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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Structural and Biochemical Studies on the Regulation of Biotin Carboxylase by Substrate Inhibition and Dimerization

Biotin carboxylase (BC) activity is shared among biotin-dependent carboxylases and catalyzes the Mg-ATP-dependent carboxylation of biotin using bicarbonate as the CO{sub 2} donor. BC has been studied extensively over the years by structural, kinetic, and mutagenesis analyses. Here we report three new crystal structures of Escherichia coli BC at up to 1.9 {angstrom} resolution, complexed with different ligands. Two structures are wild-type BC in complex with two ADP molecules and two Ca{sup 2+} ions or two ADP molecules and one Mg{sup 2+} ion. One ADP molecule is in the position normally taken by the ATP substrate, whereas the other ADP molecule occupies the binding sites of bicarbonate and biotin. One Ca{sup 2+} ion and the Mg{sup 2+} ion are associated with the ADP molecule in the active site, and the other Ca{sup 2+} ion is coordinated by Glu-87, Glu-288, and Asn-290. Our kinetic studies confirm that ATP shows substrate inhibition and that this inhibition is competitive against bicarbonate. The third structure is on the R16E mutant in complex with bicarbonate and Mg-ADP. Arg-16 is located near the dimer interface. The R16E mutant has only a 2-fold loss in catalytic activity compared with the wild-type enzyme. Analytical ultracentrifugation experiments showed that the mutation significantly destabilized the dimer, although the presence of substrates can induce dimer formation. The binding modes of bicarbonate and Mg-ADP are essentially the same as those to the wild-type enzyme. However, the mutation greatly disrupted the dimer interface and caused a large re-organization of the dimer. The structures of these new complexes have implications for the catalysis by BC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A complex approach to assessing porous structure of structured ceramics obtained by SPS technique

Highlights: • A complex approach to microstructural analysis of nanostructured SPS ceramics was presented. • A bunch of gas, intrusion and microscopic methods were applied for open/closed porosity determination in nanoceramics. • Kinetic TPR analysis for structural changes in nanoceramic was carried out. • 3D pore visualization for nanoceramics was provided via SEM/FIB tomography • Porosity calculations were performed via BET, BJH, t-plot, Washburn equation, FEI Avizo 9.1 software results. - Abstract: Spark plasma sintering (SPS) is a highly prospective technology providing rapid consolidation of nano-disperse compositions into structured ceramics with complex structural organization. Characterizing pore structure of such systems remains a challenge due to different types, size and shape of the pores as well as structural defects occurring in the material, thus requiring special methods to quantify certain porosity type. The paper presents a complex approach to studying structure of SPS hematite-based structured ceramics. The method involves a number of gas, intrusion and electron microscopy probing techniques to characterize open and closed pores in the ceramics bulk. Low temperature nitrogen sorption has been implemented to estimate open micro- and mesoporosity in the size range 0.7–50 nm using BET, BJH and t-plot methods to process experimental data. Additionally, structural peculiarities of consolidated structured ceramics have been studied using temperature-programmed reduction (TPR) with the kinetic analysis of the results being carried out. Volume of macropores sized above 50 nm has been measured with mercury intrusion. Closed pores and structural defects have been quantified with SEM and FIB/SEM tomography. By comparing experimental and estimated results we have shown that addressing all porosity types provides a highly precise structural characterization of the material.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials

The rigid constraints of chemistry-dictated by quantum mechanics and the discrete nature of the atom-limit the set of observable atomic crystal structures. What structures are possible in the absence of these constraints? Here, we systematically crystallize one-component systems of particles interacting with isotropic multiwell pair potentials. We investigate two tunable families of pairwise interaction potentials. Our simulations self-assemble a multitude of crystal structures ranging from basic lattices to complex networks. Sixteen of the structures have natural analogs spanning all coordination numbers found in inorganic chemistry. Fifteen more are hitherto unknown and occupy the space between covalent and metallic coordination environments. The discovered crystal structures constitute targets for self-assembly and expand our understanding of what a crystal structure can look like.

crystal structures↗
DOE OSTI2018

Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition

Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white-rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 A resolution using X-ray crystallography. Unlike the majority of the currently available C1-specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting ..beta..-strands ..beta..2 and ..beta..3 of the ..beta..-sandwich structure. Molecular dynamics (MD) simulations suggest roles for both aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active-site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1-specific LPMOs, giving a molecular-level picture of active site substrate interactions.

09 BIOMASS FUELS↗
DOE OSTI2011

Structural and Functional Studies of Fatty Acyl Adenylate Ligases from E. coli and L. pneumophila

Fatty acyl-AMP ligase (FAAL) is a new member of a family of adenylate-forming enzymes that were recently discovered in Mycobacterium tuberculosis. They are similar in sequence to fatty acyl-coenzyme A (CoA) ligases (FACLs). However, while FACLs perform a two-step catalytic reaction, AMP ligation followed by CoA ligation using ATP and CoA as cofactors, FAALs produce only the acyl adenylate and are unable to perform the second step. We report X-ray crystal structures of full-length FAAL from Escherichia coli (EcFAAL) and FAAL from Legionella pneumophila (LpFAAL) bound to acyl adenylate, determined at resolution limits of 3.0 and 1.85 {angstrom}, respectively. The structures share a larger N-terminal domain and a smaller C-terminal domain, which together resemble the previously determined structures of FAAL and FACL proteins. Our two structures occur in quite different conformations. EcFAAL adopts the adenylate-forming conformation typical of FACLs, whereas LpFAAL exhibits a unique intermediate conformation. Both EcFAAL and LpFAAL have insertion motifs that distinguish them from the FACLs. Structures of EcFAAL and LpFAAL reveal detailed interactions between this insertion motif and the interdomain hinge region and with the C-terminal domain. We suggest that the insertion motifs support sufficient interdomain motions to allow substrate binding and product release during acyl adenylate formation, but they preclude CoA binding, thereby preventing CoA ligation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Electronic and Molecular Structures of the CeB 6 Monomer

The electronic and molecular structure of the CeB 6 molecular unit has been probed by anion PE spectroscopy and DFT calculations to gain insight into structural and electronic relaxation on edge and corner sites of this ionic material. While boron in bulk lanthanide hexaboride materials assumes octahedral B 6 3– units, the monomer assumes a less compact structure to delocalize the charge. Two competitive molecular structures were identified for the anion and neutral species, which include a boat-like structure and a planar or near-planar teardrop structure. Ce adopts different orbital occupancies in the two isomers; the boat-like structure has a 4f superconfiguration while the teardrop favors a 4f 6s occupancy. The B 6 ligand in these structures carries a charge of –4 and –3, respectively. The teardrop structure, which was calculated to be isoenergetic with the boat structure, was most consistent with the experimental spectrum. B 6 -local orbitals crowd the energy window between the Ce 4f and 6s (HOMO) orbitals. A low-lying transition from the B-based orbitals is observed slightly less than 1 eV above the ground state. Here, the results suggest that edge and corner conductivity involves stabilized, highly diffuse 6s orbitals or bands rather than the bulk-favored 5d band. High-spin and open-shell low-spin states were calculated to be very close in energy for both the anion and neutral, a characteristic that reflects how decoupled the 4f electron is from the B 6 2p- and Ce 6s-based molecular orbitals.

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

Effects of rapid thermal annealing on the structural and local atomic properties of ZnO: Ge nanocomposite thin films

We have investigated the structural and local atomic properties of Ge nanocrystals (Ge-ncs) embedded ZnO (ZnO: Ge) thin films. The films were deposited by sequential sputtering of ZnO and Ge thin film layers on z-cut quartz substrates followed by an ex-situ rapid thermal annealing (RTA) at 600 °C for 30, 60, and 90 s under forming gas atmosphere. Effects of RTA time on the evolution of Ge-ncs were investigated by x-ray diffraction (XRD), scanning electron microscopy (SEM), hard x-ray photoelectron spectroscopy (HAXPES), and extended x-ray absorption fine structure (EXAFS). XRD patterns have clearly shown that fcc diamond phase Ge-ncs of sizes ranging between 18 and 27 nm are formed upon RTA and no Ge-oxide peak has been detected. However, cross-section SEM images have clearly revealed that after RTA process, Ge layers form varying size nanoclusters composed of Ge-ncs regions. EXAFS performed at the Ge K-edge to probe the local atomic structure of the Ge-ncs has revealed that as prepared ZnO:Ge possesses Ge-oxide but subsequent RTA leads to crystalline Ge structure without the oxide layer. In order to study the occupied electronic structure, HAXPES has been utilized. The peak separation between the Zn 2p and Ge 3d shows no significant change due to RTA. This implies little change in the valence band offset due to RTA.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2013

The effect of structural vacancies on the thermoelectric properties of (Cu₂Te){sub 1–x}(Ga₂Te₃) x

We have studied the effects of structural vacancies on the thermoelectric properties of the ternary compounds (Cu₂Te) 1–x (Ga₂Te₃) x (x=0.5, 0.55, 0.571, 0.6, 0.625, 0.667 and 0.75), which are solid solutions found in the pseudo-binary phase diagram for Cu₂Te and Ga₂Te₃, and possesses tunable structural vacancy concentrations. This materials system is not suitable due to the cost and scarcity of the constituent elements, but the vacancy behavior is well understood and will provide a valuable test case for other systems more suitable from the standpoint of cost and abundance of raw materials, which also possesses these vacancy features, but whose structural characterization is lacking at this stage. We find that the nominally defect free phase CuGaTe₂ possess the highest ZT (ZT=S²T/ρκ, where S is the Seebeck coefficient and ρ is the electrical resistivity κ is the thermal conductivity and T is the absolute temperature) which approaches 1 at 840 K and seems to continuously increase above this temperature. This result is due to the unexpectedly low thermal conductivity found for this material at high temperature. The low thermal conductivity was caused by strong Umklapp (thermally resistive scattering processes involving three phonons) phonon scattering. We find that due to the coincidentally strong scattering of carriers by the structural defects that higher concentrations of these features lead to poor electrical transport properties and decreased ZT. - Graphical abstract: Thermal conductivity and zT as a function of temperature for a series of compounds of the type (Cu₂Te) 1–x (Ga₂Te₃)x (x=0.5, 0.55, 0.571, 0.6, 0.625, 0.667 and 0.75). Highlights: • All the samples show p-type semiconducting behavior in the temperature dependence of the Seebeck and Hall coefficients. • The increased carrier concentration and the introduction of vacancies diminish the carrier mobility and power factor. • The low temperature k decreases significantly as the Ga₂Te₃ content increases due to increasing point defects. • The highest ZT ~ 1.0 at 840 K among the samples in this study was found in CuGaTe₂, which contains no vacancies.

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

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

Local structural similarity restraints (LSSR) provide a novel method for exploiting NCS or structural similarity to an external target structure. Two examples are given where BUSTER re-refinement of PDB entries with LSSR produces marked improvements, enabling further structural features to be modelled. Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and @@target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -target enables the correct ligand-binding structure to be found, and http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}: New crystal structure type and electronic structure

We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}, known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn{sub 2}VO{sub 6} adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO{sub 4} tetrahedra, ZnO{sub 6} octahedra and VO{sub 4} tetrahedra, and Bi{sub 2}O{sub 12} dimers. It is the only known member of the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family which does not appear to be structurally closely related to others. The electronic structure of BiZn{sub 2}VO{sub 6}, calculated by DFT methods, shows that it is an indirect gap semiconductor with a calculated band gap of 1.6 eV, which compares favourably to the experimentally measured value of 2.4 eV. - Graphical abstract: The crystal structure of BiZn{sub 2}VO{sub 6}, a new structure type in the BiM{sub 2}AO{sub 6} (M=Mg, Ca, Cd, Cu, Pb, Mn, Zn; A=V, P, As) family. - Highlights: • Structure solution from PXRD data by repeated minimisations from random starting values. • New structure type in the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family. • Electronic structure calculation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Layer-Dependent Electronic Structure of Atomically Resolved Two-Dimensional Gallium Selenide Telluride

Alloying two-dimensional (2D) semiconductors provides a powerful method to tune their physical properties, especially those relevant to optoelectronic applications. However, as the crystal structure becomes more complex, it becomes increasingly difficult to accurately correlate response characteristics to detailed atomic structure. We investigate, via annular dark-field scanning transmission electron microscopy, electron energy loss spectroscopy, and second harmonic generation, the layered III-VI alloy GaSe 0.5 Te 0.5 as a function of layer number. The local atomic structure and stacking sequence for different layers is explicitly determined. We complement the measurements with first-principles calculations of the total energy and electronic band structure of GaSe 0.5 Te 0.5 for different crystal structures and layer number. The electronic band gap as well as the π and π + σ plasmons are found to be sensitive to layer number.

2D semiconductor alloys↗
DOE OSTI2012

Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

Abstract Disulfide‐rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide‐rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C‐ and 15 N‐labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long‐time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro , but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.

Buchko, Garry W.↗
DOE OSTI2014

Structural analysis of highly porous γ-Al{sub 2}O{sub 3}

Two highly porous γ-aluminas, a commercial catalyst obtained from the calcination of boehmite and a highly mesoporous product obtained from amorphous aluminum (oxy)hydroxide via a sol–gel-based process were investigated by {sup 27}Al nuclear magnetic resonance (NMR), transmission electron microscopy (TEM), and atomic pair distribution function (PDF) analysis of synchrotron powder diffraction data. NMR data showed for both materials a distribution of tetrahedrally and octahedrally coordinated Al at a 0.30:0.70 ratio, which is typical for γ-aluminas. TEM studies revealed that rod-shaped particles with about 5 nm in thickness are the building blocks of the porous structure in both materials. These particles often extend to a length of 50 nm in the commercial catalyst and are considerably shorter in the sol–gel-based material, which has a higher surface area. Refinement of PDFs revealed the presence of a ∼1 nm scale local structure and the validity of a tetragonal average structure for both materials. This tetragonal average structure contains a substantial fraction of non-spinel octahedral Al atoms. It is argued that the presence of local structure is a general feature of γ-alumina, independent of precursor and synthesis conditions. The concentration of “non-spinel” Al atoms seems to correlate with surface properties, and increases with increasing pore size/surface area. This should have implications to the catalytic properties of porous γ-alumina. - Graphical abstract: Boehmite-derived and sol–gel synthesized porous γ-Al{sub 2}O{sub 3} possess identical structural properties, featuring a nm scale local structure and a tetragonal average structure. - Highlights: • Porous γ-Al{sub 2}O{sub 3} generally possesses a nm-scale local structure. • The tetragonal average structure contains a substantial fraction of “non-spinel” Al atoms. • The concentration of “non-spinel” Al atoms correlates with surface properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗