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At least 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Structural Basis for Promoter ;#8722;10 Element Recognition by the Bacterial RNA Polymerase [sigma] Subunit

The key step in bacterial promoter opening is recognition of the -10 promoter element (T-{sub 12}A-{sub 11}T-{sub 10}A-{sub 9}A-{sub 8}T{sub -7} consensus sequence) by the RNA polymerase {alpha} subunit. We determined crystal structures of {alpha} domain 2 bound to single-stranded DNA bearing -10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A{sub -11} and T{sub -7}, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by {alpha}. These results provide a detailed structural basis for the critical roles of A{sub -11} and T{sub -7} in promoter melting and reveal important insights into the initiation of transcription bubble formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Impact load-induced micro-structural damage and micro-structure associated mechanical response of concrete made with different surface roughness and porosity aggregates

The relationship between the nature of micro damage under impact loading and changes in mechanical behavior associated with different microstructures is studied for concretes made with two different coarse aggregates having significant differences mainly in roughness and porosity - sintered fly ash and uncrushed gravel. A range of techniques including X-ray diffraction, digital image analysis, mercury porosimetry, X-ray computed tomography, laser surface profilometry and scanning electron microscopy were used to characterize the aggregates and micro-structures. The concrete prepared with lightweight aggregates was stronger in compression than the gravel aggregate concrete due to enhanced hydration as a result of internal curing. In the lightweight concrete, it was deduced that an inhomogeneous micro-structure led to strain incompatibilities and consequent localized stress concentrations in the mix, leading to accelerated failure. The pore structure, compressibility, and surface texture of the aggregates are of paramount importance for the micro-cracking growth.

36 MATERIALS SCIENCE↗
DOE OSTI2015

A numerical approach for simulating fluid structure interaction of flexible thin shells undergoing arbitrarily large deformations in complex domains

We present a new numerical methodology for simulating fluid–structure interaction (FSI) problems involving thin flexible bodies in an incompressible fluid. The FSI algorithm uses the Dirichlet–Neumann partitioning technique. The curvilinear immersed boundary method (CURVIB) is coupled with a rotation-free finite element (FE) model for thin shells enabling the efficient simulation of FSI problems with arbitrarily large deformation. Turbulent flow problems are handled using large-eddy simulation with the dynamic Smagorinsky model in conjunction with a wall model to reconstruct boundary conditions near immersed boundaries. The CURVIB and FE solvers are coupled together on the flexible solid–fluid interfaces where the structural nodal positions, displacements, velocities and loads are calculated and exchanged between the two solvers. Loose and strong coupling FSI schemes are employed enhanced by the Aitken acceleration technique to ensure robust coupling and fast convergence especially for low mass ratio problems. The coupled CURVIB-FE-FSI method is validated by applying it to simulate two FSI problems involving thin flexible structures: 1) vortex-induced vibrations of a cantilever mounted in the wake of a square cylinder at different mass ratios and at low Reynolds number; and 2) the more challenging high Reynolds number problem involving the oscillation of an inverted elastic flag. For both cases the computed results are in excellent agreement with previous numerical simulations and/or experiential measurements. Grid convergence tests/studies are carried out for both the cantilever and inverted flag problems, which show that the CURVIB-FE-FSI method provides their convergence. Finally, the capability of the new methodology in simulations of complex cardiovascular flows is demonstrated by applying it to simulate the FSI of a tri-leaflet, prosthetic heart valve in an anatomic aorta and under physiologic pulsatile conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Synthesis Structure and Characterization of the n=4 Aurivillius Phase Bi5Ti3CrO15

The n=4 Aurivillius phase, Bi{sub 5}Ti{sub 3}CrO{sub 15}, was synthesized by solid state reaction. Rietveld analysis of high resolution neutron diffraction data demonstrated this material to adopt the polar space group A2{sub 1}am at room temperature, transforming to the aristotype I4/mmm structure above 650 C. This phase transition is coincident with an anomaly in DSC signal and relative permittivity, which are characteristic of a ferroelectric-paraelectric phase transition. Bi{sub 5}Ti{sub 3}CrO{sub 15} exhibits paramagnetic behavior at low temperature, with short range antiferromagnetic interactions, but no evidence for long range magnetic ordering. This is considered a consequence of significant disorder of Ti and Cr over the available octahedral sites, as demonstrated by analysis of neutron diffraction data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Crystal structure analysis of tungsten bronzes {beta}-SrTa{sub 2}O{sub 6} and {beta} Prime -SrTa{sub 2}O{sub 6} by synchrotron X-ray and neutron powder diffraction

Strontium ditantalum oxide SrTa{sub 2}O{sub 6} exists in {alpha}-, {beta}-, and {beta} Prime -polymorphs. Herein the crystal structures of the latter two were studied using synchrotron X-ray and constant-wavelength neutron powder diffraction. While {beta} Prime -SrTa{sub 2}O{sub 6} [space group P4/mbm, a=12.47099(1) A, c=3.898210(5) A, V=606.271(2) Angstrom-Sign {sup 3}, Z=5] belongs to the regular tetragonal tungsten bronze (TTB) family, it contains locally disordered strontium atoms within the pentagonal channel. {beta}-SrTa{sub 2}O{sub 6} [space group Pnam, a=12.36603(2) Angstrom-Sign , b=12.43467(2) A, c=7.72403(1) A, V=1187.705(4) Angstrom-Sign {sup 3}, Z=10] can be described as an orthorhombic modification of the TTB, where the octahedral tilting distortion effectively alleviates the bonding strains around TaO{sub 6} and SrO{sub 13} polyhedra. For comparison, rynersonite type {alpha}-SrTa{sub 2}O{sub 6} [space group Pnma, a=11.00610(6) Angstrom-Sign , b=7.63397(3) Angstrom-Sign , c=5.62634(3) Angstrom-Sign , V=472.727(5) Angstrom-Sign {sup 3}, and Z=4] is built from edge-shared dimer units of TaO{sub 6} octahedra. As measured by diffuse-reflection absorption spectroscopy, {alpha}-, {beta}-, and {beta} Prime -SrTa{sub 2}O{sub 6} have indirect band gap energies of 4.4, 4.0, and 3.8 eV, respectively. - Graphical Abstract: Difference Fourier map for {beta} Prime -SrTa{sub 2}O{sub 6} at z=0. Highlights: Black-Right-Pointing-Pointer Structure refinements of {beta}-SrTa{sub 2}O{sub 6} and {beta} Prime -SrTa{sub 2}O{sub 6}. Black-Right-Pointing-Pointer Strontium disorder in tetragonal tungsten bronze {beta} Prime -SrTa{sub 2}O{sub 6}. Black-Right-Pointing-Pointer Orthorhombic distortion and cell doubling in {beta}-SrTa{sub 2}O{sub 6}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Structure and physical properties of single crystal PrCr{sub 2}Al{sub 20} and CeM{sub 2}Al{sub 20} (M=V, Cr): A comparison of compounds adopting the CeCr{sub 2}Al{sub 20} structure type

Crystal growth and full structure determination of compounds adopting the CeCr{sub 2}Al{sub 20} structure type, LnTi{sub 2}Al{sub 20} (Ln=La-Pr, Sm, and Yb), LnV{sub 2}Al{sub 20} (Ln=La-Pr, and Sm), and LnCr{sub 2}Al{sub 20} (Ln=La-Pr, Sm, and Yb), are reported. Resistivity, magnetic susceptibility, and heat capacity of flux grown single crystals of the nonmagnetic CeM{sub 2}Al{sub 20} (Ln=Ce, Yb; M=Ti, V) compounds are compared to PrCr{sub 2}Al{sub 20}. Of particular interest is PrCr{sub 2}Al{sub 20} which does not show any phase transition down to the lowest temperature of the measurement (400 mK in resistivity measurement and 1.8 K for magnetic susceptibility measurements) and exhibits Kondo behavior at low temperatures. - Graphical abstract: Crystal structure of SmV{sub 2}Al{sub 20} showing the interpenetrating diamond-like samarium network and pyrochlore-like vanadium network. Highlights: Black-Right-Pointing-Pointer Single crystals of LnM{sub 2}Al{sub 20} were grown from a molten aluminum flux. Black-Right-Pointing-Pointer Magnetic, electrical, and specific heat of single crystal LnM{sub 2}Al{sub 20} are presented. Black-Right-Pointing-Pointer PrCr{sub 2}Al{sub 20} exhibits evidence of Kondo effect.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Synthesis, structures of four coordination compounds constructed from o-methacrylamidobenzoic acid and their relationship between structure and solid state luminescence

Four new coordination compounds, namely, Zn(o-MAABA){sub 2}(Phen) (1), [Cd(o-MAABA){sub 2}·2H{sub 2}O]{sub 2} (2), ([Pb{sub 2}Cl{sub 2}(o-MAABA){sub 2}(Phen){sub 4}])·2H{sub 2}O (3·2H{sub 2}O), [Pb(NO{sub 3})(o-MAABA)(Phen)]{sub n} (4), where o-MAABA=o-methacrylamidobenzoic acid and phen=1, 10-phenanthroline, have been synthesized. All compounds were fully confirmed by FT-IR, elemental analysis and TGA analysis. Their structures were determined by single crystal X-ray diffraction, in which compound 1 shows a mononuclear structure, compounds 2 and 3 have binuclear structures and compound 4 shows an infinite chain. In 2 and 4, the adjacent chains are extended into a 3D supramolecular architecture via π–π interactions. Solid-state room temperature luminescence spectra revealed that emission bands of compound 1 were located at 524 nm (λ{sub ex}=352 nm) and compound 4 at 479 and 584 nm (λ{sub ex}=390 nm) assigned to the excimer formation. The emission at 454 nm (λ{sub ex}=340 nm) of compound 2 was mainly ascribed to the Ligand–Metal Charge Transfer (LMCT). - Graphical abstract: Four coordination compounds constructed by o-methacrylamidobenzoic, phenanthroline and metal ions are reported. The photoluminescent properties is studied, which is affected by the molecular stacking and LMCT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

New hybrid lead iodides: From one-dimensional chain to two-dimensional layered perovskite structure

Two new hybrid lead halides (H{sub 2}BDA)[PbI{sub 4}] (1) (H{sub 2}BDA=1,4-butanediammonium dication) and (HNPEIM)[PbI{sub 3}] (2) (HNPEIM=N-​phenyl-ethanimidamidine cation) have been synthesized and structurally characterized. X-ray diffraction analyses reveal that compound 1 features a two-dimensional corner-sharing perovskite layer whereas compound 2 contains one-dimensional edge-sharing double chains. The N-​phenyl-ethanimidamidine cation within compound 2 was generated in-situ under solvothermal conditions. The optical absorption spectra collected at room temperature suggest that both compounds are semiconductors having direct band gaps, with estimated values of 2.64 and 2.73 eV for 1 and 2, respectively. Results from the density functional theory (DFT) calculations are consistent with the experimental data. Density of states (DOS) analysis reveals that in both compounds 1 and 2, the energy states in the valence band maximum region are iodine 5p atomic orbitals with a small contribution from lead 6s, while in the region of conduction band minimum, the major contributions are from the inorganic (Pb 6p atomic orbitals) and organic components (C and N 2p atomic orbitals) in compound 1 and 2, respectively. - Graphical abstract: Two new hybrid lead halides built on one-dimensional edge-sharing double chains and two-dimensional corner-sharing perovskite layers are synthesized and their structural and electronic properties are analyzed. - Highlights: • Two new hybrid lead iodides are designed, synthesized, and characterized. • They are closely related to, but different from, perovskite structures. • The electronic properties of both compounds are analyzed by DFT calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Synthesis, crystal structure, optical, and electronic study of the new ternary thorium selenide Ba{sub 3}ThSe{sub 3}(Se{sub 2}){sub 2}

The compound Ba{sub 3}ThSe{sub 3}(Se{sub 2}){sub 2} has been synthesized by solid-state methods at 1173 K. Its crystal structure features one-dimensional chains of {sup 1}{sub ∞}[Th(Se){sub 3}(Se{sub 2}){sub 2}{sup 6−}] separated by Ba{sup 2+} cations. Each Th atom in these chains is coordinated to two Se–Se single-bonded pairs and four Se atoms to give rise to a pseudooctahedral geometry around Th. The Th–Se distances are consistent with Th{sup 4+} and hence charge balance of Ba{sub 3}ThSe{sub 3}(Se{sub 2}){sub 2} is achieved as 3×Ba{sup 2+}, 1×Th{sup 4+}, 3×Se{sup 2−}, and 2×Se{sub 2}{sup 2−}. From optical measurements the band gap of Ba{sub 3}ThSe{sub 3}(Se{sub 2}){sub 2} is 1.96(2) eV. DFT calculations indicate that the compound is a semiconductor. - Graphical abstract: Local coordination environment of Th atoms in the Ba{sub 3}ThSe{sub 3}(Se{sub 2}){sub 2} structure. - Highlights: • Ba{sub 3}ThSe{sub 3}(Se{sub 2}){sub 2} has been synthesized by solid-state methods at 1173 K. • The structure features chains of {sup 1}{sub ∞}[Th(Se){sub 3}(Se{sub 2}){sub 2}{sup 6−}] separated by Ba{sup 2+} cations. • Ba{sub 3}ThSe{sub 3}(Se{sub 2}){sub 2} is a semiconductor with a band gap of 1.96(2) eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Syntheses, crystal Structures and electronic Structures of new metal chalcoiodides Bi{sub 2}CuSe{sub 3}I and Bi{sub 6}Cu{sub 3}S{sub 10}I

Two new metal chalcoiodides were synthesized by solid-state reactions at 400 °C. Crystal Data: Bi{sub 2}CuSe{sub 3}I, 1, monoclinic, C2/m, a=14.243(2) Å, b=4.1937(7) Å, c=14.647(2) Å, β=116.095(2)°, V=785.7(2) Å{sup 3}, and Z=4; Bi{sub 6}Cu{sub 3}S{sub 10}I, 2, orthorhombic, Pnma, a=17.476(2) Å, b=4.0078(4) Å, c=27.391(2) Å, V=1918.5(3) Å{sup 3}, and Z=4. Compound 1 adopts a three-dimensional structure formed by two alternative layers, which consist of BiSe{sub 5} square pyramids, BiSe{sub 4}I{sub 2} octahedra, CuSe{sub 4} tetrahedra, and CuSe{sub 2}I{sub 2} tetrahedra. Compound 2 possesses a new open framework built up of BiS{sub 5} square pyramides, BiS{sub 6} octahedra, BiS{sub 8} polyhedra, and CuS{sub 4} tetrahedra where I{sup −} anions are uniquely trapped within the tunnels. Both electronic structures reveal that bismuth and chalcogenide orbitals dominate the bandgaps. The Cu d and I p states contribute to the top of valence bands, in which the distribution of I orbitals may correspond to the relative bonding interactions in 1 and 2. The optical bandgaps determined by the diffuse reflectance spectra are 0.68 eV and 0.72 eV for 1 and 2, respectively. 1 is a p-type semiconductor with high Seebeck coefficients of 460–575 μV/K in the temperature range of 300–425 K. The electrical conductivity is 0.02 S/cm at 425 K for the undoped sample. The thermal conductivity is 0.22 W/mK at 425 K. - Graphical abstract: The hybridization of chalcogenides and iodides produces two new solids Bi2CuSe3I and Bi6Cu3S10I. The I{sup −} anions participate in distinct bonding interactions within the two structures and that is consistent with the analyses of density of states. 1 is a p-type semiconductor with an optical bandgap of 0.68 eV, which possesses high Seebeck coefficient and low lattice thermal conductivity in 300–425 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Copper coordination polymers constructed from thiazole-5-carboxylic acid: Synthesis, crystal structures, and structural transformation

We have successfully prepared crystals of thiazole-5-carboxylic acid (5-Htza) (L) and three new thiazole-5-carboxylate-based Cu{sup 2+} coordination polymers with different dimensionality, namely, 1D [Cu{sub 2}(5-tza){sub 2}(1,10-phenanthroline){sub 2}(NO{sub 3}){sub 2}] (1), 2D [Cu(5-tza){sub 2}(MeOH){sub 2}] (2), and 3D [Cu(5-tza){sub 2}]·H{sub 2}O (3). These have been characterized by single crystal X-ray diffraction and thermogravimetry. Interestingly, the 2D network structure of 2 can directly transform into the 3D framework of 3 upon removal of methanol molecules at room temperature. 2 can also undergo structural transformation to produce the same 2D network present in the known [Cu(5-tza){sub 2}]·1.5H{sub 2}O upon heat treatment for 2 h. This 2D network can adsorb water and convert to 3 upon exposure to air. - Highlights: • Rare examples of coordination polymers of thiazole-5-carboxylic acid were prepared. • Non-covalent interactions play a key role on the assembly of the complexes in solid state. • Structural transformation of a 2D framework to a 3D upon removal of methanol is observed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Synthesis, crystal structure and magnetic properties of K Ln Se 2 ( Ln = La, Ce, Pr, Nd) structures: A family of 2D triangular lattice frustrated magnets

Here, we report the detail synthesis, single crystal structure characterization and magnetic properties of KLnSe 2 series obtained via solid state molten flux growth method. The crystal structures were characterized using single crystal x-ray diffraction. The KLnSe 2 (Ln = La, Ce, Pr and Nd) series crystallizes in the trigonal crystal system with the space group of R-3m (No. 166). The overall structure contains two-dimensional (2D) layers made from edged shared LnSe 6 -octahedra. Ln 3+ ions form a perfect triangular magnetic lattice which propagates along ab-plane. These triangular lattices are separated by the K + ions. The magnetic properties confirm that, Ce, Pr and Nd do not show any long-range ordering down to 0.4 K indicating frustrated magnetism in the KLnSe 2 series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Structure and magnetic properties of a new anion-deficient perovskite Pb{sub 2}Ba{sub 2}BiFe{sub 4}ScO{sub 13} with crystallographic shear structure

Graphical abstract: - Highlights: • Pb{sub 2}Ba{sub 2}BiFe{sub 4}ScO{sub 13} was obtained by solid state synthesis. • Its structure was refined from combination of XPD and TEM. • It is a new member of the perovskite-related homologous series A{sub n}B{sub n}O{sub 3n−2} with n = 5. • Pb{sub 2}Ba{sub 2}BiFe{sub 4}ScO{sub 13} is antiferromagnetically ordered below T{sub N} ≈350 K. - Abstract: Pb{sub 2}Ba{sub 2}BiFe{sub 4}ScO{sub 13}, a new n = 5 member of the oxygen-deficient perovskite-based A{sub n}B{sub n}O{sub 3n−2} homologous series, was synthesized using a solid-state method. The crystal structure of Pb{sub 2}Ba{sub 2}BiFe{sub 4}ScO{sub 13} was investigated by a combination of synchrotron X-ray powder diffraction, electron diffraction, high-angle annular dark-field scanning transmission electron microscopy and Mössbauer spectroscopy. At 900 K, it crystallizes in the Ammm space group with the unit cell parameters a = 5.8459(1) Å, b = 4.0426(1) Å, and c = 27.3435(1) Å. In the Pb{sub 2}Ba{sub 2}BiFe{sub 4}ScO{sub 13} structure, quasi-two-dimensional perovskite blocks are periodically interleaved with ½[1 1 0] (1{sup ¯}01){sub p} crystallographic shear (CS) planes. At the CS planes, the corner-sharing FeO{sub 6} octahedra are transformed into chains of edge-sharing FeO{sub 5} distorted tetragonal pyramids. B-positions of the perovskite blocks between the CS planes are jointly occupied by Fe{sup 3+} and Sc{sup 3+}. The chains of the FeO{sub 5} pyramids and (Fe,Sc)O{sub 6} octahedra delimit six-sided tunnels that are occupied by double columns of cations with a lone electron pair (Pb{sup 2+}). The remaining A-cations (Bi{sup 3+}, Ba{sup 2+}) occupy positions in the perovskite block. According to the magnetic susceptibility measurements, Pb{sub 2}Ba{sub 2}BiFe{sub 4}ScO{sub 13} is antiferromagnetically ordered below T{sub N} ≈350 K.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Structural Basis for Substrate Placement by an Archaeal Box C/D Ribonucleoprotein Particle

Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Structural Insights to How Mammalian Capping Enzyme Reads the CTD Code

Physical interaction between the phosphorylated RNA polymerase II carboxyl-terminal domain (CTD) and cellular capping enzymes is required for efficient formation of the 5' mRNA cap, the first modification of nascent mRNA. Here, we report the crystal structure of the RNA guanylyltransferase component of mammalian capping enzyme (Mce) bound to a CTD phosphopeptide. The CTD adopts an extended {beta}-like conformation that docks Tyr1 and Ser5-PO{sub 4} onto the Mce nucleotidyltransferase domain. Structure-guided mutational analysis verified that the Mce-CTD interface is a tunable determinant of CTD binding and stimulation of guanylyltransferase activity, and of Mce function in vivo. The location and composition of the CTD binding site on mammalian capping enzyme is distinct from that of a yeast capping enzyme that recognizes the same CTD primary structure. Thus, capping enzymes from different taxa have evolved different strategies to read the CTD code.

59 BASIC BIOLOGICAL SCIENCES↗