1
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Hulikal Chakrapani T, Hajibeygi H, Moultos OA, Vlugt TJH. Calculating Thermodynamic Factors for Diffusion Using the Continuous Fractional Component Monte Carlo Method. J Chem Theory Comput 2024; 20:333-347. [PMID: 38113860 PMCID: PMC10782482 DOI: 10.1021/acs.jctc.3c01144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
Thermodynamic factors for diffusion connect the Fick and Maxwell-Stefan diffusion coefficients used to quantify mass transfer. Activity coefficient models or equations of state can be fitted to experimental or simulation data, from which thermodynamic factors can be obtained by differentiation. The accuracy of thermodynamic factors determined using indirect routes is dictated by the specific choice of an activity coefficient model or an equation of state. The Permuted Widom's Test Particle Insertion (PWTPI) method developed by Balaji et al. enables direct determination of thermodynamic factors in binary and multicomponent systems. For highly dense systems, for example, typical liquids, it is well known that molecular test insertion methods fail. In this article, we use the Continuous Fractional Component Monte Carlo (CFCMC) method to directly calculate thermodynamic factors by adopting the PWTPI method. The CFCMC method uses fractional molecules whose interactions with their surrounding molecules are modulated by a coupling parameter. Even in highly dense systems, the CFCMC method efficiently handles molecule insertions and removals, overcoming the limitations of the PWTPI method. We show excellent agreement between the results of the PWTPI and CFCMC methods for the calculation of thermodynamic factors in binary systems of Lennard-Jones molecules and ternary systems of Weeks-Chandler-Andersen molecules. The CFCMC method applied to calculate the thermodynamic factors of realistic molecular systems consisting of binary mixtures of carbon dioxide and hydrogen agrees well with the NIST REFPROP database. Our study highlights the effectiveness of the CFCMC method in determining thermodynamic factors for diffusion, even in densely packed systems, using relatively small numbers of molecules.
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Affiliation(s)
- Thejas Hulikal Chakrapani
- Reservoir
Engineering, Geoscience and Engineering Department, Faculty of Civil
Engineering and Geosciences, Delft University
of Technology, 2628 CN Delft, The
Netherlands
| | - Hadi Hajibeygi
- Reservoir
Engineering, Geoscience and Engineering Department, Faculty of Civil
Engineering and Geosciences, Delft University
of Technology, 2628 CN Delft, The
Netherlands
| | - Othonas A. Moultos
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, 2628 CB Delft, The
Netherlands
| | - Thijs J. H. Vlugt
- Engineering
Thermodynamics, Process and Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, 2628 CB Delft, The
Netherlands
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2
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Dohn AO, Markmann V, Nimmrich A, Haldrup K, Møller KB, Nielsen MM. Eliminating finite-size effects on the calculation of x-ray scattering from molecular dynamics simulations. J Chem Phys 2023; 159:124115. [PMID: 38127395 DOI: 10.1063/5.0164365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/01/2023] [Indexed: 12/23/2023] Open
Abstract
Structural studies using x-ray scattering methods for investigating molecules in solution are shifting focus toward describing the role and effects of the surrounding solvent. However, forward models based on molecular dynamics (MD) simulations to simulate structure factors and x-ray scattering from interatomic distributions such as radial distribution functions (RDFs) face limitations imposed by simulations, particularly at low values of the scattering vector q. In this work, we show how the value of the structure factor at q = 0 calculated from RDFs sampled from finite MD simulations is effectively dependent on the size of the simulation cell. To eliminate this error, we derive a new scheme to renormalize the sampled RDFs based on a model of the excluded volume of the particle-pairs they were sampled from, to emulate sampling from an infinite system. We compare this new correction method to two previous RDF-correction methods, developed for Kirkwood-Buff theory applications. We present a quantitative test to assess the reliability of the simulated low-q scattering signal and show that our RDF-correction successfully recovers the correct q = 0 limit for neat water. We investigate the effect of MD-sampling time on the RDF-corrections, before advancing to a molecular example system, comprised of a transition metal complex solvated in a series of water cells with varying densities. We show that our correction recovers the correct q = 0 behavior for all densities. Furthermore, we employ a simple continuum scattering model to dissect the total scattering signal from the solvent-solvent structural correlations in a solute-solvent model system to find two distinct contributions: a non-local density-contribution from the finite, fixed cell size in NVT simulations, and a local contribution from the solvent shell. We show how the second contribution can be approximated without also including the finite-size contribution. Finally, we provide a "best-practices"-checklist for experimentalists planning to incorporate explicit solvation MD simulations in future work, offering guidance for improving the accuracy and reliability of structural studies using x-ray scattering methods in solution.
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Affiliation(s)
- A O Dohn
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, Reykjavík 107, Iceland
| | - V Markmann
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - A Nimmrich
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - K Haldrup
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
| | - K B Møller
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - M M Nielsen
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark
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3
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Simon JM, Krüger P, Schnell SK, Vlugt TJH, Kjelstrup S, Bedeaux D. Kirkwood-Buff integrals: From fluctuations in finite volumes to the thermodynamic limit. J Chem Phys 2022; 157:130901. [PMID: 36209013 DOI: 10.1063/5.0106162] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The Kirkwood-Buff theory is a cornerstone of the statistical mechanics of liquids and solutions. It relates volume integrals over the radial distribution function, so-called Kirkwood-Buff integrals (KBIs), to particle number fluctuations and thereby to various macroscopic thermodynamic quantities such as the isothermal compressibility and partial molar volumes. Recently, the field has seen a strong revival with breakthroughs in the numerical computation of KBIs and applications to complex systems such as bio-molecules. One of the main emergent results is the possibility to use the finite volume KBIs as a tool to access finite volume thermodynamic quantities. The purpose of this Perspective is to shed new light on the latest developments and discuss future avenues.
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Affiliation(s)
- J-M Simon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR-6303 CNRS - Université de Bourgogne Franche-Comté, F-21078 Dijon, France
| | - P Krüger
- Graduate School of Science and Engineering, Molecular Chirality Research Center, Chiba University, Chiba 263-8522, Japan
| | - S K Schnell
- Department of Materials Science and Engineering, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - T J H Vlugt
- Process & Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - S Kjelstrup
- Center of Excellence PoreLab, Department of Chemistry, Faculty of Natural Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - D Bedeaux
- Center of Excellence PoreLab, Department of Chemistry, Faculty of Natural Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
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4
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Forero-Martinez NC, Cortes-Huerto R, Benedetto A, Ballone P. Thermoresponsive Ionic Liquid/Water Mixtures: From Nanostructuring to Phase Separation. Molecules 2022; 27:molecules27051647. [PMID: 35268747 PMCID: PMC8912101 DOI: 10.3390/molecules27051647] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/15/2022] [Accepted: 02/28/2022] [Indexed: 12/10/2022] Open
Abstract
The thermodynamics, structures, and applications of thermoresponsive systems, consisting primarily of water solutions of organic salts, are reviewed. The focus is on organic salts of low melting temperatures, belonging to the ionic liquid (IL) family. The thermo-responsiveness is represented by a temperature driven transition between a homogeneous liquid state and a biphasic state, comprising an IL-rich phase and a solvent-rich phase, divided by a relatively sharp interface. Demixing occurs either with decreasing temperatures, developing from an upper critical solution temperature (UCST), or, less often, with increasing temperatures, arising from a lower critical solution temperature (LCST). In the former case, the enthalpy and entropy of mixing are both positive, and enthalpy prevails at low T. In the latter case, the enthalpy and entropy of mixing are both negative, and entropy drives the demixing with increasing T. Experiments and computer simulations highlight the contiguity of these phase separations with the nanoscale inhomogeneity (nanostructuring), displayed by several ILs and IL solutions. Current applications in extraction, separation, and catalysis are briefly reviewed. Moreover, future applications in forward osmosis desalination, low-enthalpy thermal storage, and water harvesting from the atmosphere are discussed in more detail.
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Affiliation(s)
- Nancy C. Forero-Martinez
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany;
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Robinson Cortes-Huerto
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Correspondence:
| | - Antonio Benedetto
- School of Physics, University College Dublin, 94568 Dublin, Ireland; (A.B.); (P.B.)
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, 94568 Dublin, Ireland
- Department of Sciences, University of Roma Tre, 00146 Rome, Italy
| | - Pietro Ballone
- School of Physics, University College Dublin, 94568 Dublin, Ireland; (A.B.); (P.B.)
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, 94568 Dublin, Ireland
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5
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Ashbaugh HS, Vats M, Garde S. Bridging Gaussian Density Fluctuations from Microscopic to Macroscopic Volumes: Applications to Non-Polar Solute Hydration Thermodynamics. J Phys Chem B 2021; 125:8152-8164. [PMID: 34283590 PMCID: PMC8389927 DOI: 10.1021/acs.jpcb.1c04087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The hydration of
hydrophobic solutes is intimately related to the
spontaneous formation of cavities in water through ambient density
fluctuations. Information theory-based modeling and simulations have
shown that water density fluctuations in small volumes are approximately
Gaussian. For limiting cases of microscopic and macroscopic volumes,
water density fluctuations are known exactly and are rigorously related
to the density and isothermal compressibility of water. Here, we develop
a theory—interpolated gaussian fluctuation theory (IGFT)—that
builds an analytical bridge to describe water density fluctuations
from microscopic to molecular scales. This theory requires no detailed
information about the water structure beyond the effective size of
a water molecule and quantities that are readily obtained from water’s
equation-of-state—namely, the density and compressibility.
Using simulations, we show that IGFT provides a good description of
density fluctuations near the mean, that is, it characterizes the
variance of occupancy fluctuations over all solute sizes. Moreover,
when combined with the information theory, IGFT reproduces the well-known
signatures of hydrophobic hydration, such as entropy convergence and
solubility minima, for atomic-scale solutes smaller than the crossover
length scale beyond which the Gaussian assumption breaks down. We
further show that near hydrophobic and hydrophilic self-assembled
monolayer surfaces in contact with water, the normalized solvent density
fluctuations within observation volumes depend similarly on size as
observed in the bulk, suggesting the feasibility of a modified version
of IGFT for interfacial systems. Our work highlights the utility of
a density fluctuation-based approach toward understanding and quantifying
the solvation of non-polar solutes in water and the forces that drive
them toward surfaces with different hydrophobicities.
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Affiliation(s)
- Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Mayank Vats
- Center for Biotechnology and Interdisciplinary Studies and the Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Shekhar Garde
- Center for Biotechnology and Interdisciplinary Studies and the Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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6
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Celebi AT, Dawass N, Moultos OA, Vlugt TJH. How sensitive are physical properties of choline chloride-urea mixtures to composition changes: Molecular dynamics simulations and Kirkwood-Buff theory. J Chem Phys 2021; 154:184502. [PMID: 34241035 DOI: 10.1063/5.0049064] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Deep eutectic solvents (DESs) have emerged as a cheaper and greener alternative to conventional organic solvents. Choline chloride (ChCl) mixed with urea at a molar ratio of 1:2 is one of the most common DESs for a wide range of applications such as electrochemistry, material science, and biochemistry. In this study, molecular dynamics simulations are performed to study the effect of urea content on the thermodynamic and transport properties of ChCl and urea mixtures. With increased mole fraction of urea, the number of hydrogen bonds (HBs) between cation-anion and ion-urea decreases, while the number of HBs between urea-urea increases. Radial distribution functions (RDFs) for ChCl-urea and ChCl-ChCl pairs shows a significant decrease as the mole fraction of urea increases. Using the computed RDFs, Kirkwood-Buff Integrals (KBIs) are computed. KBIs show that interactions of urea-urea become stronger, while interactions of urea-ChCl and ChCl-ChCl pairs become slightly weaker with increasing mole fraction of urea. All thermodynamic factors are found larger than one, indicating a non-ideal mixture. Our results also show that self- and collective diffusivities increase, while viscosities decrease with increasing urea content. This is mainly due to the weaker interactions between ions and urea, resulting in enhanced mobilities. Ionic conductivities exhibit a non-monotonic behavior. Up to a mole fraction of 0.5, the ionic conductivities increase with increasing urea content and then reach a plateau.
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Affiliation(s)
- Alper T Celebi
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Noura Dawass
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Othonas A Moultos
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Thijs J H Vlugt
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
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7
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Katsuto H, Okamoto R, Sumi T, Koga K. Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions. J Phys Chem B 2021; 125:6296-6305. [PMID: 34102058 DOI: 10.1021/acs.jpcb.1c03388] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general trend of the salting-out effect on hydrophobic solutes in aqueous solution is that the smaller the size of a dissolved ion, the larger the effect of reducing the solubility of a hydrophobe. An exception is that Li+, the smallest in alkali metal ions, has a notably weaker effect than Na+. To understand the reversed order in the cation series, we performed molecular dynamics simulations of aqueous solutions of salt ions and calculated the Setschenow coefficient of methane with the ionic radius of either a cation or an anion varied in a wide range. It is confirmed that the Setschenow coefficient is correlated with the packing fraction of salt solution, as observed in earlier studies, and also correlated with the partial molar volume of an ion. Analyses of correlation function integrals, packing fractions of solvation spheres, and orientations of water molecules surrounding an ion reveal the key differences in microscopic properties between the cation and anion series, which give rise to the reversed order in the cation series of the partial molar volumes of ions and ultimately that of the Setschenow coefficients.
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Affiliation(s)
- Hiroyuki Katsuto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Ryuichi Okamoto
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Kenichiro Koga
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.,Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
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8
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Klein T, Piszko M, Kankanamge CJ, Kasapis G, Fröba AP. Fick Diffusion Coefficient in Binary Mixtures of [HMIM][NTf 2] and Carbon Dioxide by Dynamic Light Scattering and Molecular Dynamics Simulations. J Phys Chem B 2021; 125:5100-5113. [PMID: 33960781 DOI: 10.1021/acs.jpcb.1c01616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic light scattering (DLS) experiments and equilibrium molecular dynamics (EMD) simulations were performed in the saturated liquid phase of the binary mixture of 1-hexyl-3-methylimidazolium bis(trifluormethylsulfonyl)imide ([HMIM][NTf2]) and carbon dioxide (CO2) to access the Fick diffusion coefficient (D11). The investigations were performed within or close to saturation conditions at temperatures between (298.15 and 348.15) K and CO2 mole fractions (xCO2) up to 0.81. The DLS experiments were combined with polarization-difference Raman spectroscopy (PDRS) to simultaneously access the composition of the liquid phase. For the first time in an electrolyte-based system, D11 was directly calculated from EMD simulations by accessing the Maxwell-Stefan (MS) diffusion coefficient and the thermodynamic factor. Agreement within combined uncertainties was found between D11 from DLS and EMD simulations for CO2 mole fractions up to 0.5. In general, an increasing D11 with increasing xCO2 could be observed, with a local maximum present at a CO2 mole fraction of about 0.75. The local maximum could be explained by an increasing MS diffusion coefficient with increasing xCO2 over the entire studied composition range and a decreasing thermodynamic factor at xCO2 above 0.7. Finally, PDRS and EMD simulations were combined to investigate the influence of the fluid structure on the diffusive process.
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Affiliation(s)
- Tobias Klein
- Institute of Advanced Optical Technologies - Thermophysical Properties (AOT-TP), Department of Chemical and Biological Engineering (CBI) and Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Paul-Gordan-Straße 8, 91052 Erlangen, Germany
| | - Maximilian Piszko
- Institute of Advanced Optical Technologies - Thermophysical Properties (AOT-TP), Department of Chemical and Biological Engineering (CBI) and Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Paul-Gordan-Straße 8, 91052 Erlangen, Germany
| | - Chathura J Kankanamge
- Institute of Advanced Optical Technologies - Thermophysical Properties (AOT-TP), Department of Chemical and Biological Engineering (CBI) and Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Paul-Gordan-Straße 8, 91052 Erlangen, Germany
| | - Georgios Kasapis
- Institute of Advanced Optical Technologies - Thermophysical Properties (AOT-TP), Department of Chemical and Biological Engineering (CBI) and Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Paul-Gordan-Straße 8, 91052 Erlangen, Germany.,Institute for Multiscale Thermofluids, School of Engineering, University of Edinburgh, Robert Stevenson Road, Edinburgh EH9 3FB, U.K
| | - Andreas P Fröba
- Institute of Advanced Optical Technologies - Thermophysical Properties (AOT-TP), Department of Chemical and Biological Engineering (CBI) and Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Paul-Gordan-Straße 8, 91052 Erlangen, Germany
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9
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Rahbari A, Garcia-Navarro JC, Ramdin M, van den Broeke LJP, Moultos OA, Dubbeldam D, Vlugt TJH. Effect of Water Content on Thermodynamic Properties of Compressed Hydrogen. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2021; 66:2071-2087. [PMID: 34054140 PMCID: PMC8154567 DOI: 10.1021/acs.jced.1c00020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Force field-based molecular simulations were used to calculate thermal expansivities, heat capacities, and Joule-Thomson coefficients of binary (standard) hydrogen-water mixtures for temperatures between 366.15 and 423.15 K and pressures between 50 and 1000 bar. The mole fraction of water in saturated hydrogen-water mixtures in the gas phase ranges from 0.004 to 0.138. The same properties were calculated for pure hydrogen at 323.15 K and pressures between 100 and 1000 bar. Simulations were performed using the TIP3P and a modified TIP4P force field for water and the Marx, Vrabec, Cracknell, Buch, and Hirschfelder force fields for hydrogen. The vapor-liquid equilibria of hydrogen-water mixtures were calculated along the melting line of ice Ih, corresponding to temperatures between 264.21 and 272.4 K, using the TIP3P force field for water and the Marx force field for hydrogen. In this temperature range, the solubilities and the chemical potentials of hydrogen and water were obtained. Based on the computed solubility data of hydrogen in water, the freezing-point depression of water was computed ranging from 264.21 to 272.4 K. The modified TIP4P and Marx force fields were used to improve the solubility calculations of hydrogen-water mixtures reported in our previous study [Rahbari A.;J. Chem. Eng. Data2019, 64, 4103-4115] for temperatures between 323 and 423 K and pressures ranging from 100 to 1000 bar. The chemical potentials of ice Ih were calculated as a function of pressure between 100 and 1000 bar, along the melting line for temperatures between 264.21 and 272.4 K, using the IAPWS equation of state for ice Ih. We show that at low pressures, the presence of water has a large effect on the thermodynamic properties of compressed hydrogen. Our conclusions may have consequences for the energetics of a hydrogen refueling station using electrochemical hydrogen compressors.
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Affiliation(s)
- Ahmadreza Rahbari
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | | | - Mahinder Ramdin
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Leo J. P. van den Broeke
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Othonas A. Moultos
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - David Dubbeldam
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Thijs J. H. Vlugt
- Engineering
Thermodynamics, Process & Energy Department, Faculty of Mechanical,
Maritime and Materials Engineering, Delft
University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
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10
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Kumari P, Pillai VVS, Gobbo D, Ballone P, Benedetto A. The transition from salt-in-water to water-in-salt nanostructures in water solutions of organic ionic liquids relevant for biological applications. Phys Chem Chem Phys 2021; 23:944-959. [DOI: 10.1039/d0cp04959j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Computer simulations show how nano-structural motifs in organic salts/water solutions change with salt content increasing from dilute to highly concentrated.
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Affiliation(s)
- P. Kumari
- School of Physics
- University College
- Dublin
- Ireland
- Conway Institute for Biomolecular and Biomedical Research
| | - V. V. S. Pillai
- School of Physics
- University College
- Dublin
- Ireland
- Conway Institute for Biomolecular and Biomedical Research
| | - D. Gobbo
- Computational and Chemical Biology
- Fondazione Istituto Italiano di Tecnologia
- Genova
- Italy
| | - P. Ballone
- School of Physics
- University College
- Dublin
- Ireland
- Conway Institute for Biomolecular and Biomedical Research
| | - A. Benedetto
- School of Physics
- University College
- Dublin
- Ireland
- Conway Institute for Biomolecular and Biomedical Research
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11
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Celebi AT, Jamali SH, Bardow A, Vlugt TJH, Moultos OA. Finite-size effects of diffusion coefficients computed from molecular dynamics: a review of what we have learned so far. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1810685] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alper T. Celebi
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Seyed Hossein Jamali
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - André Bardow
- Energy & Process Systems Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Zürich, Switzerland
| | - Thijs J. H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
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12
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Tripathy M, Bharadwaj S, B. SJ, van der Vegt NFA. Characterizing Polymer Hydration Shell Compressibilities with the Small-System Method. NANOMATERIALS 2020; 10:nano10081460. [PMID: 32722500 PMCID: PMC7466400 DOI: 10.3390/nano10081460] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/03/2022]
Abstract
The small-system method (SSM) exploits the unique feature of finite-sized open systems, whose thermodynamic quantities scale with the inverse system size. This scaling enables the calculation of properties in the thermodynamic limit of macroscopic systems based on computer simulations of finite-sized systems. We herein extend the SSM to characterize the hydration shell compressibility of a generic hydrophobic polymer in water. By systematically increasing the strength of polymer-water repulsion, we find that the excess inverse thermodynamic correction factor (Δ1/Γs∞) and compressibility (Δχs) of the first hydration shell change sign from negative to positive. This occurs with a concurrent decrease in water hydrogen bonding and local tetrahedral order of the hydration shell water. The crossover lengthscale corresponds to an effective polymer bead diameter of 0.7 nm and is consistent with previous works on hydration of small and large hydrophobic solutes. The crossover lengthscale in polymer hydration shell compressibility, herein identified with the SSM approach, relates to hydrophobic interactions and macromolecular conformational equilibria in aqueous solution. The SSM approach may further be applied to study thermodynamic properties of polymer solvation shells in mixed solvents.
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13
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Rahbari A, Hens R, Moultos OA, Dubbeldam D, Vlugt TJH. Multiple Free Energy Calculations from Single State Point Continuous Fractional Component Monte Carlo Simulation Using Umbrella Sampling. J Chem Theory Comput 2020; 16:1757-1767. [PMID: 31999461 PMCID: PMC7066647 DOI: 10.1021/acs.jctc.9b01097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
We introduce an alternative method
to perform free energy calculations
for mixtures at multiple temperatures and pressures from a single
simulation, by combining umbrella sampling and the continuous fractional
component Monte Carlo method. One can perform a simulation of a mixture
at a certain pressure and temperature and accurately compute the chemical
potential at other pressures and temperatures close to the simulation
conditions. This method has the following advantages: (1) Accurate
estimates of the chemical potential as a function of pressure and
temperature are obtained from a single state simulation without additional
postprocessing. This can potentially reduce the number of simulations
of a system for free energy calculations for a specific temperature
and/or pressure range. (2) Partial molar volumes and enthalpies are
obtained directly from the estimated chemical potentials. We tested
our method for a Lennard-Jones system, aqueous mixtures of methanol
at T = 298 K and P = 1 bar, and
a mixture of ammonia, nitrogen, and hydrogen at T = 573 K and P = 800 bar. For pure methanol (N = 410 molecules), we observed that the estimated chemical
potentials from umbrella sampling are in excellent agreement with
the reference values obtained from independent simulations, for ΔT = ±15 K and ΔP = 100 bar (with
respect to the simulated system). For larger systems, this range becomes
smaller because the relative fluctuations of energy and volume become
smaller. Without sufficient overlap, the performance of the method
will become poor especially for nonlinear variations of the chemical
potential.
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Affiliation(s)
- Ahmadreza Rahbari
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - Remco Hens
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - Othonas A Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - David Dubbeldam
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Thijs J H Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
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14
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Barnett JW, Ashbaugh HS. Evaluation of second osmotic virial coefficients from molecular simulation following scaled-particle theory. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1639698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- J. Wesley Barnett
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, USA
| | - Henry S. Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, USA
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15
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Lbadaoui-Darvas M, Takahama S. Water Activity from Equilibrium Molecular Dynamics Simulations and Kirkwood-Buff Theory. J Phys Chem B 2019; 123:10757-10768. [DOI: 10.1021/acs.jpcb.9b06735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mária Lbadaoui-Darvas
- ENAC/IIE Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Satoshi Takahama
- ENAC/IIE Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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16
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Josephson TR, Singh R, Minkara MS, Fetisov EO, Siepmann JI. Partial molar properties from molecular simulation using multiple linear regression. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1648898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Tyler R. Josephson
- Department of Chemistry and Chemical Theory Center, Minneapolis, MN, USA
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, USA
| | - Ramanish Singh
- Department of Chemistry and Chemical Theory Center, Minneapolis, MN, USA
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, USA
| | - Mona S. Minkara
- Department of Chemistry and Chemical Theory Center, Minneapolis, MN, USA
| | - Evgenii O. Fetisov
- Department of Chemistry and Chemical Theory Center, Minneapolis, MN, USA
- Chemical Physics and Analysis, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - J. Ilja Siepmann
- Department of Chemistry and Chemical Theory Center, Minneapolis, MN, USA
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, USA
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17
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Bruce EE, van der Vegt NFA. Molecular Scale Solvation in Complex Solutions. J Am Chem Soc 2019; 141:12948-12956. [DOI: 10.1021/jacs.9b03469] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ellen E. Bruce
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
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18
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Nandy A, Smiatek J. Mixtures of LiTFSI and urea: ideal thermodynamic behavior as key to the formation of deep eutectic solvents? Phys Chem Chem Phys 2019; 21:12279-12287. [PMID: 31139787 DOI: 10.1039/c9cp01440c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We studied the dynamic and structural properties of deep eutectic solvents composed of LiTFSI salts in presence of urea.
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Affiliation(s)
- Aniruddha Nandy
- Department of Mechanical Engineering
- Indian Institute of Technology
- Kharagpur
- India
- Helmholtz-Institute Münster: Ionics in Energy Storage (HIMS-IEK 12)
| | - Jens Smiatek
- Helmholtz-Institute Münster: Ionics in Energy Storage (HIMS-IEK 12)
- Forschungszentrum Jülich GmbH
- D-48149 Münster
- Germany
- Institute for Computational Physics
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19
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Properties of Ion Complexes and Their Impact on Charge Transport in Organic Solvent-Based Electrolyte Solutions for Lithium Batteries: Insights from a Theoretical Perspective. BATTERIES-BASEL 2018. [DOI: 10.3390/batteries4040062] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Electrolyte formulations in standard lithium ion and lithium metal batteries are complex mixtures of various components. In this article, we review molecular key principles of ion complexes in multicomponent electrolyte solutions in regards of their influence on charge transport mechanisms. We outline basic concepts for the description of ion–solvent and ion–ion interactions, which can be used to rationalize recent experimental and numerical findings concerning modern electrolyte formulations. Furthermore, we discuss benefits and drawbacks of empirical concepts in comparison to molecular theories of solution for a more refined understanding of ion behavior in organic solvents. The outcomes of our discussion provide a rational for beneficial properties of ions, solvent, co-solvent and additive molecules, and highlight possible routes for further improvement of novel electrolyte solutions.
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20
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Rahbari A, Hens R, Nikolaidis IK, Poursaeidesfahani A, Ramdin M, Economou IG, Moultos OA, Dubbeldam D, Vlugt TJH. Computation of partial molar properties using continuous fractional component Monte Carlo. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1451663] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- A. Rahbari
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft, The Netherlands
| | - R. Hens
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft, The Netherlands
| | - I. K. Nikolaidis
- Molecular Thermodynamics and Modeling of Materials Laboratory, National Center for Scientific Research Demokritos, Institute of Nanoscience and Nanotechnology , Attikis, Greece
| | - A. Poursaeidesfahani
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft, The Netherlands
| | - M. Ramdin
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft, The Netherlands
| | - I. G. Economou
- Molecular Thermodynamics and Modeling of Materials Laboratory, National Center for Scientific Research Demokritos, Institute of Nanoscience and Nanotechnology , Attikis, Greece
- Chemical Engineering Program, Texas A&M University at Qatar , Doha, Qatar
| | - O. A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft, The Netherlands
| | - D. Dubbeldam
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Amsterdam, The Netherlands
| | - T. J. H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft, The Netherlands
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21
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Mamatkulov S, Schwierz N. Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties. J Chem Phys 2018; 148:074504. [DOI: 10.1063/1.5017694] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shavkat Mamatkulov
- Department of Physics, The Centre of Higher Technologies, Tashkent, Uzbekistan
| | - Nadine Schwierz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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22
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Milzetti J, Nayar D, van der Vegt NFA. Convergence of Kirkwood–Buff Integrals of Ideal and Nonideal Aqueous Solutions Using Molecular Dynamics Simulations. J Phys Chem B 2018; 122:5515-5526. [DOI: 10.1021/acs.jpcb.7b11831] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jasmin Milzetti
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
| | - Divya Nayar
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287, Darmstadt, Germany
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23
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Tang D, Delpo C, Blackmon O, Ashbaugh HS. Note: Second osmotic virial coefficients of short alkanes and their alcohol counterparts in water as a function of temperature. J Chem Phys 2018; 148:016101. [DOI: 10.1063/1.5008573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Du Tang
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
| | - Courtney Delpo
- Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, USA
| | - Odella Blackmon
- Department of Chemistry, William Carey University, Hattiesburg, Mississippi 39401, USA
| | - Henry S. Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
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24
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Narayanan Kirshnamoorthy A, Oldiges K, Winter M, Heuer A, Cekic-Laskovic I, Holm C, Smiatek J. Electrolyte solvents for high voltage lithium ion batteries: ion correlation and specific anion effects in adiponitrile. Phys Chem Chem Phys 2018; 20:25701-25715. [DOI: 10.1039/c8cp04102d] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Combined atomistic molecular dynamics, quantum chemical, and experimental study regarding the properties of two lithium conducting salts in high voltage electrolyte solvent adiponitrile.
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Affiliation(s)
| | - Kristina Oldiges
- Helmholtz Institute Münster (HI MS): Ionics in Energy Storage
- Forschungszentrum Jülich GmbH
- 48149 Münster
- Germany
| | - Martin Winter
- Helmholtz Institute Münster (HI MS): Ionics in Energy Storage
- Forschungszentrum Jülich GmbH
- 48149 Münster
- Germany
- MEET Battery Research Centre
| | - Andreas Heuer
- Institute of Physical Chemistry
- University of Münster
- 48149 Münster
- Germany
| | - Isidora Cekic-Laskovic
- Helmholtz Institute Münster (HI MS): Ionics in Energy Storage
- Forschungszentrum Jülich GmbH
- 48149 Münster
- Germany
| | - Christian Holm
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Jens Smiatek
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
- Helmholtz Institute Münster (HI MS): Ionics in Energy Storage
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25
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Dawass N, Krüger P, Schnell SK, Bedeaux D, Kjelstrup S, Simon JM, Vlugt TJH. Finite-size effects of Kirkwood–Buff integrals from molecular simulations. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1416114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- N. Dawass
- Process & Energy Laboratory, Delft University of Technology, Delft, The Netherlands
| | - P. Krüger
- Graduate School of Science and Engineering, Molecular Chirality Research Center, Chiba University, Chiba, Japan
- ICB, UMR 6303 CNRS – Université de Bourgogne, Dijon, France
| | - S. K. Schnell
- Department of Materials Science and Engineering, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - D. Bedeaux
- PoreLab, Department of Chemistry, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - S. Kjelstrup
- Process & Energy Laboratory, Delft University of Technology, Delft, The Netherlands
- PoreLab, Department of Chemistry, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - J. M. Simon
- ICB, UMR 6303 CNRS – Université de Bourgogne, Dijon, France
| | - T. J. H. Vlugt
- Process & Energy Laboratory, Delft University of Technology, Delft, The Netherlands
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26
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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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27
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Poursaeidesfahani A, Hens R, Rahbari A, Ramdin M, Dubbeldam D, Vlugt TJH. Efficient Application of Continuous Fractional Component Monte Carlo in the Reaction Ensemble. J Chem Theory Comput 2017; 13:4452-4466. [PMID: 28737933 PMCID: PMC5597954 DOI: 10.1021/acs.jctc.7b00092] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new formulation of the Reaction Ensemble Monte Carlo technique (RxMC) combined with the Continuous Fractional Component Monte Carlo method is presented. This method is denoted by serial Rx/CFC. The key ingredient is that fractional molecules of either reactants or reaction products are present and that chemical reactions always involve fractional molecules. Serial Rx/CFC has the following advantages compared to other approaches: (1) One directly obtains chemical potentials of all reactants and reaction products. Obtained chemical potentials can be used directly as an independent check to ensure that chemical equilibrium is achieved. (2) Independent biasing is applied to the fractional molecules of reactants and reaction products. Therefore, the efficiency of the algorithm is significantly increased, compared to the other approaches. (3) Changes in the maximum scaling parameter of intermolecular interactions can be chosen differently for reactants and reaction products. (4) The number of fractional molecules is reduced. As a proof of principle, our method is tested for Lennard-Jones systems at various pressures and for various chemical reactions. Excellent agreement was found both for average densities and equilibrium mixture compositions computed using serial Rx/CFC, RxMC/CFCMC previously introduced by Rosch and Maginn (Journal of Chemical Theory and Computation, 2011, 7, 269-279), and the conventional RxMC approach. The serial Rx/CFC approach is also tested for the reaction of ammonia synthesis at various temperatures and pressures. Excellent agreement was found between results obtained from serial Rx/CFC, experimental results from literature, and thermodynamic modeling using the Peng-Robinson equation of state. The efficiency of reaction trial moves is improved by a factor of 2 to 3 (depending on the system) compared to the RxMC/CFCMC formulation by Rosch and Maginn.
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Affiliation(s)
- Ali Poursaeidesfahani
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology , Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Remco Hens
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology , Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Ahmadreza Rahbari
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology , Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Mahinder Ramdin
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology , Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - David Dubbeldam
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Thijs J H Vlugt
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology , Leeghwaterstraat 39, 2628CB Delft, The Netherlands
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28
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Smiatek J. Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:233001. [PMID: 28398214 DOI: 10.1088/1361-648x/aa6c9d] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.
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Affiliation(s)
- Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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29
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Yadav HOS, Chakravarty C. Thiolated gold nanoparticle solvation in near-critical fluids: The role of density, temperature, and topology. J Chem Phys 2017; 146:174902. [DOI: 10.1063/1.4982755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hari O. S. Yadav
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
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30
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Reid JESJ, Gammons RJ, Slattery JM, Walker AJ, Shimizu S. Interactions in Water–Ionic Liquid Mixtures: Comparing Protic and Aprotic Systems. J Phys Chem B 2017; 121:599-609. [DOI: 10.1021/acs.jpcb.6b10562] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Joshua E. S. J. Reid
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
- TWI Ltd., Granta Park, Great Abington, Cambridge, CB21 6AL, U.K
| | - Richard J. Gammons
- Department
of Chemistry, University of York, Heslington, York YO10
5DD, U.K
| | - John M. Slattery
- Department
of Chemistry, University of York, Heslington, York YO10
5DD, U.K
| | - Adam J. Walker
- TWI Ltd., Granta Park, Great Abington, Cambridge, CB21 6AL, U.K
| | - Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
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31
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Kobayashi T, Reid JESJ, Shimizu S, Fyta M, Smiatek J. The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches. Phys Chem Chem Phys 2017; 19:18924-18937. [DOI: 10.1039/c7cp03717a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atomistic molecular dynamics simulations of aqueous ionic liquid mixtures were performed in order to compare the resulting Kirkwood–Buff integrals with experimental data and the corresponding integrals derived by an inverse Kirkwood–Buff approach.
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Affiliation(s)
- Takeshi Kobayashi
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Joshua E. S. J. Reid
- York Structural Biology Laboratory
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | - Seishi Shimizu
- York Structural Biology Laboratory
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | - Maria Fyta
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Jens Smiatek
- Institute for Computational Physics
- University of Stuttgart
- 70569 Stuttgart
- Germany
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32
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Pratt LR, Chaudhari MI, Rempe SB. Statistical Analyses of Hydrophobic Interactions: A Mini-Review. J Phys Chem B 2016; 120:6455-60. [PMID: 27258151 DOI: 10.1021/acs.jpcb.6b04082] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review focuses on the striking recent progress in solving for hydrophobic interactions between small inert molecules. We discuss several new understandings. First, the inverse temperature phenomenology of hydrophobic interactions, i.e., strengthening of hydrophobic bonds with increasing temperature, is decisively exhibited by hydrophobic interactions between atomic-scale hard sphere solutes in water. Second, inclusion of attractive interactions associated with atomic-size hydrophobic reference cases leads to substantial, nontrivial corrections to reference results for purely repulsive solutes. Hydrophobic bonds are weakened by adding solute dispersion forces to treatment of reference cases. The classic statistical mechanical theory for those corrections is not accurate in this application, but molecular quasi-chemical theory shows promise. Finally, because of the masking roles of excluded volume and attractive interactions, comparisons that do not discriminate the different possibilities face an interpretive danger.
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Affiliation(s)
- Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University , New Orleans, Louisiana 70118, United States
| | - Mangesh I Chaudhari
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
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33
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van der Vegt NFA, Haldrup K, Roke S, Zheng J, Lund M, Bakker HJ. Water-Mediated Ion Pairing: Occurrence and Relevance. Chem Rev 2016; 116:7626-41. [DOI: 10.1021/acs.chemrev.5b00742] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nico F. A. van der Vegt
- Eduard-Zintl-Institut
für Anorganische und Physikalische Chemie and Center of Smart
Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse
10, 64287 Darmstadt, Germany
| | - Kristoffer Haldrup
- Physics
Department, NEXMAP Section, Technical University of Denmark, Fysikvej
307, 2800 Kongens
Lyngby, Denmark
| | - Sylvie Roke
- Laboratory
for Fundamental BioPhotonics, Institute of Bioengineering, and Institute
of Materials Science, School of Engineering, and Lausanne Centre for
Ultrafast Science, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Junrong Zheng
- College
of Chemistry and Molecular Engineering, Beijing National Laboratory
for Molecular Sciences, Peking University, Beijing 100871, China
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005-1892, United States
| | - Mikael Lund
- Division
of Theoretical Chemistry, Department of Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Huib J. Bakker
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
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34
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Chaudhari MI, Rempe SB, Asthagiri D, Tan L, Pratt LR. Molecular Theory and the Effects of Solute Attractive Forces on Hydrophobic Interactions. J Phys Chem B 2016; 120:1864-70. [DOI: 10.1021/acs.jpcb.5b09552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mangesh I. Chaudhari
- Center
for Biological and Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Susan B. Rempe
- Center
for Biological and Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - D. Asthagiri
- Department
of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - L. Tan
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - L. R. Pratt
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
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35
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Balaji SP, Gangarapu S, Ramdin M, Torres-Knoop A, Zuilhof H, Goetheer EL, Dubbeldam D, Vlugt TJ. Simulating the Reactions of CO2 in Aqueous Monoethanolamine Solution by Reaction Ensemble Monte Carlo Using the Continuous Fractional Component Method. J Chem Theory Comput 2015; 11:2661-9. [DOI: 10.1021/acs.jctc.5b00160] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sayee Prasaad Balaji
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Satesh Gangarapu
- Laboratory
of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703HB Wageningen, The Netherlands
| | - Mahinder Ramdin
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Ariana Torres-Knoop
- Van’t
Hoff Institute for Molecular Sciences, University of Amsterdam, Science
Park 904, 1098XH Amsterdam, The Netherlands
| | - Han Zuilhof
- Laboratory
of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703HB Wageningen, The Netherlands
- Department
of Chemical and Materials Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - David Dubbeldam
- Van’t
Hoff Institute for Molecular Sciences, University of Amsterdam, Science
Park 904, 1098XH Amsterdam, The Netherlands
| | - Thijs J.H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
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36
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Skorpa R, Simon JM, Bedeaux D, Kjelstrup S. The reaction enthalpy of hydrogen dissociation calculated with the Small System Method from simulation of molecular fluctuations. Phys Chem Chem Phys 2015; 16:19681-93. [PMID: 25113221 DOI: 10.1039/c4cp02768j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We show how we can find the enthalpy of a chemical reaction under non-ideal conditions using the Small System Method to sample molecular dynamics simulation data for fluctuating variables. This method, created with Hill's thermodynamic analysis, is used to find properties in the thermodynamic limit, such as thermodynamic correction factors, partial enthalpies, volumes, heat capacities and compressibility. The values in the thermodynamic limit at (T,V, μj) are then easily transformed into other ensembles, (T,V,Nj) and (T,P,Nj), where the last ensemble gives the partial molar properties which are of interest to chemists. The dissociation of hydrogen from molecules to atoms was used as a convenient model system. Molecular dynamics simulations were performed with three densities; ρ = 0.0052 g cm(-3) (gas), ρ = 0.0191 g cm(-3) (compressed gas) and ρ = 0.0695 g cm(-3) (liquid), and temperatures in the range; T = 3640-20,800 K. The enthalpy of reaction was observed to follow a quadratic trend as a function of temperature for all densities. The enthalpy of reaction was observed to only have a small pressure dependence. With a reference point close to an ideal state (T = 3640 K and ρ = 0.0052 g cm(-3)), we were able to calculate the thermodynamic equilibrium constant, and thus the deviation from ideal conditions for the lowest density. We found the thermodynamic equilibrium constant to increase with increasing temperature, and to have a negligible pressure dependence. Taking the enthalpy variation into account in the calculation of the thermodynamic equilibrium constant, we found the ratio of activity coefficients to be in the order of 0.7-1.0 for the lowest density, indicating repulsive forces between H and H2. This study shows that the compressed gas- and liquid density values at higher temperatures are far from those calculated under ideal conditions. It is important to have a method that can give access to partial molar properties, independent of the ideality of the reacting mixture. Our results show how this can be achieved with the use of the Small System Method.
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Affiliation(s)
- Ragnhild Skorpa
- Norwegian University of Science and Technology, Høgskoleringen 5, 7149 Trondheim, Norway.
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37
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Schnell SK, Skorpa R, Bedeaux D, Kjelstrup S, Vlugt TJH, Simon JM. Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation. J Chem Phys 2015; 141:144501. [PMID: 25318729 DOI: 10.1063/1.4896939] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtained with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation.
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Affiliation(s)
- Sondre K Schnell
- Process and Energy Laboratory, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Ragnhild Skorpa
- Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim, Norway
| | - Dick Bedeaux
- Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim, Norway
| | - Signe Kjelstrup
- Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim, Norway
| | - Thijs J H Vlugt
- Process and Energy Laboratory, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Jean-Marc Simon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS-Université de Bourgogne, 9, av. Savary, 21000 Dijon, France
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38
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Ashbaugh HS, Weiss K, Williams SM, Meng B, Surampudi LN. Temperature and Pressure Dependence of Methane Correlations and Osmotic Second Virial Coefficients in Water. J Phys Chem B 2015; 119:6280-94. [DOI: 10.1021/acs.jpcb.5b02056] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henry S. Ashbaugh
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Katie Weiss
- Alfred University, Alfred, New York 14802, United States
| | - Steven M. Williams
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Bin Meng
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Lalitanand N. Surampudi
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
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39
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Gutiérrez-Sevillano JJ, Leonhard K, van der Eerden JPJM, Vlugt TJH, Krooshof GJP. COSMO-3D: Incorporating Three-Dimensional Contact Information into the COSMO-SAC Model. Ind Eng Chem Res 2015. [DOI: 10.1021/ie504285x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. J. Gutiérrez-Sevillano
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - K. Leonhard
- Lehrstuhl
fur Technische Thermodynamik, RWTH Aachen University, 52056 Aachen, Germany
| | - J. P. J. M. van der Eerden
- Donders
Centre for Cognitive Neuroimaging, Radboud University Nijmegen, P.O. Box 9101, 6500 HB, The Netherlands
| | - T. J. H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - G. J. P. Krooshof
- Advanced
Chemical
Engineering Solutions (ACES), DSM ChemTech Center,
P.O. Box 18, 6160 MD Geleen, The Netherlands
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40
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Chaudhari MI, Sabo D, Pratt LR, Rempe SB. Hydration of Kr(aq) in Dilute and Concentrated Solutions. J Phys Chem B 2014; 119:9098-102. [DOI: 10.1021/jp508866h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Mangesh I. Chaudhari
- Center
for Biological and
Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
| | - Dubravko Sabo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Lawrence R. Pratt
- Department of Chemical
and
Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Susan B. Rempe
- Center for Biological and
Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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