Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling

The kinetic and thermodynamic aspects of the helix-coil transition in polyalanine-based peptides have been studied at the ensemble level using a distributed computing network. This study builds on a previous report, which critically assessed the performance of several contemporary force fields in reproducing experimental measurements and elucidated the complex nature of helix-coil systems. Here we consider the effects of modifying backbone torsions and the scaling of noncovalent interactions. Although these elements determine the potential of mean force between atoms separated by three covalent bonds (and thus largely determine the local conformational distributions observed in simulation), we demonstrate that the interplay between these factors is both complex and force field dependent. We quantitatively assess the heliophilicity of several helix-stabilizing potentials as well as the changes in heliophilicity resulting from such modifications, which can "make or break" the accuracy of a given force field, and our findings suggests that future force field development may need to better consider effect that vary with peptide length. This report also serves as an example of the utility of distributed computing in analyzing and improving upon contemporary force fields at the level of absolute ensemble equilibrium, the next step in force field development.     

The silicon vacancy in SiC

The isolated silicon vacancy is one of the basic intrinsic defects in SiC. We present new experimental data as well as new calculations on the silicon vacancy defect levels and a new model that explains the optical transitions and the magnetic resonance signals observed as occurring in the singly negative charge state of the silicon vacancy in 4H and 6H SiC.     

Synthesis and optical properties of N-In codoped ZnO nanobelts

N-In codoped ZnO nanobelts were successfully synthesized via high-temperature chemical vapor deposition for the first time, using the mixture of In/ZnO as a precursor. The EDX spectrum showed that In was introduced into ZnO nanobelts. In order to better understand the optical properties of N-In codoped ZnO nanobelts, the Raman and low-temperature PL spectra of the undoped, In-doped and N-In codoped ZnO nanostructures were measured. By contrasting, N is incorporated into the nanobelts. The temperature dependent photoluminescence (PL) spectra were investigated. Their PL spectra in the temperature from 9 K to room temperature were dominated by an A^oX emission of excitons bound to 2No-In_Zn acceptor complexes. The dissociation energy of the acceptor complexes is estimated to be 89-112 meV.     

Structural and electrical properties of iron molybdenum phosphate glasses

Summary  Iron molybdenum phosphate glasses [xMoO₃ · (0.6 -x)P₂O₅ · 0.4Li₂O] :yFe₂O₃ with 0 ≤x ≤ 0.6 andy = 0.03 (mol%) prepared in ambient atmosphere using the melt quenching technique were studied by using DC electrical conductivity,⁵⁷Fe M?ssbauer and infrared spectroscopies. The DC conductivity depends on the MoO₃ concentrationx. It was observed that, with increasingx, the ratio Fe²⁺ /(Fe³⁺ + Fe²⁺) and the DC conductivity increase. Infrared spectroscopy and X-ray powder diffraction indicate that a Li₂ MoO₄ crystalline phase is present for high MoO₃ content samples (x = 0.5, 0.6). This work was partly sponsored by FINEP, CNPq (Brazilian agencies) and UECE (Universidade Estadual do Cearà).     

Micro-Raman spectroscopy in polycrystalline CuInSe2 formation

The crystalline formation of CuInSe₂ thin films has been investigated using micro-Raman spectroscopy and AES composition analysis. It is confirmed that the Raman peaks are stongly dependent on the surface morphology and the Cu:In:Se ratio. In the films annealed at 315°C, crystalline grains larger than 2 m show Raman peaks at 174 cm^–1 and 258 cm^–1. The In content is very low and the Cu:Se ratio is about 1:1 in these grains. The low In concentration is thought to be due to the formation of In₂O₃ on the surface. On the other hand, random structures of 1–2 m grains found in films annealed at temperatures below 305°C show peaks at 174 cm^–1 and 186 cm^–1 instead of 258 cm^–1 and have a Cu:In:Se ratio of 1:1:3–4. Thus the 186 cm^–1 peak is thought to be related to a Cu, In-deficient phase when compared to stoichiometric CuInSe₂. The optimum annealing condition was found by analyzing the Raman spectra and composition of different crystalline CuInSe₂ grains. Films annealed under this condition exhibited a clear Raman peak at 174 cm^–1 and consisted of clusters of crystals less than 1 m in size.     

Percolation transition of siloxane domain in partially phenylated organic/inorganic hybrid glass

Organic-inorganic hybrid glass undergoes a percolation transition of the organic or inorganic moiety at a certain volume fraction of either phase. At the percolation threshold, various properties of the hybrid glass exhibit an abrupt change. We attempted to evaluate the threshold volume fraction of the percolation transition in partially phenylated glass from the measurable or observable behavior at the percolation transition. The volume fraction of the phenyl moiety in the hybrid glass was varied by variation of the mixed fraction of two starting silicon alkoxides, TEOS (tetraethylorthosilicate) and PTES (phenyltriethoxysilane). The threshold volume fraction was estimated as the point at which the dye-colored state with hydrophilic/hydrophobic dye, the Vickers hardness and siloxane bonding length exhibited a significant change. The percolation threshold of the phenyl moiety was estimated to be approximately 50 vol.%. At this threshold, the Vickers hardness showed a abrupt and almost discrete decrease and noticeable elasticity appeared. At the same time, the siloxane bondings were stretched by approximately 20% on the percolation of the phenyl part. In partially phenylated glass prepared from mixture of TEOS and PTES, the siloxane bondings seem to have a strong tendency to form a percolated siloxane network, and as a result of that, only the percolation of the phenyl moiety could be captured from the experimentally measurable quantities.     

A new criterion for the glass-forming ability of liquids

Based on theoretical calculations using the fragility concept and the nucleation theory for a model glass-forming system, we propose a dimensionless criterion, ?, expressed by T_rg(ΔT_x/T_g)^a, with T_rg, the reduced glass-transition temperature, ΔT_x, the width of the supercooled liquid region when heating a glass, T_g, the glass transition temperature, and a, the exponent. The application of this simple criterion to various glasses, including network, metallic, and molecular glasses (except pure water), indicates an excellent correlation between the critical cooling rate R_c and ? in a Log R_c-? single master plot with a = 0.143.     

Evolution of the local environment of lanthanum during simplified SON68 glass leaching

The evolution of the short- and medium-range local environment of lanthanum was determined by L_III-edge X-ray absorption spectroscopy (XAS) during leaching of simplified SON68-type glasses. In glass without phosphorus, lanthanum is found in a silicate environment, and its first coordination sphere comprises eight oxygen atoms at a mean distance of 2.51 Å. When this glass was leached at a high renewal rate, the lanthanum local environment was significantly modified: it was present at hydroxycarbonate and silicate sites with a mean La-O distance of 2.56 Å, and the second neighbors consisted of La atoms instead of Si for the glass. Conversely, in the gel formed at low renewal rates, lanthanum was found in a silicate environment similar to that of the glass. In phosphorus-doped glass, lanthanum is found in a phosphate environment, although the Si/P atomic ratio is 20:1. Lanthanum is surrounded by seven oxygen atoms at a mean distance of 2.37 Å. When phosphorus-doped glass is leached, regardless of the leaching solution flow rate, the short- and medium-range lanthanum local environment remains almost constant; the most significant change is a 0.05 Å increase in the La-O distance.     

Investigation of the chemical solubility of mixed-alkali fluorcanasite forming glasses

There is currently significant interest in all-ceramic dental restorations due to the demand to replace metals as the primary load-bearing tooth restorative material. A promising non-metallic material for such restorations is fluorcanasite, a chain-silicate glass-ceramic that is castable using conventional dental metal-casting techniques and which exhibits enhanced fracture toughness and flexural strength compared with currently available resin-bonded ceramics. Unfortunately, because of its relatively low silica content, it exhibits poor chemical durability. The aim of this study was to assess the influence of compositional changes on the formation and chemical solubility of the fluorcanasite forming glass, crystalline phase and residual glass. To this end, mixed-alkali compositions have been investigated and it has been shown that the solubility of the glass is a function of the alkali species present in the glass. By changing the alkali ratio of the fluorcanasite forming glass from 0.33 ([K]/[K + Na]) of the base composition derived from stoichiometry to 0.47, it was possible to reduce the chemical solubility of the fluorcanasite material significantly. The addition of extra CaF₂ to refine the grain structure resulted in a decrease in the durability of the material, making it currently unacceptable for dental applications. The glass-ceramic exhibits a minimum chemical solubility at the composition K⁷/Na⁸. The residual glass may have a slightly elevated K content compared to the original glass. The addition of extra CaF₂ to refine the grain structure resulted in an unacceptable decrease in the durability of the material.     

Molecular dynamics simulations of calcium aluminate glasses

Molecular dynamics simulations of a series of calcium aluminate glasses have been carried out using empirical potentials with a covalent term. The simulations closely reproduce the total neutron correlation function of glasses with 30 and 38 mol% Al₂O₃ and physical properties such as elastic constants. For compositions close to the eutectic 37 mol% Al₂O₃, aluminum is tetrahedrally coordinated by oxygen, but the proportion of five-fold and six-fold coordination and also edge-sharing tetrahedra gradually increases with increasing Al₂O₃ content. The coordination number for oxygen around calcium atoms is close to 6 and this involves a larger coordination at a shorter, well-defined distance, followed by a smaller coordination with a broader range of distances. When the Al₂O₃ content decreases, the calcium aluminate structure becomes depolymerised and the average ring size increases. Also reported is an X-ray photoelectron spectroscopy measurement on a glass sample with 38 mol% Al₂O₃, which shows that 38.6 ± 0.9% of the oxygens are non-bridging, in excellent agreement with the simulations.