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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 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Trigonal polymorph of Li 2 MnO 3

We report the discovery of a trigonal polymorph of the prospective Li ion battery material Li 2 MnO 3 and its synthesis in bulk, single crystal form. Crystal growth of trigonal Li 2 MnO 3 is strongly dependent upon the quality of a polycrystalline LiMnO 2 precursor consumed in the synthesis process. The crystal structure of the new trigonal phase is composed of ordered honeycomb layers of LiO 6 and MnO 6 octahedra segregated by layers of LiO 6 octahedra and represents an ordered stacking variant of the known monoclinic polymorph. Diffuse reflectance spectroscopy reveals a direct optical gap of 2.47 ± 0.11 eV and a series of charge excitations that are well explained by the expected Mn 4+ 3d 3 valence. Density functional theory calculations are in excellent agreement with the spectroscopic measurements and find a near degeneracy in the formation energies of the two polymorphs. Furthermore, our results suggest that the trigonal structure resolves the compositional and structural disorder often manifested in the monoclinic phase.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural Basis for EPC1-Mediated Recruitment of MBTD1 into the NuA4/TIP60 Acetyltransferase Complex

MBTD1, a H4K20me reader, has recently been identified as a component of the NuA4/TIP60 acetyltransferase complex, regulating gene expression and DNA repair. NuA4/TIP60 inhibits 53BP1 binding to chromatin through recognition of the H4K20me mark by MBTD1 and acetylation of H2AK15, blocking the ubiquitination mark required for 53BP1 localization at DNA breaks. The NuA4/TIP60 non-catalytic subunit EPC1 enlists MBTD1 into the complex, but the detailed molecular mechanism remains incompletely explored. Here, we present the crystal structure of the MBTD1-EPC1 complex, revealing a hydrophobic C-terminal fragment of EPC1 engaging the MBT repeats of MBTD1 in a site distinct from the H4K20me binding site. Different cellular assays validate the physiological significance of the key residues involved in the MBTD1-EPC1 interaction. Our study provides a structural framework for understanding the mechanism by which MBTD1 recruits the NuA4/TIP60 acetyltransferase complex to influence transcription and DNA repair pathway choice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Design, synthesis, evaluation and X-ray structural studies of potent HIV-1 protease inhibitors containing substituted oxaspirocyclic carbamates as the P2 ligands

Here, we report here the design, synthesis and evaluation of a series of HIV-1 protease inhibitors that incorporate substituted oxaspirocyclic carbamate derivatives to serve as the P2 ligands. Various substituted ligand derivatives were synthesized in a racemic manner, using a tandem Prins/pinacol reaction as the key reaction. This reaction sets the relative stereochemistry of the oxaspirocyclic template in a highly diastereoselective manner. Reaction of the resulting ketone with enantiopure (S)-tert-butyl sulfinamide provided a convenient pathway to resolve the oxaspirocyclic ketone derivatives. The absolute stereochemical identity was determined by X-ray crystallography. The structure-activity studies demonstrate the effect of the stereochemistry of the oxaspirocyclic ring systems as well as the substitution effect on the aromatic ring. Several inhibitors exhibited potent HIV-1 protease inhibitory activity. One of these inhibitors displayed subnanomolar HIV-1 protease affinity and also exhibited potent antiviral activity. A high-resolution X-ray crystal structure of this inhibitor-bound HIV-1 protease show that the oxaspirocyclic P2 ligand forms an unconventional C–H⋯O bond with the backbone carboxyl group of Gly48’ and an interesting N–H … π interaction with the aromatic ring in the S2 subsite of HIV-1 protease active site.

Antiviral↗
DOE OSTI2021

Fast and Scalable Synthesis of LiNi 0.5 Mn 1.5 O 4 Cathode by Sol–Gel-Assisted Microwave Sintering

High-voltage spinel LiNi 0.5 Mn 1.5 O 4 (LNMO) is a promising cathode material for high-energy-density and high-power-density lithium-ion batteries (LIBs). The high cost of the currently available LIBs needs to be addressed urgently for wide application in the transport sector (electric vehicles, buses) and large-scale energy storage systems (ESS). Of significance, herein, novel fast and scalable microwave-assisted synthesis of LNMO is reported, which leads to a production cost cut. X-ray diffraction (XRD) analysis confirms the formation of the desired phase with high crystallinity. Field emission scanning (FE-SEM) and transmission electron microscopy (TEM) analyses indicate that the synthesized phase is of nanometric size (50–150 nm) due to an extremely short sintering time (20 min). The material synthesized at 750 °C shows a higher initial discharge capacity (130 mA h g -1 ) than that synthesized at 650 °C (115 mA h g -1 ). The materials heat treated at higher temperatures show better electrochemical performance in terms of initial capacity, rate capability, and improved cycling. The improved electrochemical performance of LNMO at 750 °C is attributed to the formation of a stable crystal structure, low charge transfer resistance at the electrode/electrolyte interface, high electrical conductivity due to the presence of a disorder structure, and improved ionic diffusivity.

25 ENERGY STORAGE↗
DOE OSTI2021

Binary and Ternary Colloidal Cu–Sn–Te Nanocrystals for Thermoelectric Thin Films

Recent advances in copper chalcogenide-based nanocrystals (NCs), copper sulfide, and copper selenide derived nanostructures, have drawn considerable attention. However, reports of crystal phase and shape engineering of binary or ternary copper telluride NCs remain rare. Here, a colloidal hot-injection approach for producing binary copper/tin telluride, and ternary copper tin telluride NCs with controllable compositions, crystal structures, and morphologies is reported. Here, the crystal phase and growth behavior of these tellurides are systematically studied from both experimental and theoretical perspectives.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2020

Deciphering the Solvent Effect for the Solvation Structure of Ca 2+ in Polar Molecular Liquids

Although the crystal structures for many inorganic compounds are readily available, researchers are still working hard to understand the relations between the structures and chemical properties of solutions because most of the chemical reactions take place in solutions. A huge amount of effort has been put toward modeling the ion solvation structure from the perspectives of both experiments and theories. In this study, the solvation structures of Ca 2+ ions in aqueous and alcoholic solutions at different concentrations were carefully evaluated by Ca K-edge X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses. Further, density functional theory (DFT) calculations were also performed to correlate the results with the experimental data and then further extended to other similar systems. It was found that the number of coordinating solvent molecules decreases with increasing Ca 2+ concentration and increasing solvent molecule sizes. From the EXAFS data, it was observed that the first solvation shell of Ca 2+ splits into two Ca-O distances in a methanol solution and the counter ion Cl - might also be within the first shell at high concentrations. For the first time, the effects of solvents with different polarities and sizes on the ion solvation environment were systematically evaluated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7

The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An atypical BRCT–BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex

The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break repair, a key target for PARP inhibitors in cancer cells deficient in homologous recombination. Here, we combined biophysical approaches to gain insights into the shape and conformational flexibility of the XL as well as XRCC1 and DNA ligase IIIα (LigIIIα) alone. Structurally-guided mutational analyses based on the crystal structure of the human BRCT–BRCT heterodimer identified the network of salt bridges that together with the N-terminal extension of the XRCC1 C-terminal BRCT domain constitute the XL molecular interface. Coupling size exclusion chromatography with small angle X-ray scattering and multiangle light scattering (SEC-SAXS–MALS), we determined that the XL is more compact than either XRCC1 or LigIIIα, both of which form transient homodimers and are highly disordered. The reduced disorder and flexibility allowed us to build models of XL particles visualized by negative stain electron microscopy that predict close spatial organization between the LigIIIα catalytic core and both BRCT domains of XRCC1. Together our results identify an atypical BRCT–BRCT interaction as the stable nucleating core of the XL that links the flexible nick sensing and catalytic domains of LigIIIα to other protein partners of the flexible XRCC1 scaffold.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural phase diagram for Sm-substituted BiFeO 3 multiferroics

The structural evolution of Sm substituted BiFe⁢O 3 is studied by total x-ray scattering and structure modeling. It is shown that the crystal structure changes from polar to antipolar and then to nonpolar when the Sm to Bi ratio in the material approaches 20% and 40%, respectively, with no intermixing between the structure types. The evolution is driven by lattice strain induced by the difference in the size of Sm and Bi atoms, leading to changes in the pattern of octahedral tilts and Bi off-centering, which, in turn, induce changes in the multiferroic properties. Furthermore, the substitution ratio at which the different structure types emerge appears to be tied up with the average radius of the atomic species occupying the Bi sites in the perovskite lattice and volume occupied by a formula unit, rendering both quantities useful predictor variables for guiding computational searches for substituted BiFe⁢O 3 multiferroics with improved functional properties.

Ferroelectricity↗
DOE OSTI2020

Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA

Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA–Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

On the New Oxyarsenides Eu 5 Zn 2 As 5 O and Eu 5 Cd 2 As 5 O

The new quaternary phases Eu5Zn2As5O and Eu5Cd2As5O have been synthesized by metal flux reactions and their structures have been established through single-crystal X-ray diffraction. Both compounds crystallize in the centrosymmetric space group Cmcm (No. 63, Z = 4; Pearson symbol oC52), with unit cell parameters a = 4.3457(11) Å, b = 20.897(5) Å, c = 13.571(3) Å; and a = 4.4597(9) Å, b = 21.112(4) Å, c = 13.848(3) Å, for Eu5Zn2As5O and Eu5Cd2As5O, respectively. The crystal structures include one-dimensional double-strands of corner-shared MAs4 tetrahedra (M = Zn, Cd) and As–As bonds that connect the tetrahedra to form pentagonal channels. Four of the five Eu atoms fill the space between the pentagonal channels and one Eu atom is contained within the channels. An isolated oxide anion O2– is located in a tetrahedral hole formed by four Eu cations. Applying the valence rules and the Zintl concept to rationalize the chemical bonding in Eu5M2As5O (M = Zn, Cd) reveals that the valence electrons can be counted as follows: 5 × [Eu2+] + 2 × [M2+] + 3 × [As3–] + 2 × [As2–] + O2–, which suggests an electron-deficient configuration. The presumed h+ hole is confirmed by electronic band structure calculations, where a fully optimized bonding will be attained if an additional valence electron is added to move the Fermi level up to a narrow band gap (Eu5Zn2As5O) or pseudo-gap (Eu5Cd2As5O). In order to achieve such a formal charge balance, and hence, narrow-gap semiconducting behavior in Eu5M2As5O (M = Zn, Cd), europium is theorized to be in a mixed-valent Eu2+/ Eu3+ state.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural insights into binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean

Tetrahydrofolate and its derivatives participate in one-carbon transfer reactions in all organisms. The cellular form of tetrahydrofolate (THF) is modified by multiple glutamate residues and polyglutamylation plays a key role in organellar and cellular folate homeostasis. In addition, polyglutamylation of THF is known to increase the binding affinity to enzymes in the folate cycle, many of which can utilize polyglutamylated THF as a substrate. Here, we use X-ray crystallography to provide a high-resolution view of interactions between the enzyme serine hydroxymethyltransferase (SHMT), which provides one carbon precursors for the folate cycle, and a polyglutamylated form of THF. Our 1.7 Å crystal structure of soybean SHMT8 in complex with diglutamylated 5-formyl-THF reveals, for the first time, a structural rearrangement of a loop at the entrance to the folate binding site accompanied by the formation of novel specific interactions between the enzyme and the diglutamyl tail of the ligand. Biochemical assays show that additional glutamate moieties on the folate ligand increase both enzyme stability and binding affinity. Together these studies provide new information on SHMT structure and function and inform the design of anti-folate agents.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Identification and structural analysis of a thermophilic β-1,3-glucanase from compost

β-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic β-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like β-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis for the specificity of PPM1H phosphatase for Rab GTPases

LRRK2 serine/threonine kinase is associated with inherited Parkinson’s disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal-dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity towards substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here, we have identified the molecular determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110-residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3-D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimaera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab-specific interaction domain within a conserved phosphatase fold.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

FA x Cs 1–x PbI 3 Nanocrystals: Tuning Crystal Symmetry by A-Site Cation Composition

Nanoscale semiconductors show remarkably tunable properties. For metal halide perovskite (MHP) nanocrystals (NCs), surface energy and lattice strain stabilize desirable MHP compositions and crystallographic phases that are unstable in the bulk. We report an X-ray scattering study of the average room-temperature crystal structure of ~15 nm FA x Cs 1–x PbI 3 (FA = formamidinium) NCs. All compositions crystallize in the perovskite structure; however, the average structure lowers in symmetry from the a (cubic) to ß (tetragonal) to γ (orthorhombic) perovskite phases with decreasing x (Cs addition). The corresponding a- to ß- and ß- to γ-phase transitions occur between x = 0.75–0.5 and x = 0.25–0.1, respectively. Furthermore, structural refinements also indicate large octahedral tilt angles (10–30°) in the ß- and γ-phases and an increase in (pseudo)cubic unit cell volume upon FA addition. This work establishes the composition–structure relationship for FA x Cs 1–x PbI 3 NCs and demonstrates the ability to target average crystal symmetry with facile synthetic control.

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

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization

HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD , CTD , and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.

60 APPLIED LIFE SCIENCES↗