HELFIT: Helix fitting by a total least squares method

The problem of fitting a helix to data arises in analysis of protein structure, in nuclear physics, and in engineering. A continuous helix is described by five parameters: helix axis, helix radius, and helix pitch. One of these helix parameters is frequently predefined in the helix fitting. Other algorithms find only the helix axis or determine separately the helix axis, the helix radius, or the helix pitch. Here we describe a total least squares method, HELFIT, for helix fitting. HELFIT enables one to calculate simultaneously all five of the helix parameters with high accuracy. The minimum number of data points required for the analysis is only four. HELFIT is very insensitive to noise even in short helices. HELFIT also calculates a parameter, p = rmsd/(N − 1)^1/2, which estimates the regularity of helical structures independent of the number of data points, where rmsd is the root mean square distance from the best-fit helix to data points and N is the number of data points. It should become a basic tool of structural bioinformatics.     

二甲基亚砜对乙酸气相色谱保留时间的影响及其机理

通过气相色谱、红外光谱分析和量子化学计算,探究溶于二甲基亚砜（DMSO）中乙酸保留时间发生波动的原因。 结果显示,乙酸保留时间变化与DMSO体积等量递增呈线性关系,R²=0.99301;根据红外光谱分析得出,DMSO和乙酸之间生成了氢键,以DMSO-乙酸分子的形式通过色谱柱;根据Gaussian09程序计算结果,DMSO电子密度大的部分给予电子,与乙酸之间形成了氢键,而DMSO电子密度小的部分容易获得电子与具有强偶极矩的色谱柱固定液聚乙二醇产生作用力,吸附在固定液上。因此,在上述一系列复杂的分子间作用力的共同影响下,乙酸保留时间发生了波动,且随着溶剂DMSO体积比增加,乙酸保留时间不断延长。     

The electrochemical behavior of some podands at a benzo[c]cinnoline modified glassy carbon electrode

This paper describes the grafting of benzo[c]cinnoline (BCC) molecules on glassy carbon (GC) electrode surface. The attachment of BCC molecules to carbon substrate is induced by the electrochemical reduction of the corresponding diazonium salt. The modification of GC with BCC diazonium salt was done in aprotic solution and proved by blocking of dopamine electron transfer. The presence of BCC at the GC surface was characterized by cyclic voltammetry and X-ray photoelectron spectroscopy (XPS). On modified surface, the electrochemical behavior of two different types of podands and the catalytic effects of the GC-BCC surface were studied. The XPS was used to monitor element characteristics of the adsorbates on the GC surface and confirm the attachment of BCC molecules to the GC surface.     

Variation of trace elements in snow during starting and ending of snowfall in Kyoto city measured by low power total reflection X‐ray fluorescence spectrometry

This paper reports the variation of trace element concentrations in snow samples during the starting and ending of snowfalls in Kyoto, Japan, using a low power total reflection X‐ray fluorescence spectrometer to analyze trace elements (having atomic numbers from 13 to 28) in a sample with detection limits of ppb to ppm in concentration. The difference in concentrations indicates how much the urban air is refreshed due to falling snow. Cl, K, Ca, and Fe were determined in the snow samples, and their concentrations during snow starting were higher than at snow ending.     

Antifungal activity of Mongolian medicinal plant extracts

Abstract

The in vitro antifungal activity of extracts obtained from 14 medicinal plants of the mongolian flora were investigated by measuring their minimal inhibitory concentration (MIC) against fungi cause of cutaneous diseases such as Candida species, dermatophytes and Malassezia furfur. Among the species examined, Stellaria dichotoma L., Scutellaria scordifolia L. Aquilegia sibirica Fisch. Et Schrenk. and Hyoscyamus niger L. extracts demonstrated antifungal activity against all studied fungi. In particular, S. scordifolia L. methanol extract, obtained at room temperature, showed the best activity against Candida spp., Malassezia furfur and dermatophytes with GMMIC₅₀ values of 22?µg/mL, 64?µg/mL and 32?µg/mL, respectively. The flavones, luteolin and apigenin, identified in S. scordifolia extracts, and rutin identified in S. dichotoma and Hyoscyamus niger L. extracts, could be responsible of the observed antifungal activity.     

Adsorption mechanism of arsenate by zirconyl-functionalized activated carbon

Arsenate [As(V)] and arsenite [As(III)] sorption at the solid-water interface of activated carbon impregnated with zirconyl nitrate (Zr-AC) was investigated using X-ray absorption spectroscopy (XAS) and surface complexation modeling. The XAS data at the Zr K-edge suggest that the structure of the zirconyl nitrate coating is built from chains of edge-sharing ZrO8 trigonal dodecahedra bound to each other through two double hydroxyl bridges. The 8-fold coordination of each Zr atom is completed by four O atoms, which share a bit less than the two theoretically possible bidentate nitrate groups. On impregnation, two of the O atoms may lose their nitrate group and be transformed to hydroxyl groups ready for binding to carboxylic or phenolic ligands at the AC surface. As K-edge XANES results showed the presence of only As(V) on adsorption regardless of the initial As oxidation state. Oxidation to As(V) is probably mediated by available carbon species on the AC surface as found by batch titration. Zr K-edge EXAFS data indicate that arsenate tetrahedra form monodentate mononuclear surface complexes with free hydroxyl groups of zirconyl dodecahedra, whereby each bidentate nitrate group is exchanged by up to two arsenate groups. The inner-sphere arsenate binding to the Zr-AC surface sites constrained with the spectroscopic results was used in the formulation of a surface complexation model to successfully describe the adsorption behavior of arsenate in the pH range between 4 and 12. The results suggest therefore that Zr-AC is an effective adsorbent for arsenic removal due to its high surface area and the presence of high affinity surface hydroxyl groups.     

Total synthesis of the antitumor acetogenin mosin B: desymmetrization approach to the stereodivergent synthesis of threo/trans/erythro-type acetogenins

A total synthesis of the threo/trans/erythro-type acetogenin mosin B and one of its diastereomers has been achieved. The carbon skeleton is assembled in a convergent fashion from two segments (a THF ring segment and a gamma-lactone segment) through the Nozaki-Hiyama-Kishi reaction. The THF ring segment was stereoselectively constructed by a stereodivergent synthesis starting from a common intermediate (4-cyclohexene-1,2-diol) based on a desymmetrization strategy. The gamma-lactone segment was synthesized by coupling a triflate and a chiral alpha-sulfenyl gamma-lactone. By virtue of these synthetic results, we suggest that the absolute configuration of natural mosin B is 1 a. Antiproliferative effects of 1 a and 1 b were also investigated.     

Nuclear reactions of medium and heavy target nuclei with high-energy projectiles II. Fragmentation ofnatAg and197Au by 3.65 AGeV12C-ions and 3.65 GeV protons

The cross sections of a number of target fragmentation products formed in nuclear reactions of 3·65 A GeV¹²C-ions and 3·65 GeV protons with^natAg and¹⁹⁷Au have been measured. The measurements have been done by direct counting of irradiated targets with Ge(Li) gamma-ray spectrometers. Comparisons between these and other data have been used to test the hypotheses of factorization and limiting fragmentation. The total cross section for residue production in both reactions indicates that target residues are formed mainly in central collisions.