Diffusion coefficients of nitric oxide in water: A molecular dynamics study

2016 ◽  
Vol 30 (27) ◽  
pp. 1650205 ◽  
Author(s):  
Sunil Pokharel ◽  
Nurapati Pantha ◽  
N. P. Adhikari
Keyword(s):  
Nitric Oxide ◽  
Molecular Dynamics ◽  
Mole Fraction ◽  
Diffusion Coefficients ◽  
Low Temperatures ◽  
Mean Square Displacement ◽  
Mutual Diffusion ◽  
Arrhenius Behavior ◽  
Self Diffusion ◽  
Experimental Values

Self-diffusion coefficients along with the mutual diffusion coefficients of nitric oxide (NO) and SPC/E water (H2O) as solute and solvent of the mixture, have been studied within the framework of classical molecular dynamics level of calculations using GROMACS package. The radial distribution function (RDF) of the constituent compounds are calculated to study solute–solute, solute–solvent and solvent–solvent molecular interactions as a function of temperature. A dilute solution of five NO molecules (mole fraction 0.018) and 280 H2O molecules (mole fraction 0.982) has been taken as the sample. The self-diffusion coefficient of the solvent is calculated by using mean square displacement (MSD) where as that for solute (NO) is calculated by using MSD and velocity auto-correlation function (VACF). The results are then compared with the available experimental values. The results from the present work for water come in good agreement, very precise at low temperatures, with the experimental values. The diffusion coefficients of NO, on the other hands, agree well with the available theoretical studies, and also with experiment at low temperatures (up to 310 K). The results at the higher temperatures (up to 333 K), however, deviate significantly with the experimental observations. Also, the mutual diffusion coefficients of NO in water have been calculated by using Darken’s relation. The temperature dependence of the calculated diffusion coefficients follow the Arrhenius behavior.

scholarly journals Diffusion of fructose in water: a molecular dynamics study

2020 ◽  
pp. 30-44
Author(s):  
Santosh Bhusal ◽  
Nurapati Pantha
Keyword(s):  
Molecular Dynamics ◽  
Mole Fraction ◽  
Diffusion Coefficients ◽  
Mean Square Displacement ◽  
The Self ◽  
Arrhenius Behavior ◽  
Binary Diffusion ◽  
Self Diffusion ◽  
Water Solvent ◽  
Binary Diffusion Coefficients

Present work carries the molecular dynamics (MD) simulation to study the self-diffusion coefficients of fructose (C6H12O6) and SPC/E (Extended Simple Point Charge) water (H2O) along with their binary diffusion coefficients at different temperature (298.15 K, 303.15 K, 308.15 K and 312.15 K). A dilute solution of 3 molecules of fructose (solute, mole fraction 0.0018) and 1624 molecules of water (solvent, mole fraction 0.9982) has been taken for making it relevant to the previously reported experiment. The structural analysis of the mixture has been estimated by using the radial distribution function (RDF) of its constituents. Mean square displacement (MSD) and Einstein’s relation have been used to find the self-diffusion coefficients of both the solute and solvent. Furthermore, Darken’s relation finds the binary diffusion coefficients. The temperature dependence of diffusion coefficients follows the Arrhenius behavior which further calculates activation energy of diffusion. The results from the present work agree well with the previously reported experimental values.

Molecular dynamics study of diffusion of krypton in water at different temperatures

2016 ◽  
Vol 30 (11) ◽  
pp. 1650064 ◽  
Author(s):  
Dipendra Bhandari ◽  
N. P. Adhikari
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Diffusion Coefficients ◽  
Mean Square Displacement ◽  
Mutual Diffusion ◽  
Arrhenius Behavior ◽  
Self Diffusion ◽  
Velocity Autocorrelation ◽  
Different Temperatures ◽  
Self Diffusion Coefficient

Molecular dynamics study of diffusion of two krypton atoms in 300 SPC/E water molecules at temperatures 293, 303, 313, 323 and 333 K has been carried out. Self-diffusion coefficient of krypton and water along with their mutual diffusion coefficients are estimated. Self-diffusion coefficient for krypton is calculated by using Mean Square Displacement (MSD) method and Velocity Autocorrelation (VACF) method, while that for water is calculated by using MSD method only. The mutual diffusion coefficient is estimated by using the Darken’s relation. The diffusion coefficients are found to follow the Arrhenius behavior. The structural properties of the system have been estimated by the study of solute–solute, solvent–solvent, and solute–solvent Radial Distribution Function (RDF).

MOLECULAR DYNAMICS STUDY OF DIFFUSION OF DIFFERENT INERT GASES LIKE NEON AND ARGON IN WATER AT DIFFERENT TEMPERATURES

2012 ◽  
Vol 26 (03) ◽  
pp. 1250016 ◽  
Author(s):  
H. B. MOKTAN ◽  
A. PANDAY ◽  
N. P. ADHIKARI
Keyword(s):  
Molecular Dynamics ◽  
Temperature Dependence ◽  
Radial Distribution ◽  
Diffusion Coefficients ◽  
Mean Square Displacement ◽  
Distribution Functions ◽  
Inert Gases ◽  
Self Diffusion ◽  
Arrhenius Relation ◽  
Different Temperatures

Molecular dynamics study of a binary mixture of inert gases like neon and argon in SPC/E water, with the solute mole fraction of 0.023 have been accomplished at temperatures 288, 293, 298, 303, 308 and 313 K. The solvent–solvent, solute–solute and solute–solvent radial distribution functions have been estimated. The water–water radial distribution function has been found to agree well with the experimental value. Self-diffusion coefficients of both solvent and solutes have been determined by means of respective mean square displacement (MSD) curves using the Einstein's relation. The obtained values for the self-diffusion coefficients of these gases and solvent SPC/E water is found to agree well with available experimental values. The binary diffusion coefficients of these gases in water have then been estimated by using the Darken's relation. The temperature dependence of the diffusion coefficients has also been analyzed. The temperature dependence of estimated values of self-diffusion coefficients of water have been found to obey the Arrhenius relation. Self-diffusion coefficient of neon and argon is found to vary with the temperature according as Arrhenius relation.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

scholarly journals Self-Diffusion Coefficients of Methane/n-Hexane Mixtures at High Pressures: An Evaluation of the Finite-Size Effect and a Comparison of Force Fields

2019 ◽  
Author(s):  
Thiago José Pinheiro dos Santos ◽  
Charlles Abreu ◽  
Bruno Horta ◽  
Frederico W. Tavares
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
High Pressures ◽  
Force Fields ◽  
Transport Coefficients ◽  
Finite Size ◽  
Finite Size Effect ◽  
Self Diffusion ◽  
Analytical Correction ◽  
Dynamics Simulations

Mass transport coefficients play an important role in process design and in compositional grading of oil reservoirs. As experimental measurements of these properties can be costly and hazardous, Molecular Dynamics simulations emerge as an alternative approach. In this work, we used Molecular Dynamics to calculate the self-diffusion coefficients of methane/n-hexane mixtures at different conditions, in both liquid and supercritical phases. We evaluated how the finite box size and the choice of the force field affect the calculated properties at high pressures. Results show a strong dependency between self-diffusion and the simulation box size. The Yeh-Hummer analytical correction [J. Phys. Chem. B, 108, 15873 (2004)] can attenuate this effect, but sometimes makes the results depart from experimental data due to issues concerning the force fields. We have also found that different all-atom and united-atom models can produce biased results due to caging effects and to different dihedral configurations of the n-alkane.

Molecular-Dynamics Analysis of the Structural Properties of Silica during Cooling

2008 ◽  
Vol 139 ◽  
pp. 101-106 ◽  
Author(s):  
Byoung Min Lee ◽  
Shinji Munetoh ◽  
Teruaki Motooka ◽  
Yeo Wan Yun ◽  
Kyu Mann Lee
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
Transition Temperature ◽  
Structural Properties ◽  
Diffusion Coefficients ◽  
The Self ◽  
Dynamics Analysis ◽  
Self Diffusion ◽  
Dynamics Simulations ◽  
Potential Parameters

The structural properties of SiO2 liquid during cooling have been investigated by molecular dynamics simulations. The interatomic forces acting on the particles are calculated by the modified Tersoff potential parameters. The glass transition temperature and structural properties of the resulting SiO2 system at various temperatures have been investigated. The fivefold coordinations of Si and threefold coordinations of O atoms were observed, and the coordination defects of system decrease with decreasing temperature up to 17 % at 300 K. The self-diffusion coefficients for Si and O atoms drop to almost zero below 3000 K. The structures were distorted at high temperatures, but very stable atomic network persisted up to high temperature in the liquid state.

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