1
|
O’Neill N, Shi BX, Fong K, Michaelides A, Schran C. To Pair or not to Pair? Machine-Learned Explicitly-Correlated Electronic Structure for NaCl in Water. J Phys Chem Lett 2024; 15:6081-6091. [PMID: 38820256 PMCID: PMC11181334 DOI: 10.1021/acs.jpclett.4c01030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
The extent of ion pairing in solution is an important phenomenon to rationalize transport and thermodynamic properties of electrolytes. A fundamental measure of this pairing is the potential of mean force (PMF) between solvated ions. The relative stabilities of the paired and solvent shared states in the PMF and the barrier between them are highly sensitive to the underlying potential energy surface. However, direct application of accurate electronic structure methods is challenging, since long simulations are required. We develop wave function based machine learning potentials with the random phase approximation (RPA) and second order Møller-Plesset (MP2) perturbation theory for the prototypical system of Na and Cl ions in water. We show both methods in agreement, predicting the paired and solvent shared states to have similar energies (within 0.2 kcal/mol). We also provide the same benchmarks for different DFT functionals as well as insight into the PMF based on simple analyses of the interactions in the system.
Collapse
Affiliation(s)
- Niamh O’Neill
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United
Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Benjamin X. Shi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Kara Fong
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Angelos Michaelides
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Christoph Schran
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United
Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| |
Collapse
|
2
|
Yue S, Wang L, Li N, Wan Y, Huo X, Wang X, Yang M, Zhang L. Solubility evolution of elemental sulfur in natural gas with a varying H 2S content. J Mol Model 2024; 30:149. [PMID: 38664312 DOI: 10.1007/s00894-024-05947-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
CONTEXT The solubility variations of elemental sulfur are of great importance in the prevention of sulfur deposition during the development of high-sulfur gas formations. It has been observed that the solubility varies with H2S content, which is the main solvent of elemental sulfur in natural gas. Moreover, the addition of small amounts of CH4 and/or CO2 in H2S leads to a dramatic solubility reduction of which the mechanism remains unclear. Using a modified direct coexistence method, molecular dynamics simulations are conducted to uncover the molecular mechanism of the solubility reduction. The observed solubility variations with H2S content are reproduced, and the solubility reduction is interpreted by the antisolvent effect of CH4 and CO2. While the H2S content varies in a wide range in the known high-sulfur gas formation, our simulations provide useful information for controlling the sulfur deposition in gas development. METHODS Molecular dynamics simulations are carried out using the LAMMPS package. The initial models are constructed with the Packmol software. The Ballone and Jones' potential is used for S8, the Galliero's potential for H2S and CO2, and the transferable potentials for phase equilibria-united atom (TraPPE-UA) force field for CH4. The time step is set to 1 fs, and the molecular trajectories of additional 2 ns after equilibrium are collected for analysis.
Collapse
Affiliation(s)
- Shuangli Yue
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
| | - Li Wang
- Research Institute of Exploration and Development, PetroChina Southwest Oil and Gasfield Company, Chengdu, 610213, China.
| | - Nong Li
- Research Institute of Exploration and Development, PetroChina Southwest Oil and Gasfield Company, Chengdu, 610213, China
| | - Ying Wan
- Research Institute of Exploration and Development, PetroChina Southwest Oil and Gasfield Company, Chengdu, 610213, China
| | - Xiangyu Huo
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
| | - Xian Wang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Mingli Yang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
| | - Li Zhang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China.
| |
Collapse
|
3
|
Fernández-Fernández ÁM, Bárcena Á, Conde MM, Pérez-Sánchez G, Pérez-Rodríguez M, Piñeiro MM. Modeling oceanic sedimentary methane hydrate growth through molecular dynamics simulation. J Chem Phys 2024; 160:144107. [PMID: 38591679 DOI: 10.1063/5.0203116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/23/2024] [Indexed: 04/10/2024] Open
Abstract
The crystallization process of methane hydrates in a confined geometry resembling seabed porous silica sedimentary conditions has been studied using molecular dynamics simulations. With this objective in mind, a fully atomistic quartz silica slit pore has been designed, and the temperature stability of a methane hydrate crystalline seed in the presence of water and guest molecule methane has been analyzed. NaCl ion pairs have been added in different concentrations, simulating salinity conditions up to values higher than average oceanic conditions. The structure obtained when the hydrate crystallizes inside the pore is discussed, paying special attention to the presence of ionic doping inside the hydrate and the subsequent induced structural distortion. The shift in the hydrate stability conditions due to the increasing water salinity is discussed and compared with the case of unconfined hydrate, concluding that the influence of the confinement geometry and pore hydrophilicity produces a larger deviation in the confined hydrate phase equilibria.
Collapse
Affiliation(s)
| | - Álvaro Bárcena
- Dpto. de Física Aplicada, Univ. de Vigo, Vigo 36310, Spain
| | - María M Conde
- Dpto. de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, Madrid 28006, Spain
| | | | | | | |
Collapse
|
4
|
Finney AR, Salvalaglio M. Properties of aqueous electrolyte solutions at carbon electrodes: effects of concentration and surface charge on solution structure, ion clustering and thermodynamics in the electric double layer. Faraday Discuss 2024; 249:334-362. [PMID: 37781909 DOI: 10.1039/d3fd00133d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Surfaces are able to control physical-chemical processes in multi-component solution systems and, as such, find application in a wide range of technological devices. Understanding the structure, dynamics and thermodynamics of non-ideal solutions at surfaces, however, is particularly challenging. Here, we use Constant Chemical Potential Molecular Dynamics (CμMD) simulations to gain insight into aqueous NaCl solutions in contact with graphite surfaces at high concentrations and under the effect of applied surface charges: conditions where mean-field theories describing interfaces cannot (typically) be reliably applied. We discover an asymmetric effect of surface charge on the electric double layer structure and resulting thermodynamic properties, which can be explained by considering the affinity of the surface for cations and anions and the cooperative adsorption of ions that occurs at higher concentrations. We characterise how the sign of the surface charge affects ion densities and water structure in the double layer and how the capacitance of the interface-a function of the electric potential drop across the double layer-is largely insensitive to the bulk solution concentration. Notably, we find that negatively charged graphite surfaces induce an increase in the size and concentration of extended liquid-like ion clusters confined to the double layer. Finally, we discuss how concentration and surface charge affect the activity coefficients of ions and water at the interface, demonstrating how electric fields in this region should be explicitly considered when characterising the thermodynamics of both solute and solvent at the solid/liquid interface.
Collapse
Affiliation(s)
- Aaron R Finney
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, UK.
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, UK.
| |
Collapse
|
5
|
Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. J Chem Phys 2023; 159:184110. [PMID: 37962445 DOI: 10.1063/5.0173341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.
Collapse
Affiliation(s)
- Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Bingqing Cheng
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| |
Collapse
|
6
|
Sun Y, Zhang D, Bashir A, Li C, Fan Z. Scaling Solute-Solvent Distances to Improve Solubility and Ion Paring Predictions in Rigid Ion Models. J Phys Chem B 2023; 127:9575-9586. [PMID: 37906589 DOI: 10.1021/acs.jpcb.3c05993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Force fields based on the rigid ion model (RIM) have been developed to accurately predict the various physical and chemical properties of salts and water. However, the combined use of these models often fails to accurately predict the solubility of salts in water. To address this issue, several approaches, such as charge scaling or reparameterization, have been proposed. Nevertheless, these methods require laborious reparameterization of nonbonded force field parameters. In this article, we propose a scaling solute-solvent distance (SSSD) method to improve force fields in predicting salt solubility without changing the solute-solute and solvent-solvent interactions in the original force fields. This method can also tune the ion pairing of salt in water. One main advantage of the SSSD method is that reparameterization of the crystal and water models is not needed. We use two RIMs for the NaCl-water system (JC-SPC/E and SD-SPC/E) and the CHARMM force field for the KCl-water system to demonstrate the improved accuracy in predicting solubility by the SSSD method. Furthermore, we use the RDG-SPC/Fw force field to show that the SSSD method can also be used to tune the ion pairing of CaCO3 in water. Limitations of this method are also discussed.
Collapse
Affiliation(s)
- Ying Sun
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Dan Zhang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- Department of Chemistry, Shanghai University, Shanghai 200444, P. R. China
| | - Ayesha Bashir
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Chuncheng Li
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Zhaochuan Fan
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, P. R. China
| |
Collapse
|
7
|
Li M, Lv L, Fang T, Hao L, Li S, Dong S, Wu Y, Dong X, Liu H. Self-Consistent Implementation of a Solvation Free Energy Framework to Predict the Salt Solubilities of Six Alkali Halides. J Chem Theory Comput 2023; 19:5586-5601. [PMID: 37471389 DOI: 10.1021/acs.jctc.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
To assess the salt solubilities of six alkali halides in aqueous systems, we proposed a thermodynamic cycle and an efficient molecular modeling methodology. The Gibbs free energy changes for vaporization, dissociation, and dissolution were calculated using the experimental data of ionic thermodynamic properties obtained from the NBS tables. Additionally, the Marcus' and Tissandier's solvation free energy data for Li+, Na+, K+, Cl-, and Br- ions were compared with the conventional solvation free energies by substituting into our self-consistent thermodynamic cycle. Furthermore, Tissandier's absolute solvation free energy data were used as the training set to refit the Lennard-Jones parameters of OPLS-AA force field for ions. To predict salt solubilities, an assumption of a pseudo-solvent was proposed to characterize the coupling work of a solute with its environment from infinitely diluted to saturated solutions, indicating that the Gibbs energy change of solvation process is a function of ionic strength. Following the self-consistency of the cycle, the newly derived formulas were used to determine the salt solubilities by interpolating the intersection of Gibbs free energy of dissolution and the zero free energy line. The refined ion parameters can also predict the structure and thermodynamic properties of aqueous electrolyte solutions, such as densities, pair correlation functions, hydration numbers, mean activity coefficients, vapor pressures, and the radial dependences of the net charge at 298.15 K and 1 bar. Our method can be used to characterize the solid-liquid equilibria of ions or charged particles in aqueous systems. Furthermore, for highly concentrated strong electrolyte systems, it is essential to introduce accurate water models and polarizable force fields.
Collapse
Affiliation(s)
- Miyi Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Liqiang Lv
- College of Chemical Engineering, Shijiazhuang University, Hebei, Shijiazhuang 050035, China
| | - Tao Fang
- Beijing Institute of Aerospace Testing Technology, Beijing 100074, China
| | - Long Hao
- Beijing Institute of Aerospace Testing Technology, Beijing 100074, China
| | - Shenhui Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Shoulong Dong
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Yufeng Wu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Xiao Dong
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Helei Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
- Key Laboratory of Low-Carbon Conversion Science & Engineering, Shanghai Advanced Research Institute, Chinese Academy of Sciences (Shanghai Advanced Research Institute, Chinese Academy of Sciences), Shanghai 201210, China
| |
Collapse
|
8
|
Saha D, Jana B. Decoupling of Interactions between Model-Charged Peptides Reveals Key Factors Responsible for Liquid-Liquid Phase Separation. J Phys Chem B 2023; 127:6656-6667. [PMID: 37480340 DOI: 10.1021/acs.jpcb.3c03087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Liquid-liquid phase separation (LLPS) by disordered proteins has been shown to govern biological processes and cause numerous diseases. Therefore, a deeper understanding of the interactions and their variation with external factors is key to modulating the LLPS behavior of different systems and protecting proteins from pathological aggregation. In this context, we have looked at interactions between similarly charged peptides to understand the molecular features that may drive or prevent condensate formation under various conditions. We have studied dimer formation for model peptides where charged and noncharged amino acids have been placed alternatively. Using arginine and glutamic acid as the charged residues and varying the other residues with glycine, alanine, and proline to alter hydrophobicity, we have obtained the free-energy surface (FES) for the dimer formation for these systems under high salt concentration at two different temperatures using all-atom molecular dynamics simulations and the well-tempered metadynamics method. Our results indicate that a combination of effects such as hydrophobicity, arginine-arginine interactions, or water release from the solvation shell makes dimerization free energy more favorable for the positively charged peptides with lower flexibility. For the negatively charged peptides, the crucial role of water has been found in governing the FES. Systems having charged residues and phenylalanine in the peptide sequence also have been studied at high salt concentrations using unbiased simulations. In this case, only the positively charged peptides were found to aggregate through temperature-dependent hydrophobic and cation-π interactions. Overall, our study indicates that the negatively charged peptides are more likely to remain in the dilute phase under various conditions compared to the positively charged systems. The findings from our study would be helpful in designing and controlling systems to obtain LLPS behavior for therapeutic usage.
Collapse
Affiliation(s)
- Debasis Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| |
Collapse
|
9
|
Sanchez-Burgos I, Muniz MC, Espinosa JR, Panagiotopoulos AZ. A Deep Potential model for liquid-vapor equilibrium and cavitation rates of water. J Chem Phys 2023; 158:2889532. [PMID: 37158636 DOI: 10.1063/5.0144500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/30/2023] [Indexed: 05/10/2023] Open
Abstract
Computational studies of liquid water and its phase transition into vapor have traditionally been performed using classical water models. Here, we utilize the Deep Potential methodology-a machine learning approach-to study this ubiquitous phase transition, starting from the phase diagram in the liquid-vapor coexistence regime. The machine learning model is trained on ab initio energies and forces based on the SCAN density functional, which has been previously shown to reproduce solid phases and other properties of water. Here, we compute the surface tension, saturation pressure, and enthalpy of vaporization for a range of temperatures spanning from 300 to 600 K and evaluate the Deep Potential model performance against experimental results and the semiempirical TIP4P/2005 classical model. Moreover, by employing the seeding technique, we evaluate the free energy barrier and nucleation rate at negative pressures for the isotherm of 296.4 K. We find that the nucleation rates obtained from the Deep Potential model deviate from those computed for the TIP4P/2005 water model due to an underestimation in the surface tension from the Deep Potential model. From analysis of the seeding simulations, we also evaluate the Tolman length for the Deep Potential water model, which is (0.091 ± 0.008) nm at 296.4 K. Finally, we identify that water molecules display a preferential orientation in the liquid-vapor interface, in which H atoms tend to point toward the vapor phase to maximize the enthalpic gain of interfacial molecules. We find that this behavior is more pronounced for planar interfaces than for the curved interfaces in bubbles. This work represents the first application of Deep Potential models to the study of liquid-vapor coexistence and water cavitation.
Collapse
Affiliation(s)
- Ignacio Sanchez-Burgos
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue,Cambridge CB3 0HE, United Kingdom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Maria Carolina Muniz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue,Cambridge CB3 0HE, United Kingdom
- Departamento de Química Fisica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | |
Collapse
|
10
|
Sanchez-Burgos I, Espinosa JR. Direct Calculation of the Interfacial Free Energy between NaCl Crystal and Its Aqueous Solution at the Solubility Limit. PHYSICAL REVIEW LETTERS 2023; 130:118001. [PMID: 37001068 DOI: 10.1103/physrevlett.130.118001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 06/19/2023]
Abstract
Salty water is the most abundant electrolyte aqueous mixture on Earth, however, very little is known about the NaCl-saturated solution interfacial free energy (γ_{s}). Here, we provide the first direct estimation of γ_{s} for several NaCl crystallographic planes by means of the mold integration technique, a highly efficient computational method to evaluate interfacial free energies with anisotropic crystal resolution. Making use of the JC-SPC/E model, one of the most benchmarked force fields for NaCl water solutions, we measure γ_{s} of four different crystal planes, (100), (110), (111), and (112[over ¯]) with the saturated solution at normal conditions. We find high anisotropy between the different crystal orientations with values ranging from 100 to 150 mJ m^{-2}, and the average value of the distinct planes being γ[over ¯]_{s}=137(20) mJ m^{-2}. This value for the coexistence interfacial free energy is in reasonable agreement with previous extrapolations from nucleation studies. Our Letter represents a milestone in the computational calculation of interfacial free energies between ionic crystals and aqueous solutions.
Collapse
Affiliation(s)
- Ignacio Sanchez-Burgos
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| |
Collapse
|
11
|
Tong J, Peng B, Kontogeorgis GM, Liang X. Behavior of the aqueous sodium chloride solutions from molecular simulations and theories. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2022.121086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
12
|
Khanna V, Doherty MF, Peters B. Predicting solubility and driving forces for crystallization using the absolute chemical potential route. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2155595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Vikram Khanna
- Deptartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Michael F. Doherty
- Deptartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Baron Peters
- Deptartment of Chemical & Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Deptartment of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
13
|
Kournopoulos S, Santos MS, Ravipati S, Haslam AJ, Jackson G, Economou IG, Galindo A. The Contribution of the Ion-Ion and Ion-Solvent Interactions in a Molecular Thermodynamic Treatment of Electrolyte Solutions. J Phys Chem B 2022; 126:9821-9839. [PMID: 36395498 PMCID: PMC9720728 DOI: 10.1021/acs.jpcb.2c03915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Developing molecular equations of state to treat electrolyte solutions is challenging due to the long-range nature of the Coulombic interactions. Seminal approaches commonly used are the mean spherical approximation (MSA) and the Debye-Hückel (DH) theory to account for ion-ion interactions and, often, the Born theory of solvation for ion-solvent interactions. We investigate the accuracy of the MSA and DH approaches using each to calculate the contribution of the ion-ion interactions to the chemical potential of NaCl in water, comparing these with newly computer-generated simulation data; the ion-ion contribution is isolated by selecting an appropriate primitive model with a Lennard-Jones force field to describe the solvent. A study of mixtures with different concentrations and ionic strengths reveals that the calculations from both MSA and DH theories are of similar accuracy, with the MSA approach resulting in marginally better agreement with the simulation data. We also demonstrate that the Born theory provides a good qualitative description of the contribution of the ion-solvent interactions; we employ an explicitly polar water model in these simulations. Quantitative agreement up to moderate salt concentrations and across the relevant range of temperature is achieved by adjusting the Born radius using simulation data of the free energy of solvation. We compute the radial and orientational distribution functions of the systems, thereby providing further insight on the differences observed between the theory and simulation. We thus provide rigorous benchmarks for use of the MSA, DH, and Born theories as perturbation approaches, which will be of value for improving existing models of electrolyte solutions, especially in the context of equations of state.
Collapse
Affiliation(s)
- Spiros Kournopoulos
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering,
and Institute for Molecular Science and Engineering, Imperial College, London, London SW7 2AZ, United Kingdom
| | - Mirella Simões Santos
- Laboratoire
de Chimie, École Normale Supérieure
de Lyon, 46 Allée d’Italie, 69364 Lyon, France,Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Srikanth Ravipati
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering,
and Institute for Molecular Science and Engineering, Imperial College, London, London SW7 2AZ, United Kingdom
| | - Andrew J. Haslam
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering,
and Institute for Molecular Science and Engineering, Imperial College, London, London SW7 2AZ, United Kingdom
| | - George Jackson
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering,
and Institute for Molecular Science and Engineering, Imperial College, London, London SW7 2AZ, United Kingdom
| | - Ioannis G. Economou
- Chemical
Engineering Program, Texas A&M University
at Qatar, Doha 23874, Qatar
| | - Amparo Galindo
- Department
of Chemical Engineering, Sargent Centre for Process Systems Engineering,
and Institute for Molecular Science and Engineering, Imperial College, London, London SW7 2AZ, United Kingdom,
| |
Collapse
|
14
|
Hydrophobicity of arginine leads to reentrant liquid-liquid phase separation behaviors of arginine-rich proteins. Nat Commun 2022; 13:7326. [PMID: 36443315 PMCID: PMC9705477 DOI: 10.1038/s41467-022-35001-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022] Open
Abstract
Intrinsically disordered proteins rich in cationic amino acid groups can undergo Liquid-Liquid Phase Separation (LLPS) in the presence of charge-balancing anionic counterparts. Arginine and Lysine are the two most prevalent cationic amino acids in proteins that undergo LLPS, with arginine-rich proteins observed to undergo LLPS more readily than lysine-rich proteins, a feature commonly attributed to arginine's ability to form stronger cation-π interactions with aromatic groups. Here, we show that arginine's ability to promote LLPS is independent of the presence of aromatic partners, and that arginine-rich peptides, but not lysine-rich peptides, display re-entrant phase behavior at high salt concentrations. We further demonstrate that the hydrophobicity of arginine is the determining factor giving rise to the reentrant phase behavior and tunable viscoelastic properties of the dense LLPS phase. Controlling arginine-induced reentrant LLPS behavior using temperature and salt concentration opens avenues for the bioengineering of stress-triggered biological phenomena and drug delivery systems.
Collapse
|
15
|
Silvestri A, Raiteri P, Gale JD. Obtaining Consistent Free Energies for Ion Binding at Surfaces from Solution: Pathways versus Alchemy for Determining Kink Site Stability. J Chem Theory Comput 2022; 18:5901-5919. [PMID: 36073829 DOI: 10.1021/acs.jctc.2c00787] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion incorporation or removal from a solid at the interface with solution is a fundamental part of crystal growth. Despite this, there have been few quantitative determinations of the thermodynamics for such processes from atomistic molecular dynamics due to the associated technical challenges. In this study, we compute the free energies for ion removal from kink sites at the interface between NaCl and water as an illustrative example. To examine the influence of the free energy technique used, we compare methods that follow an explicit pathway for dissolution with those that focus on the thermodynamics of the initial and final states using metadynamics and free energy perturbation, respectively. While the initial results of the two approaches are found to be completely different, it is demonstrated that the thermodynamics can be reconciled with appropriate corrections for the standard states, thus illustrating the need for caution in interpreting raw free energy curves for ion binding as widely found in the literature. In addition, a new efficient approach is introduced to correct for the system size dependence of kink site energies both due to the periodic interaction of charges in an inhomogeneous dielectric system and due to the dipolar interactions between pairs of kinks along a row. Ultimately, it is shown that with suitable care, both classes of free energy techniques are capable of producing kink site stabilities that are consistent with the solubility of the underlying bulk solid. However, the precise values for individual kink sites exhibit a small systematic offset, which can be ascribed to the contribution of the interfacial potential to the pathway-based results. For the case of NaCl, the free energies of the kink sites relative to a 1 M aqueous solution for Na+ and Cl- are found to be surprisingly different and of opposite sign, despite the ions having very similar hydration free energies.
Collapse
Affiliation(s)
- Alessandro Silvestri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| |
Collapse
|
16
|
Cheng B. Computing chemical potentials of solutions from structure factors. J Chem Phys 2022; 157:121101. [DOI: 10.1063/5.0107059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The chemical potential of a component in a solution is defined as the free energy change as the amount of the component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult, because of the convergence issues in free energy methods and finite size effects. This paper presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal-isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea--water mixtures, a NaCl aqueous solution, and a high-pressure carbon-hydrogen mixture.
Collapse
|
17
|
Saravi SH, Panagiotopoulos AZ. Activity Coefficients and Solubilities of NaCl in Water-Methanol Solutions from Molecular Dynamics Simulations. J Phys Chem B 2022; 126:2891-2898. [PMID: 35411772 DOI: 10.1021/acs.jpcb.2c00813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We obtain activity coefficients and solubilities of NaCl in water-methanol solutions at 298.15 K and 1 bar from molecular dynamics (MD) simulations with the Joung-Cheatham, SPC/E, and OPLS-AA force fields for NaCl, water, and methanol, respectively. The Lorentz-Berthelot combining rules were adopted for the unlike-pair interactions of Na+, Cl-, and the oxygen site in SPC/E water, and geometric combining rules were utilized for the remainder of the cross interactions. We found that the selection of appropriate combining rules is important in obtaining physically realistic solubilities. The solvent compositions studied range from pure water to pure methanol. Several salt concentrations were investigated at each solvent composition, from the lowest concentrations permitted by the system size used up to the experimental solubilities. We first calculated individual ion activity coefficients (IIACs) for Na+ and Cl- from the free energy change due to the gradual insertion of a single cation or anion into the solution, accompanied by a neutralizing background. We obtained the salt solubilities by comparing the chemical potentials in solution with solid NaCl chemical potentials calculated previously using the Einstein crystal method. Mean ionic activity coefficients obtained from the IIACs are in reasonable agreement with experimental data, with deviations increasing for solutions of higher methanol content. Predictions for the salt solubility are in surprisingly good agreement with experimental data, despite well-known challenges in the simultaneous calculation of activity coefficients and solubilities with classical MD simulations. The present study demonstrates that good predictions for these two important phase equilibrium properties can be obtained for mixed-solvent electrolyte solutions using existing nonpolarizable models and further suggests that the previously proposed single ion insertion technique can be extended to complex mixed-solvent solutions as well.
Collapse
Affiliation(s)
- Sina Hassanjani Saravi
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | | |
Collapse
|
18
|
Bulutoglu PS, Wang S, Boukerche M, Nere NK, Corti DS, Ramkrishna D. An investigation of the kinetics and thermodynamics of NaCl nucleation through composite clusters. PNAS NEXUS 2022; 1:pgac033. [PMID: 36713321 PMCID: PMC9802385 DOI: 10.1093/pnasnexus/pgac033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/04/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023]
Abstract
Having a good understanding of nucleation is critical for the control of many important processes, such as polymorph selection during crystallization. However, a complete picture of the molecular-level mechanisms of nucleation remains elusive. In this work, we take an in-depth look at the NaCl homogeneous nucleation mechanism through thermodynamics. Distinguished from the classical nucleation theory, we calculate the free energy of nucleation as a function of two nucleus size coordinates: crystalline and amorphous cluster sizes. The free energy surface reveals a thermodynamic preference for a nonclassical mechanism of nucleation through a composite cluster, where the crystalline nucleus is surrounded by an amorphous layer. The thickness of the amorphous layer increases with an increase in supersaturation. The computed free energy landscape agrees well with the composite cluster-free energy model, through which phase specific thermodynamic properties are evaluated. As the supersaturation increases, there is a change in stability of the amorphous phase relative to the solution phase, resulting in a change from one-step to two-step mechanism, seen clearly from the free energy profile along the minimum free energy path crossing the transition curve. By obtaining phase-specific diffusion coefficients, we construct the full mesoscopic model and present a clear roadmap for NaCl nucleation.
Collapse
Affiliation(s)
- Pelin S Bulutoglu
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
| | - Shiyan Wang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
| | - Moussa Boukerche
- Process Research and Development , AbbVie Inc, North Chicago, IL 60064, USA
| | - Nandkishor K Nere
- Process Research and Development , AbbVie Inc, North Chicago, IL 60064, USA
| | - David S Corti
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907-2100, USA
| | | |
Collapse
|
19
|
Bianco V, Conde MM, Lamas CP, Noya EG, Sanz E. Phase diagram of the NaCl–water system from computer simulations. J Chem Phys 2022; 156:064505. [DOI: 10.1063/5.0083371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- V. Bianco
- Departamento de Química Física (Unidad de I+D+i asociada al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - M. M. Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
| | - C. P. Lamas
- Departamento de Química Física (Unidad de I+D+i asociada al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - E. G. Noya
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - E. Sanz
- Departamento de Química Física (Unidad de I+D+i asociada al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| |
Collapse
|
20
|
Finney AR, Salvalaglio M. Bridging the gap between mesoscopic and molecular models of solid/liquid interfaces out-of-equilibrium. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2022.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
21
|
Blazquez S, Conde MM, Abascal JLF, Vega C. The Madrid-2019 force field for electrolytes in water using TIP4P/2005 and scaled charges: Extension to the ions F−, Br−, I−, Rb+, and Cs+. J Chem Phys 2022; 156:044505. [DOI: 10.1063/5.0077716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- S. Blazquez
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - M. M. Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006 Madrid, Spain
| | - J. L. F. Abascal
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C. Vega
- Departamento Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| |
Collapse
|
22
|
P Lamas C, R Espinosa J, M Conde M, Ramírez J, Montero de Hijes P, G Noya E, Vega C, Sanz E. Homogeneous nucleation of NaCl in supersaturated solutions. Phys Chem Chem Phys 2021; 23:26843-26852. [PMID: 34817484 DOI: 10.1039/d1cp02093e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The seeding method is an approximate approach to investigate nucleation that combines molecular dynamics simulations with classical nucleation theory. Recently, this technique has been successfully implemented in a broad range of nucleation studies. However, its accuracy is subject to the arbitrary choice of the order parameter threshold used to distinguish liquid-like from solid-like molecules. We revisit here the crystallization of NaCl from a supersaturated brine solution and show that consistency between seeding and rigorous methods, like Forward Flux Sampling (from previous work) or spontaneous crystallization (from this work), is achieved by following a mislabelling criterion to select such threshold (i.e. equaling the fraction of the mislabelled particles in the bulk parent and nucleating phases). This work supports the use of seeding to obtain fast and reasonably accurate nucleation rate estimates and the mislabelling criterion as one giving the relevant cluster size for classical nucleation theory in crystallization studies.
Collapse
Affiliation(s)
- C P Lamas
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain. .,Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - J R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0H3, UK
| | - M M Conde
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006, Madrid, Spain
| | - J Ramírez
- Departamento de Ingeniería Química Industrial y Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, 28006, Madrid, Spain
| | - P Montero de Hijes
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - E G Noya
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, CSIC, Calle Serrano 119, 28006 Madrid, Spain
| | - C Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - E Sanz
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| |
Collapse
|
23
|
Joseph JA, Reinhardt A, Aguirre A, Chew PY, Russell KO, Espinosa JR, Garaizar A, Collepardo-Guevara R. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. NATURE COMPUTATIONAL SCIENCE 2021; 1:732-743. [PMID: 35795820 PMCID: PMC7612994 DOI: 10.1038/s43588-021-00155-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Various physics- and data-driven sequence-dependent protein coarse-grained models have been developed to study biomolecular phase separation and elucidate the dominant physicochemical driving forces. Here, we present Mpipi, a multiscale coarse-grained model that describes almost quantitatively the change in protein critical temperatures as a function of amino-acid sequence. The model is parameterised from both atomistic simulations and bioinformatics data and accounts for the dominant role of π-π and hybrid cation-π/π-π interactions and the much stronger attractive contacts established by arginines than lysines. We provide a comprehensive set of benchmarks for Mpipi and seven other residue-level coarse-grained models against experimental radii of gyration and quantitative in-vitro phase diagrams; Mpipi predictions agree well with experiment on both fronts. Moreover, it can account for protein-RNA interactions, correctly predicts the multiphase behaviour of a charge-matched poly-arginine/poly-lysine/RNA system, and recapitulates experimental LLPS trends for sequence mutations on FUS, DDX4 and LAF-1 proteins.
Collapse
Affiliation(s)
- Jerelle A. Joseph
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Anne Aguirre
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Kieran O. Russell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Jorge R. Espinosa
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Adiran Garaizar
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| |
Collapse
|
24
|
Finney AR, McPherson IJ, Unwin PR, Salvalaglio M. Electrochemistry, ion adsorption and dynamics in the double layer: a study of NaCl(aq) on graphite. Chem Sci 2021; 12:11166-11180. [PMID: 34522314 PMCID: PMC8386640 DOI: 10.1039/d1sc02289j] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/14/2021] [Indexed: 12/18/2022] Open
Abstract
Graphite and related sp2 carbons are ubiquitous electrode materials with particular promise for use in e.g., energy storage and desalination devices, but very little is known about the properties of the carbon–electrolyte double layer at technologically relevant concentrations. Here, the (electrified) graphite–NaCl(aq) interface was examined using constant chemical potential molecular dynamics (CμMD) simulations; this approach avoids ion depletion (due to surface adsorption) and maintains a constant concentration, electroneutral bulk solution beyond the surface. Specific Na+ adsorption at the graphite basal surface causes charging of the interface in the absence of an applied potential. At moderate bulk concentrations, this leads to accumulation of counter-ions in a diffuse layer to balance the effective surface charge, consistent with established models of the electrical double layer. Beyond ∼0.6 M, however, a combination of over-screening and ion crowding in the double layer results in alternating compact layers of charge density perpendicular to the interface. The transition to this regime is marked by an increasing double layer size and anomalous negative shifts to the potential of zero charge with incremental changes to the bulk concentration. Our observations are supported by changes to the position of the differential capacitance minimum measured by electrochemical impedance spectroscopy, and are explained in terms of the screening behaviour and asymmetric ion adsorption. Furthermore, a striking level of agreement between the differential capacitance from solution evaluated in simulations and measured in experiments allows us to critically assess electrochemical capacitance measurements which have previously been considered to report simply on the density of states of the graphite material at the potential of zero charge. Our work shows that the solution side of the double layer provides the more dominant contribution to the overall measured capacitance. Finally, ion crowding at the highest concentrations (beyond ∼5 M) leads to the formation of liquid-like NaCl clusters confined to highly non-ideal regions of the double layer, where ion diffusion is up to five times slower than in the bulk. The implications of changes to the speciation of ions on reactive events in the double layer are discussed. CμMD reveals multi-layer electrolyte screening in the double layer beyond 0.6 M, which affects ion activities, speciation and mobility; asymmetric charge screening explains concentration dependent changes to electrochemical properties.![]()
Collapse
Affiliation(s)
- Aaron R Finney
- Thomas Young Centre and Department of Chemical Engineering, University College London London WC1E 7JE UK
| | - Ian J McPherson
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Patrick R Unwin
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London London WC1E 7JE UK
| |
Collapse
|
25
|
Polat HM, Salehi HS, Hens R, Wasik DO, Rahbari A, de Meyer F, Houriez C, Coquelet C, Calero S, Dubbeldam D, Moultos OA, Vlugt TJH. New Features of the Open Source Monte Carlo Software Brick-CFCMC: Thermodynamic Integration and Hybrid Trial Moves. J Chem Inf Model 2021; 61:3752-3757. [PMID: 34383501 PMCID: PMC8385706 DOI: 10.1021/acs.jcim.1c00652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We present several
new major features added to the Monte Carlo
(MC) simulation code Brick-CFCMC for phase- and reaction equilibria
calculations (https://gitlab.com/ETh_TU_Delft/Brick-CFCMC). The first one
is thermodynamic integration for the computation of excess chemical
potentials (μex). For this purpose, we implemented
the computation of the ensemble average of the derivative of the potential
energy with respect to the scaling factor for intermolecular interactions
(). Efficient bookkeeping is implemented
so that the quantity is updated after every MC trial
move with
negligible computational cost. We demonstrate the accuracy and reliability
of the calculation of μex for sodium chloride in
water. Second, we implemented hybrid MC/MD translation and rotation
trial moves to increase the efficiency of sampling of the configuration
space. In these trial moves, short Molecular Dynamics (MD) trajectories
are performed to collectively displace or rotate all molecules in
the system. These trajectories are accepted or rejected based on the
total energy drift. The efficiency of these trial moves can be tuned
by changing the time step and the trajectory length. The new trial
moves are demonstrated using MC simulations of a viscous fluid (deep
eutectic solvent).
Collapse
Affiliation(s)
- H Mert Polat
- CCUS and Acid Gas Entity, Liquefied Natural Gas Department, Exploration Production, TotalEnergies S.E., 92078 Paris, France.,Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands.,CTP - Centre of Thermodynamics of Processes, Mines ParisTech, PSL University, 35 rue Saint Honoré, 77305 Fontainebleau, France
| | - Hirad S Salehi
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| | - Remco Hens
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| | - Dominika O Wasik
- Materials Simulation and Modelling, Department of Applied Physics, Eindhoven University of Technology, 5600MB Eindhoven, The Netherlands
| | - Ahmadreza Rahbari
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| | - Frédérick de Meyer
- CCUS and Acid Gas Entity, Liquefied Natural Gas Department, Exploration Production, TotalEnergies S.E., 92078 Paris, France.,CTP - Centre of Thermodynamics of Processes, Mines ParisTech, PSL University, 35 rue Saint Honoré, 77305 Fontainebleau, France
| | - Céline Houriez
- CTP - Centre of Thermodynamics of Processes, Mines ParisTech, PSL University, 35 rue Saint Honoré, 77305 Fontainebleau, France
| | - Christophe Coquelet
- CTP - Centre of Thermodynamics of Processes, Mines ParisTech, PSL University, 35 rue Saint Honoré, 77305 Fontainebleau, France
| | - Sofia Calero
- Materials Simulation and Modelling, Department of Applied Physics, Eindhoven University of Technology, 5600MB Eindhoven, The Netherlands.,Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Ctra. Utrera Km. 1, Seville ES-41013, Spain
| | - David Dubbeldam
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Othonas A Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| | - Thijs J H Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| |
Collapse
|
26
|
Blow KE, Quigley D, Sosso GC. The seven deadly sins: When computing crystal nucleation rates, the devil is in the details. J Chem Phys 2021; 155:040901. [PMID: 34340373 DOI: 10.1063/5.0055248] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The formation of crystals has proven to be one of the most challenging phase transformations to quantitatively model-let alone to actually understand-be it by means of the latest experimental technique or the full arsenal of enhanced sampling approaches at our disposal. One of the most crucial quantities involved with the crystallization process is the nucleation rate, a single elusive number that is supposed to quantify the average probability for a nucleus of critical size to occur within a certain volume and time span. A substantial amount of effort has been devoted to attempt a connection between the crystal nucleation rates computed by means of atomistic simulations and their experimentally measured counterparts. Sadly, this endeavor almost invariably fails to some extent, with the venerable classical nucleation theory typically blamed as the main culprit. Here, we review some of the recent advances in the field, focusing on a number of perhaps more subtle details that are sometimes overlooked when computing nucleation rates. We believe it is important for the community to be aware of the full impact of aspects, such as finite size effects and slow dynamics, that often introduce inconspicuous and yet non-negligible sources of uncertainty into our simulations. In fact, it is key to obtain robust and reproducible trends to be leveraged so as to shed new light on the kinetics of a process, that of crystal nucleation, which is involved into countless practical applications, from the formulation of pharmaceutical drugs to the manufacturing of nano-electronic devices.
Collapse
Affiliation(s)
- Katarina E Blow
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David Quigley
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
27
|
Khanna V, Anwar J, Frenkel D, Doherty MF, Peters B. Free energies of crystals computed using Einstein crystal with fixed center of mass and differing spring constants. J Chem Phys 2021; 154:164509. [PMID: 33940822 DOI: 10.1063/5.0044833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Free energies of crystals computed using a center of mass constraint require a finite-size correction, as shown in previous work by Polson et al. [J. Chem. Phys. 112, 5339-5342 (2000)]. Their reference system is an Einstein crystal with equal spring constants. In this paper, we extend the work of Polson et al. [J. Chem. Phys. 112, 5339-5342 (2000)] to the case of differing spring constants. The generalization is convenient for constraining the center of mass in crystals with atoms of differing masses, and it helps to optimize the free energy calculations. To test the theory, we compare the free energies of LiI and NaCl crystals from calculations with differing spring constants to those computed using equal spring constants. Using these center of mass finite size corrections, we compute the true free energies of these crystals for different system sizes to eliminate the intrinsic finite-size effects. These calculations help demonstrate the size of these finite-size corrections relative to other contributions to the absolute free energy of the crystals.
Collapse
Affiliation(s)
- Vikram Khanna
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Jamshed Anwar
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - Daan Frenkel
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| | - Michael F Doherty
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Baron Peters
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
28
|
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 PMCID: PMC7889641 DOI: 10.1038/s41467-021-21181-9] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
Collapse
|
29
|
Krainer G, Welsh TJ, Joseph JA, Espinosa JR, Wittmann S, de Csilléry E, Sridhar A, Toprakcioglu Z, Gudiškytė G, Czekalska MA, Arter WE, Guillén-Boixet J, Franzmann TM, Qamar S, George-Hyslop PS, Hyman AA, Collepardo-Guevara R, Alberti S, Knowles TPJ. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 DOI: 10.1101/2020.05.04.076299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 05/26/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
Collapse
Affiliation(s)
- Georg Krainer
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Jorge R Espinosa
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Sina Wittmann
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Ella de Csilléry
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Akshay Sridhar
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Zenon Toprakcioglu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Giedre Gudiškytė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Magdalena A Czekalska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka, 44/52 01-224, Warsaw, Poland
| | - William E Arter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jordina Guillén-Boixet
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Seema Qamar
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- Division of Neurology, Department of Medicine, University of Toronto and University Health Network, Toronto, Ontario, Canada.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
| | - Rosana Collepardo-Guevara
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany.
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
| |
Collapse
|
30
|
Patel LA, Yoon TJ, Currier RP, Maerzke KA. NaCl aggregation in water at elevated temperatures and pressures: Comparison of classical force fields. J Chem Phys 2021; 154:064503. [PMID: 33588550 DOI: 10.1063/5.0030962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The properties of water vary dramatically with temperature and density. This can be exploited to control its effectiveness as a solvent. Thus, supercritical water is of keen interest as solvent in many extraction processes. The low solubility of salts in lower density supercritical water has even been suggested as a means of desalination. The high temperatures and pressures required to reach supercritical conditions can present experimental challenges during collection of required physical property and phase equilibria data, especially in salt-containing systems. Molecular simulations have the potential to be a valuable tool for examining the behavior of solvated ions at these high temperatures and pressures. However, the accuracy of classical force fields under these conditions is unclear. We have, therefore, undertaken a parametric study of NaCl in water, comparing several salt and water models at 200 bar-600 bar and 450 K-750 K for a range of salt concentrations. We report a comparison of structural properties including ion aggregation, hydrogen bonding, density, and static dielectric constants. All of the force fields qualitatively reproduce the trends in the liquid phase density. An increase in ion aggregation with decreasing density holds true for all of the force fields. The propensity to aggregate is primarily determined by the salt force field rather than the water force field. This coincides with a decrease in the water static dielectric constant and reduced charge screening. While a decrease in the static dielectric constant with increasing NaCl concentration is consistent across all model combinations, the salt force fields that exhibit more ionic aggregation yield a slightly smaller dielectric decrement.
Collapse
Affiliation(s)
- Lara A Patel
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Tae Jun Yoon
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Robert P Currier
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Katie A Maerzke
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| |
Collapse
|
31
|
Finney A, Salvalaglio M. Multiple Pathways in NaCl Homogeneous Crystal Nucleation. Faraday Discuss 2021; 235:56-80. [DOI: 10.1039/d1fd00089f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NaCl crystal nucleation from metastable solutions has long been considered to occur according to a single-step mechanism where the growth in the size and crystalline order of the emerging nuclei...
Collapse
|
32
|
Khanna V, Doherty MF, Peters B. Absolute chemical potentials for complex molecules in fluid phases: A centroid reference for predicting phase equilibria. J Chem Phys 2020; 153:214504. [PMID: 33291889 DOI: 10.1063/5.0025844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Solid-fluid phase equilibria are difficult to predict in simulations because bound degrees of freedom in the crystal phase must be converted to free translations and rotations in the fluid phase. Here, we avoid the solid-to-fluid transformation step by starting with chemical potentials for two reference systems, one for the fluid phase and one for the solid phase. For the solid, we start from the Einstein crystal and transform to the fully interacting molecular crystal. For the fluid phase, we introduce a new reference system, the "centroid," and then transform to gas phase molecules. We illustrate the new calculations by predicting the sublimation vapor pressure of succinic acid in the temperature range of 300 K-350 K.
Collapse
Affiliation(s)
- Vikram Khanna
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Michael F Doherty
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Baron Peters
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
33
|
Panagiotopoulos AZ. Simulations of activities, solubilities, transport properties, and nucleation rates for aqueous electrolyte solutions. J Chem Phys 2020; 153:010903. [DOI: 10.1063/5.0012102] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
34
|
Saric D, Kohns M, Vrabec J. Dielectric constant and density of aqueous alkali halide solutions by molecular dynamics: A force field assessment. J Chem Phys 2020; 152:164502. [PMID: 32357782 DOI: 10.1063/1.5144991] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The concentration dependence of the dielectric constant and the density of 11 aqueous alkali halide solutions (LiCl, NaCl, KCl, RbCl, CsCl, LiI, NaI, KI, CsI, KF, and CsF) is investigated by molecular simulation. Predictions using eight non-polarizable ion force fields combined with the TIP4P/ε water model are compared to experimental data. The influence of the water model and the temperature on the results for the NaCl brine are also addressed. The TIP4P/ε water model improves the accuracy of dielectric constant predictions compared to the SPC/E water model. The solution density is predicted well by most ion models. Almost all ion force fields qualitatively capture the decline of the dielectric constant with the increase of concentration for all solutions and with the increase of temperature for NaCl brine. However, the sampled dielectric constant is mostly in poor quantitative agreement with experimental data. These results are related to the microscopic solution structure, ion pairing, and ultimately the force field parameters. Ion force fields with excessive contact ion pairing and precipitation below the experimental solubility limit generally yield higher dielectric constant values. An adequate reproduction of the experimental solubility limit should therefore be a prerequisite for further investigations of the dielectric constant of aqueous electrolyte solutions by molecular simulation.
Collapse
Affiliation(s)
- Denis Saric
- Thermodynamics and Energy Technology, University of Paderborn, 33098 Paderborn, Germany
| | - Maximilian Kohns
- Laboratory of Engineering Thermodynamics, Technische Universität Kaiserslautern, 67633 Kaiserslautern, Germany
| | - Jadran Vrabec
- Thermodynamics and Process Engineering, Technical University Berlin, 10587 Berlin, Germany
| |
Collapse
|
35
|
Yagasaki T, Matsumoto M, Tanaka H. Lennard-Jones Parameters Determined to Reproduce the Solubility of NaCl and KCl in SPC/E, TIP3P, and TIP4P/2005 Water. J Chem Theory Comput 2020; 16:2460-2473. [PMID: 32207974 DOI: 10.1021/acs.jctc.9b00941] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most classical nonpolarizable ion potential models underestimate the solubility values of NaCl and KCl in water significantly. We determine Lennard-Jones parameters of Na+, K+, and Cl- that reproduce the solubility as well as the hydration free energy in dilute aqueous solutions for three water potential models, SPC/E, TIP3P, and TIP4P/2005. The ion-oxygen distance in the solution and the cation-anion distance in salt are also considered in the parametrization. In addition to the target properties, the hydration enthalpy, hydration entropy, self-diffusion coefficient, coordination number, lattice energy, enthalpy of solution, density, viscosity, and number of contact ion pairs are calculated for comparison with 17 frequently used or recently developed ion potential models. The overall performance of each ion model is represented by a global score using a scheme that was originally developed for comparison of water potential models. The global score is better for our models than for the other 17 models not only because of the quite good prediction for the solubility but also because of the relatively small deviation from the experimental value for many of the other properties.
Collapse
Affiliation(s)
- Takuma Yagasaki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Masakazu Matsumoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Hideki Tanaka
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| |
Collapse
|
36
|
Performing solvation free energy calculations in LAMMPS using the decoupling approach. J Comput Aided Mol Des 2020; 34:641-646. [PMID: 32112288 DOI: 10.1007/s10822-020-00303-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
Abstract
The decoupling approach to solvation free energy calculations requires scaling the interactions between the solute and the solution with all intramolecular interactions preserved. This paper reports a new procedure that makes it possible to these calculations in LAMMPS. The procedure is tested against built-in GROMACS capabilities. The model compounds chosen to test our methodology are ethanol and biphenyl. The LAMMPS and GROMACS results obtained are in good agreement with each other. This work should help perform solvation free energy calculations in LAMMPS and/or other molecular dynamics software having no built-in functions to implement the decoupling approach.
Collapse
|
37
|
Döpke MF, Moultos OA, Hartkamp R. On the transferability of ion parameters to the TIP4P/2005 water model using molecular dynamics simulations. J Chem Phys 2020; 152:024501. [PMID: 31941316 DOI: 10.1063/1.5124448] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Countless molecular dynamics studies have relied on available ion and water force field parameters to model aqueous electrolyte solutions. The TIP4P/2005 model has proven itself to be among the best rigid water force fields, whereas many of the most successful ion parameters were optimized in combination with SPC/E, TIP3P, or TIP4P/Ew water. Many researchers have combined these ions with TIP4P/2005, hoping to leverage the strengths of both parameter sets. To assess if this widely used approach is justified and to provide a guide in selecting ion parameters, we investigated the transferability of various commonly used monovalent and multivalent ion parameters to the TIP4P/2005 water model. The transferability is evaluated in terms of ion hydration free energy, hydration radius, coordination number, and self-diffusion coefficient at infinite dilution. For selected ion parameters, we also investigated density, ion pairing, chemical potential, and mean ionic activity coefficients at finite concentrations. We found that not all ions are equally transferable to TIP4P/2005 without compromising their performance. In particular, ions optimized for TIP3P water were found to be poorly transferable to TIP4P/2005, whereas ions optimized for TIP4P/Ew water provided nearly perfect transferability. The latter ions also showed good overall agreement with experimental values. The one exception is that no combination of ion parameters and water model considered here was found to accurately reproduce experimental self-diffusion coefficients. Additionally, we found that cations optimized for SPC/E and TIP3P water displayed consistent underpredictions in the hydration free energy, whereas anions consistently overpredicted the hydration free energy.
Collapse
Affiliation(s)
- Max F Döpke
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - Othonas A Moultos
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - Remco Hartkamp
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| |
Collapse
|
38
|
Tsironi I, Schlesinger D, Späh A, Eriksson L, Segad M, Perakis F. Brine rejection and hydrate formation upon freezing of NaCl aqueous solutions. Phys Chem Chem Phys 2020; 22:7625-7632. [DOI: 10.1039/c9cp05436g] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studying the freezing of saltwater on a molecular level is of fundamental importance for improving freeze desalination techniques.
Collapse
Affiliation(s)
- Ifigeneia Tsironi
- Department of Physics
- AlbaNova University Center
- Stockholm University
- 114 19 Stockholm
- Sweden
| | - Daniel Schlesinger
- Department of Environmental Science & Bolin Centre for Climate Research
- Stockholm University
- 114 18 Stockholm
- Sweden
| | - Alexander Späh
- Department of Physics
- AlbaNova University Center
- Stockholm University
- 114 19 Stockholm
- Sweden
| | - Lars Eriksson
- Department of Materials and Environmental Chemistry
- Stockholm University
- 106 91 Stockholm
- Sweden
| | - Mo Segad
- Department of Materials and Environmental Chemistry
- Stockholm University
- 106 91 Stockholm
- Sweden
| | - Fivos Perakis
- Department of Physics
- AlbaNova University Center
- Stockholm University
- 114 19 Stockholm
- Sweden
| |
Collapse
|
39
|
Boothroyd S, Anwar J. Solubility prediction for a soluble organic molecule via chemical potentials from density of states. J Chem Phys 2019; 151:184113. [PMID: 31731842 DOI: 10.1063/1.5117281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
While the solubility of a substance is a fundamental property of widespread significance, its prediction from first principles (starting from only the knowledge of the molecular structure of the solute and solvent) remains a challenge. Recently, we proposed a robust and efficient method to predict the solubility from the density of states of a solute-solvent system using classical molecular simulation. The efficiency, and indeed the generality, of the method has now been enhanced by extending it to calculate solution chemical potentials (rather than probability distributions as done previously), from which solubility may be accessed. The method has been employed to predict the chemical potential of Form 1 of urea in both water and methanol for a range of concentrations at ambient conditions and for two charge models. The chemical potential calculations were validated by thermodynamic integration with the two sets of values being in excellent agreement. The solubility determined from the chemical potentials for urea in water ranged from 0.46 to 0.50 mol kg-1, while that for urea in methanol ranged from 0.62 to 0.85 mol kg-1, over the temperature range 298-328 K. In common with other recent studies of solubility prediction from molecular simulation, the predicted solubilities differ markedly from experimental values, reflecting limitations of current forcefields.
Collapse
Affiliation(s)
- Simon Boothroyd
- Chemical Theory and Computation, Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Jamshed Anwar
- Chemical Theory and Computation, Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| |
Collapse
|
40
|
Zeron IM, Abascal JLF, Vega C. A force field of Li +, Na +, K +, Mg 2+, Ca 2+, Cl -, and SO 4 2- in aqueous solution based on the TIP4P/2005 water model and scaled charges for the ions. J Chem Phys 2019; 151:134504. [PMID: 31594349 DOI: 10.1063/1.5121392] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In this work, a force field for several ions in water is proposed. In particular, we consider the cations Li+, Na+, K+, Mg2+, and Ca2+ and the anions Cl- and SO4 2-. These ions were selected as they appear in the composition of seawater, and they are also found in biological systems. The force field proposed (denoted as Madrid-2019) is nonpolarizable, and both water molecules and sulfate anions are rigid. For water, we use the TIP4P/2005 model. The main idea behind this work is to further explore the possibility of using scaled charges for describing ionic solutions. Monovalent and divalent ions are modeled using charges of 0.85 and 1.7, respectively (in electron units). The model allows a very accurate description of the densities of the solutions up to high concentrations. It also gives good predictions of viscosities up to 3 m concentrations. Calculated structural properties are also in reasonable agreement with the experiment. We have checked that no crystallization occurred in the simulations at concentrations similar to the solubility limit. A test for ternary mixtures shows that the force field provides excellent performance at an affordable computer cost. In summary, the use of scaled charges, which could be regarded as an effective and simple way of accounting for polarization (at least to a certain extend), improves the overall description of ionic systems in water. However, for purely ionic systems, scaled charges will not adequately describe neither the solid nor the melt.
Collapse
Affiliation(s)
- I M Zeron
- Depto. Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J L F Abascal
- Depto. Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C Vega
- Depto. Química Física, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| |
Collapse
|
41
|
Galamba N, Paiva A, Barreiros S, Simões P. Solubility of Polar and Nonpolar Aromatic Molecules in Subcritical Water: The Role of the Dielectric Constant. J Chem Theory Comput 2019; 15:6277-6293. [DOI: 10.1021/acs.jctc.9b00505] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nuno Galamba
- Centre of Chemistry and Biochemistry and Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - Alexandre Paiva
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Susana Barreiros
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro Simões
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| |
Collapse
|
42
|
|
43
|
Luo J, Alateeqi A, Liu L, Sinno T. Carbon solubility in liquid silicon: A computational analysis across empirical potentials. J Chem Phys 2019; 150:144503. [PMID: 30981227 DOI: 10.1063/1.5088495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The nucleation and growth of SiC precipitates in liquid silicon is important in the crystallization of silicon used for the photovoltaic industry. These processes depend strongly on the carbon concentration as well as the equilibrium solubility relative to the precipitate phase. Here, using a suite of statistical thermodynamic techniques, we calculate the solubility of carbon atoms in liquid silicon relative to the β-SiC phase. We employ several available empirical potentials to assess whether these potentials may reasonably be used to computationally analyze SiC precipitation. We find that some of the Tersoff-type potentials provide an excellent picture for carbon solubility in liquid silicon but, because of their severe silicon melting point overestimation, are limited to high temperatures where the carbon solubility is several percent, a value that is irrelevant for typical solidification conditions. Based on chemical potential calculations for pure silicon, we suggest that this well-known issue is confined to the description of the liquid phase and demonstrate that some recent potential models for silicon might address this weakness while preserving the excellent description of the carbon-silicon interaction found in the existing models.
Collapse
Affiliation(s)
- Jinping Luo
- School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Abdullah Alateeqi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lijun Liu
- School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
44
|
Bellucci MA, Gobbo G, Wijethunga TK, Ciccotti G, Trout BL. Solubility of paracetamol in ethanol by molecular dynamics using the extended Einstein crystal method and experiments. J Chem Phys 2019; 150:094107. [PMID: 30849885 DOI: 10.1063/1.5086706] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Li and co-workers [Li et al., J. Chem. Phys. 146, 214110 (2017)] have recently proposed a methodology to compute the solubility of molecular compounds from first principles, using molecular dynamics simulations. We revise and further explore their methodology that was originally applied to naphthalene in water at low concentration. In particular, we compute the solubility of paracetamol in an ethanol solution at ambient conditions. For the simulations, we used a force field that we previously reparameterized to reproduce certain thermodynamic properties of paracetamol but not explicitly its solubility in ethanol. In addition, we have determined the experimental solubility by performing turbidity measurements using a Crystal16 over a range of temperatures. Our work serves a dual purpose: (i) methodologically, we clarify how to compute, with a relatively straightforward procedure, the solubility of molecular compounds and (ii) applying this procedure, we show that the solubility predicted by our force field (0.085 ± 0.014 in mole ratio) is in good agreement with the experimental value obtained from our experiments and those reported in the literature (average 0.0585 ± 0.004), considering typical deviations for predictions from first principle methods. The good agreement between the experimental and the calculated solubility also suggests that the method used to reparameterize the force field can be used as a general strategy to optimize force fields for simulations in solution.
Collapse
Affiliation(s)
- Michael A Bellucci
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Gianpaolo Gobbo
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tharanga K Wijethunga
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Bernhardt L Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
45
|
Duarte Ramos Matos G, Mobley DL. Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules. F1000Res 2019; 7:686. [PMID: 30109026 PMCID: PMC6069752 DOI: 10.12688/f1000research.14960.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/06/2018] [Indexed: 12/19/2022] Open
Abstract
Background: Solubility is a physical property of high importance to the pharmaceutical industry, the prediction of which for potential drugs has so far been a hard task. We attempted to predict the solubility of acetylsalicylic acid (ASA) by estimating the absolute chemical potentials of its most stable polymorph and of solutions with different concentrations of the drug molecule. Methods: Chemical potentials were estimated from all-atom molecular dynamics simulations. We used the Einstein molecule method (EMM) to predict the absolute chemical potential of the solid and solvation free energy calculations to predict the excess chemical potentials of the liquid-phase systems. Results: Reliable estimations of the chemical potentials for the solid and for a single ASA molecule using the EMM required an extremely large number of intermediate states for the free energy calculations, meaning that the calculations were extremely demanding computationally. Despite the computational cost, however, the computed value did not agree well with the experimental value, potentially due to limitations with the underlying energy model. Perhaps better values could be obtained with a better energy model; however, it seems likely computational cost may remain a limiting factor for use of this particular approach to solubility estimation. Conclusions: Solubility prediction of drug-like solids remains computationally challenging, and it appears that both the underlying energy model and the computational approach applied may need improvement before the approach is suitable for routine use.
Collapse
Affiliation(s)
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, Irvine, California, USA.,Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, Irvine, California, USA
| |
Collapse
|
46
|
Fernández-Fernández A, Pérez-Rodríguez M, Comesaña A, Piñeiro M. Three-phase equilibrium curve shift for methane hydrate in oceanic conditions calculated from Molecular Dynamics simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
47
|
Espinosa JR, Wand CR, Vega C, Sanz E, Frenkel D. Calculation of the water-octanol partition coefficient of cholesterol for SPC, TIP3P, and TIP4P water. J Chem Phys 2018; 149:224501. [PMID: 30553262 DOI: 10.1063/1.5054056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a numerical study of the relative solubility of cholesterol in octanol and water. Our calculations allow us to compare the accuracy of the computed values of the excess chemical potential of cholesterol for several widely used water models (SPC, TIP3P, and TIP4P). We compute the excess solvation free energies by means of a cavity-based method [L. Li et al., J. Chem. Phys. 146(21), 214110 (2017)] which allows for the calculation of the excess chemical potential of a large molecule in a dense solvent phase. For the calculation of the relative solubility ("partition coefficient," log10 P o / w ) of cholesterol between octanol and water, we use the OPLS/AA force field in combination with the SPC, TIP3P, and TIP4P water models. For all water models studied, our results reproduce the experimental observation that cholesterol is less soluble in water than in octanol. While the experimental value for the partition coefficient is log10 P o / w = 3.7, SPC, TIP3P, and TIP4P give us a value of log10 P o / w = 4.5, 4.6, and 2.9, respectively. Therefore, although the results for the studied water models in combination with the OPLS/AA force field are acceptable, further work to improve the accuracy of current force fields is needed.
Collapse
Affiliation(s)
- Jorge R Espinosa
- Departamento de Quimica Fisica, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Charlie R Wand
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Carlos Vega
- Departamento de Quimica Fisica, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Eduardo Sanz
- Departamento de Quimica Fisica, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
48
|
Jiang H, Debenedetti PG, Panagiotopoulos AZ. Communication: Nucleation rates of supersaturated aqueous NaCl using a polarizable force field. J Chem Phys 2018; 149:141102. [DOI: 10.1063/1.5053652] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hao Jiang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | | |
Collapse
|
49
|
Li L, Totton T, Frenkel D. Computational methodology for solubility prediction: Application to sparingly soluble organic/inorganic materials. J Chem Phys 2018; 149:054102. [PMID: 30089373 DOI: 10.1063/1.5040366] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solubility of a crystalline material can be estimated from the absolute free energy of the solid and the excess solvation free energy. In the earlier work, we presented a general-purpose molecular-dynamics-based methodology enabling solubility predictions of crystalline compounds, yielding accurate estimates of the aqueous solubilities of naphthalene at various pressures and temperatures. In the present work, we investigate a number of prototypical complex materials, including phenanthrene, calcite, and aragonite over a range of temperatures and pressures. Our results provide stronger evidence for the power of the methodology for universal solubility predictions.
Collapse
Affiliation(s)
- Lunna Li
- Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| | - Tim Totton
- BP Exploration Operating Co. Ltd., Sunbury-on-Thames TW16 7LN, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| |
Collapse
|
50
|
Wand CR, Totton TS, Frenkel D. Addressing hysteresis and slow equilibration issues in cavity-based calculation of chemical potentials. J Chem Phys 2018; 149:014105. [PMID: 29981554 DOI: 10.1063/1.5036963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we explore the strengths and weaknesses of a cavity-based method to calculate the excess chemical potential of a large molecular solute in a dense liquid solvent. Use of the cavity alleviates some technical problems associated with the appearance of (integrable) divergences in the integrand during alchemical particle growth. The excess chemical potential calculated using the cavity-based method should be independent of the cavity attributes. However, the performance of the method (equilibration time and the robustness) does depend on the cavity attributes. To illustrate the importance of a suitable choice of the cavity attributes, we calculate the partition coefficient of pyrene in toluene and heptane using a coarse-grained model. We find that a poor choice for the functional form of the cavity may lead to hysteresis between growth and shrinkage of the cavity. Somewhat unexpectedly, we find that, by allowing the cavity to move as a pseudo-particle within the simulation box, the decay time of fluctuations in the integrand of the thermodynamic integration can be reduced by an order of magnitude, thereby increasing the statistical accuracy of the calculation.
Collapse
Affiliation(s)
- C R Wand
- Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| | - T S Totton
- BP Exploration Operating Co. Ltd., Sunbury-on-Thames TW16 7LN, United Kingdom
| | - D Frenkel
- Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| |
Collapse
|