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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 OSTI2023

Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain

Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Synthesis and Crystal Structure of the Zintl Phases Na2CaCdSb2, Na2SrCdSb2 and Na2EuCdSb2

This work details the synthesis and the crystal structures of the quaternary Zintl phases Na2CaCdSb2, Na2SrCdSb2 and Na2EuCdSb2. They are isostructural and their noncentrosymmetric structure is with the space group Pmc21 (Pearson code oP12). All structural work is carried out via single-crystal X-ray diffraction methods. The structure features [CdSb2]4– layers of corner-shared CdSb4 tetrahedra, which are stacked along the b-crystallographic axis and are separated by cations. The results from the structure refinements suggest that in addition to full cation ordering, which is typical for this structure, there also exists a possibility for an accommodation of a small degree of cation disorder.

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

Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D – D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D – D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.

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

Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis

We report multicopper oxidases (MCOs) represent a diverse family of enzymes that catalyze the oxidation of either an organic or a metal substrate with concomitant reduction of dioxygen to water. These enzymes contain variable numbers of cupredoxin domains, two, three or six per subunit, and rely on four copper ions, a single type I copper and three additional copper ions organized in a trinuclear cluster (TNC), with one type II and two type III copper ions, to catalyze the reaction. Here, two crystal structures and the enzymatic characterization of Marinithermus hydrothermalis MCO, a two-domain enzyme, are reported. This enzyme decolorizes Congo Red dye at 70°C in the presence of high halide concentrations and may therefore be useful in the detoxification of industrial waste that contains dyes. In two distinct crystal structures, MhMCO forms the trimers seen in other two-domain MCOs, but differs from these enzymes in that four trimers interact to create a dodecamer. This dodecamer of MhMCO forms a closed ball-like structure and has implications for the sequestration of bound divalent metal ions as well as substrate accessibility. In each subunit of the dodecameric structures, a Trp residue, Trp351, located between the type I and TNC sites exists in two distinct conformations, consistent with a potential role in facilitating electron transfer in the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Synthesis and Crystal Structure of the Zintl Phases NaSrSb, NaBaSb and NaEuSb

This work details the synthesis and the crystal structures of the ternary compounds NaSrSb, NaBaSb and NaEuSb. They are isostructural and adopt the hexagonal ZrNiAl-type structure (space group P6¯2m; Pearson code hP9). The structure determination in all three cases was performed using single-crystal X-ray diffraction methods. The structure features isolated Sb3– anions arranged in layers stacked along the crystallographic c-axis. In the interstices, alkali and alkaline-earth metal cations are found in tetrahedral and square pyramidal coordination environments, respectively. The formal partitioning of the valence electrons adheres to the valence rules, i.e., Na+Sr2+Sb3–, Na+Ba2+Sb3– and Na+Eu2+Sb3– can be considered as Zintl phases with intrinsic semiconductor behavior. Electronic band structure calculations conducted for NaBaSb are consistent with this notion and show a direct gap of approx. 0.9 eV. Additionally, the calculations hint at possible inverted Dirac cones, a feature that is reminiscent of topological quantum materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Chemistry↗
DOE OSTI2021

Coexisting Multiple Martensites in Ni 57-x Mn 21+x Ga 22 Ferromagnetic Shape Memory Alloys: Crystal Structure and Phase Transition

A comprehensive study of the crystal structure and phase transition as a function of temperature and composition in Ni 57–x Mn 21+x Ga 22 (x = 0, 2, 4, 5.5, 7, 8) (at. %) magnetic shape memory alloys was performed by a temperature-dependent synchrotron X-ray diffraction technique and transmission electron microscopy. A phase diagram of this Ni 57–x Mn 21+x Ga 22 alloy system was constructed. The transition between coexisting multiple martensites with monoclinic and tetragonal structures during cooling was observed in the Ni 51.5 Mn 26.5 Ga 22 (x = 5.5) alloy, and it was found that 5M + 7M multiple martensites coexist from 300 K to 160 K and that 5M + 7M + NM multiple martensites coexist between 150 K and 100 K. The magnetic-field-induced transformation from 7M martensite to NM martensite at 140 K where 5M + 7M + NM multiple martensites coexist before applying the magnetic field was observed by in situ neutron diffraction experiments. The present study is instructive for understanding the phase transition between coexisting multiple martensites under external fields and may shed light on the design of novel functional properties based on such phase transitions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Crystal structure of silver pentazolates AgN 5 and AgN 6

Silver pentazolate, a high energy density compound containing the cyclo-N 5 – anion, has recently been synthesized under ambient conditions. However, due to high sensitivity to irradiation, its crystal structure has not been determined. In this work, silver–nitrogen crystalline compounds under ambient conditions and at high pressures, up to 100 GPa, are predicted and characterized by performing first-principles evolutionary crystal structure searching with variable stoichiometry. It is found that newly discovered AgN 5 and AgN 6 are the only thermodynamically stable silver–nitrogen compounds at pressures between 42 and 80 GPa. In contrast to AgN 5 , the pentazolate AgN 6 compound contains N 2 diatomic molecules in addition to cyclo-N 5 – . These AgN 5 and AgN 6 crystals are metastable under ambient conditions with positive formation enthalpies of 54.95 kJ mol –1 and 46.24 kJ mol –1 , respectively. Here, the underlying cause of the stability of cyclo-N 5 – silver pentazolates is the enhanced aromaticity enabled by the charge transfer from silver atoms to nitrogen rings. To aid in the experimental identification of these materials, calculated Raman spectra are reported at ambient pressure: the frequencies of N 5 – vibrational modes of AgN 5 are in good agreement with those measured in the experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

LiMo 8 O 10 : Polar Crystal Structure with Infinite Edge-Sharing Molybdenum Octahedra

Here, polycrystalline LiMo 8 O 10 was prepared in a sealed Mo crucible at 1380 °C for 48 h using the conventional high-temperature solid-state method. The polar tetragonal crystal structure (space group I4 1 md) is confirmed based on the Rietveld refinement of powder neutron diffraction and 7 Li/ 6 Li solid-state NMR. The crystal structure features infinite chains of Mo 4 O 5 (i.e., Mo 2 Mo 4/2 O 6/2 O 6/3 ) as a repeat unit containing edge-sharing Mo 6 octahedra with strong Mo–Mo metal bonding along the chain. X-ray absorption near-edge spectroscopy of the Mo-L 3 edge is consistent with the formal Mo valence/configuration. Magnetic measurements reveal that LiMo 8 O 10 is paramagnetic down to 1.8 K. Temperature-dependent resistivity [ρ(T)] measurement indicates a semiconducting behavior that can be fitted with Mott’s variable range hopping conduction mechanism in the temperature range of 215 and 45 K. The ρ(T) curve exhibits an exponential increase below 5 K with a large ratio of ρ 1.8 /ρ 300 = 435. LiMo 8 O 10 shows a negative field-dependent magnetoresistance between 2 and 25 K. Heat capacity measurement fitted with the modified Debye model yields the Debye temperature of 365 K.

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

Crystal structure of calcium-ferrite type NaAlSiO4 up to 45 GPa

Abstract Alkali-rich aluminous high-pressure phases including calcium-ferrite (CF) type NaAlSiO4 are thought to constitute ~20% by volume of subducted mid-ocean ridge basalt (MORB) under lower mantle conditions. As a potentially significant host for incompatible elements in the deep mantle, knowledge of the crystal structure and physical properties of CF-type phases is therefore important to understanding the crystal chemistry of alkali storage and recycling in the Earth’s mantle. We determined the evolution of the crystal structure of pure CF-NaAlSiO4 and Fe-bearing CF-NaAlSiO4 at pressures up to ~45 GPa using synchrotron-based, single-crystal X-ray diffraction. Using the high-pressure lattice parameters, we also determined a third-order Birch-Murnaghan equation of state, with V0 = 241.6(1) Å3, KT0 = 220(4) GPa, and KT0′ = 2.6(3) for Fe-free CF, and V0 = 244.2(2) Å3, KT0 = 211(6) GPa, and KT0′ = 2.6(3) for Fe-bearing CF. The addition of Fe into CF-NaAlSiO4 resulted in a 10 ± 5% decrease in the stiffest direction of linear compressibility along the c-axis, leading to stronger elastic anisotropy compared with the Fe-free CF phase. The NaO8 polyhedra volume is 2.6 times larger and about 60% more compressible than the octahedral (Al,Si)O6 sites, with K0NaO8 = 127 GPa and K0(Al,Si)O6 ~304 GPa. Raman spectra of the pure CF-type NaAlSiO4 sample shows that the pressure coefficient of the mean vibrational mode, 1.60(7) cm–1/GPa, is slightly higher than 1.36(6) cm−1/GPa obtained for the Fe-bearing CF-NaAlSiO4 sample. The ability of CF-type phases to contain incompatible elements such as Na beyond the stability field of jadeite requires larger and less-compressible NaO8 polyhedra. Detailed high-pressure crystallographic information for the CF phases provides knowledge on how large alkali metals are hosted in alumina framework structures with stability well into the lowermost mantle.

Geochemistry & Geophysics↗
DOE OSTI2026

AI-assisted rapid crystal structure generation towards a target local environment

In material design, traditional crystal structure prediction approaches are expensive as they require extensive structural sampling through expensive energy minimization methods. Emerging artificial intelligence (AI) generative models have shown great promise in rapidly generating realistic crystals, but they typically handle only a few tens of atoms per unit cell. To overcome this limitation, we introduce a symmetry-informed approach, the Local Environment Geometry-Oriented Crystal Generator (LEGO-xtal). Our method generates initial structures using AI models trained on an augmented dataset, and then optimizes them using structure descriptors rather than energy-based optimization. We demonstrate its effectiveness by expanding from 25 known low-energy sp2 carbon allotropes to over 1700, all within 0.5 eV/atom of the ground-state energy of graphite. This framework offers a generalizable strategy for the targeted design of materials with modular building blocks, such as metal-organic frameworks and battery materials.

Ridwan, Osman Goni [University of North Carolina a↗
DOE OSTI2026

Crystal structure, compressibility, and thermal expansion of uranium mononitride

The behavior of the uranium mononitride (UN) crystal structure at nonambient conditions is disputed, with studies proposing various mutually exclusive distortions and transformations of the conventional face-centered-cubic structure at extreme temperatures and pressures. Here, in this study, we investigated the UN lattice with diamond anvil cell x-ray diffraction experiments at pressures up to 92 GPa and with density functional theory calculations at temperatures up to 1000 K and pressures up to 90 GPa. We determined that while the UN structure is nearly cubic at ambient conditions, its lattice angle (𝛼) varies as a function of pressure and temperature, meaning its structure can be more precisely described as face-centered-rhombohedral with 𝛼 ≈ 90∘. Over the range of conditions we investigated, UN exhibits a single, isostructural phase transition at ≈ 35 GPa, where 𝛼 collapses to ≈ 86°. Measurements and calculations agree that the compressibility of UN increases significantly beyond this transition, with the bulk modulus falling from ≈ 200 GPa in the low-pressure phase to 121 ± 3 GPa (according to calculations) or 58 ± 4 GPa (according to measurements) in the high-pressure phase. Our measurements also allowed us to constrain the bulk modulus of 𝛼−U 2 ⁢N 3 to 240 ± 10 GPa.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Crystal structure and polymorphic forms of auranofin revisited

Auranofin, initially developed as a treatment for rheumatoid arthritis, is currently under extensive investigation as a potential drug for various conditions, including cancer, bacterial infections, and parasitic infections. The compound is a known inhibitor of thioredoxin reductase (TXNRD1) and related selenoproteins. Although preliminary studies on the auranofin crystal polymorphism exist, and a low-quality crystal structure has been reported, a comprehensive crystallographic characterization remains unexplored. Utilizing X-ray crystallography techniques, we conducted detailed structural analysis of auranofin and compared our findings with related organogold compounds. Implementation of Hirshfeld atom refinement (HAR) enabled a more accurate hydrogen atom positioning in the structure. The crystal packing reveals a layered arrangement stabilised by numerous weak hydrogen bonds and dispersive interactions. Notably, our attempts to reproduce the previously reported polymorphic form of auranofin, purportedly more water-soluble, were unsuccessful despite following published protocols. To our knowledge, this is the first study describing a “disappearing polymorph” phenomenon of any pharmaceutically relevant transition metal coordination compound. Our findings may have significant implications for medicinal chemistry and pharmacology of coordination complexes, suggesting the need for systematic revision of historical crystallographic data in this field.

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

The role of defect charge, crystal chemistry, and crystal structure on positron lifetimes of vacancies in oxides

Density functional theory based positron lifetime (PL) calculations for cation and oxygen monovacancies in a range of oxides—hematite, magnetite, hercynite, and alumina—have been conducted to compare the impact of defect chemistry and crystal structure on the predicted lifetimes. The role of defect charge state has also been examined. A comparison across the same type of crystalline structure but different composition shows that oxygen vacancies only induce a slight increase in the positron-electron overlap and thus barely modify the PL as compared to the bulk. A much more substantial increase of PL is observed for cation monovacancies, regardless of crystal structure or the elemental nature of the vacancy, which we ascribe to an enhanced localization of charge density around the vacant site. The structural and compositional richness of the oxide leads to longer defect PLs, with defected hercynite exhibiting the longest PLs. The charge state of cation monovacancies modifies only by a small percentage the positron localization, relegating to secondary importance the metal defect's oxidation state in modifying the lifetime of positrons within vacancy traps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element

The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.

59 BASIC BIOLOGICAL SCIENCES↗