Collisional Cross-Sections with T-Wave Ion Mobility Spectrometry without Experimental Calibration

A method for relating traveling-wave ion mobility spectrometry (TWIMS) drift times with collisional cross-sections using computational simulations is presented. This method is developed using SIMION modeling of the TWIMS potential wave and equations that describe the velocity of ions in gases induced by electric fields. The accuracy of this method is assessed by comparing the collisional cross-sections of 70 different reference ions obtained using this method with those obtained from static drift tube ion mobility measurements. The cross-sections obtained here with low wave velocities are very similar to those obtained using static drift (average difference?=?0.3%) for ions formed from both denaturing and buffered aqueous solutions. In contrast, the cross-sections obtained with high wave velocities are significantly greater, especially for ions formed from buffered aqueous solutions. These higher cross-sections at high wave velocities may result from high-order factors not accounted for in the model presented here or from the protein ions unfolding during TWIMS. Results from this study demonstrate that collisional cross-sections can be obtained from single TWIMS drift time measurements, but that low wave velocities and gentle instrument conditions should be used in order to minimize any uncertainties resulting from high-order effects not accounted for in the present model and from any protein unfolding that might occur. Thus, the method presented here eliminates the need to calibrate TWIMS drift times with collisional cross-sections measured using other ion mobility devices.

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The importance of glyceraldehyde radiolysis in chemical evolution

Studies in chemical evolution are intended to demonstrate how compounds of biological importance are generated from substances that could have been found in abiotic conditions on the primitive Earth or in extraterrestrial environments. In this context, the aim of the present work was to examine the behavior of dl-glyceraldehyde in both aqueous solution and solid samples under gamma irradiation. We irradiated dl-glyceraldehyde at different doses and temperatures with a gamma source; even at low doses and temperature (77 K), free radicals were detected. Among the products formed were ethylene glycol and glycolaldehyde. Some sugar-like compounds were also detected.

     

On the geometric–arithmetic index by decompositions-CMMSE

The concept of geometric–arithmetic index was introduced in the chemical graph theory recently, but it has shown to be useful. There are many papers studying different kinds of indices (as Wiener, hyper–Wiener, detour, hyper–detour, Szeged, edge–Szeged, PI, vertex–PI and eccentric connectivity indices) under particular cases of decompositions. The main aim of this paper is to show that the computation of the geometric-arithmetic index of a graph G is essentially reduced to the computation of the geometric-arithmetic indices of the so-called primary subgraphs obtained by a general decomposition of G. Furthermore, using these results, we obtain formulas for the geometric-arithmetic indices of bridge graphs and other classes of graphs, like bouquet of graphs and circle graphs. These results are applied to the computation of the geometric-arithmetic index of Spiro chain of hexagons, polyphenylenes and polyethene.     

Investigation of Cold Atmospheric Plasma-Activated Water for the Dental Unit Waterline System Contamination and Safety Evaluation in Vitro

The disinfection of the inner surface of a medical device has long been a challenge for the central sterile supply departments. Dental unit waterline system (DUWLs) foster the attachment of microorganisms and development of biofilm, which lead to continuous contamination of the outlet water from dental units; this contamination may be responsible for a potential risk of infection due to the exposure of patients and medical staff. The present study investigated the disinfection effects of cold atmospheric plasma-activated water (CAPAW) on DUWLs using a model of 5-day-old Enterococcus faecalis biofilm. The results showed that the colony-forming unit was reduced from 10⁷ to 0 after 5 min of treatment. The physicochemical properties of CAPAW were evaluated, including the pH value, oxidation reduction potential, and NO radical. The results showed that the inactivation mechanisms were mainly triggered by the reactive oxygen/nitrogen species. Additionally, CAPAW had a metal corrosion rate same as that of deionized water. We conclude that CAPAW can be applied as an appropriate alternative disinfectant against biofilm contamination of DUWLs.     

Hydrogenation of diacetyl over composite-supported egg-shell noble metal catalysts

Two composite supports with a mixed inorganic–organic structure were synthesized: BTAl and UTAl. Hydrophilic–hydrophobic dual properties of the supports were suitable for preparing egg-shell-supported metal catalysts for selective hydrogenation reactions. The catalysts were characterized by ICP, XRD, OM, TEM, EPMA, XPS and TGA. Their mechanical resistance was assessed. Activity and selectivity were tested with the hydrogenation of 2,3-butanedione (diacetyl) to 3-hydroxy-2-butanoneacetoin (acetoin). The same order of increasing metal particle size was found for the two tested supports: Pt < Ru < Pd. The XPS analysis showed that the metal/composite catalysts reduced in H2 at 503 K had two kinds of active sites: reduced (Me°) and electron-deficient (Me⁺). It was rationalized that the hydrogen bond cleavage was performed on the Me° active sites, while reactant adsorption occurred on the Me⁺ sites. The differences in activity and selectivity between the composite catalysts were attributed to electronic effects on the different metals and to different adsorptive properties of the different polymers. The high selectivity to acetoin was attributed to the preferential adsorption of diacetyl as compared to the adsorption of acetoin. The BTAl catalysts were slightly more active and selective than the UTAl ones. This was attributed to electronic effects caused by remnant organic groups on the composite supports (urethane or biphenyl on UTAl or BTAl, respectively). Pd-BTAl was the most active and selective catalyst, a fact related to electronic effects of both palladium and the support.     

Immobilization and Stabilization of Beta-Xylosidases from Penicillium janczewskii

β-Xylosidases are critical for complete degradation of xylan, the second main constituent of plant cell walls. A minor β-xylosidase (BXYL II) from Penicillium janczewskii was purified by ammonium sulfate precipitation (30% saturation) followed by DEAE-Sephadex chromatography in pH 6.5 and elution with KCl. The enzyme presented molecular weight (MW) of 301 kDa estimated by size exclusion chromatography. Optimal activity was observed in pH 3.0 and 70–75 °C, with higher stability in pH 3.0–4.5 and half-lives of 11, 5, and 2 min at 65, 70, and 75 °C, respectively. Inhibition was moderate with Pb⁺² and citrate and total with Cu⁺², Hg⁺², and Co⁺². Partially purified BXYL II and BXYL I (the main β-xylosidase from this fungus) were individually immobilized and stabilized in glyoxyl agarose gels. At 65 °C, immobilized BXYL I and BXYL II presented half-lives of 4.9 and 23.1 h, respectively, therefore being 12.3-fold and 33-fold more stable than their unipuntual CNBr derivatives (reference mimicking soluble enzyme behaviors). During long-term incubation in pH 5.0 at 50 °C, BXYL I and BXYL II glyoxyl derivatives preserved 85 and 35% activity after 25 and 7 days, respectively. Immobilized BXYL I retained 70% activity after 10 reuse cycles of p-nitrophenyl-β-D-xylopyranoside hydrolysis.

     

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

\(\alpha\)-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577–585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.     

Effect of heterocyclic ring system on formation of dimeric quinolones under catalyst-free conditions: a green approach

The intermediate-dependent green and efficient synthesis of dimeric quinolones 4a–l and 7a–l by the Knoevenagel condensation followed by Michael-type addition of 4-hydroxy-1-methylquinolin-2(1H)-one 1a, b to indole-3-aldehydes 2a–f and aromatic aldehydes 5a–l in water through the condensed compound 3a–l under catalyst-free conditions is described. This reaction was found to be environmentally friendly, has easy-workup and shorter reaction times giving good yields of the product without the need for its isolation using column chromatography.