A Molecular Dynamics Study of Aqueous Solutions

1979 ◽  
Vol 34 (12) ◽  
pp. 1424-1435 ◽  
Author(s):  
P. Bopp ◽  
W. Dietz ◽  
K. Heinzinger
Keyword(s):  
Molecular Dynamics ◽  
Fourier Transformation ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Force Model ◽  
Hydration Water ◽  
Nacl Solution ◽  
Velocity Autocorrelation ◽  
Hydration Shells ◽  
Velocity Autocorrelation Functions

Abstract The central force model for water has been employed in a molecular dynamics simulation of a 2.2 molal NaCl solution. The structural properties of the solution obtained are compared with results of previous simulations where the ST2 model of water was used. Preliminary results on the influence of the ions on the water molecule geometry in the hydration shells are reported. The spectral densities calculated from the hydrogen velocity autocorrelation functions by Fourier transformation indicate differences in the librational and vibrational frequencies between bulk water and hydration water of Na+ and Cl-.

Molecular Dynamics Study of a KCl Aqueous Solution: Dynamical Results

1987 ◽  
Vol 42 (3) ◽  
pp. 227-230 ◽  
Author(s):  
M. Migliore ◽  
S. L. Fornili ◽  
E. Spohr ◽  
K. Heinzinger
Keyword(s):  
Diffusion Coefficients ◽  
Md Simulation ◽  
Bulk Water ◽  
Water Molecules ◽  
Hydration Water ◽  
Self Diffusion ◽  
Average Temperature ◽  
Velocity Autocorrelation ◽  
Dynamical Properties ◽  
Velocity Autocorrelation Functions

In this paper we report on dynamical properties of a 2.2 molal aqueous KCl solution as obtained from an 8.7 ps MD simulation at an average temperature of 289 K. Velocity autocorrelation functions, self-diffusion coefficients and spectral densities of the hindered translational and librational motions of the ions and the water molecules assigned to three subsystems - hydration water of the cations, hydration water of the anions and bulk water - are discussed.

Molecular Dynamics Study of the Effect of Pressure on an Aqueous NaCl Solution

1985 ◽  
Vol 40 (12) ◽  
pp. 1235-1247 ◽  
Author(s):  
G. Jancsó ◽  
K. Heinzinger ◽  
P. Bopp
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Room Temperature ◽  
Bulk Water ◽  
Force Model ◽  
Nacl Solution ◽  
Self Diffusion ◽  
Dynamical Properties ◽  
Temperature And Pressure ◽  
Dynamics Simulations

Molecular dynamics simulations of a 2.2 molal NaCI solution at room temperature and pressure of 1 bar and 10 kbar have been performed employing a modified version of the central-force model of water. The changes in the structural and dynamical properties of the solution resulting from the increase in pressure are reported. The effect of ions on the self-diffusion coefficients of hydration and bulk water and on the IR spectroscopical properties of the solution is also discussed and compared with the available experimental data.

scholarly journals Hydration and its Hydrogen Bonding State on a Protein Surface in the Crystalline State as Revealed by Molecular Dynamics Simulation

2021 ◽  
Vol 9 ◽  
Author(s):  
Hiroshi Nakagawa ◽  
Taro Tamada
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystalline State ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Protein Crystal ◽  
Hydration Water ◽  
Protein Surface ◽  
Bonding State

Protein hydration is crucial for the stability and molecular recognition of a protein. Water molecules form a hydration water network on a protein surface via hydrogen bonds. This study examined the hydration structure and hydrogen bonding state of a protein, staphylococcal nuclease, at various hydration levels in its crystalline state by all-atom molecular dynamics (MD) simulation. Hydrophilic residues were more hydrated than hydrophobic residues. As the water content increases, both types of residues were uniformly more hydrated. The number of hydrogen bonds per single water asymptotically approaches 4, the same as bulk water. The distances and angles of hydrogen bonds in hydration water in the protein crystal were almost the same as those in the tetrahedral structure of bulk water regardless of the hydration level. The hydrogen bond structure of hydration water observed by MD simulations of the protein crystalline state was compared to the Hydrogen and Hydration Database for Biomolecule from experimental protein crystals.

scholarly journals Comparative Studies on Water Self-Diffusivity Confined in Graphene Nanogap: Molecular Dynamics Simulation

2016 ◽  
Author(s):  
Mohammad Moulod ◽  
Gisuk Hwang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Surface Energy ◽  
Water Transport ◽  
Surface Interactions ◽  
Bulk Water ◽  
Water Desalination ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Interatomic Potentials

Fundamental understanding of the water in graphene is crucial to optimally design and operate the sustainable energy, water desalination, and bio-medical systems. A numerous atomic-scale studies have been reported, primarily articulating the surface interactions (interatomic potentials) between the water and graphene. However, a systematic comparative study among the various interatomic potentials is rare, especially for the water transport confined in the graphene nanostructure. In this study, the effects of different interatomic potentials and gap sizes on water self-diffusivity are investigated using the molecular dynamics simulation at T = 300 K. The water is confined in the rigid graphene nanogap with the various gap sizes Lz = 0.7 to 4.17 nm, using SPC/E and TIP3P water models. The water self-diffusivity is calculated using the mean squared displacement approach. It is found that the water self-diffusivity in the confined region is lower than that of the bulk water, and it decreases as the gap size decreases and the surface energy increases. Also, the water self-diffusivity nearly linearly decreases with the increasing surface energy to reach the bulk water self-diffusivity at zero surface energy. The obtained results provide a roadmap to fundamentally understand the water transport properties in the graphene geometries and surface interactions.

Molecular Dynamics Simulation Study of the Liquid Crystal Phase in a Small Mesogene Cluster (5CB)22

2008 ◽  
Vol 140 ◽  
pp. 89-96 ◽  
Author(s):  
W. Gwizdała ◽  
A. Dawid ◽  
Z. Gburski
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystal ◽  
Rigid Bodies ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Total Dipole Moment ◽  
Lennard Jones ◽  
Nanoscale System ◽  
Velocity Autocorrelation ◽  
Vaporization Temperature

The molecular dynamics (MD) technique was used to investigate the nano droplet composed of twenty mesogene molecules 4-cyano-4-n-pentylbiphenyl (5CB). The 5CB molecules were treated as rigid bodies, the intermolecular interaction was taken to be the full site-site pairwise additive Lennard-Jones (LJ) potential plus a Coulomb interaction. The radial distribution functions in the temperature range from 150 to 400 K, were calculated as well as the linear and angular velocity autocorrelation functions. In addition the total dipole moment autocorrelation function and dielectric loss of (5CB)22 mesogene cluster were calculated and the liquid crystal ordering in the nanoscale system was studied up to its vaporization temperature.

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