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.

A density functional theory study on the structure stability of silica nanoclusters.

The studies of silica nanoclusters are of substantial interest for large potential in applications as diverse as photonics/optics, microelectronics and catalysis. In this study, we used the basing-hopping method with Buckingham potential to get the stable structures of silica nanoclusters ((SiO2)(n) = 1-13). The global minimum geometry of silica nanoclusters were determined by density functional theory calculation. We investigated the energy gap, binding energy and second order energy difference of nanoclusters to determine their structural stability with different sizes. We also calculate the second-order energy difference, binding energy to determine the magic number.

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.

Combined molecular dynamics and dissipative particle dynamics to study of the microstructure of poly(L-lactide)/polyethylene blends.

Different type of polymers miscibility has been induced great interest, owing to its relevance to the understanding of processing and performance properties of blends containing different type of polymers. In this article, we investigate the microstructure of poly(L-lactide) (PLLA)/polyethylene (PE) blends. The simulation method is adopted molecular dynamics and dissipative particle dynamics. The results show that the stable microstructures are type of cylinder and lamellae with volume ratio (VPE/VPLLA = 3/7). Furthermore, the lateral compression test is also used to study the stability of microstructure.

Structure-activity relationships of alphaS1-casomorphin using AM1 calculations and molecular dynamics simulations.

This paper investigates the structure-activity relationships of alphaS1-casomorphin (alphaS1-CM) using AM1 calculations and molecular dynamics (MD) simulations. Previous studies have shown that this peptide has remarkable opioid actions, and not only has a high affinity toward all three subtypes (kappa1-kappa3) of the kappa-opioid sites, but also inhibits the proliferation of the T47D human breast cancer cell line. The systematic conformer search performed by the AM1 calculations is based on the torsional angles of the Val2-Pro3 (omega2) and Phe4-Pro5 (omega4) amide bonds. The AM1 results reveal that the alphaS1-CM conformers strongly favor the cis/cis pair of the omega2/omega4 amide bonds in the minimized energy state. Furthermore, the picture of these stable conformers is found to be a strong interaction of the coulomb's force between two terminuses. MD simulations are performed to investigate the features of both the structural stability and pharmacological activity of alphaS1-CM in aqueous solution. The simulation results reveal that the omega2/omega4 amide bonds favor the cis/cis status in the stable state. Furthermore, the pharmacophoric distance between two aromatic rings is found to be 5.0 approximately 5.4A. The chi1 rotamers of the Tyr and Phe residues show a preference for gauche (-) and trans, respectively. The side chain rotamers of alphaS1-CM are competed to those of other opioid ligands with a known potency and selectivity for delta- and mu-opioid receptors. Finally, we address a likely kappa pharmacophore model compared to the delta pharmacophore model.

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.

The effects of confinement on the behavior of water molecules between parallel Au plates of (001) planes.

Molecular dynamics simulation is utilized to investigate the behavior of water molecules confined between two Au plates of (001) planes separated by gaps of 24.48, 16.32, 12.24, 11.22, and 10.20 A. The simulation results indicate that the arrangements of the water molecules are dependent on the gap size. For the largest gap size, adsorption of the Au surface creates two permanent water layers in the vicinity of each Au plate. Furthermore, in this case, the gap size is sufficiently large to permit the formation of a central region within which the water molecules are randomly oriented in a similar manner to bulk water molecules. The results indicate that the orientation of the first water layer directly absorbed by the plate surface does not change as the gap size between the two Au plates is reduced. However, the orientations of the O-H bonds in the second water layer parallel to the surface rearrange to form hydrogen bonds between the water layers as the separation between the plates is decreased. Finally, an inspection of the variation of the self-diffusion coefficients with the gap size suggests that the difference between the dynamic properties of the water molecules in the z direction and the x-y plane decreases as the distance between the two Au plates increases.