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. We also calculate the partial density of state (PDOS) and election density difference. In addition, our calculated results demonstrate that the bonding between H2O and Pd nanowire is contributed by d orbitals of Pd nanowire and p orbitals of O atom. The nudged elastic band (NEB) method is applied to locate transition states and minimum energy pathways (MEP), and we discuss the dissociation behavior of the side-on H2O molecules on the top site of hexagonal and tetragonal planes, respectively.

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. The FMM is utilized to obtain the suitable parameters of tight-binding potential bystable amorphous structures and corresponding energies. Finally, we employ molecular dynamics (MD) simulation to study mechanical properties of Ni/Ta crystallization and BMG, such as atomistic stress-strain, plastic and elastic deformation, and elastic modulus.

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 electronic properties of CO on nanoparticles are studied by the analysis of density of state and charge density. The characteristic of CO on W(n) nanoparticles are also compared with that of W bulk.

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. Finally, the square displacement (SD) is utilized the dynamics behavior of different size Rh nanoclusters at different temperatures.

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. From the study, it was found that the bicrystal interfaces can provide resistance to the motion of dislocations, and can strengthen the mechanical properties of copper materials.

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 results show that the hydrogen bond distribution profile of compressive system is different from that of the release system at the same strain. It demonstrates that the characteristic structure of water/PMMA interface under a compression-release cycle is not reversible.

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). We find that there is an existing of little barriers for the dissociations reaction of O2 molecule. Ab initio molecular dynamics simulation is also preformed to study the adsorption and dissociation mechanism of O2 molecules on the W(111) surface. Our results indicate that O2 molecule will be dissociated by inclined deposition at temperature of 10 K, but can stable adsorb on top site by normal deposition. The change of bond length and adsorption energy in process of dissociation of O2 molecules on the W(111) surface are also calculated. The O2 coverage effect is also discussed in this paper.

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. The narrowing effect is more significant for longer SWCNC tips. Two categories of SWCNCs are therefore classified according to whether the SWCNC tip buckles at its part inside or outside the substrate. SWCNCs of the first category defined in this paper are found able to indent into the substrate up to a desired depth. Further analyses demonstrate that a longer SWCNC tip of the first category will encounter smaller repulsive force during the indentation and thus require less net work to accomplish the indentation process. Raising temperatures will weaken the narrowing effect, so an SWCNC tip of the first category also encounters greater repulsive force and larger net work in the indentation process performed at a higher temperature. Notably, a permanent hollow hole with high aspect ratio will be produced on the copper substrate, while copper atoms in close proximity to the hole are only slightly disordered, especially when the indentation is manipulated at a lower temperature by using a longer SWCNC tip.

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. Chem., 2012, 22, 20319). The low-lying adsorption configurations as well as the adsorption energies for O2 and CO molecules on different PdNW adsorption sites were obtained by DFT calculation. The most stable adsorption configurations for the Langmuir-Hinshelwood (LH) mechanism processes were considered for investigating the CO oxidation mechanism. The nudged elastic band (NEB) method was adopted to obtain the transition state configuration and the minimum energy pathways (MEPs).

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 results show that the diffusion in the axial direction can be enhanced by the tensile strain and the water molecule flow can be blocked at a higher strain once the deformed areas appear at the higher strain. Moreover, the deformed (5,5) CNC at strain of 2.8 can recover its original structure at strain of 0, indicating that the adjustment of diffusion coefficient is repeatable by applying different strains in the axial direction.

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. The local structural transformation among different local structures and the recrystalline process of amorphous ZnO at higher temperatures are observed and can explain the structural transformation and recrystalline mechanism in a corresponding experiment [Bruncko et al., Thin Solid Films 520, 866-870 (2011)].

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. In aqueous solution, the simulations suggest that endomorphin conformers strongly favor the trans/trans pair of the ω(1)/ω(2) amide bonds. From two-dimensional probability distributions of the ring-to-ring distances with respect to the pharmacophoric angles for EMs, a selectivity range of µ(1) is ca. 8.3 ~ 10.5 Å for endomorphin-2 and selectivity range of µ(2) is ca. 10.5 ~ 13.0 Å for endomorphin-1 were determined. Four-component µ-pharmacophore models are proposed for EMs and are compared to the previously published δ- and κ-pharmacophore models.

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. This constrained side chain torsion angle not only significantly increases the δ receptor binding affinity but also makes most of the δ receptor binding conformations of biphalin bind to the δ receptor through the fragment containing the mentioned residue Phe.

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. Such a model was demonstrated to match the delta-opioid pharmacophore query derived from the non-peptides SIOM, TAN-67, and OMI perfectly. This result thus strongly supports the assumption that the dimer structure of Met-enkephalin is a possible delta-receptor binding conformation.