Evaluation of different virtual screening programs for docking in a charged binding pocket

Virtual screening of small molecules against a protein target often identifies the correct pose, but the ranking in terms of binding energy remains a difficult problem, resulting in unacceptable numbers of false positives and negatives. To investigate this problem, the performance of three docking programs, FRED, QXP/FLO, and GLIDE, along with their five different scoring functions, was evaluated with the engineered cavity in cytochrome c peroxidase (CCP). This small cavity is negatively charged and completely buried from solvent. A test set of 60 molecules, experimentally identified as 43 "binders" and 17 "non-binders", were tested with the CCP binding site. The docking methods' performance is quantified by the ROC curve and their reproduction of crystal poses. The effects from generation of different ligand tautomers and inclusion of water molecule in the cavity are also discussed.     

Ferric hydroxide supported gold subnano clusters or quantum dots: enhanced catalytic performance in chemoselective hydrogenation

An attempt to prepare ferric hydroxide supported Au subnano clusters via modified co-precipitation without any calcination was made. High resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) have been employed to study the structure and chemical states of these catalysts. No Au species could be observed in the HRTEM image nor from the XRD pattern, suggesting that the sizes of the Au species in and on the ferric hydroxide support were less than or around 1 nm. Chemoselective hydrogenation of aromatic nitro compounds and alpha,beta-unsaturated aldehydes was selected as a probe reaction to examine the catalytic properties of this catalyst. Under the same reaction conditions, such as 100 degrees C and 1 MPa H2 in the hydrogenation of aromatic nitro compounds, a 96-99% conversion (except for 4-nitrobenzonitrile) with 99% selectivity was obtained over the ferric hydroxide supported Au catalyst, and the TOF values were 2-6 times higher than that of the corresponding ferric oxide supported catalyst with 3-5 nm size Au particles. For further evaluation of this Au catalyst in the hydrogenation of citral and cinnamaldehyde, selectivity towards unsaturated alcohols was 2-20 times higher than that of the corresponding ferric oxide Au catalyst.     

Facile synthesis of superparamagnetic Fe3O4@Au nanoparticles for photothermal destruction of cancer cells

Superparamagnetic Fe(3)O(4) nanoparticles with positive surface ξ-potential were synthesized via a solvothermal route. After Fe(3)O(4) was mixed with HAuCl(4) and NaBH(4), the reduced Au nanoparticles could be directly adsorbed onto the surface of Fe(3)O(4) nanoparticles. The as-synthesized nanocomposites were successfully applied to photothermal destruction of cancer cells.     

Effect of film thickness on morphological evolution in dewetting and crystallization of polystyrene/poly(ε-caprolactone) blend films

In this Article, the morphological evolution in the blend thin film of polystyrene (PS)/poly(ε-caprolactone) (PCL) was investigated via mainly AFM. It was found that an enriched two-layer structure with PS at the upper layer and PCL at the bottom layer was formed during spinning coating. By changing the solution concentration, different kinds of crystal morphologies, such as finger-like, dendritic, and spherulitic-like, could be obtained at the bottom PCL layer. These different initial states led to the morphological evolution processes to be quite different from each other, so the phase separation, dewetting, and crystalline morphology of PS/PCL blend films as a function of time were studied. It was interesting to find that the morphological evolution of PS at the upper layer was largely dependent on the film thickness. For the ultrathin (15 nm) blend film, a liquid-solid/liquid-liquid dewetting-wetting process was observed, forming ribbons that rupture into discrete circular PS islands on voronoi finger-like PCL crystal. For the thick (30 nm) blend film, the liquid-liquid dewetting of the upper PS layer from the underlying adsorbed PCL layer was found, forming interconnected rim structures that rupture into discrete circular PS islands embedded in the single lamellar PCL dendritic crystal due to Rayleigh instability. For the thicker (60 nm) blend film, a two-step liquid-liquid dewetting process with regular holes decorated with dendritic PCL crystal at early annealing stage and small holes decorated with spherulite-like PCL crystal among the early dewetting holes at later annealing stage was observed. The mechanism of this unusual morphological evolution process was discussed on the basis of the entropy effect and annealing-induced phase separation.     

Impact of sugar stereochemistry on natural killer T cell stimulation by bacterial glycolipids

Natural killer T (NKT) cells recognize glycolipids produced by Sphingomonas bacteria, and these glycolipids contain C6-oxidized sugars, either glucuronic acid or galacturonic acid, linked to ceramides. Glycolipids with gluco stereochemistry are the most prevalent. Multiple studies have demonstrated that galactosylceramides are more potent stimulators of NKT cells than their glucose isomers. To determine if this stereoselectivity is retained in the context of the C6-oxidized sugars found in bacterial glycolipids, we prepared two sets of gluco and galacto-glycolipids oxidized at their C6 positions and compared their NKT stimulatory properties. In the context of carboxylic acid groups at C6, gluco stereochemistry gave the more potent responses. We also prepared bacterial glycolipids containing more complex ceramide groups to determine if these chains impact NKT cell responses.     

Synthesis, characterization, crystal structure and DFT studies on 1',3'-dihydrospiro[fluorene-9,2'-perimidine

The title compound, 1′,3′-dihydrospiro[fluorene-9,2′-perimidine] has been synthesized and characterized by NMR, ESI-MS, IR, elemental analysis, UV–vis and fluorescence spectroscopy. The crystal structures of the title compound and its co-crsytal with 9-fluorenone have also been determined by X-ray single crystal diffraction. Density functional theory (DFT) calculations and vibrational frequencies have been performed at B3LYP/6-31G* level. The comparisons between the experimental vibrational frequencies and the predicted data show that B3LYP/6-31G* method can simulate the IR of the title compound on the whole. The theoretical electronic absorption spectra have been calculated by using TD-DFT method and compared with the experimental result. The solid-fluorescence determination of the title compound reveals two emission bans at 430 and 590 nm while its co-crystal reveals only one emission band at 590 nm.     

一种新型铜离子荧光分子探针的合成与性能研究

设计合成了一种新型的以二苯乙烯为荧光团、双(2-吡啶甲基)胺(DPA)为识别基团的铜离子荧光分子探针(E)-4-(4-(双吡啶甲基胺)苯乙烯基)氰基苯(1),其结构用UV,IR,1H NMR,13C NMR和GC/MS进行了表征,并考察了其荧光性能.结果表明该荧光分子探针在CH3CN/H2O(1/9,V/V)溶液中,能...     

过渡金属脒配合物的合成与应用研究进展

脒及其衍生物是一类具有广泛而良好生物活性的有机物,也是重要的有机合成中间体.脒作为一类良好的配体,具有多种成键类型,所生成的脒过渡会属配合物也具有很多特殊性质与重要用途.本文主要综述了脒配合物合成方法的进展及其性能与应用.其中腈胺加成"一锅"法制备脒配合物的有效性和方便性.不但可以利用过渡金属诱导有机腈与胺耦合成眯,而...     

Synthesis and properties of a novel polyester containing bithiazole

A novel Schiff base type polyester containing 2,2’-diamino-4,4’-bithiazole(DABT) was prepared by low-temperature interface polycondensation of 1,4-benzenedicarbonyl dichloride with 4,4’-(4,4’-bithiazole-2,2’-diylbis(imine-2,1-diyl)diphenol(BDDP), which is derived from a 2,2’-diamino-4,4’-bithiazole(DABT) Schiff base reacted with a 4-hydroxybenzaldehyde monomer.The newly generated polyester was evaluated based on characterization of its solubility,FTIR spectroscopy,elemental analysis,X-ray diffraction measurements and thermogravimetric analysis(TGA) studies.