Femtosecond IR Studies of Solvation by Directly Probing the Solvent
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The response of solvent to the change of charge or dipole of solute molecules has been intensely studied in recent years 1 . In previous solvation experiments, time dependent fluorescence Stokes shift of dye molecules in different solvents were measured, from which the solvation time for the solvents were determined 1 , 2 . Various theories, from the simple dielectric continuum model to instantaneous solvent normal mode analysis, have been used to relate solvent motions to solvation time 3 , 4 . MD simulations have also been carried out to understand the nature of these solvent motions in the solvation process 5 . However, these time dependent Stokes shift experiments, which measure the solute fluorescence, can only provide an indirect microscopic picture of the relevant solvent motions during the solvation process.Keywords:
Stokes shift
Implicit solvation
Solvation shell
We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.
Solvation shell
Implicit solvation
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AbstractMost chemical (or biochemical) reactions take place in a liquid solvent. Water is the natural solvent of biochemical reactions, and is increasingly used for organic synthesis. As water is not an inert solvent, modelling such a complex environment and evaluating the solvation effects on the electronic structure of the solute is a challenge. The unusual weak bond is used here as a probe of the solvation effects. Several solvation models were tested: a continuum, 1027 TIP3P water molecules and a microsolvation model complemented by a continuum or by TIP3P molecules. First, we show that the combination of the topological analysis of the electron localisation function (ELF) and the theory of atoms in molecules (AIM) is a robust way to evaluate and rationalise the strength and the accuracy of a given solvation model. These analyses demonstrate that a polarisable continuum model (PCM) is less accurate than a quantum mechanics/molecular mechanics (QM/MM) calculation where only the probe molecule is included in the QM region. We also show that solvating the solute and its first solvation shell embedded in a PCM leads to the same polarisation effect as a costly QM/MM calculation with 30 H2O included in the QM part and approximately 1000 classical water molecules. Finally, beyond this work, we show here that the combined ELF and AIM analyses can open up new opportunities for the electronic description of environment effects, for example in dynamical calculations.Keywords:: electron localisation functionatoms in moleculesCPMDsolvation effectsliquid water AcknowledgementThis work has been achieved with the help of the resources of PSMN (Pôle Scientifique de modélisation Numérique).
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Implicit solvation
QM/MM
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A study on the explicit and implicit solvation models for calculation of solvation free energy of ions and pKa of amino acids presented recently [ Gupta , M. ; J. Chem.Comput. 2013 , 9 , 5021 - 5031 ] is extended for the study of amines and alkanolamines. Solvation free energies and pKa's of a data set of 25 amines and alkanolamines are calculated using the explicit solvation shell (ESS) model given by da Silva et al. [ J. Phys. Chem. A 2009 , 113 , 6404 ] and continuum solvation models (polarized continuum solvation model (PCM), SM8T, and DivCon). An extensive overview involving the gas-phase basicity and proton affinity, calculated using density functional methods (B3LYP/6-311++G(d,p)) and composite methods (G3MP2B3, G3MP2, CBS-QB3, G4MP2) and compared with corresponding experimental results for amines and alkanolamines, is also included in the present work. This data set was selected based on the components' potential as solvents for postcombustion CO2 capture (PCC) processes. Results of gaseous-phase thermochemistry and pKa obtained from different models employed in this work are analyzed against experimental results for obtaining error estimates involved in each theoretical model. The ESS model for the calculation of the solvation free energy of ions combined with composite methods for gaseous-phase thermochemistry is found to give reasonable accuracy for pKa calculations of amines and alkanolamines and thereby constitutes a method for validation of pKa for new potential PCC solvents.
Thermochemistry
Implicit solvation
Solvation shell
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The study of the Explicit Solvation Shell Model (ESS) presented recently [da Silva, E. F.; Svendsen, H. F.; Merz, K. M. J. Phys. Chem. A 2009, 113, 6404.] for calculation of solvation free energy of ions is extended for the study for amino acids. Solvation free energies and pKa of a data set of 10 amino acids is calculated using ESS. The data set of amino acids is selected based on their potential to be regarded as solvents for postcombustion CO2 capture processes. Calculated results are compared against experimental pKa and pKa calculated from PCM, SM8T, and DivCon continuum solvation models. Error estimates of pKa from different models vs experimental pKa data are also given to evaluate the results calculated by different solvation models. This study also involves a comprehensive study of gas phase basicity, proton affinity,ΔGacid0, ΔHacid0, protonation entropy with density functional methods (B3LYP/6-311++G(d,p)) and composite methods (G3MP2B3, G3MP2, CBS-QB3, G4MP2) and their comparison with experimental results for amino acids.
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Implicit solvation
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Solvation shell
Implicit solvation
Force Field
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Solvation shell
Implicit solvation
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A method is presented to explicitly represent the first solvation shell in continuum solvation calculations. Initial solvation shell geometries were generated with classical molecular dynamics simulations. Clusters consisting of solute and 5 solvent molecules were fully relaxed in quantum mechanical calculations. The free energy of solvation of the solute was calculated from the free energy of formation of the cluster, and the solvation free energy of the cluster was calculated with continuum solvation models. The method has been implemented with two continuum solvation models, a Poisson−Boltzmann model and the IEF-PCM model. Calculations were carried out for a set of 60 ionic species. Implemented with the Poisson−Boltzmann model the method gave an unsigned average error of 2.1 kcal/mol and a rmsd of 2.6 kcal/mol for anions; for cations the unsigned average error was 2.8 kcal/mol and the rmsd 3.9 kcal/mol. Similar results were obtained with the IEF-PCM model.
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Implicit solvation
Poisson–Boltzmann equation
Solvent models
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We develop a microscopic theory of the time-resolved Stokes shift of a chromophore in a polar solvent which incorporates both non-Debye dielectric relaxation and solvation shell structure. The present theory depends on the direct correlation function of the pure solvent, the measured frequency-dependent dielectric constant, and a microscopically derived translational diffusion parameter. We compare the predictions of the theory given here to a variety of experimental results on solvation in protic and aprotic solvents. Good agreement with experiment is found. Our theory compares favorably with the dynamical mean spherical approximation (MSA) theory of time-dependent solvation.
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Stokes shift
Debye
Implicit solvation
Chromophore
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Electron density-based implicit solvation models are a class of techniques for quantifying solvation effects and calculating free energies of solvation without an explicit representation of solvent molecules. Integral to the accuracy of solvation modeling is the proper definition of the solvation shell separating the solute molecule from the solvent environment, allowing for a physical partitioning of the free energies of solvation. Unlike state-of-the-art implicit solvation models for molecular quantum chemistry calculations,
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Many hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were analyzed and compared with the properties of solvation water present at the surface of ice. The most striking observations concerned the temperature dependence of changes in water structure. In the case of solvation water of the ice-binding plane, the difference between the overall structural ordering of solvation water and bulk water diminished with increasing temperature; in the case of solvation water of the rest of the protein, the trend was opposite. In this respect, the solvation water of the ice-binding plane roughly resembled the hydration layer of ice. Simultaneously, the whole solvation shell of the protein displayed some features that are typical for solvation shells of many other proteins and are not encountered in the solvation water of ice. In the first place, this is an increase in density of water around the protein. The opposite is true for the solvation water of ice – it is less dense than bulk water. Therefore, even though the structure of solvation water of ice-binding plane and the structure of solvation water of ice seem to share some similarities, densitywise they differ.
Solvation shell
Antifreeze protein
Implicit solvation
Antifreeze
Properties of water
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