arXiv subjects

Daniel Borgis

Publications and source records attributed to Daniel Borgis.

At least 19 recordsLinked to original sources

arXiv2026

Accurate Solvation Properties in supercritical CO$_2$ with Molecular Density Functional Theory

Supercritical CO$_2$ is a highly efficient solvent for the development of more environmentally benign chemical processes. It is crucial to predict its solvation properties -- the solvation free energy and the solvation structure -- both accurately and at low computational cost. We show here that classical density functional theory (cDFT) can reproduce the solvation properties obtained from conventional molecular simulations, while requiring a computational effort that is several orders of magnitude lower. This excellent agreement is achieved using a molecular cDFT formalism based on a density that depends on both the positions and orientations of CO$_2$ molecules in the vicinity of the solute. We further examine several levels of approximation for the excess free-energy functional in cDFT and demonstrate that the homogeneous reference fluid approximation is sufficient to recover the molecular dynamics (MD) benchmark results. These findings open the way to extending molecular cDFT to other thermodynamic conditions.

physics.chem-ph↗

arXiv2025

A Molecular Density Functional Theory of aqueous electrolytic solution

We propose a generalisation of molecular density functional theory to describe inhomogeneous solvent mixture, with the objective of modelling electrolytic solutions. Two electrolytic models are presented, both within the HNC approximation. The first one is a two-components mixture representing a primitive-like model of sodium chloride, where the solvent is described as a dielectric continuum. This popular model has the advantage of simplicity, as the ions densities solely depend on spatial coordinates. Additionally, we develop a realistic three-components electrolyte model, in which water solvent is described by a third density field that depends on both spatial and orientational coordinates. The proposed methodology and its tridimensional implementation (3 spatial coordinates and 3 Euler angles) are validated by comparing the solvation properties of a sodium cation with the predictions of integral equation theory solved in 1D (1 intermolecular distance and 5 Euler angles), showing near-perfect agreement. This methodology enables the study of solvation properties of solutes of arbitrary shapes in electrolytic solutions, as demonstrated with the prototypical N-methylacetamide molecule immersed in both electrolytic solution models.

physics.chem-ph↗

arXiv2024

The orientational structure of a model patchy particle fluid: simulations, integral equations, density functional theory and machine learning

We investigate the orientational properties of a homogeneous and inhomogeneous tetrahedral 4-patch fluid (Kern--Frenkel model). Using integral equations, either (i) HNC or (ii) a modified HNC scheme with simulation input, the full orientational dependence of pair and direct correlation functions is determined. Density functionals for the inhomogeneous problem are constructed via two different methods. The first, molecular density functional theory, utilizes the full direct correlation function and an isotropic hard-sphere bridge functional. The second method, a machine learning approach, uses a decomposition of the functional into an isotropic reference part and a mean-field orientational part, where both parts are improved by machine learning techniques. Comparison to simulation data at hard walls and around hard tracers show a similar performance of the two functionals. Machine learning strategies are discussed to eliminate residual differences, with the goal of obtaining machine-learning enhanced functionals for the general anisotropic fluid.

cond-mat.soft↗

arXiv2023

Molecular integral equations theory in the near critical region of CO2

Environmental concerns are driving the search for greener yet efficient solvents. Supercritical CO2 (scCO2) is a promising candidate due to its non-toxicity and the potential for reusing CO2 emissions. It also offers a versatile range of properties that can be finely tuned by pressure adjustments. This adaptability is exploited in chemical industry processes such as separation or extraction. The development of new green processes using scCO2 requires an efficient tool for predicting the solvation properties under different conditions. Existing parametric equations for solubility prediction depend on known experimental data, while molecular dynamics (MD) simulations remain expensive for studying different conditions. Both methods are unsuitable for advancing new technologies. The molecular density functional theory (MDFT) offers a promising alternative, combining an accurate microscopic modeling with fast calculations. MDFT necessitates the bulk direct correlation functions, which can be calculated from expensive MD simulations or from approximate yet rapid molecular integral equations. The development of MDFT as a powerful tool to study the solvation in scCO2 will require the construction of an accurate molecular integral equations for scCO2.This paper presents the exact direct correlation functions of scCO2 obtained from MD and compares them with the results of the simplest molecular integral equations, the hypernetted chain approximation (HNC). If HNC fails to provide correct long-range correlations and thermodynamics, it succeeds in reproducing the short-range structure. By using the direct correlation functions obtained from MD and HNC, we demonstrate the efficacy of MDFT in calculating the chemical potential of CO2 in scCO2. The results open the door to the application of MDFT to a wider range of solutes dissolved in scCO2 with different thermodynamic conditions.

physics.chem-ph↗

arXiv2023

Dielectric response of confined water films: Insights from classical DFT

We re-examine the problem of the dielectric response of highly polar liquids such as water in confinement between two walls using a simple two-variable density functional theory involving number and polarisation densities. In the longitudinal polarisation case where a perturbing field is applied perpendicularly to the walls, we show that the notion of local dielectric constant, although ill-defined at a microscopic level, makes sense when a coarse-graining over the typical size of a particle is introduced. The approach makes it possible to study the effective dielectric response of thin liquid films of various thicknesses in connection to the recent experiments of [Fumagalli et al. , Science, 2018, 360, 1339-1342], and to discuss the notion interfacial dielectric constant. We argue that the observed properties as function of slab dimension, in particular the very low dielectric constants of the order of 2-3 measured for thin slabs of 1 nm thickness do not highlight any special property of water but can be recovered for a generic polar solvent having similar particle size and the same high dielectric constant. Regarding the transverse polarisation case where the perturbing field is parallel to the walls, the associated effective dielectric constant as a function of the slab dimension reaches bulk-like values at much shorter widths than in the longitudinal case.

cond-mat.stat-mech↗

arXiv2020

Tackling solvent effect by coupling electronic and molecular Density Functional Theory

Solvation effect might have a tremendous influence on chemical reactions. However, precise quantum chemistry calculations are most often done either in vacuum neglecting the role of the solvent or using continuum solvent model ignoring its molecular nature. We propose a new method coupling a quantum description of the solute using electronic density functional theory with a classical grand-canonical treatment of the solvent using molecular density functional theory. Unlike previous work, both densities are minimized self consistently, accounting for mutual polarization of the molecular solvent and the solute. The electrostatic interaction is accounted using the full electron density of the solute rather than fitted point charges. The introduced methodology represents a good compromise between the two main strategies to tackle solvation effect in quantum calculation. It is computationally more effective than a direct quantum-mechanics/molecular mechanics coupling, requiring the exploration of many solvent configurations. Compared to continuum methods it retains the full molecular-level description of the solvent. We validate this new framework onto two usual benchmark systems: a water solvated in water and the symmetrical nucleophilic substitution between chloromethane and chloride in water. The prediction for the free energy profiles are not yet fully quantitative compared to experimental data but the most important features are qualitatively recovered. The method provides a detailed molecular picture of the evolution of the solvent structure along the reaction pathway.

physics.chem-ph↗

arXiv2020

Predicting hydration free energies of the FreeSolv database of druglike molecules with molecular density functional theory

We assess the performance of molecular densityfunctional theory (MDFT) to predict hydration freeenergies of the small drug-like molecules benchmark,FreeSolv. MDFT in the hyper-netted chain approx-imation (HNC) coupled with a pressure correctionpredicts experimental hydration free energies of theFreeSolv database within 1 kcal/mol with an averagecomputation time of two cpu.min per molecule. Thisis the same accuracy as for simulation based free en-ergy calculations that typically require hundreds ofcpu.h or tens of gpu.h per molecule.

physics.chem-ph↗

arXiv2019

Study of a water-graphene capacitor with molecular density functional theory

Most of the performances of electrochemical devices are governed by molecular processes taking place at the solution-electrode interfaces and molecular simulation are the main way to study these processes. Aqueous electrochemical systems have often been studied using classical DFT but with too crude approximations to consider the system description to be realistic. We study the interface between graphene electrodes and liquid water at different applied voltage using molecular DFT, improving the state of the art by the following key points: 1) electrodes have a realistic atomic resolution, 2) classical DFT calculations are carried out at fixed imposed potential difference and 3) water is described by a molecular model. This allows to reveal the structural modification of water adsorbed at the graphene interface and the evolution of water dielectric permittivity when a voltage is applied. The computed capacitance of this device is in agreement with molecular dynamics simulations. This demonstrates the relevance of molecular DFT to study electrochemical systems at the molecular level.

physics.chem-ph↗

arXiv2019

Computing three-dimensional densities from force densities improves statistical efficiency

The extraction of inhomogeneous 3-dimensional densities around tagged solutes from molecular simulations is known to have a very high computational cost because this is traditionally performed by collecting histograms, with each discrete voxel in three-dimensional space needing to be visited significantly. This paper presents an extension of a previous methodology for the extraction of 3D solvent number densities with a reduced variance principle [Borgis et al., Mol. Phys. 111, 3486-3492 (2013)] to other 3D densities such as charge and polarization densities. The approach is also generalized to cover molecular solvents with structures described using rigid geometrical constraints, which include in particular popular water models such as SPC/E and TIPnP class of models. The noise reduction is illustrated for the microscopic hydration structure of a small molecule, in various simulation conditions, and for a protein. The method has large applicability to simulations of solvation in many fields, for example around biomolecules, nanoparticles, or within porous materials.

physics.chem-ph↗

arXiv2018

A Molecular Density Functional Theory Approach to Electron Transfer Reactions

Beyond the dielectric continuum description initiated by Marcus theory, the nowadays standard theoretical approach to study electron transfer (ET) reactions in solution or at interfaces is to use classical force field or ab initio Molecular Dynamics simulations. We propose here an alternative method based on liquid-state theory, namely molecular density functional theory, which is numerically much more efficient than simulations while still retaining the molecular nature of the solvent. We begin by reformulating molecular ET theory in a density functional language and show how to compute the various observables characterizing ET reactions from an ensemble of density functional minimizations. In particular, we define in that formulation the relevant order parameter of the reaction, the so-called vertical energy gap, and determine the Marcus free energy curves of both reactant and product states along that coordinate. Important thermodynamic quantities such as the reaction free energy and the reorganization free energies follow. We assess the validity of the method by studying the model Cl$^0\rightarrow$ Cl$^+$ and Cl$^0\rightarrow$ Cl$^-$ ET reactions in bulk water for which molecular dynamics results are available. The anionic case is found to violate the standard Marcus theory. Finally, we take advantage of the computational efficiency of the method to study the influence of confinement on the ET, by investigating the evolution of the reorganization free energy of the Cl$^0\rightarrow$ Cl$^+$ reaction when the atom approaches an atomistically resolved wall.

physics.chem-ph↗

arXiv2018

High-throughput free energies and water maps for drug discovery by molecular density functional theory

The hydration or binding free energy of a drug-like molecule is a key data for early stage drug discovery. Hundreds of thousands of evaluations are needed, which rules out the exhaustive use of atomistic simulations and free energy methods. Instead, the current docking and screening processes are today relying on numerically efficient scoring functions that lose much of the atomic scale information and hence remain error-prone. In this article, we show how a probabilistic description of molecular liquids as implemented in the molecular density functional theory predicts hydration free energies of a state-of-the-art benchmark of small drug-like molecules within 0.5 kJ/mol (0.1 kcal/mol) of atomistic simulations, along with water and polarization maps, for a computation time compatible with screening and docking.

physics.chem-ph↗

arXiv2018

Screened Coulombic Orientational Correlations in Dilute Aqueous Electrolytes

The ion-induced long-range orientational order between water molecules recently observed in second harmonic scattering experiments and illustrated with large scale molecular dynamics simulations is quantitatively explained using the Ornstein-Zernike integral equation approach of liquid physics. This general effect, not specific to hydrogen-bonding solvents, is controlled by electroneutrality condition, dipolar interactions and dielectric+ionic screening. As expected, all numerical theories recover the well-known analytical expressions established 40 years ago.

physics.chem-ph↗

arXiv2017

Bridge functional for the molecular density functional theory with consistent pressure and surface tension and its importance for solvation in water

We address the problem of predicting the solvation free energy and equilibrium solvent density profile in fews minutes from the molecular density functional theory beyond the usual hypernetted-chain approximation. We introduce a bridge functional of a coarse-grained, weighted solvent density. In few minutes at most, for solutes of sizes ranging from small compounds to large proteins, we produce (i) an estimation of the free energy of solvation within 1 kcal/mol of the experimental data for the hydrophobic solutes presented here, and (ii) the solvent distribution around the solute. Contrary to previous propositions, this bridge functional is thermodynamically consistent in that it produces the correct liquid-vapor coexistence and the experimental surface tension. We show this consistency to be of crucial importance for water at room temperature and pressure. This bridge functional is designed to be simple, local, and thus numerically efficient. Finally, we illustrate this new level of molecular theory of solutions with the study of the hydration shell of a protein.

physics.chem-ph↗

arXiv2017

Efficient molecular density functional theory using generalized spherical harmonics expansions

We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density $\rho(\mathbf{r},\mathbf{\Omega})$ around the solute is a function of the position $\mathbf{r}\equiv(x,y,z)$ and of the three Euler angles $\mathbf{\Omega}\equiv(\theta,\phi,\psi)$ describing the solvent orientation. The standard density functional, equivalent to the HNC closure for the solute-solvent correlations in the liquid theory, is minimized with respect to $\rho(\mathbf{r},\mathbf{\Omega})$. The up-to-now very expensive angular convolution products are advantageously replaced by simple products between projections onto generalized spherical harmonics. The dramatic gain in speed of resolution enables to explore in a systematic way molecular solutes of up to nanometric sizes in arbitrary solvents and to calculate their solvation free energy and associated microscopic solvent structure in at most a few minutes. We finally illustrate the formalism by tackling the solvation of molecules of various complexity in water.

physics.chem-ph↗

arXiv2016

Molecular density functional theory of water including density-polarization coupling

We present a three-dimensional molecular density functional theory (MDFT) of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: ($i$) a scalar density and a vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and ($ii$) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.

physics.chem-ph↗

arXiv2015

Solvation free-energy pressure corrections in the Three Dimensional Reference Interaction Site Model

Solvation free energies are efficiently predicted by molecular density functionnal theory (MDFT) if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [Sergiievskyi et al., JPCL, 2014, 5, 1935-1942] recently derived the rigorous compensation of this excess of pressure (PC) and proposed an empirical "ideal gas" supplementary correction (PC+) that further enhances the calculated solvation free energies. In a recent paper [Misin et al, JCP, 2015, 142, 091105], those corrections were applied to solvation free energy calculations using the three-dimensional reference interaction site model (3D-RISM). As for classical DFT, PC and PC+ corrections improve greatly the predictions of 3D-RISM, but PC+ is described as decreasing the accuracy. In this article, we first derive rigorously the PC and PC+ corrections for 3D-RISM. We show the reported discrepancy is then taken off by introducing the correct expression of the pressure in 3D-RISM. This provides a consistent way to correct the solvation free-energies calculated by 3D-RISM method.

cond-mat.stat-mech↗

arXiv2015

Pressure Correction in Classical Density Functional Theory: Hyper Netted Chain and Hard Sphere Bridge Functionals

Low accuracy of the Solvation Free Energy (SFE) calculation is a known problem of the numerical methods of the Integral Equation Theory of Liquids and the Classical Density Functional Theory (Classical DFT). Although functionals with empirical corrections can essentially improve the predictability of the methods, their universality is still a question. In our recent paper we connected the SFE calculation errors with the incorrect pressure in the Classical DFT and proposed the a posteriory correction to improve the results (J. Phys. Chem. Lett., 5, 1925-1942 ). This paper raised a discussion in the community. In particular, recently appeared a critical reply where pointed some thermodynamical inconsistencies of the derivations in our paper (J. Chem. Theory Comput., 11, 378-380). In the present work we re-derive the pressure correction in a more simple way and show that despite the inaccuracies during the derivation, the final form of the previously derived correction is correct. We also test the applicability of the proposed correction to the functionals which include a three- and many- body terms from the fundamental measure theory (FMT) for hard sphere fluid. We test all the functionals on a set of model systems and discuss the obtained results.

cond-mat.soft↗

arXiv2015

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.

physics.chem-ph↗