1
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Neha, Aggarwal M, Soni A, Karmakar T. Polymorph-Specific Solubility Prediction of Urea Using Constant Chemical Potential Molecular Dynamics Simulations. J Phys Chem B 2024; 128:8477-8483. [PMID: 39186699 DOI: 10.1021/acs.jpcb.4c02027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Molecular dynamics simulations offer a robust approach to understanding the material properties within a system. Solubility is defined as the analytical composition of a saturated solution expressed as a proportion of designated solute in a designated solvent, according to IUPAC. It is a critical property of compounds and holds significance across numerous fields. Various computational techniques have been explored for determining solubility, including methods based on chemical potential determination, enhanced sampling simulation, and direct coexistence simulation, and lately, machine learning-based methods have shown promise. In this investigation, we have utilized Constant Chemical Potential Molecular Dynamics, a method rooted in direct coexistence simulation, to predict the solubility of urea polymorphs in aqueous solution. The primary purpose of using this method is to overcome the limitation of the direct simulation method by maintaining a constant chemical potential for a sufficiently long time. Urea is chosen as a prototypical system for our study, with a particular focus on three of its polymorphs. Our approach effectively discriminates between the polymorphs of urea based on their respective solubility values; polymorph III is found to have the highest solubility, followed by forms IV and I.
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Affiliation(s)
- Neha
- Department of Chemistry, Indian Institute of Technology, Delhi, New Delhi 110016, India
| | - Manya Aggarwal
- Department of Chemistry, Indian Institute of Technology, Delhi, New Delhi 110016, India
| | - Aashutosh Soni
- Department of Chemistry, Indian Institute of Technology, Delhi, New Delhi 110016, India
| | - Tarak Karmakar
- Department of Chemistry, Indian Institute of Technology, Delhi, New Delhi 110016, India
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2
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Izarra AD, Coudert FX, Fuchs AH, Boutin A. Alchemical Osmostat for Monte Carlo Simulation: Sampling Aqueous Electrolyte Solution in Open Systems. J Phys Chem B 2023; 127:766-776. [PMID: 36634303 DOI: 10.1021/acs.jpcb.2c07902] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Molecular simulations involving electrolytes are usually performed at a fixed amount of salt ions in the simulation box, reproducing macroscopic concentration. Although this statement is valid in the bulk, the concentration of an electrolyte confined in nanoporous materials such as MOFs or zeolites is greatly affected and remains a priori unknown. The nanoporous material in equilibrium with the bulk electrolyte exchange water and ions at a given chemical potential Δμ in the semi-grand-canonical ensemble, that must be calibrated in order to determine the concentration in the nanoporous material. In this work, we propose an algorithm based on nonequilibrium candidate Monte Carlo (NCMC) moves to ultimately perform MC simulations in contact with a saline reservoir. First, we adapt the Widom insertion technique to calibrate the chemical potential by alchemically transmuting water molecules into ions by using NCMC moves. The chemical potential defines a Monte Carlo osmostat in the semi-grand-constant volume and temperature ensemble (Δμ, N, V, T) to be added in a Monte Carlo simulation where the number of ions fluctuates. In order to validate the method, we adapted the NCMC move to determine the free energy of water solvation and subsequently explore thermodynamics of electrolyte solvation at infinite dilution in water. Finally, we implemented the osmostat in MC simulations initialized with bulk water that are driven toward electrolyte solutions of similar concentration as the saline reservoir. Our results demonstrate that alchemical osmostat for MC simulation is a promising tool for use to sample electrolyte insertion in nanoporous materials.
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Affiliation(s)
- Ambroise de Izarra
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.,Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, Paris75005, France
| | - François-Xavier Coudert
- Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, Paris75005, France
| | - Alain H Fuchs
- Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, Paris75005, France
| | - Anne Boutin
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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3
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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
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4
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DeFever RS, Maginn EJ. Computing the Liquidus of Binary Monatomic Salt Mixtures with Direct Simulation and Alchemical Free Energy Methods. J Phys Chem A 2021; 125:8498-8513. [PMID: 34543018 DOI: 10.1021/acs.jpca.1c06107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe and validate a free-energy-based method for computing the liquidus for binary solid-liquid phase diagrams in molecular simulations of monatomic salts. The method is demonstrated by calculating the liquidus for LiCl-KCl and MgCl2-KCl salt mixtures with the polarizable ion model (PIM). The free-energy-based method is cross-validated with direct coexistence simulations. Both techniques show excellent agreement with one another. Though the predictions of the PIM disagree with experiments, we use our free-energy-based approach to decouple the contributions of liquid mixture nonidealities and pure component solid-liquid equilibrium to the phase diagram. In both mixtures, the PIM accurately reproduces the liquid phase nonidealities but fails to predict the liquidus because it does not accurately predict the pure component melting temperature of LiCl or MgCl2.
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Affiliation(s)
- Ryan S DeFever
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Edward J Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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5
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Ansari N, Karmakar T, Parrinello M. Molecular Mechanism of Gas Solubility in Liquid: Constant Chemical Potential Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:5279-5286. [PMID: 32551636 DOI: 10.1021/acs.jctc.0c00450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Accurate prediction of gas solubility in a liquid is crucial in many areas of chemistry, and a detailed understanding of the molecular mechanism of the gas solvation continues to be an active area of research. Here, we extend the idea of the constant chemical potential molecular dynamics (CμMD) approach to the calculation of the gas solubility in the liquid under constant gas chemical potential conditions. As a representative example, we utilize this method to calculate the isothermal solubility of carbon dioxide in water. Additionally, we provide microscopic insight into the mechanism of solvation that preferentially occurs in areas of the surface where the hydrogen network is broken.
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Affiliation(s)
- Narjes Ansari
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8092 Zurich, Switzerland.,Facoltà di informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Tarak Karmakar
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8092 Zurich, Switzerland.,Facoltà di informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8092 Zurich, Switzerland.,Facoltà di informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland.,Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
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6
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Qiao C, Zhang J, Jiang P, Zhao S, Song X, Yu J. A molecular approach for predicting phase diagrams of ternary aqueous saline solutions. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2019.115278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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7
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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: 131] [Impact Index Per Article: 26.2] [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.
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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
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8
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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
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9
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10
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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.
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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
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11
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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.
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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
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12
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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.
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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
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13
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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.
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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
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14
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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.
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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
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15
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Moučka F, Kolafa J, Lísal M, Smith WR. Chemical potentials of alkaline earth metal halide aqueous electrolytes and solubility of their hydrates by molecular simulation: Application to CaCl2, antarcticite, and sinjarite. J Chem Phys 2018; 148:222832. [DOI: 10.1063/1.5024212] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Filip Moučka
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
- Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Ústí nad Labem, Czech Republic
| | - Jiří Kolafa
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, 166 28 Praha 6, Czech Republic
| | - Martin Lísal
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
- Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Ústí nad Labem, Czech Republic
| | - William R. Smith
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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16
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Li L, Totton T, Frenkel D. Computational methodology for solubility prediction: Application to the sparingly soluble solutes. J Chem Phys 2018; 146:214110. [PMID: 28595415 DOI: 10.1063/1.4983754] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solubility of a crystalline substance in the solution can be estimated from its absolute solid free energy and excess solvation free energy. Here, we present a numerical method, which enables convenient solubility estimation of general molecular crystals at arbitrary thermodynamic conditions where solid and solution can coexist. The methodology is based on standard alchemical free energy methods, such as thermodynamic integration and free energy perturbation, and consists of two parts: (1) systematic extension of the Einstein crystal method to calculate the absolute solid free energies of molecular crystals at arbitrary temperatures and pressures and (2) a flexible cavity method that can yield accurate estimates of the excess solvation free energies. As an illustration, via classical Molecular Dynamic simulations, we show that our approach can predict the solubility of OPLS-AA-based (Optimized Potentials for Liquid Simulations All Atomic) naphthalene in SPC (Simple Point Charge) water in good agreement with experimental data at various temperatures and pressures. Because the procedure is simple and general and only makes use of readily available open-source software, the methodology should provide a powerful tool for universal solubility prediction.
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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
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17
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Heidari M, Kremer K, Cortes-Huerto R, Potestio R. Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids. J Chem Theory Comput 2018; 14:3409-3417. [DOI: 10.1021/acs.jctc.8b00002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Maziar Heidari
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | | | - Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Physics Department, University of Trento, via Sommarive 14 Povo, Trento 38123, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
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18
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Bergström CAS, Larsson P. Computational prediction of drug solubility in water-based systems: Qualitative and quantitative approaches used in the current drug discovery and development setting. Int J Pharm 2018; 540:185-193. [PMID: 29421301 PMCID: PMC5861307 DOI: 10.1016/j.ijpharm.2018.01.044] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/20/2018] [Accepted: 01/22/2018] [Indexed: 01/18/2023]
Abstract
In this review we will discuss recent advances in computational prediction of solubility in water-based solvents. Our focus is set on recent advances in predictions of biorelevant solubility in media mimicking the human intestinal fluids and on new methods to predict the thermodynamic cycle rather than prediction of solubility in pure water through quantitative structure property relationships (QSPR). While the literature is rich in QSPR models for both solubility and melting point, a physicochemical property strongly linked to the solubility, recent advances in the modelling of these properties make use of theory and computational simulations to better predict these properties or processes involved therein (e.g. solid state crystal lattice packing, dissociation of molecules from the lattice and solvation). This review serves to provide an update on these new approaches and how they can be used to more accurately predict solubility, and also importantly, inform us on molecular interactions and processes occurring during drug dissolution and solubilisation.
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Affiliation(s)
- Christel A S Bergström
- Department of Pharmacy, Uppsala University, Biomedical Centre P.O. Box 580, SE-751 23 Uppsala, Sweden.
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Biomedical Centre P.O. Box 580, SE-751 23 Uppsala, Sweden
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19
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Boothroyd S, Kerridge A, Broo A, Buttar D, Anwar J. Solubility prediction from first principles: a density of states approach. Phys Chem Chem Phys 2018; 20:20981-20987. [DOI: 10.1039/c8cp01786g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solubility is a fundamental property of widespread significance. Its accurate prediction remains a major challenge. We present a novel, efficient approach to solubility prediction for molecules over a range of conditions based on density of states.
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Affiliation(s)
- Simon Boothroyd
- Chemical Theory and Computation
- Department of Chemistry
- Lancaster University
- Lancaster LA1 4YB
- UK
| | - Andy Kerridge
- Chemical Theory and Computation
- Department of Chemistry
- Lancaster University
- Lancaster LA1 4YB
- UK
| | - Anders Broo
- Pharmaceutical Science IMED Biotech unit
- AstraZeneca
- Mölndal
- Sweden
| | - David Buttar
- Pharmaceutical Science IMED Biotech unit
- AstraZeneca
- Macclesfield
- UK
| | - Jamshed Anwar
- Chemical Theory and Computation
- Department of Chemistry
- Lancaster University
- Lancaster LA1 4YB
- UK
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20
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Benavides AL, Portillo MA, Chamorro VC, Espinosa JR, Abascal JLF, Vega C. A potential model for sodium chloride solutions based on the TIP4P/2005 water model. J Chem Phys 2017; 147:104501. [DOI: 10.1063/1.5001190] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. L. Benavides
- Departamento de Ingeniería Física, División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, Col. Lomas del Campestre, CP 37150 León, Mexico
| | - M. A. Portillo
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - V. C. Chamorro
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J. R. Espinosa
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J. L. F. Abascal
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C. Vega
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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21
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Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2017; 62:1559-1569. [PMID: 29056756 PMCID: PMC5648357 DOI: 10.1021/acs.jced.7b00104] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review "alchemical" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.
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Affiliation(s)
- Guilherme Duarte Ramos Matos
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Daisy Y Kyu
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Hannes H Loeffler
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - John D Chodera
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Michael R Shirts
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
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22
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Di Lecce S, Albrecht T, Bresme F. A computational approach to calculate the heat of transport of aqueous solutions. Sci Rep 2017; 7:44833. [PMID: 28322266 PMCID: PMC5359663 DOI: 10.1038/srep44833] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/13/2017] [Indexed: 12/22/2022] Open
Abstract
Thermal gradients induce concentration gradients in alkali halide solutions, and the salt migrates towards hot or cold regions depending on the average temperature of the solution. This effect has been interpreted using the heat of transport, which provides a route to rationalize thermophoretic phenomena. Early theories provide estimates of the heat of transport at infinite dilution. These values are used to interpret thermodiffusion (Soret) and thermoelectric (Seebeck) effects. However, accessing heats of transport of individual ions at finite concentration remains an outstanding question both theoretically and experimentally. Here we discuss a computational approach to calculate heats of transport of aqueous solutions at finite concentrations, and apply our method to study lithium chloride solutions at concentrations >0.5 M. The heats of transport are significantly different for Li+ and Cl− ions, unlike what is expected at infinite dilution. We find theoretical evidence for the existence of minima in the Soret coefficient of LiCl, where the magnitude of the heat of transport is maximized. The Seebeck coefficient obtained from the ionic heats of transport varies significantly with temperature and concentration. We identify thermodynamic conditions leading to a maximization of the thermoelectric response of aqueous solutions.
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Affiliation(s)
- Silvia Di Lecce
- Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| | - Tim Albrecht
- Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| | - Fernando Bresme
- Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
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23
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Benavides A, Portillo M, Abascal J, Vega C. Estimating the solubility of 1:1 electrolyte aqueous solutions: the chemical potential difference rule. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1288939] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- A.L. Benavides
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Guanajuato, Mexico
| | - M.A. Portillo
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J.L.F. Abascal
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C. Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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24
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Noroozi J, Paluch AS. Microscopic Structure and Solubility Predictions of Multifunctional Solids in Supercritical Carbon Dioxide: A Molecular Simulation Study. J Phys Chem B 2017; 121:1660-1674. [DOI: 10.1021/acs.jpcb.6b12390] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Javad Noroozi
- Department
of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Andrew S. Paluch
- Department
of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
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25
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Cox CE, Phifer JR, Ferreira da Silva L, Gonçalves Nogueira G, Ley RT, O’Loughlin EJ, Pereira Barbosa AK, Rygelski BT, Paluch AS. Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection. J Comput Aided Mol Des 2017; 31:183-199. [DOI: 10.1007/s10822-016-0001-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
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26
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Benavides AL, Aragones JL, Vega C. Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route. J Chem Phys 2016; 144:124504. [PMID: 27036458 DOI: 10.1063/1.4943780] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The solubility of NaCl in water is evaluated by using three force field models: Joung-Cheatham for NaCl dissolved in two different water models (SPC/E and TIP4P/2005) and Smith Dang NaCl model in SPC/E water. The methodology based on free-energy calculations [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] and [J. L. Aragones et al., J. Chem. Phys. 136, 244508 (2012)] has been used, except, that all calculations for the NaCl in solution were obtained by using molecular dynamics simulations with the GROMACS package instead of homemade MC programs. We have explored new lower molalities and made longer runs to improve the accuracy of the calculations. Exploring the low molality region allowed us to obtain an analytical expression for the chemical potential of the ions in solution as a function of molality valid for a wider range of molalities, including the infinite dilute case. These new results are in better agreement with recent estimations of the solubility obtained with other methodologies. Besides, two empirical simple rules have been obtained to have a rough estimate of the solubility of a certain model, by analyzing the ionic pairs formation as a function of molality and/or by calculating the difference between the NaCl solid chemical potential and the standard chemical potential of the salt in solution.
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Affiliation(s)
- A L Benavides
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J L Aragones
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - C Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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27
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Phifer JR, Solomon KJ, Young KL, Paluch AS. Computing MOSCED parameters of nonelectrolyte solids with electronic structure methods in SMD and SM8 continuum solvents. AIChE J 2016. [DOI: 10.1002/aic.15413] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jeremy R. Phifer
- Dept. of Chemical, Paper and Biomedical Engineering; Miami University; Oxford OH 45056
| | - Kimberly J. Solomon
- Dept. of Chemical, Paper and Biomedical Engineering; Miami University; Oxford OH 45056
| | - Kayla L. Young
- Dept. of Chemical, Paper and Biomedical Engineering; Miami University; Oxford OH 45056
| | - Andrew S. Paluch
- Dept. of Chemical, Paper and Biomedical Engineering; Miami University; Oxford OH 45056
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28
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Affiliation(s)
- Roman Shevchuk
- Department
for Mathematics
and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
- Institute
for Microbiology
and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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29
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Ley RT, Fuerst GB, Redeker BN, Paluch AS. Developing a Predictive Form of MOSCED for Nonelectrolyte Solids Using Molecular Simulation: Application to Acetanilide, Acetaminophen, and Phenacetin. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.5b04807] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan T. Ley
- Department
of Chemical, Paper
and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Georgia B. Fuerst
- Department
of Chemical, Paper
and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Bryce N. Redeker
- Department
of Chemical, Paper
and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Andrew S. Paluch
- Department
of Chemical, Paper
and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
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30
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Nezbeda I, Moučka F, Smith WR. Recent progress in molecular simulation of aqueous electrolytes: force fields, chemical potentials and solubility. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1165296] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ivo Nezbeda
- Faculty of Science, J.E. Purkinje University, Ústí nad Labem, Czech Republic
- Institute of Chemical Process Fundamentals, Academy of Sciences, Prague 6, Czech Republic
| | - Filip Moučka
- Faculty of Science, J.E. Purkinje University, Ústí nad Labem, Czech Republic
| | - William R. Smith
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
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31
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Liu S, Cao S, Hoang K, Young KL, Paluch AS, Mobley DL. Using MD Simulations To Calculate How Solvents Modulate Solubility. J Chem Theory Comput 2016; 12:1930-41. [PMID: 26878198 DOI: 10.1021/acs.jctc.5b00934] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, our interest is in predicting solubility in general, and we focus particularly on predicting how the solubility of particular solutes is modulated by the solvent environment. Solubility in general is extremely important, both for theoretical reasons - it provides an important probe of the balance between solute-solute and solute-solvent interactions - and for more practical reasons, such as how to control the solubility of a given solute via modulation of its environment, as in process chemistry and separations. Here, we study how the change of solvent affects the solubility of a given compound. That is, we calculate relative solubilities. We use MD simulations to calculate relative solubility and compare our calculated values with experiment as well as with results from several other methods, SMD and UNIFAC, the latter of which is commonly used in chemical engineering design. We find that straightforward solubility calculations based on molecular simulations using a general small-molecule force field outperform SMD and UNIFAC both in terms of accuracy and coverage of the relevant chemical space.
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Affiliation(s)
| | | | | | - Kayla L Young
- Department of Chemical, Paper and Biomedical Engineering, Miami University , Oxford, Ohio 45056, United States
| | - Andrew S Paluch
- Department of Chemical, Paper and Biomedical Engineering, Miami University , Oxford, Ohio 45056, United States
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32
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Affiliation(s)
- Raúl Fuentes-Azcatl
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
| | - Marcia C. Barbosa
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
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33
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Zimmermann NER, Vorselaars B, Quigley D, Peters B. Nucleation of NaCl from Aqueous Solution: Critical Sizes, Ion-Attachment Kinetics, and Rates. J Am Chem Soc 2015; 137:13352-61. [DOI: 10.1021/jacs.5b08098] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Bart Vorselaars
- Department
of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, U.K
| | - David Quigley
- Department
of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, U.K
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34
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Mester Z, Panagiotopoulos AZ. Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations. J Chem Phys 2015; 142:044507. [PMID: 25637995 DOI: 10.1063/1.4906320] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mean ionic activity coefficients of aqueous NaCl solutions of varying concentrations at 298.15 K and 1 bar have been obtained from molecular dynamics simulations by gradually turning on the interactions of an ion pair inserted into the solution. Several common non-polarizable water and ion models have been used in the simulations. Gibbs-Duhem equation calculations of the thermodynamic activity of water are used to confirm the thermodynamic consistency of the mean ionic activity coefficients. While the majority of model combinations predict the correct trends in mean ionic activity coefficients, they overestimate their values at high salt concentrations. The solubility predictions also suffer from inaccuracies, with all models underpredicting the experimental values, some by large factors. These results point to the need for further ion and water model development.
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Affiliation(s)
- Zoltan Mester
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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35
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Mester Z, Panagiotopoulos AZ. Temperature-dependent solubilities and mean ionic activity coefficients of alkali halides in water from molecular dynamics simulations. J Chem Phys 2015; 143:044505. [DOI: 10.1063/1.4926840] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zoltan Mester
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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36
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Valiskó M, Boda D. The effect of concentration- and temperature-dependent dielectric constant on the activity coefficient of NaCl electrolyte solutions. J Chem Phys 2015; 140:234508. [PMID: 24952553 DOI: 10.1063/1.4883742] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Our implicit-solvent model for the estimation of the excess chemical potential (or, equivalently, the activity coefficient) of electrolytes is based on using a dielectric constant that depends on the thermodynamic state, namely, the temperature and concentration of the electrolyte, ε(c, T). As a consequence, the excess chemical potential is split into two terms corresponding to ion-ion (II) and ion-water (IW) interactions. The II term is obtained from computer simulation using the Primitive Model of electrolytes, while the IW term is estimated from the Born treatment. In our previous work [J. Vincze, M. Valiskó, and D. Boda, "The nonmonotonic concentration dependence of the mean activity coefficient of electrolytes is a result of a balance between solvation and ion-ion correlations," J. Chem. Phys. 133, 154507 (2010)], we showed that the nonmonotonic concentration dependence of the activity coefficient can be reproduced qualitatively with this II+IW model without using any adjustable parameter. The Pauling radii were used in the calculation of the II term, while experimental solvation free energies were used in the calculation of the IW term. In this work, we analyze the effect of the parameters (dielectric constant, ionic radii, solvation free energy) on the concentration and temperature dependence of the mean activity coefficient of NaCl. We conclude that the II+IW model can explain the experimental behavior using a concentration-dependent dielectric constant and that we do not need the artificial concept of "solvated ionic radius" assumed by earlier studies.
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Affiliation(s)
- Mónika Valiskó
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Dezső Boda
- Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
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37
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38
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Paluch AS, Parameswaran S, Liu S, Kolavennu A, Mobley DL. Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation. J Chem Phys 2015; 142:044508. [PMID: 25637996 PMCID: PMC4312346 DOI: 10.1063/1.4906491] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/12/2015] [Indexed: 01/13/2023] Open
Abstract
We present a general framework to predict the excess solubility of small molecular solids (such as pharmaceutical solids) in binary solvents via molecular simulation free energy calculations at infinite dilution with conventional molecular models. The present study used molecular dynamics with the General AMBER Force Field to predict the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol solvents. The simulations are able to predict the existence of solubility enhancement and the results are in good agreement with available experimental data. The accuracy of the predictions in addition to the generality of the method suggests that molecular simulations may be a valuable design tool for solvent selection in drug development processes.
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Affiliation(s)
- Andrew S Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, USA
| | - Sreeja Parameswaran
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - Shuai Liu
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, USA
| | - Anasuya Kolavennu
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, USA
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39
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Kobayashi K, Liang Y, Sakka T, Matsuoka T. Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water. J Chem Phys 2014; 140:144705. [DOI: 10.1063/1.4870417] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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40
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Moučka F, Nezbeda I, Smith WR. Molecular Force Field Development for Aqueous Electrolytes: 1. Incorporating Appropriate Experimental Data and the Inadequacy of Simple Electrolyte Force Fields Based on Lennard-Jones and Point Charge Interactions with Lorentz–Berthelot Rules. J Chem Theory Comput 2013; 9:5076-85. [DOI: 10.1021/ct4006008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filip Moučka
- Faculty
of Science, University of Ontario Institute of Technology, Oshawa, ON
L1H7K4, Canada
- Faculty
of Science, J. E. Purkinje University, 400 96 Ústí n. Lab., Czech Republic
| | - Ivo Nezbeda
- Faculty
of Science, J. E. Purkinje University, 400 96 Ústí n. Lab., Czech Republic
- E. Hála
Laboratory of Thermodynamics, Institute of
Chemical Process Fundamentals, Academy of Sciences, 165 02 Prague 6, Czech Republic
| | - William R. Smith
- Faculty
of Science, University of Ontario Institute of Technology, Oshawa, ON
L1H7K4, Canada
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41
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Moučka F, Nezbeda I, Smith WR. Molecular simulation of aqueous electrolytes: Water chemical potential results and Gibbs-Duhem equation consistency tests. J Chem Phys 2013; 139:124505. [DOI: 10.1063/1.4821153] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Paluch AS, Maginn EJ. Efficient Estimation of the Equilibrium Solution-Phase Fugacity of Soluble Nonelectrolyte Solids in Binary Solvents by Molecular Simulation. Ind Eng Chem Res 2013. [DOI: 10.1021/ie401295j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew S. Paluch
- Department
of Chemical and Biomolecular Engineering, University of Notre Dame, Notre
Dame, Indiana 46556, United States
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43
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44
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Paluch AS, Maginn EJ. Predicting the Solubility of Solid Phenanthrene: A Combined Molecular Simulation and Group Contribution Approach. AIChE J 2013. [DOI: 10.1002/aic.14020] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Andrew S. Paluch
- Dept. of Chemical and Biomolecular Engineering; University of Notre Dame; Notre Dame; IN; 46556
| | - Edward J. Maginn
- Dept. of Chemical and Biomolecular Engineering; University of Notre Dame; Notre Dame; IN; 46556
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45
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Aragones JL, Sanz E, Vega C. Solubility of NaCl in water by molecular simulation revisited. J Chem Phys 2012; 136:244508. [DOI: 10.1063/1.4728163] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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46
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Moučka F, Lísal M, Škvor J, Jirsák J, Nezbeda I, Smith WR. Molecular Simulation of Aqueous Electrolyte Solubility. 2. Osmotic Ensemble Monte Carlo Methodology for Free Energy and Solubility Calculations and Application to NaCl. J Phys Chem B 2011; 115:7849-61. [DOI: 10.1021/jp202054d] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filip Moučka
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON L1H7K4, Canada
| | - Martin Lísal
- E. Hála Laboratory of Thermodynamics, Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague 6, Czech Republic
| | - Jiří Škvor
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON L1H7K4, Canada
| | - Jan Jirsák
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON L1H7K4, Canada
- E. Hála Laboratory of Thermodynamics, Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague 6, Czech Republic
| | - Ivo Nezbeda
- E. Hála Laboratory of Thermodynamics, Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague 6, Czech Republic
| | - William R. Smith
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON L1H7K4, Canada
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47
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Paluch AS, Jayaraman S, Shah JK, Maginn EJ. A method for computing the solubility limit of solids: application to sodium chloride in water and alcohols. J Chem Phys 2011; 133:124504. [PMID: 20886947 DOI: 10.1063/1.3478539] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We present an adaptable method to compute the solubility limit of solids by molecular simulation, which avoids the difficulty of reference state calculations. In this way, the method is highly adaptable to molecules of complex topology. Results are shown for solubility calculations of sodium chloride in water and light alcohols at atmospheric conditions. The pseudosupercritical path integration method is used to calculate the free energy of the solid and gives results that are in good agreement with previous studies that reference the Einstein crystal. For the solution phase calculations, the self-adaptive Wang-Landau transition-matrix Monte Carlo method is used within the context of an expanded isothermal-isobaric ensemble. The method shows rapid convergence properties and the uncertainty in the calculated chemical potential was 1% or less for all cases. The present study underpredicts the solubility limit of sodium chloride in water, suggesting a shortcoming of the molecular models. Importantly, the proper trend for the chemical potential in various solvents was captured, suggesting that relative solubilities can be computed by the method.
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Affiliation(s)
- Andrew S Paluch
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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48
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Pi HL, Aragones JL, Vega C, Noya EG, Abascal JL, Gonzalez MA, McBride C. Anomalies in water as obtained from computer simulations of the TIP4P/2005 model: density maxima, and density, isothermal compressibility and heat capacity minima. Mol Phys 2010. [DOI: 10.1080/00268970902784926] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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49
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Mason PE, Heyda J, Fischer HE, Jungwirth P. Specific Interactions of Ammonium Functionalities in Amino Acids with Aqueous Fluoride and Iodide. J Phys Chem B 2010; 114:13853-60. [DOI: 10.1021/jp104840g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Philip E. Mason
- Department of Food Science, Cornell University, Ithaca, New York 14853, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 16610 Prague 6, Czech Republic, and Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, Grenoble Cedex 9 F-38042, France
| | - Jan Heyda
- Department of Food Science, Cornell University, Ithaca, New York 14853, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 16610 Prague 6, Czech Republic, and Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, Grenoble Cedex 9 F-38042, France
| | - Henry E. Fischer
- Department of Food Science, Cornell University, Ithaca, New York 14853, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 16610 Prague 6, Czech Republic, and Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, Grenoble Cedex 9 F-38042, France
| | - Pavel Jungwirth
- Department of Food Science, Cornell University, Ithaca, New York 14853, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 16610 Prague 6, Czech Republic, and Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, Grenoble Cedex 9 F-38042, France
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50
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Zhang C, Raugei S, Eisenberg B, Carloni P. Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength. J Chem Theory Comput 2010; 6:2167-75. [DOI: 10.1021/ct9006579] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Chao Zhang
- German Research School for Simulation Sciences, FZ-Juelich/RWTH Aachen University, Aachen, Germany, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352, Rush University Medical Center, 1653 W. Congress Parkway, Chicago, Illinois 60612, and SISSA, CNR-INFN-DEMOCRITOS, and Italian Institue of Technology (IIT), SISSA Unit, Trieste, Italy
| | - Simone Raugei
- German Research School for Simulation Sciences, FZ-Juelich/RWTH Aachen University, Aachen, Germany, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352, Rush University Medical Center, 1653 W. Congress Parkway, Chicago, Illinois 60612, and SISSA, CNR-INFN-DEMOCRITOS, and Italian Institue of Technology (IIT), SISSA Unit, Trieste, Italy
| | - Bob Eisenberg
- German Research School for Simulation Sciences, FZ-Juelich/RWTH Aachen University, Aachen, Germany, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352, Rush University Medical Center, 1653 W. Congress Parkway, Chicago, Illinois 60612, and SISSA, CNR-INFN-DEMOCRITOS, and Italian Institue of Technology (IIT), SISSA Unit, Trieste, Italy
| | - Paolo Carloni
- German Research School for Simulation Sciences, FZ-Juelich/RWTH Aachen University, Aachen, Germany, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352, Rush University Medical Center, 1653 W. Congress Parkway, Chicago, Illinois 60612, and SISSA, CNR-INFN-DEMOCRITOS, and Italian Institue of Technology (IIT), SISSA Unit, Trieste, Italy
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