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     

微机在“醋酸,磷酸电位滴定”实验中的应用

微机在“醋酸、磷酸电位滴定”实验中的应用王苏文（南京师范大学化学系南京２１００２４）袁立新（南京师范大学物理系南京２１００２４）关键词计算机，Ａ／Ｄ模数转换器，电位滴定许多化学实验使用传统的方法对实验数据进行人工读数、记录、处理等。在这一过程中就必定...     

X-射线荧光分析散射幂函数法原理及其应用I·RhKα相干散射平方法

本文发现6~40号元素对能量为20keV的X_射线的质量吸收系数和质量相干散射系数之间呈二次幂函数关系,并据此提出了X_射线荧光定量分析校正基体效应的新方法——RhKa相干散射平方法.用国家标准物质GBW对该原理进行了验证.本法用于硅酸盐地质样品中微量元素的测定取得令人满意的结果.     

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.     

High-vacuum pyrolysis of 1,1,1-trifluoro-2-bromo-2-chloroethane. IR spectrum of 1,1,1-trifluoro-2-chloroethyl radical in an argon matrix

The products of high-vacuum pyrolysis of 1,1,1-trifluoro-2-bromo-2-chloroethane were studied by matrix IR spectroscopy. The decomposition of 1,1,1-trifluoro-2-bromo-2-chloroethane was shown to occur predominantlyvia two directions: to form the 1,1,1-trifluoro-2-chloroethyl radical and trifluoromethylcarbene isomerizing to trifluoroethylene. The CF₃CHCl radical has been detected in the matrix for the first time. The bands observed in the IR spectrum were calculated by the quantum-chemical B3LYP/6-311 G(d,p) method and assigned to normal vibrations of the radical. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2085–2088, October, 1998.     

高分辨等离子体质谱法直接测定高纯镓中的痕量元素

建立高分辨电感耦合等离子体质谱法(HR-ICP-MS)测定高纯镓样品中Be、Mg、A l、S i、Ti、V、Cr、Mn、Fe、Co、N i、Cu、Zn、Ge、As、Mo、Ag、Cd、In、Sb、Ba、Pb、B i等痕量元素的方法。样品用HNO3 HC l经微波消解后,试液直接进样用HR-ICP-MS法同时测定上述元素,在高分辨质谱测量模式下避免了大量的质谱干扰,详细地研究了HC l和高纯镓所产生的基体效应,以Sc、Rh、Tl作为内标元素校正了基体效应,讨论和确定了实验的最佳测定条件。结果表明,23种痕量元素的检出限在0.001~0.21μg/L之间;回收率在89.8%~111.6%之间,相对标准偏差(RSD)小于3.3%。     

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.     

生物体系中电子转移机理的研究Ⅱ: 分子间电子转移及 电子供、受体间不同基 团的影响

利用自编程序MOPAC-ET中AM1方法,及KT(Koopman'sTheorem)法,研究了二苯负离子体系的分子间电子转移现象,计算了其电子供、受体在不同距离下的V~A~B及它们之间的相关性,另外,还对两苯环间不同介入基团对电子转移的影响做了初步研究,发现不同的介入基团存在着较大的差异。