pyMolDyn: Identification,structure, and properties of cavities/vacancies in condensed matter and molecules

pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc.     

Synthesis, characterization and hydrodesulfurization activity of silica-dispersed NiMoW trimetallic catalysts

Silica-dispersed NiMoW trimetallic hydrodesulfurization catalysts were prepared by deposition-precipitation method. For comparative purposes, bulk NiMoW trimetallic catalysts were obtained by co-precipitation. Silica was employed to disperse active metals for full utilization of active components and silica-dispersed NiMoW catalyst had high active metal content. BET analysis showed that silica-dispersed NiMoW trimetallic catalysts had a high surface area (165.1 m²/g) and pore volume (0.27 ml/g). Transmission electron microscopy results proved that active components were well dispersed. Hydrodesulfurization activity of silica-dispersed NiMoW catalysts was much higher than that of comparative catalysts and up to twice greater than those of commercial NiMo alumina-supported systems per gram of catalyst.     

UNIQUAC correlation of liquid–liquid equilibrium in systems involving ionic liquids: The DFT–PCM approach. Part II

In this work, new UNIQUAC structural parameters r and q for the ionic liquids were determined by quantum chemistry calculations performed with the Gaussian 03 and GAMESS 7.1 packages, including the density functional theory (DFT) for the optimization of the structures and the polarizable continuum method (PCM) for the calculation of molecular areas and volumes. Data liquid–liquid equilibrium (LLE) of 41 ternary systems involving 15 different ionic liquids, comprising 379 experimental tie-lines, was correlated by the UNIQUAC model for the activity coefficient. The results, expressed by deviations between experimental and calculated compositions, are very satisfactory, with deviation values about 1.93%.     

Advantages of using a modified orthogonal sampling configuration originally designed for LC-ESI-MS to couple CE and MS for the determination of antioxidant phenolic compounds found in virgin olive oil

A ThermoFinnigan sheath liquid flow capillary electrophoresis-mass spectrometry system designed for coupling via a co-axial interface was coupled through an adapted via an alternative, commercially available interface for orthogonal sampling. The affordable, reversible structural alterations made in the commercial LC-MS interface resulted in improved analytical performance.The results of a conventional capillary electrophoresis (CE) method using a commercial co-axial source to determine antioxidant phenolic acids present in virgin olive oil, were compared with those obtained by using a modified orthogonal sampling position. In both cases, separations were done using a 10 mM ammonium acetate/ammonium hydroxide buffer solution at pH 10.0 and a constant applied voltage of 25 kV. The operating variables for the mass spectrometry interface were re-optimized for the modified orthogonal orientation. This allowed the sheath liquid, sheath gas flow rates and capillary voltage to be lowered with respect to the co-axial coupling configuration. In addition, the orthogonal sampling position provided a higher selectivity by effect of ion sampling excluding larger droplets—with an increased momentum along the axis—which were drained through the sink at the bottom of the ion source. Also, the new configuration facilitated sample ionization, improved electrospray stability and led to stronger signals as a result.The new system was validated in terms of precision (repeatability), linearity, and limits of detection and quantification. A comparison of the validation data with the results previously obtained by using a commercial co-axial configuration revealed the adapted orthogonal sampling position to provide better repeatability in both migration times and relative peak areas (<1% and 7% respectively with n = 15 replicates), a good linear range (with levels in the microgram-per-litre region) and lower limits of detection—especially for the compounds detected with the lowest sensitivity when co-axial ESI was used, as HFA, GEN, FER and VAN finding LOD among 24-3.0 μg L⁻¹ respectively.     

Speciation of aluminium fluoride complexes and Al in soils from the vicinity of an aluminium smelter plant by hyphenated High Performance Ion Chromatography Flame Atomic Absorption Spectrometry technique

The paper presents a new tool for the determination of inorganic speciation forms of aluminium: AlF_n^{(3 − n)+}, and Al³⁺ by means of the HPIC-FAAS. The proposed method has been successfully used for speciation analysis (qualitative and quantitative) of inorganic aluminium forms AlF_n^{(3 − n)+} in soil samples. In order to isolate the most environmentally available fraction, 5 g of the sample was collected and extracted in deionised water (water soluble fraction) for 1 h using a magnetic stirrer. The determinations in a hyphenated technique system were performed for a number of prepared water extracts. Concentration determinations of particular aluminium forms were performed based on model studies and real samples. The separation of Al species with nominal charge of + 1, + 2, and + 3 required a run time of less than 4 min during a single analysis. Based on the analysis of water extracts of soil, it was obtained that aluminium forms elute in the following order: 1PA (first signal) — AlF₂⁺ and/or AlF₄⁻; 2PA (second signal) — AlF²⁺ and/or AlF₃⁰; 3PA (third signal) — Al³⁺. In order to confirm the occurrence of these forms a simulation using the Mineql program was conducted. The details of speciation analysis of aluminium fluoride forms by means of an HPIC-FAAS instrument equipped are presented. Interpretation of the speciation analysis of the water soluble fraction of soil samples is proposed, based on the separation during chromatographic run and calculated data by Mineql.     

Effect of drying technique on the physicochemical properties of sodium silicate-based mesoporous precipitated silica

The conventional drying (oven drying) method used for the preparation of precipitated mesoporous silica with low surface area (>300 m²/g) and small pore volume is often associated with a high production cost and a time consuming process. Therefore, the main goal of this study was to develop a cost-effective and fast drying process for the production of precipitated mesoporous silica using inexpensive industrial grade sodium silicate and spray drying of the precipitated wet-gel silica slurry. The precipitated wet-gel silica slurry was prepared from an aqueous sodium silicate solution through the drop-wise addition of sulfuric acid. Mesoporous precipitated silica powder was prepared by drying the wet-gel slurry with different drying techniques. The effects of the oven drying (OD), microwave drying (MD), and spray drying (SD) techniques on the physical (oil, water absorption, and tapping density), and textural properties (specific BET surface area, pore volume, pore size, and % porosity) of the precipitated mesoporous silica powder were studied. The dried precipitated mesoporous silica powders were characterized with field-emission scanning electron microscopy; Brunauer, Emmett and Teller and BJH nitrogen gas adsorption/desorption methods; Fourier-transform infrared spectroscopy; thermogravimetric and differential analysis; N₂ physisorption isotherm; pore size distribution and particle size analysis. There was a significant effect of drying technique on the textural properties, such as specific surface area, pore size distribution and cumulative pore volume of the mesoporous silica powder. Additionally, the effect of the microwave-drying period on the physicochemical properties of the precipitated mesoporous silica powder was investigated and discussed.     

Influence of superalloy substrate roughness on adhesion and oxidation behavior of magnetron-sputtered NiCoCrAlY coatings

The present study has been conducted in order to determine the influence of superalloy substrate roughness on adhesion and oxidation behavior of magnetron-sputtered NiCoCrAlY coatings. Six types of coating samples with different substrate roughness were tested. The surface roughness and real surface area of both the substrates and coatings were studied by atomic force microscopy (AFM) techniques. The scratch tests performed at progressive loads were employed to evaluate the adhesion of the coatings. Cyclic oxidation tests were performed at 1100 °C in air for 50 cycles, each cycle consisting of 1 h heating in the tube furnace followed by 15 min cooling in the open air. The AFM measurements exhibit that the surface roughness of the sputtered NiCoCrAlY coating increases with the increasing of the superalloy substrate roughness. The NiCoCrAlY coatings present slightly lower roughness than the corresponding superalloy substrate. The scratch adhesion tests indicate that the coatings on substrates with a smoother surface possess better adhesion than on those with a rougher surface. Both the real surface area and oxidation weight gain of the coatings decrease with the decreasing of the superalloy substrate roughness. The NiCoCrAlY coating sputtered on the superalloy substrate with lower roughness provides relatively higher antioxidant protection than that provided by the coating with rougher substrate.     

Self-organized critical model for protein folding

The major factor that drives a protein toward collapse and folding is the hydrophobic effect. At the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We study the fractal behavior of 5526 protein structures present in the Brookhaven Protein Data Bank. Power laws of protein mass, volume and solvent-accessible surface area are measured independently. The present findings indicate that self-organized criticality is an alternative explanation for the protein folding. Also we note that the protein packing is an independent and constant value because the self-similar behavior of the volumes and protein masses have the same fractal dimension. This power law guarantees that a protein is a complex system. From the analyzed data, q-Gaussian distributions seem to fit well this class of systems.