42 research outputs found
A molecular density functional theory to study solvation in water
A classical density functional theory is applied to study solvation of
solutes in water. An approx- imate form of the excess functional is proposed
for water. This functional requires the knowledge of pure solvent direct
correlation functions. Those functions can be computed by using molecular
simulations such as molecular dynamic or Monte Carlo. It is also possible to
use functions that have been determined experimentally. The functional
minimization gives access to the solvation free energy and to the equilibrium
solvent density. Some correction to the functional are also proposed to get the
proper tetrahedral order of solvent molecules around a charged solute and to
reproduce the correct long range hydrophobic behavior of big apolar solutes. To
proceed the numerical minimization of the functional, the theory has been
discretized on two tridimensional grids, one for the space coordinates, the
other for the angular coordinates, in a functional minimization code written in
modern Fortran, mdft. This program is used to study the solvation in water of
small solutes of several kind, atomic and molecular, charged or neutral. More
complex solutes, a neutral clay and a small protein have also been studied by
functional minimization. In each case the classical density functional theory
is able to reproduce the exact results predicted by MD. The computational cost
is at least three order of magnitude less than in explicit methods.Comment: PhD Manuscript 157 pages, written in Frenc
Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections
Molecular Density Functional Theory (MDFT) offers an efficient implicit-
solvent method to estimate molecule solvation free-energies whereas conserving
a fully molecular representation of the solvent. Even within a second order ap-
proximation for the free-energy functional, the so-called homogeneous reference
uid approximation, we show that the hydration free-energies computed for a
dataset of 500 organic compounds are of similar quality as those obtained from
molecular dynamics free-energy perturbation simulations, with a computer cost
reduced by two to three orders of magnitude. This requires to introduce the
proper partial volume correction to transform the results from the grand
canoni- cal to the isobaric-isotherm ensemble that is pertinent to experiments.
We show that this correction can be extended to 3D-RISM calculations, giving a
sound theoretical justifcation to empirical partial molar volume corrections
that have been proposed recently.Comment: Version with correct equation numbers is here:
http://compchemmpi.wikispaces.com/file/view/sergiievskyi_et_al.pdf/513575848/sergiievskyi_et_al.pdf
Supporting information available online at:
http://compchemmpi.wikispaces.com/file/view/SuppInf_sergiievskyi_et_al_07-04-2014.pdf/513576008/SuppInf_sergiievskyi_et_al_07-04-2014.pd
Hydration of Clays at the Molecular Scale: The Promising Perspective of Classical Density Functional Theory
We report here how the hydration of complex surfaces can be efficiently
studied thanks to recent advances in classical molecular density functional
theory. This is illustrated on the example of the pyrophylite clay. After
presenting the most recent advances, we show that the strength of this implicit
method is that (i) it is in quantitative or semi-quantitative agreement with
reference all-atoms simulations (molecular dynamics here) for both the
solvation structure and energetics, and that (ii) the computational cost is two
to three orders of magnitude less than in explicit methods. The method remains
imperfect, in that it locally overestimates the polarization of water close to
hydrophylic sites of the clay. The high numerical efficiency of the method is
illustrated and exploited to carry a systematic study of the electrostatic and
van der Waals components of the surface-solvant interactions within the most
popular force field for clays, CLAYFF. Hydration structure and energetics are
found to weakly depend upon the electrostatics. We conclude on the consequences
of such findings in future force-field development.Comment: 24 pages, 8 figures. Molecular Physics (2014
Simulating electrochemical systems by combining the finite field method with a constant potential electrode
International audienceA better understanding of interfacial mechanisms is needed to improve the performances of elec-trochemical devices. Yet, simulating an electrode surface at fixed electrolyte composition remains a challenge. Here we apply a finite electric field to a single electrode held at constant potential and in contact with an aqueous ionic solution, using classical molecular dynamics. The polarization yields two electrochemical interfaces on opposite sides of the same metal slab. While the net charge on one electrode surface is the opposite of the net charge on the other, maintaining overall charge neutrality of the metal. The electrode surface charges fluctuations are compensated by the adsorption of ions from the electrolyte, forming a pair of electric double layers with aligned dipoles. This opens the way towards the efficient simulation of electrochemical interfaces using any flavor of molecular dynamics, from classical to first principles-based methods
Molecular Density Functional Theory for water with liquid-gas coexistence and correct pressure
The solvation of hydrophobic solutes in water is special because liquid and
gas are almost at coexistence. In the common hypernetted chain approximation to
integral equations, or equivalently in the homogenous reference fluid of
molecular density functional theory, coexistence is not taken into account.
Hydration structures and energies of nanometer-scale hydrophobic solutes are
thus incorrect. In this article, we propose a bridge functional that corrects
this thermodynamic inconsistency by introducing a metastable gas phase for the
homogeneous solvent. We show how this can be done by a third order expansion of
the functional around the bulk liquid density that imposes the right pressure
and the correct second order derivatives. Although this theory is not limited
to water, we apply it to study hydrophobic solvation in water at room
temperature and pressure and compare the results to all-atom simulations. With
this correction, molecular density functional theory gives, at a modest
computational cost, quantitative hydration free energies and structures of
small molecular solutes like n-alkanes, and of hard sphere solutes whose radii
range from angstroms to nanometers. The macroscopic liquid-gas surface tension
predicted by the theory is comparable to experiments. This theory gives an
alternative to the empirical hard sphere bridge correction used so far by
several authors.Comment: 18 pages, 6 figure
Molecular Density Functional Theory of Water describing Hydrophobicity at Short and Long Length Scales
We present an extension of our recently introduced molecular density
functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619,
2013] to the solvation of hydrophobic solutes of various sizes, going from
angstroms to nanometers. The theory is based on the quadratic expansion of the
excess free energy in terms of two classical density fields, the particle
density and the multipolar polarization density. Its implementation requires as
input a molecular model of water and three measurable bulk properties, namely
the structure factor and the k-dependent longitudinal and transverse dielectric
susceptibilities. The fine three-dimensional water structure around small
hydrophobic molecules is found to be well reproduced. In contrast the computed
solvation free-energies appear overestimated and do not exhibit the correct
qualitative behavior when the hydrophobic solute is grown in size. These
shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by
complementing the functional with a truncated hard-sphere functional acting
beyond quadratic order in density. It makes the resulting functional compatible
with the Van-der-Waals theory of liquid-vapor coexistence at long range.
Compared to available molecular simulations, the approach yields reasonable
solvation structure and free energy of hard or soft spheres of increasing size,
with a correct qualitative transition from a volume-driven to a surface-driven
regime at the nanometer scale.Comment: 24 pages, 8 figure
Une théorie de la fonctionnelle de la densité moléculaire pour la solvatation dans l'eau
A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation functions. Those functions can be computed by using molecular simulations such as molecular dynamic or Monte Carlo. It is also possible to use functions that have been determined experimentally. The functional minimization gives access to the solvation free energy and to the equilibrium solvent density. Some correction to the functional are also proposed to get the proper tetrahedral order of solvent molecules around a charged solute and to reproduce the correct long range hydrophobic behavior of big apolar solutes. To proceed the numerical minimization of the functional, the theory has been discretized on two tridimensional grids, one for the space coordinates, the other for the angular coordinates, in a functional mini- mization code written in modern Fortran, mdft. This program is used to study the solvation in water of small solutes of several kind, atomic and molecular, charged or neutral. More complex solutes, a neutral clay and a small protein have also been studied by functional minimization. In each case the classical density functional theory is able to reproduce the exact results predicted by MD. The computational cost is at least three order of magnitude less than in explicit methods.La théorie de la fonctionnelle de la densité classique est utilisée pour étudier la solvatation de solutés quelconques dans le solvant eau. Une forme approchée de la fonctionnelle d’excès pour l’eau est proposée. Cette fonctionnelle nécessite l’utilisation de fonctions de corrélation du solvant pur. Celles-ci peuvent être calculées par simulations numériques, dynamique moléculaire ou Monte Carlo ou obtenues expérimentalement. La minimisation de cette fonctionnelle donne accès à l’énergie libre de solvatation ainsi qu’à la densité d’équilibre du solvant. Différentes corrections de cette fonctionnelle approchée sont proposées. Une correction permet de renforcer l’ordre tétraédrique du solvant eau autour des solutés chargés, une autre permet de reproduire le comportement hydrophobe à longue distance de solutés apolaires. Pour réaliser la minimisation numérique de la fonctionnelle, la théorie a été implémentée sur une double grille tridimensionnelle pour les coordonnées angulaires et spatiales, dans un code de minimisation fonctionnelle écrit en Fortran moderne, mdft. Ce programme a été utilisé pour étudier la solvatation en milieu aqueux de petits solutés atomiques neutres et chargés et de petites molécules polaires et apolaires ainsi que de solutés plus complexes, une argile hydrophobe et une petite protéine. Dans chacun des cas la théorie de la fonctionnelle de la densité classique permet d’obtenir des résultats similaires à ceux théoriquement exacts obtenus par dynamique moléculaire, avec des temps de calculs inférieurs d’au moins trois ordres de grandeurs