Structural analysis of PEKEKK(T/I) using WAXD, imaging plates and SAXS

Structures and crystal form transition of the novel aryl ether ketone polymer containing meta-phenylene linkage: PEKEKK(T/I) were investigated by wide angle X-ray diffraction (WAXD), imaging plates (IPs) and small angle X-ray scattering (SAXS). The energy of activation of the decomposition reaction and degree of crystallinity of PEKEKK(T/I) were determined by WAXD and thermo-gravimetric analysis (TGA), respectively. Results obtained from WAXD and IPs show that crystal forms I and II coexist in the PEKEKK(T/I) samples isothermally cold crystallized in the temperature range from 180degreesC to 240degreesC and only form I occurs in PEKEKK(T/I) samples isothermally cold crystallized at 270degreesC. The radius of gyration (Rg), thickness of microregions with electron-density fluctuations (E) and distribution of particle sizes were investigated by SAXS.

Structural analysis of saponins from medicinal herbs using electrospray ionization tandem mass spectrometry

The underivatized saponins from Tribulus terrestris and Panax ginseng have been investigated by electrospray ionization multi-stage tandem mass spectrometry (ESI-MSn). In ESI-MS spectra, a predominant [M + Na](+) ion in positive mode and [M - H](-) ion in negative mode were observed for molecular mass information. Multi-stage tandem mass spectrometry of the molecular ions was used for detailed structural analysis. Fragment ions from glycoside cleavage can provide information on the mass of aglycone and the primary sequence and branching of oligosaccharide chains in terms of classes of monosaccharides. Fragment ions from cross-ring cleavages of sugar residues can give some information about the linkages between sugar residues. It was found that different alkali metal-cationized adducts with saponins have different degrees of fragmentation, which may originate from the different affinity of a saponin with each alkali metal in the gas phase. ESI-MSn has been proven to be an effective tool for rapid determination of native saponins in extract mixtures, thus avoiding tedious derivatization and separation steps.

Crystal growth and structural analysis of PrMnO3 and TbMnO3

Single crystals of PrMnO3 and TbMnO3 were grown by floating zone method and the crystal structure was determined by single crystal X-ray diffractometry. The structure of these compounds belongs to the orthorhombic system (space group is Pnma, No. 62) with the lattice parameters alpha approximate to root (.) - a(p), b approximate to 2 (.) a(p) , c approximate to root 2.a(p) and Z = 4, where a(p) is ideal cubic perovskite cell parameter.

Metal ion adducts in the structural analysis of ginsenosides by electrospray ionization with multi-stage mass spectrometry

The effect of metal (Li+, Na+, K+, Ag+) cationization on collision-induced dissociation of ginsenosides was investigated by electrospray ionization mass spectrometry combined with multi-stage mass spectrometry (ESI-MSn). The fragments of sodiated and lithiated molecules give valuable structural information regarding the nature of the aglycone and the sequence and linkage information of sugar moieties. However, the number and relative abundances of fragment ions from lithiated ginsenosides are significantly greater than for the sodiated species, The K+ adducts undergo glycosidic cleavages and very limited cross-ring reactions. The silver ion adducts fragment mainly through glycosidic cleavages. Copyright (C) 2001 John Wiley & Sons, Ltd.

Application of acetone and dimethyl ether chemical ionization reagent gases to structural analysis

Acetone and dimethyl ether( DME) have been shown to be reagent gases of exceptional utitlity and versatility for the characterization of a variety of class of organic compounds. The fragmentation mechanisms of the adduct product ions, formed by ion/molceule reaction of the substrate with the ionized gases, have been studied and substantiated by experiments with acetone-d(6) and DME-d(6).

Structural analysis of nonlinearities of Ca4ReO(BO3)(3) (Re = La, Nd, Sm, Gd, Er, Y)

From the chemical bond viewpoint, second-order nonlinear optical (NLO) tensor coefficients of the family of new oxoborates Ca4ReO(BO3)(3) (CReOB, Re = La, Nd, Sm, Gd, Er, and Y) have been theoretically predicted. The d(11) tensor coefficient of CReOB is predicted to be -11 d(36)(KDP), which is the largest d(ij) tensor that has been found in borate crystals. From the structural characteristic of CReOB, we find the isolated BO33- clusters play a dominant role in contributions to the total nonlinearity, and the largest d(11) tensor of CReOB-type crystals is also ascribed to these BO33- clusters. We also find the NLO property of this family does not change dramatically for different rare-earth elements. The details of the calculation of CGdOB only are presented.

Structural analysis of peptides of PSII light-harvesting complexes in siphonous green algae, Codium fragile

peptide composition and arrangement of 4 major light-harvesting complexes LHCP1-3 and LHCP3, isolated from siphonous green algae (Codium fragile (Sur.) Hariot.) were investigated. LHCP1 showed five main peptides, 34.4, 31.5, 29.5, 28.2 and 26.5 kD in SDS-PAGE, the 34.4 and 31.5 kD peptides were never found in higher plants. LHCP3 contained the other four kinds of LHCP1 peptides except 34.4 kD, while LHCP3, consisted of only 28.2 and 26.5 kD peptides. We found that 34.4, 28.2 and 26.5 kD peptides were easy to decompose from LHCP1 when subjected to SDS-PACE without pretreatment. They might be located at the exterior of LHCP1, while the 31.5 and 29.5 kD peptides were at the central part. The 28.2 and 26.5 kD peptides often occurred in CPa, the center complex of PS II. They are possibly the LHC II peptides tightly associated with CC II. According to the results described above, a peptide map of LHCP1 was sketched.

Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches. (C) 2007 Elsevier Ltd. All rights reserved.

Structural Analysis of Network Traffic Flows

Network traffic arises from the superposition of Origin-Destination (OD) flows. Hence, a thorough understanding of OD flows is essential for modeling network traffic, and for addressing a wide variety of problems including traffic engineering, traffic matrix estimation, capacity planning, forecasting and anomaly detection. However, to date, OD flows have not been closely studied, and there is very little known about their properties. We present the first analysis of complete sets of OD flow timeseries, taken from two different backbone networks (Abilene and Sprint-Europe). Using Principal Component Analysis (PCA), we find that the set of OD flows has small intrinsic dimension. In fact, even in a network with over a hundred OD flows, these flows can be accurately modeled in time using a small number (10 or less) of independent components or dimensions. We also show how to use PCA to systematically decompose the structure of OD flow timeseries into three main constituents: common periodic trends, short-lived bursts, and noise. We provide insight into how the various constituents contribute to the overall structure of OD flows and explore the extent to which this decomposition varies over time.

A structural analysis of G-quadruplex/ligand interactions

This focused review article discusses in detail, all available high-resolution small molecule ligand/G-quadruplex structural data derived from crystallographic and NMR based techniques, in an attempt to understand key factors in ligand binding and to highlight the biological importance of these complexes. In contrast to duplex DNA, G-quadruplexes are four-stranded nucleic acid structures folded from guanine rich repeat sequences stabilized by the stacking of guanine G-quartets and extensive Watson-Crick/Hoogsteen hydrogen bonding. Thermally stable, these topologies can play a role in telomere regulation and gene expression. The core structures of G-quadruplexes form stable scaffolds while the loops have been shown, by the addition of small molecule ligands, to be sufficiently adaptable to generate new and extended binding platforms for ligands to associate, either by extending G-quartet surfaces or by forming additional planar dinucleotide pairings. Many of these structurally characterised loop rearrangements were totally unexpected opening up new opportunities for the design of selective ligands. However these rearrangements do significantly complicate attempts to rationally design ligands against well defined but unbound topologies, as seen for the series of napthalene diimides complexes. Drawing together previous findings and with the introduction of two new crystallographic quadruplex/ligand structures we aim to expand the understanding of possible structural adaptations available to quadruplexes in the presence of ligands, thereby aiding in the design of new selective entities. (C) 2011 Elsevier Masson SAS. All rights reserved.