Molecular dynamics simulations of hydration shell on montmorillonite (001) in water

2016 ◽  
Vol 48 (9) ◽  
pp. 976-980 ◽  
Author(s):  
Hao Yi ◽  
Xian Zhang ◽  
Yunliang Zhao ◽  
Lingyun Liu ◽  
Shaoxian Song
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydration Shell ◽  
Dynamics Simulations

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.

First and Second Hydration Shell of Ni2+ Studied by Molecular Dynamics Simulations

2006 ◽  
Vol 115 (2-3) ◽  
pp. 170-176 ◽  
Author(s):  
Andrei V. Egorov ◽  
Andrei V. Komolkin ◽  
Alexander P. Lyubartsev ◽  
Aatto Laaksonen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydration Shell ◽  
Dynamics Simulations

Anisotropic structure and dynamics of the solvation shell of a benzene solute in liquid water from ab initio molecular dynamics simulations

2016 ◽  
Vol 18 (8) ◽  
pp. 6132-6145 ◽  
Author(s):  
Ashu Choudhary ◽  
Amalendu Chandra
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid Water ◽  
Hydration Shell ◽  
Solvation Shell ◽  
Ab Initio Molecular Dynamics ◽  
Anisotropic Structure ◽  
Structure And Dynamics ◽  
Dynamics Simulations

The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke–Lee–Yang–Parr) and dispersion corrected BLYP-D functionals.

scholarly journals Ion-triggered selectivity in bacterial sodium channels

2018 ◽  
Vol 115 (21) ◽  
pp. 5450-5455 ◽  
Author(s):  
Simone Furini ◽  
Carmen Domene
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydration Shell ◽  
Membrane Potentials ◽  
Free Energy Calculations ◽  
Selectivity Filter ◽  
Atomic Scale ◽  
Steric Effects ◽  
Potassium Ions ◽  
Dynamics Simulations

Since the availability of the first crystal structure of a bacterial Na+ channel in 2011, understanding selectivity across this family of membrane proteins has been the subject of intense research efforts. Initially, free energy calculations based on molecular dynamics simulations revealed that although sodium ions can easily permeate the channel with their first hydration shell almost intact, the selectivity filter is too narrow for efficient conduction of hydrated potassium ions. This steric view of selectivity was subsequently questioned by microsecond atomic trajectories, which proved that the selectivity filter appears to the permeating ions as a highly degenerate, liquid-like environment. Although this liquid-like environment looks optimal for rapid conduction of Na+, it seems incompatible with efficient discrimination between similar ion species, such as Na+ and K+, through steric effects. Here extensive molecular dynamics simulations, combined with Markov state model analyses, reveal that at positive membrane potentials, potassium ions trigger a conformational change of the selectivity toward a nonconductive metastable state. It is this transition of the selectivity filter, and not steric effects, that prevents the outward flux of K+ at positive membrane potentials. This description of selectivity, triggered by the nature of the permeating ions, might have implications on the current understanding of how ion channels, and in particular bacterial Na+ channels, operate at the atomic scale.

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