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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Nucleophilic Thiols Reductively Cleave Ether Linkages in Lignin Model Polymers and Lignin

Lignin may serve as a renewable feedstock for the production of chemicals and fuels if mild, scalable processes for its depolymerization can be devised. The use of small organic thiols represents a bioinspired strategy to cleave the β–O–4 bond, the most common linkage in lignin. In the present study, synthetic β–O–4 linked polymers were treated with organic thiols, yielding up to 90 % cleaved monomer products. Lignin extracted from poplar was also treated with organic thiols resulting in molecular weight reductions as high as 65 % (Mn) in oxidized lignin. Thiol–based cleavage of other lignin linkages was also explored in small–molecule model systems to uncover additional potential pathways by which thiols might depolymerize lignin. The success of thiol–mediated cleavage on model dimers, polymers, and biomass–derived lignin illustrates the potential utility of small redox–active molecules to penetrate complex polymer matrices for depolymerization and subsequent valorization of lignin into fuels and chemicals.

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

Emitter Reconstruction for Cleaved CdSexTe1-x Devices with Cu vs. As Doping

CdTe absorbers have had historically low carrier densities of ~10^14 cm-3 due to the self-compensating nature of copper dopants. Recent advances in group-V (e.g., arsenic) doping have increased this to 10^16-10^17 cm-3, but modeling suggests that the front interface and emitter properties become limiting in this case. By cleaving arsenic- and copper-doped CdTe device stacks at the emitter/absorber interface, we gain the ability to reconstruct emitters with known properties, which will not change during subsequent device processing, and directly test the modeling. By doing so, we find a much larger performance drop in arsenic devices; this is attributed to insufficient electron density in the emitter and increased sensitivity to interface changes due to collapsed depletion width. This work can help guide emitter engineering for highly-doped CdTe devices in both the as-grown-superstrate- and cleaved-substrate configurations.

As-doped↗
DOE OSTI2023

Pseudomonas aeruginosa Dps (PA0962) Functions in H 2 O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity

We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe 2+ utilizing H 2 O 2 (not O 2 ) as an oxidant, suggesting Pa Dps functions to aid P. aeruginosa to survive H 2 O 2 -mediated oxidative stress. In agreement, a P. aeruginosa Δdps mutant is significantly more susceptible to H 2 O 2 than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe 2+ oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H 2 O 2 or O 2 but requires divalent cations and 12-mer Pa Dps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Thermomechanical Cleave of Polycrystalline CdTe Solar Cells and its Applications: A Review

One of the primary research challenges for cadmium telluride (CdTe) solar cells is addressing its open‐circuit voltage ( V OC ) deficit. While theoretical studies and single crystal work show V OC > 1 V is possible, devices remain stubbornly low at ≈800–900 mV. As absorber opto‐electronic properties (e.g., hole density, carrier lifetime) are improved, device modeling suggests that interfaces become limiting. Because CdTe‐based devices are typically grown in the superstrate configuration, the back interface is relatively accessible for manipulation and study, while the front interface (i.e., the heterojunction region) is buried under microns of material and inaccessible. NREL has developed a novel technique to thermomechanically cleave polycrystalline CdTe device stacks directly at the front interface, enabling characterization and controlled manipulation of this important region. Herein, recent work, primarily from NREL, will be reviewed, including considerations for achieving successful delamination; key scientific discoveries about the front interface that have been enabled by this technique; and practical applications, such as flexible, low‐cost solar with high power‐to‐weight ratio.

14 SOLAR ENERGY↗
DOE OSTI2020

Crystal Structure and C–H Bond-Cleaving Reactivity of a Mononuclear Co IV –Dinitrate Complex

High-valent Fe IV =O intermediates with a terminal metal–oxo moiety are key oxidants in many enzymatic and synthetic C–H bond oxidation reactions. While generating stable metal–oxo species for late transition metals remains synthetically challenging, notably, a number of high-valent non-oxo–metal species of late transition metals have been recently described as strong oxidants that activate C–H bonds. In this work, we obtained an unprecedented mononuclear Co IV –dinitrate complex (2) upon one-electron oxidation of its Co(III) precursor supported by a tridentate dianionic N3 ligand. 2 was structurally characterized by X-ray crystallography, showing a square pyramidal geometry with two coordinated nitrate anions. Furthermore, characterization of 2 using combined spectroscopic and computational methods revealed that 2 is a low-spin (S = 1/2) Co(IV) species with the unpaired electron located on the cobalt d z2 orbital, which is well positioned for substrate oxidations. Indeed, while having a high thermal stability, 2 is able to cleave sp 3 C–H bonds up to 87 kcal/mol to afford rate constants and kinetic isotope effects (KIEs) of 2–6 that are comparable to other high-valent metal oxidants. The ability to oxidize strong C–H bonds has yet to be observed for Co IV –O and Co III =O species previously reported. Therefore, 2 represents the first high-valent Co(IV) species that is both structurally characterized by X-ray crystallography and capable of activating strong C–H bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA

Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, Caenorhabditis elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1’s helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity

DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic 5 engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas 6 genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, in this paper we report 7 peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand 8 DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on 9 target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much 10 smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, 11 demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs

We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5'caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data from PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity

DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, we herein report peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.

Conversion↗
DOE OSTI2022

Targeting a proteolytic neoepitope on CUB domain containing protein 1 ( CDCP1 ) for RAS -driven cancers

Extracellular proteolysis is frequently dysregulated in disease and can generate proteoforms with unique neoepitopes not found in healthy tissue. Here, we demonstrate that Abs that selectively recognize a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) could enable more effective and safer treatments for solid tumors. CDCP1 is highly overexpressed in RAS-driven cancers, and its ectodomain is cleaved by extracellular proteases. Biochemical, biophysical, and structural characterization revealed that the 2 cleaved fragments of CDCP1 remain tightly associated with minimal proteolysis-induced conformational change. Using differential phage display, we generated recombinant Abs that are exquisitely selective to cleaved CDCP1 with no detectable binding to the uncleaved form. These Abs potently targeted cleaved CDCP1-expressing cancer cells as an Ab-drug conjugate, an Ab-radionuclide conjugate, and a bispecific T cell engager. In a syngeneic pancreatic tumor model, these cleaved-specific Abs showed tumor-specific localization and antitumor activity with superior safety profiles compared with a pan-CDCP1 approach. Targeting proteolytic neoepitopes could provide an orthogonal "AND" gate for improving the therapeutic index.

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 OSTI2019

Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å

HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the ‘PD-D/EXK’ superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Rapid Prototyping for Nanoparticle-Based Photonic Crystal Fiber Sensors

The advent of nanotechnology has motivated a revolution in the development of miniaturized sensors. Such sensors can be used for radiation detection, temperature sensing, radio-frequency sensing, strain sensing, and more. At the nanoscale, integrating the materials of interest into sensing platforms can be a common issue. One promising platform is photonic crystal fibers, which can draw in optically sensitive nanoparticles or have its optical properties changed by specialized nanomaterials. However, testing these sensors at scale is limited by the the need for specialized equipment to integrate these photonic crystal fibers into optical fiber systems. Having a method to enable rapid prototyping of new nanoparticle-based sensors in photonic crystal fibers would open up the field to a wider range of laboratories that could not have initially studied these materials in such a way before. This manuscript discusses the improved processes for cleaving, drawing, and rapidly integrating nanoparticle-based photonic crystal fibers into optical system setups. The method proposed in this manuscript achieved the following innovations: cleaving at a quality needed for nanoparticle integration could be done more reliably (≈100% acceptable cleaving yield versus ≈50% conventionally), nanoparticles could be drawn at scale through photonic crystal fibers in a safe manner (a method to draw multiple photonic crystal fibers at scale versus one fiber at a time), and the new photonic crystal fiber mount was able to be finely adjusted when increasing the optical coupling before inserting it into an optical system (before, expensive fusion splicing was the only other method).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗