Solvation Effects on Molecules and Biomolecules (eBook)

Prof. Sylvio Canuto (editor of this review volume) is a professor of physics at University of Sao Paulo and is presently serving as: A member of the advisory editorial board of the Chemical Physics Letters (Elsevier); a member of the editorial board of the International Journal of Quantum Chemistry (John Wiley); a specialist editor of the Computer Physics Communications (North Holland); an associate editor of the Brazilian Journal of Physics; a member of the editorial board of the Journal of Computational Methods in Science and Engineering; a member of the International Scientific Advisory Board of the Journal of the Argentine Chemical Society. In addition to these duties, he is co-editor of the following SI volumes: an International Journal of Quantum Chemistry, 106 (2006) issue no. 13; an International Journal of Quantum Chemistry, 103 (2005) issue no. 5.; the Journal of Molecular Structure (Theochem), 464 (1999) issue 1-3.; the Brazilian Journal of Physics, 34 (2004) issue 1.; and the Brazilian Journal of Physics, 24 (1994) (part of) issue 4. Prof. Canuto has co-edited the following books: Electronic Structure of Atoms, Molecules and Solids. Proceedings of the 2nd Brazilian School on Electronic Structure. J. DÁ. Castro, S. Canuto and F. Paixao. World Scientific, 1990.; and I Escola Brasileira de Estrutura Eletrônica, Ed. Universidade de Brasília (1989), 587 pages (in portuguese) and co-authored: Teoria Quântica de Moléculas e Sólidos, ed. Livraria da Física, (2004), 400 pages (in portuguese) J D M Vianna, A. Fazzio and S. Canuto.

Preface 9
1 Solvation Models for Molecular Properties:Continuum Versus Discrete Approaches 11
Introduction 11
Focussed Models 12
QM/MM 13
QM/continuum 14
Modeling Solvent Effects on Properties 16
QM Evaluation of NMR Nuclear Shieldings 17
An Application to Solvated Systems: N Nuclear Shieldings of Diazines 19
QM/continuum: Polarity Versus H-bond 20
QM/MM Versus QM/continuum 24
Conclusions 28
2 The multipole moment expansion solvent continuum model: a brief review 32
Introduction 32
Development of the model: main contributions 33
Basic equations 34
Cavity definition 36
Distributed multipoles 37
Solvation energy convergence 38
Non-electrostatic contributions 42
Comparison with other solvent models 42
Conclusions and perspectives 43
3 The Discrete Reaction Field Approachfor Calculating Solvent Effects 48
Introduction 48
Theory 54
Perturbation Theory 54
Electrostatic Potentials: The Point Charges 58
The Many-Body Polarization 60
Bulk Effects: The Dielectric Continuum 67
Implementations 68
Macroscopic and Microscopic Properties 74
Some validation 76
The Water Dimer 76
Benzene Dimer 79
Many-Body Interactions 82
Concluding the Validation 83
Applications 83
Sudden Polarization in Excited States of Symmetric Ethylenes 83
Spectra 85
The n transition in acetone 85
Absorption and emission spectra of N-(1-pyrenyl)-methyluracil- 5-carboxamide-1-aminopyrene (PAUMe) 87
The visible spectrum of Fe-(PyPepS)2-- 90
Circular dichroism spectrum of '133Co(en)3'1353+ in water 92
(Hyper-)polarizabilities and Macroscopic Properties in Solution 93
Response properties of liquid water 94
The first hyperpolarizability of pNA in 1,4-dioxane solution 97
Chemistry in Solution 98
The dissociation of ter-butyl-chloride in water 98
Tautomerism of substituted cyclic imidazoline 99
Summary and conclusion 101
4 Thermochemical Analysis of the Hydrationof Neutral Solutes 112
Introduction 112
The MST-PCM continuum method 114
The enthalpy of solvation 115
Experimental data and computational details 116
Thermochemical analysis of the hydration 117
Concluding remarks 120
5 Electronic Properties of Hydrogen BondNetworks: Implications for Solvent Effectsin Polar Liquids 123
Introduction 123
Polarization Effects and Charge Fluctuations in Polar Hydrogen Bonding Liquids 124
Electronic Polarization and the Dipole Moment in Liquid Phase 124
Charge Fluctuations in Hydrogen Bonding Liquids 127
Structure of the Hydrogen Bond Network and Electronic Properties of Water 128
Hydrogen Bonding and the Dipole Moment of Liquid Water 128
Hydrogen Bonding and Electron Binding Energies 130
Charge Fluctuations of the Hydrogen Bond Network and Proton Transfer Assisted by the Solvent in Phenol--Water Clusters 132
Born--Oppenheimer Molecular Dynamics of Proton Transfer in Phenol--Water Clusters 132
Dynamics of PT in Phenol--Water Clusters 133
Proton (Deuterium) Transfer in Phenol--Water Clusters and Fluctuations of the HB Network 135
Conclusions 139
6 The Sequential QM/MM Method and itsApplications to Solvent Effects in Electronicand Structural Properties of Solutes 142
INTRODUCTION 142
METHOD 145
Fundament of the ASEP/MD Method 145
Ground and Excited State Gradients 148
Location of Conical Intersections and Singlet--Triplet Crossing Points in Solution 150
Free Energy Differences 153
De-Excitation Pathways In Acrolein 155
Absorption Spectra 156
Emission Spectra 158
Non-radiative Excited State Decay 159
Concluding Remarks 162
7 The Sequential QM/MM Method and itsApplications to Solvent Effects in Electronicand Structural Properties of Solutes 165
INTRODUCTION 165
METHODOLOGY 167
Description of the Statistical Analyses 168
Statistical correlation or statistical inefficiency 169
Structural analysis: solvent distribution 173
APPLICATIONS 176
Nonpolar Solutes 176
Solvent effects on the UV-vis spectra of benzene 177
Hydration effects on the structure, band gap and UV-vis spectrum of C60 181
Including Solute Polarization 184
Average Solvent Electrostatic Configuration 189
SUMMARY AND CONCLUSIONS 191
8 Statistical Mechanical Modeling of ChemicalReactions in Condensed Phase Systems 196
Introduction 196
PMM basic derivations 197
Statistical mechanics in the infinite dilution conditions 199
The free-energy reaction surface 201
Modeling the reaction kinetics 206
The Diffusion Equation 206
Evaluation of the Reaction Rate Constants 208
Applications 210
Binding--Unbinding Reaction of CO in Myoglobin 210
Intramolecular Proton Transfer in Aqueous Malonaldehyde 214
9 An explicit quantum chemical solvent modelfor strongly coupled solute--solvent systems in groundor excited state 219
Introduction 219
The model, QMSTAT 223
Intermolecular Interactions 223
The Quantum Chemical Methods 230
Statistical Mechanical Method 235
Parametrization and Simulation Protocol 236
Examples of applications 238
The Polarization and Repulsion Are Coupled in Some Monatomic Ions 239
Asymmetric Solvation from Many-Body Interactions 241
Solute--Solvent Interactions in the La and Lb Excited States of Indole 242
Summary 245
10 Molecular Dynamics Simulation Methods including Quantum Effects 251
Introduction 251
Methodologies for Simulating Liquid Systems 253
Molecular Mechanics 254
Quantum Mechanics 256
The Quantum Mechanical/Molecular Mechanical Scheme 258
The Quantum Mechanical Charge Field Framework 259
The charge field approach 259
Electrostatic embedding and the periodic box 261
A general electrostatic embedding scheme for QM/MM simulations 265
Implementation of Consistent Embedding in the QMCF MD Approach 267
Results of QMCF MD Simulations 269
Conclusion and Outlook 278
11 Solvation Effects on Molecules and Biomolecules 283
INTRODUCTION 283
Classical Thermodynamics Of Solvation 284
Statistical Mechanics Of Solvation 285
Polymer Solutions 288
Comparison Of Flory--Huggins And Classical Solution Theories 290
Effect of Internal Degrees of Freedom 292
Coupling of the Center of Mass of One Molecule to the Excluded Volume of Another (Polymer Solutions) 292
Effect of Molecular Shape and Architecture 294
Solvation In Polymers 296
Sorption of Gases in Polymers 296
Molecular simulation methods for calculation of phase equilibria 298
Grand equilibrium method: application to the calculation of solubility of gases in polystyrene 299
Concentrated Solutions of Polymers in Solvents 303
Solvation structure: mixtures of nonpolar polymers with nonpolar solvents 304
Solvation structure: mixtures of polar polymers with polar solvents 308
Hydrogen bonding in polar polymer--solvent mixtures 309
Solvent Effect on Polymer Size in the Solution 311
The Solvent Effect on Dynamics of Polymer Collapse 313
Time-Dependent Solvation Response 315
Experimental Methods 316
Theoretical Studies 318
Computer Simulations and the Mechanisms of Solvation 319
SUMMARY 321
12 Hydrogen Bonds And Solvent Effects In Soil Processes: A Theoretical View 325
INTRODUCTION 325
SIMULATON METHODS 328
ORGANIC FUNCTIONAL GROUPS AS MODELS FOR HUMIC SUBSTANCES 329
Binary Complexes with Acetic Acid and Acetate 330
Binary Complexes of 2,4-Dichlorophenoxyacetic Acid (2,4-D) 333
HYDROGEN-BONDED INTERACTIONS IN SOIL MINERALS AND THEIR SURFACES 337
Hydrogen-Bonded Interactions of Surfaces of the Isolated Kaolinite Layer 337
Interactions of 2,4-D with the Octahedral Kaolinite Surface 340
Interaction of Broken Clay Surfaces with Water and Model Organic Molecules 343
Hydrogen Bond Interactions of Goethite Surface 344
CONCLUSIONS 347
13 Linear Response Theory in Connection to Density Functional Theory/Molecular Dynamics and Coupled Cluster/Molecular Dynamics Methods 352
Introduction 352
The Combined Quantum Mechanics and Molecular Mechanics model 354
Combined Density Functional Theory and Molecular Mechanics model 359
Response functions for the Density Functional Theory/Molecular Mechanics method 361
The Combined Coupled Cluster/Molecular Mechanics Method 366
Coupled Cluster/Molecular Mechanics Response Theory 370
Linear Response Calculations on Solvated Acetone 377
Conclusion 379
14 Combined QM/MM methods for the simulation of condensed phase processes using an approximate DFT approach 384
Introduction 384
SCC-DFTB 386
Performance of SCC-DFTB 388
Methods to treat environmental effects 388
Small polypeptides in aqueous solution 390
Ace-Lala-NME 391
Helix Formation in Ace-Lalan-NME Peptides with n = 4--20 394
Study of Non-natural peptides: and / -peptides 396
Gas-Phase Benchmark 396
Solution Results 398
Studying proton-transfer reactions in complex environments 400
Minimum Energy Pathways (MEPs) 400
Free Energy Simulations Using Multi-scale Approaches 402
Conclusions 405
15 Solvation of Hydrogen Bonded Systems: CHO, OHO, and Cooperativity 409
INTRODUCTION 409
Early Applications of Rudimentary SCRF 411
Solvation Of ChO And OhO H-Bonds 412
Biologically Important H-Bonds 416
Amino Acids 417
Dipeptide 419
COOPERATIVITY 421
One-Dimensional Chains 421
Clusters 426
16 Solvation in Supercritical Fluids 435
INTRODUCTION 435
NON-POLAR SCF 437
Solvation of Alkaloids in SC-CO2 437
Effects from Adding a Co-solvent 442
POLAR SCFs 443
Dielectric Behavior SC-Water 443
Excess Electrons in Polar SCFs -- Equilibrium Aspects 447
Excess Electrons in Polar SCFs -- Solvation Dynamics 451
CONCLUDING REMARKS 453
17 A Quantum Chemical Approach to Free Energy Calculation for Chemical Reactions in Condensed System: Combination of a Quantum Chemical Method with a Theory of Statistical Mechanics 456
INTRODUCTION 456
REAL-SPACE GRID QM/MM APPROACH 460
Kohn--Sham Density Functional Theory 460
Kohn--Sham DFT with Real-Space Grids 462
Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Approach 468
THEORY OF SOLUTIONS IN THE ENERGY REPRESENTATION 470
Free-Energy Perturbation and Thermodynamic Integration Methods 470
Distribution Functions in Solution 474
Density-Functional Theory 476
Radial Distribution Functions and Reference Interaction Site Model 479
Method of Energy Representation 480
COMBINATION OF THE QM/MM METHOD WITH THE THEORY OF SOLUTIONS 486
Division of the Total Solvation Free Energy 487
Contribution of the Many-Body Effect 490
APPLICATION OF THE QM/MM-ER APPROACH 493
Solvation Free Energy of a Water Molecule 493
Free Energy Change Associated with a Proton Transfer Process 497
18 Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study 507
Introduction 507
Theory 509
Hybrid Quantum Mechanics--Molecular Mechanics (QM/MM) 509
Replica Exchange Molecular Dynamics 510
Computational Method 510
System Preparation 511
REMD of Alanine Dipeptide in Explicit Water 511
Molecular Dynamics of Alanine Dipeptide in Vacuum 511
Free Energy Surfaces 511
Dipolar Couplings 512
Results and Discussions 512
Molecular Dynamics of Alanine Dipeptide in Vacuum 512
Replica Exchange Molecular Dynamics of Alanine Dipeptide in Explicit Water 514
Radial Distribution Functions 515
Conclusions 516
Index 517