Search results for "molecular dynamics"
showing 10 items of 1075 documents
Structural features of selected protic ionic liquids based on a super-strong base
2019
Protic ionic liquids (PIL) were prepared from a super-strong base 1,7-diazabicyclo[5.4.0]undec-7-ene (DBU) and super-strong acids, trifluoromethane sulfonic acid (TfOH), and (trifluoromethanesulfonyl)-(nonafluorobutylsulfonyl)imide, (IM14H), ([DBUH][TfO] and [DBUH][IM14], respectively; the latter for the first time) and their chemical and physical properties and structural features have been explored using a synergy of experimental and computational tools. The short range order in neat DBU, as well as the long range structural correlations induced by charge correlation and hydrogen bonding interactions in the ionic liquids, have been explored under ambient conditions, where these compounds …
Modeling the Interaction of Carbon Monoxide with Flexible Graphene: From Coupled Cluster Calculations to Molecular-Dynamics Simulations
2018
The interaction of CO with graphene was studied at different theoretical levels. Quantum-mechanical calculations on finite graphene models with the use of coronene for coupled cluster calculations and circumcoronene for B97D calculations showed that there was no preferential site for adsorption and that the most important factor was the orientation of CO relative to graphene. The parallel orientation was preferred, with binding energies around 9 kJ mol-1 at the CCSD(T) and B97D levels, which was in good agreement with experimental findings. From a large number of CO-circumcoronene and CO-CO interactions, computed at different distances and randomly generated orientations, parameters were fi…
Effect of melting on ionization potential of sodium clusters
2003
The effect of melting transition on the ionization potential has been studied for sodium clusters with 40, 55, 142, and 147 atoms, using ab initio and classical molecular dynamics. Classical and ab initio simulations were performed to determine the ionization potential of Na142 and Na147 for solid, partly melted, and liquid structures. The results reveal no correlation between the vertical ionization potential and the degree of surface disorder, melting, or the total energy of the cluster obtained with the ab initio method. However, in the case of 40 and 55 atom clusters, the ionization potential seems to decrease when the cluster melts.
Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection
2013
Bioprotection by sugars, and in particular trehalose peculiarity, is a relevant topic due to the implications in several fields. The underlying mechanisms are not yet clearly elucidated, and remain the focus of current investigations. Here we revisit data obtained at our lab on binary sugar/water and ternary protein/sugar/water systems, in wide ranges of water content and temperature, in the light of the current literature. The data here discussed come from complementary techniques (Infrared Spectroscopy, Molecular Dynamics simulations, Small Angle X-ray Scattering and Calorimetry), which provided a consistent description of the bioprotection by sugars from the atomistic to the macroscopic …
Water orientation and hydrogen-bond structure at the fluorite/water interface
2016
AbstractWater in contact with mineral interfaces is important for a variety of different processes. Here, we present a combined theoretical/experimental study which provides a quantitative, molecular-level understanding of the ubiquitous and important CaF2/water interface. Our results show that, at low pH, the surface is positively charged, causing a substantial degree of water ordering. The surface charge originates primarily from the dissolution of fluoride ions, rather than from adsorption of protons to the surface. At high pH we observe the presence of Ca-OH species pointing into the water. These OH groups interact remarkably weakly with the surrounding water and are responsible for the…
Piezoelectric coefficients by molecular dynamics simulations in the constant stress ensemble: A case study of quartz
2006
Piezoelectric (strain) coefficients dij of quartz are calculated in terms of molecular dynamics as a function of pressure and temperature. We review the necessary formulas for the computation of electromechanical materials coefficients obtained at constant stress and temperature, and discuss how to overcome complications of the definition of polarization variations due to fluctuating box geometries. A method is employed suppressing significantly stochastic fluctuations of the estimators for piezoelectric coefficients. A recently suggested force field for the simulation of SiO2 reproduces available experimental data quite accurately. Predictions are made for the pressure dependence of dij of…
Nucleus-driven crystallization of amorphous Ge2Sb2Te5: A density functional study
2012
Early stages of nucleus-driven crystallization of the prototype phase change material Ge${}_{2}$Sb${}_{2}$Te${}_{5}$ have been studied by density functional/molecular dynamics simulations for amorphous samples (460 and 648 atoms) at 500, 600, and 700 K. All systems assumed a fixed cubic seed of 58 atoms and 6 vacancies. Crystallization occurs within 600 ps for the 460-atom system at 600 and 700 K, and signs of crystallization (nucleus growth, percolation) are present in the others. Crystallization is accompanied by an increase in the number of ``$ABAB$ squares'' ($A$: Ge, Sb, $B$: Te), and atoms of all elements move significantly. There is no evidence of cavity movement to the crystal-glass…
Chain Motion in an Unentangled Polyethylene Melt: A Critical Test of the Rouse Model by Molecular Dynamics Simulations and Neutron Spin Echo Spectros…
1998
We have investigated the dynamic structure factor for single-chain relaxation in a polyethylene melt by means of molecular dynamics simulations and neutron spin echo spectroscopy. After accounting for a 20% difference in the chain self-diffusion coefficient between simulation and experiment we find a perfect quantitative agreement of the intermediate dynamic structure factor over the whole range of momentum transfer studied. Based on this quantitative agreement one can test the experimental results for deviations from standard Rouse behavior reported so far for only computer simulations of polymer melt dynamics.
Amorphous silica between confining walls and under shear: a computer simulation study
2002
Molecular dynamics computer simulations are used to investigate a silica melt confined between walls at equilibrium and in a steady-state Poisseuille flow. The walls consist of point particles forming a rigid face-centered cubic lattice and the interaction of the walls with the melt atoms is modelled such that the wall particles have only a weak bonding to those in the melt, i.e. much weaker than the covalent bonding of a Si-O unit. We observe a pronounced layering of the melt near the walls. This layering, as seen in the total density profile, has a very irregular character which can be attributed to a preferred orientational ordering of SiO4 tetrahedra near the wall. On intermediate lengt…
Oxidation of nanocrystalline aluminum by variable charge molecular dynamics
2010
International audience; We investigate the oxidation of nanocrystalline aluminum surfaces using molecular dynamics (MD) simulations with the variable charge model that allows charge dynamically transfer among atoms. The interaction potential between atoms is described by the electrostatic plus (Es+) potential model, which is composed of an embedded atom method potential and an electrostatic term. The simulations were performed from 300 to 750K on polycrystalline samples with a mean grain size of 5 nanometers. We mainly focused on the effect of the temperature parameter on the oxidation kinetic. The results show that, beyond a first linear regime, the kinetics follow a direct logarithmic law…