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Sun Y, Zhang D, Bashir A, Li C, Fan Z. Scaling Solute-Solvent Distances to Improve Solubility and Ion Paring Predictions in Rigid Ion Models. J Phys Chem B 2023; 127:9575-9586. [PMID: 37906589 DOI: 10.1021/acs.jpcb.3c05993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Force fields based on the rigid ion model (RIM) have been developed to accurately predict the various physical and chemical properties of salts and water. However, the combined use of these models often fails to accurately predict the solubility of salts in water. To address this issue, several approaches, such as charge scaling or reparameterization, have been proposed. Nevertheless, these methods require laborious reparameterization of nonbonded force field parameters. In this article, we propose a scaling solute-solvent distance (SSSD) method to improve force fields in predicting salt solubility without changing the solute-solute and solvent-solvent interactions in the original force fields. This method can also tune the ion pairing of salt in water. One main advantage of the SSSD method is that reparameterization of the crystal and water models is not needed. We use two RIMs for the NaCl-water system (JC-SPC/E and SD-SPC/E) and the CHARMM force field for the KCl-water system to demonstrate the improved accuracy in predicting solubility by the SSSD method. Furthermore, we use the RDG-SPC/Fw force field to show that the SSSD method can also be used to tune the ion pairing of CaCO3 in water. Limitations of this method are also discussed.
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Affiliation(s)
- Ying Sun
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Dan Zhang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- Department of Chemistry, Shanghai University, Shanghai 200444, P. R. China
| | - Ayesha Bashir
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Chuncheng Li
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Zhaochuan Fan
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, P. R. China
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2
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Xie L, Chan KY, Li VCY. Molecular dynamics simulation of hydration and free energy of ions in nanochannels of polyelectrolyte threaded metal organic framework and the impacts on selective ion transport. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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3
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Takahashi K, Nakano H, Sato H. Unified polarizable electrode models for open and closed circuits: Revisiting the effects of electrode polarization and different circuit conditions on electrode-electrolyte interfaces. J Chem Phys 2022; 157:014111. [DOI: 10.1063/5.0093095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A precise understanding of the interfacial structure and dynamics is essential for the optimal design of various electrochemical devices. Herein, we propose a method for classical molecular dynamics simulations to deal with electrochemical interfaces with polarizable electrodes under the open circuit condition. Less attention has been paid to electrochemical circuit conditions in computation despite being often essential for a proper assessment, especially comparison between different models. The present method is based on the chemical potential equalization principle, as is a method developed previously to deal with systems under the closed circuit condition. These two methods can be interconverted through the Legendre transformation, so that the difference in the circuit conditions can be compared on the same footing. Furthermore, the electrode polarization effect can be correctly studied by comparing the present method with the conventional simulations with the electrodes represented by fixed charges, since both of the methods describe systems under the open circuit condition. The method is applied to a parallel-plate capacitor composed of platinum electrodes and an aqueous electrolyte solution. The electrode polarization effects have an impact on the interfacial structure of the electrolyte solution. We found that the difference in the circuit conditions significantly affects the dynamics of the electrolyte solution. The electric field at the charged electrode surface is poorly screened by the nonequilibrium solution structure in the open circuit condition, which accelerates the motion of the electrolyte solution.
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Affiliation(s)
| | | | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University - Katsura Campus, Japan
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4
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Priya P, Nguyen TC, Saxena A, Aluru NR. Machine Learning Assisted Screening of Two-Dimensional Materials for Water Desalination. ACS NANO 2022; 16:1929-1939. [PMID: 35043618 DOI: 10.1021/acsnano.1c05345] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
There exists a vast expanse of data in the literature which can be harnessed for accelerated design and discovery of advanced materials for various applications of importance ─ for example, desalination of seawater. Here, we develop a machine learning (ML) model, training it with ∼260 molecular dynamics (MD) computation results, to predict the desalination performance of 2D membranes that exist in the literature. The desalination performance variables of water flux and salt rejection rates are correlated to 49 material features related to the chemistry of the pores and the membranes along with applied pressure, salt concentration, partial charges on the atoms, geometry of the pore, the mechanical properties of the membranes, and the properties of water for the water model used. We used the ML model to screen 3814 structurally optimized 2D materials for maximum water flux and salt rejection rates from the literature. We found some candidates that perform ∼4 times better than the more popularly known 2D materials such as graphene and MoS2. This result is verified using data obtained from MD simulations performed on several representative 2D membranes for different classes. Such validated statistical frameworks using literature data can be very useful in guiding experiments in the field of functional materials for varied applications.
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Affiliation(s)
- Pikee Priya
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Thanh C Nguyen
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Anshul Saxena
- Walker Department of Mechanical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Narayana R Aluru
- Walker Department of Mechanical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
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5
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Shi P, Luo H, Tan X, Lu Y, Zhang H, Yang X. Molecular dynamics simulation study of adsorption of anionic–nonionic surfactants at oil/water interfaces. RSC Adv 2022; 12:27330-27343. [PMID: 36276041 PMCID: PMC9514088 DOI: 10.1039/d2ra04772a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/10/2022] [Indexed: 11/21/2022] Open
Abstract
Four anionic–nonionic surfactants with the same headgroups and different units of oxygen ethyl (EO) and oxygen propyl (PO) were adopted to investigate the influence on oil/water interfacial tensions in this article. Molecular dynamics (MD) simulations were conducted to study the interfacial property of the four surfactants. Four parameters were proposed to reveal the effecting mechanism of molecular structure on interfacial tension, which included the interfacial thickness, order parameter of the hydrophobic chain, radial distribution function, and the solvent accessible surface area. In addition, the electrostatic potential of the four surfactants was calculated. The research results indicated that the interface facial mask formed by the surfactants, which contained three EO or three PO units was more stable, and it was easier for the surfactants of six EO or six PO units to form a microemulsion at higher concentrations. The adsorption mechanism of the anionic–nonionic surfactant systems at the oil/water interfaces was supplemented at a molecular level, which provided fundamental guidance for an in-depth understanding of the optimal selection of the surfactants in enhancing oil recovery. Four anionic–nonionic surfactants with the same headgroups and different units of oxygen ethyl (EO) and oxygen propyl (PO) were adopted to investigate the influence on oil/water interfacial tensions in this article.![]()
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Affiliation(s)
- Peng Shi
- College of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin 150026, People's Republic of China
- College of Chemical Engineering, Harbin Institute of Petroleum, Harbin 150028, People's Republic of China
| | - Haibin Luo
- College of Chemical Engineering, Harbin Institute of Petroleum, Harbin 150028, People's Republic of China
| | - Xuefei Tan
- College of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin 150026, People's Republic of China
| | - Yang Lu
- College of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin 150026, People's Republic of China
| | - Hui Zhang
- College of Science, Harbin University of Science and Technology, Harbin 150080, People's Republic of China
| | - Xin Yang
- College of Chemical Engineering, Harbin Institute of Petroleum, Harbin 150028, People's Republic of China
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6
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Li Y, Yue X, Huang G, Wang M, Zhang Q, Wang C, Yi H, Wang S. Li + Selectivity of Carboxylate Graphene Nanopores Inspired by Electric Field and Nanoconfinement. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006704. [PMID: 33666333 DOI: 10.1002/smll.202006704] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/13/2021] [Indexed: 06/12/2023]
Abstract
The regulation of the ion selectivity by electric field and ion association on the Li+ selectivity of carboxyl functionalized graphene nanopores are investigated by molecular dynamics simulation. Carboxylate graphene nanopores of sub-2 nm exhibit excellent Li+ selectivity under the electric field of 1.0 V nm-1 . The results show that ion association inspired by electric field may be a key factor affecting ion selectivity of sub-2 nm nanopores. The ion association of Mg2+ and Cl- can be promoted obviously near the nanopores under the electric field of 1.0 V nm-1 . The migrating of Mg2+ can be retarded by stable clusters of Mg2+ and Cl- formed near nanopores. The degree of association of Li+ with Cl- is relatively low and the disassociation of the Li+ cluster is easier so that Li+ can more easily pass through the nanopores. These results gain insight into the effect of ion association inspired by electric field and nanoconfinement of graphene nanopore on Mg2+ /Li+ separation, and provide helpful information for the application of nanoporous materials in extraction of Li+ ion from salt-lake brine.
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Affiliation(s)
- Yingying Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Xingyi Yue
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Gen Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Mei Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Qingwen Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Chunchang Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Haibo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Shuangyin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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7
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Drecun O, Striolo A, Bernardini C. Structural and dynamic properties of some aqueous salt solutions. Phys Chem Chem Phys 2021; 23:15224-15235. [PMID: 34235528 DOI: 10.1039/d0cp05331g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aqueous salt solutions are utilized and encountered in wide-ranging technological applications and natural settings. Towards improved understanding of the effect of salts on the dynamic properties of such systems, dilute aqueous salt solutions (up to 1 molar concentration) are investigated here, via experiments and molecular simulations. Four salts are considered: sodium chloride, for which published results are readily available for comparison, ammonium acetate, barium acetate and barium nitrate, for which published data are scarce. In the present work, molecular dynamics (MD) simulations are conducted to quantify viscosity and water self-diffusion coefficients, together with rheometry and Pulsed Field Gradient Spin Echo (PFGSE)-NMR experiments for validation. Simulation predictions are consistent with experimental observations in terms of trend and magnitude of salt-specific effects. Combining insights from the approaches considered, an interpretation of the results is proposed whereby the capacity of salts to influence bulk dynamics arises from their molecular interfacial area and strength of interaction with first hydration-shell water molecules. For the concentration range investigated, the interpretation could be useful in formulating aqueous systems for applications including the manufacturing of advanced catalysts.
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Affiliation(s)
- Olivera Drecun
- Department of Chemical Engineering, University College London, UK.
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8
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Niblett SP, Limmer DT. Ion Dissociation Dynamics in an Aqueous Premelting Layer. J Phys Chem B 2021; 125:2174-2181. [DOI: 10.1021/acs.jpcb.0c11286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Samuel P. Niblett
- Materials Science Division, Lawrence Berkeley Laboratory, Berkeley, California 94720, United States
| | - David T. Limmer
- Chemistry Department, University of California, Berkeley, California 94720, United States
- Chemical Science Division, Lawrence Berkeley Laboratory, Berkeley, California 94720, United States
- Kavli Energy Nanosciences Institute, University of California, Berkeley, California 94720, United States
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9
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Alıcı H, Demir K. Investigation of the stability and the helix-tail interaction of sCT and its various charged mutants based on comparative molecular dynamics simulations. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2020.111057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Lim VT, Hahn DF, Tresadern G, Bayly CI, Mobley DL. Benchmark assessment of molecular geometries and energies from small molecule force fields. F1000Res 2020; 9:Chem Inf Sci-1390. [PMID: 33604023 PMCID: PMC7863993 DOI: 10.12688/f1000research.27141.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing.
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Affiliation(s)
- Victoria T. Lim
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - David F. Hahn
- Computational Chemistry, Janssen Research & Development, Beerse, B-2340, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Beerse, B-2340, Belgium
| | | | - David L. Mobley
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
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11
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Self-assembly of the surfactant mixtures on graphene in the presence of electrolyte: a molecular simulation study. ADSORPTION 2020. [DOI: 10.1007/s10450-020-00264-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Takahashi K, Nakano H, Sato H. A polarizable molecular dynamics method for electrode–electrolyte interfacial electron transfer under the constant chemical-potential-difference condition on the electrode electrons. J Chem Phys 2020; 153:054126. [DOI: 10.1063/5.0020619] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Ken Takahashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Nakano
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
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13
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Slapikas R, Dabo I, Sinnott SB. Optimized utilization of COMB3 reactive potentials in LAMMPS. J Chem Phys 2020; 152:224702. [PMID: 32534521 DOI: 10.1063/5.0009011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
An investigation to optimize the application of the third-generation charge optimized many-body (COMB3) interatomic potential and associated input parameters was carried out through the study of solid-liquid interactions in classical molecular dynamics simulations. The rates of these molecular interactions are understood through the wetting rates of water nano-droplets on a bare copper (111) surface. Implementing the Langevin thermostat, the influence of simulation time step, the number of atoms in the system, the frequency at which charge equilibration is performed, and the temperature relaxation rate are all examined. The results indicate that time steps of 0.4 fs are possible when using longer relaxation times for the system temperature, which is almost double the typical time step used for reactive potentials. The use of the charge equilibration allows for a fewer atomic layers to be used in the Cu slab. In addition, charge equilibrium schemes do not need to be performed every time step to ensure accurate charge transfer. Interestingly, the rate of wetting for the nanodroplets is dominantly dependent on the temperature relaxation time, which is predicted to significantly change the viscosity of the water droplets. This work provides a pathway for optimizing simulations using the COMB3 reactive interatomic potential.
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Affiliation(s)
- Robert Slapikas
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16801, USA
| | - Ismaila Dabo
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16801, USA
| | - Susan B Sinnott
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16801, USA
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14
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Rimsza JM, Kuhlman KL. Surface Energies and Structure of Salt-Brine Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2482-2491. [PMID: 32097016 DOI: 10.1021/acs.langmuir.9b03172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Permeability of salt formations is controlled by the equilibrium between the salt-brine and salt-salt interfaces described by the dihedral angle, which can change with the composition of the intergranular brine. Here, classical molecular dynamics (MD) simulations were used to investigate the structure and properties of the salt-brine interface to provide insight into the stability of salt systems. Mixed NaCl-KCl brines were investigated to explore differences in ion size on the surface energy and interface structure. Nonlinearity was noted in the salt-brine surface energy with increasing KCl concentration, and the addition of 10% KCl increased surface energies by 2-3 times (5.0 M systems). Size differences in Na+ and K+ ions altered the packing of dissolved ions and water molecules at the interface, impacting the surface energy. Additionally, ions at the interface had lower numbers of coordinating water molecules than those in the bulk and increased hydration for ions in systems with 100% NaCl or 100% KCl brines. Ultimately, small changes in brine composition away from pure NaCl altered the structure of the salt-brine interface, impacting the dihedral angle and the predicted equilibrium permeability of salt formations.
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Affiliation(s)
- Jessica M Rimsza
- Geochemistry Department, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
| | - Kristopher L Kuhlman
- Applied Systems Analysis & Research, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
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15
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Mason PE, Tavagnacco L, Saboungi ML, Hansen T, Fischer HE, Neilson GW, Ichiye T, Brady JW. Molecular Dynamics and Neutron Scattering Studies of Potassium Chloride in Aqueous Solution. J Phys Chem B 2019; 123:10807-10813. [PMID: 31769976 DOI: 10.1021/acs.jpcb.9b08422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Neutron diffraction with isotopic substitution (NDIS) experiments were done on both natural abundance potassium and isotopically labeled 41KCl heavy water solutions to characterize the solvent structuring around the potassium ion in water. Preliminary measurements suggested that the literature value for the coherent neutron scattering length (2.69 fm) for 41K was significantly in error. This value was remeasured using a neutron powder diffractometer and found to be 2.40 fm. This revision increases significantly the contrast between the natural abundance K and 41K by about 30% (from 1.0 to 1.3 fm). The experimentally determined structure factor of the potassium ion was then compared to that calculated from molecular dynamics (MD) simulations. Previous neutron scattering measurements of potassium gave a solvation number of 5.5 (see below). In this study, the NDIS and MD results are in good agreement and allowed us to derive a coordination number of 6.1 for water molecules and 0.8 for chloride ions around each K+ ion in 4 molal aqueous KCl solution.
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Affiliation(s)
- Philip E Mason
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic & Center for Biomolecules and Complex Molecular Systems , 16610 Prague 6 , Czech Republic
| | - Letizia Tavagnacco
- Department of Food Science , Cornell University , Ithaca , New York 14853 , United States
| | - Marie-Louise Saboungi
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie , UMR 7590 CNRS - Sorbonne Université, Campus Pierre et Marie Curie , 4, Place Jussieu , 75005 Paris , France
| | - Thomas Hansen
- Institut Laue-Langevin , 71 Avenue des Martyrs , 38042 Grenoble Cedex 9 , France
| | - Henry E Fischer
- Institut Laue-Langevin , 71 Avenue des Martyrs , 38042 Grenoble Cedex 9 , France
| | - George W Neilson
- H.H. Wills Physics Laboratory , University of Bristol , BS8 1TL Bristol , U.K
| | - Toshiko Ichiye
- Department of Chemistry , Georgetown University , Box 571227, Washington , DC 20057 , United States
| | - John W Brady
- Department of Food Science , Cornell University , Ithaca , New York 14853 , United States
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16
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Lee SH. Ionic mobilities of Na+ and Cl− at 25°C as a function of Ewald sum parameter: a comparative molecular dynamics simulation study. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1696966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Song Hi Lee
- Chemistry Institute for Functional Materials, Pusan National University, Pusan, South Korea
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17
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Tolmachev DA, Boyko OS, Lukasheva NV, Martinez-Seara H, Karttunen M. Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections. J Chem Theory Comput 2019; 16:677-687. [DOI: 10.1021/acs.jctc.9b00813] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- D. A. Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, St. Petersburg 199004, Russia
| | - O. S. Boyko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, St. Petersburg 199004, Russia
| | - N. V. Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, St. Petersburg 199004, Russia
| | - H. Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 6 CZ166 10, Czech Republic
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, St. Petersburg 199004, Russia
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18
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Bachler J, Handle PH, Giovambattista N, Loerting T. Glass polymorphism and liquid-liquid phase transition in aqueous solutions: experiments and computer simulations. Phys Chem Chem Phys 2019; 21:23238-23268. [PMID: 31556899 DOI: 10.1039/c9cp02953b] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the most intriguing anomalies of water is its ability to exist as distinct amorphous ice forms (glass polymorphism or polyamorphism). This resonates well with the possible first-order liquid-liquid phase transition (LLPT) in the supercooled state, where ice is the stable phase. In this Perspective, we review experiments and computer simulations that search for LLPT and polyamorphism in aqueous solutions containing salts and alcohols. Most studies on ionic solutes are devoted to NaCl and LiCl; studies on alcohols have mainly focused on glycerol. Less attention has been paid to protein solutions and hydrophobic solutes, even though they reveal promising avenues. While all solutions show polyamorphism and an LLPT only in dilute, sub-eutectic mixtures, there are differences regarding the nature of the transition. Isocompositional transitions for varying mole fractions are observed in alcohol but not in ionic solutions. This is because water can surround alcohol molecules either in a low- or high-density configuration whereas for ionic solutes, the water ion hydration shell is forced into high-density structures. Consequently, the polyamorphic transition and the LLPT are prevented near the ions, but take place in patches of water within the solutions. We highlight discrepancies and different interpretations within the experimental community as well as the key challenges that need consideration when comparing experiments and simulations. We point out where reinterpretation of past studies helps to draw a unified, consistent picture. In addition to the literature review, we provide original experimental results. A list of eleven open questions that need further consideration is identified.
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Affiliation(s)
- Johannes Bachler
- Institute of Physical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria.
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20
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Chattaraj KG, Paul S. How does temperature modulate the structural properties of aggregated melamine in aqueous solution—An answer from classical molecular dynamics simulation. J Chem Phys 2019; 150:064501. [DOI: 10.1063/1.5066388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
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21
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Lukasheva NV, Tolmachev DA, Karttunen M. Mineralization of phosphorylated cellulose: crucial role of surface structure and monovalent ions for optimizing calcium content. Phys Chem Chem Phys 2019; 21:1067-1077. [PMID: 30511059 DOI: 10.1039/c8cp05767b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cellulose can be phosphorylated to produce organic matrices with highly adsorptive properties for, e.g., biocompatible materials for biomedical applications. We focus on the effects of phosphorylation of surfaces of crystalline nanocellulose and, in particular, on the competitive adsorption of mono- and divalent cations (Na+ and Ca2+) typically contained in mineralizing salt mixtures using all-atom molecular dynamics (MD) simulations. Phosphorylation was applied at 12% and 25% both in water and CaCl2 solutions. Our main result shows that Na+ and Ca2+ cations are concentrated in different interfacial layers with Na+ ions penetrating much closer to the surface. This behavior cannot be described by the Poisson-Boltzmann theory or implicit solvent simulations. Our analysis shows that the physical origin of this observation is due to a balance between the electrostatic interactions and hydration free energy associated with the ions. Adsorption levels of the different ions also respond differently to changes in the degree of phosphorylation. We show that the number of adsorbed Na+ ions per phosphate group increases whereas the number of adsorbed Ca2+ ions decreases with an increasing degree of phosphorylation (or when the number of binding sites increases). The decrease in the number of adsorbed Ca2+ ions can be explained by an increasing "charge-charge" repulsion between the Ca2+ ions attracted by the charged surface. Importantly, our results demonstrate the existence of an optimum degree of phosphorylation in terms of adsorbed Ca2+ ions and can be used as a guideline in materials design, for example, when choosing the cellulose matrix or with other similarly structured biomolecular and polymer surfaces.
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Affiliation(s)
- Natalia V Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj pr. V.O., 31, 199004 St. Petersburg, Russia.
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22
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Nguyen CT, Beskok A. Charged nanoporous graphene membranes for water desalination. Phys Chem Chem Phys 2019; 21:9483-9494. [DOI: 10.1039/c9cp01079c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water desalination using positively and negatively charged single-layer nanoporous graphene membranes.
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Affiliation(s)
- Chinh Thanh Nguyen
- Department of Mechanical Engineering
- Southern Methodist University
- Dallas
- USA
| | - Ali Beskok
- Department of Mechanical Engineering
- Southern Methodist University
- Dallas
- USA
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23
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Lee SH, Kim J. Transport properties of bulk water at 243–550 K: a Comparative molecular dynamics simulation study using SPC/E, TIP4P, and TIP4P/2005 water models. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1562123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Song Hi Lee
- Chemistry Institute for Functional Materials, Pusan National University, Pusan, South Korea
| | - Jahun Kim
- Center for Instrumental Analysis, Kyungsung University, Pusan, South Korea
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24
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Shi P, Zhang H, Lin L, Song C, Chen Q, Li Z. Molecular dynamics study of the effect of inorganic salts on the monolayer of four surfactants at the oil/water interface. J DISPER SCI TECHNOL 2018. [DOI: 10.1080/01932691.2018.1462200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Peng Shi
- Key Laboratory of Engineering Dielectrics and Its Application of Ministry of Education & College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, People's Republic of China
- College of Chemical Engineering, Harbin Institute of Petroleum, Harbin, People's Republic of China
| | - Hui Zhang
- Key Laboratory of Engineering Dielectrics and Its Application of Ministry of Education & College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, People's Republic of China
| | - Lin Lin
- Key Laboratory of Engineering Dielectrics and Its Application of Ministry of Education & College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, People's Republic of China
| | - Chunhui Song
- Key Laboratory of Engineering Dielectrics and Its Application of Ministry of Education & College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, People's Republic of China
| | - Qingguo Chen
- Key Laboratory of Engineering Dielectrics and Its Application of Ministry of Education & College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, People's Republic of China
| | - Zesheng Li
- Key Laboratory of Cluster Science of Ministry of Education & School of Chemistry, Beijing Institute of Technology, Beijing, People's Republic of China
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25
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Yao G, Zhao J, Ramisetti SB, Wen D. Atomistic Molecular Dynamic Simulation of Dilute Poly(acrylic acid) Solution: Effects of Simulation Size Sensitivity and Ionic Strength. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b03549] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guice Yao
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, U.K
| | - Jin Zhao
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, U.K
| | | | - Dongsheng Wen
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, U.K
- School of Aeronautic Science and Engineering, Beihang University, Beijing, 100191, China
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26
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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27
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Cerdan AH, Martin NÉ, Cecchini M. An Ion-Permeable State of the Glycine Receptor Captured by Molecular Dynamics. Structure 2018; 26:1555-1562.e4. [DOI: 10.1016/j.str.2018.07.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 05/07/2018] [Accepted: 07/26/2018] [Indexed: 11/16/2022]
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28
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Structure, interactions and action of Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase. Biochem J 2018; 475:2457-2471. [DOI: 10.1042/bcj20180271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 11/17/2022]
Abstract
Biochemical and crystallographic studies on Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase (MtHIBADH), a member of the 3-hydroxyacid dehydrogenase superfamily, have been carried out. Gel filtration and blue native PAGE of MtHIBADH show that the enzyme is a dimer. The enzyme preferentially uses NAD+ as the cofactor and is specific to S-hydroxyisobutyric acid (HIBA). It can also use R-HIBA, l-serine and 3-hydroxypropanoic acid (3-HP) as substrates, but with much less efficiency. The pH optimum for activity is ∼11. Structures of the native enzyme, the holoenzyme, binary complexes with NAD+, S-HIBA, R-HIBA, l-serine and 3-HP and ternary complexes involving the substrates and NAD+ have been determined. None of the already known structures of HIBADH contain a substrate molecule at the binding site. The structures reported here provide for the first time, among other things, a clear indication of the location and interactions of the substrates at the active site. They also define the entrance of the substrates to the active site region. The structures provide information on the role of specific residues at the active site and the entrance. The results obtained from crystal structures are consistent with solution studies including mutational analysis. They lead to the proposal of a plausible mechanism of the action of the enzyme.
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29
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Rezaei Sani SM, Akhavan M, Jalili S. Salt-induced effects on natural and inverse DPPC lipid membranes: Molecular dynamics simulation. Biophys Chem 2018; 239:7-15. [DOI: 10.1016/j.bpc.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/22/2018] [Accepted: 04/22/2018] [Indexed: 11/29/2022]
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30
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Nguyen CT, Beskok A. Saltwater transport through pristine and positively charged graphene membranes. J Chem Phys 2018; 149:024704. [DOI: 10.1063/1.5032207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Chinh Thanh Nguyen
- Department of Mechanical Engineering, Southern Methodist University, Dallas, Texas 75205, USA
| | - Ali Beskok
- Department of Mechanical Engineering, Southern Methodist University, Dallas, Texas 75205, USA
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31
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Shadrack Jabes B, Klein R, Delle Site L. Structural Locality and Early Stage of Aggregation of Micelles in Water: An Adaptive Resolution Molecular Dynamics Study. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- B. Shadrack Jabes
- Institute for Mathematics Freie Universität Berlin D‐14195 Berlin Germany
| | - Rupert Klein
- Institute for Mathematics Freie Universität Berlin D‐14195 Berlin Germany
| | - Luigi Delle Site
- Institute for Mathematics Freie Universität Berlin D‐14195 Berlin Germany
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32
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Su Z, Ravindhran G, Dias CL. Effects of Trimethylamine-N-oxide (TMAO) on Hydrophobic and Charged Interactions. J Phys Chem B 2018; 122:5557-5566. [DOI: 10.1021/acs.jpcb.7b11847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Zhaoqian Su
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| | - Gopal Ravindhran
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| | - Cristiano L. Dias
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
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33
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Liang T, Antony AC, Akhade SA, Janik MJ, Sinnott SB. Applied Potentials in Variable-Charge Reactive Force Fields for Electrochemical Systems. J Phys Chem A 2018; 122:631-638. [DOI: 10.1021/acs.jpca.7b06064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Andrew C. Antony
- Department
of Materials Science and Engineering, The University of Florida, Gainesville, Florida 32611, United States
| | - Sneha A. Akhade
- Institute
for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, Washington 99352 United States
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34
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Li K, Liu L, Wu H, Li S, Yu C, Zhou Y, Huang W, Yan D. Understanding the temperature effect on transport dynamics and structures in polyamide reverse osmosis system via molecular dynamics simulations. Phys Chem Chem Phys 2018; 20:29996-30005. [DOI: 10.1039/c8cp05825c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Molecular simulations could disclose the transport dynamics, membrane structures and temperature effect on reverse osmosis process.
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Affiliation(s)
- Ke Li
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University
- Shanghai
- China
| | - Lifen Liu
- Center for Membrane and Water Science & Technology, Ocean College, Zhejiang University of Technology
- Hangzhou
- China
| | - Hao Wu
- Center for Membrane and Water Science & Technology, Ocean College, Zhejiang University of Technology
- Hangzhou
- China
| | - Shanlong Li
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University
- Shanghai
- China
| | - Chunyang Yu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University
- Shanghai
- China
| | - Yongfeng Zhou
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University
- Shanghai
- China
| | - Wei Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University
- Shanghai
- China
| | - Deyue Yan
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University
- Shanghai
- China
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35
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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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36
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Hunt PA. Quantum Chemical Modeling of Hydrogen Bonding in Ionic Liquids. Top Curr Chem (Cham) 2017; 375:59. [PMID: 28523638 PMCID: PMC5480408 DOI: 10.1007/s41061-017-0142-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/16/2017] [Indexed: 01/18/2023]
Abstract
Hydrogen bonding (H-bonding) is an important and very general phenomenon. H-bonding is part of the basis of life in DNA, key in controlling the properties of water and ice, and critical to modern applications such as crystal engineering, catalysis applications, pharmaceutical and agrochemical development. H-bonding also plays a significant role for many ionic liquids (IL), determining the secondary structuring and affecting key physical parameters. ILs exhibit a particularly diverse and wide range of traditional as well as non-standard forms of H-bonding, in particular the doubly ionic H-bond is important. Understanding the fundamental nature of the H-bonds that form within ILs is critical, and one way of accessing this information, that cannot be recovered by any other computational method, is through quantum chemical electronic structure calculations. However, an appropriate method and basis set must be employed, and a robust procedure for determining key structures is essential. Modern generalised solvation models have recently been extended to ILs, bringing both advantages and disadvantages. QC can provide a range of information on geometry, IR and Raman spectra, NMR spectra and at a more fundamental level through analysis of the electronic structure.
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Affiliation(s)
- Patricia A Hunt
- Imperial College of Science, Technology and Medicine, London, UK.
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37
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Giri AK, Spohr E. Cluster formation of NaCl in bulk solutions: Arithmetic vs. geometric combination rules. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.09.089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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38
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Jia F, Yang L, Wang Q, Song S. Correlation of natural muscovite exfoliation with interlayer and solvation forces. RSC Adv 2017. [DOI: 10.1039/c6ra26560j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Natural muscovite exfoliation was correlated with interlayer and solvation forces respectively in this work.
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Affiliation(s)
- Feifei Jia
- Hubei Key Laboratory of Mineral Resources Processing and Environment
- Wuhan University of Technology
- Wuhan
- China
- School of Resources and Environmental Engineering
| | - Lang Yang
- School of Resources and Environmental Engineering
- Wuhan University of Technology
- Wuhan
- China
| | - Qingmiao Wang
- School of Resources and Environmental Engineering
- Wuhan University of Technology
- Wuhan
- China
| | - Shaoxian Song
- Hubei Key Laboratory of Mineral Resources Processing and Environment
- Wuhan University of Technology
- Wuhan
- China
- School of Resources and Environmental Engineering
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39
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Lovrić J, Duflot D, Monnerville M, Toubin C, Briquez S. Water-Induced Organization of Palmitic Acid at the Surface of a Model Sea Salt Particle: A Molecular Dynamics Study. J Phys Chem A 2016; 120:10141-10149. [DOI: 10.1021/acs.jpca.6b07792] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josip Lovrić
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
| | - Denis Duflot
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
| | - Maurice Monnerville
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
| | - Céline Toubin
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
| | - Stéphane Briquez
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
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40
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Misin M, Vainikka PA, Fedorov MV, Palmer DS. Salting-out effects by pressure-corrected 3D-RISM. J Chem Phys 2016; 145:194501. [DOI: 10.1063/1.4966973] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Maksim Misin
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
| | - Petteri A. Vainikka
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Maxim V. Fedorov
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Moscow 143026, Russian Federation
| | - David S. Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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41
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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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42
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Hanasaki I, Fujiwara D, Kawano S. Departure of microscopic friction from macroscopic drag in molecular fluid dynamics. J Chem Phys 2016; 144:094503. [DOI: 10.1063/1.4943045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Wong-Ekkabut J, Karttunen M. Molecular dynamics simulation of water permeation through the alpha-hemolysin channel. J Biol Phys 2016; 42:133-46. [PMID: 26264478 PMCID: PMC4713412 DOI: 10.1007/s10867-015-9396-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 07/21/2015] [Indexed: 02/05/2023] Open
Abstract
The alpha-hemolysin (AHL) nanochannel is a non-selective channel that allows for uncontrolled transport of small molecules across membranes leading to cell death. Although it is a bacterial toxin, it has promising applications, ranging from drug delivery systems to nano-sensing devices. This study focuses on the transport of water molecules through an AHL nanochannel using molecular dynamics (MD) simulations. Our results show that AHL can quickly transport water across membranes. The first-passage time approach was used to estimate the diffusion coefficient and the mean exit time. To study the energetics of transport, the potential of mean force (PMF) of a water molecule along the AHL nanochannel was calculated. The results show that the energy barriers of water permeation across a nanopore are always positive along the channel and the values are close to thermal energy (kBT). These findings suggest that the observed quick permeation of water is due to small energy barriers and a hydrophobic inner channel surface resulting in smaller friction. We speculate that these physical mechanisms are important in how AHL causes cell death.
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Affiliation(s)
- Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University, 50 Phahon Yothin Rd, Chatuchak, Bangkok, Thailand, 10900.
| | - Mikko Karttunen
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1.
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, MetaForum, 5600 MB, Eindhoven, The Netherlands.
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Do TN, Choy WY, Karttunen M. Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations. J Chem Theory Comput 2015; 12:395-404. [PMID: 26636721 DOI: 10.1021/acs.jctc.5b00868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Keap1 protein plays an essential role in regulating cellular oxidative stress response and is a crucial binding hub for multiple proteins, several of which are intrinsically disordered proteins (IDP). Among Kelch's IDP binding partners, NRF2 and PTMA are the two most interesting cases. They share a highly similar binding motif; however, NRF2 binds to Kelch with a binding affinity of approximately 100-fold higher than that of PTMA. In this study, we perform an exhaustive sampling composed of 6 μs well-tempered metadynamics and 2 μs unbiased molecular dynamics (MD) simulations aiming at characterizing the binding mechanisms and structural properties of these two peptides. Our results agree with previous experimental observations that PTMA is remarkably more disordered than NRF2 in both the free and bound states. This explains PTMA's lower binding affinity. Our extensive sampling also provides valuable insights into the vast conformational ensembles of both NRF2 and PTMA, supports the hypothesis of coupled folding-binding, and confirms the essential role of linear motifs in IDP binding.
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Affiliation(s)
- Trang Nhu Do
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, ON, Canada N2L 3G1
| | - Wing-Yiu Choy
- Department of Biochemistry, University of Western Ontario , 1151 Richmond Street, London, ON, Canada N6A 3K7
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, MetaForum, 5600 MB, Eindhoven, The Netherlands
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Marchand G, Soetens JC, Jacquemin D, Bopp PA. Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution. J Chem Phys 2015; 143:224505. [DOI: 10.1063/1.4937156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Gabriel Marchand
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière, BP 92208, FR-44322 Nantes Cedex 3, France
| | - Jean-Christophe Soetens
- Institut des Sciences Moléculaires (ISM), Université de Bordeaux, Bât A12, FR-33405 Talence Cedex, France
| | - Denis Jacquemin
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS 6230, Université de Nantes, 2 rue de la Houssinière, BP 92208, FR-44322 Nantes Cedex 3, France
| | - Philippe A. Bopp
- Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
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46
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Auffinger P, Cheatham TE, Vaiana AC. Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue? J Chem Theory Comput 2015; 3:1851-9. [PMID: 26627627 DOI: 10.1021/ct700143s] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Realistic all-atom simulation of biological systems requires accurate modeling of both the biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to the rapid growth of KCl or NaCl clusters in the vicinity of biomolecular systems have been reported. To better understand this phenomenon, molecular dynamics simulations of KCl aqueous solutions at three (1.0, 0.25, and 0.10 M) concentrations were performed. Two popular water models (TIP3P and SPC/E) and two Lennard-Jones parameter sets (AMBER and Dang) were combined to produce a total of 80 ns of molecular dynamics trajectories. Results suggest that the use of the Dang cation Lennard-Jones parameters instead of those adopted by the AMBER force-field produces a more accurate description of the ionic solution. In the later case, formation of salt aggregates is probably indicative of an artifact resulting from misbalanced force-field parameters. Because similar results were obtained with two different water parameter sets, the simulations exclude a water model dependency in the formation of anomalous ionic clusters. Overall, the results strongly suggest that for accurate modeling of ions in biomolecular systems, great care should be taken in choosing balanced ionic parameters even when using the most popular force-fields. These results invite a reexamination of older data obtained using available force-fields and a thorough check of the quality of current parameters sets by performing simulations at finite (>0.25 M) instead of minimal salt conditions.
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Affiliation(s)
- Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France, and Department of Medical Chemistry, Pharmaceutical Chemistry and Pharmaceutics and Bioengineering, University of Utah, Salt Lake City, Utah 84112
| | - Thomas E Cheatham
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France, and Department of Medical Chemistry, Pharmaceutical Chemistry and Pharmaceutics and Bioengineering, University of Utah, Salt Lake City, Utah 84112
| | - Andrea C Vaiana
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France, and Department of Medical Chemistry, Pharmaceutical Chemistry and Pharmaceutics and Bioengineering, University of Utah, Salt Lake City, Utah 84112
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47
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Jensen KP, Jorgensen WL. Halide, Ammonium, and Alkali Metal Ion Parameters for Modeling Aqueous Solutions. J Chem Theory Comput 2015; 2:1499-509. [PMID: 26627020 DOI: 10.1021/ct600252r] [Citation(s) in RCA: 275] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A complete set of Lennard Jones parameters for the halide ions, F(-), Cl(-), Br(-), and I(-), ammonium ion, and the alkali metal ions is reported. The parameters have been optimized using Monte Carlo simulations and free energy perturbation theory with the TIP4P water model to reproduce experimental free energies of hydration and locations of the first maxima of the ion-oxygen radial distribution functions, to provide water coordination numbers consistent with experimental ranges, and to exhibit gas-phase monohydrate energies in reasonable agreement with ab initio values. Average errors for absolute and relative free energies of hydration for the ions are ca. 1 kcal/mol. For the halides, this is the first self-consistent set of parameters that has been optimized for aqueous-phase performance. The good results for relative free energies of hydration are particularly auspicious for use of the new parameters in a wide variety of liquid-phase simulations where halide and alkali cations are systematically varied.
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Affiliation(s)
- Kasper P Jensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
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Cordomí A, Edholm O, Perez JJ. Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers. J Chem Theory Comput 2015; 5:2125-34. [PMID: 26613152 DOI: 10.1021/ct9000763] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The behavior of electrolytes in molecular dynamics simulations of zwitterionic phospholipid bilayers is very sensitive to the force field parameters used. Here, several 200 ns molecular dynamics of simulations of dipalmitoyl phosphotidylcholine (PC) bilayers in 0.2 M sodium or potassium chloride using various common force field parameters for the cations are presented. All employed parameter sets give a larger number of Na(+) ions than K(+) ions that bind to the lipid heads, but depending on the parameter choice quite different results are seen. A wide range of coordination numbers for the Na(+) and K(+) ions is also observed. These findings have been analyzed and compared to published experimental data. Some simulations produce aggregates of potassium chloride, indicating (in accordance with published simulations) that these force fields do not reproduce the delicate balance between salt and solvated ions. The differences between the force fields can be characterized by one single parameter, the electrostatic radius of the ion, which is correlated to σMO (M represents Na(+)/K(+)), the Lennard-Jones radius. When this parameter exceeds a certain threshold, binding to the lipid heads is no longer observed. One would, however, need more accurate experimental data to judge or rank the different force fields precisely. Still, reasons for the poor performance of some of the parameter sets are clearly demonstrated, and a quality control procedure is provided.
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Affiliation(s)
- Arnau Cordomí
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
| | - Olle Edholm
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
| | - Juan J Perez
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
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49
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Kohagen M, Mason PE, Jungwirth P. Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering. J Phys Chem B 2015; 120:1454-60. [PMID: 26172524 DOI: 10.1021/acs.jpcb.5b05221] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modeled ions, described by nonpolarizable force fields, can suffer from unphysical ion pairing and clustering in aqueous solutions well below their solubility limit. The electronic continuum correction takes electronic polarization effects of the solvent into account in an effective way by scaling the charges on the ions, resulting in a much better description of the ionic behavior. Here, we present parameters for the sodium ion consistent with this effective polarizability approach and in agreement with experimental data from neutron scattering, which could be used for simulations of complex aqueous systems where polarization effects are important.
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Affiliation(s)
- Miriam Kohagen
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
| | - Philip E Mason
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
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50
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Antipina AY, Gurtovenko AA. Molecular Mechanism of Calcium-Induced Adsorption of DNA on Zwitterionic Phospholipid Membranes. J Phys Chem B 2015; 119:6638-45. [DOI: 10.1021/acs.jpcb.5b01256] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandra Yu. Antipina
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi
Prospect V.O. 31, St. Petersburg 199004, Russia
- Faculty
of Physics, St. Petersburg State University, Ulyanovskaya str. 1, Petrodvorets, St. Petersburg 198504, Russia
| | - Andrey A. Gurtovenko
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi
Prospect V.O. 31, St. Petersburg 199004, Russia
- Faculty
of Physics, St. Petersburg State University, Ulyanovskaya str. 1, Petrodvorets, St. Petersburg 198504, Russia
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