Molecular Dynamics Simulations of Water and Ion Structures Near Charged Surfaces

Author(s):  
Dongyan Xu ◽  
Deyu Li ◽  
Yongsheng Leng

Extensive research has been devoted to nanofluidics in the past decade because of its potential applications in single molecule sensing and manipulations. Fundamental studies have attracted significant attention in this research field since the success of nanofluidic devices depends on a thorough understanding of the fluidic, ionic, and molecular behavior in highly confined nano-environments. In this paper, we report on molecular dynamics simulations of the effect of surface charge densities on the ion distribution and the water density profile close to a charged surface. We demonstrate that surface charges not only interact with mobile ions in the electrolyte, but also interact with water molecules due to their polarizability, and hence influence the orientation of water molecules in the near wall region. For the first time, we show that as the surface charge density increases, the water molecules within ∼ 5 Å of the {100} silicon surface will evolve from one layer into two layers. Meanwhile, the orientation of the water molecules is more aligned instead of randomly distributed. This layering effect may have important implications on electroosmotic flow through nanochannels and heat transfer across the solid-liquid interface.

Author(s):  
Dongyan Xu ◽  
Deyu Li ◽  
Yongsheng Leng ◽  
Yunfei Chen

Fundamental studies in nanofluidics have attracted significant attention in the past decade since the success of nanofluidic devices depends on a thorough understanding of the fluidic, ionic, and molecular behaviors in highly confined nano-environments. In this work, molecular dynamics simulations of the effect of surface charge densities on the ion and water distribution in the near wall region has been performed for both (100) and (111) silicon surfaces. We demonstrate that surface charges not only interact with mobile ions in the electrolyte, but also interact with water molecules due to their polarizability and hence influence the orientation of water molecules close to the charged surface. It is shown that as the surface charge density increases, water molecules within ∼ 5 Å from the (100) silicon surface can evolve from one layer into two layers and meanwhile, the orientation of water molecules is more aligned instead of randomly distributed. However, no extra water layer is observed near a (111) silicon surface even under a surface charge density of as high as −0.2034 C/m2. The above phenomenon may be related to the different surface atom densities of (100) and (111) silicon surfaces.


2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  

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.


2020 ◽  
Vol 65 (6) ◽  
pp. 510
Author(s):  
S. Perepelytsya

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.


Biopolymers ◽  
2007 ◽  
Vol 85 (2) ◽  
pp. 169-184 ◽  
Author(s):  
S. Elizabeth McDowell ◽  
Nad'a Špačková ◽  
Jiří Šponer ◽  
Nils G. Walter

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 ◽  
...  

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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