Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

Simple preparation and characteristics of silk fibroin microsphere

We investigated the biomaterial and pharmaceutical utility of pure silk fibroin (SF) protein as a possible for separation, using Sephadex G-25 gel filtration chromatography and simply preparing SF microsphere particles (SFMP) by spray dryer. Also, some of its physicochemical properties and morphology were investigated. Obtaining microspheres and/or submicronic particles by spray dryer method was accelerated or completed with the transition from the random coil to the β-sheet structure during spray dryer treatment. It was identified by the basic Fourier transform infrared spectroscopy of SFMP. The various pH range of SFMP’s swelling ratio is dependent on the pH of the solution, not on the occurred gelation. Morphologically, SFMP was spherical in shape, and particles, average 2±10 μm in size, were observed by scanning electron microscope and particle analyzer, respectively. The average molecular weight (M_W) of pure SF protein dissolved in calcium chloride is about 61,500 g/mol as measured by gel permeation chromatography.     

Structure and Magnetic Properties of Nickel–Zinc Ferrite Nanoparticles Prepared by Glass Crystallization Method

Summary. The magnetic and microstructure properties of Fe₂O₃–0.4NiO–0.6ZnO–B₂O₃ glass system, which was subjected to heat treatment in order to induce a magnetic crystalline phase (Ni_0.4Zn_0.6-Fe₂O₄ crystals) within the glass matrix, were investigated. DSC measurement was performed to reveal the crystallization temperature of the prepared glass sample. The obtained samples, produced by heat treatment at 765°C for various times (1, 1.5, 2, and 3 h), were characterized by X-ray diffraction, IR spectra, transmission electron microscopy, and vibrating sample magnetometer. The results indicated the formation of spinel Ni–Zn ferrite in the glass matrix. Particles of the ferrite with sizes ranging from 28 to 120 nm depending on the sintering time were observed. The coercivity values for different heat-treatment samples were found to be in the range from 15.2 to 100 Oe. The combination of zinc content and sintering times leads to samples with saturation magnetization ranging from 12.25 to 17.82 emu/g.     

Synthesis and properties of coumarin-derived organogelators

A new family of coumarin derivatives containing amide group with different alkyl chain lengths was synthesized and their properties as organogelators were evaluated. It was found that the organogelation abilities were not obviously affected by the alkyl spacer length of amide group. Helical morphologies formed either in nonpolar or high polar solvents by most of the gelators. Occurrence of reversible and stereoselective photodimerization of the gel formed by 4-(7′-coumarinoxy)-N-octadecylbutanamide (3a) in cyclohexane was confirmed by ¹H NMR, UV absorption, and fluorescence spectra. The photoreaction of the gel proceeded without any dissolution, but the drastic microscopic changes of gel morphologies accompanied with the irradiation were identified using SEM and AFM investigations.     

A simple scheme for calculating the energy levels and the spectra of molecular crystals

A simple matrix method for calculating the vibrational and electron energy levels and spectra in molecular crystals is proposed.     

A Closed-Form Relation for Dimension-Dependent Two-Electron Matrix Elements of the Interelectronic Distance

The evaluation of matrix elements of two electron atoms is fundamental for the study of the electronic properties of those systems. We add to this knowledge by presenting an explicit expression for the matrix elements of the inverse of the interelectronic distance of two-electron atoms in any spatial dimension D. The basis functions used are the D-dependent hydrogenic wavefunctions {1s ²,2p ²,3d ²,4f ²,5g ²,...,21y ²,...}, extending and including, in this way, the results of the previous basis set {1s ²,2p ²,3d ²,4f ²}. The methodology used does not employ Fourier integral transforms as in previous works but hypergeometric transformation formulas.     

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

石墨炉原子吸收光谱无标样分析法的研究：Ⅰ.消除基体干扰

实现石墨炉原子吸收光谱绝对分析必须消除基体干扰，本研究采用有机基体改进剂，管壁原子化、热解涂层石墨管，峰面积积分吸收信号，Ｄ２灯或Ｚｅｅｍａｎ效应扣除背景，有效地控制和消除了海水基体对Ａｓ，Ｃｄ，Ｃｏ，Ｃｒ，Ｃｕ，Ｍｎ，Ｎｉ，Ｐｂ和Ｖ等元素的干扰，实现了无干扰测定。     

钯镁基体改进剂对铅,铋,锗在石墨炉中原子化影响的研究

通过原子吸收和X-射线衍射分析证明,加入钯镁基体改进剂在预热处理后对Pb、Bi和Ge三个元素分别生成金属间化合物PbPd_3、BiPd_3、Ge_9Pd_(23)和其他化合物,从而提高了最高允许灰化温度,改变了原子化机理。在原子化阶段这些金属间化合物直接分解为金属原子,结果提高测定灵敏度。     

Matrix separation of palladium and iridium by the cellulose anion exchanger Cellex T and the subsequent determination of palladium at theμg/g-level

The preconcentration and separation of palladium and iridium from base metals is studied with cellulose (Cellex T) and styrene-divinylbenzene (Varion AT 400) anion exchangers. In spite of lower capacity of Cellex T to chloride complexes of Pd and Ir, it allowed to get a higher preconcentration factor. Yields of 92–99% are achieved for Pd and 96–97% for Ir from the solutions containing great excess of base and heavy metals. Graphite furnace atomic absorption spectrometry is used for the final measurements. The procedure has been applied to the determination of palladium in natural samples.