Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “active sites”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Development of LpxH Inhibitors Chelating the Active Site Dimanganese Metal Cluster of LpxH

Abstract Despite the widespread emergence of multidrug‐resistant nosocomial Gram‐negative bacterial infections and the major public health threat it brings, no new class of antibiotics for Gram‐negative pathogens has been approved over the past five decades. Therefore, there is an urgent medical need for developing effective novel antibiotics against multidrug‐resistant Gram‐negative pathogens by targeting previously unexploited pathways in these bacteria. To fulfill this crucial need, we have been investigating a series of sulfonyl piperazine compounds targeting LpxH, a dimanganese‐containing UDP‐2,3‐diacylglucosamine hydrolase in the lipid A biosynthetic pathway, as novel antibiotics against clinically important Gram‐negative pathogens. Inspired by a detailed structural analysis of our previous LpxH inhibitors in complex with K. pneumoniae LpxH ( Kp LpxH), here we report the development and structural validation of the first‐in‐class sulfonyl piperazine LpxH inhibitors, JH‐LPH‐45 ( 8 ) and JH‐LPH‐50 ( 13 ), that achieve chelation of the active site dimanganese cluster of Kp LpxH. The chelation of the dimanganese cluster significantly improves the potency of JH‐LPH‐45 ( 8 ) and JH‐LPH‐50 ( 13 ). We expect that further optimization of these proof‐of‐concept dimanganese‐chelating LpxH inhibitors will ultimately lead to the development of more potent LpxH inhibitors for targeting multidrug‐resistant Gram‐negative pathogens.

Pharmacology & Pharmacy↗
DOE OSTI2020

The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases

Arginine acts as a precursor of polyamines in plants in two known pathways, agmatine and ornithine routes. It is decarboxylated to agmatine by arginine decarboxylase, and then transformed to putrescine by the consecutive action of agmatine iminohydrolase and N-carbamoylputrescine amidohydrolase. Alternatively, it can be hydrolyzed to ornithine by arginase and then decarboxylated by ornithine decarboxylase to putrescine. Some plants lack a functional ornithine pathway, but all have one or two arginases that can have dual cellular localization, in mitochondria and plastids. It was recently shown that arginases from Arabidopsis thaliana and soybean act also as agmatinases, thus they can produce putrescine directly from agmatine. Therefore, arginase (together with arginine decarboxylase) can complement putrescine production in plastids, providing a third polyamine biosynthesis pathway in plants. Phylogenetic analysis suggests that arginases, highly conserved in the plant kingdom, create the only group of enzymes recognized in the family of ureohydrolases in plants. Arginases are metalloenzymes with binuclear manganese cluster in the active site. In this work, two arginases from A. thaliana and Medicago truncatula are structurally characterized and their binding properties are discussed. Crystal structures with bound ornithine show that plant hexameric arginases engage a long loop from the neighboring subunit to stabilize α-amino and carboxyl groups of the ligand. This unique ligand binding mode is unobserved in arginases from other domains of life. Structural analysis shows that substrate binding by residues from two neighboring subunits might also characterize some prokaryotic agmatinases. This feature of plant arginases is most likely the determinant of their ability to recognize not only arginine but also agmatine as their substrates, thus, to act as arginase and agmatinase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Lithium superoxide-based high rate Li-Air batteries enabled by Di-iridium sulfur bridge active sites

Li-oxygen (Li-O 2 ) batteries can potentially provide much higher energy density than Li-ion batteries; however, the practical application of these batteries is hindered due to several drawbacks such as low current rates and high overpotential for the charging process. Here, in this paper, we report a novel Li-Air battery system that operates under high current rates (up to 1mAcm -2 ) with LiO 2 as the primary discharge product instead of the commonly reported Li 2 O 2 . This LiO 2 based battery at high rates is through a combination of an as-synthesized new one-dimensional (1D) transition metal trichalcogenide mid-entropy alloy of SnIrS 3.6 as a cathode catalyst and an electrolyte blend with a SnI 2 bi-functional additive. It is revealed that SnIrS 3.6 has a microporous structure composed of six- and five-coordinated metal atoms, forming octahedral and triangular bipyramids which has not been observed in other layered chalcogeide materials. DFT calculations reveal that the SnIrS 3.6 structure can result in LiO 2 formation through di-iridium sulfur bridge active sites that results in strong binding of O 2 and LiO 2 preventing disproportionation to Li 2 O 2 and enabling high rates. This finding will open a new perspective in designing advanced LiO 2 -based Li-O 2 batteries for real practices.

25 ENERGY STORAGE↗
DOE OSTI2023

Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity

DNA polymerases catalyze DNA synthesis with high efficiency, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during the DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rNs) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes ribonucleotide triphosphate binding, the mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η error incorporation efficiency increases significantly across different sequence contexts. Finally, our systematic structural studies suggest that the rN at the primer end improves primer alignment and reduces barriers in C2'-endo to C3'-endo sugar conformational change. Overall, our work provides further mechanistic insights into the effects of rN incorporation on DNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effects of the method of active site characterization for determining structure-sensitivity in Ag-catalyzed ethylene epoxidation

We report catalysts have been prepared on a low surface area α-Al 2 O 3 support used commercially for previous generation olefin epoxidation catalysts. Prescreening of the low surface area alumina (0.73 m 2 /g) indicated the absence of acid catalyzed isomerization of EO at an evaluation temperature of 210 °C. A 0.1 wt% Ag base material synthesized by incipient wetness impregnation of AgNO 3 was used as a base material for electroless deposition (ED) of additional Ag to increase particle sizes by controlled reduction of Ag + directly onto the preexisting Ag surface to form weight loadings between 0.3 and 5.0 wt% metal. A 12 wt% Ag/α-Al 2 O 3 using Ag 2 C 2 O 4 as the Ag precursor was also prepared to compare performance of the ED samples with a catalyst more typical of industrial formulations. Characterization by SEM, STEM, and hydrogen titration of oxygen precovered Ag characterized before and after catalytic evaluation indicated that microscopy is required to accurately represent distributions of Ag particle sizes, but H 2 titration of O-precovered Ag gives the best representation of active sites since it directly counts the number of Ag surface sites. Larger particles >100 nm are resistant to both Ag sintering and carbon foulant; TOF values were relatively insensitive to particle size with only a 2.2 × difference between the best and worst performing samples. Selectivity, which is not a function of TOF, shows the most significant structure sensitivity effect where particle sizes follow the trend 67 nm ≈ 92 nm (58% EO) < 157 nm (67% EO) < 211–542 nm (73% EO). The lower EO selectivities were also correlated with increased fouling for the smaller Ag sizes, suggesting that more strongly bound EO precursor(s) leads to combustion and CO 2 /H 2 O formation.

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

An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation

Human uracil DNA-glycosylase (UDG) is the prototypic and first identified DNA glycosylase with a vital role in removing deaminated cytosine and incorporated uracil and 5-fluorouracil (5-FU) from DNA. UDG depletion sensitizes cells to high APOBEC3B deaminase and to pemetrexed (PEM) and floxuridine (5-FdU), which are toxic to tumor cells through incorporation of uracil and 5-FU into DNA. To identify small-molecule UDG inhibitors for pre-clinical evaluation, we optimized biochemical screening of a selected diversity collection of >3,000 small-molecules. We found aurintricarboxylic acid (ATA) as an inhibitor of purified UDG at an initial calculated IC 50 < 100 nM. Subsequent enzymatic assays confirmed effective ATA inhibition but with an IC50 of 700 nM and showed direct binding to the human UDG with a K D of <700 nM. ATA displays preferential, dose-dependent binding to purified human UDG compared to human 8-oxoguanine DNA glycosylase. ATA did not bind uracil-containing DNA at these concentrations. Yet, combined crystal structure and in silico docking results unveil ATA interactions with the DNA binding channel and uracil-binding pocket in an open, destabilized UDG conformation. Biologically relevant ATA inhibition of UDG was measured in cell lysates from human DLD1 colon cancer cells and in MCF-7 breast cancer cells using a host cell reactivation assay. Collective findings provide proof-of-principle for development of an ATA-based chemotype and “door stopper” strategy targeting inhibitor binding to a destabilized, open pre-catalytic glycosylase conformation that prevents active site closing for functional DNA binding and nucleotide flipping needed to excise altered bases in DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Self-Sacrificial Template Synthesis of Fe-N-C Catalysts with Dense Active Sites Deposited on A Porous Carbon Network for High Performance in PEMFC

In this study, iron-nitrogen-carbon (Fe-N-C) single-atom catalysts are promising sustainable alternatives to the costly and scarce platinum (Pt) to catalyze the oxygen reduction reactions (ORR) at the cathode of proton exchange membrane fuel cells (PEMFCs). However, Fe-N-C cathodes for PEMFC are made thicker than Pt/C ones, in order to compensate for the lower intrinsic ORR activity and site density of Fe-N-C materials. The thick electrodes are bound with mass transport issues that limit their performance at high current densities, especially in H 2 /air PEMFCs. Practical Fe-N-C electrodes must combine high intrinsic ORR activity, high site density, and fast mass transport. Herein, it has achieved an improved combination of these properties with a Fe-N-C catalyst prepared via a two-step synthesis approach, constructing first a porous zinc-nitrogen-carbon (Zn-N-C) substrate, followed by transmetallating Zn by Fe via chemical vapor deposition. A cathode comprising this Fe-N-C catalyst has exhibited a maximum power density of 0.53 W cm -2 in H 2 /air PEMFC at 80 °C. The improved power density is associated with the hierarchical porosity of the Zn-N-C substrate of this work, which is achieved by epitaxial growth of ZIF-8 onto g-C 3 N 4 , leading to a micro-mesoporous substrate.

25 ENERGY STORAGE↗
DOE OSTI2023

Active Site Engineering via Optimizing the Heterogeneous Support Structure for Single-Atom Catalysis

Supported single-atom catalysts show a large range of activities and selectivities that depend on the local environment of the catalytic sites. Here a theory-based optimization strategy is presented that is based on a density functional theory determination of the transition states and intermediates for a low-dimensional coordinate representation of the heterogeneity of the active sites. The approach is applied to a vanadium catalyst on an amorphous SiO 2 support that involves a large kinetic network described using a full chemistry model. Without assuming a priori scaling relations or mechanism reduction, the optimal state of heterogeneity is found to lie at atomic configurations where the activation energies for two distinct key chemical processes are equal. It is found a posteriori that the behavior of the system is consistent with linear free energy scaling relations in the randomness parameters. The energetic span theory proves quite useful in reducing the full chemistry model to a small number of key reactions. The use of a nonlinear optimization algorithm in combination with energetic span theory provides significant simplification in treating disordered systems.

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

Single-Facet Dominant Anatase TiO 2 (101) and (001) Model Catalysts to Elucidate the Active Sites for Alkanol Dehydration

Alkanol dehydration on Lewis acid-base pairs of transition metal oxide catalysts is a reaction of importance in oxygen removal from biomass-derived feedstocks and their conversion to chemicals in general. However, catalysts with a high degree of structural heterogeneity, such as commercial TiO 2 powders, are not well-suited to establish rigorous structure-function relationships at an atomic level. Here, we provide compelling evidence for the effects of surface orientation of TiO 2 catalyst on elimination reactions of alcohols. Two anatase titania model catalysts, with preferential exposure of (101) and (001) facets, were synthesized and studied for 2-propanol dehydration using kinetic, isotopic, microscopic, and spectroscopic measurements, coupled with DFT calculations. Surface Lewis acid sites were found to be active for 2-propanol dehydration and (101) facets are more reactive than (001) facets under the reaction conditions studied. On both anatase surfaces, 2-propanol was found to dehydrate via concerted E2 elimination pathways, but with different initial states and thus also different intrinsic activation barriers. Molecular 2-propanol dehydration dominates on TiO2 (101) while on TiO 2 (001), 2-propanol simultaneously converts to more stable 2-propoxide before dehydration, which then requires higher activation energies for E2 elimination.

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

Precise Identification and Characterization of Catalytically Active Sites on the Surface of γ‐Alumina**

Abstract γ‐alumina is one of the oldest and most important commercial catalytic materials with high surface area and stability. These attributes enabled its use as the first commercial large‐scale heterogeneous catalyst for ethanol dehydration. Despite progress in materials characterization the nature of the specific sites on the surface of γ‐alumina that are responsible for its unique catalytic properties has remained obscure and controversial. By using combined infrared spectroscopy, electron microscopy and solid‐state nuclear magnetic resonance measurements we identify the octahedral, amphoteric (O) 5 Al(VI)‐OH sites on the (100) segments of massively restructured (110) facets on typical rhombus‐platelet γ‐alumina as well as the (100) segments of irrational surfaces (invariably always present in all γ‐alumina samples) responsible for its unique catalytic activity. Such (O) 5 Al(VI)‐OH sites are also present on the macroscopically defined (100) facets of γ‐alumina with elongated/rod‐like geometry. The mechanism by which these sites lose ‐OH groups upon thermal dehydroxylation resulting in coordinatively unsaturated penta‐coordinate Al +3 O 5 sites is clarified. These coordinatively unsaturated penta‐coordinate Al sites produce well‐defined thermally stable Al‐carbonyl complexes. Our findings contribute to the understanding of the nature of coordinatively unsaturated Al sites on the surface of γ‐alumina and their role as catalytically active sites.

Khivantsev, Konstantin↗
DOE OSTI2023

Chemical Kinetic Method for Active-Site Quantification in Fe-N-C Catalysts and Correlation with Molecular Probe and Spectroscopic Site-Counting Methods

Mononuclear Fe ions ligated by nitrogen (FeN x ) dispersed on nitrogen-doped carbon (Fe-N-C) serve as active centers for electrocatalytic O 2 reduction and thermocatalytic aerobic oxidations. Despite their promise as replacements for precious metals in a variety of practical applications, such as fuel cells, the discovery of new Fe-N-C catalysts has relied primarily on empirical approaches. In this context, the development of quantitative structure–reactivity relationships and benchmarking of catalysts prepared by different synthetic routes and by different laboratories would be facilitated by the broader adoption of methods to quantify atomically dispersed FeN x active centers. In the present study, we develop a kinetic probe reaction method that uses the aerobic oxidation of a model hydroquinone substrate to quantify the density of FeN x centers in Fe- N-C catalysts. The kinetic method is compared with low-temperature Mössbauer spectroscopy, CO pulse chemisorption, and electrochemical reductive stripping of NO derived from NO 2 – on a suite of Fe-N-C catalysts prepared by diverse routes and featuring either the exclusive presence of Fe as FeN x sites or the coexistence of aggregated Fe species in addition to FeN x . The FeN x site densities derived from the kinetic method correlate well with those obtained from CO pulse chemisorption and Mössbauer spectroscopy. The broad survey of Fe-N-C materials also reveals the presence of outliers and challenges associated with each site quantification approach. Furthermore, the kinetic method developed here does not require pretreatments that may alter active-site distributions nor specialized equipment beyond reaction vessels and analytical instrumentation (e.g., NMR).

36 MATERIALS SCIENCE↗
DOE OSTI2021

Precise Identification and Characterization of Catalytically Active Sites on the Surface of γ-Alumina

γ-alumina is one of the oldest and most important commercial catalytic materials with high surface area and stability. These attributes enabled its use as the first commercial large-scale heterogeneous catalyst for ethanol dehydration. Despite progress in materials characterization the nature of the specific sites on the surface of γ-alumina that are responsible for its unique catalytic properties has remained obscure and controversial. By using combined infrared spectroscopy, electron microscopy and solid-state nuclear magnetic resonance measurements we identify the octahedral, amphoteric (O) 5 Al(VI)-OH sites on the (100) segments of massively restructured (110) facets on typical rhombus-platelet γ-alumina as well as the (100) segments of irrational surfaces (invariably always present in all γ-alumina samples) responsible for its unique catalytic activity. Such (O) 5 Al(VI)-OH sites are also present on the macroscopically defined (100) facets of γ-alumina with elongated/rod-like geometry. The mechanism by which these sites lose -OH groups upon thermal dehydroxylation resulting in coordinatively unsaturated penta-coordinate Al +3 O 5 sites is clarified. These coordinatively unsaturated penta-coordinate Al sites produce well-defined thermally stable Al-carbonyl complexes. Overall, our findings contribute to the understanding of the nature of coordinatively unsaturated Al sites on the surface of γ-alumina and their role as catalytically active sites.

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

Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site

Background: Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production. Results: Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H 2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains. Conclusion: The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O 2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Decoupling the catalytic and degradation mechanisms of cobalt active sites during acidic water oxidation

Advancement of iridium-free catalysts for the low-pH oxygen evolution reaction (OER) is required to enable multi-gigawatt-scale proton-exchange water electrolysis. Cobalt-based materials might address this requirement, but little is known about the mechanism of operation of these OER catalysts at low pH. Here we investigate the nature and evolution of the active cobalt sites along with charge- and mass-transfer processes that support their catalytic function within a cobalt–iron–lead oxide material using in situ spectroscopic, gravimetric and electrochemical techniques. We demonstrate that corrosion of the cobalt sites and their reformation through electrooxidation of dissolved Co 2+ do not affect the catalytic mechanism and are decoupled from the OER. The OER-coupled charge transfer is supported by Co (3+δ)+ -oxo-species, which are structurally different from those reported for alkaline/near-neutral conditions and are formed on a relatively slow timescale of minutes. These mechanistic insights might assist in developing genuinely practical catalysts for this vital technology.

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

Enhanced Catalytic Dechlorination of Polyvinyl Chloride (PVC) and H2 Production Enabled by Synergistic Gaδ+/Ga0 Active Sites in Liquid Metal Particles

Polyvinyl chloride (PVC) is ubiquitous yet challenging to recycle due to its tendency to thermally decompose above 250 °C, releasing toxic, corrosive chlorinated compounds, and its inability to melt. Here, we report a catalytic strategy for PVC upcycling at 160 °C using gallium liquid metal particles (Ga-LMP) featuring a dynamic Ga-GaOOH core–shell architecture. These catalysts enable concurrent dechlorination and hydrogen evolution, yielding up to 7% H2 (based on initial hydrogen atoms in PVC) along with a highly dechlorinated (>95%) carbonaceous solid and aqueous HCl. Mechanistic investigations combining X-ray photoelectron spectroscopy, infrared spectroscopy, solid-state NMR, inelastic neutron scattering, and ab initio molecular dynamics reveal a synergistic interplay between Gaδ+ sites in the GaOOH shell and metallic Ga0 in the core. Cationic Ga initiates C–Cl bond activation and HCl formation, while progressive reduction of the shell exposes Ga0 sites that promote C–H activation and H2 evolution. Control experiments with a Ga salt and bulk Ga liquid metal confirmed that neither oxidation state alone can achieve both transformations efficiently. This work establishes a dynamic dual-site paradigm for liquid metal catalysis, in which the in situ evolution and coexistence of oxidized and metallic species enable sequential and cooperative bond activation pathways. These findings provide a general design principle for novel liquid metal catalysts that target challenging polymer transformations under mild conditions.

Zingg, Benjamin [ORNL] (ORCID:0009000914530153)↗