Two Methods,One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses

In lead optimization, protein crystallography is an indispensable tool to analyze drug binding. Binding modes and non-covalent interaction inventories are essential to design follow-up synthesis candidates. Two protocols are commonly applied to produce protein–ligand complexes: cocrystallization and soaking. Because of its time and cost effectiveness, soaking is the more popular method. Taking eight ligand hinge binders of protein kinase A, we demonstrate that cocrystallization is superior. Particularly for flexible proteins, such as kinases, and larger ligands cocrystallization captures more reliable the correct binding pose and induced protein adaptations. The geometrical discrepancies between soaking and cocrystallization appear smaller for fragment-sized ligands. For larger flexible ligands that trigger conformational changes of the protein, soaking can be misleading and underestimates the number of possible polar interactions due to inadequate, highly impaired positions of protein amino-acid side and main chain atoms. Thus, if applicable cocrystallization should be the gold standard to study protein–ligand complexes.     

Rare-earth free sensitizer in NaLuCrF4:Er upconversion material

Upconversion phosphors are known as a material system that can convert near-infrared light into visible/ultraviolet emissions by sequentially absorbing multiple photons. The studies on upconversion materials often use two rare earth (RE) ions as a sensitizer-activator pair. We investigated the influences on luminescence intensity depending on Cr-doping content (x) of hexagonal NaLu_0.98–xCr_xF₄Er_0.02 (x = 0–0.9) upconversion material by substituting Lu³⁺ ions with Cr³⁺in the absence of Gd³⁺. The change in upconversion luminescence intensity appears with saddle-like shape. We suggest that Cr³⁺ ions play the dual role as a constituent in host lattice and a sensitizer in the upconversion process. Optimal conditions for gaining the strongest upconversion emission correspond to x = 0.3–0.5, where there are effective energy transfers between Cr³⁺ and Er³⁺ ions and CrEr dimers. Apart from these values, the emission intensity decreases rapidly which can be ascribed to the absence of multiple-photon absorption for the case of low Cr³⁺ contents, and to the coupling between Cr³⁺ and/or Er³⁺ ions for the case of high Cr³⁺ contents. Magnetization and electron-spin-resonant measurements were performed to understand the correlation between the optical and magnetic properties.     

Pull-Down of Metalloproteins in Their Native States by Using Desthiobiotin-Based Probes

One-third of all proteins are estimated to require metals for structural stability and/or catalytic activity. Desthiobiotin probes containing metal binding groups can be used to capture metalloproteins with exposed active-site metals under mild conditions so as to prevent changes in metallation state. The proof-of-concept was demonstrated with carbonic anhydrase (CA), an open active site, Zn²⁺-containing protein. CA was targeted by using sulfonamide derivatives. Linkers of various lengths and structures were screened to determine the optimal structure for capture of the native protein. The optimized probes could selectively pull down CA from red blood cell lysate and other protein mixtures. Pull-down of differently metallated CAs was also investigated.     

Performance comparison of parallel ILU preconditioners for the incompressible Navier-Stokes equations

Journal of Mechanical Science and Technology - In this paper, the performances of various ILU type parallel preconditioners for the finite element discretization of the incompressible Naiver-Stokes...     

Hydrogen production enhancement using hot gas cleaning system combined with prepared Ni-based catalyst in biomass gasification

This paper investigates the hot gas temperature effect on enhancing hydrogen generation and minimizing tar yield using zeolite and prepared Ni-based catalysts in rice straw gasification. Results obtained from this work have shown that increasing hot gas temperature and applying catalysts can enhance energy yield efficiency. When zeolite catalyst and hot gas temperature were adjusted from 250 °C to 400 °C, H₂ and CO increased slightly from 7.31% to 14.57%–8.03% and 17.34%, respectively. The tar removal efficiency varies in the 70%–90% range. When the zeolite was replaced with prepared Ni-based catalysts and hot gas cleaning (HGC) operated at 250 °C, H₂ contents were significantly increased from 6.63% to 12.24% resulting in decreasing the hydrocarbon (tar), and methane content. This implied that NiO could promote the water-gas shift reaction and CH₄ reforming reaction. Under other conditions in which the hot gas temperature was 400 °C, deactivated effects on prepared Ni-based catalyst were observed for inhibiting syngas and tar reduction in the HGC system. The prepared Ni-based catalyst worked at 250 °C demonstrate higher stability, catalyst activity, and less coke decomposition in dry reforming. In summary, the optimum catalytic performance in syngas production and tar elimination was achieved when the catalytic temperature was 250 °C in the presence of prepared Ni-based catalysts, producing 5.92 MJ/kg of lower heating value (LHV) and 73.9% tar removal efficiency.     

Dielectric strength of Al2O3/silicone composites after high‐temperature aging

Silicones are widely used for electrical insulation owing to their high dielectric strength and thermal stability. However, recent studies revealed insufficient stability of silicone for high‐temperature applications. To study the effect of Al₂O₃ fiber on silicone stability, we measured the dielectric strength of unfilled silicone and Al₂O₃/silicone composites as a function of aging time at 250°C in air and analyzed data by Weibull probability distribution to determine characteristic dielectric strength (E₀) and shape parameter (β). Prior to aging, unfilled silicone and composites had similar behavior, with E₀ at about 20 kV/mm and β > 15. During aging, unfilled silicone developed both micro‐ and macrocracks, with β dropped below five in 240 h and E₀ decreased significantly. Composites developed microcracks, with β dropped below 5 in longer time and E₀ remained almost constant. Addition of Al₂O₃ slowed down crack growth in silicone matrix, resulting in longer lasting high‐temperature dielectric materials. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 41170.     

Regioselective Synthesis of Naphtho‐fused Heterocycles via Palladium(0)‐Catalyzed Tandem Reaction of N‐Tosylhydrazones

We have developed a palladium(0)‐catalyzed tandem process which involves the cross‐coupling reaction of N‐tosylhydrazones with dibromide compounds followed by a sequence of intramolecular 5‐exo‐trig, 3‐exo‐trig cyclization, ring opening, and β‐hydride elimination to produce 6‐endo‐trig cyclized products. The strategy was successfully applied for the regioselective synthesis of substituted benzo[b]naphtho[2,1‐d]thiophenes, naphtho[1,2‐b]benzofurans, and benzo[a]carbazoles in moderate to excellent yields.

     

Adsorptive interaction of bisphenol A with mesoporous titanosilicate/reduced graphene oxide nanocomposite materials: FT-IR and Raman analyses

Nanocomposite materials containing graphene oxide have attracted tremendous interest as catalysts and adsorbents for water purification. In this study, mesoporous titanosilicate/reduced graphene oxide composite materials with different Ti contents were employed as adsorbents for removing bisphenol A (BPA) from water systems. The adsorptive interaction between BPA and adsorption sites on the composite materials was investigated by Fourier transform infrared (FT-IR) and Raman spectroscopy. Adsorption capacities of BPA at equilibrium, q _e (mg/g), decreased with increasing Ti contents, proportional to the surface area of the composite materials. FT-IR observations for fresh and spent adsorbents indicated that BPA adsorbed onto the composite materials by the electrostatic interaction between OH functional groups contained in BPA and on the adsorbents. The electrostatic adsorption sites on the adsorbents were categorized into three hydroxyl groups: Si-OH, Ti-OH, and graphene-OH. In Raman spectra, the intensity ratios of D to G band were decreased after the adsorption of BPA, implying adsorptive interaction of benzene rings of BPA with the sp² hybrid structure of the reduced graphene oxide.     

Deformation and Fracture of β‐Silicon Nitride Micropillars

Room‐temperature deformation and fracture behaviors under microcompression of single crystal β‐silicon nitride (Si₃N₄) micropillars were investigated. Pillars were fabricated by focused ion beam (FIB) in large Si₃N₄ grains, located close to the basal and prismatic orientations, selected by electron backscatter diffraction (EBSD). The micromechanical test and the damage characterization were performed by nanoindentation and scanning electron microscopy (SEM), respectively. The elastic, plastic, and fracture properties, such as Young's modulus, yield stress, and rupture stress are considerably influenced by the pillar orientation. The activation of the type slip system was identified in case of basal oriented micropillars.