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Understanding Water Structure in an Ion-Pair Solvation Shell in the Vicinity of a Water/Membrane Interface.

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TLDR
This study reveals that the effect of the aqueous interface on the first solvation shell of the ion pair and thus on the ion pairing thermodynamics becomes more pronounced in the polarizable model, and that the free energy profile along the interionic distance cannot capture the difference in the degree of solvent participation in ion pairing at the water/membrane interface.
Abstract
The anomalous properties of interfacial water at the surface of a lipid membrane and their implications on nearby chemical processes are well recognized. However, we have found that ion pairing thermodynamics may not be significantly affected by interfacial water in a classical, nonpolarizable force field. To trace the root cause of such a counterintuitive finding, we performed atomistic molecular dynamics simulations to explore the impact of polarizable interactions and characterize the hydration structure of a sodium chloride (NaCl) ion pair at the surface of a model lipid membrane and in a bulk phase. Our study reveals that the effect of the aqueous interface on the first solvation shell of the ion pair and thus on the ion pairing thermodynamics becomes more pronounced in the polarizable model, and that the free energy profile along the interionic distance cannot capture the difference in the degree of solvent participation in ion pairing at the water/membrane interface. This study also forms the basis for the future design of a reaction coordinate that takes the behavior of the interfacial water into account.

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Effect of Cholesterol on the Structure of Networked Water at the Surface of a Model Lipid Membrane.

TL;DR: Cholesterol provides a more bulk-like environment for the interfacial water molecules, as evidenced by enhancement of local water density, a reduction in their orientational bias, and increases in both the number of hydrogen bonds and the topological complexity of the hydrogen bond network.
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Ion Association and Electrolyte Structure at Surface Films in Lithium-Ion Batteries

TL;DR: In this article, the authors describe the degradation of carbonate electrolytes from redox side reactions to produce electrode surface films, and the composition of these films depends on the compo...
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Decoding Interfacial Water Orientation to Predict Surface Charge Density on a Model Sheet Using a Deep Learning Algorithm

TL;DR: In this paper, the anomalous behavior of water at the aqueous interface of a surface has been thoroughly investigated over the past decades, and indirect surface characterization based on the properties of i...
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The lung surfactant activity probed with molecular dynamics simulations.

TL;DR: In this article , the surface of pulmonary alveolar subphase is covered with a mixture of lipids and proteins, and it shows a complex phase behavior which can be altered by the interaction with third molecules such as drugs or pollutants.
References
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Journal ArticleDOI

VMD: Visual molecular dynamics

TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
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Comparison of simple potential functions for simulating liquid water

TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
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Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes

TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
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Canonical dynamics: Equilibrium phase-space distributions

TL;DR: The dynamical steady-state probability density is found in an extended phase space with variables x, p/sub x/, V, epsilon-dot, and zeta, where the x are reduced distances and the two variables epsilus-dot andZeta act as thermodynamic friction coefficients.
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Scalable molecular dynamics with NAMD

TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
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