Canuto Solvation Effects on Molecules and Biomolecules

Computational Methods and Applications
1. Auflage 2010
ISBN: 978-1-4020-8270-2
Verlag: Springer-Verlag
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 500 Seiten

The incessant development of quantum chemistry since the appearance of the Schrodinger ¨ equation has turned this area into a respectable branch of science with unprecedented capabilities. It is now a well-recognized eld of research with pred- tive power that is an important component in physical–chemical laboratories. Very important developments were conducted in the early days by bright theoretical s- entists that were ready to absorb the incredible and unpredicted computer revolution which was only just beginning. Isolated medium-size molecular systems can now be accurately studied theoretically by quantum chemical methods. However, it was also long recognized that all biomolecular phenomena necessary to obtain and sustain living systems take place in solution, as well as the vast majority of chemical p- cesses. Indeed solvent and liquid systems are germane in chemistry experiments. In physics, aconstant concern isthedescription of theroleplayed by theenvironment in modifying the properties of the system as compared to the isolated situation. Hence, the importance of studying atoms, molecules and biomolecules in the solvent en- ronment can hardly be denied. The quantum chemical studies of molecular systems affected by the interaction with a solvent had its own turning point before the end of the 1970s, when some pioneering work was done, including the dielectric pr- erties of the medium in an effective nonlinear Hamiltonian. This naturally led to the development of the so-called continuum models that are important and now popular. Continuum models can be implemented from the simplest to the most sophisticated quantum chemical methods.

Autoren/Hrsg.

Canuto, Sylvio

Inhaltsverzeichnis

1;Preface;9
2;1 Solvation Models for Molecular Properties:Continuum Versus Discrete Approaches;11
2.1;Introduction;11
2.2;Focussed Models;12
2.2.1;QM/MM;13
2.2.2;QM/continuum;14
2.3;Modeling Solvent Effects on Properties;16
2.3.1;QM Evaluation of NMR Nuclear Shieldings;17
2.3.2;An Application to Solvated Systems: N Nuclear Shieldings of Diazines;19
2.3.2.1;QM/continuum: Polarity Versus H-bond;20
2.3.2.2;QM/MM Versus QM/continuum;24
2.4;Conclusions;28
3;2 The multipole moment expansion solvent continuum model: a brief review;32
3.1;Introduction;32
3.2;Development of the model: main contributions;33
3.3;Basic equations;34
3.4;Cavity definition;36
3.5;Distributed multipoles;37
3.6;Solvation energy convergence;38
3.7;Non-electrostatic contributions;42
3.8;Comparison with other solvent models;42
3.9;Conclusions and perspectives;43
4;3 The Discrete Reaction Field Approachfor Calculating Solvent Effects;48
4.1;Introduction;48
4.2;Theory;54
4.2.1;Perturbation Theory;54
4.2.2;Electrostatic Potentials: The Point Charges;58
4.2.3;The Many-Body Polarization;60
4.2.4;Bulk Effects: The Dielectric Continuum;67
4.2.5;Implementations;68
4.2.6;Macroscopic and Microscopic Properties;74
4.3;Some validation;76
4.3.1;The Water Dimer;76
4.3.2;Benzene Dimer;79
4.3.3;Many-Body Interactions;82
4.3.4;Concluding the Validation;83
4.4;Applications;83
4.4.1;Sudden Polarization in Excited States of Symmetric Ethylenes;83
4.4.2;Spectra;85
4.4.2.1;The n transition in acetone;85
4.4.2.2;Absorption and emission spectra of N-(1-pyrenyl)-methyluracil- 5-carboxamide-1-aminopyrene (PAUMe);87
4.4.2.3;The visible spectrum of Fe-(PyPepS)2--;90
4.4.2.4;Circular dichroism spectrum of '133Co(en)3'1353+ in water;92
4.4.3;(Hyper-)polarizabilities and Macroscopic Properties in Solution;93
4.4.3.1;Response properties of liquid water;94
4.4.3.2;The first hyperpolarizability of pNA in 1,4-dioxane solution;97
4.4.4;Chemistry in Solution;98
4.4.4.1;The dissociation of ter-butyl-chloride in water;98
4.4.4.2;Tautomerism of substituted cyclic imidazoline;99
4.5;Summary and conclusion;101
5;4 Thermochemical Analysis of the Hydrationof Neutral Solutes;112
5.1;Introduction;112
5.2;The MST-PCM continuum method;114
5.3;The enthalpy of solvation;115
5.4;Experimental data and computational details;116
5.5;Thermochemical analysis of the hydration;117
5.6;Concluding remarks;120
6;5 Electronic Properties of Hydrogen BondNetworks: Implications for Solvent Effectsin Polar Liquids;123
6.1;Introduction;123
6.2;Polarization Effects and Charge Fluctuations in Polar Hydrogen Bonding Liquids;124
6.2.1;Electronic Polarization and the Dipole Moment in Liquid Phase;124
6.2.2;Charge Fluctuations in Hydrogen Bonding Liquids;127
6.3;Structure of the Hydrogen Bond Network and Electronic Properties of Water;128
6.3.1;Hydrogen Bonding and the Dipole Moment of Liquid Water;128
6.3.2;Hydrogen Bonding and Electron Binding Energies;130
6.4;Charge Fluctuations of the Hydrogen Bond Network and Proton Transfer Assisted by the Solvent in Phenol--Water Clusters;132
6.4.1;Born--Oppenheimer Molecular Dynamics of Proton Transfer in Phenol--Water Clusters;132
6.4.2;Dynamics of PT in Phenol--Water Clusters;133
6.4.3;Proton (Deuterium) Transfer in Phenol--Water Clusters and Fluctuations of the HB Network;135
6.5;Conclusions;139
7;6 The Sequential QM/MM Method and itsApplications to Solvent Effects in Electronicand Structural Properties of Solutes;142
7.1;INTRODUCTION;142
7.2;METHOD;145
7.2.1;Fundament of the ASEP/MD Method;145
7.2.2;Ground and Excited State Gradients;148
7.2.3;Location of Conical Intersections and Singlet--Triplet Crossing Points in Solution;150
7.2.4;Free Energy Differences;153
7.3;De-Excitation Pathways In Acrolein;155
7.3.1;Absorption Spectra;156
7.3.2;Emission Spectra;158
7.3.3;Non-radiative Excited State Decay;159
7.4;Concluding Remarks;162
8;7 The Sequential QM/MM Method and itsApplications to Solvent Effects in Electronicand Structural Properties of Solutes;165
8.1;INTRODUCTION;165
8.2;METHODOLOGY;167
8.2.1;Description of the Statistical Analyses;168
8.2.1.1;Statistical correlation or statistical inefficiency;169
8.2.1.2;Structural analysis: solvent distribution;173
8.3;APPLICATIONS;176
8.3.1;Nonpolar Solutes;176
8.3.1.1;Solvent effects on the UV-vis spectra of benzene;177
8.3.1.2;Hydration effects on the structure, band gap and UV-vis spectrum of C60;181
8.3.2;Including Solute Polarization;184
8.3.3;Average Solvent Electrostatic Configuration;189
8.4;SUMMARY AND CONCLUSIONS;191
9;8 Statistical Mechanical Modeling of ChemicalReactions in Condensed Phase Systems;196
9.1;Introduction;196
9.2;PMM basic derivations;197
9.3;Statistical mechanics in the infinite dilution conditions;199
9.4;The free-energy reaction surface;201
9.5;Modeling the reaction kinetics;206
9.5.1;The Diffusion Equation;206
9.5.2;Evaluation of the Reaction Rate Constants;208
9.6;Applications;210
9.6.1;Binding--Unbinding Reaction of CO in Myoglobin;210
9.6.2;Intramolecular Proton Transfer in Aqueous Malonaldehyde;214
10;9 An explicit quantum chemical solvent modelfor strongly coupled solute--solvent systems in groundor excited state;219
10.1;Introduction;219
10.2;The model, QMSTAT;223
10.2.1;Intermolecular Interactions;223
10.2.2;The Quantum Chemical Methods;230
10.2.3;Statistical Mechanical Method;235
10.2.4;Parametrization and Simulation Protocol;236
10.3;Examples of applications;238
10.3.1;The Polarization and Repulsion Are Coupled in Some Monatomic Ions;239
10.3.2;Asymmetric Solvation from Many-Body Interactions;241
10.3.3;Solute--Solvent Interactions in the La and Lb Excited States of Indole;242
10.4;Summary;245
11;10 Molecular Dynamics Simulation Methods including Quantum Effects;251
11.1;Introduction;251
11.2;Methodologies for Simulating Liquid Systems;253
11.2.1;Molecular Mechanics;254
11.2.2;Quantum Mechanics;256
11.2.3;The Quantum Mechanical/Molecular Mechanical Scheme;258
11.2.4;The Quantum Mechanical Charge Field Framework;259
11.2.4.1;The charge field approach;259
11.2.4.2;Electrostatic embedding and the periodic box;261
11.2.4.3;A general electrostatic embedding scheme for QM/MM simulations;265
11.2.5;Implementation of Consistent Embedding in the QMCF MD Approach;267
11.3;Results of QMCF MD Simulations;269
11.4;Conclusion and Outlook;278
12;11 Solvation Effects on Molecules and Biomolecules;283
12.1;INTRODUCTION;283
12.2;Classical Thermodynamics Of Solvation;284
12.3;Statistical Mechanics Of Solvation;285
12.4;Polymer Solutions;288
12.5;Comparison Of Flory--Huggins And Classical Solution Theories;290
12.5.1;Effect of Internal Degrees of Freedom;292
12.5.2;Coupling of the Center of Mass of One Molecule to the Excluded Volume of Another (Polymer Solutions);292
12.5.3;Effect of Molecular Shape and Architecture;294
12.6;Solvation In Polymers;296
12.6.1;Sorption of Gases in Polymers;296
12.6.1.1;Molecular simulation methods for calculation of phase equilibria;298
12.6.1.2;Grand equilibrium method: application to the calculation of solubility of gases in polystyrene;299
12.6.2;Concentrated Solutions of Polymers in Solvents;303
12.6.2.1;Solvation structure: mixtures of nonpolar polymers with nonpolar solvents;304
12.6.2.2;Solvation structure: mixtures of polar polymers with polar solvents;308
12.6.2.3;Hydrogen bonding in polar polymer--solvent mixtures;309
12.6.3;Solvent Effect on Polymer Size in the Solution;311
12.6.4;The Solvent Effect on Dynamics of Polymer Collapse;313
12.7;Time-Dependent Solvation Response;315
12.7.1;Experimental Methods;316
12.7.2;Theoretical Studies;318
12.7.3;Computer Simulations and the Mechanisms of Solvation;319
12.8;SUMMARY;321
13;12 Hydrogen Bonds And Solvent Effects In Soil Processes: A Theoretical View;325
13.1;INTRODUCTION;325
13.2;SIMULATON METHODS;328
13.3;ORGANIC FUNCTIONAL GROUPS AS MODELS FOR HUMIC SUBSTANCES;329
13.3.1;Binary Complexes with Acetic Acid and Acetate;330
13.3.2;Binary Complexes of 2,4-Dichlorophenoxyacetic Acid (2,4-D);333
13.4;HYDROGEN-BONDED INTERACTIONS IN SOIL MINERALS AND THEIR SURFACES;337
13.4.1;Hydrogen-Bonded Interactions of Surfaces of the Isolated Kaolinite Layer;337
13.4.2;Interactions of 2,4-D with the Octahedral Kaolinite Surface;340
13.4.3;Interaction of Broken Clay Surfaces with Water and Model Organic Molecules;343
13.4.4;Hydrogen Bond Interactions of Goethite Surface;344
13.5;CONCLUSIONS;347
14;13 Linear Response Theory in Connection to Density Functional Theory/Molecular Dynamics and Coupled Cluster/Molecular Dynamics Methods;352
14.1;Introduction;352
14.2;The Combined Quantum Mechanics and Molecular Mechanics model;354
14.3;Combined Density Functional Theory and Molecular Mechanics model;359
14.4;Response functions for the Density Functional Theory/Molecular Mechanics method;361
14.5;The Combined Coupled Cluster/Molecular Mechanics Method;366
14.6;Coupled Cluster/Molecular Mechanics Response Theory;370
14.7;Linear Response Calculations on Solvated Acetone;377
14.8;Conclusion;379
15;14 Combined QM/MM methods for the simulation of condensed phase processes using an approximate DFT approach;384
15.1;Introduction;384
15.2;SCC-DFTB;386
15.2.1;Performance of SCC-DFTB;388
15.3;Methods to treat environmental effects;388
15.4;Small polypeptides in aqueous solution;390
15.4.1;Ace-Lala-NME;391
15.4.2;Helix Formation in Ace-Lalan-NME Peptides with n = 4--20;394
15.5;Study of Non-natural peptides: and / -peptides;396
15.5.1;Gas-Phase Benchmark;396
15.5.2;Solution Results;398
15.6;Studying proton-transfer reactions in complex environments;400
15.6.1;Minimum Energy Pathways (MEPs);400
15.6.2;Free Energy Simulations Using Multi-scale Approaches;402
15.7;Conclusions;405
16;15 Solvation of Hydrogen Bonded Systems: CHO, OHO, and Cooperativity;409
16.1;INTRODUCTION;409
16.1.1;Early Applications of Rudimentary SCRF;411
16.2;Solvation Of ChO And OhO H-Bonds;412
16.3;Biologically Important H-Bonds;416
16.3.1;Amino Acids;417
16.3.2;Dipeptide;419
16.4;COOPERATIVITY;421
16.4.1;One-Dimensional Chains;421
16.4.2;Clusters;426
17;16 Solvation in Supercritical Fluids;435
17.1;INTRODUCTION;435
17.2;NON-POLAR SCF;437
17.2.1;Solvation of Alkaloids in SC-CO2;437
17.2.2;Effects from Adding a Co-solvent;442
17.3;POLAR SCFs;443
17.3.1;Dielectric Behavior SC-Water;443
17.3.2;Excess Electrons in Polar SCFs -- Equilibrium Aspects;447
17.3.3;Excess Electrons in Polar SCFs -- Solvation Dynamics;451
17.4;CONCLUDING REMARKS;453
18;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
18.1;INTRODUCTION;456
18.2;REAL-SPACE GRID QM/MM APPROACH;460
18.2.1;Kohn--Sham Density Functional Theory;460
18.2.2;Kohn--Sham DFT with Real-Space Grids;462
18.2.3;Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Approach;468
18.3;THEORY OF SOLUTIONS IN THE ENERGY REPRESENTATION;470
18.3.1;Free-Energy Perturbation and Thermodynamic Integration Methods;470
18.3.2;Distribution Functions in Solution;474
18.3.3;Density-Functional Theory;476
18.3.4;Radial Distribution Functions and Reference Interaction Site Model;479
18.3.5;Method of Energy Representation;480
18.4;COMBINATION OF THE QM/MM METHOD WITH THE THEORY OF SOLUTIONS;486
18.4.1;Division of the Total Solvation Free Energy;487
18.4.2;Contribution of the Many-Body Effect;490
18.5;APPLICATION OF THE QM/MM-ER APPROACH;493
18.5.1;Solvation Free Energy of a Water Molecule;493
18.5.2;Free Energy Change Associated with a Proton Transfer Process;497
19;18 Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study;507
19.1;Introduction;507
19.2;Theory;509
19.2.1;Hybrid Quantum Mechanics--Molecular Mechanics (QM/MM);509
19.2.2;Replica Exchange Molecular Dynamics;510
19.3;Computational Method;510
19.3.1;System Preparation;511
19.3.2;REMD of Alanine Dipeptide in Explicit Water;511
19.3.3;Molecular Dynamics of Alanine Dipeptide in Vacuum;511
19.3.4;Free Energy Surfaces;511
19.3.5;Dipolar Couplings;512
19.4;Results and Discussions;512
19.4.1;Molecular Dynamics of Alanine Dipeptide in Vacuum;512
19.4.2;Replica Exchange Molecular Dynamics of Alanine Dipeptide in Explicit Water;514
19.4.3;Radial Distribution Functions;515
19.5;Conclusions;516
20;Index;517