Solvation Effects on Molecules and Biomolecules: Computational Methods and Applications (Challenges and Advances in Computational Chemistry and Physics, 6)

✍ Scribed by Sylvio Canuto (editor)

• Publisher: Springer
• Year: 2008
• Tongue: English
• Leaves: 536
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Preface
1 Solvation Models for Molecular Properties:Continuum Versus Discrete Approaches
Introduction
Focussed Models
QM/MM
QM/continuum
Modeling Solvent Effects on Properties
QM Evaluation of NMR Nuclear Shieldings
An Application to Solvated Systems: N Nuclear Shieldings of Diazines
QM/continuum: Polarity Versus H-bond
QM/MM Versus QM/continuum
Conclusions
2 The multipole moment expansion solvent continuum model: a brief review
Introduction
Development of the model: main contributions
Basic equations
Cavity definition
Distributed multipoles
Solvation energy convergence
Non-electrostatic contributions
Comparison with other solvent models
Conclusions and perspectives
3 The Discrete Reaction Field Approachfor Calculating Solvent Effects
Introduction
Theory
Perturbation Theory
Electrostatic Potentials: The Point Charges
The Many-Body Polarization
Bulk Effects: The Dielectric Continuum
Implementations
Macroscopic and Microscopic Properties
Some validation
The Water Dimer
Benzene Dimer
Many-Body Interactions
Concluding the Validation
Applications
Sudden Polarization in Excited States of Symmetric Ethylenes
Spectra
The n transition in acetone
Absorption and emission spectra of N-(1-pyrenyl)-methyluracil- 5-carboxamide-1-aminopyrene (PAUMe)
The visible spectrum of Fe-(PyPepS)2--
Circular dichroism spectrum of '133Co(en)3'1353+ in water
(Hyper-)polarizabilities and Macroscopic Properties in Solution
Response properties of liquid water
The first hyperpolarizability of pNA in 1,4-dioxane solution
Chemistry in Solution
The dissociation of ter-butyl-chloride in water
Tautomerism of substituted cyclic imidazoline
Summary and conclusion
4 Thermochemical Analysis of the Hydrationof Neutral Solutes
Introduction
The MST-PCM continuum method
The enthalpy of solvation
Experimental data and computational details
Thermochemical analysis of the hydration
Concluding remarks
5 Electronic Properties of Hydrogen BondNetworks: Implications for Solvent Effectsin Polar Liquids
Introduction
Polarization Effects and Charge Fluctuations in Polar Hydrogen Bonding Liquids
Electronic Polarization and the Dipole Moment in Liquid Phase
Charge Fluctuations in Hydrogen Bonding Liquids
Structure of the Hydrogen Bond Network and Electronic Properties of Water
Hydrogen Bonding and the Dipole Moment of Liquid Water
Hydrogen Bonding and Electron Binding Energies
Charge Fluctuations of the Hydrogen Bond Network and Proton Transfer Assisted by the Solvent in Phenol--Water Clusters
Born--Oppenheimer Molecular Dynamics of Proton Transfer in Phenol--Water Clusters
Dynamics of PT in Phenol--Water Clusters
Proton (Deuterium) Transfer in Phenol--Water Clusters and Fluctuations of the HB Network
Conclusions
6 The Sequential QM/MM Method and itsApplications to Solvent Effects in Electronicand Structural Properties of Solutes
INTRODUCTION
METHOD
Fundament of the ASEP/MD Method
Ground and Excited State Gradients
Location of Conical Intersections and Singlet--Triplet Crossing Points in Solution
Free Energy Differences
De-Excitation Pathways In Acrolein
Absorption Spectra
Emission Spectra
Non-radiative Excited State Decay
Concluding Remarks
7 The Sequential QM/MM Method and itsApplications to Solvent Effects in Electronicand Structural Properties of Solutes
INTRODUCTION
METHODOLOGY
Description of the Statistical Analyses
Statistical correlation or statistical inefficiency
Structural analysis: solvent distribution
APPLICATIONS
Nonpolar Solutes
Solvent effects on the UV-vis spectra of benzene
Hydration effects on the structure, band gap and UV-vis spectrum of C60
Including Solute Polarization
Average Solvent Electrostatic Configuration
SUMMARY AND CONCLUSIONS
8 Statistical Mechanical Modeling of ChemicalReactions in Condensed Phase Systems
Introduction
PMM basic derivations
Statistical mechanics in the infinite dilution conditions
The free-energy reaction surface
Modeling the reaction kinetics
The Diffusion Equation
Evaluation of the Reaction Rate Constants
Applications
Binding--Unbinding Reaction of CO in Myoglobin
Intramolecular Proton Transfer in Aqueous Malonaldehyde
9 An explicit quantum chemical solvent modelfor strongly coupled solute--solvent systems in groundor excited state
Introduction
The model, QMSTAT
Intermolecular Interactions
The Quantum Chemical Methods
Statistical Mechanical Method
Parametrization and Simulation Protocol
Examples of applications
The Polarization and Repulsion Are Coupled in Some Monatomic Ions
Asymmetric Solvation from Many-Body Interactions
Solute--Solvent Interactions in the La and Lb Excited States of Indole
Summary
10 Molecular Dynamics Simulation Methods including Quantum Effects
Introduction
Methodologies for Simulating Liquid Systems
Molecular Mechanics
Quantum Mechanics
The Quantum Mechanical/Molecular Mechanical Scheme
The Quantum Mechanical Charge Field Framework
The charge field approach
Electrostatic embedding and the periodic box
A general electrostatic embedding scheme for QM/MM simulations
Implementation of Consistent Embedding in the QMCF MD Approach
Results of QMCF MD Simulations
Conclusion and Outlook
11 Solvation Effects on Molecules and Biomolecules
INTRODUCTION
Classical Thermodynamics Of Solvation
Statistical Mechanics Of Solvation
Polymer Solutions
Comparison Of Flory--Huggins And Classical Solution Theories
Effect of Internal Degrees of Freedom
Coupling of the Center of Mass of One Molecule to the Excluded Volume of Another (Polymer Solutions)
Effect of Molecular Shape and Architecture
Solvation In Polymers
Sorption of Gases in Polymers
Molecular simulation methods for calculation of phase equilibria
Grand equilibrium method: application to the calculation of solubility of gases in polystyrene
Concentrated Solutions of Polymers in Solvents
Solvation structure: mixtures of nonpolar polymers with nonpolar solvents
Solvation structure: mixtures of polar polymers with polar solvents
Hydrogen bonding in polar polymer--solvent mixtures
Solvent Effect on Polymer Size in the Solution
The Solvent Effect on Dynamics of Polymer Collapse
Time-Dependent Solvation Response
Experimental Methods
Theoretical Studies
Computer Simulations and the Mechanisms of Solvation
SUMMARY
12 Hydrogen Bonds And Solvent Effects In Soil Processes: A Theoretical View
INTRODUCTION
SIMULATON METHODS
ORGANIC FUNCTIONAL GROUPS AS MODELS FOR HUMIC SUBSTANCES
Binary Complexes with Acetic Acid and Acetate
Binary Complexes of 2,4-Dichlorophenoxyacetic Acid (2,4-D)
HYDROGEN-BONDED INTERACTIONS IN SOIL MINERALS AND THEIR SURFACES
Hydrogen-Bonded Interactions of Surfaces of the Isolated Kaolinite Layer
Interactions of 2,4-D with the Octahedral Kaolinite Surface
Interaction of Broken Clay Surfaces with Water and Model Organic Molecules
Hydrogen Bond Interactions of Goethite Surface
CONCLUSIONS
13 Linear Response Theory in Connection to Density Functional Theory/Molecular Dynamics and Coupled Cluster/Molecular Dynamics Methods
Introduction
The Combined Quantum Mechanics and Molecular Mechanics model
Combined Density Functional Theory and Molecular Mechanics model
Response functions for the Density Functional Theory/Molecular Mechanics method
The Combined Coupled Cluster/Molecular Mechanics Method
Coupled Cluster/Molecular Mechanics Response Theory
Linear Response Calculations on Solvated Acetone
Conclusion
14 Combined QM/MM methods for the simulation of condensed phase processes using an approximate DFT approach
Introduction
SCC-DFTB
Performance of SCC-DFTB
Methods to treat environmental effects
Small polypeptides in aqueous solution
Ace-Lala-NME
Helix Formation in Ace-Lalan-NME Peptides with n = 4--20
Study of Non-natural peptides: and / -peptides
Gas-Phase Benchmark
Solution Results
Studying proton-transfer reactions in complex environments
Minimum Energy Pathways (MEPs)
Free Energy Simulations Using Multi-scale Approaches
Conclusions
15 Solvation of Hydrogen Bonded Systems: CHO, OHO, and Cooperativity
INTRODUCTION
Early Applications of Rudimentary SCRF
Solvation Of ChO And OhO H-Bonds
Biologically Important H-Bonds
Amino Acids
Dipeptide
COOPERATIVITY
One-Dimensional Chains
Clusters
16 Solvation in Supercritical Fluids
INTRODUCTION
NON-POLAR SCF
Solvation of Alkaloids in SC-CO2
Effects from Adding a Co-solvent
POLAR SCFs
Dielectric Behavior SC-Water
Excess Electrons in Polar SCFs -- Equilibrium Aspects
Excess Electrons in Polar SCFs -- Solvation Dynamics
CONCLUDING REMARKS
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
INTRODUCTION
REAL-SPACE GRID QM/MM APPROACH
Kohn--Sham Density Functional Theory
Kohn--Sham DFT with Real-Space Grids
Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Approach
THEORY OF SOLUTIONS IN THE ENERGY REPRESENTATION
Free-Energy Perturbation and Thermodynamic Integration Methods
Distribution Functions in Solution
Density-Functional Theory
Radial Distribution Functions and Reference Interaction Site Model
Method of Energy Representation
COMBINATION OF THE QM/MM METHOD WITH THE THEORY OF SOLUTIONS
Division of the Total Solvation Free Energy
Contribution of the Many-Body Effect
APPLICATION OF THE QM/MM-ER APPROACH
Solvation Free Energy of a Water Molecule
Free Energy Change Associated with a Proton Transfer Process
18 Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study
Introduction
Theory
Hybrid Quantum Mechanics--Molecular Mechanics (QM/MM)
Replica Exchange Molecular Dynamics
Computational Method
System Preparation
REMD of Alanine Dipeptide in Explicit Water
Molecular Dynamics of Alanine Dipeptide in Vacuum
Free Energy Surfaces
Dipolar Couplings
Results and Discussions
Molecular Dynamics of Alanine Dipeptide in Vacuum
Replica Exchange Molecular Dynamics of Alanine Dipeptide in Explicit Water
Radial Distribution Functions
Conclusions
Index