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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Unusually large 254 Atoms Counter‐Ion for 5 Atoms [Ge 5 ] 2– Cluster

Abstract . With the attempt to synthesize Nb‐enclosed germanium Zintl cluster ion in ethylenediamine ( en ) / toluene solution, the reaction of K 4 Ge 9 /Na 4 Ge 9 with Nb( mes ) 2 ( mes = mesitylene) gives unexpected 18‐crown‐6 cleavage product of [K 14 Na 2 (NbO 2 ) 2 (C 8 H 16 O 5 ) 8 ](Ge 5 ) ( en ) · solv in the form of very air‐sensitive, light‐brown, plate‐like crystals. This unique compound crystallizes in monoclinic Pn (No. 7) space group, the cleavage of crown linked the 14 potassium, 2 sodium, and 2 niobium atoms into the bulky 2+ charged cation, which balances the [Ge 5 ] 2– anion. This compound represents the rare example of heteronuclear metal alkoxide / Zintl ion hybrid.

Zavalij, Peter Y.↗
DOE OSTI2021

Temperature and radiation effects on brittle versus ductile fracture behavior in miscible phase boundaries: insight from atomistic simulations

Temperature- and irradiation-assisted failure mechanisms in miscible phase boundaries are clarified via atomistic calculations. We first establish the temperature-dependent brittle-to-ductile transition in U–Zr miscible phase boundaries. Our results confirm that these boundaries are mostly brittle at low temperatures and ductile at elevated temperatures. We then investigate the changes induced by irradiation on the fracture mechanisms in such phase boundaries. The irradiation-induced defect accumulation follows a multi-stage process that starts with the accumulation of isolated small dislocation loops before transitioning to the saturation and growth of larger dislocation loops and end up with a reorganization into forest dislocations. The accumulation of loops is the primary feature to participate in the delineation between brittle and ductile interfacial fracture in irradiated phase boundaries. At low damage levels, radiation defect interactions with the crack tip are limited and U–Zr miscible boundaries fail through the emission of dislocations ahead of the crack tip followed by brittle cleavage in agreement with the classical Griffith’s criterion for crack stability. At higher damage levels, the failure mode transitions from brittle crack growth to ductile void growth. In this case, the microcrack tip is blunted by the high density of pre-existing, radiation-induced defects in the vicinity of the crack. This interaction leads to the development and growth of a cavity at the interface as opposed to interfacial cleavage.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A General Model for the Ductility of Intermetallics Applied to Fe-Co Alloys

The mechanical properties, specifically ductility, of high performing soft magnets such as Fe-Co alloys are a limiting factor to their broader use in a number of systems. The understanding of the mechanical robustness in these materials is currently insufficient to be able to support the growing interest in applications such as magnetic shielding or electric motors. Fe-Co alloys provide the highest commercially available magnetic saturation and high magnetic permeability but have very poor ductility. The addition of vanadium to these alloys has allowed for significant commercialization and some ductility improvements, but the fundamental reasons for the observed improvements are not well understood. In most published work on mechanical properties in these alloys, the precise chemistry of the alloys investigated, often a critical aspect of intermetallics, is not reported or controlled and thermal history is unclear. This work creates a ductility model that is sensitive to changes in chemistry and can predict relative strain to failure as well as brittle fracture mode for intermetallics and is applied to Fe-Co alloys. Through the application of density functional theory (DFT), this model identifies defect stabilities, anti-phase boundary (APB) energies, the energy necessary to cross-slip, and cleavage energies and combines them through energetic competition to determine a relative failure strain. The model correctly predicts ductility improvements with the addition of vanadium as well as the transition from intergranular to transgranular cleavage, though more precise experiments are necessary to appropriately validate the various improvements observed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites

Bleomycins constitute a family of anticancer natural products that bind DNA through intercalation of a C-terminal tail/bithiazole moiety and hydrogen-bonding interactions between the remainder of the drug and the minor groove. The clinical utility of the bleomycins is believed to result from single- and double-strand DNA cleavage mediated by the HOO-Fe(III) form of the drug. The bleomycins also serve as a model system to understand the nature of complex drug-DNA interactions that may guide future DNA-targeted drug discovery. In this study, the impact of the C-terminal tail on bleomycin-DNA interactions was investigated. Toward this goal, we determined two crystal structures of HOO-Co(III)•BLMA 2 “green” (a stable structural analogue of the active HOO-Fe(III) drug) bound to duplex DNA containing 5'-TAGTT, one in which the entire drug is bound (fully bound) and a second with only the C-terminal tail/bithiazole bound (partially bound). The structures reported here were captured by soaking HOO-Co(III)•BLMA 2 into preformed host–guest crystals including a preferred DNA-binding site. While the overall structure of DNA-bound BLMA 2 was found to be similar to those reported earlier at the same DNA site for BLMB 2 , the intercalated bithiazole of BLMB 2 is “flipped” 180° relative to DNA-bound BLMA 2 . Further, this finding highlights an unidentified role for the C-terminal tail in directing the intercalation of the bithiazole. In addition, these analyses identified specific bond rotations within the C-terminal domain of the drug that may be relevant for its reorganization and ability to carry out a double-strand DNA cleavage event.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Revealing the mechanism of lignin re-polymerization inhibitor in acidic pretreatment and its impact on enzymatic hydrolysis

Phenolic additives, including 2-naphthol, 2-naphthol-7-sulfonate, and resorcinol were evaluated for their impact on the lignin re-polymerization and subsequent hydrolysis of bamboo residues. Low surface lignin concentration (65.68%) of the substrate and high Tg value (185 °C) of lignin was observed for 2-naphthol-7-sulfonate assisted pretreatment, leading to the most significant increase (14%) in enzymatic hydrolysis efficiency of pretreated bamboo residues. Meanwhile, physicochemical properties of lignin revealed that the introduced sulfonic acid groups increased the surface charge, decreased the molecular weight, promoted the cleavage of β-O-4 linkages, and prevented the re-condensation of lignin. Even though resorcinol-assisted pretreatment, by contrast, was found to be an inhibitor for enzymatic hydrolysis. NMR analysis of modified lignin showed that resorcinol led to a higher amount of non-condensed phenolic OH groups and promoted the cleavage of β-O-4 linkages, acting as an inhibitor in lignin re-polymerization during the dilute acidic pretreatment. In short, the above findings present a detailed view of suppressing lignin re-polymerization for boosting the utilization of bioresources with acidic pretreatment.

09 BIOMASS FUELS↗
DOE OSTI2021

Kinetic analysis of Cas12a and Cas13a RNA-Guided nucleases for development of improved CRISPR-Based diagnostics

Bacterial CRISPR systems provide acquired immunity against invading nucleic acids by activating RNA-programmable RNases and DNases. Cas13a and Cas12a enzymes bound to CRISPR RNA (crRNA) recognize specific nucleic acid targets, initiating cleavage of the targets as well as non-target (trans) nucleic acids. Here, we examine the kinetics of single-turnover target and multi-turnover trans-nuclease activities of both enzymes. High-turnover, non-specific Cas13a trans-RNase activity is coupled to rapid binding of target RNA. By contrast, low-turnover Cas12a trans-nuclease activity is coupled to relatively slow cleavage of target DNA, selective for DNA over RNA, indifferent to base identity, and preferential for single-stranded substrates. Combining multiple crRNA increases detection sensitivity of targets, an approach we use to quantify pathogen DNA in samples from patients suspected of Buruli ulcer disease. Results reveal that these enzymes are kinetically adapted to play distinct roles in bacterial adaptive immunity and show how kinetic analysis can be applied to CRISPR-based diagnostics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The exo-β- N -acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases

Endo-β-N-acetylmuramidases, commonly known as lysozymes, are well-characterized antimicrobial enzymes that catalyze an endo-lytic cleavage of peptidoglycan; i.e., they hydrolyze the β-1,4-glycosidic bonds connecting N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc). In contrast, little is known about exo-β-N-acetylmuramidases, which catalyze an exo-lytic cleavage of β-1,4-MurNAc entities from the non-reducing ends of peptidoglycan chains. Such an enzyme was identified earlier in the bacterium Bacillus subtilis, but the corresponding gene has remained unknown so far. We now report that ybbC of B. subtilis, renamed namZ, encodes the reported exo-β-N-acetylmuramidase. A ΔnamZ mutant accumulated specific cell wall fragments and showed growth defects under starvation conditions, indicating a role of NamZ in cell wall turnover and recycling. Recombinant NamZ protein specifically hydrolyzed the artificial substrate para-nitrophenyl β-MurNAc and the peptidoglycan-derived disaccharide MurNAc-β-1,4-GlcNAc. Together with the exo-β-N-acetylglucosaminidase NagZ and the exo-muramoyl-L-alanine amidase AmiE, NamZ degraded intact peptidoglycan by sequential hydrolysis from the non-reducing ends. A structure model of NamZ, built on the basis of two crystal structures of putative orthologs from Bacteroides fragilis, revealed a two-domain structure including a Rossmann-fold-like domain that constitutes a unique glycosidase fold. Thus, NamZ, a member of the DUF1343 protein family of unknown function, is now classified as the founding member of a new family of glycosidases (CAZy GH171). NamZ-like peptidoglycan hexosaminidases are mainly present in the phylum Bacteroidetes and less frequently found in individual genomes within Firmicutes (Bacilli, Clostridia), Actinobacteria, and γ-proteobacteria.

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

An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11

Human cleavage and polyadenylation specificity factor (CPSF)73 (also known as CPSF3) is the endoribonuclease that catalyzes the cleavage reaction for the 3'-end processing of pre-mRNAs. The active site of CPSF73 is located at the interface between a metallo-β-lactamase domain and a β-CASP domain. Two metal ions are coordinated by conserved residues, five His and two Asp, in the active site, and they are critical for the nuclease reaction. The metal ions have long been thought to be zinc ions, but their exact identity has not been examined. Here we present evidence from inductively coupled plasma mass spectrometry and X-ray diffraction analyses that a mixture of metal ions, including Fe, Zn, and Mn, is present in the active site of CPSF73. The abundance of the various metal ions is different in samples prepared from different expression hosts. Zinc is present at less than 20% abundance in a sample expressed in insect cells, but the sample is active in cleaving a pre-mRNA substrate in a reconstituted canonical 3'-end processing machinery. Zinc is present at 75% abundance in a sample expressed in human cells, which has comparable endonuclease activity. We also observe a mixture of metal ions in the active site of the CPSF73 homolog INTS11, the endonuclease for Integrator. Taken together, our results provide further insights into the role of metal ions in the activity of CPSF73 and INTS11 for RNA 3'-end processing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Spectroscopy and crystallography define carotenoid oxygenases as a new subclass of mononuclear non-heme Fe II enzymes

Carotenoid cleavage dioxygenases (CCDs) are non-heme Fe II enzymes that catalyze the oxidative cleavage of alkene bonds in carotenoids, stilbenoids, and related compounds. How these enzymes control the reaction of dioxygen (O 2 ) with their alkene substrates is unclear. Here, we apply spectroscopy in conjunction with X-ray crystallography to define the iron coordination geometry of a model CCD, CAO1 (Neurospora crassa carotenoid oxygenase 1), in its resting state and following substrate binding and coordination sphere substitutions. Resting CAO1 exhibits a five-coordinate (5C), square pyramidal Fe II center that undergoes steric distortion toward a trigonal bipyramidal geometry in the presence of piceatannol. Titrations with the O 2 -analog, nitric oxide, show a >100-fold increase in iron–nitric oxide affinity upon substrate binding, defining a crucial role for the substrate in activating the Fe II site for O 2 reactivity. The importance of the 5C Fe II structure for reactivity was probed through mutagenesis of the second-sphere Thr151 residue of CAO1, which occludes ligand binding at the sixth coordination position. A T151G substitution resulted in the conversion of the iron center to a six-coordinate state and a 135-fold reduction in apparent catalytic efficiency toward piceatannol compared with the wildtype enzyme. Substrate complexation resulted in partial six-coordinate to 5C conversion, indicating solvent dissociation from the iron center. Additional substitutions at this site demonstrated a general functional importance of the occluding residue within the CCD superfamily. Taken together, these data suggest an ordered mechanism of CCD catalysis occurring via substrate-promoted solvent replacement by O 2 . CCDs thus represent a new class of mononuclear non-heme Fe II enzymes.

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

Selective activation of methane C–H bond in the presence of methanol

Direct methane to methanol (MTM) conversion over heterogeneous catalysts is a promising route for valorization of methane. The methane C-H bond activation is considered as the key step of the MTM and is the focus of considerable research activity. However, the formed methanol typically suffers from overoxidation largely due to the cleavage of a methanol C-H bond, whose bond dissociation energy is ca. 0.5 eV lower than that of the methane C-H bond, which usually translates to a transition state energy of the methanol C-H bond cleavage that is ca. 0.55 eV lower than that of methane whenever the reactions proceed through a radical mechanism. Furthermore, we propose a general approach for decreasing the transition state energy difference between the CH 4 and CH 3 OH C-H bond dissociation. When a metal-oxide supported cationic transition metal atom and a neighboring oxygen on the oxide surface serve as the active site, the transition state energy difference through a surface-stabilized pathway can be noticeably narrowed as compared with that of a radical pathway. For Ir, Pt and Rh-doped anatase TiO 2 (101), the CH 4 C-H bond activation can be preferred over that of CH 3 OH at significant methanol mole fraction. Also, for PdAu alloys containing adsorbed oxygen and positively charged Pd, calculations suggest in agreement with recent experiments (Science 367 (6474), 193-197) that the CH 4 C-H bond can be selectively activated in the presence of CH 3 OH.

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

Molecular dynamics studies of helium bubble effects on grain boundary fracture vulnerabilities in an Fe 70 Ni 11 Cr 19 –1%H austenitic stainless steel

Comprehensive molecular dynamics tensile test simulations have been performed to study the delamination processes of seven different grain boundaries / cleavage planes (Σ1{111}, Σ3{111}, Σ5{100}, Σ7{111}, Σ9{411}, Σ11{311}, and R{100}/{411}) containing a helium bubble. Combinations of a variety of conditions are explored including different strain rates, system dimensions, bubble density, bubble radius, bubble pressure, and temperature. We found that in general, grain boundaries absorb less energies with decreasing strain rate but increasing bubble areal density, bubble pressure, bubble radius, and temperature. The propensity of grain boundary delamination is sensitive to grain boundary type: The random grain boundary R{100}/{411} is one of the most brittle boundaries whereas the Σ1{111} cleavage plane and the Σ3{111} twin boundary are two of the toughest boundaries. The sorted list of grain boundary fracture vulnerability obtained from our dynamic tensile test simulations differs from the one obtained from our decohesion energy calculations, confirming the important role of plastic deformation during fracture. Finally, detailed mechanistic analyses are performed to interpret the simulated results.

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

The mechanism of carboxylative cyclization of propargylamine by N-heterocyclic carbene complexes of Au(I)

Here, the complex [Au(IPr)(2-oxazolidinone)] (1 = IKa) was prepared from reaction of [Au(IPr)Cl] (2), K 2 CO 3 , and propargyl amine (PPA). Kinetic studies have been performed for acid cleavage of 1 to yield the oxazolidinone product and an [Au(IPr)(X)] adduct. The fastest rates of cleavage were found to occur for the hydrogen chloride salt of PPA (PPA-HCl) and for the CO 2 adduct of PPA, PPA-CO 2 = the carbamic acid (CA). This transformation was studied as a function of [CA], pressure of CO 2 as well as temperature. Detailed computational studies support the formation of a key intermediate and are also in agreement with a rapid carbonylation/decarbonylation reaction. The computed reactions mechanisms for addition of PPA-HCl and CA are also presented as well as the crystal structure of 1.

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

Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA

Metazoan microRNAs require specificmaturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding of how Microprocessor recognizes primary microRNA transcripts (pri-miRNAs). In this paper we present a cryoelectron microscopy structure of human Microprocessor with a pri-miRNA docked in the active site, poised for cleavage. The basal junction is recognized by a four-way intramolecular junction in Drosha, triggered by the Belt and Wedge regions that clamp over the ssRNA. The belt is important for efficiency and accuracy of pri-miRNA processing. TwodsRBDs form a molecular ruler tomeasure the stem length between the twodsRNA-ssRNAjunctions. The specific organization of thedsRBDs near the apical junction is independent of Drosha core domains, as observed in a second structure in the partially docked state. Collectively, we derive a molecular model to explain how Microprocessor recognizes a pri-miRNA and accurately identifies the cleavage site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Effects of low-temperature neutron irradiation on the microstructure and tensile properties of duplex 2304 stainless steel and its electron-beam welds

A lean duplex stainless steel material (2304-grade) in its base metal and electron beam (e-beam) welded conditions were studied microstructurally and mechanically as a function of irradiation conditions to evaluate its use as a structural material at low temperatures (60–100 °C). Neutron irradiation up to a fluence of 1.40 × 10 19 n/cm 2 (E > 0.1 MeV) or ~0.011 dpa decreased the total elongation of both base metal and e-beam welded samples. Overall, radiation hardening was observed in all the samples. The transversely cut irradiated samples showed some nonuniform quasi-cleavage and shearing in their fracture surfaces, indicating the variance of ductile nature of the two-phased (deformable austenite and harder ferrite) duplex structure. The e-beam welded samples also showed quasi-cleavage fracture, which is a characteristic of radiation-induced embrittlement. Furthermore, these observations of the e-beam welded samples were attributed to the formation of coarse ferrites, grain boundary and intragranular phases such as γ 2 and γ 3 , and minor impurity phases such as CrN and Cr 2 N in the weld pool and/or heat-affected zone of the samples. Radiation-induced elemental segregation was also identified in the post-irradiated base metal.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser

NendoU from SARS-CoV-2 is responsible for the virus’s ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Bimetallic-Derived Catalytic Structures for CO 2 -Assisted Ethane Activation

In recent years, the simultaneous upgrading of CO 2 and ethane has emerged as a promising approach for generating valuable gaseous (CO, H 2 , and ethylene) and liquid (aromatics and C 3 oxygenates) chemicals from the greenhouse gas CO 2 and large-reserved shale gas. The key challenges for controlling product selectivity lie in the selective C-H and C-C bond cleavage of ethane with the assistance of CO 2 . Bimetallic-derived catalysts likely undergo alloying or oxygen-induced segregation under reaction conditions, thus providing diverse types of interfacial sites, e.g., metal/support (M/M'O x ) interface and metal oxide/metal (M'O x /M) inverse interface, that are beneficial for selective CO 2 -assisted ethane upgrading. The alloying extent can be initially predicted by cohesive energy and atomic radius (or Wigner-Seitz radius), while the preference for segregation to form the on-top suboxide can be approximated using the work function, electronegativity, and binding strength of adsorbed oxygen. Furthermore, bimetallic-derived catalysts are typically supported on high surface area oxides. Modifying the reducibility and acidity/basicity of the oxide supports and introducing surface defects facilitate CO 2 activation and oxygen supplies for ethane activation. Using in situ synchrotron characterization and density functional theory (DFT) calculations, we found that the electronic properties of oxygen species influence the selective cleavage of C-H/C-C bonds in ethane, with electron-deficient oxygen over the metal (or alloy) surface promoting nonselective bond scission to produce syngas and electron-enriched oxygen over the metal oxide/metal interface enhancing selective C-H scission to yield ethylene. Here, we further demonstrate that the preferred structures of the catalyst surfaces, either alloy surfaces or metal oxide/metal inverse interfaces, can be controlled through the appropriate choice of metal combinations and their atomic ratios. Through a comprehensive comparison of experimental results and DFT calculations, the selectivity of C-C/C-H bond scission is correlated with the thermodynamically favorable bimetallic-derived structures (i.e., alloy surfaces or metal oxide/metal inverse interfaces) under reaction conditions over a wide range of bimetallic catalysts. These findings not only offer structural and mechanistic insights into bimetallic-derived catalysts but also provide design principles for selective catalysts for CO 2 -assisted activation of ethane and other light alkanes. This Account concludes by discussing challenges and opportunities in designing advanced bimetallic-derived catalysts, incorporating new reaction chemistries for other products, employing precise synthesis strategies for well-defined structures with optimized site densities, and leveraging time/spatial/energy-resolved in situ spectroscopy/scattering/microscopy techniques for comprehensive structural analysis. The research methodologies established here are helpful for the investigation of dynamic alloy and interfacial structures and should inspire more efforts toward the simultaneous upgrading of CO 2 and shale gas.

03 NATURAL GAS↗