scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2020 ◽  
Author(s):  
Miraslau Barabash ◽  
William Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Molecules ◽  
Complex Interplay ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

Abstract In order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. We now address the questions of the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in terms of experimentally accessible radial distributions functions, yielding results that agree well with molecular dynamics simulations. We show that the patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

A Molecular Dynamics Study of Ionic Hydration Near a Platinum Surface

1991 ◽  
Vol 46 (10) ◽  
pp. 876-886 ◽  
Author(s):  
J. Seitz-Beywl ◽  
M. Poxleitner ◽  
K. Heinzinger
Keyword(s):  
Boundary Layer ◽  
Molecular Dynamics ◽  
Distribution Functions ◽  
Water Molecules ◽  
Molecular Orbital Calculations ◽  
Platinum Surface ◽  
Average Temperature ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Dynamics Simulations

AbstractTwo Molecular Dynamics simulations have been performed where a Pt(100) surface is covered with three layers of water molecules and a lithium or an iodide ion is placed additionally in the boundary layer. The flexible BJH model of water is employed in the simulations and the ion-water, platinum-water and platinum-ion potentials are derived from molecular orbital calculations. The simulations extended over 7.5 ps at an average temperature of 298 K. The effect of the Pt(100) surface on the ionic hydration is demonstrated by the comparison of the radial distribution functions, the orientation of the water molecules and their geometrical arrangement in the first hydration shells of the ions in the boundary layer with those in a 2.2 molal bulk Lil solution.

scholarly journals Positively and Negatively Hydrated Counterions in Molecular Dynamics Simulations of DNA Double Helix

2020 ◽  
Vol 65 (6) ◽  
pp. 510
Author(s):  
S. Perepelytsya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Double Helix ◽  
Dipole Moments ◽  
Hydration Shell ◽  
Minor Groove ◽  
Water Molecules ◽  
Negative Hydration ◽  
Dynamics Simulations ◽  
Dna Double Helix

The DNA double helix is a polyanionic macromolecule that is neutralized in water solutions by metal ions (counterions). The property of counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na+ counterions and negative hydration of K+ and Cs+ counterions incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations. The results have shown that the dynamics of the hydration shell of counterions depends on the region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions localized in the minor groove of the double helix (about 50 ps for Na+ and lower than 10 ps for K+ and Cs+). The estimated potentials of the mean force for the hydration shells of counterions show that the water molecules are constrained too strongly, and the effect of negative hydration for K+ and Cs+ counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.

Anomalous diffusion of water molecules at grain boundaries in ice Ih

2018 ◽  
Vol 20 (20) ◽  
pp. 13944-13951 ◽  
Author(s):  
Pedro Augusto Franco Pinheiro Moreira ◽  
Roberto Gomes de Aguiar Veiga ◽  
Ingrid de Almeida Ribeiro ◽  
Rodrigo Freitas ◽  
Julian Helfferich ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Grain Boundaries ◽  
Anomalous Diffusion ◽  
First Principles ◽  
Water Molecules ◽  
Diffusive Behavior ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

First-principles and classical molecular dynamics simulations show that diffusion of water molecules at pre-melted grain boundaries in ice is glassy-like, showing sub-diffusive behavior.

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