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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 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions

Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here in this paper, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box–tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate ‘discriminator’ structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA

NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identifed as a 3'→5' exonuclease, but we show here that NrnA is bidirectional, degrading 2–5 nucleotide long RNA oligomers from the 3' end, and longer RNA substrates from the 5' end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5'→3' DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3'→5' activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT

Abstract Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H 2 O 2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H 2 O 2 -treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H 2 O 2 . The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H 2 O 2 -consumption assays. Furthermore, an entrance channel for H 2 O 2 was identified and key residues implicated in H 2 O 2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Structural Effects of Lanthanide Dopants on Alumina

Lanthanide (Ln 3+ ) doping in alumina has shown great promise for stabilizing and promoting desirable phase formation to achieve optimized physical and chemical properties. However, doping alumina with Ln elements is generally accompanied by formation of new phases (i.e. LnAlO3, Ln2O3), and therefore inclusion of Ln-doping mechanisms for phase stabilization of the alumina lattice is indispensable. In this study, Ln-doping (400 ppm) of the alumina lattice crucially delays the onset of phase transformation and enables phase population control, which is achieved without the formation of new phases. The delay in phase transition (θ → α), and alteration of powder morphology, particle dimensions, and composition ratios between α- and θ-alumina phases are studied using a combination of solid state nuclear magnetic resonance, electron microscopy, digital scanning calorimetry, and high resolution X-ray diffraction with refinement fitting. Loading alumina with a sparse concentration of Ln-dopants suggests that the dopants reside in the vacant octahedral locations within the alumina lattice, where complete conversion into the thermodynamically stable α-domain is shown in dysprosium (Dy)- and lutetium (Lu)-doped alumina. This study opens up the potential to control the structure and phase composition of Ln-doped alumina for emerging applications.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Electronic structure and characterization of a uranyl di-15-crown-5 complex with an unprecedented sandwich structure

Understanding of the nature and extent of chemical bonding in uranyl coordination complexes is crucial for the design of new ligands for nuclear waste separation, uranium extraction from seawater, and other applications. We report in this paper the synthesis, infrared spectroscopic characterization, and quantum chemical studies of a molecular uranyl–di-15-crown-5 complex. The structure and bonding of this unique complex featuring a distinctive 6-fold coplanar coordination staggered sandwich structure and an unusual non-perpendicular orientation of the uranyl moiety are evaluated using density functional theory and chemical bonding analyses. Finally, the results provide fundamental understanding of the coordination interaction of uranyl with oxygen-donor ligands.

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

Examining the structural evolution of bicarbonate–water clusters: insights from photoelectron spectroscopy, basin-hopping structural search, and comparison with available IR spectral studies

Bicarbonate serves a crucial biochemical role in the physiological pH buffering system and also has important atmospheric implications. In the current study, HCO 3 $-$ (H 2 O) n (n = 0-13) clusters were successfully produced via electrospray ionization of corresponding bulk salt solution, and were characterized by combining negative ion photoelectron spectroscopy and theoretical calculations. The photoelectron spectra reveal that the electron binding energy monotonically increases with the cluster size up to n = 10 and remains largely the same after n > 10. The photo-detaching feature of the solute HCO3$-$itself, which dominates in the small clusters, diminishes with increase of water coverage. Based on the charge distribution and molecular orbital analyses, the universal high electron binding energy tail that dominates in the larger clusters can be attributed to ionization of water. Thus, the transition of ionization from solute to solvent at the size larger than n=10 has been observed. Extensive theoretical structural search based on the Basin-Hopping unbiased method was carried out, and a plethora of low energy isomers have been obtained for each medium and large size. By comparing the simulated photoelectron spectra and calculated electron binding energies with the experiments, as well as by comparing the simulated infrared spectra with previously reported IR spectra, the probable global minima and the structural evolutionary routes are presented. The nature of bicarbonate-water interactions are mainly electrostatic as implied by the electron localization function (ELF) analysis.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2017

Flexible monomer-based covalent organic frameworks: design, structure and functions

The design and synthesis of flexible monomer-based covalent organic frameworks (COFs) have been considered a challenge. We describe the design and synthesis of a new flexible monomer-based COF, termed PPN-30 (PPN meaning porous polymer network), by the use of a flexible alkyl amine, 1,4-cyclohexanediamine, combined with 1,3,5-triformylbenzene. The structure and gas adsorption properties of PPN-30 were carefully investigated.

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

High temperature hydrothermal synthesis of rare-earth titanates: synthesis and structure of RE 5 Ti 4 O 15 (OH) (RE = La, Er), Sm 3 TiO 5 (OH) 3 , RE 5 Ti 2 O 11 (OH) (RE = Tm–Lu) and Ce 2 Ti 4 O 11

Reactions of rare-earth oxides with TiO 2 were performed in high temperature (650–700 °C) hydrothermal fluids. Two different mineralizer fluids were examined, 20 M KOH and 30 M CsF, and their respective products analyzed. When concentrated KOH fluids were used, single crystals of a variety of new OH - containing species were isolated and structurally characterized: RE 5 Ti 4 O 15 (OH) (RE = La, Er) I, Sm 3 TiO 5 (OH) 3 II and RE 5 Ti 2 O 11 (OH) (RE = Tm–Lu) III. La 5 Ti 4 O 15 (OH) I crystallizes in the orthorhombic space group Pnnm with unit cell dimensions of a = 30.5152(12) Å, b = 5.5832(2) Å, c = 7.7590(3) Å and V = 1321.92(9) Å 3 , Z = 4. Sm 3 TiO 5 (OH) 3 II crystallizes in the monoclinic space group P21/m with unit cell parameters of a = 5.6066(2) Å, b = 10.4622(4) Å, c = 6.1258(2) Å and β = 104.7390(10)°, V = 347.50(2) Å3, Z = 2. Lu5Ti2O11(OH) III crystallizes in the monoclinic space group C2/m with unit cell dimensions of a = 12.1252(9) Å, b = 5.8243(4) Å, c = 7.0407(5) Å, β = 106.939(3)° and V = 475.65(6) Å3, Z = 2. When concentrated fluoride solutions are used, mostly RE 2 Ti 2 O 7 type compounds were isolated in either cubic or monoclinic phases. In the case of cerium, Ce2Ti4O11IV was isolated that crystallizes in the monoclinic space group C2/c with unit cell parameters of a = 13.6875(7) Å, b = 5.0955(3) Å, c = 12.8592(7) Å, β = 108.964(2)° and V = 848.18(8) Å 3 , Z = 4. The synthesis, structural characterization, and supporting characterization are reported for all compounds. The work highlights the complementary nature of hydroxide and fluoride fluids in studying the reactivity of refractory oxides.

36 MATERIALS SCIENCE↗
DOE OSTI2017

The structure and unconventional dihydrogen bonding of a pressure-stabilized hydrogen-rich (NH 3 BH 3 )(H 2 ) x (x = 1.5) compound

Combining X-ray diffraction, Raman spectroscopy, and ab initio simulations we characterize an extremely hydrogen-rich phase with the chemical formula (NH 3 BH 3 )(H 2 ) x (x = 1.5). This phase was formed by compressing ammonia borane (AB, NH 3 BH 3 ) in an environment with an excess of molecular hydrogen (H 2 ). This compound can store a total of 26.8 wt% hydrogen, both as molecular hydrogen and chemically bonded hydrogen in AB, making it one of the most hydrogen-rich solids currently known. The new compound possesses a layered AB structure where additional H 2 molecules reside in channels created through the weaving of AB layers. The unconventional dihydrogen bonding network of the new compound is significantly modified from its parent AB phase and contains H•••H contacts between adjacent AB molecules and between AB and H 2 molecules. H–H can be either a proton donor or a proton acceptor that forms new types of dihydrogen bonding with the host AB molecules, which are depicted as H–H•••H–B or H–H•••H–N, respectively. Furthermore, this study not only demonstrates the strategy and the promise of using pressure for new material synthesis, but also unleashes the power of combining experiments and ab initio calculations for elucidating novel structures and unusual bonding configurations in dense low-Z materials.

36 MATERIALS SCIENCE↗