Solvation Effects on Molecules and Biomolecules: Computational Methods and Applications (Challenges and Advances in Computational Chemistry and Physics)

Cover......Page 1
Solvation Effects on Molecules and Biomolecules......Page 2
CHALLENGES AND ADVANCES IN
COMPUTATIONAL CHEMISTRY AND PHYSICS
Volume 6......Page 3
ISBN: 140208269X......Page 5
CONTENTS......Page 6
Preface......Page 9
Introduction......Page 11
Focussed Models......Page 12
QM/MM......Page 13
QM/continuum......Page 14
Modeling Solvent Effects on Properties......Page 16
QM Evaluation of NMR Nuclear Shieldings......Page 17
An Application to Solvated Systems: N Nuclear Shieldings of Diazines......Page 19
QM/continuum: Polarity Versus H-bond......Page 20
QM/MM Versus QM/continuum......Page 24
Conclusions......Page 28
Introduction......Page 32
Development of the model: main contributions......Page 33
Basic equations......Page 34
Cavity definition......Page 36
Distributed multipoles......Page 37
Solvation energy convergence......Page 38
Comparison with other solvent models......Page 42
Conclusions and perspectives......Page 43
Introduction......Page 48
Perturbation Theory......Page 54
Electrostatic Potentials: The Point Charges......Page 58
The Many-Body Polarization......Page 60
Bulk Effects: The Dielectric Continuum......Page 67
Implementations......Page 68
Macroscopic and Microscopic Properties......Page 74
The Water Dimer......Page 76
Benzene Dimer......Page 79
Many-Body Interactions......Page 82
Sudden Polarization in Excited States of Symmetric Ethylenes......Page 83
The n  transition in acetone......Page 85
Absorption and emission spectra of N-(1-pyrenyl)-methyluracil- 5-carboxamide-1-aminopyrene (PAUMe)......Page 87
The visible spectrum of Fe-(PyPepS)2--......Page 90
Circular dichroism spectrum of '133Co(en)3'1353+ in water......Page 92
(Hyper-)polarizabilities and Macroscopic Properties in Solution......Page 93
Response properties of liquid water......Page 94
The first hyperpolarizability of pNA in 1,4-dioxane solution......Page 97
The dissociation of ter-butyl-chloride in water......Page 98
Tautomerism of substituted cyclic imidazoline......Page 99
Summary and conclusion......Page 101
Introduction......Page 112
The MST-PCM continuum method......Page 114
The enthalpy of solvation......Page 115
Experimental data and computational details......Page 116
Thermochemical analysis of the hydration......Page 117
Concluding remarks......Page 120
Introduction......Page 123
Electronic Polarization and the Dipole Moment in Liquid Phase......Page 124
Charge Fluctuations in Hydrogen Bonding Liquids......Page 127
Hydrogen Bonding and the Dipole Moment of Liquid Water......Page 128
Hydrogen Bonding and Electron Binding Energies......Page 130
Born--Oppenheimer Molecular Dynamics of Proton Transfer in Phenol--Water Clusters......Page 132
Dynamics of PT in Phenol--Water Clusters......Page 133
Proton (Deuterium) Transfer in Phenol--Water Clusters and Fluctuations of the HB Network......Page 135
Conclusions......Page 139
INTRODUCTION......Page 142
Fundament of the ASEP/MD Method......Page 145
Ground and Excited State Gradients......Page 148
Location of Conical Intersections and Singlet--Triplet Crossing Points in Solution......Page 150
Free Energy Differences......Page 153
De-Excitation Pathways In Acrolein......Page 155
Absorption Spectra......Page 156
Emission Spectra......Page 158
Non-radiative Excited State Decay......Page 159
Concluding Remarks......Page 162
INTRODUCTION......Page 165
METHODOLOGY......Page 167
Description of the Statistical Analyses......Page 168
Statistical correlation or statistical inefficiency......Page 169
Structural analysis: solvent distribution......Page 173
Nonpolar Solutes......Page 176
Solvent effects on the UV-vis spectra of benzene......Page 177
Hydration effects on the structure, band gap and UV-vis spectrum of C60......Page 181
Including Solute Polarization......Page 184
Average Solvent Electrostatic Configuration......Page 189
SUMMARY AND CONCLUSIONS......Page 191
Introduction......Page 196
PMM basic derivations......Page 197
Statistical mechanics in the infinite dilution conditions......Page 199
The free-energy reaction surface......Page 201
The Diffusion Equation......Page 206
Evaluation of the Reaction Rate Constants......Page 208
Binding--Unbinding Reaction of CO in Myoglobin......Page 210
Intramolecular Proton Transfer in Aqueous Malonaldehyde......Page 214
Introduction......Page 219
Intermolecular Interactions......Page 223
The Quantum Chemical Methods......Page 230
Statistical Mechanical Method......Page 235
Parametrization and Simulation Protocol......Page 236
Examples of applications......Page 238
The Polarization and Repulsion Are Coupled in Some Monatomic Ions......Page 239
Asymmetric Solvation from Many-Body Interactions......Page 241
Solute--Solvent Interactions in the La and Lb Excited States of Indole......Page 242
Summary......Page 245
Introduction......Page 251
Methodologies for Simulating Liquid Systems......Page 253
Molecular Mechanics......Page 254
Quantum Mechanics......Page 256
The Quantum Mechanical/Molecular Mechanical Scheme......Page 258
The charge field approach......Page 259
Electrostatic embedding and the periodic box......Page 261
A general electrostatic embedding scheme for QM/MM simulations......Page 265
Implementation of Consistent Embedding in the QMCF MD Approach......Page 267
Results of QMCF MD Simulations......Page 269
Conclusion and Outlook......Page 278
INTRODUCTION......Page 283
Classical Thermodynamics Of Solvation......Page 284
Statistical Mechanics Of Solvation......Page 285
Polymer Solutions......Page 288
Comparison Of Flory--Huggins And Classical Solution Theories......Page 290
Coupling of the Center of Mass of One Molecule to the Excluded Volume of Another (Polymer Solutions)......Page 292
Effect of Molecular Shape and Architecture......Page 294
Sorption of Gases in Polymers......Page 296
Molecular simulation methods for calculation of phase equilibria......Page 298
Grand equilibrium method: application to the calculation of solubility of gases in polystyrene......Page 299
Concentrated Solutions of Polymers in Solvents......Page 303
Solvation structure: mixtures of nonpolar polymers with nonpolar solvents......Page 304
Solvation structure: mixtures of polar polymers with polar solvents......Page 308
Hydrogen bonding in polar polymer--solvent mixtures......Page 309
Solvent Effect on Polymer Size in the Solution......Page 311
The Solvent Effect on Dynamics of Polymer Collapse......Page 313
Time-Dependent Solvation Response......Page 315
Experimental Methods......Page 316
Theoretical Studies......Page 318
Computer Simulations and the Mechanisms of Solvation......Page 319
SUMMARY......Page 321
INTRODUCTION......Page 325
SIMULATON METHODS......Page 328
ORGANIC FUNCTIONAL GROUPS AS MODELS FOR HUMIC SUBSTANCES......Page 329
Binary Complexes with Acetic Acid and Acetate......Page 330
Binary Complexes of 2,4-Dichlorophenoxyacetic Acid (2,4-D)......Page 333
Hydrogen-Bonded Interactions of Surfaces of the Isolated Kaolinite Layer......Page 337
Interactions of 2,4-D with the Octahedral Kaolinite Surface......Page 340
Interaction of Broken Clay Surfaces with Water and Model Organic Molecules......Page 343
Hydrogen Bond Interactions of Goethite Surface......Page 344
CONCLUSIONS......Page 347
Introduction......Page 352
The Combined Quantum Mechanics and Molecular Mechanics model......Page 354
Combined Density Functional Theory and Molecular Mechanics model......Page 359
Response functions for the Density Functional Theory/Molecular Mechanics method......Page 361
The Combined Coupled Cluster/Molecular Mechanics Method......Page 366
Coupled Cluster/Molecular Mechanics Response Theory......Page 370
Linear Response Calculations on Solvated Acetone......Page 377
Conclusion......Page 379
Introduction......Page 384
SCC-DFTB......Page 386
Methods to treat environmental effects......Page 388
Small polypeptides in aqueous solution......Page 390
Ace-Lala-NME......Page 391
Helix Formation in Ace-Lalan-NME Peptides with n = 4--20......Page 394
Gas-Phase Benchmark......Page 396
Solution Results......Page 398
Minimum Energy Pathways (MEPs)......Page 400
Free Energy Simulations Using Multi-scale Approaches......Page 402
Conclusions......Page 405
INTRODUCTION......Page 409
Early Applications of Rudimentary SCRF......Page 411
Solvation Of ChO And OhO H-Bonds......Page 412
Biologically Important H-Bonds......Page 416
Amino Acids......Page 417
Dipeptide......Page 419
One-Dimensional Chains......Page 421
Clusters......Page 426
INTRODUCTION......Page 435
Solvation of Alkaloids in SC-CO2......Page 437
Effects from Adding a Co-solvent......Page 442
Dielectric Behavior SC-Water......Page 443
Excess Electrons in Polar SCFs -- Equilibrium Aspects......Page 447
Excess Electrons in Polar SCFs -- Solvation Dynamics......Page 451
CONCLUDING REMARKS......Page 453
INTRODUCTION......Page 456
Kohn--Sham Density Functional Theory......Page 460
Kohn--Sham DFT with Real-Space Grids......Page 462
Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Approach......Page 468
Free-Energy Perturbation and Thermodynamic Integration Methods......Page 470
Distribution Functions in Solution......Page 474
Density-Functional Theory......Page 476
Radial Distribution Functions and Reference Interaction Site Model......Page 479
Method of Energy Representation......Page 480
COMBINATION OF THE QM/MM METHOD WITH THE THEORY OF SOLUTIONS......Page 486
Division of the Total Solvation Free Energy......Page 487
Contribution of the Many-Body Effect......Page 490
Solvation Free Energy of a Water Molecule......Page 493
Free Energy Change Associated with a Proton Transfer Process......Page 497
Introduction......Page 507
Hybrid Quantum Mechanics--Molecular Mechanics (QM/MM)......Page 509
Computational Method......Page 510
Free Energy Surfaces......Page 511
Molecular Dynamics of Alanine Dipeptide in Vacuum......Page 512
Replica Exchange Molecular Dynamics of Alanine Dipeptide in Explicit Water......Page 514
Radial Distribution Functions......Page 515
Conclusions......Page 516
Index......Page 0