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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure and stability of alkali gallates structurally reminiscent of hollandite

Abstract Single crystals of CsGa 7 O 11 , RbGa 7 O 11 , and RbGa 4 In 5 O 14 were grown from alkali halide melts and their structures were characterized by single crystal and powder X‐ray diffraction. CsGa 7 O 11 and RbGa 7 O 11 adopt the same structure type, reminiscent of the hollandite structure type, as it contains nearly rectangular channels made up of two dimers of edge‐sharing GaO 6 octahedra, and two corner‐sharing octahedron/tetrahedron pairs. The structure of RbGa 4 In 5 O 14 is more complex and is comprised of indium octahedra, gallium trigonal bipyramids, and gallium tetrahedra, and contains similar sized tunnels as CsGa 7 O 11 and RbGa 7 O 11 . CsGa 7 O 11 and RbGa 4 In 5 O 14 were further characterized by TGA, ion exchange experiments, and DFT studies revealing that both structures are thermodynamically stable up to 850°C; however, CsGa 7 O 11 decomposes to GaO(OH) xH 2 O when heated in warm aqueous solutions. CsGa 7 O 11 undergoes ion exchange in both an aqueous solution of RbCl and a RbNO 3 melt, as predicted by DFT studies, where the ion exchange is more extensive in the RbNO 3 melt.

Juillerat, Christian A.↗
DOE OSTI2021

Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B

Toxin B (TcdB) is a primary cause of Clostridioides difficile infection (CDI). This toxin acts by glucosylating small GTPases in the Rho/Ras families, but the structural basis for TcdB recognition and selectivity of specific GTPase substrates remain unsolved. Here, we report the cocrystal structures of the glucosyltransferase domain (GTD) of two distinct TcdB variants in complex with human Cdc42 and R-Ras, respectively. These structures reveal a common structural mechanism by which TcdB recognizes Rho and R-Ras. Furthermore, we find selective clustering of adaptive residue changes in GTDs that determine their substrate preferences, which helps partition all known TcdB variants into two groups that display distinct specificities toward Rho or R-Ras. Mutations that selectively disrupt GTPases binding reduce the glucosyltransferase activity of the GTD and the toxicity of TcdB holotoxin. These findings establish the structural basis for TcdB recognition of small GTPases and reveal strategies for therapeutic interventions for CDI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Rational Selection of Transition-Metal Oxide Electrocatalysts from Structure Electronic Structure-Activity Relations: The Role of Defects, Strain, and Sub-Surface Layering

This BES research investigates the physicochemical properties of metal oxides and how they affect electrocatalytic functionalities. The goal is to develop a predictive framework for realizing top-performing electrocatalytic materials for energy-critical reactions. The hypothesis is that well-defined thin films allow detailed mapping of structural-activity relationships because flat surfaces are more straightforward to characterize. Furthermore, the well-defined nature of thin-film metal oxides allows precise tuning of structural and chemical variables for structure-activity-relationship mapping. The proposed research has two technical objectives. The first is to experimentally assess whether the binding energies of surface oxygen can serve as an activity descriptor for oxygen electrocatalysis on metal oxides and then how to control them by tuning the structure and chemical variables. The second is to find the rate-limiting process in oxygen electrocatalysis and other small-molecule reactions. Similar mechanistic insights have been developed on well-defined platinum surfaces but not yet on oxides. This research addresses this gap and uses electrochemistry and X-ray photoemission spectroscopy to study oxide surface chemistry. The obtained insights are collectively analyzed to reveal how the oxides’ structural and chemical variables affect kinetics and can be used to design more active electrocatalysts for energy-critical reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Nucleon off-shell structure and the free neutron valence structure from A=3 inclusive electron scattering measurements

Understanding the differences between the distribution of quarks bound in protons and neutrons is key for constraining the mechanisms of SU(6) spin-flavor symmetry breaking in Quantum Chromodynamics (QCD). While vast amounts of proton structure measurements were done, data on the structure of the neutron is much more spars as experiments typically extract the structure of neutrons from measurements of light atomic nuclei using model-dependent corrections for nuclear effects. Recently the MARATHON collaboration performed such an extraction by measuring inclusive deep-inelastic electron-scattering on helium-3 and tritium mirror nuclei where nuclear effects are expected to be similar and thus be suppressed in the helium-3 to tritium ratio. Here we evaluate the model dependence of this extraction by examining a wide range of models including the effect of using instant-form and light-cone nuclear wave functions and several different parameterizations of nucleon modification effects, including those with and without isospin dependence. We find that, while the data cannot differentiate among the different models of nuclear structure and nucleon modification, they consistently prefer a neutron-to-proton structure function ratio of at $x_B \rightarrow 1$ of $\sim 0.4$ with a typical uncertainty ($1\sigma$) of $\sim0.05$ and $\sim0.10$ for isospin-independent and isospin-dependent modification models, respectively. While strongly favoring SU(6) symmetry breaking models based on perturbative QCD and the Schwinger-Dyson equation calculation, the MARATHON data do not completely rule out the scalar di-quark models if an isospin-dependent modification exist.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Anisotropic Structural Collapse of Mg 3 Sb 2 and Mg 3 Bi 2 at High Pressure

Alloys between Mg 3 Sb 2 and Mg 3 Bi 2 have recently been shown to be exceptional thermoelectric materials due in part to their anomalously low thermal conductivity. In the present study, in situ high-pressure synchrotron X-ray diffraction was used to investigate the structure and bonding in Mg 3 Sb 2 and Mg 3 Bi 2 at pressures up to 50 GPa. Our results confirm prior predictions of isotropic in-plane and out-of-plane compressibility but reveal large disparities between the bond strength of the two distinct Mg sites. Using single-crystal diffraction, we show that the octahedral Mg–Sb bonds are significantly more compressible than the tetrahedral Mg–Sb bonds in Mg 3 Sb 2 , which lends support to prior arguments that the weaker octahedral Mg bonds are responsible for the anomalous thermal properties of Mg 3 Sb 2 and Mg 3 Bi 2 . Further, we report the discovery of a displacive and reversible phase transition in both Mg 3 Sb 2 and Mg 3 Bi 2 above 7.8 and 4.0 GPa, respectively. Furthermore, the transition to the high-pressure structure involves a highly anisotropic volume collapse, in which the out-of-plane axis compresses significantly more than the in-plane axes. Single-crystal diffraction at high pressure was used to solve the monoclinic high-pressure structure ( C 2/ m ), which is a distorted variant of the ambient-pressure structure containing four unique Mg coordination environments.

36 MATERIALS SCIENCE↗
DOE OSTI2021

X-ray Crystal Structure of Thorium Tetrahydroborate, Th(BH 4 ) 4 , and Computational Studies of An(BH 4 ) 4 (An = Th, U)

Here the crystal structure of Th(BH 4 ) 4 is described. Two of the four BH 4 – ions are terminal and tridentate (κ 3 ), whereas the other two bridge between neighboring Th IV centers in a κ 2 ,κ 2 (i.e., bis-bidentate) fashion. Thus, each thorium center is bound to six BH 4 – groups by 14 Th–H bonds. The six boron atoms describe a distorted octahedron in which the κ 3 -BH 4 – ions are mutually cis; the 14 ligating hydrogen atoms define a highly distorted bicapped hexagonal antiprism. The thorium centers are linked into a polymer consisting of interconnected helical chains wound about 4-fold screw axes. The structures of An(BH 4 ) 4 (An = Th, U) were also investigated by DFT. The geometries of [An(BH 4 ) 6 ] 2– , [An3(BH 4 ) 16 ] 4– , and [An 5 (BH 4 ) 26 ] 6– fragments of the polymeric structures were optimized at the B3LYP and/or PBE levels. Most calculated geometries are 14-coordinate and agree with the experimental structures, but isolated [Th(BH 4 ) 6 ] 2– units are predicted to feature 16-coordinate Th IV centers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Improved quasiparticle self-consistent electronic band structure and excitons in β – LiGaO 2

The band structure of β–LiGaO 2 is calculated using the quasiparticle self-consistent QSGWˆ method where the screened Coulomb interaction Wˆ is evaluated including electron-hole interaction ladder diagrams and G is the one-electron Green's function. Improved convergence compared to previous calculations leads to a significantly larger band gap of about 7.0 eV. However, exciton binding energies are found to be large and lead to an exciton gap of about 6.0 eV if also a zero-point-motion correction of about –0.4 eV is included. Furthermore, these results are in excellent agreement with recent experimental results on the onset of absorption. Besides the excitons observed thus far, the calculations indicate the existence of a Rydberg-like series of exciton excited states, which is however modified from the classical Wannier exciton model by the anisotropies of the material and the more complex mixing of Bloch states in the excitons resulting from the Bethe-Salpeter equation. The exciton fine structure and the exciton wave functions are visualized and analyzed in various ways.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Synthesis, structural characterization, and electronic structure of the novel Zintl phase Ba 2 ZnP 2

The novel Zintl phase dibarium zinc diphosphide (Ba 2 ZnP 2 ) was synthesized for the first time. This was accom­plished using the Pb flux technique, which allowed for the growth of crystals of adequate size for structural determination via single-crystal X-ray diffraction methods. The Ba 2 ZnP 2 com­pound was determined to crystallize in a body-centered ortho­rhom­bic space group, Ibam (No. 72). Formally, this crystallographic arrangement belongs to the K 2 SiP 2 structure type. Therefore, the structure can be best described as infinite [ZnP 2 ] 4– polyanionic chains with divalent Ba 2+ cations located between the chains. All valence electrons are partitioned, which conforms to the Zintl–Klemm concept and suggests that Ba 2 ZnP 2 is a valence-precise com­position. In conclusion, the electronic band structure of this new com­pound, com­puted with the aid of the TB–LMTO–ASA code, shows that Ba 2 ZnP 2 is an intrinsic semiconductor with a band gap of ca 0.6 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Interstitial Atoms and the Frustrated and Allowed Structural Transitions Principle: Tunability in the Electronic Structure of AuCu 3 ‐type Frameworks in Dy 4 T 1− x Ga 12 (T = Ag, Ir)

In this Article, we explore how the chemical pressure (CP) features of an intermetallic phase may provide opportunities to couple perturbations in electron count with the stabilization of the underlying geometrical structure. AuCu 3 ‐type LnGa 3 (Ln = lanthanide or group 3 metal) phases contain octahedral cavities of negative CP held open by overly compressed Ln–Ga interactions, leading to a series of transition metal‐stuffed derivatives. We present new additions to this family with the synthesis and crystal structures of Dy 4 T 1−x Ga 12 with (T, x) = (Ag, 0.29) and (Ir, 0.15), adopting Y 4 PdGa 12 ‐type superstructures of the AuCu 3 ‐type. density functional Ttheory (DFT)‐CP calculations, when adjusted to avoid dipolar CP features, affirm that T atom incorporation provides a mechanism for the relief of packing tensions, while electronic density of states distributions illustrate that the T atoms serve largely as electron or hole donors to the band structure, as needed for them to attain d 10 configurations. The maximum obtainable value for x may be limited by a mismatch between the Fermi energy and pseudogap, in line with the balance of factors envisioned by the frustrated and allowed structural transitions principle. Furthermore, trends in resistivity measurements on T = Ir, Pd, and Ag compounds are interpretable in terms of the varying degrees of disorder arising from x < 1.0.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Heterometallic UO 2 2+ /Ag + Complexes: Structural Design and Luminescence Properties

Reported here are the synthesis, structural characterization, and luminescence properties of 11 novel UO 2 2+ /Ag + heterometallic complexes. Halogenated benzoic acids (2,6-dihalobenzoic acid (halo = F, Br), 3,5-dichlorobenzoic acid, and 3-halobenzoic acid (halo = Br, I)) and N-donor polycyclic ligands (2,2′-bipyridine, 2,2’;6′,2″-terpyridine, 1,10-phenanthroline, 2,2′-bipyrimidine) were employed to synthesize a set of compounds and induce structural diversity. The primary mode of coordination with the uranyl cation is hexagonal bipyramidal monomeric units with three halobenzoate ligands in the equatorial plane, though 1-D chains with pentagonal bipyramidal uranyl centers also form. The Ag + cations coordinate preferentially to the N-donor ligands and serve as counter-cations for the anionic uranyl motifs. The soft ligand character of the N-donor molecules is found to be a requirement for the inclusion of the Ag + cation into the structures. Anionic uranyl units and cationic silver units assemble via noncovalent interactions between π systems on adjacent rings and between halogens (when Br and I are present). Solid-state emission spectra display the usual uranyl band with superimposed vibronic fine structure, except for that of compound 1 , which shows emission from the 2,2′-bipyridine center. This family of compounds represents a substantial contribution to the already rich library of UO 2 2+ /Ag + compounds, and the synthetic parameters discussed within reveal a platform for the design of new heterometallic uranyl-containing materials.

anions↗
DOE OSTI2022

Structural Complexity and Tuned Thermoelectric Properties of a Polymorph of the Zintl Phase Ca 2 CdSb 2 with a Non-centrosymmetric Monoclinic Structure

The Zintl phase Ca 2 CdSb 2 was found to be dimorphic. Besides the orthorhombic Ca 2 CdSb 2 (-o), here we report on the synthesis, the structural characterization, and the thermoelectric transport properties of its monoclinic form, Ca 2 CdSb 2 (-m), and its Lu-doped variant Ca 2–x Lu x CdSb 2 (x ≈ 0.02). The monoclinic structure exhibits complex structural characteristics and constitutes a new structure type with the non-centrosymmetric space group Cm (Z = 30). The electrical resistivity ρ(T) measured on single crystals of both phases portrays a transition from a semiconductor to a degenerate p-type semiconductor upon doping with Lu and with an attendant change in the Hall carrier concentration nH from 7.15 × 10 18 to 2.30 × 10 19 cm –3 at 300 K. The Seebeck coefficient S(T) of both phases are comparable and indicate a hole-dominated carrier transport mechanism with magnitudes of 133 and 116 μV/K at 600 K for Ca 2 CdSb 2 (-m) and Ca 2–x Lu x CdSb 2 , respectively. The convoluted atomic bonding with an attendant large unit cell volume of ~4365 Å 3 drives a putative low thermal conductivity in these materials resulting in a power factor PF of 1.63 μW/cm K 2 and an estimated thermoelectric figure of merit zT of ~0.5 for Ca 2–x Lu x CdSb 2 at 600 K. Furthermore, differential scanning calorimetry results reveal the stability of these phases up to about 960 K, making them candidates for moderate temperature thermoelectric materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Three-dimensional atomic packing in amorphous solids with liquid-like structure

Liquids and solids are two fundamental states of matter. However, our understanding of their three-dimensional atomic structure is mostly based on physical models. Here we use atomic electron tomography to experimentally determine the three-dimensional atomic positions of monatomic amorphous solids, namely a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into pentagonal bipyramid networks with medium-range order. Molecular dynamics simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic metallic liquids, which rapidly grow in size and form more icosahedra during the quench from the liquid to the glass state. Furthermore, these results expand our understanding of the atomic structures of amorphous solids and will encourage future studies on amorphous–crystalline phase and glass transitions in non-crystalline materials with three-dimensional atomic resolution.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Evolution of structure and transport properties of the Ba 8 Cu 16 P 30 clathrate-I framework with the introduction of Ga

Two type-I clathrates were synthesized by introducing Ga into the framework of the Ba 8 Cu 16 P 30 type-I clathrate. The introduction of minute amounts of Ga, 1.9% Ga/M total (where M total = Cu + Ga), resulted in the disturbance of the completely ordered Pbcn superstructure of Ba 8 Cu 16 P 30 . Ba 8 Cu 15.43(2) Ga 0.3 P 30.26(3) crystallizes in a partially ordered orthorhombic Pmna clathrate-I superstructure with five out of 15 framework sites being jointly occupied by metal+phosphorus. Increasing the Ga content resulted in all framework sites being occupied by metal + phosphorus in the archetype cubic Pm n clathrate-I crystal structure of Ba 8 Cu 14.5(3) Ga 1.3 P 30.2(4) with 8.2% Ga/M total . A combination of energy dispersive x-ray spectroscopy, inductively coupled plasma mass spectroscopy, and single crystal x-ray diffraction was used to determine the structures alongside the compositions. The positional disorder was verified by 31 P solid state NMR spectroscopy. Characterization of the transport properties indicated that the Ga-substituted samples exhibit higher Seebeck coefficients and electrical resistivities compared to its pristine counterpart, in line with the expected reduction of the hole concentration due to Ga/Cu substitution. Moderate improvements in the thermoelectric power factor and overall figure-of-merit were observed for samples with 6.9% and 3.8% Ga/M total as compared to those for the pristine Ba 8 Cu 16 P 30 clathrate. Finally, band structure calculations shed light on how Ga substitution affects the electronic structure and thermoelectric properties of studied clathrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗