Understanding the carbon-monoxide oxidation mechanism on ultrathin palladium nanowires: a density functional theory study.

The CO oxidation mechanism catalyzed by ultrathin helical palladium nanowires (PdNW) was investigated by density functional theory (DFT) calculation. The helical PdNW structure was constructed on the basis of the simulated annealing basin-hopping (SABH) method with the tight-binding potential and the penalty method in our previous studies (J. Mater.

Water molecular flow control with a (5,5) nanocoil switch.

Molecular dynamics simulation was employed to investigate the diffusion behaviors of water molecules within a (5,5) carbon nanocoil (CNC) at different tensile strains, the length and coil diameter of CNC are 22 and 6.83 Ǻ, respectively. Condensed-phase, optimized molecular potentials for atomistic simulation studies were employed to model the interaction between atoms.

The dynamics behavior of Rh nanoclusters on boron nitride sheet.

The configurations and corresponding adsorption energies of Rh(n) (n = 4-13) nanoclusters on the boron nitride sheet are investigated by density functional theory (DFT). We use the force-matching method (FMM) to modify parameters of Morse and Tersoff potential functions. To elucidate the dynamical behaviors of Rh nanoclusters on the boron nitride sheet, molecular dynamics (MD) is applied with modified Morse potential function parameter.

Density function theory study of the adsorption and dissociation of carbon monoxide on tungsten nanoparticles.

The adsorption and dissociation properties of carbon monoxide (CO) molecule on tungsten W(n) (n = 10-15) nanoparticles have been investigated by density-functional theory (DFT) calculations. The lowest-energy structures for W(n) (n = 10-15) nanoparticles are found by the basin-hopping method and big-bang method with the modified tight-binding many-body potential. We calculated the corresponding adsorption energies, C-O bond lengths and dissociation barriers for adsorption of CO on nanoparticles.

The deformation mechanism of Ni-Ta bulk metallic glasses after tensile: molecular dynamics study.

The mechanical properties of Ni-Ta crystallizationand binary bulk metallic glasses (BMG) were investigated for this study at the nanoscale. First, the Ta9Ni3 crystals are formed by space group, and structures with different ratios (Ta1Ni1, BTa8Ni4, BTa9Ni3, BTa7Ni5) were put into unit cell randomly. The optimizations of BMG structures are performed by Density functional theory (DFT) calculation to find the stable amorphous structures and corresponding energy.

Density function theory study on adsorption and dissociation of H2O on Pd nanowire.

The adsorption and dissociation of H2O in Pd nanowire have been investigated by the density functional theory (DFT) studies. First, we construct Pd nanowire by basin-hopping method and use DFT calculation to find the ground state of Pd nanowire, and put the H2O molecular on different adsorption sites and the H2O molecule is found to preferentially absorb on a Top (T) site. The H2O molecule lies parallel to the Pd nanowire surface, while the O atom is bound at a Top site.

Observation of the amorphous zinc oxide recrystalline process by molecular dynamics simulation.

The detailed structural variations of amorphous zinc oxide (ZnO) as well as wurtzite (B4) and zinc blende (B3) crystal structures during the temperature elevation process were observed by molecular dynamics simulation. The amorphous ZnO structure was first predicted through the simulated-annealing basin-hopping algorithm with the criterion to search for the least stable structure. The density and X-ray diffraction profiles of amorphous ZnO of the structure were in agreement with previous reports.

Four-component pharmacophore model for endomorphins toward μ opioid receptor subtypes.

In the present work, a series of simulation tools were used to determine structure-activity relationships for the endomorphins (EMs) and derive μ-pharmacophore models for these peptides. Potential lowest energy conformations were determined in vacuo by systematically varying the torsional angles of the Tyr(1)-Pro(2) (ω(1)) and Pro(2)-Trp(3)/Phe(3) (ω(2)) as tuning parameters in AM1 calculations. These initial models were then exposed to aqueous conditions via molecular dynamics simulations.

A molecular dynamics study on opioid activities of biphalin molecule.

Molecular dynamics simulations of the biphalin molecule, (Tyr-D-Ala-Gly-Phe-NH)(2), and the active tetrapeptide hydrazide, Tyr-D-Ala-Gly-Phe-NH-NH(2) were performed to investigate the cause of the increased μ and δ receptor binding affinities of the former over the latter. The simulation results demonstrate that the acylation of the two equal tetrapeptide fragments of biphalin produces the constrained hydrazide bridges [Formula: see text] and [Formula: see text], which in turn increase the opportunity of conformations for binding to μ or δ receptors. Meanwhile, the connection of the two active tetrapeptide fragments of biphalin also results in the constrained side chain torsion angle χ(2) at one of the two residues Phe.

Adsorption and dissociation of the O2 on W(111) surface: a density functional theory study.

The adsorption and dissociation of O2 molecules on W(111) surface have been studied at the density functional theory (DFT) level in conjunction with the projector augmented wave (PAW) method. All passable dissociation reaction paths of O2 molecule on W(111) surface are considered. The nudged elastic band (NEB) method is applied to locate transition states, and minimum energy pathways (MEP).

The interfacial behavior of water/PMMA thin film under normal compression.

Molecular dynamics simulation (MD) has been used to investigate the structure property of water/PMMA interface under compression and compression release. A virtual repulsive wall was employed to generate a normal compression strain on the simulation model, leading a compressive system. In order to understand the difference of interfacial phenomenon between the system under strain and under release, the hydrogen bond and density distributions of water and PMMA along the normal direction are calculated.

The scratch behaviors of copper bi-layers by a diamond tip: a molecular statics study.

The scratch deformation behaviors of two bicrystal coppers (Cu(100)/Cu(110) and Cu(110)/Cu(100)) during the nanoscratching process were explored and compared with their single crystal ingredients by the molecular statics simulations. The effects of lattice configuration and scratch depth were investigated in this study. The results showed that the motion of dislocations was blocked in the bicrystal interface until the dislocations accumulated enough energy to move.

The nanoindentation of a copper substrate by single-walled carbon nanocone tips: a molecular dynamics study.

This study dealt with deep nanoindentation of a copper substrate with single-walled carbon nanocones (SWCNCs) as the proximal probe tip, using molecular dynamics (MD) simulations. As an important feature, during the indentation the end part of the SWCNC tip will suffer a narrowing effect due to the radial component of resistant compression from the substrate and then forms into a somewhat flat arrowhead-like shape. The effective cross-sectional area of the SWCNC tip inside the substrate that the resistant force is acting on therefore is reduced to lower the normal resistant force on the tip.

Conformational stability and three-dimensional model of the delta-opioid pharmacophore for the extended antiparallel dimer structure of Met-enkephalin in water.

The conformational stability of the extended antiparallel dimer structure of Met-enkephalin in water was analyzed by examining the hydration structure of enkephalin using molecular dynamics simulations. The result shows that, despite of the hydrophicility of the terminal atoms in the pentapeptide, the main contributor for the stability of the dimer in water is the four intermolecular hydrogen bonds between the Gly(2) and Phe(4) groups. The three-dimensional model of the delta-opioid pharmacophore for this dimer structure was also established.