Search NASA⌕ Search

SEARCH · Search NASA

Results for “CLEAVAGE”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Deciphering decomposition pathways of high explosives with cryogenic X-ray Raman spectroscopy

We employed cryogenic X-ray Raman spectroscopy to investigate the early-stage decomposition of the high explosive molecule hexanitrohexaazaisowurtzitane (CL-20). By systematically varying the radiation dose under cryogenic conditions, we induced the decomposition of the molecule using ionizing radiation and observed the evolution of spectral features at the carbon, nitrogen, and oxygen K edges. Through extensive first-principles calculations, we identified key intermediates in the early stages of the decomposition process, resulting from C–C and C–N bond cleavage which leads to the opening of the internal cage structure. A detailed analysis of spectral trends and fingerprints provided evidence supporting N–NO 2 homolytic cleavage as the primary initial decomposition pathway. The combination of advanced core-level spectroscopy methods and state-of-the-art theoretical calculations enabled a comprehensive characterization of the molecular changes induced by controlled radiation dose exposures. In conclusion, our findings establish a benchmark for understanding the decomposition chemistry of high-explosive materials, offering important insights into their stability and reactivity under extreme conditions.

X-ray Raman spectroscopy↗
DOE OSTI2024

Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader

Abstract Bacteria that are chronically exposed to high levels of pollutants demonstrate genomic and corresponding metabolic diversity that complement their strategies for adaptation to hydrocarbon-rich environments. Whole genome sequencing was carried out to infer functional traits of Serratia marcescens strain SMTT recovered from soil contaminated with crude oil. The genome size (Mb) was 5,013,981 with a total gene count of 4,842. Comparative analyses with carefully selected S. marcescens strains, 2 of which are associated with contaminated soil, show conservation of central metabolic pathways in addition to intra-specific genetic diversity and metabolic flexibility. Genome comparisons also indicated an enrichment of genes associated with multidrug resistance and efflux pumps for SMTT. The SMTT genome contained genes that enable the catabolism of aromatic compounds via the protocatechuate para-degradation pathway, in addition to meta-cleavage of catechol (meta-cleavage pathway II); gene enrichment for aromatic compound degradation was markedly higher for SMTT compared to the other S. marcescens strains analysed. Our data presents a valuable genetic inventory for future studies on strains of S. marcescens and provides insights into those genomic features of SMTT with industrial potential.

Genetics & Heredity↗
DOE OSTI2021

Flavonoids naringenin chalcone, naringenin, dihydrotricin, and tricin are lignin monomers in papyrus

Recent studies demonstrate that several polyphenolic compounds produced from beyond the canonical monolignol biosynthetic pathways can behave as lignin monomers, participating in radical coupling reactions and being incorporated into lignin polymers. Here, we show various classes of flavonoids, the chalconoid naringenin chalcone, the flavanones naringenin and dihydrotricin, and the flavone tricin, incorporated into the lignin polymer of papyrus (Cyperus papyrus L.) rind. These flavonoids were released from the rind lignin by Derivatization Followed by Reductive Cleavage (DFRC), a chemical degradative method that cleaves the β-ether linkages, indicating that at least a fraction of each was integrated into the lignin as β-ether-linked structures. Due to the particular structure of tricin and dihydrotricin, whose C-3' and C-5' positions at their B-rings are occupied by methoxy groups, these compounds can only be incorporated into the lignin through 4'–O–β bonds. However, naringenin chalcone and naringenin have no substituents at these positions and can therefore form additional carbon–carbon linkages, including 3'– or 5'–β linkages that form phenylcoumaran structures not susceptible to cleavage by DFRC. Furthermore, Nuclear Magnetic Resonance analysis indicated that naringenin chalcone can also form additional linkages through its conjugated double bond. The discovery expands the range of flavonoids incorporated into natural lignins, further broadens the traditional definition of lignin, and enhances the premise that any phenolic compound present at the cell wall during lignification could be oxidized and potentially integrated into the lignin structure, depending only on its chemical compatibility. This study indicates that papyrus lignin has a unique structure, as it is the only lignin known to date that integrates such a diversity of phenolic compounds from different classes of flavonoids. This discovery will open up new ways to engineer and design lignins with specific properties and for enhanced value.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Probing the local electronic structure of isovalent Bi atoms in InP

Cross-sectional scanning tunneling microscopy (X-STM) is used to experimentally study the influence of isovalent Bi atoms on the electronic structure of InP. In this work, we map the spatial pattern of the Bi impurity state, which originates from Bi atoms down to the sixth layer below the surface, in topographic, filled-state X-STM images on the natural {110} cleavage planes. The Bi impurity state has a highly anisotropic bowtielike structure and extends over several lattice sites. These Bi-induced charge redistributions extend along the $\langle$110$\rangle$ directions, which define the bowtielike structures we observe. Local tight-binding calculations reproduce the experimentally observed spatial structure of the Bi impurity state. In addition, the influence of the Bi atoms on the electronic structure is investigated in scanning tunneling spectroscopy measurements. These measurements show that Bi induces a resonant state in the valence band, which shifts the band edge toward higher energies. Furthermore, we show that the energetic position of the Bi-induced resonance and its influence on the onset of the valence band edge depend crucially on the position of the Bi atoms relative to the cleavage plane.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Programming PAM antennae for efficient CRISPR-Cas9 DNA editing

Bacterial CRISPR-Cas9 nucleases have been repurposed as powerful genome editing tools. Whereas engineering guide RNAs or Cas nucleases have proven to improve the efficiency of CRISPR editing, modulation of protospacer-adjacent motif (PAM), indispensable for CRISPR, has been less explored. Here, we develop a DNA origami–based platform to program a PAM antenna microenvironment and address its performance at the single-molecule level with submolecular resolution. To mimic spatially controlled in vivo PAM distribution as may occur in chromatin, we investigate the effect of PAM antennae surrounding target DNA. We find that PAM antennae effectively sensitize the DNA cleavage by recruiting Cas9 molecules. Super-resolution tracking of single single-guide RNA/Cas9s reveals localized translocation of Cas9 among spatially proximal PAMs. We find that the introduction of the PAM antennae effectively modulates the microenvironment for enhanced target cleavage (up to ~50%). These results provide insight into factors that promote more efficient genome editing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro

SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2

Targeting the main protease of SARS-CoV-2 Inside host cells, the RNA genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is translated into two polyproteins that are cleaved to give the individual viral proteins. The main viral protease, known as Mpro or 3CLpro, plays a key role in these cleavages, making it an important drug target. Drayman et al . identified eight drugs that target 3CLpro from a library of 1900 clinically safe drugs. Because of the challenge of working with SARS-CoV-2, they started by screening for drugs that inhibit the replication of a human coronavirus that causes the common cold. They then evaluated the top hits for inhibiting SARS-CoV-2 replication and for inhibiting 3CLpro. Masitinib, a broad antiviral, inhibited the main proteases of coronaviruses and picornaviruses and was effective in reducing SARS-CoV-2 replication in mice.

Drayman, Nir↗
DOE OSTI2022

Craspase is a CRISPR RNA-guided, RNA-activated protease

The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo–electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5' region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain–binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA–activated protease with self-regulatory capacity.

Science & Technology - Other Topics↗
DOE OSTI2024

Electrically driven proton transfer promotes Brønsted acid catalysis by orders of magnitude

Electric fields play a key role in enzymatic catalysis and can enhance reaction rates by 100,000-fold, but the same rate enhancements have yet to be achieved in thermochemical heterogeneous catalysis. In this work, we probe the influence of catalyst potential and interfacial electric fields on heterogeneous Brønsted acid catalysis. We observed that variations in applied potential of ~380 mV led to a 100,000-fold rate enhancement for 1-methylcyclopentanol dehydration, which was catalyzed by carbon-supported phosphotungstic acid. Mechanistic studies support a model in which the interfacial electrostatic potential drop drives quasi-equilibrated proton transfer to the adsorbed substrate prior to rate-limiting C–O bond cleavage. Large increases in rate with potential were also observed for the same reaction catalyzed by Ti/TiO y H x and for the Friedel Crafts acylation of anisole with acetic anhydride by carbon-supported phosphotungstic acid.

Science & Technology - Other Topics↗
DOE OSTI2020

Improved analysis of arabinoxylan-bound hydroxycinnamate conjugates in grass cell walls

Background: Arabinoxylan in grass cell walls is acylated to varying extents by ferulate and p-coumarate at the 5-hydroxy position of arabinosyl residues branching off the xylan backbone. Some of these hydroxycinnamate units may then become involved in cell wall radical coupling reactions, resulting in ether and other linkages amongst themselves or to monolignols or oligolignols, thereby crosslinking arabinoxylan chains with each other and/or with lignin polymers. This crosslinking is assumed to increase the strength of the cell wall, and impedes the utilization of grass biomass in natural and industrial processes. A method for quantifying the degree of acylation in various grass tissues is, therefore, essential. We sought to reduce the incidence of hydroxycinnamate ester hydrolysis in our recently introduced method by utilizing more anhydrous conditions. Results: The improved methanolysis method minimizes the undesirable ester-cleavage of arabinose from ferulate and p-coumarate esters, and from diferulate dehydrodimers, and produces more methanolysis vs. hydrolysis of xylan-arabinosides, improving the yields of the desired feruloylated and p-coumaroylated methyl arabinosides and their diferulate analogs. Free ferulate and p-coumarate produced by ester-cleavage were reduced by 78% and 68%, respectively, and 21% and 39% more feruloyl and p-coumaroyl methyl arabinosides were detected in the more anhydrous method. The new protocol resulted in an estimated 56% less combined diferulate isomers in which only one acylated arabinosyl unit remained, and 170% more combined diferulate isomers conjugated to two arabinosyl units. Conclusions: Overall, the new protocol for mild acidolysis of grass cell walls is both recovering more ferulate- and p-coumarate-arabinose conjugates from the arabinoxylan and cleaving less of them down to free ferulic acid, p-coumaric acid, and dehydrodiferulates with just one arabinosyl ester. This cleaner method, especially when coupled with the orthogonal method for measuring monolignol hydroxycinnamate conjugates that have been incorporated into lignin, provides an enhanced tool to measure the extent of crosslinking in grass arabinoxylan chains, assisting in identification of useful grasses for biomass applications.

09 BIOMASS FUELS↗
DOE OSTI2026

Next-Generation Sequencing Data from a CUT&RUN Study of R. toruloides IFO0880 Cse4 and Orc1 Binding Sites

Rhodotorula toruloides has been increasingly explored as a host for bioproduction of lipids, fatty acid derivatives and terpenoids. Various genetic tools have been developed, but neither a centromere nor an autonomously replicating sequence (ARS), both necessary elements for stable episomal plasmid maintenance, has yet been reported. In this study, cleavage under targets and release using nuclease (CUT&RUN), a method used for genome-wide mapping of DNA–protein interactions, was used to identify R. toruloides IFO0880 genomic regions associated with the centromeric histone H3 protein Cse4, a marker of centromeric DNA. Fifteen putative centromeres ranging from 8 to 19 kb in length were identified and analyzed, and four were tested for, but did not show, ARS activity. These centromeric sequences contained below average GC content, corresponded to transcriptional cold spots, were primarily nonrepetitive and shared some vestigial transposon-related sequences but otherwise did not show significant sequence conservation. Future efforts to identify an ARS in this yeast can utilize these centromeric DNA sequences to improve the stability of episomal plasmids derived from putative ARS elements.

Genome Engineering↗
DOE OSTI2026

MnRhBi3: A Cleavable Antiferromagnetic Metal

This dataset contains DFT input and output files supporting the theoretical modeling in the associated publication (Chem. Mater. 2024, 36, 11306-11316). The calculations characterize MnRhBi3, an orthorhombic (Cmmm) van der Waals-layered intermetallic compound that cleaves easily between neighboring Bi layers. The dataset is organized into three calculation types: (i) Bulk: Structural relaxations of the periodic MnRhBi3 crystal in antiferromagnetic (AFM) and ferromagnetic (FM) configurations, using the vdW-DF-optB86b functional. These provide the equilibrium lattice constants, magnetic energy differences (AFM is 0.5 meV/f.u. lower than FM), and magnetic moments (4.4 µB/Mn, 0.17 µB/Rh, 0.18 µB/Bi) reported in Table 1 of the main text. (ii) Slab: Same magnetic configurations computed with an 18 Ang vacuum layer introduced between Bi layers, used to calculate the cleavage energy Ec = 0.56 J/m2 (AFM) and 0.57 J/m2 (FM), establishing MnRhBi3 as a van der Waals-layered material comparable to graphite, MoS2, and CrI3. (iii) ELF: Single-point calculation on the relaxed bulk AFM geometry with LELF=.TRUE., producing the ELFCAR file used to generate electron localization function isosurfaces and contour maps (Fig. 2, main text) showing Bi lone pairs directed into the van der Waals gaps. All folders contain CONTCAR, INCAR, KPOINTS, OUTCAR, and POSCAR. The ELF/ folder additionally contains ELFCAR. Calculations were performed using VASP 6.3.2 with PBE + vdW-DF-optB86b, PAW potentials, and an energy cutoff of 800 eV.

36 MATERIALS SCIENCE↗
DOE OSTI2021

High Throughput expression and characterization of laccases in Saccharomyces cerevisiae [Poster]

We are working to generate fundamental understanding of enzymatic depolymerization of lignin and using this understanding to engineer mixtures of enzymes that catalyze the reactions necessary to efficiently depolymerize lignin into defined fragments. Over the years the enzymes involved in these processes have been difficult to study, because 1) the enzymes thought to be most important, fungal laccases and peroxidases, are very difficult to express in soluble, active form; 2) the full complement of required enzymes and whether or not they act synergistically is not known; 3) analysis of bond cleavage events is difficult due to the lack of analytical tools for measuring bond cleavage events in either polymeric lignin or model lignin-like compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Catalytic Activation of Pyran Ethers in Self-Solvating Saccharides with Alkaline Earth Metals (Final Report)

Catalytic activation of cellulose ethers occurs via hydroxyl-stabilized cleavage of inter-monomer glycosidic bonds. Cooperativity between two hydroxyl groups lowers the ether cleavage transition state necessary to break apart long carbohydrate chains to initiate small molecule formation as fuel precursors. Metals existing with lignocellulosic materials including alkaline earth metals (Ca 2+ , Mg 2+ ) or alkali (Na + , K + ) also can catalyze ether scission cooperatively. By bonding with carbohydrate hydroxyl groups, a metal cation disrupt the hydrogen bonding network and free carbohydrate functional groups to react; a second metal cation stabilizes the carbohydrate ether transition state and enhances the rate of polymer scission. In this work, we expanded our initial understanding of metal-catalyzed glycoside ether scission. Within polysaccharides such as cellulose, two ether groups exist: one between monomers (glycosidic linkages) and one within a pyran ring. The hydroxyl-group hydrogen bonding network and bound metal ions form low energy binding states that interact with both ether oxygens simultaneously. Based on this interaction, our primary hypothesis was that the competition between stabilizing the two ether scission transition states determines the extent of the major pathways. Metals that disrupt the hydrogen bonding network of the C6 of sugars and stabilize the glycosidic ether promote transglycosylation to levoglucosan; in contrast, metals that stabilize the pyran ether oxygen promote sugar ring fragmentation to furans such as furfural. Varying characteristics of metal cation catalysts and configurations of bound polysaccharide chains dictate the relative rates of ether scission.

09 BIOMASS FUELS↗
DOE OSTI2023

Triphenylborane in Metal-Free Catalysis

The development and application of new organoboron reagents as Lewis acids in synthesis and metal-free catalysis have dramatically expanded over the past 20 years. In this context, we will show the recent uses of the simple and relatively weak Lewis acid BPh 3 —discovered 100 years ago—as a metal-free catalyst for various organic transformations. The first part will highlight catalytic applications in polymer synthesis such as the copolymerization of epoxides with CO 2 , isocyanate, and organic anhydrides to various polycarbonate copolymers and controlled diblock copolymers as well as alternating polyurethanes. This is followed by a discussion of BPh 3 as a Lewis acid component in the frustrated Lewis pair (FLP) mediated cleavage of hydrogen and hydrogenation catalysis. In addition, BPh 3 -catalyzed reductive N-methylations and C-methylations with CO 2 and silane to value-added organic products will be covered as well along with BPh 3 -catalyzed cycloadditions and insertion reactions. Collectively, this mini-review showcases the underexplored potential of commercially available BPh3 in metal-free catalysis.

Lewis acid↗
DOE OSTI2023

Site-Selective Polyolefin Hydrogenolysis on Atomic Ru for Methanation Suppression and Liquid Fuel Production

Catalytic hydrogenolysis of end-of-life polyolefins can produce value-added liquid fuels and therefore holds great promises in plastic waste reuse and environmental remediation. The major challenge limiting the recycling economic benefit is the severe methanation (usually >20%) induced by terminal C–C cleavage and fragmentation in polyolefin chains. Here, we overcome this challenge by demonstrating that Ru single-atom catalyst can effectively suppress methanation by inhibiting terminal C–C cleavage and preventing chain fragmentation that typically occurs on multi-Ru sites. The Ru single-atom catalyst supported on CeO 2 shows an ultralow CH 4 yield of 2.2% and a liquid fuel yield of over 94.5% with a production rate of 314.93 g fuels g Ru -1 h -1 at 250 °C for 6 h. Such remarkable catalytic activity and selectivity of Ru single-atom catalyst in polyolefin hydrogenolysis offer immense opportunities for plastic upcycling.

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

Shinkolobweite, from the Shinkolobwe Mine, Democratic Republic of Congo: A New Mineral Containing Uranium in the Rare Pentavalent Oxidation State

ABSTRACT Shinkolobweite, Pb1.333[U5+O(OH)(UO2)5O4.67(OH)5.33](H2O)5, is a new lead uranyl oxide-hydroxide hydrate mineral containing hexavalent and pentavalent uranium from the Shinkolobwe mine, Democratic Republic of Congo. Crystals of shinkolobweite are dark reddish-brown prisms up to 0.5 mm in length, occurring on a matrix of massive uraninite associated with fourmarierite, rutherfordine, soddyite, and sklodowskite. Crystals are translucent with subadamantine luster and light bronze-yellow streak, are flattened on {010}, are elongated on [001], and exhibit the forms {100}, {010}, {101}, and . The mineral is non-fluorescent under both longwave and shortwave ultraviolet illumination. It has a Mohs hardness of ∼2 and exhibits brittle tenacity with perfect cleavage on {010}, imperfect cleavage on {100}, and even fracture. The calculated density is 5.853 g/cm3 based on the empirical formula. Electron probe microanalysis provided the empirical formula Pb1.290U6+4.876U5+1.166O27H16.633 based on 27 O apfu and U5+:U6+ determined by X-ray photoelectron spectroscopy. Shinkolobweite is orthorhombic, superspace group Pnnm(0b0)000, a = 14.4808(4), b = 7.0681(8), c = 11.9423(3) Å, V = 1222.32(15) Å3, modulation wave vector [0 1/3 0], and Z = 2. The structure was refined from 8959 reflections to a final R1 = 0.0736 for all reflections. Uranyl oxide-hydroxide sheets in shinkolobweite adopt the β-U3O8 topology and possess (3 + 1) commensurately modulated ordering that results from the long-range ordering of U5+ and U6+ in the sheet, as well as the position and occupancy of interlayer Pb2+ cations. Observations of a topological transition between α-U3O8 and β-U3O8 type sheets in shinkolobweite supplements our understanding of U5+ mineral oxidation and stability.

Mineralogy↗
DOE OSTI2023

Beyond n-dopants for organic semiconductors: use of bibenzo[ d ]imidazoles in UV-promoted dehalogenation reactions of organic halides

2,2’-Bis(4-dimethylaminophenyl)- and 2,2'-dicyclohexyl-1,1',3,3'-tetramethyl-2,2',3,3'-tetrahydro-2,2'-bibenzo[ d ]imidazole ((N-DMBI) 2 and (Cyc-DMBI) 2 ) are quite strong reductants with effective potentials of ca. −2 V vs ferrocenium/ferrocene, yet are relatively stable to air due to the coupling of redox and bond-breaking processes. Here, we examine their use in accomplishing electron transfer-induced bond-cleavage reactions, specifically dehalogenations. The dimers reduce halides that have reduction potentials less cathodic than ca. −2 V vs ferrocenium/ferrocene, especially under UV photoexcitation (using a 365 nm LED). In the case of benzyl halides, the products are bibenzyl derivatives, whereas aryl halides are reduced to the corresponding arenes. The potentials of the halides that can be reduced in this way, quantum-chemical calculations, and steady-state and transient absorption spectroscopy suggest that UV irradiation accelerates the reactions via cleavage of the dimers to the corresponding radical monomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗