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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin

Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tuning metal-support interactions in nickel–zeolite catalysts leads to enhanced stability during dry reforming of methane

Ni-based catalysts are highly reactive for dry reforming of methane (DRM) but they are prone to rapid deactivation due to sintering and/or coking. In this study, we present a straightforward approach for anchoring dispersed Ni sites with strengthened metal-support interactions, which leads to Ni active sites embedded in dealuminated Beta zeolite with superior stability and rates for DRM. The process involves solid-state grinding of dealuminated Beta zeolites and nickel nitrate, followed by calcination under finely controlled gas flow conditions. By combining in situ X-ray absorption spectroscopy and ab initio simulations, it is elucidated that the efficient removal of byproducts during catalyst synthesis is conducted to strengthen Ni–Si interactions that suppress coking and sintering after 100 h of time-on-stream. Transient isotopic kinetic experiments shed light on the differences in intrinsic turnover frequency of Ni species and explain performance trends. This work constructs a fundamental understanding regarding the implication of facile synthesis protocols on metal-support interaction in zeolite-supported Ni sites, and it lays the needed foundations on how these interactions can be tuned for outstanding DRM performance.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Oil and Natural Gas Development near and beneath Uranium Tailings Cells and Other Remediated Sites - 20358

DOE LM is responsible for maintaining remedies at more than 50 remediated sites that require active long-term surveillance and maintenance (LTS and M). Institutional controls (ICs) were established to limit human and environmental exposures to residual contamination by controlling land use, restricting access to potential hazards, and making the public aware of potential dangers from the residual contamination. ICs for each site were developed based on current and foreseeable conditions; however, these controls should evolve to mitigate potential human health and other environmental risks from unanticipated changes in activities or site conditions. Activities conducted beyond the DOE long-term care boundaries by non-DOE parties may impact the effectiveness of ICs or even the long-term stability of disposal cells and groundwater remedies. Several sites that LM manages or that will transfer to LM for LTS and M are in active oil and gas production basins. The sites are associated with uranium ore milling or nuclear test sites and have been remediated or are in the process of remediation and have no ongoing DOE mission. Particularly since 2005, hydraulic fracturing ('fracking') combined with directional drilling has dramatically increased oil and natural gas (oil/gas) production in the United States, now making it the number one hydrocarbon-producing country. Fracking has allowed production from shale and other rocks of low natural permeability that were historically not considered viable oil/gas resources. Also, because wellbores can now be drilled as many as 5 kilometers or more horizontally, hydrocarbons can be recovered from zones without having access to the surface above them. Drilling activity near Rulison, Colorado, the location of an underground nuclear detonation managed by LM, has raised public concerns that remnant radioactivity in the detonation zone could migrate to producing wells and enter the natural gas distribution system. At sites like the Falls City, Texas, Disposal site, transitioned to LM with a split estate, increased production in the region has resulted in wellbores beneath the long-term care boundary of the site. While the DOE license for Falls City was approved by the NRC in 1997 without the acquisition of the subsurface rights, NRC has raised concerns on whether this activity impacts the integrity of the cell and/or groundwater remedies. In Wyoming, LM is anticipating receiving the license for the Bear Creek site and manages the Spook site, both locations of uranium mill tailings disposal cells. These Wyoming sites are in an active region of major oil and gas development. This change in surrounding land use will require LM to work collaboratively with NRC to address these concerns. At several DOE sites radioactive waste, and often intermixed nonradioactive constituents, is permanently isolated in engineered disposal cells. At other sites, residual contamination can be present in groundwater, blast cavities, and infinite amounts within soil. Areas targeted for oil and gas development at the Texas and Wyoming sites range from depths of 2440 to 3350 meters (8000-11000 feet) below ground surface. When most site remedies were designed, oil and gas development was not considered to be an issue within the site boundary. With the more recent uses of directional drilling, fracking, and associated wastewater injections, the evaluative criteria for incoming sites and ICs for managing long-term protectiveness and regulatory compliance are changing. Although DOE surface ownership was previously thought to be a robust IC to prevent surface and subsurface development, particularly at disposal sites, that may no longer be the case. Whereas the subsurface development at Texas and Wyoming sites is currently occurring at thousands of meters beneath the surface, shallower and direct onsite development would be more of a concern for LM. The energy introduced when a well is hydraulically fractured causes microseismic events (magnitude -2 to 1.0) as the fractures propagate but does not directly cause seismic events (earthquakes) of sufficient magnitude to damage surface structures. Additionally, the extent of the hydraulic fractures is limited to the targeted depths, which are far below the surface. However, earthquakes of sufficient magnitude to damage surface structures have been attributed to the injection of wastewater into disposal wells. States that have experienced these effects have enacted regulations that limit the rate and pressures that wastewater can be injected into disposal wells. Items LM may consider are the need for monitoring the volume of water injected into nearby disposal wells and possibly installing seismic stations at sites most susceptible to damage. While the need to demonstrate that no impact from oil and gas extraction activities on a site groundwater remedy or disposal cells will vary from site to site, LM is assessing risk criteria for this activity. Though LM has not experienced an issue yet at a uranium tailings disposal site, it cannot assume that there will be none, and must address NRC concerns. LM is building on past experiences at other sites and beginning to form new processes with the hope that these concepts can be applied for other future sites. (authors)

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2020

Thermal Stability of Silica for Application in Thermal Energy Storage

Free from siting constraints, thermal energy storage (TES) shows promise as an economical alternative to traditional pumped-storage hydropower (PSH) and compressed air energy storage (CAES). As potential thermal energy storage media, many solid particles demonstrate stability over wide temperature ranges which allows for increased sensible energy storage density and is essential in achieving low-cost storage. Silica sand, in the form of a-quartz, is one such candidate. This work presents a brief review of relevant silica thermophysical properties and further investigates the thermal stability of silica particles as a candidate TES media by subjecting them to two different thermal campaigns: (1) a 500-hour thermal treatment at 1200°C under varied atmospheres; and (2) cycling 25, 50, and 100 times between 300°C and 1200°C. For both campaigns, particle stability is examined by means of pre- and post-treatment Mie scattering. An additional XRD analysis is conducted for the 500-hour treatment in air. Results indicate limited changes in both particle distribution and crystallographic structure which is promising for the application as solid particle media for thermal energy storage.

27 ARPA - Advanced Research Projects Agency-Energy↗
DOE OSTI2025

Fast product release requires active-site water dynamics in carbonic anhydrase

Water plays an essential role in enzyme structure, stability, and the substantial rate enhancement of enzyme catalysis. However, direct observations linking enzyme catalysis and active-site water dynamics pose a significant challenge due to experimental difficulties. By integrating an ultraviolet (UV) photolysis technique with temperature-controlled X-ray crystallography, we track the catalytic pathway of carbonic anhydrase II (CAII) at 1.2 Å resolution. This approach enables us to construct molecular movies of CAII catalysis, encompassing substrate (CO 2 ) binding, conversion from substrate to product (bicarbonate), and product release. In the catalytic pathway, we identify an unexpected configuration in product binding and correlate it with sub-nanosecond rearrangement of active-site water. Based on these experimental observations, we propose a comprehensive mechanism of CAII and describe the detailed structure and dynamics of active-site water in CAII. Our findings suggest that CAII has evolved to utilize the structure and fast dynamics of the active-site waters for its diffusion-limited catalytic efficiency.

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

Polyethylene Upcycling to Liquid Alkanes in Molten Salts under Neat and External Hydrogen Source-Free Conditions

Development of facile approaches to convert plastic waste into liquid fuels under neat conditions is highly desired but challenging, particularly without noble metal catalysts and an external hydrogen source. Herein, highly efficient and selective polyethylene-to-gasoline oil (branched C 6 –C 12 alkanes) conversion was achieved under mild conditions (<170 °C) using commercially available AlCl 3 -containing molten salts as reaction media and to provide catalytic sites (no extra solvents, additives, or hydrogen feeding). The high catalytic efficiency and selectivity was ensured by the abundant active Al sites with strong Lewis acidity (comparable to the Al type in acidic zeolite) and highly ionic nature of the molten salts to stabilize the carbenium intermediates. Dynamic genesis of the Al sites was elucidated via time-resolved Al K-edge soft X-ray and 27 Al NMR, confirming the tricoordinated Al 3+ as active sites and its coordination with the as-generated alkene/aromatic intermediates. Further, the carbenium formation and polyethylene chain variation was illustrated by inelastic neutron scattering (INS) and an isotope-labeling experiment. Theoretical simulations further demonstrated the successive hydride abstraction, β-scission, isomerization, and internal hydrogen transfer reaction pathway with AlCl 3 as active sites. This facile catalytic system can further achieve the conversion of robust, densely assembled, and high molecular weight plastic model compounds to liquid alkane products in the diesel range.

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

Disentangling natural and anthropogenic effects on benthic macroinvertebrate assemblages in western US streams

Abstract Stream macroinvertebrate assemblages are shaped by natural and human‐related factors that operate through complex hierarchical pathways. Quantifying these relationships can provide additional insights into stream ecological assessment. We applied a structural equation modeling framework to evaluate hypothesized pathways by which watershed, riparian, and in‐stream factors affect benthic macroinvertebrate condition in the Western Mountains (WMT) and Xeric (XER) ecoregions in the United States. We developed a conceptual model grounded in theory, empirical evidence, and expert opinion to evaluate the following hypotheses: (1) macroinvertebrate assemblages are primarily driven by proximal, in‐stream factors (e.g., water quality and physical habitat); (2) anthropogenic land uses affect macroinvertebrates indirectly by altering in‐stream characteristics; and (3) riparian vegetation cover attenuates land use effects. We tested our model separately on three measures of benthic macroinvertebrate assemblage condition: ratio of observed‐to‐expected taxonomic richness (O/E); a multimetric index (MMI); and richness of Ephemeroptera, Plecoptera, and Trichoptera taxa (EPT). In the WMT, site‐level riparian cover, in‐stream physical habitat (relative bed stability), and water chemistry (total nitrogen) were the top three predictors of macroinvertebrate assemblages, each having over two times the magnitude of effect on macroinvertebrates compared with watershed‐level predictors. In the arid XER, annual precipitation and stream flow characteristics were top predictors of macroinvertebrate assemblages and had similar magnitudes of effect as in‐stream water chemistry. Path analyses revealed that land use activities in the watershed and at the stream site degraded macroinvertebrate assemblages indirectly by altering relative bed stability, water quality, and riparian cover/complexity. Increased riparian cover was associated with greater macroinvertebrate condition by reducing land use impacts on stream flow, streambed substrate, and water quality, but the pathways differed among ecoregions. In the WMT, site‐level riparian cover affected macroinvertebrate assemblages partly through indirect pathways associated with greater streambed stability and reduced total nitrogen concentrations. In contrast, in the XER, watershed‐level riparian cover affected macroinvertebrate assemblages through greater specific stream power. Identifying the relative effects of and pathways by which natural and anthropogenic factors affect macroinvertebrates can serve as a framework for prioritizing management and conservation efforts.

Environmental Sciences & Ecology↗
DOE OSTI2022

Design of Ru-Ni diatomic sites for efficient alkaline hydrogen oxidation

Anion exchange membrane fuel cells are limited by the slow kinetics of alkaline hydrogen oxidation reaction (HOR). Here, we establish HOR catalytic activities of single-atom and diatomic sites as a function of *H and *OH binding energies to screen the optimal active sites for the HOR. As a result, the Ru-Ni diatomic one is identified as the best active center. Guided by the theoretical finding, we subsequently synthesize a catalyst with Ru-Ni diatomic sites supported on N-doped porous carbon, which exhibits excellent catalytic activity, CO tolerance, and stability for alkaline HOR and is also superior to single-site counterparts. In situ scanning electrochemical microscopy study validates the HOR activity resulting from the Ru-Ni diatomic sites. Furthermore, in situ x-ray absorption spectroscopy and computational studies unveil a synergistic interaction between Ru and Ni to promote the molecular H 2 dissociation and strengthen OH adsorption at the diatomic sites, and thus enhance the kinetics of HOR.

25 ENERGY STORAGE↗
DOE OSTI2023

B56$δ$ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan’s syndrome mutations

Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by PPP2R5D) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in PPP2R5D cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Steering the Methane Dry Reforming Reactivity of Ni/La 2 O 3 Catalysts by Controlled In Situ Decomposition of Doped La 2 NiO 4 Precursor Structures

The influence of A- and/or B-site doping of Ruddlesden-Popper perovskite materials on the crystal structure, stability, and dry reforming of methane (DRM) reactivity of specific A 2 BO 4 phases (A = La, Ba; B = Cu, Ni) has been evaluated by a combination of catalytic experiments, in situ X-ray diffraction, X-ray absorption spectroscopy (XAS), X-ray photoelectron spectroscopy (XPS), and aberration-corrected electron microscopy. At room temperature, B-site doping of La 2 NiO 4 with Cu stabilizes the orthorhombic structure ( Fmmm ) of the perovskite, while A-site doping with Ba yields a tetragonal space group ( I 4/ mmm ). We observed the orthorhombic-to-tetragonal transformation above 170 °C for La 2 Ni 0.9 Cu 0.1 O 4 and La 2 Ni 0.8 Cu 0.2 O 4 , slightly higher than for undoped La 2 NiO 4 . Loss of oxygen in interstitial sites of the tetragonal structure causes further structure transformations for all samples before decomposition in the temperature range of 400 °C-600 °C. Controlled in situ decomposition of the parent or A/B-site doped perovskite structures in a DRM mixture (CH 4 :CO 2 = 1:1) in all cases yields an active phase consisting of exsolved nanocrystalline metallic Ni particles in contact with hexagonal La 2 O 3 and a mixture of (oxy)carbonate phases (hexagonal and monoclinic La 2 O 2 CO 3 , BaCO 3 ). Differences in the catalytic activity evolve because of (i) the in situ formation of Ni-Cu alloy phases (in a composition of >7:1 = Ni:Cu) for La 2 Ni 0.9 Cu 0.1 O 4 , La 2 Ni 0.8 Cu 0.2 O 4 , and La 1.8 Ba 0.2 Ni 0.9 Cu 0.1 O 4 , (ii) the resulting Ni particle size and amount of exsolved Ni, and (iii) the inherently different reactivity of the present (oxy)carbonate species. Based on the onset temperature of catalytic DRM activity, the latter decreases in the order of La 2 Ni 0.9 Cu 0.1 O 4 ~ La 2 Ni 0.8 Cu 0.2 O 4 ≥ La 1.8 Ba 0.2 Ni 0.9 Cu 0.1 O 4 > La 2 NiO 4 > La 1.8 Ba 0.2 NiO 4 . Simple A-site doped La 1.8 Ba 0.2 NiO 4 is essentially DRM inactive. The Ni particle size can be efficiently influenced by introducing Ba into the A site of the respective Ruddlesden-Popper structures, allowing us to control the Ni particle size between 10 nm and 30 nm both for simple B-site and A-site doped structures. Hence, it is possible to steer both the extent of the metal-oxide-(oxy)carbonate interface and its chemical composition and reactivity. Counteracting the limitation of the larger Ni particle size, the activity can, however, be improved by additional Cu-doping on the B-site, enhancing the carbon reactivity. Exemplified for the La 2 NiO 4 based systems, we show how the delicate antagonistic balance of doping with Cu (rendering the La 2 NiO 4 structure less stable and suppressing coking by efficiently removing surface carbon) and Ba (rendering the La 2 NiO 4 structure more stable and forming unreactive surface or interfacial carbonates) can be used to tailor prospective DRM-active catalysts.

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

Superoxide Dismutase 1 Folding Stability as a Target for Molecular Tweezers in SOD1-Related Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation are hallmarks of many severe neurodegenerative diseases including Alzheimer's, Parkinson's and Huntington's disease. As a supramolecular ligand that binds to lysine and arginine residues, the molecular tweezer CLR01 was found to modify the aggregation pathway of disease-relevant proteins in vitro and in vivo with beneficial effects on toxicity. However, the molecular mechanisms of how tweezers exert these effects remain mainly unknown, hampering further drug development. Here, we investigate the modulation mechanism of unfolding and aggregation pathways of SOD1, which are involved in amyotrophic lateral sclerosis (ALS), by CLR01. Using a truncated version of the wildtype SOD1 protein, SOD1 bar , we show that CLR01 acts on the first step of the aggregation pathway, the unfolding of the SOD1 monomer. CLR01 increases, by ~10 °C, the melting temperatures of the A4V and G41D SOD1 mutants, which are commonly observed mutations in familial ALS. Molecular dynamics simulations and binding free energy calculations as well as native mass spectrometry and mutational studies allowed us to identify K61 and K92 as binding sites for the tweezers to mediate the stability increase. The data suggest that the modulation of SOD1 conformational stability is a promising target for future developments of supramolecular ligands against neurodegenerative diseases.

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

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

One of the seven natural CO 2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO 2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

bacterial metabolism↗
DOE OSTI2020

In-situ structure and catalytic mechanism of NiFe and CoFe layered double hydroxides during oxygen evolution

NiFe and CoFe (MFe) layered double hydroxides (LDHs) are among the most active electrocatalysts for the alkaline oxygen evolution reaction (OER). Herein, we combine electrochemical measurements, operando X-ray scattering and absorption spectroscopy, and density functional theory (DFT) calculations to elucidate the catalytically active phase, reaction center and the OER mechanism. We provide the first direct atomic-scale evidence that, under applied anodic potentials, MFe LDHs oxidize from as-prepared α-phases to activated γ-phases. The OER-active γ-phases are characterized by about 8% contraction of the lattice spacing and switching of the intercalated ions. DFT calculations reveal that the OER proceeds via a Mars van Krevelen mechanism. The flexible electronic structure of the surface Fe sites, and their synergy with nearest-neighbor M sites through formation of O-bridged Fe-M reaction centers, stabilize OER intermediates that are unfavorable on pure M-M centers and single Fe sites, fundamentally accounting for the high catalytic activity of MFe LDHs.

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

Rational design of heterogeneous single-site catalysts via surface organometallic chemistry

Single-site heterogeneous catalysts offer an attractive route to unite the molecular precision of homogeneous catalysis with the durability and practical advantages of solids. Surface organometallic chemistry (SOMC) provides a particularly powerful strategy for this purpose by grafting molecular precursors onto tailored surfaces and converting support functionalities into ligand environments for isolated metal centers. As a result, SOMC brings the language and logic of coordination chemistry to heterogeneous catalysis, where the support becomes an integral part of the active site coordination sphere. This Review surveys recent progress in the rational design of SOMC-derived single-site catalysts, with emphasis on synthetic routes, post synthetic transformations, and the deliberate tuning of catalytic behavior through metal-support interactions. Discussions are made on how support identity, hydroxyl topology, acidity, and redox activity shape the geometry, electronic structure, and oxidation state of supported metal sites, as well as how these factors determine activity, selectivity, and stability. We also examine a central limitation of these systems: despite their molecularly informed design, supported single sites often exist as structurally distributed ensembles rather than uniform species, particularly on amorphous supports. This site heterogeneity, along with catalyst dynamics under operating conditions, remains a major barrier to definitive structure-activity relationships. Therefore, emerging approaches that combine advanced characterization, first-principles modeling, ensemble kinetics, and machine learning to resolve active-site structure and guide catalyst development are highlighted. Together, these advances position SOMC as a versatile coordination chemistry framework for the predictive design of heterogeneous catalysts with well-defined molecularly tailored active sites.

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

CRISPR-COPIES: Web Tool

CRISPR/Cas system has emerged as a powerful genome-editing tool for metabolic engineering and human gene therapy. However, the conundrum of where to integrate heterologous genes on the chromosome using the CRISPR/Cas system remains an open question. Selecting a site for gene integration requires incorporation of complex criteria such as factors involved in CRISPR/Cas-mediated integration, genetic stability, and gene expression and therefore, usually requires strenuous characterization of sites on particular or different chromosomal locations. To address these issues, we developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. The tool applies ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. This submission contains the code we developed to create a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate CRISPR-COPIES will serve as a useful tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, and human gene and cell therapy.

Bioinformatics↗
DOE OSTI2021

Binary Atomically Dispersed Metal-Site Catalysts with Core–Shell Nanostructures for O 2 and CO 2 Reduction Reactions

Engineering atomically dispersed metal site catalysts with controlled local coordination environments and 3D nanostructures effectively improves the catalytic performance for the oxygen reduction reaction (ORR) and the carbon dioxide reduction reaction (CO 2 RR), which are critical for clean energy conversion and chemical production. Herein, an innovative approach for preparing core-shell nanostructured catalysts with different single-metal sites in the core and the shell, respectively, is developed. In particular, as the shell precursors, covalent organic polymers with a thin layered structure that is polymerized in situ and coated on a metal-doped ZIF-derived carbon core are used, followed by a controlled thermal activation. The selective combination and construction of different metal sites increase active site density in the surface layers, promote structural robustness, facilitate mass/charge transfer, and yield a possible synergy of active sites in the core and the shell. The p-FeNC(shell)@CoNC(core), consisting of a polymerized FeTPPCl-derived carbon layer (p-FeNC) on a Co-doped ZIF-derived carbon (CoNC), exhibits remarkable ORR activity and stability in acidic media along with encouraging durability in H 2 –air fuel cells. Likewise, a p-FeNC(shell)@NiNC(core) catalyst demonstrates outstanding CO 2 RR activity and stability. Hence, integrating two appropriate single-metal sites in core and shell precursors, respectively, can modulate morphological and catalytic properties for a possible synergy toward different electrocatalysis processes.

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

Mechanistic study of direct coupling of CO 2 and C 2 H 4 over atomically dispersed metal at graphene edges

Direct coupling of CO 2 and ethylene (hereinafter DCCE) to acrylic acid is valuable for valorizing CO 2 to manufacture acrylate-derived products. However, previous studies in DCCE have been limited on molecular catalysts with challenges in improving catalytic performance. In this work, we employed density functional theory calculations and ab initio molecular dynamics simulations to investigate the heterogeneous catalysis of DCCE over atomically dispersed metal centers at nitrogen-doped zigzag edge of graphene. Based on competitive adsorption and structural stability, Mo, Cr, V, Ru, and Ni active sites are chosen to explore the reaction kinetics. Here, we find that the activation barriers are determined by the charge redistribution at transition states, which explains the trend of activity for the C-C coupling and the hydrogen transfer, two key steps in DCCE. Furthermore, we show that the intramolecular hydrogen transfer (rate-limiting step) is hindered due to the lack of local coordinate at the active sites. We thus propose to use co-adsorbed water as a “proton-exchanger” following a water-assisted route, and show that the activation barriers are reduced over all metal centers. Particularly, water promotes the hydrogen transfer over metals with strong CO 2 -ethylene co-activation and facile C-C coupling kinetics, which could be considered promising for DCCE. In both mechanisms, the stability of metallactone intermediate can be used to predict the catalytic activity. It is anticipated that the insights from this work can provide guidelines for mimicking well-defined multifunctional active sites in molecular catalysts to design heterogeneous catalysts for such C-C coupling, which advances catalytic utilization of CO 2 .

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

Thermal Stability of Silica for Application in Thermal Energy Storage: Preprint

Free from siting constraints, thermal energy storage (TES) shows promise as an economical alternative to traditional pumped-storage hydropower (PSH) and compressed air energy storage (CAES). As potential thermal energy storage media, many solid particles demonstrate stability over wide temperature ranges which allows for increased sensible energy storage density and is essential in achieving low-cost storage. Silica sand, in the form of a-quartz, is one such candidate. This work presents a brief review of relevant silica thermophysical properties and further investigates the thermal stability of silica particles as a candidate TES media by subjecting them to two different thermal campaigns: (1) a 500-hour thermal treatment at 1200°C under varied atmospheres; and (2) cycling 25, 50, and 100 times between 300°C and 1200°C. For both campaigns, particle stability is examined by means of pre- and post-treatment Mie scattering. An additional XRD analysis is conducted for the 500-hour treatment in air. Results indicate limited changes in both particle distribution and crystallographic structure which is promising for the application as solid particle media for thermal energy storage.

27 ARPA - Advanced Research Projects Agency-Energy↗