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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state

The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered and most widespread riboswitches. Numerous structural studies have been reported for this riboswitch bound with various ligands. However, the ligand-free (apo) structure remains unknown. Here, we report a 3.1 Å resolution crystal structure of Escherichia coli TPP riboswitch in the apo state, which exhibits an extended, Y-shaped conformation further supported by small-angle X-ray scattering data and driven molecular dynamics simulations. The loss of ligand interactions results in helical uncoiling of P5 and disruption of the key tertiary interaction between the sensory domains. Opening of the aptamer propagates to the gene-regulatory P1 helix and generates the key conformational flexibility needed for the switching behavior. Much of the ligand-binding site at the three-way junction is unaltered, thereby maintaining a partially preformed pocket. Together, these results paint a dynamic picture of the ligand-induced conformational changes in TPP riboswitches that confer conditional gene regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Crystal structures and formation mechanisms of boron-rich tungsten borides

Boron-rich tungsten borides tend to adopt mechanically unfavorable layered structures but experimentally exhibit excellent mechanical properties rivalling traditional superhard solids. Unravelling the contraindicated structure-property relationship, however, has been impeded by their structural ambiguities because of the difficulty in probing boron and atomic deficiency of these borides. Here, we study crystal structures of boron-rich tungsten borides WB 3+x and WB 2+x by neutron diffraction based on high-quality samples prepared by a high-pressure method, leading to definitive structural resolutions for both borides with unique compositions of WB 5.14 and WB 2.34 . Combined with theoretical calculations, their structural stability is revealed to be closely related to atomic deficiency, which is governed by the valence-band filling with an optimal valence-electron concentration of ~10 per cell. The presence of interstitial boron trimers at the vacant W : 2b sites in WB 5.14 alters the crystal symmetry, making the Wyckoff 2d site more favorably occupied by W, rather than the 2c site, as previously misassigned. Here, the staggered planar boron layers and wrinkled boron bonding in WB 2.34 are identified to be crucial for stabilizing its structure. These findings unveil the longstanding structural mysteries of boron-rich tungsten borides and offer powerful insights for rational design of borides by defect chemistry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Investigation into the crystal structure–dielectric property correlation in barium titanate nanocrystals of different sizes

For high capacitance multilayer ceramic capacitors, high dielectric constant and lead-free ceramic nanoparticles are highly desired. However, as the particle size decreases to a few tens of nanometers, their dielectric constant significantly decreases, and the underlying mechanism has yet to be fully elucidated. Herein, we report a systematic investigation into the crystal structure–dielectric property relationship of combustion-made BaTiO 3 (BTO) nanocrystals. When the nanocrystal size was 100 nm and below, a metastable paraelectric cubic phase was found in the as-received BTO (denoted as arBTO) nanocrystals based on an X-ray diffraction (XRD) study. A stable ferroelectric tetragonal phase was present when the nanocrystal size was above 200 nm. Notably, the cubic arBTO (particle size ≤100 nm) exhibited tetragonal fluctuations as revealed by Raman spectroscopy, whereas the tetragonal arBTO (particle size ≥200 nm) contained ~10% cubic fraction according to the Rietveld fitting of the XRD profiles. Thermal annealing of the multi-grain tetragonal arBTO at 950 °C yielded single crystals of annealed BTO (denoted as anBTO), whose dielectric constants were higher than those of arBTO. However, the single crystalline anBTO prevented the formation of 90° domains; therefore, they exhibited a low dielectric constant of ~300. Although X-ray photoelectron spectroscopy and high-resolution transmission electron microscopy could not identify the exact structural defects, our study revealed that surface and bulk defects formed during synthesis affect the final crystal structures and thus the dielectric properties of BTO nanocrystals with different sizes. Finally, the understanding obtained from this study will help us design high dielectric constant perovskite nanocrystals for next-generation multilayer ceramic capacitor applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The crystal structure of Fe2S at 90 GPa based on single-crystal X-ray diffraction techniques

The Fe-S system was explored in a laser-heated diamond-anvil cell at 89(2) GPa and 2380(120) K to better understand the phase stability of Fe 2 S. Upon temperature quenching, crystallites of Fe 2 S were identified, and their structure was investigated using single-crystal X-ray diffraction techniques. At these conditions, Fe 2 S adopts the C23 structure (anti-PbCl 2 , Co 2 P) with space group Pnma (Z = 4). This structure consists of columns of corner-sharing, FeS 4 tetrahedra, and columns of edge-sharing FeS 5 square pyramids linked along edges in the b direction. Sulfur is in ninefold coordination with Fe. This work marks the first high-pressure structural solution and refinement of Fe 2 S synthesized in a multigrain Fe+FeS sample at 90 GPa and 2400 K and establishes the stability of C23 Fe 2 S at these conditions. A previous powder diffraction study reports an orthorhombic Fe 2 S phase with a C37, Co 2 Si-like unit cell above 190 GPa. A C23–C37 structural transition is inferred to explain the previously observed unit-cell parameters at higher pressures and temperatures. These results highlight the utility of applying single-crystal X-ray diffraction techniques to high P-T multigrain samples to explore the structural properties of iron-rich phases in Earth and planetary cores.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Crystal structure of nicarbazin, (C 13 H 10 N 4 O 5 )(C 6 H 8 N 2 O)

The crystal structure of nicarbazin has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Nicarbazin is a co-crystal of 4,4′-dinitrocarbanilide (DNC) and 2-hydroxy-4,6-dimethylpyrimidine (HDP) molecules. Nicarbazin crystallizes in space groupP-1(#2) witha= 6.90659(8),b= 12.0794(4),c= 13.5040(7) Å,α= 115.5709(11),β= 102.3658(6),γ= 91.9270(4)°,V= 982.466(5) Å 3 , andZ= 2. The DNC and HDP molecules are linked by two strong N–H⋯O and N–H⋯N hydrogen bonds, and the HDP molecules are linked into centrosymmetric dimers by another N–H⋯O hydrogen bond. These strong hydrogen bonds link the molecules into layers parallel to theab-plane and parallel stacking of both DNC and HDP molecules is prominent in the structure. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Materials Science↗
DOE OSTI2022

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Low-Temperature Crystal Structure and Mean-Field Modeling of Er x Dy 1- x Al 2 Intermetallics

Low-temperature crystal structure of the Er x Dy 1-x Al 2 alloys with x = 0.45, 0.67, 0.90 was examined using temperature-dependent powder X-ray diffraction. The Er-rich sample, Er 0.9 Dy 0.1 Al 2 , exhibits a rhombohedral distortion associated with the magnetic ordering that occurs around 20 K. The rhombohedral distortion is suppressed in Er 0.67 Dy 0.33 Al 2 , while a weak low-temperature tetragonal distortion is observed in Er 0.45 Dy 0.55 Al 2 . The mean-field theory supports the correlation between the type of structural distortion and the variable easy magnetization axis in Er x Dy 1-x Al 2 intermetallics.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature

Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL . Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.

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

The theory of transport in helical spin-structure crystals

Abstract We study helical structures in spin-spiral single crystals. In the continuum approach for the helicity potential energy the simple electronic band splits into two non-parabolic bands. For low exchange integrals, the lower band is described by a surface with a saddle shape in the direction of the helicity axis. Using the Boltzmann equation with the relaxation due to acoustic phonons, we discover the dependence of the current on the angle between the electric field and helicity axis leading to the both parallel and perpendicular to the electric field components in the electroconductivity. The latter can be interpreted as a planar Hall effect. In addition, we find that the transition rates depend on an electron spin allowing the transition between the bands. The electric conductivities exhibit nonlinear behaviors with respect to chemical potential µ . We explain this effect as the interference of the band anisotropy, spin conservation, and interband transitions. The proposed theory with the spherical model in the effective mass approximation for conduction electrons can elucidate nonlinear dependencies that can be identified in experiments. We find the excellent agreement between the theoretical and experimental data for parallel resistivity depending on temperature at the phase transition from helical to ferromagnetic state in a M n P single crystal. In addition, we predict that the perpendicular resistivity abruptly drops to zero in the ferromagnetic phase.

Physics↗
DOE OSTI2020

Caught in the H inact : Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O 2 -stable State of [FeFe] Hydrogenase

[FeFe] hydrogenases are the most active H 2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O 2 -stable state called H inact . To date, the structure and mechanism of formation of H inact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in-depth spectroscopic characterization by X-ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O 2 -stable hydrogenases and molecular catalysts.

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

The crystal structure of feitknechtite (β-MnOOH) and a new MnOOH polymorph

Studies suggest that feitknechtite (β-MnOOH) is a prevalent, and perhaps necessary, intermediate phase during the synthesis of birnessite-like phases, the abiotic oxidation of Mn2+, and the transformation of biogenic hexagonal phyllomanganates to more complex Mn oxides in laboratory and natural systems. Researchers have generally described feitknechtite as consisting of pyrochroite-like (or cadmium iodide-like) Mn-O octahedral layers, but a detailed crystal structure has not been reported. For this work, we used TEM/SAED and powder XRD and Rietveld refinements to derive the unit cell and, for the first time, report a complete structure description for feitknechtite (β-MnOOH). Rietveld refinements were also completed for three natural feitknechtite/hausmannite samples, and time-resolved synchrotron XRD experiments were used to follow the thermal transformation of feitknechtite to hausmannite. Additionally, we identified and report the structure for a second, and perhaps novel, MnOOH polymorph (proposed designation ε-MnOOH), mixed with the synthetic feitknechtite, that is similar to β-MnOOH but with a different layer stacking.

58 GEOSCIENCES↗
DOE OSTI2023

Synthesis, crystal structure, and magnetic properties of CoMoFeAl and related compounds

We have carried out joint theoretical and experimental investigations of three Heusler compounds CoMoFeAl, CoMo 0.5 Fe 1.5 Al, and Co 1.5 Mo 0.5 FeAl. Our first-principle calculations show that all three compounds show either ferro- or ferrimagnetic order with CoMoFeAl and CoMo 0.5 Fe 1.5 Al exhibiting high spin polarization of almost 80%. The investigated samples were prepared using arc melting and high vacuum annealing. All the samples show cubic crystal structure with disorder. The parent compound CoMoFeAl shows a small saturation magnetization of 12 emu/g, and a Curie temperature of 440 K. The other two compounds, namely, Co 1.5 Mo 0.5 FeAl and CoMo 0.5 Fe 1.5 Al, show much higher saturation magnetizations of 62 emu/g and 59 emu/g, and substantially higher Curie temperatures of 950 K and 780 K, respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal structures of ‘ALternative Isoinformational ENgineered’ DNA in B-form

The first structural model of duplex DNA reported in 1953 by Watson & Crick presented the double helix in B-form, the form that genomic DNA exists in much of the time. Thus, artificial DNA seeking to mimic the properties of natural DNA should also be able to adopt B-form. Using a host–guest system in which Moloney murine leukemia virus reverse transcriptase serves as the host and DNA as the guests, we determined high-resolution crystal structures of three complexes including 5'-CTTBPPBBSSZZSAAG, 5'-CTTSSPBZPSZBBAAG and 5'-CTTZZPBSBSZPPAAG with 10 consecutive unnatural nucleobase pairs in B-form within self-complementary 16 bp duplex oligonucleotides. We refer to this ALternative Isoinformational ENgineered (ALIEN) genetic system containing two nucleobase pairs (P:Z, pairing 2-amino-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one with 6-amino-5-nitro-(1H)-pyridin-2-one, and B:S, 6-amino-4-hydroxy-5-(1H)-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one) as ALIEN DNA. We characterized both position- and sequence-specific helical, nucleobase pair and dinucleotide step parameters of P:Z and B:S pairs in the context of B-form DNA. We conclude that ALIEN DNA exhibits structural features that vary with sequence. Further, Z can participate in alternative stacking modes within a similar sequence context as captured in two different structures. This finding suggests that ALIEN DNA may have a larger repertoire of B-form structures than natural DNA.

59 BASIC BIOLOGICAL SCIENCES↗