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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Effect of Phosphorus Modulation in Iron Single‐Atom Catalysts for Peroxidase Mimicking

Abstract Fe–N–C single‐atom catalysts (SACs) exhibit excellent peroxidase (POD)‐like catalytic activity, owing to their well‐defined isolated iron active sites on the carbon substrate, which effectively mimic the structure of natural peroxidase's active center. To further meet the requirements of diverse biosensing applications, SAC POD‐like activity still needs to be continuously enhanced. Herein, a phosphorus (P) heteroatom is introduced to boost the POD‐like activity of Fe–N–C SACs. A 1D carbon nanowire (FeNCP/NW) catalyst with enriched Fe–N 4 active sites is designed and synthesized, and P atoms are doped in the carbon matrix to affect the Fe center through long‐range interaction. The experimental results show that the P‐doping process can boost the POD‐like activity more than the non‐P‐doped one, with excellent selectivity and stability. The mechanism analysis results show that the introduction of P into SAC can greatly enhance POD‐like activity initially, but its effect becomes insignificant with increasing amount of P. As a proof of concept, FeNCP/NW is employed in an enzyme cascade platform for highly sensitive colorimetric detection of the neurotransmitter acetylcholine.

Ding, Shichao↗
DOE OSTI2020

Characterization of SETD3 methyltransferase–mediated protein methionine methylation

Most characterized protein methylation events encompass arginine and lysine N-methylation, and only a few cases of protein methionine thiomethylation have been reported. Newly discovered oncohistone mutations include lysine-to-methionine substitutions at positions 27 and 36 of histone H3.3. In these cases, the methionine substitution localizes to the active-site pocket of the corresponding histone lysine methyltransferase, thereby inhibiting the respective transmethylation activity. SET domain–containing 3 (SETD3) is a protein (i.e. actin) histidine methyltransferase. Here, we generated an actin variant in which the histidine target of SETD3 was substituted with methionine. As for previously characterized histone SET domain proteins, the methionine substitution substantially (76-fold) increased binding affinity for SETD3 and inhibited SETD3 activity on histidine. Unexpectedly, SETD3 was active on the substituted methionine, generating S-methylmethionine in the context of actin peptide. The ternary structure of SETD3 in complex with the methionine-containing actin peptide at 1.9 Å resolution revealed that the hydrophobic thioether side chain is packed by the aromatic rings of Tyr 312 and Trp 273 , as well as the hydrocarbon side chain of Ile 310 . Our results suggest that placing methionine properly in the active site—within close proximity to and in line with the incoming methyl group of SAM—would allow some SET domain proteins to selectively methylate methionine in proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

Modeling the Uptake of Hydrogen Chloride onto Interior Spacecraft Materials

Hydrogen chloride (HCl) is a major combustion product from the pyrolysis of polyvinyl chloride (PVC) insulated electrical wires, a common spacecraft fire safety concern. Models at two different scales were developed to predict HCl uptake on anodized, chromate conversion coated (Iridite), and bare aluminum surfaces, as well as on Nomex fabric: a macroscopic one-step global surface reaction model where all the active sites are on the exterior surface, and a pore model where the interior active sites deeper into the oxide layer can also be accessed by HCl. Experiments were performed to calibrate kinetic and diffusion constants in the models. A cast acrylic test cell was used to measure the differences between the inlet and outlet concentration of HCl after inserting a sample rod of the test material. For the materials with a thin (< 200 µm) or no oxide layer, the macroscopic surface reaction model adequately predicts the experimental measurements. For the anodized aluminum with a thicker oxide layer, the pore model provided a better match to experimental results. The results will be discussed with respect to the spacecraft fire safety project (Saffire).

modeling↗
NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗
DOE OSTI2022

Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6

The E1 enzyme Uba6 initiates signal transduction by activating ubiquitin and the ubiquitin-like protein FAT10 in a two-step process involving sequential catalysis of adenylation and thioester bond formation. To gain mechanistic insights into these processes, we determined the crystal structure of a human Uba6/ubiquitin complex. Two distinct architectures of the complex are observed: one in which Uba6 adopts an open conformation with the active site configured for catalysis of adenylation, and a second drastically different closed conformation in which the adenylation active site is disassembled and reconfigured for catalysis of thioester bond formation. Surprisingly, an inositol hexakisphosphate (InsP6) molecule binds to a previously unidentified allosteric site on Uba6. Our structural, biochemical, and biophysical data indicate that InsP6 allosterically inhibits Uba6 activity by altering interconversion of the open and closed conformations of Uba6 while also enhancing its stability. In addition to revealing the molecular mechanisms of catalysis by Uba6 and allosteric regulation of its activities, our structures provide a framework for developing Uba6-specific inhibitors and raise the possibility of allosteric regulation of other E1s by naturally occurring cellular metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Revisiting Competing Paths in Electrochemical CO 2 Reduction on Copper via Embedded Correlated Wavefunction Theory

We re-evaluate two key steps in the mechanism of CO 2 reduction on copper at a higher level of theory capable of correcting inherent errors in density functional theory (DFT) approximations, namely, embedded correlated wavefunction (ECW) theory. Here, we consider the CO reduction step on Cu(111), which is critical to understanding reaction selectivity. Here, we optimize embedding potentials at the periodic plane-wave DFT level using density functional embedding theory (DFET). All possible adsorption sites (adsites) for each adsorbate then are screened with ECW theory at the catalytically active site to refine the local electronic structure. Unsurprisingly, DFT and ECW theory predict different adsite preferences, largely because of DFT’s inability to properly situate the CO 2π* level. Differing preferred adsites suggest that different reaction pathways could emerge from DFT versus ECW theory. Starting from these preferred ECW theory adsites, we then obtain reaction pathways at the plane-wave DFT level using the climbing-image nudged elastic band method to determine minimum energy paths. Thereafter, we perform ECW calculations at the catalytically active site to correct the energetics at each interpolated structure (image) along the reaction pathways. Via this approach, we confirm that the first step in CO reduction via hydrogen transfer on Cu(111) is to form hydroxymethylidyne (*COH) instead of formyl (*CHO). Although the prediction to preferentially form *COH is consistent with that of DFT, the two theories predict quite different structural and mechanistic behaviors, suggesting that verification is needed for other parts of the mechanism of CO 2 reduction, which is the subject of ongoing work.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

Low temperature dry reforming of methane using Ru-Ni-Mg/ceria-zirconia catalysts: Effect of Ru loading and reduction temperature

Dry reforming catalysts, especially those with activity at moderate temperatures, have been intensely investigated to enhance the conversion of biogas. Here, Ru is evaluated as a promoter for Ni-Mg based catalysts. Catalysts based on 1.4 wt%Ni-1.0 wt%Mg-Ce 0.6 Zr 0.4 O 2 with Ru (0.02–0.32 wt%) were prepared using incipient wetness. The reducibility of the catalysts and conversions increased with increasing Ru content. Increases in conversions with increasing Ru loading was attributed to the additional active sites and synergistic effect between Ru and Ni, which weakened Ni-Mg interactions. Samples showed dry reforming activity at low temperatures (450–510 °C). Reaction rates and activation energies of higher loading Ru samples (1.4 wt%Ni-1.0 wt%Mg/Ce 0.6 Zr 0.4 O 2 with 0.16 and 0.32 wt%Ru) decreased when the reduction temperature was raised from 300 to 400 °C. A 20 h TOS study showed stable catalytic activity with minimal coke deposition. Furthermore, the results suggest that Ru is an alternative to Pt in promoting low temperature dry reforming of methane.

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

Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases

Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized -- but only from archaeal methanogens that are anaerobic, O 2 -sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O 2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O 2 -sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Room temperature synthesis of high-entropy Prussian blue analogues

High-entropy Prussian blue analogues (HEPBAs) integrating the highly dispersed active sites of high-entropy materials with intrinsic 3D diffusion channels and the redox-active sites of Prussian blue analogues have great potential in electrochemical applications but have not been realized. Herein, a series of HEPBAs were successfully synthesized under room temperature combining mechanochemistry with wet chemistry for the first time.

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

Crystal structure of Methanococcus jannaschii dihydroorotase with substrate bound

Here, we report the X-ray structural analysis of dihydroorotase from Methanococcus jannaschii co-crystallized with dihydroorotate at pH 6.5. The crystals are isomorphous with the crystals of the apoenzyme, with space group P3 2 21 and unit-cell dimensions a = b = 111.4, c = 101.2 Å. The structure was refined to R = 0.169 and R free = 0.186 at a resolution of 1.87 Å at room temperature. During crystallization the degradative reaction took place, and the electron density in the active site corresponds to the substrate carbamoyl aspartate. Carbamoyl aspartate interacts with the protein in the active site in a manner similar to that observed for Escherichia coli and human dihydroorotases. However, the flexible loop (residues 140–151) adopts both conformations in the crystal, loop-out and loop-in, with the loop-out conformation having higher occupancy. This contrasts with our expectations for the flexible loop to be exclusively in the loop-in conformation, which is the conformation that it adopts to stabilize the binding of the substrate in the known systems. Additional studies with substrate analogs that resemble carbamoyl aspartate and different crystallization conditions would provide further insight into the conformation of the flexible loop in this system.

Methanococcus jannaschii↗
DOE OSTI2020

Multi-modal surface analysis of porous films under operando conditions

Practical catalysts with a porous framework, such as zeolites, host catalytic reactions at active sites engrained in the pores and channels of the scaffold. The mechanism of interaction at these active sites, defining catalyst performance, remains elusive, in large part, due to the lack of surface characterization methods available for thick films or powders. Here, we present thin film analogs of practical catalysts that allow for the implementation of surface characterization tools, including advanced microscopy and operando spectroscopy methodologies. Specifically, we investigated bilayer silica, MFI nanosheets, and UiO-66 thin films using a multi-modal approach addressing film growth, characterization, and gas adsorption aimed at understanding catalytic activity, reactivity, and selectivity properties, as defined by molecular-level changes in the reaction mechanism.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Performance enhancement and degradation mechanism identification of a single-atom Co–N–C catalyst for proton exchange membrane fuel cells

Development of platinum group metal (PGM)-free catalysts for oxygen reduction reaction (ORR) has been a strategic research topic for proton exchange membrane (PEM) fuel cells. Present state-of-art PGM-free ORR catalysts are Fe, N co-doped carbon (Fe-N-C) catalysts, which unfortunately exhibit instability concerns. Herein, we report a stable atomically dispersed Co, N co-doped carbon (Co-N-C) catalyst with high Co content of 1.0 at% and the active site, i.e., the coordination of Co, is CoN2+2 in nature. The Co-N-C catalyst demonstrated high ORR activity comparable to, and high stability over 3 times better than, that of the Fe-N-C catalyst. It also achieved a high activity of 22 mA cm2 at 0.9 ViR-free and a power density of 0.61 W cm-2 under 1.0 bar H2/O2. Further, we identify two main degradation mechanisms of the PGM-free catalysts: catalyst oxidation by H2O2/radicals and demetalation. The improved stability of Co-N-C relative to Fe-N-C is attributed to less Fenton-reactive nature of Co and significantly enhanced resistance to demetalation of Co-N-C.

Xie, Xiaohong↗
DOE OSTI2023

Assessing factors that determine adatom migration and clustering on a thin film oxide; Pt 1 and Rh 1 on the “29” Cu x O/Cu(1 1 1) surface

The dynamical nature of single-site catalysts under non-equilibrium conditions poses significant challenges in the full characterization of their active sites. The “29” oxide is a thin Cu x O film grown on Cu(111) which provides a well-defined surface on which to study the structure and chemistry of atomically dispersed precious metals. A combination of experimental and first-principles approaches is used to investigate the factors that influence the mobility of metal adatoms and their clustering tendencies. Our work elucidates how a homogenous coordination environment of neutral single-atoms can be obtained when its tendency to break oxide bonds within its vicinity is low. Herein we demonstrate that this in turn affects the chemical atomically dispersed species on thin-film oxides, as defects on the oxide would in fact allow such species to be more accessible to CO. We thus highlight the importance of understanding the relationship between defects and atomically dispersed active sites upon designing single-site catalysts.

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

Intra-crystalline mesoporous zeolite encapsulation-derived thermally robust metal nanocatalyst in deep oxidation of light alkanes

Zeolite-confined metal nanoparticles (NPs) have attracted much attention owing to their superior sintering resistance and broad applications for thermal and environmental catalytic reactions. However, the pore size of the conventional zeolites is usually below 2 nm, and reactants are easily blocked to access the active sites. Herein, a facile in situ mesoporogen-free strategy is developed to design and synthesize palladium (Pd) NPs enveloped in a single-crystalline zeolite (silicalite-1, S-1) with intra-mesopores (termed Pd@IM-S-1). Pd@IM-S-1 exhibited remarkable light alkanes deep oxidation performances, and it should be attributed to the confinement and guarding effect of the zeolite shell and the improvement in mass-transfer efficiency and active metal sites accessibility. The Pd–PdO interfaces as a new active site can provide active oxygen species to the first C–H cleavage of light alkanes. This work exemplifies a promising strategy to design other high-performance intra-crystalline mesoporous zeolite-confined metal/metal oxide catalysts for high-temperature industrial thermal catalysis.

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

Controlled site coverage of strong metal–support interaction (SMSI) on Pd NP catalysts

Here, strong metal–support interaction catalysts have been shown to improve desired product selectivity at the cost of fractional rates due to active site coverage. The goal of this study was to determine if the active site coverage of metallic nanoparticles could be controlled to lower levels than have been previously reported in SMSI catalysts with the aim of improving the rate while maintaining high selectivity. 2Pd–XTi/SiO 2 (2 wt% Pd, X wt% Ti) strong metal–support interaction (SMSI) catalysts with Ti loadings between 0–1.0 wt% were synthesized to control Pd nanoparticle coverage. Calcination at 450 °C and reduction at 550 °C were sufficient for forming ~2 nm sized Pd particles in all catalysts. Increasing the Ti loading from 0.1 to 1.0 wt% increased the surface coverage from 40 to 85% at a fixed reduction temperature of 550 °C. The IR spectra of the SMSI catalysts were similar with a high fraction of linear bonded CO which was much higher than that of Pd nanoparticles of similar size. The SMSI overlayer could be removed by oxidation at 350 °C and re-reduction at 200 °C. EXAFS of the oxidized catalysts indicates that nearly full oxidation of the metallic nanoparticle was required to remove the SMSI overlayer. Oxidation temperatures from 30 to 300 °C partially oxidized the Pd nanoparticles and subsequent re-reduction at 200 °C partially decreases the SMSI coverage. The fractional surface coverage was determined by measuring the rate of propylene hydrogenation with and without the SMSI overlayer. Increasing the reduction temperature from 200 to 550 °C increased the SMSI coverage from 0 to 85% depending on the Ti loading and temperature. In conclusion, after reduction at 550 °C and oxidation at 350 °C, the range of coverages varied between ~10% with 0.1 wt% Ti after re-reduction at 300 °C and ~85% with 1 wt% Ti after reduction at 550 °C.

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

Structural elucidation of the cis -prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation

Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme’s active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme’s active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.

59 BASIC BIOLOGICAL SCIENCES↗