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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Using Complementary Methods of Synchrotron Radiation Powder Diffraction and Pair Distribution Function to Refine Crystal Structures with High Quality Parameters—A Review

Determination of the atomic-scale structures of certain fine-grained minerals using single-crystal X-ray diffraction (XRD) has been challenging because they commonly occur as submicron and nanocrystals in the geological environment. Synchrotron powder diffraction and scattering techniques are useful complementary methods for studying this type of minerals. In this review, we discussed three example studies investigated by combined methods of synchrotron radiation XRD and pair distribution function (PDF) techniques: (1) low-temperature cristobalite; (2) kaolinite; and (3) vernadite. Powder XRD is useful to determine the average structure including unit-cell parameters, fractional atomic coordinates, occupancies and isotropic atomic displacement parameters. X-ray/Neutron PDF methods are sensitive to study the local structure with anisotropic atomic displacement parameters (ADP). The results and case studies suggest that the crystal structure and high-quality ADP values can be obtained using the combined methods. The method can be useful to characterize crystals and minerals that are not suitable for single-crystal XRD.

58 GEOSCIENCES↗
DOE OSTI2023

New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class

Class II Fructose-1,6-bisphosphatases (FBPaseII) (EC: 3.1.3.11) are highly conserved essential enzymes in the gluconeogenic pathway of microorganisms. Previous crystallographic studies of FBPasesII provided insights into various inactivated states of the enzyme in different species. Presented here is the first crystal structure of FBPaseII in an active state, solved for the enzyme from Francisella tularensis (FtFBPaseII), containing native metal cofactor Mn 2+ and complexed with catalytic product fructose-6-phosphate (F6P). Another crystal structure of the same enzyme complex is presented in the inactivated state due to the structural changes introduced by crystal packing. Analysis of the interatomic distances among the substrate, product, and divalent metal cations in the catalytic centers of the enzyme led to a revision of the catalytic mechanism suggested previously for class II FBPases. We propose that phosphate-1 is cleaved from the substrate fructose-1,6-bisphosphate (F1,6BP) by T89 in a proximal α-helix backbone (G88-T89-T90-I91-T92-S93-K94) in which the substrate transition state is stabilized by the positive dipole of the $\langle$-helix backbone. Once cleaved a water molecule found in the active site liberates the inorganic phosphate from T89 completing the catalytic mechanism. Additionally, a crystal structure of Mycobacterium tuberculosis FBPaseII (MtFBPaseII) containing a bound F1,6BP is presented to further support the substrate binding and novel catalytic mechanism suggested for this class of enzymes.

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

Operando single crystal neutron diffraction reveals insight into the field response mechanisms in the hydrogen-bonded KH 2 PO 4 ferroelectric

The mechanism that facilitates polarization reorientation in KH 2 PO 4 (KDP) was investigated using operando single-crystal neutron diffraction. Diffraction data were measured from a KDP single crystal during the application of alternating electric fields and were then binned into 40 increments to enable field-dependent single-crystal structure refinements. The field-dependent structures are compared with an as-grown crystal to determine how the lattice and atomic sites evolve in response to the applied electric fields. These analyses provide evidence that the reorientation of the macroscopic polarization is facilitated through a cooperative change in hydrogen bonding, which results in the reversal of the spontaneous dipole. In addition, a decrease in secondary extinction near the coercive field indicates that the inversion of the macroscopic polarization is achieved through the nucleation and subsequent growth of new domains.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Trebiskyite, the First Titanium-Decavanadate Mineral

Abstract Trebiskyite, Na3Mg2[TiV9O28]·22H2O, from the Pickett Corral mine, Bull Canyon, Montrose County, Colorado, USA, is the first mineral containing essential Ti as a component of a decavanadate polyanion. Crystals are thin prisms or needles up to ∼0.3 mm in length, occurring as individuals and in divergent sprays. Trebiskyite crystals are translucent yellow with vitreous luster and pale-yellow streak and are non-fluorescent under both longwave and shortwave ultraviolet illumination. The crystals exhibit elongation on [001] and are modified by several 0kl prism forms, possibly corresponding to {010}, {011}, and {012}. The Mohs hardness is ca. 2 based on scratch tests. Crystals have brittle tenacity with irregular fracture. No apparent cleavage, nor twinning, was evident, and the mineral is readily soluble in H2O. The density measured by flotation in methylene iodide-toluene mixture is 2.38(2) g/cm3. The calculated density is 2.352 g/cm3 for the empirical formula and 2.343 g/cm3 for the ideal formula. Electron microprobe analyses provided the empirical formula Na3.39Mg1.87V8.75Ti1.25O50H44.00, based on Ti + V = 10 apfu, O = 50 apfu, with the Na content having been determined from the refined crystal structure. Trebiskyite is monoclinic, space group P21/c, a = 9.478(4), b = 21.426(11), c = 11.267(5) Å, β = 114.572(7)°, V = 2080.8(13) Å3, Z = 2. The structure was refined from 6642 reflections to a final R1 = 0.0517 for reflections I > 2σ(I). The structural unit of trebiskyite, (TiV9O28)7−, is built from a Ti-substituted decavanadate polyanion, (V10O28)6−, found in other members of the pascoite family. Chemically, trebiskyite is closely related to lasalite, Na2Mg2[V10O28]·20H2O, and huemulite, Na4Mg[V10O28]·24H2O; however, trebiskyite contains a novel structural arrangement that is unique among the decavanadate minerals. The interstitial complex in trebiskyite has the ideal formula {[Na3Mg2(H2O)19](H2O)3} and consists of chains of distorted octahedrally coordinated Na+ and regular Mg[O(H2O)5] octahedra. The observed low incident bond valence to the V1 site (4.45 vu) and marked deviation in vanadyl and V–Oeq bond lengths indicate that this site is host to the essential Ti4+ identified during chemical analyses.

Mineralogy↗
DOE OSTI2024

Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors

Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.

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

An idealized model for the crystal structure of intermetallic compounds isostructural with Mg 3 Cr 2 Al 18

Mg 3 Cr 2 Al 18 (abbreviated in this report as MCA) is the parent phase for a large class of intermetallic compounds that belong to the cubic crystal space group, $Fd\overline{3}m$. The purpose of this paper is to introduce an ideal, unrelaxed crystal structure for compounds isostructural with MCA. There are five distinct atomic sublattices in MCA compounds, which can be denoted, $A, B, C, D,$ and $E$. With this, a general description for MCA structures can be written as $A^{8a}_{1}B^{16c}_{2}C^{16d}_{2}D^{48f}_{6}E^{96g}_{12}$, where the superscripts represent the Wyckoff special equipoints associated with the various sublattices in MCA, and the subscripts indicate the contributions of each sublattice to the stoichiometry of one formula unit in an any given MCA structured compound. Sublattices D and E are where deviations from ideality occur in real, MCA-like compounds. This paper examines MCA bond lengths, nearest-neighbour polyhedral arrangements, 3-D sublattice crystal structures, 2-D atom tessellation patterns, and crystal chemical effects associated with atomic relaxations on the $D$ and $E$ sublattices. The ideal MCA crystal structure developed in this report provides an appropriate initial structure for use as input to crystal structure refinements of diffraction data for MCA-like phases being examined experimentally, or as input for computational, atomistic simulations of the structures of such compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Mo 4 FeGa 17.25– x Ge x : Complementary Point Substitutions, Buffering Frameworks, and Merging of the 18-n and Octet Bonding Schemes

We present the discovery of Mo 4 FeGa 17.25–x Ge x (x ∼ 2.1(4), based on determination of Ge content), a complex gallide featuring a variety of point substitution phenomena. Its crystal structure is derived from the Ti 2 Ni type, in which a diamond network of face-sharing octahedra is interpenetrated by a second diamond network of vertex-sharing stella quadrangula. However, while in the ideal Ti 2 Ni type these two frameworks run uninterrupted through the crystal, Mo 4 FeGa 17.25–x Ge x shows three variations. First, the inner tetrahedron of every other stella quadrangula is replaced with a main group atom, creating tetrahedra reminiscent of the Zintl phase NaTl. Next, a selection of Ga 6 octahedra are filled with Fe atoms, in a manner analogous to the stuffed AuCu 3 -type phases. Finally, the refined crystal structure shows that in each unit cell a single Ga2 atom in the octahedral network is substituted with a dumbbell of Ga/Ge atoms. Electronic structure calculations on ordered models of Mo 4 FeGa 17.25–x Ge x reveal a narrow band near the Fermi energy, which is explained in terms of the 18-n and octet bonding schemes using reversed approximation Molecular Orbital analysis. A DFT-chemical pressure analysis connects the tetrahedron/atom and atom/dumbbell substitutions to the relief of atomic packing tensions and highlights soft atomic motions within the octahedral framework and driving forces for atom/dumbbell substitution. The combination of soft vibrational modes, disorder, and a narrow band gap could make this phase of interest for potential thermoelectric properties.

Chemical structure↗
DOE OSTI2020

Synthesis, Crystal Structure, and Cooperative 3d–5d Magnetism in Rock Salt Type Li 4 NiOsO 6 and Li 3 Ni 2 OsO 6

Two new transition metal oxides with the nominal chemical compositions of Li 4 NiOsO 6 and Li 3 Ni 2 OsO 6 were successfully synthesized. Both compounds crystallize in an ordered rock salt structure type in the monoclinic C2/m space group. The crystal structures were determined using both synchrotron X-ray and time-of-flight neutron, powder diffraction data. In both phases, Ni2+ ions are present while oxidation states of osmium are +6 and +5 in Li 4 NiOsO 6 and Li 3 Ni 2 OsO 6 , respectively. Ni2+ ions in the hypothetical fully ordered phase form a honeycomb arrangement in the ab crystallographic plane and these hexagons are centered by osmium ions. Furthermore, the magnetic layers are separated along the c axis by the octahedra, which are centered by Li+ (or Li+/Ni 2+ , depending on the chemical compositions). Crystal structure refinements reveal that there is some degree of mixed occupancy in cationic positions. Temperature dependent magnetic susceptibility data for both phases show ferrimagnetic transitions with predominant antiferromagnetic (AFM) interactions among 3d electrons of nickel and Sd electrons of osmium. Iso-thermal magnetization loops as a function of the applied magnetic field below the transition temperatures confirm the ferrimagnetic nature in magnetic transitions. Temperature dependent heat capacity data, however, did not exhibit any anomaly in either phase, indicating the absence of long-range magnetic ordering. The lack of long-range order for both Os 5+ and Os 6+ -based compounds was also confirmed by low temperature neutron diffraction data down to 10 K. Temperature dependent AC magnetic susceptibility data in various frequencies for both samples indicate that Li 4 NiOsO 6 exhibits spin-glass-like behavior, while the transition temperature for Li 3 Ni 2 OsO 6 is nearly frequency independent.

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

Synthesis and ion-irradiation tolerance of the Dy2TiO5 polymorphs

In developing improvements in nuclear fuels, work has been conducted in replacing boron with lanthanides to act as neutron absorbent materials. To further this development for the first time the three major polymorphs of Dy2TiO5 have been fabricated as bulk, single-phase materials in a systematic study. Crystal structure refinement has been carried out from powder x-ray diffraction data, with further structural detail attained via electron diffraction. A cubic phase, defect-pyrochlore, Fd-3m space group, was found with cell parameter a = 10.2996 (1) angstrom and oxygen x48f positional parameter = 0.331 (1). Dy2TiO5 was also fabricated as a bulk, single-phase compound with hexagonal symmetry, P6(3)/mmc space group, with cell parameters a = b = 3.6307(2), c = 11.8963(8) angstrom. The radiation response for each of the polymorphs has been investigated in-situ via 1 MeV Kr - ion-irradiation and transmission electron microscopy characterisation at the IVEM-TANDEM facility, Argonne National Laboratory. Critical temperatures, T-c, for maintaining crystallinity during irradiation were determined and showed Dy2TiO5 with either orthorhombic or cubic symmetry to perform the best, with the lowest T-c values of 711 and 761 K respectively when compared with the hexagonal form. These relatively low T-c values may be attributed to different characteristics for each phase; high anti-site defect formation energy for the orthorhombic symmetry, and the ability to accommodate disorder for the cubic symmetry.

Burnable poison↗
DOE OSTI2020

Microstructure Evolution of U–Zr System in A Thermal Cycling Neutron Diffraction Experiment: Extruded U–10Zr (wt. %)

Microstructure evolution of 1073 K extruded U–10Zr (wt. %) fuel during thermal cycling (303–1073 K with a ~9 hour hold at 873 K during cooling) was investigated using in situ neutron diffraction. Analysis was performed using Rietveld texture and crystal structure refinements from time–of–flight neutron diffraction data, with a focus on the evolution of textures and lattice parameters as a function of temperature. The α–U phase exhibits lattice contraction with increasing temperature along the b lattice direction and lattice expansion in the other directions while the other phases exhibit lattice expansion with temperature in all directions. Contrary to the established phase diagram, the β–U phase is absent at the temperatures of the thermal cycling. (001) α and (110) γ plane normals are observed with a strong preferred orientation along the extrusion direction. Finally, the variant selection of (001) α ||(110) γ is observed for the first time.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Antiferromagnetic Ordering in Quasi-One-Dimensional FeBi 4 S 7

Here, we report a detailed study of the synthesis, composition, magnetic structure, and transport properties of a quasi-one-dimensional antiferromagnet FeBi 4 S 7 that contains chains of edge-sharing FeS 6 octahedra. High-resolution powder X-ray diffraction (PXRD) analysis, aided by variation of synthetic conditions, suggests that the true formula of the material is Fe 1.2 Bi 3.8 S 7 , due to the minor substitution of Fe into Bi sites. This finding is in agreement with crystal structure refinement from neutron powder diffraction data as well as with the small band gap of 0.23 eV determined from electrical transport measurements. Analysis of the neutron diffraction pattern collected below the antiferromagnetic ordering temperature of 64 K revealed ferromagnetic coupling between the Fe moments in the chains of FeS 6 octahedra. The overall ordering, however, is antiferromagnetic due to the antiparallel arrangement of moments on neighboring chains. The collinear spin arrangement is described by a k-vector (1, 0, 1/2), which indicates doubling of the unit cell in the c direction and the loss of the C-centering translation as compared to the nuclear cell. The ferromagnetic nature of the sulfide-bridged chains of Fe 2+ ions in FeBi 4 S 7 , in contrast to the antiferromagnetic coupling between Fe moments in compounds with similar structural fragments, can be justified by the analysis of metric parameters that characterize the Fe–S bonding in these materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing

Antibody therapeutics are one of the most important classes of drugs. Antibody structures have become an integral part of predicting the behavior of potential therapeutics, either directly or as the basis of modeling. Structures of Fab:antigen complexes have even greater value. While the crystallization and structure determination of Fabs is easy relative to many other protein classes, especially membrane proteins, broad screening and optimization of crystalline hits is still necessary. Through a comprehensive review of rabbit Fab crystal contacts and their incompatibility with human Fabs, we identified a small secondary structural element from the rabbit light chain constant domain potentially responsible for hindering the crystallization of human Fabs. Upon replacing the human kappa constant domain FG loop (HQGLSSP) with the two residue shorter rabbit loop (QGTTS), we dramatically improved the crystallization of human Fabs and Fab:antigen complexes. Our design, which we call “Crystal Kappa”, enables rapid crystallization of human fabs and fab complexes in a broad range of conditions, with less material in smaller screens or from dilute solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of meglumine diatrizoate, (C 7 H 18 NO 5 )(C 11 H 8 I 3 N 2 O 4 )

The crystal structure of meglumine diatrizoate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Meglumine diatrizoate crystallizes in space group P2 1 (#4) with a = 10.74697(4), b = 6.49364(2), c = 18.52774(7) Å, β = 90.2263(3), V = 1292.985(5) Å 3 , and Z = 2. Two different crystal structures, which yielded essentially identical refinement residuals and positions of the non-H atoms, were obtained. The differences were in the H atom positions and the hydrogen bonding. One structure was 123.0 kJ/mol/cell lower in energy than the other and was adopted for the final description. The crystal structure consists of alternating double layers of cations and anions along the c-axis. The hydrogen bonds link the cations and anions into a three-dimensional framework. Each of the hydrogen atoms on the ammonium nitrogen of the cation acts as a donor in a strong N–H∙∙∙O hydrogen bond. One of these is to a hydroxyl group of another cation, and the other is to the carboxylate group of the anion. Each of the amide nitrogen atoms of the anion forms a strong N–H∙∙∙O intermolecular hydrogen bond, one to a carbonyl and the other to a carboxylate group. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2022

Crystal structure of vismodegib, C 19 H 14 Cl 2 N 2 O 3 S

The crystal structure of vismodegib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Vismodegib crystallizes in space group P2 1 /a (#14) with a = 16.92070(20), b = 10.20235(4), c = 12.16161(10) Å, β = 108.6802(3)°, V = 1988.873(9) Å 3 , and Z = 4. The crystal structure consists of corrugated layers of molecules parallel to the bc-plane. There is only one classical hydrogen bond in the structure, between the amide nitrogen atom and the N atom of the pyridine ring. Pairs of these hydrogen bonds link the molecules into dimers, with a graph set R2,2(14) > a > a. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2020

A Possible Radiation-Induced Transition from Monazite-(Ce) to Xenotime-(Y)

This study examines two pegmatitic monazite samples (2a and 4b, these numbers are related to a previous study) to determine their crystal chemistry and effects of internal radiation damage using synchrotron high-resolution powder X-ray diffraction and electron-probe micro-analysis. Both the huttonite and cheralite substitutions are discussed. Rietveld structure refinement of sample 2a shows three different phases [2a = monazite-(Ce), 2b = monazite-(Ce), and 2c = xenotime-(Y)] with distinct structural parameters. The changes among the unit-cell parameters between the two monazite-(Ce) phases is more pronounced in the a followed by the b and c unit-cell parameters. Sample 4a is a single-phase monazite-(Sm) that contains 0.164 apfu Th. Phase 2c with space group I41/amd arises from redistribution of La, Ce, Pr, Nd, Sm, Gd, Dy, Si, and Y atoms from those in monazite (space group P21/n). A possible cause for the phase transition from monazite-(Ce) to xenotime-(Y) is α-radiation events over a long geological time. However, other chemical processes cannot be ruled out as a cause for the transition.

structural variations↗
DOE OSTI2023

Crystal structure of encorafenib, C 22 H 27 ClFN 7 O 4 S

The crystal structure of encorafenib, C 22 H 27 ClFN 7 O 4 S, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Encorafenib crystallizes in space group P2 1 (#4) with a = 16.17355(25), b = 9.52334(11), c = 17.12368(19) Å, β = 89.9928(22)°, V = 2637.50(4) Å 3 , and Z = 4. The crystal structure consists of alternating layers of stacked halogenated phenyl rings and the other parts of the molecules perpendicular to the a-axis. One molecule participates in two strong N–H∙∙∙N hydrogen bonds (one intra- and the other intermolecular), which are not present for the other molecule. The intermolecular hydrogen bonds link molecule 2 into a spiral chain along the b-axis. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗