Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses

We analysed Hordeum spontaneum accessions from 21 different locations to understand the genetic diversity of HsDhn3 alleles and effects of single base mutations on the intrinsically disordered structure of the resulting polypeptide (HsDHN3). HsDHN3 was found to be YSK2-type with a low-frequency 6-aa deletion in the beginning of Exon 1. There is relatively high diversity in the intron region of HsDhn3 compared to the two exon regions. We have found subtle differences in K segments led to changes in amino acids chemical properties. Predictions for protein interaction profiles suggest the presence of a protein-binding site in HsDHN3 that coincides with the K1 segment. Comparison of DHN3 to closely related cereals showed that all of them contain a nuclear localization signal sequence flanking to the K1 segment and a novel conserved region located between the S and K1 segments [E(D/T)DGMGGR]. We found that H. vulgare, H. spontaneum, and Triticum urartu DHN3s have a greater number of phosphorylation sites for protein kinase C than other cereal species, which may be related to stress adaptation. Our results show that the nature and extent of mutations in the conserved segments of K1 and K2 are likely to be key factors in protection of cells.

The structure of crystallisable copolymers of L-lactide, epsilon-caprolactone and glycolide

We apply a new X-ray scattering approach to the study of melt-spun filaments of tri-block and random terpolymers prepared from lactide, caprolactone and glycolide. Both terpolymers contain random sequences, in both cases the overall fraction of lactide units is similar to 0.7 and C-13 and H-1 NMR shows the lactide sequence length to be similar to 9-10. A novel representation of the X-ray fibre pattern as series of spherical harmonic functions considerably facilitates the comparison of the scattering from the minority crystalline phase with hot drawn fibres prepared from the poly(L-lactide) homopolymer. Although the fibres exhibit rather disordered structures we show that the crystal structure is equivalent to that displayed by poly(L-lactide) for both the block and random terpolymers. There are variations in the development of a two-phase structure which reflect the differences in the chain architectures. There is evidence that the random terpolymer includes non-lactide units in to the crystal interfaces to achieve a well defined two-phase structure. (c) 2005 Published by Elsevier Ltd.

Synthesis and crystal structure of the thiophene-3-acetonitrile complex fac-[Mo(CO)(3){NCCH2(C4H3S-3)}(3)]

Reaction of fac-[ Mo( CO)(3)( NCMe)(3)] with three equivalents of NCCH2(C4H3S- 3) in acetonitrile gives the tris(thiophene- 3- acetonitrile) complex, fac-[Mo(CO)(3){NCCH2(C4H3S-3)}(3)] (1) in 7% yield. Complex 1 crystallizes out in the orthorhombic space group Pnma with a = 12.714( 17), b = 16.41( 2), c = 11.304(16) Angstrom, Z = 4. The structure has crystallographic m symmetry and the metal is in an almost perfect octahedral environment, with a facial arrangement of carbonyl and thiophene- 3- acetonitrile groups. The thiophene rings are disordered.

Crystal and molecular structure of the thioether-analogue of PEEK from X-ray powder data and diffraction-modelling

Analysis of X-ray powder data for the melt-crystallisable aromatic poly(thioether thioether ketone) [-S-Ar-S-Ar-CO-Ar](n), ('PTTK', Ar= 1,4-phenylene), reveals that it adopts a crystal structure very different from that established for its ether-analogue PEEK. Molecular modelling and diffraction-simulation studies of PTTK show that the structure of this polymer is analogous to that of melt-crystallised poly(thioetherketone) [-SAr-CO-Ar](n) in which the carbonyl linkages in symmetry-related chains are aligned anti-parallel to one another. and that these bridging units are crystallographically interchangeable. The final model for the crystal structure of PTTK is thus disordered, in the monoclinic space group 121a (two chains per unit cell), with cell dimensions a = 7.83, b = 6.06, c = 10.35 angstrom, beta = 93.47 degrees. (c) 2005 Elsevier Ltd. All rights reserved.

The exclusive use of integer-order spots for LEED-IV structure analysis of adsorption systems: p(2×2)-O on Ni{111}

Two different ways of performing low-energy electron diffraction (LEED) structure determinations for the p(2 x 2) structure of oxygen on Ni {111} are compared: a conventional LEED-IV structure analysis using integer and fractional-order IV-curves collected at normal incidence and an analysis using only integer-order IV-curves collected at three different angles of incidence. A clear discrimination between different adsorption sites can be achieved by the latter approach as well as the first and the best fit structures of both analyses are within each other's error bars (all less than 0.1 angstrom). The conventional analysis is more sensitive to the adsorbate coordinates and lateral parameters of the substrate atoms whereas the integer-order-based analysis is more sensitive to the vertical coordinates of substrate atoms. Adsorbate-related contributions to the intensities of integer-order diffraction spots are independent of the state of long-range order in the adsorbate layer. These results show, therefore, that for lattice-gas disordered adsorbate layers, for which only integer-order spots are observed, similar accuracy and reliability can be achieved as for ordered adsorbate layers, provided the data set is large enough.

Unsaturated σ-hydrocarbyl transition-metal complexes. Part 3. Crystal and molecular structure of trans-chlorobis(diethylphenylphosphine)(vinyl)platinum(II)

The molecular structure of trans-[PtCl(CHCH2)(PEt2Ph)2] has been determined by X-ray diffraction methods. The crystals are orthorhombic, space group Pbcn, with a= 10.686(2), b= 13.832(4), c= 16.129(4)Å, and Z= 4. The structure has been solved by the heavy-atom method and refined by full-matrix least squares to R 0.044 for 1 420 diffractometric intensity data. The crystals contain discrete molecules in which the platinum co-ordination is square planar. The Pt–Cl bond vector coincides with a crystallographic diad axis about which the atoms of the vinyl group are disordered. Selected bond lengths (Å) are Pt–Cl 2.398(4), Pt–P 2.295(3), and Pt–C 2.03(2). The Pt–CC angle is 127(2)°. From a survey of the available structural data it is concluded that there is little, if any, back donation from platinum to carbon in platinum–alkenyl linkages.

Structure variation and evolution in microphase-separated grafted diblock copolymer films

The phase behavior of grafted d-polystyrene-block-poly(methyl methacrylate) diblock copolymer films is examined, with particular focus on the effect of solvent and annealing time. It was observed that the films undergo a two-step transformation from an initially disordered state, through an ordered metastable state, to the final equilibrium configuration. It was also found that altering the solvent used to wash the films, or complete removal of the solvent prior to thermal annealing using supercritical CO2, could influence the structure of the films in the metastable state, though the final equilibrium state was unaffected. To aid in the understanding to these experimental results, a series of self-consistent field theory calculations were done on a model diblock copolymer brush containing solvent. Of the different models examined, those which contained a solvent selective for the grafted polymer block most accurately matched the observed experimental behavior. We hypothesize that the structure of the films in the metastable state results from solvent enrichment of the film near the film/substrate interface in the case of films washed with solvent or faster relaxation of the nongrafted block for supercritical CO2 treated (solvent free) films. The persistence of the metastable structures was attributed to the slow reorganization of the polymer chains in the absence of solvent.

Extracting quantitative structural parameters for disordered polymers from neutron scattering data

The organization of non-crystalline polymeric materials at a local level, namely on a spatial scale between a few and 100 a, is still unclear in many respects. The determination of the local structure in terms of the configuration and conformation of the polymer chain and of the packing characteristics of the chain in the bulk material represents a challenging problem. Data from wide-angle diffraction experiments are very difficult to interpret due to the very large amount of information that they carry, that is the large number of correlations present in the diffraction patterns.We describe new approaches that permit a detailed analysis of the complex neutron diffraction patterns characterizing polymer melts and glasses. The coupling of different computer modelling strategies with neutron scattering data over a wide Q range allows the extraction of detailed quantitative information on the structural arrangements of the materials of interest. Proceeding from modelling routes as diverse as force field calculations, single-chain modelling and reverse Monte Carlo, we show the successes and pitfalls of each approach in describing model systems, which illustrate the need to attack the data analysis problem simultaneously from several fronts.

Extracting and validating force fields for disordered polymeric materials from neutron scattering data

We present a new approach that allows the determination and refinement of force field parameters for the description of disordered macromolecular systems from experimental neutron diffraction data obtained over a large Q range. The procedure is based on tight coupling between experimentally derived structure factors and computer modelling. By separating the potential into terms representing respectively bond stretching, angle bending and torsional rotation and by treating each of them separately, the various potential parameters are extracted directly from experiment. The procedure is illustrated on molten polytetrafluoroethylene.

Extracting force fields for disordered polymeric materials from neutron scattering data

We present a new approach that allows the determination of force-field parameters for the description of disordered macromolecular systems from experimental neutron diffraction data obtained over a large Q range. The procedure is based on a tight coupling between experimentally derived structure factors and computer modelling. We separate the molecular potential into non-interacting terms representing respectively bond stretching, angle bending and torsional rotation. The parameters for each of the potentials are extracted directly from experimental data through comparison of the experimental structure factor and those derived from atomistic level molecular models. The viability of these force fields is assessed by comparison of predicted large-scale features such as the characteristic ratio. The procedure is illustrated on molten poly(ethylene) and poly(tetrafluoroethylene).

Local and average structure in zinc cyanide: towards an understanding of the atomistic origin of negative thermal expansion

Neutron diffraction at 11.4 and 295 K and solid-state 67Zn NMR are used to determine both the local and average structures in the disordered, negative thermal expansion (NTE) material, Zn(CN)2. Solid-state NMR not only confirms that there is head-to-tail disorder of the C≡N groups present in the solid, but yields information about the relative abundances of the different Zn(CN)4-n(NC)n tetrahedral species, which do not follow a simple binomial distribution. The Zn(CN)4 and Zn(NC)4 species occur with much lower probabilities than are predicted by binomial theory, supporting the conclusion that they are of higher energy than the other local arrangements. The lowest energy arrangement is Zn(CN)2(NC)2. The use of total neutron diffraction at 11.4 K, with analysis of both the Bragg diffraction and the derived total correlation function, yields the first experimental determination of the individual Zn−N and Zn−C bond lengths as 1.969(2) and 2.030(2) Å, respectively. The very small difference in bond lengths, of ~0.06 Å, means that it is impossible to obtain these bond lengths using Bragg diffraction in isolation. Total neutron diffraction also provides information on both the average and local atomic displacements responsible for NTE in Zn(CN)2. The principal motions giving rise to NTE are shown to be those in which the carbon and nitrogen atoms within individual Zn−C≡N−Zn linkages are displaced to the same side of the Zn···Zn axis. Displacements of the carbon and nitrogen atoms to opposite sides of the Zn···Zn axis, suggested previously in X-ray studies as being responsible for NTE behavior, in fact make negligible contribution at temperatures up to 295 K.