29 Spin-Orbit Coupling in \rEnzymatic Reactions and theRole of Spin in Biochemistry......Page 1068
Introduction......Page 1069
O2 Interaction with Heme, FAD, and Oxidases......Page 1070
Definition of Spin and the Angular Momentum Conservation......Page 1072
Molecular Oxygen Structure and Spectra......Page 1073
Spin-Prohibition of Dioxygen Reactions......Page 1075
Cytochrome Oxidases and Related Heme-Containing Enzymes......Page 1076
Dioxygen Reaction with Glucose Oxidase......Page 1078
Dioxygen Binding to Heme......Page 1080
Spin-Orbit Coupling in O2-Heme Interaction......Page 1083
External Magnetic Field Effects in Biochemistry......Page 1086
Spin Neuroscience......Page 1088
Conclusions......Page 1089
References......Page 1091
30 Protein Modeling......Page 1096
Experiment......Page 1097
Structure Solution......Page 1098
Refinement and Validation......Page 1099
Data Acquisition......Page 1100
Restraint Collection......Page 1101
Computer Modeling......Page 1102
Molecular Mechanics......Page 1103
Homology Modeling......Page 1105
Molecular Graphics......Page 1106
Electrostatics......Page 1108
Solvent-Accessible Surface......Page 1110
Time Scales......Page 1111
Dynamical Structures......Page 1113
Interactions......Page 1114
Ligand Binding......Page 1115
Protein–Protein Interactions......Page 1117
Enzyme Mechanisms......Page 1120
Conclusion and Outlook......Page 1122
References......Page 1123
31 Applications of Computational Methods to Simulations of Proteins Dynamics......Page 1128
Introduction......Page 1130
Formalism of Molecular Mechanics and Molecular Dynamics Methods – A \rShort Presentation......Page 1131
On the Origin of Potential Energy Surface (PES) Concept......Page 1132
Force Fields......Page 1134
General Molecular Dynamics Scheme......Page 1136
MD Codes......Page 1138
Review of Reviews......Page 1139
Protein Folding Studies......Page 1141
Functionally Important Motions (FIM)......Page 1142
Transport Phenomena in Proteins......Page 1143
Charge Transfer in Protein Complexes......Page 1144
Simulations of Single Molecule AFM Experiments......Page 1145
Acknowledgment......Page 1146
References......Page 1147
32 Molecular Dynamics and Advanced Sampling \rSimulations of Nucleic Acids......Page 1156
Molecular Dynamics Simulations of Nucleic Acids......Page 1157
Induced Conformational Changes During Molecular \rDynamics Simulations......Page 1160
Replica-Exchange Molecular Dynamics Simulations......Page 1162
Combining Replica-Exchange and Umbrella \rSampling Simulations......Page 1164
Simulation Studies on DNA Bending......Page 1165
Conformational Transitions of Nucleic Acid Backbone States......Page 1167
References......Page 1171
33 Model Systems for Dynamics of \rpi -Conjugated Biomolecules in Excited States......Page 1176
Introduction......Page 1178
Mixed Quantum-Classical Dynamics Simulations......Page 1180
The Primary Mechanism of Vision......Page 1181
Model 1: PSB3......Page 1183
Model 2: PSB4......Page 1184
Current Status of the Field......Page 1187
Photostability of DNA and RNA......Page 1188
Model 1: Aminopyrimidine......Page 1190
Model 2: Pyrrole......Page 1193
Current Status of the Field......Page 1196
Probing Photoexcitation of Proteins......Page 1198
Model 1: Formamide......Page 1199
Model 2: Protonated Formamide......Page 1201
Current Status of the Field......Page 1203
Conclusions and Outlook......Page 1204
References......Page 1205
34 Low-Energy Electron (LEE)-Induced DNA Damage: Theoretical Approaches to Modeling Experiment......Page 1216
Introduction......Page 1217
Proposed Mechanism of LEE Induced DNA Strand Breaks......Page 1220
Electron–Molecule Interaction Events......Page 1221
Resonance (TNI) Formation: A Molecular Orbital Approach......Page 1223
Shape Resonances of DNA Bases......Page 1226
Electron Attachment to DNA/RNA Bases in Gas-Phase......Page 1230
Choice of the Basis Set......Page 1231
Effect of Solvation (Condensed Media)......Page 1233
Proposed Theoretical Models of DNA Damage......Page 1236
Excited States of TNI (Resonance Formation)......Page 1241
LEE Induced Base Release......Page 1245
Effect of Solvation on Strand Break Formation......Page 1247
References......Page 1250
35 Computational Modeling of DNA and RNA Fragments......Page 1258
Introduction......Page 1259
Hydrogen Bonding and Stacking Interactions in Nucleic Acids......Page 1263
Level of Computations......Page 1264
Gold Standard......Page 1265
Other Approaches......Page 1266
Geometries......Page 1267
Interpreting the Computations......Page 1270
References......Page 1272
36 Metal Interactions with Nucleobases, Base Pairs, and Oligomer Sequences; Computational Approach......Page 1278
Introduction......Page 1279
Interaction of Bare Cations with Bases......Page 1280
Metal Interactions in Implicit Solvent Model......Page 1285
Hydrated Alkaline Earth and Zinc-Group Metal Cations......Page 1286
Complexes of Hydrated Copper Cations with Guanine......Page 1288
Interaction with Platinum Metal Complexes......Page 1290
The Tautomeric Equilibrium of the Metalated Nucleobases......Page 1291
Interaction of Nucleobases with Half-Sandwich Ru(II) Complexes......Page 1292
Metal Cations From Ia, Ib, IIa, and IIb Groups......Page 1296
Interactions of Hydrated Cations with Nucleotides......Page 1300
Metal Interactions with Stacked Bases......Page 1302
Metal Adducts in Oligomeric Sequences......Page 1303
Conclusion......Page 1304
References......Page 1305
37 Predictive QSAR Modeling: Methods and Applications in Drug Discovery and Chemical Risk Assessment......Page 1310
Data Preparation......Page 1312
QSAR Model Development......Page 1316
Target Functions......Page 1319
Target Functions and Validation Criteria for Classification QSAR Models......Page 1320
Target Functions and Validation Criteria for Category QSAR Models......Page 1321
Distance-based AD.......Page 1322
Y-randomization......Page 1323
\"Good Practices\'\' in QSAR Modeling: Examples of Models and Their Application toVirtual Screening and Lead Identification......Page 1324
QSAR Methods......Page 1317
QSAR-Aided Discovery of Novel Anticonvulsant Compounds......Page 1325
QSAREnabledDiscoveryofNovelGeranylgeranyltransferaseIInhibitors(GGTIs)......Page 1327
\"Good Practices\'\' in QSAR Model Development: Applications to Toxicity Modeling......Page 1329
Quantitative Structure In Vitro–In Vivo Relationship Modeling......Page 1330
Using \"Hybrid\'\' Descriptors for QSIIR Modeling of Rodent Carcinogenicity......Page 1331
Using \"Hybrid\'\' Descriptors for the QSIIR Modeling of Rodent Acute Toxicity......Page 1332
Collaborative and Consensus Modeling of Aquatic Toxicity......Page 1333
Universal Statistical Figures of Merit for All Models......Page 1334
Consensus QSAR Models of Aquatic Toxicity; comparison BetweenMethods and Models......Page 1335
Conclusions: Emerging Chemical/Biological Data and QSAR Research Strategies......Page 1336
References......Page 1337
38 Quantitative Structure–Activity Relationships of Antimicrobial Compounds......Page 1344
Introduction......Page 1345
Quantitative Structure–Activity Relationship (QSAR)......Page 1346
Mapping the Descriptors to Activity......Page 1347
Coumarins......Page 1348
Benzamides......Page 1349
Flavanones......Page 1350
Furan Derivatives......Page 1351
mt-QSAR Studies......Page 1352
Conclusions......Page 1353
References......Page 1354
39 Ab Initio Investigation of Photochemical Reaction Mechanisms: From Isolated Molecules to Complex Environments......Page 1360
Introduction......Page 1361
Multiconfigurational Quantum Chemistry......Page 1365
QM/MM Methodology......Page 1369
Photoisomerization in a Rhodopsin Chromophore Model......Page 1372
Photofragmentation Through a Conical Intersection: The Photodenitrogenation \rof a Bicyclic Azoalkane......Page 1378
Charge Transfer and Intermolecular Hydrogen Transfer Mediated by a Conical \rIntersection: Quenching the Fluorescence of Bicyclic Azoalkanes......Page 1380
Green Fluorescent Proteins (GFP)......Page 1386
Understanding the Spectral Tuning in Retinal Proteins......Page 1388
Deactivation Mechanism in Cytosine-Guanine DNA Base Pair......Page 1393
Absorption Spectra of a Coumarin in Solution......Page 1395
Tracking the Photoisomerization of Retinal in Different Environments......Page 1397
References......Page 1399