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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Mild, Electroreductive Lignin Cleavage: Optimizing the Depolymerization of Authentic Lignins

Among candidate strategies to depolymerize lignin, electroreduction has promise as a mild, environmentally friendly, low-cost method to cleave lignin’s most common linkage, the β-O-4 bond. Much of the prior work on lignin electrolysis has focused on anodic (oxidative) approaches, while most available electroreduction studies have studied lignin model compounds rather than authentic lignin. Here, after optimizing with a model system, we investigated the room-temperature electroreductive cleavage of four common lignin samples from different pretreatment approaches, including Kraft, Soda, GVL, and Cu-AHP lignin. This mild electrolysis process resulted in the solubilization of 45% of the GVL lignin and 60% of the Cu-AHP lignin, affording approximately 17.6 and 19.4 wt % of monomeric materials, respectively. Furthermore, the present work is an encouraging first step toward an electroreductive strategy for lignin depolymerization and upgrading.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Depolymerization of Hydroxylated Polymers via Light-Driven C–C Bond Cleavage

The accumulation of persistent plastic waste in the environment is widely recognized as an ecological crisis. New chemical technologies are necessary both to recycle existing plastic waste streams into high-value chemical feedstocks and to develop next-generation materials that are degradable by design. Here, we report a catalytic methodology for the depolymerization of a commercial phenoxy resin and high molecular weight hydroxylated polyolefin derivatives upon visible light irradiation near ambient temperature. Proton-coupled electron transfer (PCET) activation of hydroxyl groups periodically spaced along the polymer backbone furnishes reactive alkoxy radicals that promote chain fragmentation through C–C bond β-scission. The depolymerization produces well-defined and isolable product mixtures that are readily diversified to polycondensation monomers. In addition to controlling depolymerization, the hydroxyl group modulates the thermomechanical properties of these polyolefin derivatives, yielding materials with diverse properties. Furthermore, these results demonstrate a new approach to polymer recycling based on light-driven C–C bond cleavage that has the potential to establish new links within a circular polymer economy and influence the development of new degradable-by-design polyolefin materials.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Synthetically Reversible, Proton-Mediated Nitrite N–O Bond Cleavage at a Dicopper Site

A monocationic dicopper(I,I) nitrite complex [Cu 2 (μ-κ 1 :κ 1 -O 2 N)DPFN][NTf 2 ] (2) (DPFN = 2,7-bis(fluoro-di(2-pyridyl)methyl)-1,8-naphthyridine, NTf 2 – = N(SO 2 CF 3 ) 2 – ), was synthesized by treatment of a dicopper acetonitrile complex, [Cu 2 (μ-MeCN)DPFN][NTf 2 ] 2 (1), with tetrabutylammonium nitrite ([nBu 4 N][NO 2 ]). DFT calculations indicate that 2 is one of three linkage isomers that are close in energy and presumably accessible in solution. Reaction of the μ-κ 1 :κ 1 -O 2 N complex with p-TolSH produces nitrous acid (HONO) and the corresponding dicopper thiolate species via an acid–base exchange reaction. Notably, treatment of 2 with HNTf 2 results in N–O bond cleavage in the putative, HONO-ligated complex to form the more thermodynamically favorable nitrosyl-bridged dicopper complex [Cu 2 (μ-NO)(μ-OH)DPFN][NTf 2 ] 2 (4). This scission can be reversed via deprotonation of the hydroxy ligand with KO t Bu. X-ray diffraction studies confirmed the solid-state molecular structures of 2 and 4. DFT calculations were used to construct a reaction coordinate diagram detailing formation of the μ-NO complex and to describe its electronic structure. The nitrosyl ligand in 4 is chemically labile, as demonstrated by its ready displacement in reactions with CO or NO 2 – .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Photochemical Tungsten–Carbon Bond Cleavage in Bicyclic Tungstacyclopentanes

W(NCPh 3 )(OSiPh 3 ) 2 (C7H 12 ) (1) and W(NAd)(OSiPh 3 ) 2 (C 7 H 12 ) (2) undergo photochemical α-hydrogen abstraction to form alkylidenes. Transient absorption studies suggest that fast W–C homolysis precedes thermal α-hydrogen abstraction. Radical trapping experiments in the presence of 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) support formation of an alkyl radical in these reactions. DFT calculations of models of 1 and 2 are also consistent with formation of W(V)-alkyl-radical intermediates that ultimately abstract an α-hydrogen to form the alkylidene. This article provides evidence for W–C bond cleavage in reac-tions that convert catalytically inactive d 0 tungstacyclopentanes into metathesis-active alkylidenes.

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

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Abstract In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226–234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Catalytic carbon–carbon bond cleavage in lignin via manganese–zirconium-mediated autoxidation

Abstract Efforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl–ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon–carbon (C–C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C–C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to cis,cis -muconic acid in an engineered strain of Pseudomonas putida KT2440 that conducts aromatic O -demethylation reactions at the 4-position. This work demonstrates that autoxidation of lignin with Mn and Zr offers a catalytic strategy to increase the yield of valuable aromatic monomers from lignin.

09 BIOMASS FUELS↗
DOE OSTI2024

Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes

FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme’s biological significance, the molecular architecture of the FAM111A serine protease domain (SPD) is unknown. Here, we show that FAM111A is a dimerization-dependent protease containing a narrow, recessed active site that cleaves substrates with a chymotrypsin-like specificity. X-ray crystal structures and mutagenesis studies reveal that FAM111A dimerizes via the N-terminal helix within the SPD. This dimerization induces an activation cascade from the dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. Dimerization is essential for proteolytic activity in vitro and for facilitating DNA replication at DNA-protein crosslink obstacles in cells, while it is dispensable for autocleavage. These findings underscore the role of dimerization in FAM111A’s function and highlight the distinction in its dimerization dependency between substrate cleavage and autocleavage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enzymatic cleavage of model lignin dimers depends on pH, enzyme, and bond type

Lignin is composed of phenylpropanoid monomers linked by ether and carbon-carbon bonds to form a complex heterogeneous structure. Bond-specific studies of lignin-modifying enzymes (LMEs; e.g., laccases and peroxidases) are limited by the polymerization of model lignin substrates and repolymerization of cleavage products. Here we present a high throughput platform to screen LME activities on four tagged model lignin compounds that represent the β-O-4’, β-β’, 5–5’, and 4-O-5’ linkages in lignin. We utilized nanostructure-initiator mass spectrometry (NIMS) and model lignin compounds with tags containing perfluorinated and cationic moieties, which effectively limit polymerization and condensation of the substrates and their degrading products. Sub-microliter sample droplets were printed on the NIMS chip with a novel robotics method. This rapid platform enabled characterization of LMEs across a range of pH 3–10 and relative quantification of modified (typically oxidized), cleaved, and polymerized products. All tested enzymes oxidized the four substrates and cleaved the β-O-4’ and β-β’ substrates to monomeric products. We discovered that the active pH range depended on both the substrate and the enzyme type. This has important applications for biomass conversion to biofuels and bioproducts, where the relative percentages of different bond types in lignin varies depending on feedstock and chemical pretreatment methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Electrocatalytic cleavage of lignin model dimers using ruthenium supported on activated carbon cloth

Biomass lignin is the largest natural source of renewable aromatic compounds, creating an opportunity for its use as a feedstock provided that deconstruction and upgrading methods become available. Valorization of lignin is challenging because its complex structure is naturally recalcitrant to biological degradation. Deconstruction of this amorphous cross-linked polymer requires cleavage of aryl ether bonds, which account for more than half of the linkages between lignin's phenylpropanoid building blocks. High temperature cracking of lignin is possible via pyrolysis, but linkages such as 4-O-5 bonds are resistant to thermal degradation. Electrocatalytic hydrogenation offers a mild alternative; operated at low temperature and atmospheric pressure, it cleaves ether bonds while saturating aromatic rings with in situ generated hydrogen. To investigate the use of catalytic ruthenium supported on activated carbon cloth to cleave 4-O-5 bonds, model compounds that exhibit this linkage were selected, including 3-phenoxyphenol, 4-phenoxyphenol, 3-phenoxyanisole, and 3-phenoxytoluene. The two phenols, 3-phenoxyphenol and 4-phenoxyphenol, were cleaved and hydrogenated to form cyclohexanol. 3-Phenoxyanisole and 3-phenoxytoluene were also cleaved but with lower conversion rates and cyclohexanol yields. Alkaline electrolyte solutions showed the highest cyclohexanol yields for both substrates. Increasing substrate concentrations from 10 mM to 40 mM increased faradaic efficiency to 25%, while decreasing current density from 100 mA (33.33 mA cm -2 ) to 20 mA (6.67 mA cm -2 ) greatly improved the faradaic efficiency to 96%.

09 BIOMASS FUELS↗
DOE OSTI2025

The importance of ester cleavage in the butylamine pretreatment of hybrid poplar

Butylamine is an effective in-and-out pretreatment solvent for hybrid poplar. It penetrates the cell walls and breaks ester cross-linkages, facilitating lignin release and improving enzymatic digestion. This work explores the “in-and-out” pretreatment of hybrid poplar with butylamine as a distillable protic solvent and reagent. The butylamine solvent can be removed by vacuum distillation with >95% solvent removal in all cases, providing a valuable scheme for efficient solvent recovery and recycling. Running the reaction with neat butylamine at 140 °C for 3 hours results in high yields of monosaccharides (90% glucose and 71% xylose) after enzymatic digestion, and a good tolerance to water content with no significant reduction in glucose yield up to an 8 : 1 water : butylamine ratio. We investigate the mechanisms of this pretreatment using powder X-ray diffraction, thermogravimetric analysis, fluorescence microscopy, elemental analysis, solid state and solution state nuclear magnetic spectroscopy to observe chemical and material markers of the pretreatment chemistry. The results suggest that the butylamine leaves the macro and microstructural properties of the lignocellulose relatively unaltered, but conducts targeted ester cleavage chemistry to remove cross-links between the various biopolymers and partially solubilize the lignin component of the biomass. These findings should act to guide future development of pretreatment chemistry for the development of biorefinery processes, and assist in the utilization of biomass as a starting point for chemical syntheses.

Palasz, Joseph M↗
DOE OSTI2023

Facile and dynamic cleavage of every iron–sulfide bond in cuboidal iron–sulfur clusters

Nature employs weak-field metalloclusters to support a wide range of biological processes. The most ubiquitous metalloclusters are the cuboidal Fe–S clusters, which are comprised of Fe sites with locally high-spin electronic configurations. Such configurations enhance rates of ligand exchange and imbue the clusters with a degree of structural plasticity that is increasingly thought to be functionally relevant. Here, we examine this phenomenon using isotope tracing experiments. Specifically, we demonstrate that synthetic [Fe 4 S 4 ] and [MoFe 3 S 4 ] clusters exchange their Fe atoms with Fe 2+ ions dissolved in solution, a process that involves the reversible cleavage and reformation of every Fe–S bond in the cluster core. This exchange is facile—in most cases occurring at room temperature on the timescale of minutes—and documented over a range of cluster core oxidation states and terminal ligation patterns. In addition to suggesting a highly dynamic picture of cluster structure, these results provide a method for isotopically labeling pre-formed clusters with spin-active nuclei, such as 57 Fe. Such a protocol is demonstrated for the radical S -adenosyl- l -methionine enzyme, RlmN.

Science & Technology - Other Topics↗
DOE OSTI2024

Structural insights into RNA cleavage by a novel family of bacterial RNases

Abstract Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.

Biochemistry & Molecular Biology↗
DOE OSTI2020

A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions

Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry–based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo–assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar Populus × canescens 717-1B4 in interaction with the ectomycorrhizal basidiomycete Laccaria bicolor . In total, we identified 1,660 and 2,870 Populus and L. bicolor unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of L. bicolor . These PCPs mapped to 64 Populus proteins and 69 L. bicolor proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.

59 BASIC BIOLOGICAL SCIENCES↗