Melt-quenched and as-deposited structures of amorphous selenium: a density functional/ molecular dynamics comparison.

Molecular dynamics simulations using a density functional description of energies and forces have been carried out for a model of an as-deposited (AD) surface of amorphous selenium. The deposition model assumed the annealing (at 400 K) of layers of randomly located single atoms, followed by compression to the density used in earlier melt-quenched (MQ) simulations of amorphous Se, and by further annealing. The AD and MQ structures are predominantly twofold coordinated and similar, for example in the pair distribution functions, with notable differences: the AD structures have more defects (atoms with one and three neighbours), and the ring distributions differ. These differences are also reflected in the electronic structures of the AD and MQ samples, where the increased presence of defects in the former influences the Bader charges and the edge states of the band gap. The dominance of rings found in a previous simulation of AD structures is not found.

Density functional study of structure and dynamics in liquid antimony and Sbn clusters.

Density functional/molecular dynamics simulations have been performed on liquid antimony (588 atoms and six temperatures between 600 K and 1300 K) and on neutral Sb clusters with up to 14 atoms. We study structural patterns (coordination numbers, bond angles, and ring patterns, structure factors, pair distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra, dynamical structure factors, viscosity) and compare with available experimental results and with the results of our previous simulations on Bi. Three short covalent bonds characteristic of pnictogens are common in the clusters, and higher temperatures lead in the liquid to broader bond angle distributions, larger total cavity volumes, and weaker correlations between neighboring bond lengths. There are clear similarities between the properties of Sb and Bi aggregates.

Structure of amorphous Ag/Ge/S alloys: experimentally constrained density functional study.

Density functional/molecular dynamics simulations have been performed to determine structural and other properties of amorphous Ag/Ge/S and Ge/S alloys. In the former, the calculations have been combined with experimental data (x-ray and neutron diffraction, extended x-ray absorption fine structure). Ag/Ge/As alloys have high ionic conductivity and are among the most promising candidates for future memristor technology. We find excellent agreement between the experimental results and large-scale (500 atoms) simulations in Ag/Ge/S, and we compare and contrast the structures of Ge/S and Ag/Ge/S. The calculated electronic structures, vibrational densities of states, ionic mobilities, and cavity distributions of the amorphous materials are discussed and compared with data on crystalline phases where available. The high mobility of Ag in solid state electrolyte applications is related to the presence of cavities and can occur via jumps to a neighbouring vacant site.

Structure and dynamics in liquid bismuth and Bi(n) clusters: a density functional study.

Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available. While the three short covalent bonds typical to pnictogens are characteristic in both liquid and clusters, the number of large voids and the total cavity volume is much larger in the liquid at 1023 K, with larger local concentration variations. The inclusion of spin-orbit coupling results in a lowering of the cohesive energies in Bin clusters of 0.3-0.5 eV/atom.

Density functional simulations of structure and polymorphism in Ga/Sb films.

Thin films of gallium/antimony alloys are promising candidates for phase change memories requiring rapid crystallization at high crystallization temperatures. Prominent examples are the stoichiometric form GaSb and alloys near the eutectic composition GaSb(7), but little is known about their amorphous structures or the differences between the 'as-deposited' (AD) and 'melt-quenched' (MQ) forms. We have generated these structures using 528-atom density functional/molecular dynamics simulations, and we have studied in detail and compared structural parameters (pair distribution functions, structure factors, coordination numbers, bond and ring size distributions) and electronic properties (densities of states, bond orders) for all structures. There is good agreement with x-ray diffraction data from deposited films of GaSb, and there is evidence for Sb segregation in GaSb(7).

Amorphous Ge15Te85: density functional, high-energy x-ray and neutron diffraction study.

The structure and electronic properties of amorphous Ge(15)Te(85) have been studied by combining density functional (DF) simulations with high-energy x-ray and neutron diffraction measurements. Three models with 560 atoms have been constructed using reverse Monte Carlo methods constrained to (1) agree with the experimental structure factors S(Q), and have (2) energies close to the DF minimum and (3) a semiconducting band structure. The best structure is based on the melt-quenched DF structure and has a small number of Ge-Ge bonds. It shows interlocking networks of Te and GeTe with a significant fraction (22-24%) of voids (cavities). Ge occurs with both tetrahedral and 3 + 3 defective octahedral configurations, and the coordination of Te is slightly higher than indicated by the '8 - N rule' (N is the number of valence electrons). The GeTe network includes clusters of ABAB squares (A = Ge, B = Te), and the bonding is characterized by the chemical bond orders.

Relationship between topological order and glass forming ability in densely packed enstatite and forsterite composition glasses.

The atomic structures of magnesium silicate melts are key to understanding processes related to the evolution of the Earth's mantle and represent precursors to the formation of most igneous rocks. Magnesium silicate compositions also represent a major component of many glass ceramics, and depending on their composition can span the entire fragility range of glass formation. The silica rich enstatite (MgSiO(3)) composition is a good glass former, whereas the forsterite (Mg(2)SiO(4)) composition is at the limit of glass formation. Here, the structure of MgSiO(3) and Mg(2)SiO(4) composition glasses obtained from levitated liquids have been modeled using Reverse Monte Carlo fits to diffraction data and by density functional theory. A ring statistics analysis suggests that the lower glass forming ability of the Mg(2)SiO(4) glass is associated with a topologically ordered and very narrow ring distribution. The MgO(x) polyhedra have a variety of irregular shapes in MgSiO(3) and Mg(2)SiO(4) glasses and a cavity analysis demonstrates that both glasses have almost no free volume due to a large contribution from edge sharing of MgO(x)-MgO(x) polyhedra. It is found that while the atomic volume of Mg cations in the glasses increases compared to that of the crystalline phases, the number of Mg-O contacts is reduced, although the effective chemical interaction of Mg(2+) remains similar. This unusual structure-property relation of Mg(2)SiO(4) glass demonstrates that by using containerless processing it may be possible to synthesize new families of dense glasses and glass ceramics with zero porosity.

Bright beaches of nanoscale potassium islands on graphite in STM imaging.

We demonstrate, via scanning tunneling microscopy (STM) measurements performed at 48 K, the existence of "bright beaches" at the edges of K islands (diameter approximately 5-500 nm) on the graphite surface. The enhanced tunneling current is only observed in monolayer-high islands on graphite, and not in islands of similar geometry on top of a K monolayer film. First-principles density functional calculations and STM simulations suggest that this is an STM field effect, which appears as the positive tip attracts donated electrons back to the metallic K islands. The restored charge accumulates preferentially at the island edges.

Binary alloys of Ge and Te: order, voids, and the eutectic composition.

The liquid and amorphous structures of Ge0.15Te0.85 and GeTe alloys are characterized using combined density functional/molecular dynamics simulations. Te is threefold coordinated, in contrast with predictions of the "8-N rule," and Ge atoms (fourfold coordinated) show octahedral and tetrahedral bonding angles. Cubic local environment occurs in both materials, and GeTe shows a pronounced alternation of atomic types. Tetrahedral Ge coordination is more common in the eutectic Ge0.15Te0.85, which comprises corner- and edge-sharing GeTe4 units surrounded by Te. There is no Te segregation, and the material resembles neither GeTe nor Te. The ubiquitous cavities (voids) have been overlooked in Ge0.15Te0.85, where they comprise over 25% of the volume.

Density functional study of amorphous, liquid and crystalline Ge(2)Sb(2)Te(5): homopolar bonds and/or AB alternation?

The amorphous, liquid and crystalline phases of the phase change material Ge(2)Sb(2)Te(5) (GST) have been studied by means of density functional/molecular dynamics simulations. The large sample (460 atoms and 52 vacancies in the unit cell) and long simulations (hundreds of picoseconds) provide much new information. Here we extend our original analysis (2007 Phys. Rev. B 76 235201) in important ways: partial coordination numbers and radial distribution functions, bond angle distributions, new local order parameters, vibration frequencies, and the charges on atoms and vacancies. The valence band densities of states in amorphous and crystalline GST are compared with ones from x-ray photoemission spectroscopy. The results for the liquid phase are new and those for the crystalline phase much expanded. GST shows pronounced AB alternation (A: Ge, Sb; B: Te), especially in its amorphous phase, and ABAB squares play a central role in the amorphous to crystalline transition. We comment on earlier speculations concerning the nature of the amorphous to crystalline transition.

Density functional calculations of ATP systems. 1. Crystalline ATP hydrates and related molecules.

Adenosine 5'-triphosphate (ATP) is an essential energy carrier in mammalian and other cells, and its hydrolysis to the diphosphate (ADP) in the presence of metal cations (e.g., Mg(2+) or Ca(2+)) is one of the most prevalent biochemical reactions. We describe here density functional (DF) calculations on closely related systems and compare the results with other calculations and available experimental data: Na(H2O)n +, Mg(H2O)n 2+, and Ca(H2O)n 2+ clusters (n = 1, 4-7), the crystalline pyrophosphates Mg(2)P(2)O(7).6H2O and alpha-CaNa(2)P(2)O(7).4H2O, and crystalline Na(2)ATP.3H2O. The last of these comprises asymmetric units of ATP dimers (monomers A and B) in a double-protonated state H(2)(ATP)(2-). The calculated structures agree well with available measurements and provide additional information, including the location of the H atoms. Analysis of the dipole moments of individual ATP monomers and their dimers shows that the crystal comprises blocks of opposing dipoles. Replacing one Na+ ion with Mg2+ or Ca2+ results in a significant elongation of the terminal bridging P-O bond. The calculations provide benchmarks for the use of DF methods in ATP systems and are used in the companion paper to study the hydrolysis of ATP at the active site of the protein actin.

Density functional calculations of ATP systems. 2. ATP hydrolysis at the active site of actin.

The hydrolysis of adenosine 5'-triphosphate (ATP) at the active site of actin has been studied using density functional calculations. The active site is modeled by the triphosphate tail of ATP, an Mg cation, surrounding water molecules, and the nearby protein residues. Four reaction paths have been followed by constraining coordinates that allow phosphate stretching, nucleophilic attack of the catalytic water, and OH(-) formation via water deprotonation. The lowest-energy barrier (21.0 kcal/mol) is obtained for a dissociative reaction where the terminal phosphate breaks on approaching the catalytic water, followed by proton release via a proton wire mechanism. A higher barrier (39.6 kcal/mol) results for an associative reaction path where OH(-) is formed first, with a pentacoordinated phosphorus atom (P-O distances 2.1 A). Stretching the terminal bridging P-O bond results in bond rupture at 2.8 A with an energy barrier of 28.8 kcal/mol. The residues Gln137 and His161 are not important in the reactions, but insight into their roles in vivo has been obtained. The favored coordination of the end products H(2)PO(4)(-) and ADP(3-) includes a hydrogen bond and an O-Mg-O bridge between the phosphates as well as a hydrogen bond between H(2)PO(4)(-) and the Ser14 side chain. The total energy is 2.1 kcal/mol lower than in the initial reactants. Classical simulations of ATP- and ADP.P(i)-actin show few hydrolysis-induced differences in the protein structure, indicating that phosphate migration is necessary for a change in conformation.

Thermal expansion in small metal clusters and its impact on the electric polarizability

The thermal expansion coefficients of Na(N) clusters with 8