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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Direct Electrochemical Reduction of CO 2 to C 2+ Chemicals: Catalysts, Microenvironments, and Mechanistic Understanding

The electrochemical reduction reaction of CO 2 (eCO 2 RR) to chemicals presents a viable solution for addressing climate change and sustainable manufacturing. In this Review, we describe the recent advancements in eCO 2 RR for multicarbon (C 2+ ) chemicals production from the aspects of catalyst structure, reaction microenvironments, and mechanistic understanding. Here, we draw experimental and theoretical comparisons between the catalyst systems containing bulk and highly dispersed metals, alloys, and metal compounds and recount new results of microenvironmental impacts as well as the catalytic mechanism. From our own recent studies, we offer some viewpoints on the electrocatalytic mechanism during complex multistep proton-coupled electron transfers and propose several research directions in unlocking the full potential of eCO 2 RR as a scalable industrial solution for CO 2 -to-C 2+ conversion.

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

Accessing Photoredox Transformations with an Iron(III) Photosensitizer and Green Light

Efficient excited-state electron transfer between an iron(III) photosensitizer and organic electron donors was realized with green light irradiation. This advance was enabled by the use of the previously reported iron photosensitizer, [Fe(phtmeimb) 2 ]+ (phtmeimb = {phenyl[tris(3-methyl-imidazolin-2-ylidene)]borate}, that exhibited long-lived and luminescent ligand-to-metal charge transfer (LMCT) excited states. A benchmark dehalogenation reaction was investigated with catalytic yieldsthat exceed 90% and an enhanced stability relative to the prototypical photosensitizer [Ru(bpy) 3 ] 2+ . The initial catalytic step is electron transfer from an amine to the photoexcited iron sensitizer that is shown to occur with a large cage-escape yield. For LMCT excited states, this reductive electron transfer is vectoral and may be a general advantage of Fe(III) photosensitizers. In-depth time-resolved spectroscopic methods, that include transient absorption characterization from the ultraviolet to the infrared regions, provided a quantitative description of the catalytic mechanism with associated rate constants and yields.

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

Low-Temperature Non-Oxidative Coupling of Methane on Atomically Dispersed Titanium–Aluminum–Boron Nanopowder

Nonoxidative coupling of methane represents a long-standing challenge in heterogeneous catalysis, as it requires activation of the carbon–hydrogen (C–H) bond, controlled carbon–carbon (C–C) bond formation, and effective hydrogen management without relying on oxidants. Here, we report a low-temperature C–H activation and nonoxidative C–C coupling of methane over atomically dispersed titanium–aluminum–boron nanopowder (Ti–Al–B NP) utilizing a catalytic microreactor coupled to synchrotron single-photon photoionization reflectron time-of-flight mass spectrometry. The soft-ionization, in situ probing method detects the nascent reaction products and radical intermediates under operando conditions, including methyl radical, C2 hydrocarbons, and molecular hydrogen. Methane activation is initiated at 800 K, approximately 700 K below the gas-phase decomposition threshold, leading predominantly to ethylene formation with selectivity reaching up to 78% among the C–C coupled products. Electronic structure calculations on model Ti–Al–B clusters elucidate a cooperative catalytic mechanism in which titanium enables methane adsorption and C–H activation, boron acts as a reversible hydrogen reservoir, and aluminum stabilizes methylene intermediates, thereby facilitating selective C–C coupling and dehydrogenation. These findings establish a distinct catalyst architecture for nonoxidative methane coupling based on earth abundant elements alternative to expensive platinum and other noble metal-containing conventional catalysts and provide molecular-level design principles for controlling dehydrogenation and subsequent C–C bond formation in challenging light alkane conversions.

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

Discovery of the cryptic function of terpene cyclases as aromatic prenyltransferases

Catalytic versatility is an inherent property of many enzymes. In nature, terpene cyclases comprise the foundation of molecular biodiversity as they generate diverse hydrocarbon scaffolds found in thousands of terpenoid natural products. Here, we report that the catalytic activity of the terpene cyclases AaTPS and FgGS can be switched from cyclase to aromatic prenyltransferase at basic pH to generate prenylindoles. The crystal structures of AaTPS and FgGS provide insights into the catalytic mechanism of this cryptic function. Moreover, aromatic prenyltransferase activity discovered in other terpene cyclases indicates that this cryptic function is broadly conserved among the greater family of terpene cyclases. We suggest that this cryptic function is chemoprotective for the cell by regulating isoprenoid diphosphate concentrations so that they are maintained below toxic thresholds.

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

Three-dimensional strain dynamics govern the hysteresis in heterogeneous catalysis

Understanding catalysts strain dynamic behaviours is crucial for the development of cost-effective, efficient, stable and long-lasting catalysts. Here, we reveal in situ three-dimensional strain evolution of single gold nanocrystals during a catalytic CO oxidation reaction under operando conditions with coherent X-ray diffractive imaging. We report direct observation of anisotropic strain dynamics at the nanoscale, where identically crystallographically-oriented facets are qualitatively differently affected by strain leading to preferential active sites formation. Interestingly, the single nanoparticle elastic energy landscape, which we map with attojoule precision, depends on heating versus cooling cycles. The hysteresis observed at the single particle level is following the normal/inverse hysteresis loops of the catalytic performances. This approach opens a powerful avenue for studying, at the single particle level, catalytic nanomaterials and deactivation processes under operando conditions that will enable profound insights into nanoscale catalytic mechanisms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M pro inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Toward a mechanistic understanding of electrocatalytic nanocarbon

Electrocatalytic nanocarbon (EN) is a class of material receiving intense interest as a potential replacement for expensive, metal-based electrocatalysts for energy conversion and chemical production applications. The further development of EN will require an intricate knowledge of its catalytic behaviors, however, the true nature of their electrocatalytic activity remains elusive. This review highlights work that contributed valuable knowledge in the elucidation of EN catalytic mechanisms. Experimental evidence from spectroscopic studies and well-defined molecular models, along with the survey of computational studies, is summarized to document our current mechanistic understanding of EN-catalyzed oxygen, carbon dioxide and nitrogen electrochemistry. We hope this review will inspire future development of synthetic methods and in situ spectroscopic tools to make and study well-defined EN structures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

In crystallo observation of three metal ion promoted DNA polymerase misincorporation

Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase η. The resulting molecular snapshots suggest primer 3´-OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain

ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster . Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The structural basis for 2′−5′/3′−5′-cGAMP synthesis by cGAS

Abstract cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2′−5′/3′−5′-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria

In Gram-negative bacteria, the enzymatic modification of Lipid A with aminoarabinose (L-Ara4N) leads to resistance against polymyxin antibiotics and cationic antimicrobial peptides. ArnC, an integral membrane glycosyltransferase, attaches a formylated form of aminoarabinose to the lipid undecaprenyl phosphate, enabling its association with the bacterial inner membrane. Here, we present cryo-electron microscopy structures of ArnC from S. enterica in apo and nucleotide-bound conformations. These structures reveal a conformational transition that takes place upon binding of the partial donor substrate. Using coarse-grained and atomistic simulations, we provide insights into substrate coordination before and during catalysis, and we propose a catalytic mechanism that may operate on all similar metal-dependent polyprenyl phosphate glycosyltransferases. The reported structures provide a new target for drug design aiming to combat polymyxin resistance.

Ashraf, Khuram U. [Rutgers University, Newark, NJ ↗
DOE OSTI2022

Polymerization of the backbone of the pectic polysaccharide rhamnogalacturonan I

Rhamnogalacturonan I (RG-I) is a major plant cell wall pectic polysaccharide defined by its repeating disaccharide backbone structure of [4)-α-d-GalA- (1,2)-α-l-Rha-(1,]. A family of RG-I:Rhamnosyltransferases (RRT) has previously been identified, but synthesis of the RG-I backbone has not been demonstrated in vitro because the identity of Rhamnogalacturonan I:Galaturonosyltransferase (RG-I:GalAT) was unknown. Here a putative glycosyltransferase, At1g28240/MUCI70, is shown to be an RG-I:GalAT. The name RGGAT1 is proposed to reflect the catalytic activity of this enzyme. When incubated together with the rhamnosyltransferase RRT4, the combined activities of RGGAT1 and RRT4 result in elongation of RG-I acceptors in vitro into a polymeric product. RGGAT1 is a member of a new GT family categorized as GT116, which does not group into existing GT-A clades and is phylogenetically distinct from the GALACTURONOSYLTRANSFERASE (GAUT) family of GalA transferases that synthesize the backbone of the pectin homogalacturonan. RGGAT1 has a predicted GT-A fold structure but employs a metal-independent catalytic mechanism that is rare among glycosyltransferases with this fold type. Furthermore, the identification of RGGAT1 and the 8-member Arabidopsis GT116 family provides a new avenue for studying the mechanism of RG-I synthesis and the function of RG-I in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Highly selective electrocatalytic CO 2 reduction to ethanol by metallic clusters dynamically formed from atomically dispersed copper

Direct electrochemical conversion of CO 2 to ethanol offers a promising strategy of lowering CO 2 emission while storing energy from renewable electricity. However, current electrocatalysts offer only limited selectivity toward ethanol. Here we report a copper catalyst synthesized by a unique Cu-Li amalgm method over a commercial carbon support that achieved Faradaic efficiency (FE) higher than 91% at -0.7 V (RHE) and the active potential as low as -0.4 V (RHE) during direct electrocatalytic CO 2 -to-ethanol conversion. The catalyst also demonstrated stability over an extended period of operation. A strong correlation between the catalytic selectivity and the initial Cu atoms dispersion was found and Operando X-ray absorption spectroscopy identified a dynamic and reversible transformation from atomically dispersed copper atoms to Cu n (n = 3 and 4) under the electrochemical reaction. Frist-principles calculations further elucidate the possible catalytic mechanism of CO 2 reduction over Cu n .

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

Structural basis of broad-spectrum β-lactam resistance in Staphylococcus aureus

Abstract Broad-spectrum β-lactam antibiotic resistance in Staphylococcus aureus is a global healthcare burden 1,2 . In clinical strains, resistance is largely controlled by BlaR1 3 , a receptor that senses β-lactams through the acylation of its sensor domain, inducing transmembrane signalling and activation of the cytoplasmic-facing metalloprotease domain 4 . The metalloprotease domain has a role in BlaI derepression, inducing blaZ (β-lactamase PC1) and mecA (β-lactam-resistant cell-wall transpeptidase PBP2a) expression 3–7 . Here, overcoming hurdles in isolation, we show that BlaR1 cleaves BlaI directly, as necessary for inactivation, with no requirement for additional components as suggested previously 8 . Cryo-electron microscopy structures of BlaR1—the wild type and an autocleavage-deficient F284A mutant, with or without β-lactam—reveal a domain-swapped dimer that we suggest is critical to the stabilization of the signalling loops within. BlaR1 undergoes spontaneous autocleavage in cis between Ser283 and Phe284 and we describe the catalytic mechanism and specificity underlying the self and BlaI cleavage. The structures suggest that allosteric signalling emanates from β-lactam-induced exclusion of the prominent extracellular loop bound competitively in the sensor-domain active site, driving subsequent dynamic motions, including a shift in the sensor towards the membrane and accompanying changes in the zinc metalloprotease domain. We propose that this enhances the expulsion of autocleaved products from the active site, shifting the equilibrium to a state that is permissive of efficient BlaI cleavage. Collectively, this study provides a structure of a two-component signalling receptor that mediates action—in this case, antibiotic resistance—through the direct cleavage of a repressor.

Science & Technology - Other Topics↗
DOE OSTI2021

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family that is highly conserved in coronaviruses. As endoribonuclease activity seems to be responsible for the interference with the innate immune response, Nsp15 emerges as an attractive target for therapeutic intervention. Here we report the first structures with bound nucleotides and show how the enzyme specifically recognizes uridine moiety. In addition to a uridine site we present evidence for a second base binding site that can accommodate any base. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. This acquired knowledge was instrumental in identifying Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. Using crystallography, biochemical, and whole-cell assays, we demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site. Our findings provide new insights for the development of uracil scaffold-based drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Electrospun porous La–Sr–Co–Ni–O nanofibers for highly sensitive non-enzymatic glucose detection

Glucose biosensors are widely used for clinical, industrial, and environmental applications. Nonenzymatic electrochemical glucose biosensors based on metal oxides with a perovskite structure have exhibited high sensitivity, excellent stability, and cost efficiency. In this work, porous La–Sr–Co–Ni–O (LSCNO) nanofibers, with an ABO 3 -type perovskite structure, were prepared through optimizing the A-site and B-site elements by electrospinning, followed with calcination at 700 °C for 5 h. Characterized by scanning and transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy, fabricated nanofibers were confirmed to be porous and nanosized polycrystalline grains with high crystallinity. A novel La 0.75 Sr 0.25 Co 0.5 Ni 0.5 O 3 -based nonenzymatic electrochemical biosensor was developed, which is sensitive to glucose because of an electrochemically catalytic mechanism, a mediated electron transfer involving Ni(II)/Ni(III) or Co(II)/Co(III), accompanying with gluconic acid complexation. The glucose biosensor presented a linear response in the range of 0.1–1.0 mM with a calibration sensitivity of 924 ± 28 μA mM –1 , a proportion of the variance of 0.9926, and a lower limit of detection of 0.083 mM, respectively, demonstrating an outstanding analytical performance. The biosensor showed no response to the most widely used anionic surfactant, sodium dodecyl sulfate, and low sensitivity to other biomolecules, such as fructose, lactose, galactose, mannose, dopamine, and ascorbic acid. A urine sample was tested by this novel nonenzymatic electrochemical biosensor by standard addition method, suggesting a potential application for clinical test.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The Mycobacterium tuberculosis mycothiol S -transferase is divalent metal-dependent for mycothiol binding and transfer

Mycothiol S-transferase (MST) (encoded by the rv0443 gene) was previously identified as the enzyme responsible for the transfer of Mycothiol (MSH) to xenobiotic acceptors in Mycobacterium tuberculosis (M.tb) during xenobiotic stress. To further characterize the functionality of MST in vitro and the possible roles in vivo, X-ray crystallographic, metal-dependent enzyme kinetics, thermal denaturation studies, and antibiotic MIC determination in rv0433 knockout strain were performed. The binding of MSH and Zn 2+ increases the melting temperature by 12.9 °C as a consequence of the cooperative stabilization of MST by both MSH and metal. The co-crystal structure of MST in complex with MSH and Zn 2+ to 1.45 Å resolution supports the specific utilization of MSH as a substrate as well as affording insights into the structural requirements of MSH binding and the metal-assisted catalytic mechanism of MST. Further, contrary to the well-defined role of MSH in mycobacterial xenobiotic responses and the ability of MST to bind MSH, cell-based studies with an M.tb rv0443 knockout strain failed to provide evidence for a role of MST in processing of rifampicin or isoniazid. These studies suggest the necessity of a new direction to identify acceptors of the enzyme and better define the biological role of MST in mycobacteria.

59 BASIC BIOLOGICAL SCIENCES↗