scholarly journals Icephobicity of Functionalized Graphene Surfaces

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Xiang-Xiong Zhang ◽  
Min Chen
Keyword(s):  
Molecular Dynamics ◽  
Freezing Temperature ◽  
Ice Nucleation ◽  
Chloride Ions ◽  
Water Molecules ◽  
Sodium Ions ◽  
Functionalized Graphene ◽  
Functionalized Surfaces ◽  
The Difference ◽  
Dynamics Simulations

Manipulating the ice nucleation ability of liquid water by solid surface is of fundamental importance, especially in the design of icephobic surfaces. In this paper, the icephobicity of graphene surfaces functionalized by sodium ions, chloride ions, or methane molecules is investigated using molecular dynamics simulations. The icephobicity of the surface is evaluated by the freezing temperature. The freezing temperature on surface functionalized by methane molecules decreases at first and then increases as a function of the number groups, while the freezing temperature increases monotonically as a function of the number groups upon surfaces functionalized by sodium ions or chloride ions. The difference can be partially explained by the potential morphologies near the surfaces. Additionally, the validity of indicating the ice nucleation ability of water molecules using the number of six rings in the system is examined. Current study shows that the ice nucleation upon functionalized surfaces is inhibited when compared with smooth graphene substrate, which proves the feasibility of changing the icephobicity of the surfaces by functionalizing with certain ions or molecules.

A Molecular Dynamics Study of Aqueous Solutions

1976 ◽  
Vol 31 (5) ◽  
pp. 476-481 ◽  
Author(s):  
P. C. Vogel ◽  
K. Heinzinger
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solutions ◽  
Internal Pressure ◽  
Chloride Ions ◽  
Water Molecules ◽  
Sodium Ions ◽  
Nacl Solution ◽  
Hydration Shells

Abstract Results of a molecular dynamics study of a 0.55 molal aqueous NaCl solution are reported. The basic periodic box contained 200 water molecules, 2 sodium ions and 2 chloride ions. The calculated properties of this solution are compared with those obtained previously for a 2.2 molal NaCl solution. The formation of second hydration shells, an increase of the number of water molecules in the first hydration shells, and a release of internal pressure are the main changes connected with a decrease of the concentration.

scholarly journals Mechanism of dehydration in a non-porous variable hydrate

2014 ◽  
Vol 70 (a1) ◽  
pp. C1000-C1000
Author(s):  
Laszlo Fabian
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Chloride Ions ◽  
Smooth Transition ◽  
Water Molecules ◽  
Present Contribution ◽  
Gated Channel ◽  
Mechanism Of Dehydration ◽  
Paroxetine Hydrochloride ◽  
Dynamics Simulations

Paroxetine hydrochloride form II (PHCl-II) is a variable hydrate with a peculiar behaviour [1]. It changes its water content in response to changes in relative humidity with remarkable speed and in a completely reversible fashion. This is commonly observed for channel hydrates, but no continuous channels exist in the PHCl-II structure [2]. Powder diffraction results showed that loss of water produces an isostructural anhydrate, suggesting a simple, non-destructive mechanism of dehydration. The aim of the present contribution is to explain this unusual behaviour at a molecular level by using molecular dynamics simulations. Models of both the hydrated and anhydrous state could be created from the experimental hydrate structure by simple energy minimisation, which is in accordance with the experimentally observed smooth transition. A partially dehydrated supercell model was used to study the mechanism which allows water molecules to cross the steric barrier between adjacent solvent cavities. Since such transitions are rare on the simulation timescale (µs to ms), a steered molecular dynamics approach was applied. The results show that the passage of water molecules is facilitated by conformational changes, in which a ring system acts as a gate between cavities. When passing through the 'gate', water molecules are relayed between two chloride ions: as one Cl...HOH hydrogen bond is broken, another HOH...Cl one is formed. The progress of water molecules along the gated channel is not continuous, they spend a significant amount of time in each cavity between consecutive passages.

Molecular Dynamics Simulation of Quasi-Two-Dimensional Water Network on Ice Nucleation Protein

2011 ◽  
Author(s):  
Daisuke Murakami ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Water Clusters ◽  
Ice Nucleation ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Two Dimensional ◽  
Threshold Density ◽  
Ice Nucleation Protein ◽  
Network Of Hydrogen Bonds ◽  
Dynamics Simulations

An ice nucleation protein induces a phase transition from liquid water to ice in air. A specific hydrophilic surface of the protein may have an influence on the network of hydrogen bonds touching on the protein. However, microscopic characteristics of the ice nucleation protein and behavior of water molecules on it have not been clarified. So we carried out molecular dynamics simulations in various quasi-two-dimensional densities of water molecules on the ice nucleation protein. The percolation threshold of water clusters was confirmed. Comparing another hydrophilic protein, the threshold density in both cases had nearly the same value. But percolation probabilities and mean cluster sizes near the threshold were different between both cases. Those results implied that the threshold density was consistent with the conventional theory, but the forming of water clusters near the threshold was influenced by the hydrophilicity on the ice nucleation protein.

Nanocomputational Observation of Interaction of Two Cytotoxins and Nanobio Membrane: Molecular Dynamics Simulation Study

2011 ◽  
Vol 110-116 ◽  
pp. 3888-3892
Author(s):  
N. Maftouni ◽  
M. Amininassab ◽  
F. Kowsari
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Small Proteins ◽  
Steered Molecular Dynamics Simulation ◽  
The Difference ◽  
Dynamics Simulations ◽  
Naja Atra

Experimental observations have shown that cardio toxins (cobra cytotoxins), small proteins of three-fingered cytotoxin group, damage nanobiomembranes in different cells and vesicles. However, the molecular mechanism of this damage is not yet completely cleared. Molecular dynamics simulations have been used here to study the interaction of cardiotoxins A3 and A4 from Naja atra cobra venom with hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid bilayer in two separate systems. Each of studied systems included one cytotoxin molecule, 128 lipid molecules (64 molecules in each monolayer) and 11817 water molecules. It has been found that the toxin interacts with zwitterionic bilayer formed by POPC. At the beginning of simulation the cytotoxins have been oriented toward nanobiomembrane surface by their loops’ tips. This orientation has changed during first 50 ns of classical molecular dynamics simulation for both of studied cytotoxins. The A3 toxin finally meets POPC nanobiomembrane with sides of loops near tips including cytotoxin region THR148 and VAL155. The A4 cytotoxin molecule has been finally oriented toward surface of nanobiomembrane with base and one of loop's tip including THR184, ARG186 and LEU158 amino acids, after 50 ns molecular dynamics simulation. Then 25 ns steered molecular dynamics simulation has been done for both of systems. The obtained data suggest that cytotoxin A3 meets the nanobiomembrane with sides of loops near tips and A4 meets POPC nanobiomembrane with base and one of loop's tips. The difference between final orientations of these two cytotoxins comes from the difference in the structure of them.

scholarly journals Electrical Breakdown Mechanism of Transformer Oil with Water Impurity: Molecular Dynamics Simulations and First-Principles Calculations

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 123
Author(s):  
Bin Cao ◽  
Ji-Wei Dong ◽  
Ming-He Chi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Diffusion ◽  
First Principles ◽  
Electrical Breakdown ◽  
Transformer Oil ◽  
Water Molecules ◽  
Conducting Channel ◽  
Breakdown Mechanism ◽  
Water Impurity ◽  
Dynamics Simulations

Water impurity is the essential factor of reducing the insulation performance of transformer oil, which directly determines the operating safety and life of a transformer. Molecular dynamics simulations and first-principles electronic-structure calculations are employed to study the diffusion behavior of water molecules and the electrical breakdown mechanism of transformer oil containing water impurities. The molecular dynamics of an oil-water micro-system model demonstrates that the increase of aging acid concentration will exponentially expedite thermal diffusion of water molecules. Density of states (DOS) for a local region model of transformer oil containing water molecules indicates that water molecules can introduce unoccupied localized electron-states with energy levels close to the conduction band minimum of transformer oil, which makes water molecules capable of capturing electrons and transforming them into water ions during thermal diffusion. Subsequently, under a high electric field, water ions collide and impact on oil molecules to break the molecular chain of transformer oil, engendering carbonized components that introduce a conduction electronic-band in the band-gap of oil molecules as a manifestation of forming a conductive region in transformer oil. The conduction channel composed of carbonized components will be eventually formed, connecting two electrodes, with the carbonized components developing rapidly under the impact of water ions, based on which a large number of electron carriers will be produced similar to “avalanche” discharge, leading to an electrical breakdown of transformer oil insulation. The water impurity in oil, as the key factor for forming the carbonized conducting channel, initiates the electric breakdown process of transformer oil, which is dominated by thermal diffusion of water molecules. The increase of aging acid concentration will significantly promote the thermal diffusion of water impurities and the formation of an initial conducting channel, accounting for the degradation in dielectric strength of insulating oil containing water impurities after long-term operation of the transformer.

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 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.

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