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.

SourceResearch connectionFrom yearThrough year

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

At least 559 records · Page 31

All sources NASA NTRS DOE OSTI

DOE OSTI2024

Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway

Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this study, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Correlating surface adsorbate configuration and electrochemical performance of IrO 2 during seawater-relevant electrolysis

Seawater electrolysis alleviates freshwater demand to produce clean hydrogen while eliminating the need for water purification steps. The anodic process, seawater oxidation, typically requires high overpotentials and yields low selectivity to oxygen via the oxygen evolution reaction (OER), primarily due to the competing chlorine evolution reaction (CER) and hypochlorite evolution reaction (HCER) in pH-neutral conditions. Here, combining in situ surface-enhanced Raman characterization, grand canonical density functional theory-based calculations, and kinetic Monte Carlo simulations, we report the evolution of surface adsorbate configurations driven by applied potential and pH during seawater-relevant OER over IrO 2 , a highly OER-active and chloride-corrosion-resistant catalyst. As a result, the chemical properties of active sites, and thereby the kinetics of OER and CER/HCER, are effectively tuned. However, it is revealed that there is no optimal combination of potential and pH to achieve both high activity and high selectivity for seawater-relevant OER. To address this limitation, we establish a correlation between activity/selectivity and surface adsorbate configurations, enabling the optimization of highly active and OER-selective IrO 2 -based catalysts in seawater-relevant oxidation by modulating the local adsorbate environment of active sites.

08 HYDROGEN↗

DOE OSTI2021

Identifying higher oxygenate synthesis sites in Cu catalysts promoted and stabilized by atomic layer deposited Fe 2 O 3

The conversion of syngas to higher oxygenates is an important step in the pathway towards the long-term sustainable production of fuels and chemicals. Mixed Cu/Fe catalysts combine metals with different CO activation characteristics, a property that makes them promising candidates for higher oxygenate production. However, Cu/Fe catalysts suffer from instability due to sintering and phase separation, and the active sites for higher oxygenate formation on these materials are not well understood. In this work, we use atomic layer deposition (ALD) to modify silica-supported Cu nanoparticles with monolayer precise amounts of Fe 2 O 3 and study the effects on catalyst structure, reactivity, and stability. We demonstrate that the Fe 2 O 3 ALD process is inherently selective towards deposition on the SiO 2 surface versus the Cu nanoparticles. As a result, a sufficiently thick Fe 2 O 3 layer surrounding the Cu nanoparticles acts as a barrier against Cu migration, preventing catalyst deactivation through sintering without covering the Cu. In syngas conversion reactions, we find that higher oxygenate selectivity increases with Fe 2 O 3 loading at low and intermediate ALD cycle numbers. Furthermore, using in situ X-ray absorption spectroscopy, we demonstrate that the Fe near the Cu nanoparticles is reduced to a metallic state under reaction conditions. From these measurements, we identify these metallic Cu/Fe interfaces as the active sites for higher oxygenate formation, which are most abundant at intermediate Fe 2 O 3 ALD cycle numbers. As the Fe 2 O 3 loading increases, higher oxygenate selectivity falls, resulting from encapsulation of the Cu nanoparticles by thick Fe 2 O 3 layers. Overall, the results demonstrate how thickness-controlled ALD Fe 2 O 3 can be used as both a promoter and stabilizer of Cu-based higher oxygenate synthesis catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase

Mevalonate diphosphate decarboxylases (MDDs) catalyze the ATP-dependent-Mg 2+ -decarboxylation of mevalonate-5-diphosphate (MVAPP) to produce isopentenyl diphosphate (IPP), which is essential in both eukaryotes and prokaryotes for polyisoprenoid synthesis. The substrates, MVAPP and ATP, have been shown to bind sequentially to MDD. Here we report crystals in which the enzyme remains active, allowing the visualization of conformational changes in Enterococcus faecalis MDD that describe sequential steps in an induced fit enzymatic reaction. Initial binding of MVAPP modulates the ATP binding pocket with a large loop movement. Upon ATP binding, a phosphate binding loop bends over the active site to recognize ATP and bring the molecules to their catalytically favored configuration. Positioned substrates then can chelate two Mg 2+ ions for the two steps of the reaction. Closure of the active site entrance brings a conserved lysine to trigger dissociative phosphoryl transfer of γ-phosphate from ATP to MVAPP, followed by the production of IPP.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Multimetallic Metal-Organic Frameworks as Heterogeneous Catalysts for Gas Phase Hydroformylation and Hydrogenation Reactions

This project focused on the development bimetallic metal-organic frameworks (MOFs) as gas phase heterogeneous catalysts for hydrogenation and hydroformylation reactions. MOFs are a new class of hybrid inorganic/organic materials that are highly crystalline, with structures consisting of metal nodes of specific geometries connected by organic linkers. Although there have been a number of studies of catalysis at MOF nodes in solution, there is little experimental data in the literature for gas phase reactions despite the fact that industrial heterogeneous catalysis on MOFs is more economically viable than homogeneous catalysis. The use of MOFs as heterogeneous catalysts presents the unique opportunity to carefully control the composition, geometry and ensemble sizes of the active sites, which are all critical factors for the rational design of new catalysts. Specific objectives of the project are as follows: (1) to tailor the geometry, composition and ensemble size of the active sites; (2) to understand how the adsorption of molecules at metal sites can be modified by interactions with a neighboring metal site; (3) to determine how oxidation states of the metal change during reaction and how these states can be modified by metal-metal electronic interactions; and (4) to elucidate reaction mechanisms and intermediates. For these studies, we have chosen to investigate selective hydrogenation of hydrocarbons and hydroformylation, which are industrially relevant reactions. Our interdisciplinary team of Chen, Shustova and Vogiatzis/Henkelman provides critical expertise in novel MOF synthesis (Shustova), atomic-scale surface science and catalysis (Chen) and computational studies of reaction mechanisms (Vogiatzis/Henkelman) that are necessary for the development of these catalysts. We believe that this work will lead directly to the rational design of new catalysts that are versatile, highly active/selective and suitable for industrial processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Discovery of an autoinhibited conformation in mesotrypsin reveals a strategy for selective serine protease inhibition

Selective inhibition of the more than 100 S1 family serine proteases is a long-standing challenge due to their active site similarity. Mesotrypsin, implicated in cancer progression, exemplifies these difficulties; no current inhibitors achieve selectivity over other human trypsins. We found an unexpected autoinhibited conformation of mesotrypsin via x-ray crystallography, revealing a cryptic pocket adjacent to the active site. Using high-throughput virtual screening targeting this cryptic pocket, we identified a conformationally selective small-molecule inhibitor that stabilizes the inactive state of mesotrypsin. This inhibitor demonstrates selectivity for mesotrypsin over other trypsins. Our findings challenge the accepted view of digestive trypsins as constitutively active enzymes lacking potential for allosteric regulation. Furthermore, analyses of other structures suggest that dynamic sampling of closed states with analogous allosteric cryptic pockets appears widespread among S1 serine proteases. These observations point to a potentially generalizable strategy to achieve selective inhibition, offering broad implications for drug development targeting serine proteases in cancer and other diseases.

Coban, Matt↗

DOE OSTI2021

Operando leaching of pre-incorporated Al and mechanism in transition-metal hybrids on carbon substrates for enhanced charge storage

Insufficient exposure and utilization of active sites often induces an inferior reactivity for transition-metal-based two-dimensional (2D) materials. In response, we for the first time propose a universal "nano-tailoring" strategy to incorporate abundant defects and active sites into low-crystallinity nanosheets by electrochemically leaching of Al species. With MnAl layered double hydroxides (LDHs) as a representative example, potassium-birnessite MnO 2 (AK-MnO 2 ) with oxygen vacancies and abundant edge sites is successfully produced. The oxygen vacancies are shown to help optimize the electron-transfer and ion-adsorption capability. These integrated advantages endow the AK-MnO 2 with a high capacitance value of 239 F g –1 at 100 A g –1 . By further combining with soft X-ray absorption spectroscopy techniques, we unravel that the reducibility of M 2+ in M 2+ Al-LDH serves as the key descriptor for the reconstruction rate. Here, this "nano-tailoring" strategy can provide some important implications and clues to manipulating 2D materials for efficient energy storage and conversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Suppressing Universal Cathode Crossover in High‐Energy Lithium Metal Batteries via a Versatile Interlayer Design**

Abstract The universal cathode crossover such as chemical and oxygen has been significantly overlooked in lithium metal batteries using high‐energy cathodes which leads to severe capacity degradation and raises serious safety concerns. Herein, a versatile and thin (≈25 μm) interlayer composed of multifunctional active sites was developed to simultaneously regulate the Li deposition process and suppress the cathode crossover. The as‐induced dual‐gradient solid‐electrolyte interphase combined with abundant lithiophilic sites enable stable Li stripping/plating process even under high current density of 10 mA cm −2 . Moreover, X‐ray photoelectron spectroscopy and synchrotron X‐ray experiments revealed that N‐rich framework and CoZn dual active sites can effectively mitigate the undesired cathode crossover, hence significantly minimizing Li corrosion. Therefore, assembled lithium metal cells using various high‐energy cathode materials including LiNi 0.7 Mn 0.2 Co 0.1 O 2 , Li 1.2 Co 0.1 Mn 0.55 Ni 0.15 O 2 , and sulfur demonstrate significantly improved cycling stability with high cathode loading.

Xie, Chuyi↗

DOE OSTI2023

Suppressing Universal Cathode Crossover in High‐Energy Lithium Metal Batteries via a Versatile Interlayer Design**

25 ENERGY STORAGE↗

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 OSTI2022

Oxygen Evolution Reaction in Alkaline Environment: Material Challenges and Solutions

Abstract The oxygen evolution reaction (OER) generally exists in electrochemistry‐enabled applications that are coupled with cathodic reactions like hydrogen evolution, carbon dioxide reduction, ammonia synthesis, and electrocatalytic hydrogenation. The OER heavily impacts the overall energy efficiency of these devices because the sluggish OER kinetics result in a huge overpotential, thus, a large amount of efficient catalysts are needed. The benchmark iridium and ruthenium (Ir/Ru)‐based materials (mostly used in acid media) are, however, significantly limited by their scarcity. Non‐precious metal‐based catalysts (NPMCs) have emerged as the most promising alternatives; however, they tend to degrade quickly under the harsh operating conditions of typical OER devices. Another challenge is the unsatisfying performance of OER catalysts when integrated in real‐world devices. Herein, the OER active sites for three mainstream types of NPMCs including non‐precious transition metal oxides/(oxy)hydroxides, metal‐free carbon materials, and hybrid non‐precious metal and carbon composites are reviewed. In addition, possible degradation mechanisms for active sites and mitigation strategies are discussed in detail. This review also provides insights into the gaps between R&D of NPMCs for the OER and their applications in practical devices.

Xie, Xiaohong↗

DOE OSTI2023

Theoretical assessments of CO 2 activation and hydrogenation pathways on transition-metal surfaces

Carbon dioxide (CO 2 ) hydrogenation on transition-metal active sites offers a promising carbon utilization route toward mitigating greenhouse gas emissions. C 1 products are often formed in parallel during CO 2 hydrogenation, prompting investigations into the intrinsic properties of transition metals that drive activity and product selectivity. Here, in this work, close-packed surfaces of a selection of transition-metal catalysts (Ni, Co, Rh, Ru, Pd, and Pt) were studied with density functional theory (DFT) calculations to understand their fundamental reactivities for CO 2 transformation reactions. Results indicate that CO 2 conversion proceeds through CO* formation and hydrogenation to form C 1 products (* denotes an adsorbed species). Ni, Co, Rh, and Ru favor CO/CH 4 formation, while Pd and Pt favor CO/CH 3 OH formation. The ability of a metal to dissociate C-O bonds drives selectivity between CH 4 and CH 3 OH, while competition between CO* desorption and surface hydrogenation describes CO selectivities. The C-O bond dissociation steps often impose the highest barrier along CH 4 formation reaction profiles, suggesting their kinetic relevance for CH 4 formation rates. The provided DFT-derived data sets detail a comprehensive reaction network of elementary steps relevant to C 1 chemistries, ultimately offering a benchmark for insights into design strategies for materials that exploit transition-metal active sites in carbon capture or utilization processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose–bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Effects of surface diffusion in electrocatalytic CO 2 reduction on Cu revealed by kinetic Monte Carlo simulations

We report Kinetic Monte Carlo (KMC) methods are frequently used for mechanistic studies of thermally driven heterogeneous catalysis systems but are underused for electrocatalysis. Here, we develop a lattice KMC approach for electrocatalytic CO 2 reduction. The work is motivated by a prior experimental report that performed electroreduction of a mixed feed of 12 CO 2 and 13 CO on Cu; differences in the 13 C content of C2 products ethylene and ethanol (Δ 13 C) were interpreted as evidence of site selectivity. The lattice KMC model considers the effect of surface diffusion on this system. In the limit of infinitely fast diffusion (mean-field approximation), the key intermediates 12 CO* and 13 CO* would be well mixed on the surface and no evidence of site selectivity could have been observed. Using a simple two-site model and adapting a previously reported microkinetic model, we assess the effects of diffusion on the relative isotope fractions in the products using the estimated surface diffusion rate of CO* from literature reports. We find that the size of the active sites and the total surface adsorbate coverage can have a large influence on the values of Δ 13 C that can be observed. Δ 13 C is less sensitive to the CO* diffusion rate as long as it is within the estimated range. We further offer possible methods to estimate surface distribution of intermediates and to predict intrinsic selectivity of active sites based on experimental observations. This work illustrates the importance of considering surface diffusion in the study of electrochemical CO 2 reduction to multi-carbon products. Our approach is entirely based on a freely available open-source code, so will be readily adaptable to other electrocatalytic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Site and Structural Requirements for the Dehydra-Decyclization of Cyclic Ethers on ZrO2

In this study, we examined the site and structural requirements for the dehydra-decyclization of cyclic ethers, tetrahydrofuran, and tetrahydropyran to produce conjugated dienes over ZrO2-based catalysts, a reaction that could be an important step in the use of biomass-derived sugars as a starting material to produce monomers for the plastics industry. To help identify the active sites for this reaction, studies were conducted in which ZrO2 surfaces were decorated with Na. These studies showed that Na was effective at poisoning the activity for the ring opening of cyclic ethers, but much less so for the dehydration of the resulting adsorbed alkoxides. The studies of the activity of different types of ZrO2 for the dehydra-decyclization reaction, including single crystals and ultra-thin films supported on MgAl2O4 and silica, also showed that the reaction was dependent on the local structure of the ZrO2 surface. The insights these results provide for identifying the active sites on the ZrO2 surface are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

An N$\cdots$H$\cdots$N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction

Pyridoxal 5'-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the electronic states of PLP and the electrostatics of enzyme active sites, responsible for the reaction specificities, by enabling direct visualization of hydrogen atom positions. Here we report a room-temperature joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5'-phosphate (PMP), the cofactor product of the first half reaction catalyzed by the enzyme. Between PMP N SB and catalytic Lys258 Nζ amino groups an equally shared deuterium is observed in an apparent low-barrier hydrogen bond (LBHB). Density functional theory calculations were performed to provide further evidence of this LBHB interaction. The structural arrangement and the juxtaposition of PMP and Lys258, facilitated by the LBHB, suggests active site preorganization for the incoming ketoacid substrate that initiates the second half-reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Oxidation, Oligomerization, Isomerization of Hydrocarbons Using Metal–Organic Frameworks

The selective conversion of hydrocarbons into higher-value fuels and feedstocks is essential to the global energy and chemistry landscape. While porous inorganic materials have enabled significant progress in these transformations, achieving high activity, selectivity, and stability under industrially relevant conditions remains challenging. Metal–organic frameworks (MOFs) are a promising platform to precisely control active-site environments and interrogate structure–function relationships due to their crystallinity, tunability, and porosity. This review highlights relevant hydrocarbon transformations and outlines the general mechanisms for oxidation, oligomerization, and isomerization. Metal node acidity, confinement effects, and active site dispersion are analyzed for their impact on reactivity and selectivity across the three reactions. Lastly, we discuss current limitations in catalyst stability and offer a perspective on integrating reticular chemistry with high-throughput experimentation and machine learning to accelerate the discovery and design of robust, next-generation MOF catalysts.

Catalysts↗

DOE OSTI2022

Platinum Graphene Catalytic Condenser for Millisecond Programmable Metal Surfaces

Accelerating catalytic chemistry and tuning surface reactions require precise control of the electron density of metal atoms. In this work, nanoclusters of platinum were supported on a graphene sheet within a catalytic condenser device that facilitated electron or hole accumulation in the platinum active sites with negative or positive applied potential, respectively. The catalytic condenser was fabricated by depositing on top of a p-type Si wafer an amorphous HfO 2 dielectric (70 nm), on which was placed the active layer of 2–4 nm platinum nanoclusters on graphene. A potential of ±6 V applied to the Pt/graphene layer relative to the silicon electrode moved electrons into or out of the active sites of Pt, attaining charge densities more than 1% of an electron or hole per surface Pt atom. At a level of charge condensation of ±10% of an electron per surface atom, the binding energy of carbon monoxide to a Pt(111) surface was computed via density functional theory to change 24 kJ mol –1 (0.25 eV), which was consistent with the range of carbon monoxide binding energies determined from temperature-programmed desorption (ΔBE CO of 20 ± 1 kJ mol –1 or 0.19 eV) and equilibrium surface coverage measurements (ΔBE CO of 14 ± 1 kJ mol –1 or 0.14 eV). Impedance spectroscopy indicated that Pt/graphene condensers with potentials oscillating at 3000 Hz exhibited negligible loss in capacitance and charge accumulation, enabling programmable surface conditions at amplitudes and frequencies necessary to achieve catalytic resonance.

Inorganic carbon compounds↗