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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Structure–activity relationship of Au/ZrO 2 catalyst on formation of hydroxyl groups and its influence on CO oxidation

We studied the effect of changes in morphology and surface hydroxyl species upon thermal treatment of zirconia on the oxidation activity of Au/ZrO 2 catalyst. We observed using transmission Fourier transform infrared (FTIR) spectroscopy progressive changes in the presence of monodentate (type I), bidentate (type II) and hydrogen bridged species (type III) for each of the thermally treated (85 to 500 °C) supports consisting of bare zirconia and Au/ZrO 2 catalysts. Furthermore, structural changes in zirconia were accompanied by an increase in crystal size (7 to 58 nm) and contraction of the supports porosity (SSA 532 to 7 m 2 g -1 ) with increasing thermal treatment. Deposition of gold nanoparticles under similar preparation conditions on different thermally treated zirconia resulted in changes in the mean gold cluster size, ranging from 3.7 to 5.6 nm. Changes in the surface hydroxyl species, support structure and size of the gold centers are important parameters responsible for the observed decrease (>90%) in CO conversion activity for the Au/ZrO 2 catalysts. Density functional theory calculations provide evidence of increased CO binding to Au nanoclusters in the presence of surface hydroxyls on zirconia, which increases charge transfer at the perimeter of the gold nanocluster on zirconia support. This further helps in reducing a model CO-oxidation reaction barrier in the presence of surface hydroxyls. Lastly, this work demonstrates the need to understand the structure–activity relationship of both the support and active particles for the design of catalytic materials.

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

Structure and properties of rhombohedral CePd{sub 3}Ga{sub 8}: A variant of the cubic parent compound with BaHg{sub 11} structure type

Single crystals of a new intermetallic gallide, R-CePd{sub 3}Ga{sub 8}, have been synthesized from excess molten gallium. Single-crystal X-ray diffraction reveals that R-CePd{sub 3}Ga{sub 8} crystallizes in the R-3m space group with a=b=c=8.4903(10) A and {alpha}={beta}={gamma}=89.993(17). R-CePd{sub 3}Ga{sub 8} is a variant of the cubic BaHg{sub 11} structure type with three structural units: a Ce-centered polyhedron, a distorted cube of Pd{sub 2}Ga{sub 6} and a Pd-centered cuboctahedron. The distortions of these units are compared to undistorted analogous units in intermetallic compounds with BaHg{sub 11} structure type. Field and temperature-dependent magnetization measurements on R-CePd{sub 3}Ga{sub 8} reveal a paramagnetic material with strong antiferromagnetic correlations and a magnetization consistent with Ce{sup 3+}. Electrical resistance measurements indicate Kondo behavior between localized Ce{sup 3+} magnetic moments. - Graphical Abstract: Single crystals of CePd{sub 3}Ga{sub 8} have been synthesized from Ga flux. This new compound is the first rhombohedral variant of the cubic BaHg{sub 11} structure type. Highlights: Black-Right-Pointing-Triangle Single crystals of CePd{sub 3}Ga{sub 8} were synthesized from gallium flux. Black-Right-Pointing-Triangle CePd{sub 3}Ga{sub 8} is the first rhombohedral variant of the cubic BaHg{sub 11} structure type. Black-Right-Pointing-Triangle Paramagnetic with antiferromagnetic correlations. Black-Right-Pointing-Triangle Magnetization consistent with Ce{sup 3+}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Structure-Guided, Single-Point Modifications in the Phosphinic Dipeptide Structure Yield Highly Potent and Selective Inhibitors of Neutral Aminopeptidases

Seven crystal structures of alanyl aminopeptidase from Neisseria meningitides (the etiological agent of meningitis, NmAPN) complexed with organophosphorus compounds were resolved to determine the optimal inhibitor-enzyme interactions. The enantiomeric phosphonic acid analogs of Leu and hPhe, which correspond to the P1 amino acid residues of well-processed substrates, were used to assess the impact of the absolute configuration and the stereospecific hydrogen bond network formed between the aminophosphonate polar head and the active site residues on the binding affinity. For the hPhe analog, an imperfect stereochemical complementarity could be overcome by incorporating an appropriate P1 side chain. The constitution of P1'-extended structures was rationally designed and the lead, phosphinic dipeptide hPhePψ[CH2]Phe, was modified in a single position. Introducing a heteroatom/heteroatom-based fragment to either the P1 or P1' residue required new synthetic pathways. The compounds in the refined structure were low nanomolar and subnanomolar inhibitors of N. meningitides, porcine and human APNs, and the reference leucine aminopeptidase (LAP). The unnatural phosphinic dipeptide analogs exhibited a high affinity for monozinc APNs associated with a reasonable selectivity versus dizinc LAP. Another set of crystal structures containing the NmAPN dipeptide ligand were used to verify and to confirm the predicted binding modes; furthermore, novel contacts, which were promising for inhibitor development, were identified, including a π-π stacking interaction between a pyridine ring and Tyr372.

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

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A , which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

Details of five very high-resolution accurate structures of bovine trypsin are compared in the context of the reproducibility of models obtained from crystals grown under identical conditions. Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C{sup α} and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

The structures of penicillin-binding protein 4 (PBP4) and PBP5 from Enterococci provide structural insights into β-lactam resistance

The final steps of cell-wall biosynthesis in bacteria are carried out by penicillin-binding proteins (PBPs), whose transpeptidase domains form the cross-links in peptidoglycan chains that define the bacterial cell wall. These enzymes are the targets of β-lactam antibiotics, as their inhibition reduces the structural integrity of the cell wall. Bacterial resistance to antibiotics is a rapidly growing concern; however, the structural underpinnings of PBP-derived antibiotic resistance are poorly understood. PBP4 and PBP5 are low-affinity, class B transpeptidases that confer antibiotic resistance to Enterococcus faecalis and Enterococcus faecium, respectively. We report the crystal structures of PBP4 (1.8 Å) and PBP5 (2.7 Å) in their apo and acyl-enzyme complexes with the β-lactams benzylpenicillin, imipenem, and ceftaroline. We found that, although these three β-lactams adopt geometries similar to those observed in other class B PBP structures, there are small, but significant, differences that likely decrease antibiotic efficacy. Further, we also discovered that the N-terminal domain extensions in this class of PBPs undergo large rigid-body rotations without impacting the structure of the catalytic transpeptidase domain. Together, our findings are defining the subtle functional and structural differences in the Enterococcus PBPs that allow them to support transpeptidase activity while also conferring bacterial resistance to antibiotics that function as substrate mimics.

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

Canonical symplectic structure and structure-preserving geometric algorithms for Schrödinger–Maxwell systems

An infinite dimensional canonical symplectic structure and structure-preserving geometric algorithms are developed for the photon–matter interactions described by the Schrödinger–Maxwell equations. The algorithms preserve the symplectic structure of the system and the unitary nature of the wavefunctions, and bound the energy error of the simulation for all time-steps. This new numerical capability enables us to carry out first-principle based simulation study of important photon–matter interactions, such as the high harmonic generation and stabilization of ionization, with long-term accuracy and fidelity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Structure and thermodynamics of uranium-containing iron garnets

Use of crystalline garnet as a waste form phase appears to be advantageous for accommodating actinides from nuclear waste. Previous studies show that large amounts of uranium (U) and its analogues such as cerium (Ce) and thorium (Th) can be incorporated into the garnet structure. In this study, we synthesized U loaded garnet phases, Ca 3 U x Zr 2–x Fe 3 O 12 (x = 0.5–0.7), along with the endmember phase, Ca 3 (Zr 2 )SiFe 3+ 2 O 12 , for comparison. The oxidation states of U were determined by X-ray photoelectron and absorption spectroscopies, revealing the presence of mixed pentavalent and hexavalent uranium in the phases with x = 0.6 and 0.7. The oxidation states and coordination environments of Fe were measured using transmission 57 Fe-Mössbauer spectroscopy, which shows that all iron is tetrahedrally coordinated Fe 3+ . U substitution had a significant effect on local environments, the extent of U substitution within this range had a minimal effect on the structure, and unlike in the x = 0 sample, Fe exists in two different environments in the substituted garnets. The enthalpies of formation of garnet phases from constituent oxides and elements were first time determined by high temperature oxide melt solution calorimetry. The results indicate that these substituted garnets are thermodynamically stable under reducing conditions. Furthermore, our structural and thermodynamic analysis further provides explanation for the formation of natural uranium garnet, elbrusite-(Zr), and supports the potential use of Ca 3 U x Zr 2–x Fe 3 O 12 as viable waste form phases for U and other actinides.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2015

Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures

Whereas the structures of small to medium-sized well folded RNA molecules often can be determined by either X-ray crystallography or NMR spectroscopy, obtaining structural information for large RNAs using experimental, computational, or combined approaches remains a major interest and challenge. RNA is very sensitive to small-angle X-ray scattering (SAXS) due to high electron density along phosphate-sugar backbones, whose scattering contribution dominates SAXS intensity. For this reason, SAXS is particularly useful in obtaining global RNA structural information that outlines backbone topologies and, therefore, molecular envelopes. Such information is extremely valuable in bridging the gap between the secondary structures and three-dimensional topological structures of RNAmolecules, particularly those that have proven difficult to study using other structuredetermination methods. Here we review published results of RNA topological structures derived from SAXS data or in combination with other experimental data, as well as details on RNA sample preparation for SAXS experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Pressure-Induced Local Structure Distortions in Cu(pyz)F(2)(H(2)O)(2)

We employed infrared spectroscopy along with complementary lattice dynamics and spin density calculations to investigate pressure-driven local structure distortions in the copper coordination polymer Cu(pyz)F{sub 2}(H{sub 2}O){sub 2}. Here, pyz is pyrazine. Our study reveals rich and fully reversible local lattice distortions that buckle the pyrazine ring, disrupt the bc-plane O-H {hor_ellipsis} F hydrogen-bonding network, and reinforce magnetic property switching. The resiliency of the soft organic ring is a major factor in the stability of this material. Interestingly, the collective character of the lattice vibrations masks direct information on the Cu-N and Cu-O linkages through the series of pressure-induced Jahn-Teller axis switching transitions, although Cu-F bond softening is clearly identified above 3 GPa. These findings illustrate the importance of combined bulk and local probe techniques for microscopic structure determination in complex materials.

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

Structural and chemical ordering of Heusler C o x M n y G e z epitaxial films on Ge (111): Quantitative study using traditional and anomalous x-ray diffraction techniques

Epitaxial films of C o x M n y G e z grown on Ge (111) substrates by molecular-beam-epitaxy techniques have been investigated as a continuous function of composition using combinatorial synchrotron x-ray diffraction (XRD) and x-ray fluorescence (XRF) spectroscopy techniques. A high-resolution ternary epitaxial phase diagram is obtained, revealing a small number of structural phases stabilized over large compositional regions. Ordering of the constituent elements in the compositional region near the full Heusler alloy C o 2 MnGe has been examined in detail using both traditional XRD and a new multiple-edge anomalous diffraction (MEAD) technique. Multiple-edge anomalous diffraction involves analyzing the energy dependence of multiple reflections across each constituent absorption edge in order to detect and quantify the elemental distribution of occupation in specific lattice sites. Results of this paper show that structural and chemical ordering are very sensitive to the Co : Mn atomic ratio, such that the ordering is the highest at an atomic ratio of 2 but significantly reduced even a few percent off this ratio. The in-plane lattice is nearly coherent with that of the Ge substrate, while the approximately 2% lattice mismatch is accommodated by the out-of-plane tetragonal strain. The quantitative MEAD analysis further reveals no detectable amount (<0.5%) of Co-Mn site swapping, but instead high levels (26%) of Mn-Ge site swapping. Increasing Ge concentration above the Heusler stoichiometry ( C o 0.5 M n 0.25 G e 0.25 ) is shown to correlate with increased lattice vacancies, antisites, and stacking faults, but reduced lattice relaxation. The highest degree of chemical ordering is observed off the Heusler stoichiometry with a Ge enrichment of 5 at.%.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Structural and Physical Property Studies of Amorphous Zn-In-Sn-O Thin Films

The structures in amorphous (a-) Zn, Sn co-doped In 2 O 3 (ZITO) thin films grown by pulsed laser deposition on glass under varying oxygen pressure or with varying Sn:Zn ratios were determined using X-ray absorption spectroscopy and anomalous X-ray scattering. Typical structures around cations in a-ZITO films are described and compared with crystalline (c-) ZITO films. The results show that the Zn cations are fourfold coordinated with Zn–O bond lengths of 1.98 ± 0.02 Å, which is close to that in bulk ZnO. As a consequence, the second coordination shells around Zn contract. At longer distances away from Zn, the structure is commensurate with the averaged structure. The unit volume around In also contracts slightly compared to bulk In 2 O 3 , whereas the Sn–O bond length is similar to the one in bulk SnO 2 . These unique structural characteristics may account for the films' superior thermal stability over amorphous Sn-doped In 2 O 3 , and suggest that Zn and Sn act as network-forming cations. Like in c-ZITO, coordination numbers (N) around Sn, In, and Zn follow the order N Sn > N In > N Zn . Unlike in c-ZITO, where electrical properties change significantly with a slight variation in the Sn:Zn ratio, this variation does not markedly alter the electrical properties, or the local structures, of a-ZITO films. Dramatic changes in the electrical properties occur for films grown under various oxygen pressures, which point to oxygen “defects” as the source of charge carriers.

Proffit, Diana E↗
DOE OSTI2014

Structural characterization of Bi{sub 2}Te{sub 3} and Sb{sub 2}Te{sub 3} as a function of temperature using neutron powder diffraction and extended X-ray absorption fine structure techniques

The structure of Bi{sub 2}Te{sub 3} (Seebeck coefficient Standard Reference Material (SRM™ 3451)) and the related phase Sb{sub 2}Te{sub 3} have been characterized as a function of temperature using the neutron powder diffraction (NPD) and the extended X-ray absorption fine structure (EXAFS) techniques. The neutron structural studies were carried out from 20 K to 300 K for Bi{sub 2}Te{sub 3} and from 10 K to 298 K for Sb{sub 2}Te{sub 3}. The EXAFS technique for studying the local structure of the two compounds was conducted from 19 K to 298 K. Bi{sub 2}Te{sub 3} and Sb{sub 2}Te{sub 3} are isostructural, with a space group of R3{sup ¯}m. The structure consists of repeated quintuple layers of atoms, Te2-M-Te1-M-Te2 (where M = Bi or Sb) stacking along the c-axis of the unit cell. EXAFS was used to examine the bond distances and static and thermal disorders for the first three shells of Bi{sub 2}Te{sub 3} and Sb{sub 2}Te{sub 3} as a function of temperature. The temperature dependencies of thermal disorders were analyzed using the Debye and Einstein models for lattice vibrations. The Debye and Einstein temperatures for the first two shells of Bi{sub 2}Te{sub 3} are similar to those of Sb{sub 2}Te{sub 3} within the uncertainty in the data. However, the Debye and Einstein temperatures for the third shell of Bi-Bi are significantly lower than those of the third shell of Sb-Sb. The Einstein temperature for the third shell is consistent with a soft phonon mode in both Bi{sub 2}Te{sub 3} and Sb{sub 2}Te{sub 3}. The lower Einstein temperature of Bi-Bi relative to Sb-Sb is consistent with the lower value of thermal conductivity of Bi{sub 2}Te{sub 3} relative to Sb{sub 2}Te{sub 3}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗