Driven water/ion transport through narrow nanopores: a molecular dynamics perspective

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water molecules through the cutin biopolymer. The theoretical analysis gives evidence that water permeation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

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Effects of Hydrogen Bonding on the Rotational Dynamics of Water-Like Molecules in Liquids: Insights from Molecular Dynamics Simulations

Australian Journal of Chemistry ◽

10.1071/ch19537 ◽

2020 ◽

Vol 73 (8) ◽

pp. 734

Author(s):

W. A. Monika Madhavi ◽

Samantha Weerasinghe ◽

Konstantin I. Momot

Keyword(s):

Molecular Dynamics ◽

Hydrogen Bonding ◽

Hydrogen Sulfide ◽

Spin Relaxation ◽

Rotational Diffusion ◽

Molecular Geometry ◽

Md Simulations ◽

Water Molecules ◽

Molecular Reorientation ◽

Nmr Spin Relaxation

Rotational motion of molecules plays an important role in determining NMR spin relaxation properties of liquids. The textbook theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of molecules is described by a continuous time rotational diffusion random walk with a single rotational diffusion coefficient. Previously we and others have shown that reorientation of water molecules on the timescales of picoseconds is not consistent with the Debye rotational-diffusion model. In particular, multiple timescales of molecular reorientation were observed in liquid water. This was attributed to the hydrogen bonding network in water and the consequent presence of collective rearrangements of the molecular network. In order to better understand the origins of the complex reorientational behaviour of water molecules, we carried out molecular dynamics (MD) simulations of a liquid that has a similar molecular geometry to water but does not form hydrogen bonds: hydrogen sulfide. These simulations were carried out at T=208K and p=1 atm (~5K below the boiling point). Ensemble-averaged Legendre polynomial functions of hydrogen sulfide exhibited a Gaussian decay on the sub-picosecond timescale but, unlike water, did not exhibit oscillatory behaviour. We attribute these differences to hydrogen sulfide’s absence of hydrogen bonding.

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Stabilization of DPPC lipid bilayers in the presence of co-solutes: molecular mechanisms and interaction patterns

Physical Chemistry Chemical Physics ◽

10.1039/d1cp03052c ◽

2021 ◽

Author(s):

Fabian Keller ◽

Andreas Heuer ◽

Hans-Joachim Galla ◽

Jens Smiatek

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Lipid Bilayers ◽

Density Functional ◽

Molecular Mechanisms ◽

Md Simulations ◽

Water Molecules ◽

Interaction Patterns ◽

Conceptual Density Functional Theory ◽

Functional Theory

The interactions between DPPC lipid bilayers in different phases with ectoine, amino ectoine and water molecules are studied by means of atomistic molecular dynamics (MD) simulations and conceptual density functional theory (DFT) calculations.

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Gating Mechanism of Hv1 Studied by Molecular Dynamic Simulations

Materials Proceedings ◽

10.3390/iocn2020-07862 ◽

2020 ◽

Vol 4 (1) ◽

pp. 20

Author(s):

Thi Tuong Vy Phan

Keyword(s):

Molecular Dynamics ◽

Cancer Progression ◽

Md Simulations ◽

Proton Channel ◽

Water Molecules ◽

State Structure ◽

Ph Homeostasis ◽

Dynamic Simulations ◽

Closed State ◽

Gating Mechanism

The voltage-gated proton channel (Hv1) plays the important role in proton extrusion, pH homeostasis, sperm motility, and cancer progression. The closed-state structure of Hv1 was recently revealed by X-ray crystallography. However, the opened-state structure has not been captured yet. To investigate the mechanism of proton transfer in Hv1, molecular dynamics (MD) simulations were performed with the closed-state structure of Hv1 under electric field and pH conditions. The residues arrangement on the closed-state structure revealed that the selectivity filter (Asp108) which is located in the hydrophobic layer (consists of two Phe residues 146 and 179) might prevent water penetration. In molecular dynamics simulations, we observed that the channel opened by moving 3 Arg up on the S4 helix and a continuous hydrogen-bonded chain of water molecules (a “water wire”) went through the channel when it opened. During simulations, the open channel allowed water molecules to pass through the channel but excluded other ions. This indicates the Hv1 channel is highly selective for protons. Our results clearly showed the Hv1 channel is voltage-and pH-gradient sensing.

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Polarizable force field for molecular dynamics simulations of silver nanoparticles

Kharkov University Bulletin Chemical Series ◽

10.26565/2220-637x-2019-32-03 ◽

2019 ◽

Cited By ~ 1

Keyword(s):

Molecular Dynamics ◽

Polarization Effect ◽

Md Simulations ◽

Water Molecules ◽

Interfacial Water ◽

Silver Surface ◽

Polarizable Force Field ◽

Rod Model ◽

Adsorption Of Water ◽

Rigid Rod

Contact of silver metal surfaces with water, ions and organic ligands experiences induced charges, leading to attractive polarization. These forces play an important role at inorganic/organic interfaces and complement other non-bonded surface interactions. Despite the importance of these interactions, it, however, remains difficult to implement polarization effects to classical molecular dynamics (MD) simulations. In this contribution, we first present an overview of two popular polarizable models, such as Drude oscillator and the rigid rod model, which are utilized to mimic the polarizability of bulk metals. Second, we implemented the rigid rod model to the polarizable force field (FF) for a silver atom, which was further adapted for atomistic MD simulations of silver nanoparticles (AgNPs) composed of 1397 atoms. In our model, induced charge polarization is represented by the displacement of a charge-carrying virtual site attached rigidly to an original Ag atom. To explore the role of polarization, we compared the performance of the classical nonpolarizable FF and the new polarizable model in the MD simulations of adsorption of water and ions onto quasi-spherical AgNP and the flat crystalline silver surface. The analysis of the radial distribution function of Ag-Ag atoms demonstrated that the introduction of the polarization effect had minor effects on face-centered cubic (fcc) packing of silver atoms of bare and water-solvated AgNPs. We found that the polarizable FF causes some increase in attractive interactions between the silver surface and water molecules and Na+ ions. As a crucial test of the developed polarizable model, the structure of adsorbed interfacial water molecules was analyzed. Our data suggest that the environment-induced polarization of the silver surface contributes significantly to the structure of adsorbed interfacial water layers and it also plays an important role in the adsorption of positive ions. However, it was also found out that the polarization effect has a rather short-range effect, so that a minor contribution of silver polarization was seen for adsorption of water molecules and ions from distant solvation shells.

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Structure of Water Saturated CTMA-Montmorillonite Hybrid: Molecular Dynamics Simulation Investigation

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.233-235.1872 ◽

2011 ◽

Vol 233-235 ◽

pp. 1872-1877 ◽

Cited By ~ 2

Author(s):

Run Liang Zhu ◽

Thomas V. Shapley ◽

Marco Molinari ◽

Ge Fei ◽

Stephen C. Parker

Keyword(s):

Molecular Dynamics ◽

Interlayer Space ◽

Md Simulations ◽

Dynamics Simulation ◽

Basal Spacing ◽

Water Molecules ◽

Surface Oxygen ◽

Hydrogen Atoms ◽

Structure Of Water ◽

Water Saturated

Molecular dynamics (MD) simulations have been used to investigate the interlayer structure of water saturated organoclays. The basal spacing values of cetyltrimethylammonium (CTMA) intercalated montmorillonite (CTMA-Mont) in dry and water saturated states were detected using XRD. Then the results were compared with simulation results of dry CTMA-Mont. The MD simulations show that the CTMA cations form layer structures on siloxane surface and aggregate in the interlayer space. Water molecules can access part of the siloxane surface and form H-bonds with surface oxygen atoms by donating one or two of the hydrogen atoms. Thus, the water molecules close to the surface have a preferred orientation with the dipole pointing towards the surface, while in the interlayer space, the water molecules aggregate to form large clusters. The H-bonds between surface oxygen and water molecules are shown to be slightly weaker than those between water molecules. Although water molecules within interlayer space can form strong H-bonds as in bulk water the number of H-bond for each water molecule is reduced. Our results indicate that MD simulations represent a useful tool for exploring the microstructure of water saturated organoclays.

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Determination of Reference Chemical Potential Using Molecular Dynamics Simulations

Journal of Thermodynamics ◽

10.1155/2010/342792 ◽

2010 ◽

Vol 2010 ◽

pp. 1-5 ◽

Cited By ~ 3

Author(s):

Krishnadeo Jatkar ◽

Jae W. Lee ◽

Sangyong Lee

Keyword(s):

Molecular Dynamics ◽

Gas Hydrates ◽

Chemical Potential ◽

Md Simulations ◽

Water Molecules ◽

Chemical Potential Difference ◽

Guest Molecules ◽

Experimental Values ◽

Dynamics Simulations

A new method implementing molecular dynamics (MD) simulations for calculating the reference properties of simple gas hydrates has been proposed. The guest molecules affect interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed simulations to validate the experimental data for determining , the chemical potential difference between water and theoretical empty cavity at the reference state, for structure II type gas hydrates. Simulations have also been used to observe the variation of the hydrate unit cell volume with temperature. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. The values were close to the experimental values obtained by the Lee-Holder model, considering lattice distortion.

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Molecular dynamics simulation on the interfacial features of supercritical 1-butene/subcritical water

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633614500667 ◽

2014 ◽

Vol 13 (08) ◽

pp. 1450066 ◽

Cited By ~ 1

Author(s):

Huidong Zheng ◽

Jingjing Chen ◽

Fangdi Wu ◽

Suying Zhao

Keyword(s):

Molecular Dynamics ◽

Diffusion Coefficients ◽

Subcritical Water ◽

Md Simulations ◽

Extraction Process ◽

Supercritical Condition ◽

Dynamics Simulation ◽

Water Molecules ◽

Butanol Concentration ◽

Subcritical Condition

We studied the interfacial features of 1-butene/water and extraction process of 2-butanol by molecular dynamics (MD) simulations. The infinite dilute diffusion coefficients of 1-butene in water is larger than that of 2-butanol, and one important reason is that 2-butanol molecules can form hydrogen bonds with water molecules. 1-butene is more soluble in water under supercritical condition than that under subcritical condition. 1-butene under supercritical condition can extract more 2-butanol from aqueous solution than that under other conditions. A process of producing 2-butanol by the direct hydration of 1-butene is more competive when it operates under the supercritical conditions of 1-butene which due to a higher solubility of 1-butene in water, a larger diffusion coefficient of 1-butene and a lower 2-butanol concentration in water.

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Excess Properties of Water-Methanol Mixtures as Studied by MD Simulations

Zeitschrift für Naturforschung A ◽

10.1515/zna-1991-1-215 ◽

1991 ◽

Vol 46 (1-2) ◽

pp. 95-99 ◽

Cited By ~ 14

Author(s):

G. Pálinkás ◽

I. Bakó

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Mole Fraction ◽

Extreme Values ◽

Md Simulations ◽

Excess Properties ◽

Water Molecules ◽

Methanol Mixture ◽

Dynamics Simulations ◽

Pair Interactions

AbstractMolecular dynamics simulations with pair interactions reproduce experimental excess properties of methanol-water mixtures. Water molecules lose, and methanol molecules gain neighbours in the mixtures as compared to the solvents. The water-methanol mixture with 0.25 mole fraction of methanol, resulting in extreme values for different excess properties, is characterized by the highest number of molecules with maximal number of H-bonded neighbours.

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Structure and Ion Transport Pathways in 0.45Li2O-(0.55-x)P2O5-xB2O3 Glasses

MRS Proceedings ◽

10.1557/proc-1266-cc06-03 ◽

2010 ◽

Vol 1266 ◽

Author(s):

Tho Duc Thieu ◽

R. Prasada Rao ◽

Stefan Adams

Keyword(s):

Molecular Dynamics ◽

Ion Transport ◽

Photoelectron Spectroscopy ◽

Md Simulations ◽

Structural Effects ◽

Transport Pathways ◽

Xps Spectra ◽

X Ray ◽

Coordination Numbers ◽

Bond Valence Analysis

AbstractLithium borophosphate glasses 0.45Li2O-(0.55-x)P2O5-xB2O3 (where 0 ≤ x ≤ 0.40) were investigated focusing on the influence of cation mobility changes due to mixed glass former effect. It was found that glass transition temperature (Tg) increases and molar volume decreases with B2O3 addition. X-ray photoelectron spectroscopy (XPS) spectra showed that besides P-O-P, B-O-B and P=O, P-O-, B-O- bond peaks, an intermediate O1s peak due to P-O-B bonds emerges in glasses with B2O3 contents x ≥ 0.15. Molecular dynamics (MD) simulations for the same systems have been performed with an optimized potential, fitted to match bond lengths, coordination numbers and ionic conductivity (σdc). Structural effects on ion transport as the origin of the mixed glass former effect can be quantified by applying the bond valence analysis (BV) approach to the equilibrated MD trajectories.

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