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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Crystal structures of LaO{sub 1−x}F{sub x}BiS{sub 2} (x∼0.23, 0.46): Effect of F doping on distortion of Bi–S plane

The crystal structures of superconducting LaO{sub 1−x}F{sub x}BiS{sub 2} (x∼0.23, 0.46) were determined by single-crystal X-ray diffraction analysis. Their space group was P4/nmm. Distortion of the Bi–S plane changed when the F content was increased from 0.23 to 0.46, and a nearly flat Bi–S plane was formed at x∼0.46. Computational calculations supported this effect of F doping on distortion of Bi–S plane. LaO{sub 1−x}F{sub x}BiS{sub 2} with higher F contents were computationally predicted to be thermodynamically more unstable under ambient pressure. We discussed the bonding, conductivities, and synthetic routes of LaO{sub 1−x}F{sub x}BiS{sub 2}. - Graphical abstract: Distortion of the Bi–S plane in LaO{sub 1−x}F{sub x}BiS{sub 2} changed when the F content was increased from 0.23 to 0.46, and a nearly flat Bi–S plane was formed at x∼0.46 with the appearance of superconductivity. - Highlights: • Crystal structure of LaO{sub 1−x}F{sub x}BiS{sub 2} was determined by single-crystal XRD. • Doping amount of F changes the distortion of the Bi–S plane. • Nearly flat Bi–S planes were found in superconductive LaO{sub 1−x}F{sub x}BiS{sub 2} (x∼0.46). • LaO{sub 1−x}F{sub x}BiS{sub 2} with higher F contents was thermodynamically more unstable. • Bonding, superconductivities, and synthetic routes of LaO{sub 1−x}F{sub x}BiS{sub 2} were discussed.

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

Crystal structure of a plectonemic RNA supercoil

Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid superstructures. Crystal structures of DNA coiled coils indicate that their geometries can vary according to sequence and/or the presence of stabilizers such as proteins or small molecules. However, such superstructures have not been revealed for RNA. Here we report the crystal structure of an RNA supercoil, which displays one level higher molecular organization than previously reported structures of DNA coiled coils. In the presence of an RNA-binding protein, two interlocking RNA coiled coils of double-stranded RNA, a 'coil of coiled coils', form a plectonemic supercoil. Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Crystal structure details of La- and Bi-substituted hydroxyapatites: Evidence for LaO{sup +} and BiO{sup +} with a very short metal–oxygen bond

Crystal structures of substituted apatites with general formula Ca{sub 10−x}M{sub x}(PO{sub 4}){sub 6}(OH{sub 1−δ}){sub 2−x}O{sub x}, where M=La, Bi, 0≤x<2, were refined using high-resolution X-ray powder diffraction patterns. Individual positions for Ca{sup 2+} and M{sup 3+}-ions localized near Ca2-site were determined. The M{sup 3+}-ion was found shifted toward the hexagonal channel center with respect to the Ca{sup 2+}-ion, forming very short bond with the intrachannel O{sup 2−}, while leaving considerably longer distances to other oxygen atoms, which suggested the existence of a MO{sup +} ion. Distinct bands of stretching M–O modes were observed in the Raman and FT-IR spectra of the compounds. The bond lengths for BiO{sup +} and LaO{sup +} were estimated to be 2.05(1) and 2.09(1) Å correspondingly. The latter was almost 0.3 Å lower than the shortest La–O bond in La{sub 2}O{sub 3}. The realization of such a strong lanthanide–oxygen bond in a crystal lattice could provide a very high axial ligand field and might be implemented to develop high-energy-barrier single-molecule magnets as well as to tune properties of lanthanide-based luminophores. - Graphical abstract: A fragment of the La-for-Ca substituted apatite crystal structure focusing on the La–O bond. - Highlights: • Individual positions in the apatite crystal lattice for a doping atom (La, Bi) and Ca. • The doping atom shifts toward the center of the hexagonal channel. • BiO{sup +} and LaO{sup +} with estimated short bond lengths of 2.05 and 2.09 Å respectively.

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

A High-Resolution Crystal Structure of a Psychrohalophilic α–Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface

Bacterial α–carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO 2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α–CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an “in-gel” carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highly conserved “knot-topology” that is characteristic of α–CA’s. Similar to other bacterial α–CA’s, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α–CA’s characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α–CA’s.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Synthesis and single-crystal structure determination of the zinc nitride halides Zn{sub 2}NX (X=Cl, Br, I)

A series of zinc nitride halides, Zn{sub 2}NX (X=Cl, Br, I), has been synthesized from solid–liquid reactions of zinc nitride with the respective zinc halides under vacuum, and their crystal structures were determined using single-crystal and powder X-ray diffraction. While Zn{sub 2}NCl and Zn{sub 2}NBr crystallize in the acentric orthorhombic space group Pna2{sub 1}, Zn{sub 2}NI adopts the centrosymmetric space group Pnma; Zn{sub 2}NCl and Zn{sub 2}NBr can be considered to belong to the anti-β-NaFeO{sub 2} type, and Zn{sub 2}NI is closely related. Each N{sup 3−} is tetrahedrally coordinated by zinc atoms, and the X{sup −} anions are located in the vacancies of the framework formed by corner-sharing [NZn{sub 4}] tetrahedra. According to TGA/DTA analyses, the Zn{sub 2}NX compounds exhibit good thermal stability. The electronic structure has been analyzed by employing density-functional theory and the HSE06 hybrid functional. - Graphical abstract: Zn{sub 2}NCl, Zn{sub 2}NBr, and Zn{sub 2}NI have been synthesized, and their crystal structures (Cl and Br phases: Pna2{sub 1}; I phase: Pnma) have been determined from XRD; the direct band gap of Zn{sub 2}NCl is theoretically (HSE06 hybrid functional) predicted as 3.7 eV. - Highlights: • Zn{sub 2}NCl, Zn{sub 2}NBr, and Zn{sub 2}NI have been synthesized from solid–liquid reactions. • The crystal structures of Zn{sub 2}NCl, Zn{sub 2}NBr, and Zn{sub 2}NI have been determined from single-crystal X-ray diffraction. • Zn{sub 2}NCl and Zn{sub 2}NBr crystallize in the acentric space group Pna2{sub 1} whereas Zn{sub 2}NI adopts the centrosymmetric space group Pnma. • Zn{sub 2}NCl and Zn{sub 2}NBr are stable up to 750 °C whereas Zn{sub 2}NI decays at 600 °C already. • The direct band gap of Zn{sub 2}NCl is theoretically predicted as 3.7 eV using the HSE06 hybrid functional.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Crystal Structures of the Kainate Receptor GluR5 Ligand Binding Core Dimer with Novel GluR5-Selective Antagonists

Glutamate receptor (GluR) ion channels mediate fast synaptic transmission in the mammalian CNS. Numerous crystallographic studies, the majority on the GluR2-subtype AMPA receptor, have revealed the structural basis for binding of subtype-specific agonists. In contrast, because there are far fewer antagonist-bound structures, the mechanisms for antagonist binding are much less well understood, particularly for kainate receptors that exist as multiple subtypes with a distinct biology encoded by the GluR5-7, KA1, and KA2 genes. We describe here high-resolution crystal structures for the GluR5 ligand-binding core complex with UBP302 and UBP310, novel GluR5-selective antagonists. The crystal structures reveal the structural basis for the high selectivity for GluR5 observed in radiolabel displacement assays for the isolated ligand binding cores of the GluR2, GluR5, and GluR6 subunits and during inhibition of glutamate-activated currents in studies on full-length ion channels. The antagonists bind via a novel mechanism and do not form direct contacts with the E723 side chain as occurs in all previously solved AMPA and kainate receptor agonist and antagonist complexes. This results from a hyperextension of the ligand binding core compared with previously solved structures. As a result, in dimer assemblies, there is a 22 {angstrom} extension of the ion channel linkers in the transition from antagonist- to glutamate-bound forms. This large conformational change is substantially different from that described for AMPA receptors, was not possible to predict from previous work, and suggests that glutamate receptors are capable of much larger movements than previously thought.

36 MATERIALS SCIENCE↗
NASA NTRS2003

Structural Basis for Flip-Flop Action of Thiamin-Dependent Enzymes Revealed by Crystal Structure of Human Pyruvate Dehydrogenase

The biologically active derivative of vitamin B1; thiamin pyrophosphate; is used as cofactor by many enzymes that perform a wide range of catalytic functions in the pathways of energy production. In alpha2beta2-heterotetrameric human pyruvate dehydrogenase, the first catalytic component enzyme of human pyruvate dehydrogenase complex, this cofactor is used to cleave the C(sup alpha)-C(=0) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase, the second catalytic component of the complex. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites have puzzled researchers from earlier functional studies of this enzyme. In order to gain insight into the mechanism of action of this enzyme, we determined the crystal structure of the holoform of human pyruvate dehydrogenase at 1.958, resolution. We propose a kinetic model for the flip-flop action of this enzyme through the concerted approx. 2A, shuttle-like motion of the heterodimers. The similarity of thiamin pyrophosphate binding in human pyruvate dehydrogenase and other functionally related enzymes suggests this newly defined mechanism of shuttle-like motion of domains to be common for the family of thiamin pyrophosphate-dependent enzymes.

Ciszak, Ewa↗
DOE OSTI2016

2.4 Å resolution crystal structure of human TRAP1 NM , the Hsp90 paralog in the mitochondrial matrix

TRAP1 is an organelle-specific Hsp90 paralog that is essential for neoplastic growth. As a member of the Hsp90 family, TRAP1 is presumed to be a general chaperone facilitating the late-stage folding of Hsp90 client proteins in the mitochondrial matrix. Interestingly, TRAP1 cannot replace cytosolic Hsp90 in protein folding, and none of the known Hsp90 co-chaperones are found in mitochondria. Thus, the three-dimensional structure of TRAP1 must feature regulatory elements that are essential to the ATPase activity and chaperone function of TRAP1. Here, the crystal structure of a human TRAP1 NM dimer is presented, featuring an intact N-domain and M-domain structure, bound to adenosine 5'-β,γ-imidotriphosphate (ADPNP). The crystal structure together with epitope-mapping results shows that the TRAP1 M-domain loop 1 contacts the neighboring subunit and forms a previously unobserved third dimer interface that mediates the specific interaction with mitochondrial Hsp70.

36 MATERIALS SCIENCE↗
DOE OSTI2010

The Crystal Structure of Coxsackievirus A21 and Its Interaction with ICAM-1

CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 {angstrom} resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 {angstrom} resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1{sup Kilifi}. The cryo-EM map was fitted with the crystal structures of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Ternary mixed-anion semiconductors with tunable band gaps from machine-learning and crystal structure prediction

In this paper, we report the computational investigation of a series of ternary $X_4Y_2Z$ and $X_5Y_2Z_2$ compounds with $X$ =Mg, Ca, Sr, Ba; $Y$ =P, As, Sb, Bi; and $Z$ =S, Se, Te. The compositions for these materials were predicted through a search guided by machine learning, while the structures were resolved using the minima hopping crystal structure prediction method. Based on ab initio calculations, we predict that many of these phases are thermodynamically stable. In particular, 21 of the $X_4Y_2Z$ compounds crystallize in a tetragonal structure with $I\bar{4}2d$ symmetry, and exhibit band gaps in the range of 0.8 and 1.8 eV, well suited for various energy applications. We show that several candidates (in particular $X_4Y_2$ Te and $X_4\mathrm{Sb_2Se}$) exhibit good photo absorption in the visible range, while others (e.g., $\mathrm{Ba_4Sb_2Se}$) show excellent thermoelectric performance due to high power factors and extremely low lattice thermal conductivities.

36 MATERIALS SCIENCE↗
DOE OSTI2011

An Insight into the Interaction Mode Between CheB and Chemoreceptor from Two Crystal Structures of CheB Methylesterase Catalytic Domain

We have determined 2.2 {angstrom} resolution crystal structure of Thermotoga maritima CheB methylesterase domain to provide insight into the interaction mode between CheB and chemoreceptors. T. maritima CheB methylesterase domain has identical topology of a modified doubly-wound {alpha}/{beta} fold that was observed from the previously reported Salmonella typhimurium counterpart, but the analysis of the electrostatic potential surface near the catalytic triad indicated considerable charge distribution difference. As the CheB demethylation consensus sites of the chemoreceptors, the CheB substrate, are not uniquely conserved between T. maritima and S. typhimurium, such surfaces with differing electrostatic properties may reflect CheB regions that mediate protein-protein interaction. Via the computational docking of the two T. maritima and S. typhimurium CheB structures to the respective T. maritima and Escherichia coli chemoreceptors, we propose a CheB:chemoreceptor interaction mode.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum

Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1 {angstrom}, respectively. The apoenzyme crystallized in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with two molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4{sub 3} with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan

Syndesmos, nucleoside diphosphate linked moiety X (nudix)-type motif 16-like 1 (Nudt16l1), is evolutionarily divergent from the Nudt16 family. Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain (Syn4{sup cyto}) in focal contacts, interacts with various cell adhesion adaptor proteins to control cell signaling. We determined the X-ray crystal structure of syndesmos; it is composed of seven α-helices and seven β-strands. Although syndesmos has a molecular topology similar to that of nudix hydrolase proteins, the structure of the nudix motif differs from that of X29. The dimeric interface of syndesmos is composed of α-helix 4, 7 and β-strand 2, 7, which primarily form hydrophobic interactions. The binding interaction between syndesmos and syn4{sup cyto} was characterized as a low-affinity interaction (K{sub d} = 62 μM) by surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR). The NMR resonances of Lys (177, 178, 179), Gly182, and Ser183 in the C1 region and Lys193 and Lys194 in the V region of syndecan-4 are perturbed upon syndesmos binding. Our results provide structural insight into the molecular function of syndesmos in the regulation of cell signaling via binding to syndecan-4. - Highlights: • Crystal structure of syndesmos has been determined as a dimer at 2.01 Å resolution. • The molecular topology of syndesmos resembles that of the Nudix hydrolase protein. • The structure of the Nudix motif of syndesmos is quite different from that of X29. • Syndesmos binds cytoplasmic domain of syndecan-4 proteoglycan with low affinity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

A small-box approach to the local crystal structure of Y 3 NbO 7

The local crystal structure of Y 3 NbO 7 was probed using neutron total scattering. Five different structural models were fit to the experimental pair distribution function of this material up to 15 Å. Fits of defect fluorite (Fm$\overline{3}$m), pyrochlore (Fd$\overline{3}$m), and orthorhombic C weberite models (C222 1 ) were attempted based on prior structural investigations of Y 3 NbO 7 and related fluorite-based materials. Orthorhombic P weberite (P222 1 ) and monoclinic weberite models (P112 1 ) were derived via symmetry reduction of the orthorhombic C weberite structure. All models except monoclinic weberite failed to reproduce the experimental pair distribution function. Misfits were clearly visible for peaks arising from atom pairs within the first coordination shell (defect fluorite and pyrochlore) and beyond (orthorhombic C and P weberite). By contrast, monoclinic weberite (γ ≈ 91.8°) provided an excellent fit, with no major misfits observed. This unit cell features distorted YO 8 dodecahedra, YO 7 monocapped octahedra, and NbO 6 octahedra as building blocks. Comparison between the topologies of the cationic and anionic substructures in monoclinic weberite and its parent orthorhombic C structure revealed displacements of the metal atoms along the [100] direction and a less compact spatial distribution of oxygen atoms along the a axis. In conclusion, the monoclinic weberite model presented herein may serve as a starting point to revisit structural modeling of fluorite-based materials with challenging local structures.

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

Effect of the Crystal Structure on the Electrical Properties of Thin-Film PZT Structures

A new method of two-stage crystallization of lead zirconate–titanate (PZT) films using a seed sublayer with a low excess lead content has been proposed and realized. A seed layer with a strong texture of perovskite Pe(111) grains is formed from a solution with a lead excess of 0–5 wt %; the fast growth of the grains is provided by the deposition of the main film from a solution with high lead content. As a result, a strong Pe(111) texture with complete suppression of the Pe(100) orientation forms. An analysis of current–voltage dependences of the transient currents and the distributions of the local conductivity measured by the contact AFM method reveals two various mechanisms of current percolation that are determined by traps in the bulk and at the perovskite grain interfaces.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Synthesis and crystal structure of iron zeolitic frameworks

Iron-based crystal structures including FeO.sub.4 tetrahedrally coordinated in three dimensions in a framework analogous to a zeolite. The structures having the general formula A.sub.yB.sub.8Fe.sub.12O.sub.24(O/OH).sub.6.xH.sub.2O in which A is Na, K, Cs, Rb or a combination thereof and B is an alkaline earth element or a combination of alkaline earth elements.

36 MATERIALS SCIENCE↗