Lanthanoids(III) and actinoids(III) in water: Diffusion coefficients and hydration enthalpies from polarizable molecular dynamics simulations

2012 ◽  
Vol 85 (1) ◽  
pp. 237-246 ◽  
Author(s):  
Fausto Martelli ◽  
Sacha Abadie ◽  
Jean-Pierre Simonin ◽  
Rodolphe Vuilleumier ◽  
Riccardo Spezia
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Heavy Ions ◽  
Md Simulations ◽  
Contradictory Result ◽  
Dielectric Friction ◽  
Water Interaction ◽  
Diffusive Regime ◽  
Dynamics Simulations ◽  
Good Agreement

By using polarizable molecular dynamics (MD) simulations of lanthanoid(III) and actinoid(III) ions in water, we obtained ionic diffusion coefficients and hydration enthalpies for both series. These values are in good agreement with experiments. Simulations thus allow us to relate them to microscopic structure. In particular, across the series the diffusion coefficients decrease, reflecting the increase of ion–water interaction. Hydration enthalpies also show that interactions increase from light to heavy ions in agreement with experiment. The apparent contradictory result of the decrease of the diffusion coefficient with decreasing ionic radius is tentatively explained in terms of dielectric friction predominance on Stokes’ diffusive regime.

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.

Molecular Dynamics Simulations of Atoms Diffusion in Solid

2018 ◽  
Vol 15 ◽  
pp. 51-64
Author(s):  
Yu Lu Zhou ◽  
Xiao Ma Tao ◽  
Qing Hou ◽  
Yi Fang Ouyang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Einstein Relation ◽  
Interatomic Potentials ◽  
Body System ◽  
Many Body ◽  
Point Particles ◽  
Bulk Surface ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations, which treat atoms as point particles and trace their individual trajectories, are always employed to investigate the transport properties of a many-body system. The diffusion coefficients of atoms in solid can be obtained by the Einstein relation and the Green-Kubo relation. An overview of the MD simulations of atoms diffusion in the bulk, surface and grain boundary is provided. We also give an example of the diffusion of helium in tungsten to illustrate the procedure, as well as the importance of the choice of interatomic potentials. MD simulations can provide intuitive insights into the atomic mechanisms of diffusion.

Predicting Methane Diffusivity in Polymeric Membranes by Molecular Dynamics

2015 ◽  
Vol 1119 ◽  
pp. 461-465
Author(s):  
M.K. Hadj-Kali ◽  
A. Bessadok-Jemai ◽  
S. Haider ◽  
Y. Alzeghayer
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Polymeric Membranes ◽  
Transport Mechanisms ◽  
Fluid Equation ◽  
Cell Modules ◽  
Dynamics Simulations ◽  
Materials Studio

Diffusion coefficients of methane (CH4) have been obtained by Molecular Dynamics (MD) simulations combined with Einstein fluid equation. Three polymers were considered, namely polyethylene, polypropylene and poly (cis-1,4-butadiene). All calculations were performed by means of Polymer Builder and Amorphous Cell modules within Materials Studio (Accelrys). The obtained diffusivity results are within the range of published results for similar small molecules. Molecular dynamics simulations proved to be a useful tool for understanding the detailed descriptions and transport mechanisms occurring within the material.

scholarly journals Thermal Conductivity of Polybutadiene Rubber from Molecular Dynamics Simulations and Measurements by the Heat Flow Meter Method

Materials ◽  
2021 ◽  
Vol 14 (24) ◽  
pp. 7737
Author(s):  
Aleksandr Vasilev ◽  
Tommy Lorenz ◽  
Vikram G Kamble ◽  
Sven Wießner ◽  
Cornelia Breitkopf
Keyword(s):  
Molecular Dynamics ◽  
Heat Flow ◽  
Md Simulations ◽  
Flow Meter ◽  
Polybutadiene Rubber ◽  
Polymeric Chains ◽  
Dynamics Simulations ◽  
Heat Flow Meter ◽  
Good Agreement ◽  
Thermal Conductivities

Thermal conductivities of polybutadiene rubbers crosslinked by 2.4 and 2.8 phr of sulfur have been found to be functions of temperature via molecular dynamics (MD) simulations using the Green–Kubo method. From an analysis of the heat flux autocorrelation functions, it has been revealed that the dominant means of heat transport in rubbers is governed by deformations of polymeric chains. Thermal conductivities of rubber samples vulcanized by 2.4 and 2.8 phr of sulfur have been measured by the heat flow meter method between 0 ∘C and 60 ∘C at atmospheric pressure. The temperature dependencies of the thermal conductivities of rubbers and their glass transition temperatures derived from MD simulations are in good agreement with the literature and experimental data. Details are discussed in the paper.

Some Properties of Molten KCl at High Density Studied by MD Simulation

1981 ◽  
Vol 36 (10) ◽  
pp. 1106-1111 ◽  
Author(s):  
Ryuzo Takagi ◽  
Isao Okada ◽  
Kazutaka Kawamura
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Thermodynamic Properties ◽  
Diffusion Coefficients ◽  
Md Simulation ◽  
Ambient Pressure ◽  
The Self ◽  
Self Diffusion ◽  
Dynamics Simulations ◽  
Good Agreement

Molecular dynamics simulations of molten KCl have been performed at 1173 K with the molar volumes of 52.0 (the value under ambient pressure), 50.0, 48.0 and 45.0 cm3 mol-1 . Some thermodynamic properties at higher densities have been evaluated, which are generally in good agreement with the experimentally obtained ones and Monte Carlo results. Both at normal and higher densities, the self-exchange velocities of neighbouring unlike ions (SEV) are found to be proportional to the internal mobilities with nearly the same constant as derived previously for molten LiCl, RbCl and their 1 : 1 mixture. Calculated transport properties such as the SEV and the self-diffusion coefficients considerably decrease with increasing density, while the configuration does not change much.

Molecular Dynamics Simulations of Nanoparticle Interactions with a Planar Wall: Does Shape Matter?

2013 ◽  
Vol 13 (3) ◽  
pp. 900-915 ◽  
Author(s):  
Andreas Fuchs ◽  
David Kauzlarić ◽  
Andreas Greiner ◽  
Sauro Succi ◽  
Jan. G. Korvink
Keyword(s):  
Molecular Dynamics ◽  
Continuum Theory ◽  
Md Simulations ◽  
Nano Particles ◽  
Hydrodynamic Theory ◽  
Rigid Particles ◽  
Nanoparticle Interactions ◽  
Planar Wall ◽  
Dynamics Simulations ◽  
Good Agreement

AbstractWe investigate the hydrodynamic interactions of spherical colloidal nano particles and nano tetrahedra near a planar wall by means of molecular dynamics (MD) simulations of rigid particles within an all-atom solvent. For both spherical and nano-tetrahedral particles, we find that the parallel and perpendicular components of the local diffusion coefficient and viscosity, show good agreement with hydrodynamic theory of Faxén and Brenner. This provides further evidence that low perturbations from sphericality of a nanoparticle’s shape has little influence on its local diffusive behaviour, and that for this particular case, the continuum theory fluid dynamics is valid even down to molecular scales.

scholarly journals Thermal Conductivity of Polyisoprene and Polybutadiene from Molecular Dynamics Simulations and Transient Measurements

Polymers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1081 ◽  
Author(s):  
Aleksandr Vasilev ◽  
Tommy Lorenz ◽  
Cornelia Breitkopf
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Weight ◽  
Atmospheric Pressure ◽  
Md Simulations ◽  
Wire Method ◽  
Dynamics Simulations ◽  
Transient Measurements ◽  
Good Agreement ◽  
Thermal Conductivities

The thermal conductivities of untreated polyisoprene and polybutadiene were calculated by molecular dynamics (MD) simulations using a Green-Kubo approach between −10 °C and 50 °C at atmospheric pressure. For comparison, the thermal conductivities of untreated polyisoprene with a molecular weight of 54,000 g/mol and untreated polybutadiene with a molecular weight of 45,000 g/mol were measured by the transient hot wire method in similar conditions. The simulation results of both polymers are in good agreement with the experimental data. We observed that the MD simulations slightly overestimate the thermal conductivity due to the chosen force field description. Details are discussed in the paper.

scholarly journals Thermal Conductivities of Crosslinked Polyisoprene and Polybutadiene from Molecular Dynamics Simulations

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 315
Author(s):  
Aleksandr Vasilev ◽  
Tommy Lorenz ◽  
Cornelia Breitkopf
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Temperature Dependence ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Dynamics Simulations ◽  
First Time ◽  
Soft Rubber ◽  
Good Agreement ◽  
Thermal Conductivities

For the first time, the thermal conductivities of vulcanized polybutadiene and polyisoprene have been investigated according to their degree of crosslinking. The C-C and C-S-S-C crosslink bridges, which can be obtained via vulcanization processes using peroxides and sulfur, respectively, are considered. The temperature dependence of the thermal conductivity of soft rubber derived from molecular dynamics (MD) simulations is in very good agreement with the experimental results. The contributions of bonded and non-bonded interactions in the MD simulations and their influence on the thermal conductivities of polyisoprene and polybutadiene are presented. The details are discussed in this paper.

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

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