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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Towards automated crystallographic structure refinement with phenix.refine

phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods. phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Solving the Structure and Dynamics of Metal Nanoparticles by Combining X-Ray Absorption Fine Structure Spectroscopy and Atomistic Structure Simulations

Extended X-ray absorption fine structure (EXAFS) spectroscopy is a premiere method for analysis of the structure and structural transformation of nanoparticles. Extraction of analytical information about the three-dimensional structure and dynamics of metal–metal bonds from EXAFS spectra requires special care due to their markedly non-bulk-like character. In recent decades, significant progress has been made in the first-principles modeling of structure and properties of nanoparticles. Here, we summarize new approaches for EXAFS data analysis that incorporate particle structure modeling into the process of structural refinement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Synthesis Crystal Structure and Magnetism of beta-Fe1.00(2)Se1.00(3) Single Crystals

Understanding iron-based superconductors requires high-quality impurity-free single crystals. So far they have been elusive for {beta}-FeSe and extraction of intrinsic materials properties has been compromised by several magnetic-impurity phases. Here, we report synchrotron-clean {beta}-FeSe superconducting single crystals grown via LiCl/CsCl flux method. Phase purity yields evidence for a defect-induced weak ferromagnetism that coexists with superconductivity below T{sub c}. In contrast to Fe{sub 1+y}Te-based superconductors, our results reveal that the interstitial Fe(2) site is not occupied and that all contribution to density of states at the Fermi level must come from in-plane Fe(1).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

Structural Changes of (KGd)2Ta2O7 Pyrochlore at High Pressure

The structure of K-bearing tantalate pyrochlore (K{sub 2-x}Gd{sub x})Ta{sub 2}O{sub 6+x}(x {approx} 0.4) was studied at high pressures using in situ X-ray diffraction and Raman scattering methods. Experimental results indicated that (K{sub 2-x}Gd{sub x})Ta{sub 2}O{sub 6+x}(x {approx} 0.4) retains the pyrochlore structure up to 40 GPa, but partial amorphization occurred at pressures above 23 GPa. The amorphous phase was also confirmed in the quenched sample by means of transmission electron microscopy. The tantalate pyrochlore lattice is more stable than pyrochlore compounds in other systems, such as rare earth titanates, zirconates and stannates. The structural stability of pyrochlore tantalate may be mainly related to the size ratio of cations on the 16d and 16c sites in the lattice.

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

Synthesis and structural characterization of the Zintl phases Na{sub 3}Ca{sub 3}TrPn{sub 4}, Na{sub 3}Sr{sub 3}TrPn{sub 4}, and Na{sub 3}Eu{sub 3}TrPn{sub 4} (Tr=Al, Ga, In; Pn=P, As, Sb)

15 new quaternary Zintl phases have been synthesized by solid-state reactions from the respective elements, and their structures have been determined by single-crystal X-ray diffraction. Na{sub 3}E{sub 3}TrPn{sub 4} (E=Ca, Sr, Eu; Tr=Al, Ga, In; Pn=P, As, Sb) crystallize in the hexagonal crystal system with the non-centrosymmetric space group P6{sub 3}mc (No. 186). The structure represents a variant of the K{sub 6}HgS{sub 4} structure type (Pearson index hP22) and features [TrPn{sub 4}]{sup 9–} tetrahedral units, surrounded by Na{sup +} and Ca{sup 2+}, Sr{sup 2+}, Eu{sup 2+} cations. The nominal formula rationalization [Na{sup +}]{sub 3}[E{sup 2+}]{sub 3}[TrPn{sub 4}]{sup 9–} follows the octet rule, suggesting closed-shell configurations for all atoms and intrinsic semiconducting behavior. However, structure refinements for several members hint at disorder and mixing of cations that potentially counteract the optimal valence electron count. - Graphical abstract: The hexagonal, non-centrosymmetric structure of Na{sub 3}E{sub 3}TrPn{sub 4} (E=Ca, Sr, Eu; Tr=Al, Ga, In; Pn=P, As, Sb) features [TrPn{sub 4}]{sup 9–} tetrahedral units, surrounded by Na{sup +} and Ca{sup 2+}, Sr{sup 2+}, Eu{sup 2+} cations. - Highlights: • 15 quaternary phosphides, arsenides, and antimonides are synthesized and structurally characterized. • The structure is a variant of the hexagonal K{sub 6}HgS{sub 4}-type, with distinctive pattern for the cations. • Occupational and/or positional disorder of yet unknown origin exists for some members of the series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Structural unit charge density and molecular cation templating effects on orientational geometric isomerism and interlayer spacing in 2-D uranyl sulfates

The new uranyl aqua sulfate compound [({CH_3}{sub 3}N{sub 2}C{sub 3}H{sub 3}{CH_2COOH})(H{sub 3}O)] [(UO{sub 2}){sub 2}(SO{sub 4}){sub 3}(H{sub 2}O)]·1.5H{sub 2}O was synthesized and the crystal structure determined. The two-dimensional uranyl-aqua sulfate compound exhibits a previously reported anionic structural unit topology, but features an interstitial complex incorporating hydronium in the form of a disorder Zundel cation and the cation moiety from the ionic liquid 1-carboxymethyl 3-methylimidazolium bistriflimide [HBetMIm][Tf{sub 2}N], which forms hydrogen bonding dimer pairs. An analysis of similar uranyl sulfate complexes from the literature is conducted to explore the relative importance and role of structure directing factors in alkylammonium charge-balanced two-dimensional uranyl sulfates. A correlation is observed between structural unit charge density and interlayer spacing, with a concomitant direction of structural and orientational geometric isomerism of the anionic structural unit. We discuss the role of synthetic conditions and molecular cation properties in directing structural unit formation through charge density matching and hydrogen bonding.

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

Large-Scale Screening of Zeolite Structures for CO2 Membrane Separations

We have conducted large-scale screening of zeolite materials for CO2/CH4 and CO2/N-2 membrane separation applications using the free energy landscape of the guest molecules inside these porous materials. We show how advanced molecular simulations can be integrated with the design of a simple separation process to arrive at a metric to rank performance of over 87 000 different zeolite structures, including the known IZA zeolite structures. Our novel, efficient algorithm using graphics processing units can accurately characterize both the adsorption and diffusion properties of a given structure in just a few seconds and accordingly find a set of optimal structures for different desired purity of separated gases from a large database of porous materials in reasonable wall time. Our analysis reveals that the optimal structures for separations usually consist of channels with adsorption sites spread relatively uniformly across the entire channel such that they feature well-balanced CO2 adsorption and diffusion properties. Our screening also shows that the top structures in the predicted zeolite database outperform the best known zeolite by a factor of 4-7. Finally, we have identified a completely different optimal set of zeolite structures that are suitable for an inverse process, in which the CO2 is retained while CH4 or N-2 is passed through a membrane.

Kim, JH↗
DOE OSTI2015

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.

Handley, Kim M↗
NASA NTRS1980

Comparison of structural behavior of superplastically formed/diffusion-bonded sandwich structures and honeycomb core sandwich structures

A superplasticity formed/diffusion-bonded (SPF/DB) orthogonally corrugated core sandwich structure is discussed and its structural behavior is compared to that of a conventional honeycomb core sandwich structure. The stiffness and buckling characteristics of the two types of sandwich structures are compared under conditions of equal structural density. It is shown that under certain conditions, the SPF/DB orthogonally corrugated core sandwich structure is slightly more efficient than the optimum honeycomb core (square-cell core) sandwich structure. However, under different conditions, this effect can be reversed.

Ko, W. L.↗
DOE OSTI2011

Crystal Structure of the FimD Usher Bound to its Cognate FimC-FimH Substrate

Type 1 pili are the archetypal representative of a widespread class of adhesive multisubunit fibres in Gram-negative bacteria. During pilus assembly, subunits dock as chaperone-bound complexes to an usher, which catalyses their polymerization and mediates pilus translocation across the outer membrane. Here we report the crystal structure of the full-length FimD usher bound to the FimC-FimH chaperone-adhesin complex and that of the unbound form of the FimD translocation domain. The FimD-FimC-FimH structure shows FimH inserted inside the FimD 24-stranded {beta}-barrel translocation channel. FimC-FimH is held in place through interactions with the two carboxy-terminal periplasmic domains of FimD, a binding mode confirmed in solution by electron paramagnetic resonance spectroscopy. To accommodate FimH, the usher plug domain is displaced from the barrel lumen to the periplasm, concomitant with a marked conformational change in the {beta}-barrel. The amino-terminal domain of FimD is observed in an ideal position to catalyse incorporation of a newly recruited chaperone-subunit complex. The FimD-FimC-FimH structure provides unique insights into the pilus subunit incorporation cycle, and captures the first view of a protein transporter in the act of secreting its cognate substrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia

Macrophage migration inhibitory factor (MIF) is a eukaryotic cytokine that affects a broad spectrum of immune responses and its activation/inactivation is associated with numerous diseases. During protozoan infections MIF is not only expressed by the host, but, has also been observed to be expressed by some parasites and released into the host. To better understand the biological role of parasitic MIF proteins, the crystal structure of the MIF protein from Giardia lamblia (Gl-MIF), the etiological agent responsible for giardiasis, has been determined at 2.30 Å resolution. The 114-residue protein adopts an α/β fold consisting of a four-stranded β-sheet with two anti-parallel α-helices packed against a face of the β-sheet. An additional short β-strand aligns anti-parallel to β4 of the β-sheet in the adjacent protein unit to help stabilize a trimer, the biologically relevant unit observed in all solved MIF crystal structures to date, and form a discontinuous β-barrel. The structure of Gl-MIF is compared to the MIF structures from humans (Hs-MIF) and three Plasmodium species (falciparum, berghei, and yoelii). The structure of all five MIF proteins are generally similar with the exception of a channel that runs through the center of each trimer complex. Relative to Hs-MIF, there are differences in solvent accessibility and electrostatic potential distribution in the channel of Gl-MIF and the Plasmodium-MIFs due primarily to two “gate-keeper” residues in the parasitic MIFs. For the Plasmodium MIFs the gate-keeper residues are at positions 44 (Y==>R) and 100 (V==>D) and for Gl-MIF it is at position 100 (V==>R). If these gate-keeper residues have a biological function and contribute to the progression of parasitemia they may also form the basis for structure-based drug design targeting parasitic MIF proteins.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2012

Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Structure changes in {sup 160}Er from low to ultrahigh spin

A spectroscopic investigation of the {gamma} decays from excited states in {sup 160}Er has been performed in order to study the changing structural properties exhibited from low spin up toward ultrahigh spin (I{approx}60({h_bar}/2{pi})). The nucleus {sup 160}Er was populated by the reaction {sup 116}Cd({sup 48}Ca,4n{gamma}) at a beam energy of 215 MeV, and resulting {gamma} decays were studied using the Gammasphere spectrometer. New rotational structures and extensions to existing bands were observed, revealing a diverse range of quasiparticle configurations, which are discussed in terms of the cranked shell model. At spins around 50({h_bar}/2{pi}) there is evidence for oblate states close to the yrast line. Three rotational bands that have the characteristics of strongly deformed triaxial structures are observed, marking a return to collectivity at even higher spin. The high-spin data are interpreted within the framework of cranked Nilsson-Strutinsky calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Terminating states in the positive-parity structures of As67

The energy levels and γ-ray decay scheme of the positive-parity states in the Tz=12 nucleus 67As have been studied by using the 40Ca(36Ar,2αp)67As reaction at a beam energy of 145 MeV. Two new band structures have been identified which can be connected to the previously known levels. The results for these bands are compared with configuration-dependent cranked Nilsson–Strutinsky calculations. The good level of agreement between theory and experiment suggests that these structures can be interpreted in terms of configurations that involve three g92 particles and that both possess noncollective terminating states.

59 ≤ A ≤ 89↗