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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 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues

Drug resistance to front-line malarial treatments represents an ongoing threat to control malaria, a vector borne infectious disease. The malarial parasite, Plasmodium falciparum has developed genetic variants, conferring resistance to the current standard therapeutic artemisinin and its derivatives commonly referred to as artemisinin-combination therapies (ACTs). Emergence of multi-drug resistance parasite genotypes is a warning of potential treatment failure, reaffirming the urgent and critical need to find and validate alternate drug targets to prevent the spread of disease. An attractive and novel drug target includes glucose-regulated protein 78 kDa (GRP78, or BiP), an essential molecular chaperone protein involved in the unfolded protein response that is upregulated in ACT treated P. falciparum parasites. We have shown that both sequence and structure are closely related to human GRP78 (hGRP78), a chaperone belonging to the HSP70 class of ATPase proteins, which is often upregulated in cellular stress responses and cancer. By screening a library of nucleoside analogues, we identified eight ‘hit’ compounds binding at the active site of the ATP binding domain of P. falciparum GRP78 using a high-throughput ligand soaking screen using x-ray crystallography. These compounds were further evaluated using protein thermal shift assays to assess target binding activity. The nucleoside analogues identified from our screen provide a starting point for the development of more potent and selective antimalarial inhibitors. In addition, we have established a well-defined, high-throughput crystal-based screening approach that can be applied to many crystallizable P. falciparum proteins for generating anti-Plasmodium specific compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Durable Mn-Based PGM-Free Catalysts for Polymer Electrolyte Membrane Fuel Cells

This proposed project aims to develop and evaluate novel manganese based, nitrogen-derived, PGM-free electrocatalysts (denoted as Mn-N-C) to fully address the membrane electrolyte assemblies (MEA)’s ionomer degradation issue resulting from iron. Four thrusts will be pursed in this proposed project. First, advanced first-principles computation methods will be employed to accelerate the rational catalyst design and synthesis. Second, an effective hydro-gel method will be used to maximize atomic Mn active sites embedded in carbon matrix. Next, state-of-the art methods in fuel cell companies will be used to fabricate MEAs containing the Mn-N-C catalysts. Finally, industry standards will be rigorously followed to evaluate fuel cell performance and durability of the Mn-N-C catalysts. With successful completion of the project, it is expected that the following outcomes will be achieved. (1) A set of MEAs containing the Mn-N-C catalysts and with active area large than 50 cm 2 for independent testing, (2) testing results demonstrating that the MEAs of Mn-N-C catalysts have mass activity of 0.044 A/cm 2 at 0.9 VIR-free and H 2 /air performance of 0.50 V at 1.0 A/cm 2 ; (3) fundamental understanding of the composition-structure-property relation of the PGM-free Mn- N-C catalysts, and (4) computational data, measurement data, and publications deposited into the database of ElectroCat Consortium.

08 HYDROGEN↗
DOE OSTI2023

University Coalition for Fossil Fuel Energy Research

Following a nationwide open competition, the University Coalition for Fossil Energy Research (UCFER) was established in October 2015 through a cooperative agreement between Penn State and the Department of Energy (DOE) National Energy Technology Laboratory (NETL). Penn State lead UCFER with the objective of advancing basic and applied research for clean and low-carbon energy based on fossil fuels in support of the DOE’s mission. UCFER focused on research that improves the efficiency of production and use of fossil energy resources, while minimizing the environmental impacts and reducing greenhouse gas emissions. Penn State lead a team of nine universities (Massachusetts Institute of Technology, The Pennsylvania State University, Princeton University, Texas A&M University, University of Kentucky, University of Southern California, The University of Tulsa, University of Wyoming, and Virginia Polytechnic and State University) during the competition stage, adding seven more universities in 2017 (Carnegie Mellon University, Louisiana State University, The Ohio State University, University of North Dakota, University of Pittsburgh, University of Utah, and West Virginia University). This Coalition exhibited a wide geographical distribution across the U.S. bringing a wide variety of fossil energy expertise. This national university alliance was a major collaborative effort with NETL to address specific topics of R&D in NETL’s mission area, which involved one or more of NETL’s five core competencies (Geologic and Environmental Systems, Materials Engineering and Manufacturing, Energy Conversion Engineering, Systems Engineering and Analysis, and Computational Science and Engineering). The first five to six months of the project was the definitization stage. During this period, Penn State worked closely with NETL to finalize the Coalition organizational structure and By- Laws, prepare a statement of substantial involvement and a statement of project objectives, and develop operations and membership plans. A major component of this stage included preparing an execution plan to solicit research, evaluate proposals, recommend selected projects to NETL, and award projects. In addition, a plan was prepared to monitor projects, review projects, disseminate knowledge from research projects and develop an online system for Coalition research portfolio management. This included developing a website and several databases. The first of six rounds of solicitations started in mid-2016. Projects from the sixth solicitation started February 1, 2021, and ended January 31, 2023. Projects that were selected represented twelve technology lines. Approximately $16.6 million in funding was available for the six solicitations. Most of the funding was provided by DOE, Office of Fossil Energy (DOEFE) with the DOE Fuel Cells Technologies Office (DOE-FCTO) providing funding for a few projects. Coalition universities submitted 259 proposals in response to the solicitations, requesting approximately $67.0 million in funding, and forty-three projects were selected. However, one project withdrew after the principal investigator left the university. The management of the Coalition projects was a major activity by Penn State. Managing the Coalition projects consisted of monitoring the projects, reviewing the projects through annual technical review meetings, disseminating knowledge from the research projects, and developing an online system for Coalition research portfolio management. Penn State’s OMT monitored projects to ensure that all milestones (technical, schedule, budget) were met, expenditures were allowable, cost share (when applicable) were reported, and all technical reports were submitted. The OMT also posted the technical reports electronically on a secure members-only website for access and review by the Coalition members. Disseminating knowledge from the research projects was done through a website, newsletters, various meetings, conferences, journal articles, publicity/press releases, and project summaries that were prepared after each project was completed. Penn State kept NETL apprised of UCFER progress through quarterly reports (thirtyone were submitted by Penn State), verbal and written communications, yearly updates at the annual technical review meetings, and cost accrual reports. The UCFER project had a significant impacty. The UCFER program established the first national university alliance in fossil energy research with a major collaboration effort with DOE NETL that addressed specific topics in NETL’s research and development mission areas. It generated inter-university collaborations, which was another program interest. Twenty-two out of 259 proposals contained collaborations (≈8.5%) and three of forty-two funded projects involved inter-university collaborations (≈7.0%). The forty-two funded projects provided support at fourteen universities involving 269 personnel. Research was conducted by 106 faculty, 115 graduate and undergraduate students, forty-six research staff and post-doctoral scholars, and two visiting scholars. Students and post-doctoral scholars were also on-site at NETL through CRADAs. In addition, non-Coalition participants included six universities and sixteen companies and national laboratories. The non-Coalition participants were involved as subcontractors, providers of cost share, performed unpaid consultation and sample analysis, served as advisory board members, or were providers of samples and materials for testing. UCFER also produced visibility in that fifty-six refereed journal articles were published, fifty-seven conference papers and twenty-three posters were prepared, 190 presentations were given, eight patent applications were filed, two books/book chapters were written, and ten software codes were developed. Collaboration between NETL and the individual projects was a major requirement for all funded projects. This included NETL staff time to support collaboration, consultation, technical guidance, sample preparation and analysis, internships at NETL, on-site testing and equipment usage by Coalition participants at NETL, co-mentoring students, and coauthoring journal articles and conference papers. Collaboration was impacted by COVID-19 in that not all on-site activities could be performed. NETL personnel were coauthors on eight of the conference papers (fourteen percent of the conference papers that were prepared) and seventeen of the journal articles (thirty percent of the journal articles that were prepared). A website was developed for an online proposal solicitation and review process and to provide exposure to UCFER. A website analysis highlighted the large amount of member and general public interest in UCFER by interpreting access statistics from March 2016 through June 2023. Visitors to the site originated from many different organizations, businesses, and countries. The website provided a means to disseminate information to both the general public and the UCFER members and was successfully used for outreach activities. In addition, NETL required that RFP release, proposal submission, and proposal reviews all be performed online. Penn State successfully developed these capabilities in a secure section of the website, which were used throughout the UCFER project. It is recognized that each project had its technical successes. In addition, highlighted successes were compiled and summarized from the research projects. Information was requested from the PIs of completed projects. In addition, Penn State’s Operations Management Team reviewed subcontract reports to identify project successes. Examples of information requested from PIs included (not all-inclusive): new projects that have been funded as a result of UCFER funding; new commercial products; establishment of a new center; new patent; new software; best paper awards; highly-cited work; and graduate student successes. A total of forty-eight highlighted successes were reported.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2021

Elucidating Electron Storage and Distribution within the Pentaheme Scaffold of Cytochrome c Nitrite Reductase (NrfA)

Cytochrome c nitrite reductases (CcNIR or NrfA) play important roles in the global nitrogen cycle by conserving the usable nitrogen in the soil. Here, the electron storage and distribution properties within the pentaheme scaffold of Geobacter lovleyi NrfA were investigated via EPR spectroscopy coupled with chemical titration experiments. Initially, a chemical reduction method was established to sequentially add electrons to the fully oxidized protein, one equivalent at a time. The step–by–step reduction of the hemes was then followed using UV–Vis and EPR spectroscopy. EPR–spectral simulations elucidate the sequence of heme reduction within the pentaheme scaffold, and identify the signals of all five hemes in the EPR spectra. Electrochemical experiments ascertain the reduction potentials for each heme, observed in a narrow +11 (Heme 5) to –212 mV (Heme 3) range (vs SHE). Based on quantitative analysis/simulation of the EPR data, we demonstrate that Hemes 4 and 5 are reduced first (before the active site Heme 1) and serve the purpose of an electron storage unit within the protein. To probe the role of the central Heme 3, a H108M NrfA variant was generated where the reduction potential of Heme 3 is shifted positively (from –212 mV to +29 mV). Here, the H108M mutation significantly impacts the distribution of electrons within the pentaheme scaffold and the reduction potentials of the hemes, reducing the catalytic activity of the enzyme to 3% compared to wild–type. We propose that this is due to Heme 3’s important role as an electron gateway in the wild–type enzyme.

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

Mechanistic insights explain the transforming potential of the T507K substitution in the protein-tyrosine phosphatase SHP2

The protein-tyrosine phosphatase SHP2 is an allosteric enzyme critical for cellular events downstream of growth factor receptors. Mutations in the SHP2 gene have been linked to many different types of human diseases, including developmental disorders, leukemia, and solid tumors. Unlike most SHP2-activating mutations, the T507K substitution in SHP2 is unique in that it exhibits oncogenic Ras-like transforming activity. However, the biochemical basis of how the SHP2/T507K variant elicits transformation remains unclear. By combining kinetic and biophysical methods, X-ray crystallography, and molecular modeling, as well as using cell biology approaches, in this work we uncovered that the T507K substitution alters both SHP2 substrate specificity and its allosteric regulatory mechanism. We found that although SHP2/T507K exists in the closed, autoinhibited conformation similar to the WT enzyme, the interactions between its N-SH2 and protein-tyrosine phosphatase domains are weakened such that SHP2/T507K possesses a higher affinity for the scaffolding protein Grb2-associated binding protein 1 (Gab1). We also discovered that the T507K substitution alters the structure of the SHP2 active site, resulting in a change in SHP2 substrate preference for Sprouty1, a known negative regulator of Ras signaling and a potential tumor suppressor. Our results suggest that SHP2/T507K's shift in substrate specificity coupled with its preferential association of SHP2/T507K with Gab1 enable the mutant SHP2 to more efficiently dephosphorylate Sprouty1 at pTyr-53. This dephosphorylation hyperactivates Ras signaling, which is likely responsible for SHP2/T507K's Ras-like transforming activity.

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

Structural mechanism of Escherichia coli cyanase

Cyanase plays a vital role in the detoxification of cyanate and supplies a continuous nitrogen source for soil microbes by converting cyanate to ammonia and carbon dioxide in a bicarbonate-dependent reaction. The structures of cyanase complexed with dianion inhibitors, in conjunction with biochemical studies, suggest putative binding sites for substrates. However, the substrate-recognition and reaction mechanisms of cyanase remain unclear. Here, crystal structures of cyanase from Escherichia coli were determined in the native form and in complexes with cyanate, bicarbonate and intermediates at 1.5–1.9 Å resolution using synchrotron X-rays and an X-ray free-electron laser. Cyanate and bicarbonate interact with the highly conserved Arg96, Ser122 and Ala123 in the active site. Further, in the presence of a mixture of cyanate and bicarbonate, three different electron densities for intermediates were observed in the cyanase structures. Moreover, the observed electron density could explain the dynamics of the substrate or product. In addition to conformational changes in the substrate-binding pocket, dynamic movement of Leu151 was observed, which functions as a gate for the passage of substrates or products. These findings provide a structural mechanism for the substrate-binding and reaction process of cyanase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The Role of Cooperative Interactions Among Surfaces, Solvents, and Reactive Intermediates on Catalysis at Liquid–Solid Interfaces (Final Report DE-SC0020224)

This project established quantitative links between inner‑sphere chemistry (active metal identity, coordination, and zeolite topology) and outer‑sphere organization (solvent identity, hydrogen‑bond networks, and pore condensation) that govern rates, activation barriers, and selectivities for alkene epoxidation and epoxide ring‑opening at solid–liquid and quasi‑liquid–solid interfaces. We deconvoluted contributions from covalent interactions at active sites and noncovalent, solvent‑mediated interactions within pores by pairing well‑defined metal substituted zeolites with controlled solvent environments. We then mapped those contributions onto measurable kinetics (ΔH‡, ΔS‡), adsorption thermodynamics (ITC), and in situ spectroscopy. The transferrable outcomes include a set of design rules that include the following understandings. First, tune silanol ((SiOH)x) density and pore topology to organize solvent networks that selectively stabilize transition states. Second, exploit activity‑coefficient‑normalized rates and adsorption– barrier correlations to diagnose when solvent reorganization rather than surface chemistry limits performance. Third, use partial pore condensation (e.g., acetonitrile, water but also generalizable to other solvents) to elicit liquid‑like stabilization effects even in nominally vapor‑phase reactors. Collectively, these results provide strategies to increase epoxidation rates, improve oxidant utilization (i.e., selectivities), and steer regioselectivity in zeolite‑based catalytic processes relevant to sustainable oxidation chemistry. These outcomes should be transferable to other classes of reactions that proceed in microporous materials and under confinement provided by organized solvents (e.g., electrochemical double layers).

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

Characterizing inhibitors of human AP endonuclease 1

AP endonuclease 1 (APE1) processes DNA lesions including apurinic/apyrimidinic sites and 3´-blocking groups, mediating base excision repair and single strand break repair. Much effort has focused on developing specific inhibitors of APE1, which could have important applications in basic research and potentially lead to clinical anticancer agents. We used structural, biophysical, and biochemical methods to characterize several reported inhibitors, including 7-nitroindole-2-carboxylic acid (CRT0044876), given its small size, reported potency, and widespread use for studying APE1. Intriguingly, NMR chemical shift perturbation (CSP) experiments show that CRT0044876 and three similar indole-2-carboxylic acids bind a pocket distal from the APE1 active site. A crystal structure confirms these findings and defines the pose for 5-nitroindole-2-carboxylic acid. However, dynamic light scattering experiments show the indole compounds form colloidal aggregates that could bind (sequester) APE1, causing nonspecific inhibition. Endonuclease assays show the compounds lack significant APE1 inhibition under conditions (detergent) that disrupt aggregation. Thus, binding of the indole-2-carboxylic acids at the remote pocket does not inhibit APE1 repair activity. Myricetin also forms aggregates and lacks APE1 inhibition under aggregate-disrupting conditions. Two other reported compounds (MLS000552981, MLS000419194) inhibit APE1 in vitro with low micromolar IC50 and do not appear to aggregate in this concentration range. However, NMR CSP experiments indicate the compounds do not bind specifically to apo- or Mg 2+ -bound APE1, pointing to a non-specific mode of inhibition, possibly DNA binding. Our results highlight methods for rigorous interrogation of putative APE1 inhibitors and should facilitate future efforts to discover compounds that specifically inhibit this important repair enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Copper-Based Catalysts Confined in Carbon Nanocage Reactors for Condensed Ester Hydrogenation: Tuning Copper Species by Confined SiO 2 and Methanol Resistance

Hydrogenation of aliphatic esters to natural alcohols is an important strategy for the efficient utilization of biomass-derived oils. The synthesis of highly active copper (Cu)-based catalysts is a challenge for condensed-phase ester hydrogenation due to the difficulties in controlling active sites and catalyst deactivation. In this work, a copper-based catalyst confined in a carbon nanocage reactor was successfully designed and prepared. The copper catalyst with 56 wt % SiO 2 exhibited the best performance because of the optimum proportion of Cu + and Cu 0 sites and high dispersion. The interaction between SiO 2 and Cu particles contributes to the formation of Cu + species, which is the key site for the adsorption of carbonyl groups. Meanwhile, the confinement effect of the carbon nanocages effectively inhibited the agglomeration of the copper particles. The catalysts exhibited not only excellent thermal stability but also superior methanol resistance in comparison with the Cu/SiO 2 catalyst. On the basis of the density functional theory (DFT) calculations results, methanol resistance should be attributed to the fewer hydroxyl groups on the catalyst surface, which increase the activation barrier for the dissociation of silica, allowing the stable holding of the copper species in the methanol solvent.

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

Design and synthesis of biobased superhydrophobic biochar catalyst derived from Citrus sinensis for biodiesel production using inedible oil feedstocks

In an one-pot in situ trans/esterification of low-grade feedstocks, the simultaneous presence of triglycerides (TAGs) and free fatty acids (FFAs) presents a dual catalytic challenge. While TAGs undergo transesterification to form biodiesel and glycerol, FFAs present in the feedstocks are esterified simultaneously, producing water as a by-product. This water can deactivate acid catalysts by interacting with their active sites, reducing catalytic efficiency and reusability. To overcome this, we developed a hydrophobic sulfonic acid-functionalized biochar catalyst derived from Citrus sinensis (orange peel) via sulfonation with H 2 SO 4 and subsequent silylation using hexamethyldisilazane (HMDS). The optimized catalyst exhibited a high surface area (355.09 m 2 g −1 ), sulfur content (5.33 wt%), and strong hydrophobicity (water contact angle: 154°). Compared to non-hydrophobic analogs, it showed enhanced activity and reusability (up to 10 cycles). Using response surface methodology with central composite design, a biodiesel yield of 99.1 ± 0.4% was achieved under optimal conditions. Life cycle assessment was performed to evaluate the environmental impacts of biodiesel production utilising the synthesized catalyst, considering 1000 kg of biodiesel produced as 1 functional unit. In conclusion, the recorded results showed the cumulative abiotic depletion of fossil resources over the entire biodiesel production process as 87 243.423 MJ and global warming potential as 4103.494 kg CO 2 equivalent.

Biochar↗
DOE OSTI2023

The yeast ALA synthase C‐terminus positively controls enzyme structure and function

Abstract 5‐Aminolevulinic acid synthase (ALAS) is a pyridoxal 5′‐phosphate (PLP)‐dependent enzyme that catalyzes the first and rate‐limiting step of heme biosynthesis in α‐proteobacteria and several non‐plant eukaryotes. All ALAS homologs contain a highly conserved catalytic core, but eukaryotes also have a unique C‐terminal extension that plays a role in enzyme regulation. Several mutations in this region are implicated in multiple blood disorders in humans. In Saccharomyces cerevisiae ALAS (Hem1), the C‐terminal extension wraps around the homodimer core to contact conserved ALAS motifs proximal to the opposite active site. To determine the importance of these Hem1 C‐terminal interactions, we determined the crystal structure of S. cerevisiae Hem1 lacking the terminal 14 amino acids (Hem1 ΔCT). With truncation of the C‐terminal extension, we show structurally and biochemically that multiple catalytic motifs become flexible, including an antiparallel β‐sheet important to Fold‐Type I PLP‐dependent enzymes. The changes in protein conformation result in an altered cofactor microenvironment, decreased enzyme activity and catalytic efficiency, and ablation of subunit cooperativity. These findings suggest that the eukaryotic ALAS C‐terminus has a homolog‐specific role in mediating heme biosynthesis, indicating a mechanism for autoregulation that can be exploited to allosterically modulate heme biosynthesis in different organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Synergistic Ru Co atomic pair with enhanced activity toward levulinic acid hydrogenation

Development of efficient metal-based catalysts is of great importance for levulinic acid (LA) hydrogenation to γ-valerolactone (GVL). The widely employed Ru-based catalysts are advantageous for H 2 dissociation, however, the steric hindrance for large Ru particles hampers their coordination to C=O moiety in LA, and thereby decreasing the activity. Herein, we report a Ru 1 Co 1 -N-C double single-atom catalyst (DSAC) with synergistic Ru and Co atomic pairs for LA hydrogenation into GVL. The Ru and Co doped zeolitic imidazole frameworks (RuCo-doped ZIF-8) precursor was rationally designed ((Ru+Co)/(Zn+Ru+Co) = 2 at.%), where the Zn node spatially isolates Ru and Co species, expanding the adjacent Ru-Co distance and facilitating the formation of the Ru-Co atomic pair upon pyrolysis, with each atom coordinated with three nitrogen atoms (N 3 -Ru 1 Co 1 -N 3 ). The Ru 1 Co 1 -N-C catalyst exhibits outstanding catalytic activity, with a turnover frequency (TOF) of 1980 h –1 , surpassing previously reported Ru-based catalysts. Experimental investigation and density functional theory (DFT) calculations reveal that the electron-rich Ru induced by less electronegative Co facilitates H 2 dissociation, while atomic Ru in dual-atomic pairs promotes C=O activation, Ru and Co atomic pairs synergistically enhancing LA conversion to GVL. In conclusion, this research will shed light on the precise control of active sites at atomic scale, and also provides a new concept for designing high-performance Ru-based catalysts towards LA hydrogenation to GVL.

Double single-atom catalysts↗
DOE OSTI2023

Revolutionizing Lithium Storage Capabilities in TiO 2 by Expanding the Redox Range

TiO 2 is a widely recognized intercalation anode material for lithium-ion batteries (LIBs), yet its practical capacity is kinetically constrained due to sluggish lithium-ion diffusion, leading to a lithiation number of less than 1.0 Li + (336 mAh g -1 ). Here, the growth of TiO 2 crystallites is restrained by integrating Si into the TiO 2 framework, thereby enhancing the charge transfer and creating additional active sites potentially residing at grain boundaries for Li + storage. This strategy is corroborated by the expanded redox range of Ti, as thoroughly demonstrated via synchrotron radiation-based X-ray spectroscopy and Cs-corrected electron microscopy. Consequently, when deployed for lithium storage, the tailored material achieves an extraordinarily high reversible capacity of 559 mAh g -1 , 116% of the theoretical maximum of 483 mAh g -1 calculated based on all active species, while simultaneously retaining superior rate capability and robust cycling stability. Further, this work offers fresh perspectives on the revitalization of traditional electrode materials to achieve enhanced capacities.

25 ENERGY STORAGE↗
DOE OSTI2026

Mechanistic implications of excited high-spin states, spin–spin coupling, and differential [2Fe–2S] + cluster temperature relaxations in the electron-bifurcating NfnABC from Thermococcus sibiricus

Electron bifurcation (EB) is a mechanism of biological energy transduction in which multiple oxidation–reduction (redox) reactions are thermodynamically coupled within a single enzyme, enabling the enzyme to harness the excess free energy from an exergonic process to drive an endergonic process. Because of this unprecedented chemistry, there is interest to translate EB principles to artificial and bioengineered systems, but a hurdle is that knowledge pertaining to the fundamental design principles of EB enzymes remains scarce. Here, we investigated the fundamental physical and electronic properties of electron transfer sites in a spectroscopically uncharacterized member of the BfuABC family of EB enzymes, the NADH-dependent reduced-ferredoxin:NADP + oxidoreductase from Thermococcus sibiricus (Tsi NfnABC). Cryo-EM structures of Tsi NfnABC previously demonstrated that it contains twelve redox cofactors: two flavins (one FAD and one FMN), eight [4Fe–4S] clusters, and two [2Fe–2S] clusters. The FMN, one [4Fe–4S] cluster, and one [2Fe–2S] cluster comprise the bifurcating active site termed the electron-bifurcating flavobicluster (BF-FBC), which is found in all BfuABC family members. By using electron paramagnetic resonance spectroscopy, we identified spectral signatures originating from interactions between the FMN radical and [4Fe–4S] + cluster in the BF-FBC and observed temperature dependent behavior of the BF-FBC's [2Fe–2S] + cluster indicative of moderately slow spin–lattice relaxation. Additionally, we uncovered numerous spectral features corresponding to half-integer, S > ½ spin states of [4Fe–4S] + clusters, including one attributable to the consequences of lysine-ligation of a [4Fe–4S] cluster unique to NfnABC. We contextualize these findings to electron transfer theory and NfnABC's structure. Our insights further the understanding of how enzymes are designed to exert control over electron transfer to conduct thermodynamically challenging reactions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Chloropyridinyl Esters of Nonsteroidal Anti-Inflammatory Agents and Related Derivatives as Potent SARS-CoV-2 3CL Protease Inhibitors

We report the design and synthesis of a series of new 5-chloropyridinyl esters of salicylic acid, ibuprofen, indomethacin, and related aromatic carboxylic acids for evaluation against SARS-CoV-2 3CL protease enzyme. These ester derivatives were synthesized using EDC in the presence of DMAP to provide various esters in good to excellent yields. Compounds are stable and purified by silica gel chromatography and characterized using 1 H-NMR, 13 C-NMR, and mass spectral analysis. These synthetic derivatives were evaluated in our in vitro SARS-CoV-2 3CLpro inhibition assay using authentic SARS-CoV-2 3CLpro enzyme. Compounds were also evaluated in our in vitro antiviral assay using quantitative VeroE 6 cell-based assay with RNAqPCR. A number of compounds exhibited potent SARS-CoV-2 3CLpro inhibitory activity and antiviral activity. Compound 9a was the most potent inhibitor, with an enzyme IC 50 value of 160 nM. Compound 13b exhibited an enzyme IC 50 value of 4.9 µM. However, it exhibited a potent antiviral EC 50 value of 24 µM in VeroE6 cells. Remdesivir, an RdRp inhibitor, exhibited an antiviral EC 50 value of 2.4 µM in the same assay. We assessed the mode of inhibition using mass spectral analysis which suggested the formation of a covalent bond with the enzyme. To obtain molecular insight, we have created a model of compound 9a bound to SARS-CoV-2 3CLpro in the active site.

3CLpro inhibitors↗
DOE OSTI2024

Stabilizing *CO 2 Intermediates at the Acidic Interface using Molecularly Dispersed Cobalt Phthalocyanine as Catalysts for CO 2 Reduction

Abstract CO 2 electroreduction (CO 2 R) operating in acidic media circumvents the problems of carbonate formation and CO 2 crossover in neutral/alkaline electrolyzers. Alkali cations have been universally recognized as indispensable components for acidic CO 2 R, while they cause the inevitable issue of salt precipitation. It is therefore desirable to realize alkali‐cation‐free CO 2 R in pure acid. However, without alkali cations, stabilizing *CO 2 intermediates by catalyst itself at the acidic interface poses as a challenge. Herein, we first demonstrate that a carbon nanotube‐supported molecularly dispersed cobalt phthalocyanine (CoPc@CNT) catalyst provides the Co single‐atom active site with energetically localizeddstates to strengthen the adsorbate‐surface interactions, which stabilizes *CO 2 intermediates at the acidic interface (pH=1). As a result, we realize CO 2 conversion to CO in pure acid with a faradaic efficiency of 60 % at pH=2 in flow cell. Furthermore, CO 2 is successfully converted in cation exchanged membrane‐based electrode assembly with a faradaic efficiency of 73 %. For CoPc@CNT, acidic conditions also promote the intrinsic activity of CO 2 R compared to alkaline conditions, since the potential‐limiting step, *CO 2 to *COOH, is pH‐dependent. This work provides a new understanding for the stabilization of reaction intermediates and facilitates the designs of catalysts and devices for acidic CO 2 R.

Chemistry↗
DOE OSTI2021

Evolution of the SARS-CoV -2 proteome in three dimensions (3D) during the first 6 months of the COVID -19 pandemic

Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein–protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Here detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein–protein and protein–nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Development of Chromium and Sulfur Getter for Solid Oxide Fuel Cell (SOFC) System

Under the “real world” SOFC operating conditions, gaseous Cr and S species coexist in air stream. The combined Cr and S effect on the electrochemical poisoning of candidate LSM and LSCF electrodes has been investigated. Electrochemical and structural analysis revealed that the combined Cr and S interactions with the LSCF electrode remains significantly different from those of the individual Cr and S interactions. S reacts with the surface SrO accompanied by morphological changes whereas the hexavalent gaseous Cr species mainly deposit at the LSCF/GDC interface as is the case with Cr-only poisoning. For LSM electrode, the combined interactions of Cr and S remains similar to the sum of individual Cr and S effects as SO 2 reacts with Sr-rich regions of the bulk LSM, while Cr deposits at the electrochemically active sites. The use of getter, consisting of alkaline earth and transition metal oxides, has been proposed as a cost-effective approach to mitigate electrode poisoning. SrMnO 3 (SMO) is suggested as a robust getter material for the co-capture of airborne gaseous S and Cr species entering high-temperature electrochemical systems. The honeycomb getter forms, covered with SMO nanoparticles, were fabricated using dip coating. The SMO getter successfully maintained the electrochemical activity of LSM under the presence of gaseous Cr and S species, validating the efficacy of the getter. Post-test characterization revealed that the absorption of S and Cr contaminants led to the elongation of granular SMO particles, forming SrO nanorods and SrCrO 4 whiskers leaving Mn oxides underneath where inward-migrating Cr reside, indicating the high mutual affinity of Sr and Mn. The growth of reaction products during the long term exposure favors continued absorption of incoming S and Cr contaminants. The Mn 2 O 9 dimers, existing on the surface, are considered to help absorb S and Cr impurities, along with the Sr-terminated surface. The SMO getter also displays robust stability in humid environments at high temperatures without phase transformation or hydrolysis, fulfilling the requirement for operation in high-temperature electrochemical systems.

30 DIRECT ENERGY CONVERSION↗