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Kim J, Rotenberg B. Donnan equilibrium in charged slit-pores from a hybrid nonequilibrium molecular dynamics/Monte Carlo method with ions and solvent exchange. J Chem Phys 2024; 161:054107. [PMID: 39087531 DOI: 10.1063/5.0220913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/14/2024] [Indexed: 08/02/2024] Open
Abstract
Ion partitioning between different compartments (e.g., a porous material and a bulk solution reservoir), known as Donnan equilibrium, plays a fundamental role in various contexts such as energy, environment, or water treatment. The linearized Poisson-Boltzmann (PB) equation, capturing the thermal motion of the ions with mean-field electrostatic interactions, is practically useful to understand and predict ion partitioning, despite its limited applicability to conditions of low salt concentrations and surface charge densities. Here, we investigate the Donnan equilibrium of coarse-grained dilute electrolytes confined in charged slit-pores in equilibrium with a reservoir of ions and solvent. We introduce and use an extension to confined systems of a recently developed hybrid nonequilibrium molecular dynamics/grand canonical Monte Carlo simulation method ("H4D"), which enhances the efficiency of solvent and ion-pair exchange via a fourth spatial dimension. We show that the validity range of linearized PB theory to predict the Donnan equilibrium of dilute electrolytes can be extended to highly charged pores by simply considering renormalized surface charge densities. We compare with simulations of implicit solvent models of electrolytes and show that in the low salt concentrations and thin electric double layer limit considered here, an explicit solvent has a limited effect on the Donnan equilibrium and that the main limitations of the analytical predictions are not due to the breakdown of the mean-field description but rather to the charge renormalization approximation, because it only focuses on the behavior far from the surfaces.
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Affiliation(s)
- Jeongmin Kim
- Department of Energy Engineering, Korea Institute of Energy Technology (KENTECH), Naju 58330, Republic of Korea
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens Cedex, France
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Kim J, Belloni L, Rotenberg B. Grand-canonical molecular dynamics simulations powered by a hybrid 4D nonequilibrium MD/MC method: Implementation in LAMMPS and applications to electrolyte solutions. J Chem Phys 2023; 159:144802. [PMID: 37819001 DOI: 10.1063/5.0168878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed phases. A promising method [L. Belloni, J. Chem. Phys. 151, 021101 (2019)], one of the hybrid nonequilibrium molecular dynamics/Monte Carlo algorithms, was recently developed, which enables efficient computation of fluctuating number or charge density in dense fluids or ionic solutions. This method facilitates the exchange through an auxiliary dimension, orthogonal to all physical dimensions, by reducing initial steric and electrostatic clashes in three-dimensional systems. Here, we report the implementation of the method in LAMMPS with a Python interface, allowing facile access to grand-canonical molecular dynamics simulations with massively parallelized computation. We validate our implementation with two electrolytes, including a model Lennard-Jones electrolyte similar to a restricted primitive model and aqueous solutions. We find that electrostatic interactions play a crucial role in the overall efficiency due to their long-range nature, particularly for water or ion-pair exchange in aqueous solutions. With properly screened electrostatic interactions and bias-based methods, our approach enhances the efficiency of salt-pair exchange in Lennard-Jones electrolytes by approximately four orders of magnitude, compared to conventional grand-canonical Monte Carlo. Furthermore, the acceptance rate of NaCl-pair exchange in aqueous solutions at moderate concentrations reaches about 3% at the maximum efficiency.
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Affiliation(s)
- Jeongmin Kim
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
- Réseau sur le Stockage Électrochimique de Énergie (RS2E), FR CNRS 3459, 80039 Amiens Cedex, France
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Hoang Ngoc Minh T, Rotenberg B, Marbach S. Ionic fluctuations in finite volumes: fractional noise and hyperuniformity. Faraday Discuss 2023; 246:225-250. [PMID: 37565454 DOI: 10.1039/d3fd00031a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Observing finite regions of a bigger system is a common aim, from microscopy to molecular simulations. In the latter especially, there is ongoing interest in predicting thermodynamic properties from tracking fluctuations in finite observation volumes. However, kinetic properties have received little attention, especially not in ionic solutions, where electrostatic interactions play a decisive role. Here, we probe ionic fluctuations in finite volumes with Brownian dynamics and build an analytical framework that reproduces our simulation results and is broadly applicable to other systems with pairwise interactions. Particle number and charge correlations exhibit a rich phenomenology with time, characterized by a diversity of timescales. The noise spectrum of both quantities decays as 1/f3/2, where f is the frequency. This signature of fractional noise shows the universality of 1/f3/2 scalings when observing diffusing particles in finite domains. The hyperuniform behaviour of charge fluctuations, namely that correlations scale with the area of the observation volume, is preserved in time. Correlations even become proportional to the box perimeter at sufficiently long times. Our results pave the way to understand fluctuations in more complex systems, from nanopores to single-particle electrochemistry.
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Affiliation(s)
- Thê Hoang Ngoc Minh
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens Cedex, France
| | - Sophie Marbach
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
- Courant Institute of Mathematical Sciences, New York University, NY, 10012, USA.
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Karmakar T, Finney AR, Salvalaglio M, Yazaydin AO, Perego C. Non-Equilibrium Modeling of Concentration-Driven processes with Constant Chemical Potential Molecular Dynamics Simulations. Acc Chem Res 2023; 56:1156-1167. [PMID: 37120847 DOI: 10.1021/acs.accounts.2c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
ConspectusConcentration-driven processes in solution, i.e., phenomena that are sustained by persistent concentration gradients, such as crystallization and surface adsorption, are fundamental chemical processes. Understanding such phenomena is crucial for countless applications, from pharmaceuticals to biotechnology. Molecular dynamics (MD), both in- and out-of-equilibrium, plays an essential role in the current understanding of concentration-driven processes. Computational costs, however, impose drastic limitations on the accessible scale of simulated systems, hampering the effective study of such phenomena. In particular, due to these size limitations, closed system MD of concentration-driven processes is affected by solution depletion/enrichment that unavoidably impacts the dynamics of the chemical phenomena under study. As a notable example, in simulations of crystallization from solution, the transfer of monomers between the liquid and crystal phases results in a gradual depletion/enrichment of solution concentration, altering the driving force for phase transition. In contrast, this effect is negligible in experiments, given the macroscopic size of the solution volume. Because of these limitations, accurate MD characterization of concentration-driven phenomena has proven to be a long-standing simulation challenge. While disparate equilibrium and nonequilibrium simulation strategies have been proposed to address the study of such processes, the methodologies are in continuous development.In this context, a novel simulation technique named constant chemical potential molecular dynamics (CμMD) was recently proposed. CμMD employs properly designed, concentration-dependent external forces that regulate the flux of solute species between selected subregions of the simulation volume. This enables simulations of systems under a constant chemical drive in an efficient and straightforward way. The CμMD scheme was originally applied to the case of crystal growth from solution and then extended to the simulation of various physicochemical processes, resulting in new variants of the method. This Account illustrates the CμMD method and the key advances enabled by it in the framework of in silico chemistry. We review results obtained in crystallization studies, where CμMD allows growth rate calculations and equilibrium shape predictions, and in adsorption studies, where adsorption thermodynamics on porous or solid surfaces was correctly characterized via CμMD. Furthermore, we will discuss the application of CμMD variants to simulate permeation through porous materials, solution separation, and nucleation upon fixed concentration gradients. While presenting the numerous applications of the method, we provide an original and comprehensive assessment of concentration-driven simulations using CμMD. To this end, we also shed light on the theoretical and technical foundations of CμMD, underlining the novelty and specificity of the method with respect to existing techniques while stressing its current limitations. Overall, the application of CμMD to a diverse range of fields provides new insight into many physicochemical processes, the in silico study of which has been hitherto limited by finite-size effects. In this context, CμMD stands out as a general-purpose method that promises to be an invaluable simulation tool for studying molecular-scale concentration-driven phenomena.
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Affiliation(s)
- Tarak Karmakar
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110016, India
| | - Aaron R Finney
- Thomas Young Centre and Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| | - A Ozgur Yazaydin
- Thomas Young Centre and Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, United Kingdom
| | - Claudio Perego
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, via la Santa 1, 6962 Lugano-Viganello, Switzerland
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Borgis D, Luukkonen S, Belloni L, Jeanmairet G. Accurate prediction of hydration free energies and solvation structures using molecular density functional theory with a simple bridge functional. J Chem Phys 2021; 155:024117. [PMID: 34266282 DOI: 10.1063/5.0057506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper assesses the ability of molecular density functional theory to predict efficiently and accurately the hydration free energies of molecular solutes and the surrounding microscopic water structure. A wide range of solutes were investigated, including hydrophobes, water as a solute, and the FreeSolv database containing 642 drug-like molecules having a variety of shapes and sizes. The usual second-order approximation of the theory is corrected by a third-order, angular-independent bridge functional. The overall functional is parameter-free in the sense that the only inputs are bulk water properties, independent of the solutes considered. These inputs are the direct correlation function, compressibility, liquid-gas surface tension, and excess chemical potential of the solvent. Compared to molecular simulations with the same force field and the same fixed solute geometries, the present theory is shown to describe accurately the solvation free energy and structure of both hydrophobic and hydrophilic solutes. Overall, the method yields a precision of order 0.5 kBT for the hydration free energies of the FreeSolv database, with a computer speedup of 3 orders of magnitude. The theory remains to be improved for a better description of the H-bonding structure and the hydration free energy of charged solutes.
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Affiliation(s)
- Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Luc Belloni
- Universié Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Guillaume Jeanmairet
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
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Borgis D, Luukkonen S, Belloni L, Jeanmairet G. Simple Parameter-Free Bridge Functionals for Molecular Density Functional Theory. Application to Hydrophobic Solvation. J Phys Chem B 2020; 124:6885-6893. [DOI: 10.1021/acs.jpcb.0c04496] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, 91191, France
| | - Guillaume Jeanmairet
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, Paris, F-75005, France
- Réseau sur le Stockage Électrochimique de l’Énergie, CNRS FR3459, 33 rue Saint Leu, Amiens, Cedex 80039, France
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Luukkonen S, Belloni L, Borgis D, Levesque M. Predicting Hydration Free Energies of the FreeSolv Database of Drug-like Molecules with Molecular Density Functional Theory. J Chem Inf Model 2020; 60:3558-3565. [DOI: 10.1021/acs.jcim.0c00526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sohvi Luukkonen
- Maison de la Simulation, CNRS-CEA-Université Paris-Saclay, Gif-sur-Yvette 91191, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91191 France
| | - Daniel Borgis
- Maison de la Simulation, CNRS-CEA-Université Paris-Saclay, Gif-sur-Yvette 91191, France
- PASTEUR, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris 75005, France
| | - Maximilien Levesque
- PASTEUR, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris 75005, France
- Aqemia, Paris 75001, France
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Robert A, Luukkonen S, Levesque M. Pressure correction for solvation theories. J Chem Phys 2020; 152:191103. [DOI: 10.1063/5.0002029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Anton Robert
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Sohvi Luukkonen
- Maison de la Simulation, CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Maximilien Levesque
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
- Aqemia, Paris, France
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Luukkonen S, Levesque M, Belloni L, Borgis D. Hydration free energies and solvation structures with molecular density functional theory in the hypernetted chain approximation. J Chem Phys 2020; 152:064110. [DOI: 10.1063/1.5142651] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Maximilien Levesque
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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