scholarly journals Pair distribution functions in molecular dynamics simulations of interfaces

2006 ◽  
Author(s):  
Deng Cao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Dynamics Simulations ◽  
Pair Distribution Functions

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 Molecular Dynamics Simulations of CO2Molecules in ZIF-11 Using Refined AMBER Force Field

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
W. Wongsinlatam ◽  
T. Remsungnen
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Binding Energies ◽  
Hydrogen Atoms ◽  
Amber Force Field ◽  
Bonding Parameters ◽  
Flexible Framework ◽  
Dynamics Simulations

Nonbonding parameters of AMBER force field have been refined based onab initiobinding energies of CO2–[C7H5N2]−complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 forεandσparameters, respectively. Molecular dynamics simulations of CO2molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2molecules. One slight but notable difference is that CO2molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

Molecular Dynamics Studies of Nanoparticles of Energetic Materials

2003 ◽  
Vol 800 ◽  
Author(s):  
Saman Alavi ◽  
Gustavo F. Velardez ◽  
Donald L. Thompson
Keyword(s):  
Molecular Dynamics ◽  
Correlation Function ◽  
Solid State ◽  
Molecular Dynamics Simulations ◽  
Energetic Materials ◽  
Center Of Mass ◽  
Distribution Functions ◽  
Radial Distribution Functions ◽  
Dynamics Simulations ◽  
Dipole Correlation

ABSTRACTThe structural properties of several nanoparticles of 2,4,6,8,10,12-hexanitrohexaazaiso-wurtzitane, HNIW or CL-20, are studied by using molecular dynamics simulations. The internal structure of the CL-20 molecule is held rigid and the intermolecular interactions in the nanoparticles are taken from a previously developed force field. [Sorescu et al., J. Phys. Chem. B, 102, 948 (1998)] Molecular dynamics simulations of solid-like and annealed nanoparticles with 48 and 88 CL-20 molecules have been carried out in the solid-state range of temperatures from 50 to 500 K. The center-of-mass to center-of-mass radial distribution functions, dipole-dipole correlation function, the orientations of the surface dipoles, and the density of the nanoparticles were calculated at fixed temperatures for the nanoparticles.

scholarly journals TiCl4 Dissolved in Ionic Liquid Mixtures from Аb Initio Molecular Dynamics Simulations

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 79
Author(s):  
Lars Esser ◽  
Roberto Macchieraldo ◽  
Roman Elfgen ◽  
Melanie Sieland ◽  
Bernd Michael Smarsly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Molecular Dynamics Simulations ◽  
Interaction Network ◽  
Liquid Mixtures ◽  
Distribution Functions ◽  
Ab Initio Molecular Dynamics ◽  
Complex Interactions ◽  
Dynamics Simulations ◽  
Anion Interaction

To gain a deeper understanding of the TiCl4 solvation effects in multi-component ionic liquids, we performed ab initio molecular dynamics simulations of 1-butyl-3-methylimidazolium [C4C1Im]+, tetrafluoroborate [BF4]−, chloride [Cl]− both with and without water and titanium tetrachloride TiCl4. Complex interactions between cations and anions are observed in all investigated systems. By further addition of water and TiCl4 this complex interaction network is extended. Observations of the radial distribution functions and number integrals show that water and TiCl4 not only compete with each other to interact mainly with [Cl]−, which strongly influences the cation-[BF4]− interaction, but also interact with each other, which leads to the fact that in certain systems the cation-anion interaction is enhanced. Further investigations of the Voronoi polyhedra analysis have demonstrated that water has a greater impact on the nanosegregated system than TiCl4 which is also due to the fact of the shear amount of water relative to all other components and its higher mobility compared to TiCl4. Overall, the polar network of the IL mixture collapses by including water and TiCl4. In the case of [Cl]− chloride enters the water continuum, while [BF4]− remains largely unaffected, which deeply affects the interaction of the ionic liquid (IL) network.

Molecular dynamics simulations of EPON-862/DETDA epoxy networks: structure, topology, elastic constants, and local dynamics

Soft Matter ◽  
2019 ◽  
Vol 15 (4) ◽  
pp. 721-733 ◽  
Author(s):  
Spyros V. Kallivokas ◽  
Aristotelis P. Sgouros ◽  
Doros N. Theodorou
Keyword(s):  
Molecular Dynamics ◽  
Elastic Constants ◽  
Distribution Functions ◽  
Glass Temperature ◽  
Segmental Dynamics ◽  
Structure Topology ◽  
Xrd Patterns ◽  
Dynamics Simulations ◽  
Networks Structure ◽  
Pair Distribution Functions

Partial pair distribution functions, XRD patterns, segmental dynamics, elastic constants and glass temperature in EPON862/DETDA epoxy predicted through molecular dynamics.

QM/MM molecular dynamics simulations of the hydration of Mg(II) and Zn(II) ions

2013 ◽  
Vol 91 (7) ◽  
pp. 552-558 ◽  
Author(s):  
Saleh Riahi ◽  
Benoît Roux ◽  
Christopher N. Rowley
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Distribution Functions ◽  
Water Model ◽  
Polarizable Force Field ◽  
Water Solvent ◽  
Dynamics Simulations ◽  
Good Agreement

The hydration of Mg2+ and Zn2+ is examined using molecular dynamics simulations using 3 computational approaches of increasing complexity: the CHARMM nonpolarizable force field based on the TIP3P water model, the Drude polarizable force field based on the SWM4-NDP water model, and a combined QM/MM approach in which the inner coordination sphere is represented using a high-quality density functional theory (DFT) model (PBE/def2-TZVPP), and the remainder of the bulk water solvent is represented using the polarizable SWM4-NDP water model. The characteristic structural distribution functions (radial, angular, and tilt) are comparedand show very good agreement between the polarizable force field and QM/MM approaches. They predict an average Mg–O distance of 2.11 Å and an Zn–O distance of 2.13 Å, in good agreement with the available experimental neutron scattering and EXAFS data, while the Mg–O distances calculated using the nonpolarizable force field are 0.1 Å too short. Mg2+ (aq) and Zn2+ (aq) both have a coordination number of 6 and have a remarkably similar octahedral coordination mode, despite the chemical differences between these ions. Thermodynamic integration was used to calculate the relative hydration free energies of these ions (ΔΔGhydr). The nonpolarizable model is in error by 60 kcal mol– 1 and incorrectly predicts that Mg2+ has the more negative hydration energy. The Drude polarizable model predicts a ΔΔGhydr of only –13.2 kcal kcal mol– 1, an improvement over the results of the nonpolarizable force field, but still signficantly different than the experimental value of –30.1 kcal mol–1. The combined QM/MM approach performs much better, predicting a ΔΔGhydr of –34.8 kcal mol–1 in excellent agreement with experiment. These calculations support the experimental observation that Zn2+ has more favourable solvation free energy than Mg2+ despite having a very similar solvation structure.

scholarly journals A Master equation for the probability distribution functions of forces in soft particle packings

Soft Matter ◽  
2015 ◽  
Vol 11 (7) ◽  
pp. 1253-1258 ◽  
Author(s):  
Kuniyasu Saitoh ◽  
Vanessa Magnanimo ◽  
Stefan Luding
Keyword(s):  
Molecular Dynamics ◽  
Probability Distribution ◽  
Master Equation ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Soft Particle ◽  
Probability Distribution Functions ◽  
Soft Particles ◽  
Dynamics Simulations ◽  
Particle Packings

We study the microscopic response of force-chain networks in jammed soft particles to quasi-static isotropic (de)compressions by molecular dynamics simulations.

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