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The oxygen evolution reaction (OER) is a key anodic half-cell reaction that accompanies several critical electrochemical reduction reactions of interest to a variety of applications. Despite steady advances in understanding and qualitatively predicting OER activity and selectivity trends, a comprehensive description or prediction of material aqueous (in)stability and degradation mechanisms remains elusive, even though these processes critically influence device lifetime and economic feasibility. In this work, we investigate the interplay, or lack thereof, between OER activity and material aqueous stability across rutile oxides, with a particular focus on iridium oxide (IrO 2 ). By applying a Born–Haber cycle, we calculate the thermodynamic driving force for metal dissolution as a function of the applied bias and electrolyte conditions. We apply interpretable machine learning techniques, including principal component analysis and symbolic regression, to analyze trends across rutile oxides and find that key thermodynamic descriptors for OER activity and surface stability are only very weakly correlated. Instead, the local atomic environment─especially electronic structure signatures for interactions between the active site and its neighbors─plays a more important role in predicting material stability. Leveraging these insights, we investigate the impact of doping IrO 2 with a range of transition metals and show that the stability of Ir active sites can be tuned largely independently of its predicted OER activity. These insights lay the foundation for material design to improve stability with respect to corrosion, with the ultimate aim to enhance long-term stability without sacrificing catalytic performance in the OER.
Nitrogen-coordinated single atom iron sites (FeN 4 ) embedded in carbon (Fe–N–C) are the most active platinum group metal-free oxygen reduction catalysts for proton-exchange membrane fuel cells. Still, current Fe–N–C catalysts lack sufficient long-term durability and are not yet viable for practical applications. Here we report a highly durable and active Fe–N–C catalyst synthesized using heat treatment with ammonia chloride followed by high-temperature deposition of a thin layer of nitrogen-doped carbon on the catalyst surface. We propose that catalyst stability is improved by converting defect-rich pyrrolic N-coordinated FeN 4 sites into highly stable pyridinic N-coordinated FeN 4 sites. The stability enhancement is demonstrated in membrane electrode assemblies using accelerated stress testing and a long-term steady-state test (>300 h at 0.67 V), approaching a typical Pt/C cathode (0.1 mg Pt cm -2 ). The encouraging stability improvement represents a critical step in developing viable Fe–N–C catalysts to overcome the cost barriers of hydrogen fuel cells for numerous applications.
Abstract The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.
Abstract O-Phosphoseryl-tRNASec selenium transferase (SepSecS) catalyzes the terminal step of selenocysteine (Sec) synthesis in archaea and eukaryotes. How the Sec synthetic machinery recognizes and discriminates tRNASec from the tRNA pool is essential to the integrity of the selenoproteome. Previously, we suggested that SepSecS adopts a competent conformation that is pre-ordered for catalysis. Herein, using high-resolution X-ray crystallography, we visualized tRNA-dependent conformational changes in human SepSecS that may be a prerequisite for achieving catalytic competency. We show that tRNASec binding organizes the active sites of the catalytic protomer, while stabilizing the N- and C-termini of the non-catalytic protomer. Binding of large anions to the catalytic groove may further optimize the catalytic site for substrate binding and catalysis. Our biochemical and mutational analyses demonstrate that productive SepSecS•tRNASec complex formation is enthalpically driven and primarily governed by electrostatic interactions between the acceptor-, TΨC-, and variable arms of tRNASec and helices α1 and α14 of SepSecS. The detailed visualization of the tRNA-dependent activation of SepSecS provides a structural basis for a revised model of the terminal reaction of Sec formation in archaea and eukaryotes.
Downsizing a catalyst nanoparticle (NP) to a single atom (SA) has proven to be highly effective in increasing catalytic activity and decreasing the amount of catalyst required for various electrochemical reactions. However, insufficient stability of the single-atom site catalysts (SACs) is still a significant challenge for their practical application. Here, SACs firmly bound to stable metal oxide NPs are proposed to dramatically increase the electrochemical activity and stability of SA-based catalysts for hydrogen evolution reaction (HER). Starting from a Ru-infiltrated, Zr-based metal-organic framework (MOF), the tetragonal zirconium oxide (ZrO 2-x ) NPs-embedded carbon matrix is fabricated as support through facile pyrolysis. Simultaneously, Ru SAs as active sites are well dispersed on the surface of ZrO 2-x NPs due to the generation of oxygen vacancies in the tetragonal ZrO 2-x . Finally, the Ru-ZrO 2-x SAC exhibits a 4–5 times higher mass activity than commercial Pt and Ru catalysts and superior durability due to strong metal-support interaction (SMSI) between Ru atoms and ZrO 2-x substrate.
In the summer and fall of 2023, the Gulf of Mexico Deepwater Hydrate Coring Expedition (UT-GOM2-2) drilled, cored, made downhole measurements, and analyzed samples from the seafloor to the base of the gas hydrate stability zone in one location (Site H, WR313) in the Terrebonne basin, deepwater Gulf of Mexico. Analyses of data and samples from the expedition will inform biological, geochemical, and geomechanical models to constrain the role of gas hydrates in the carbon cycle and the potential for gas hydrates as an energy resource. Pressure and conventional cores were collected continuously to a depth of 155.1 meters below the seafloor (mbsf). At deeper depths, cores were taken periodically from hydrate-bearing sands and their bounding muds to a total depth of 861.3 mbsf. 162.6 m of conventional core and 54.8 m of pressure core were obtained. Twelve temperature measurements were made between 27.1 and 144.5 mbsf to determine the geothermal gradient. At the seafloor, more than 4 m of sandy silt of unknown origin was encountered. Beneath this sand, to a depth of ~200 mbsf, the section was composed of interbedded mud and biogenic carbonate ooze. The biogenic ooze correlated to low density and high porosity intervals observed in the previously acquired logging while drilling (LWD) data and as measured. Calcareous nannofossil biostratigraphy constrains the entire record to the Pleistocene (< 0.91 million years) with a pronounced increase in sedimentation rate with depth. Beneath 200 mbsf, the section was predominantly composed of mud with two thicker, hydrate-bearing coarse-grained intervals, which are commonly known as the Blue and Orange sands. The dissolved gas concentration was quantified from pressure cores. In the shallow section, dissolved methane concentration increased below the sulfate-methane transition zone (SMTZ) and reaches saturation (the limit of solubility for methane) at 147 mbsf. Gas expansion was very common in conventional and depressurized pressure (conventionalized) cores below the SMTZ. At deeper depths, the methane concentration within muds bounding the Blue and Orange reservoirs was generally found to be less than saturation. The dissolved and hydrate gas composition is consistent with a microbial source, containing greater than 99.99% methane and only trace concentrations of ethane, propane, and butane. The methane to ethane ratio (C 1 /C 2 ) and the methane to ethane plus propane (C 1 /(C 2 +C 3 )) decrease with depth down to at least 678 mbsf, mainly driven by the increase in ethane with depth. It is unclear if this trend continues through the Orange sand interval. The δ 13 C isotopic signature of methane ranges between -69.9 and -78.5 ‰ Vienna Pee Dee Belemnite (VPDB). Pressure core recovery of all sandy intervals was poor. However, pressure core logs of the Orange sand show intervals of low density and high velocity, which are indicative of high hydrate saturation. One core from within the Orange sand was composed of interbedded graded sandy silt and mud. The sandy silts from this core are composed of mainly quartz and feldspar with some lithics. Most of the recovered pressure core samples are maintained at near in-situ pressure and temperature (within the hydrate stability field) at the University of Texas Pressure Core Center awaiting analysis. In the shallow section, samples will be used to determine the flux of organic carbon through the basin system, find the rate at which that carbon was consumed, and understand the microbial population responsible for these processes. In the deeper section, samples from in and around the hydrate reservoirs will be used to determine the petrophysical properties of the reservoir and bounding seals in these systems.
Here, this paper describes a system-level risk assessment for the Shenhua CO 2 storage site, China, using the National Risk Assessment Partnership Integrated Assessment Model for Carbon Storage (NRAP-IAM-CS). Here, we begin by determining the optimal number of Monte Carlo (MC) simulations to achieve CO 2 and brine leakage result convergence. Then, we calculate mass CO 2 and brine leakage to the atmosphere and a hypothetical shallow aquifer. Finally, we assess the geochemical impacts in the event of leakage as if there were a shallow freshwater aquifer at the Shenhua site. Simulation results show that leakage results tend to stabilize after 300 Monte Carlo simulations. When the three wells on site are assigned a permeability of 10 -11 m 2 (representing significantly leaking wells), moderate CO 2 and brine leakages occur, and the percentage of CO 2 leakage exceeds the threshold value we set based on the Intergovernmental Panel on Climate Change (IPCC). This is, however, unlikely to be the case for the Shenhua site. For all the other scenarios, the CO 2 leakage is trivial although there is still the possibility of CO 2 leakage into the groundwater aquifer exceeding the 1% threshold over 1000 years, assuming constant legacy wellbore permeability. For the significantly leaking scenario, there is a 10% probability to have a moderate (2.7 × 10 7 m 3 ) leakage-affected volume in the shallow aquifer with the pH below 6.5, and a large (1.4 × 10 8 m 3 ) volume with the total dissolved solids (TDS) above 500 ppm, hence pH and TDS may be considered for site monitoring plans. Based on the simulation results, there is a very low probability of significant CO 2 /brine leakage through the existing wells at the Shenhua CO 2 storage site.
Propane dehydrogenation (PDH) is a commercial propylene production technology that has received much attention, but high reaction temperature results in decrease of propylene selectivity and catalyst stability. This paper describes a single-site [PtZn 4 ] catalyst by assembling atomically ordered intermetallic alloy (IMA) as a selective and ultrastable PDH catalyst. The catalyst enables more than 95% propylene selectivity from 520 to 620 oC. No obvious deactivation is observed within 160-hours test, superior to PtSn/Al 2 O 3 and state-of-the-art Pt-based catalysts. Additionally, based on in situ X-ray absorption fine-structure, X-ray photoelectron spectroscopy measurements and density functional theory calculations, we reveal that the surface [PtZn 4 ] ensembles in PtZn IMAs serve as the key active site structures, wherein the geometry-isolated and electron-rich Pt1 site in [PtZn 4 ] ensembles readily promotes the first and second C–H cleavage of propane, but inhibits further dehydrogenation of surface-bounded propylene. This significantly improves the selectivity and stability by prohibiting coke side reactions.
Understanding hydrogen evolution reaction (HER) behaviors over two-dimensional transition-metal dichalcogenides (2D-TMDs) is critical for the development of nonprecious HER electrocatalysts with better activity. Here, in this work, by combining density functional theory calculations with microkinetic modeling, we thoroughly investigated the HER mechanism on 2D-TMDs. We find an important dependence of simulated cell size on the calculated hydrogen adsorption energy and the activation barrier for MoS 2 . Distinct from previous “H migration” mechanisms proposed for the Heyrovsky reaction, the rate-determining step for MoS 2 , we propose that the Mo site only serves as the stabilized transition state rather than H adsorption. In comparison to transition-metal electrocatalysts, we find that the activation barrier of the Heyrovsky reaction on 2D-TMDs scales with the hydrogen adsorption energy exactly as for transition metals except that all activation energies are displaced upward by ca. 0.4 eV. This higher Heyrovsky activation barrier is responsible for the substantially lower activity of 2D-TMDs. We further show that this higher activation barrier stems from the more positively charged adsorbed hydrogen on the chalcogenides interacting repulsively with the incoming proton. Based on these insights, we discuss potential strategies for the design of nonprecious HER catalysts with activity comparable to Pt.
The complicated dynamics of active sites on single-atom catalysts under reducing conditions limits their applications in hydrogenation reactions and mechanistic understanding. Herein, we report that on Rh 1 /TiO 2 , *H spillover during room-temperature ethylene hydrogenation hydroxylates and reduces TiO 2 , enhancing the intrinsic activity of Rh 1 by 9-fold. Spectroscopic and kinetic evidence suggests that the spillover of *H is suppressed by their facile reaction with C 2 H 4 , most of the spilled *H are nonreactive spectators, and >99% turnovers occur on a small subset (<20%) of exposed “active Rh 1 ”. Steady-state kinetics indicates competitive adsorption between H and C 2 H 4 , H 2 dissociation is the rate-determining step, and the apparent activation barrier (E a,app ) of the reaction is ~48 kJ/mol. The evolution of Rh 1 under H 2 was further tracked by spectroscopic and microscopic techniques at elevated temperatures. At 200 °C, more Rh 1 are exposed, but these Rh 1 are at least 5-fold less active than that of the “active Rh 1 ”. At 300 °C, Rh clusters derived from Rh 1 become the main active sites, shifting E a,app to 62 kJ/mol, characteristic of Rh nanoparticles. At ≥400 °C, larger and more active Rh particles in the strong metal–support interaction state are created. In conclusion, this work revealed the unexpected regulation effects of *H spillover on M 1 active sites under ambient conditions, differentiated the minority active M 1 sites, and demonstrated how the stability of M 1 under reducing atmospheres affects hydrogenation catalysis.
Silver–copper (AgCu) bimetallic catalysts hold great potential for electrochemical carbon dioxide reduction reaction (CO 2 RR), which is a promising way to realize the goal of carbon neutrality. Although a wide variety of AgCu catalysts have been developed so far, it is relatively less explored how these AgCu catalysts evolve during CO 2 RR. The absence of insights into their stability makes the dynamic catalytic sites elusive and hampers the design of AgCu catalysts in a rational manner. Here, in this study, we synthesized intermixed and phase-separated AgCu nanoparticles on carbon paper electrodes and investigated their evolution behavior in CO 2 RR. Our time-sequential electron microscopy and elemental mapping studies show that Cu possesses high mobility in AgCu under CO 2 RR conditions, which can leach out from the catalysts by migrating to the bimetallic catalyst surface, detaching from the catalysts, and agglomerating as new particles. Besides, Ag and Cu manifest a trend to phase-separate into Cu-rich and Ag-rich grains, regardless of the starting catalyst structure. The composition of the Cu-rich and Ag-rich grains diverges during the reaction and eventually approaches thermodynamic values, i.e., Ag 0.88 Cu 0.12 and Ag 0.05 Cu 0.95 . The separation between Ag and Cu has been observed in the bulk and on the surface of the catalysts, highlighting the importance of AgCu phase boundaries for CO 2 RR. In addition, an operando high-energy-resolution X-ray absorption spectroscopy study confirms the metallic state of Cu in AgCu as the catalytically active sites during CO 2 RR. Taken together, this work provides a comprehensive understanding of the chemical and structural evolution behavior of AgCu catalysts in CO 2 RR.
Plastics play an essential role in modern society, however, the relentless growth of their production is threatening both human health and ecosystems. As a result, there are intensive efforts in developing recycling technologies to repurpose waste plastics into the building blocks for valuable materials. Here we show a binuclear complex that can catalyze the degradation of polyethylene terephthalate (PET)-the most widely used polyester globally-and a wide spectrum of other plastics including polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polycaprolactone (PCL), polyurethane (PU) and Nylon 66. Inspired by hydrolases, the group of enzymes that catalyze bond cleavages with water, the present catalyst design features biomimetic Zn-Zn sites which activate the plastic, stabilize the key intermediate, and enable intramolecular hydrolysis. This synthetic catalyst delivers activities of 36 mg PET d -1 g catal -1 toward PET depolymerization at pH 8 and 40 oC, and of 577 g PET d -1 g catal -1 at pH 13 and 90 oC for scalable PET recycling. We further demonstrate the closed-loop production of a bottle-grade PET. This work presents a practical and viable solution to the sustainable management of plastics waste.
Water is an earth-abundant source for clean hydrogen production via electrochemical water electrolysis (WE). However, the surface poisoning that occurs in aqueous electrolytes drastically deactivates the electrocatalytic performance of electrodes. Here, in this study, we report electrochemically formed In 2 O 3-x (OH) y on the surface of a large (1–1.5 mm long, 0.5–0.6 mm wide and 0.3–0.5 mm thick) single crystal of Weyl semimetal Co 3 In 2 S 2 (Co 3 In 2 S 2 /In 2 O 3-x (OH) y ) as an ultra-stable and poison tolerant electrode for the oxygen evolution reaction (OER) in 1 M KOH, addressing a bottleneck in WE. The OER activity of the powder form of Co 3 In 2 S 2 is limited by its aerophilic nature. Remarkably, the single-crystal electrodes maintained their high activity for a continuous operational period of 5 h in 1 M KOH electrolyte with/without 10 mM strong surface-poisoning ligands i.e., potassium cyanide, bipyridine, and ethylenediaminetetraacetate disodium salt. The electrodes exhibited stable OER activity for 1000 h at 100 mA cm -2 (1.73 V vs. RHE). The temperature-dependent OER polarization curves (10–70 °C) unambiguously revealed surface poisoning through the suppression of precatalytic Co-redox peaks on the bipyridine poisoned electrode, which led to the stabilization of surface Co-sites. The X-ray photoelectron spectroscopy analyses of pristine, poisoned and post-electrocatalytic single-crystal Co 3 In 2 S 2 electrodes revealed the existence of an In 2 O 3-x (OH) y surface phase, which could be the potential heterostructure for the origin of ultra-stable and poison tolerant OER activity.
Bimetallic alloys have attracted considerable attention due to the tunable catalytic activity and selectivity that can be different from those of pure metals. Here, we study the superior catalytic behaviors of the Pt 3 Ni nanowire (NW) over each individual, Pt and Ni NWs during the reverse Water Gas Shift (rWGS) reaction, using density functional theory. The results show that the promoted rWGS activity by Pt3Ni strongly depends on the ensemble effect (a particular arrangement of active sites introduced by alloying), while the contributions from ligand and strain effects, which are of great importance in electrocatalysis, are rather subtle. As a result, a unique Ni–Pt hybrid ensemble is observed at the 110/111 edge of the Pt 3 Ni NW, where the synergy between Ni and Pt sites is active enough to stabilize carbon dioxide on the surface readily for the rWGS reaction but moderate enough to allow for the facile removal of carbon monoxide and hydrogenation of hydroxyl species. Furthermore, our study highlights the importance of the ensemble effect in heterogeneous catalysis of metal alloys, enabling selective binding–tuning and promotion of catalytic activity.
Abstract Sparsomycin (SPA) is a broad-spectrum inhibitor of protein synthesis with activity across all three domains of life. Although SPA has long been known to target the ribosomal peptidyl transferase center (PTC), previous structural studies suggested that SPA binds differently to bacterial ribosomes compared to their archaeal and eukaryotic counterparts—an unexpected conclusion given the high evolutionary conservation of the ribosomal catalytic center. Here, we show that SPA inhibits a majority of elongation-competent bacterial ribosomal complexes and present X-ray crystal structures of Thermus thermophilus 70S ribosomes stalled by SPA at the initiation and early elongation stages of translation. These structures reveal that SPA binds to the bacterial ribosome in a manner essentially identical to that observed in archaeal and eukaryotic ribosomes, establishing a unified structural mechanism of SPA action across all domains of life. In this conserved binding mode, SPA occupies the A-site cleft of the PTC and forms an extensive network of interactions with universally conserved ribosomal RNA nucleotides and the CCA-end of the P-site transfer RNA (tRNA), thereby stabilizing the peptidyl-tRNA substrate while sterically blocking accommodation of an incoming aminoacyl-tRNA. By clarifying the mode of action of SPA on the bacterial ribosome, our work provides a structural framework for the rational design of SPA derivatives with improved potency and bacterial specificity.
Background/Objectives: Antibody–Drug Conjugates (ADCs) have rapidly evolved from early, rudimentary conjugates to highly targeted and precisely engineered molecules. Despite notable clinical successes, ADCs continue to face significant challenges, including aggregation and high hydrophobicity driven by high drug-to-antibody ratios (DARs), premature payload release, dose-limiting toxicities, and suboptimal pharmacokinetics. While site-specific linker–payload conjugation has improved ADC homogeneity and stability, the structural basis of antibody–linker interactions at specific sites remains underexplored. Methods: In this work, we present the crystal structures of trastuzumab Fab and Fc domains site-specifically conjugated with a cleavable linker–payload. Results: Our findings suggest that pockets within both Fab and Fc regions may interact with and shield the linker portion of the conjugate. Conclusions: These insights highlight the previously underappreciated potential of structure-based design to drive the optimization of ADC linker chemistry and facilitate the co-design of bespoke linker–payloads tailored to individual antibody conjugation sites.
During Fall and Winter quarters, Georgia Tech's School of Mechanical Engineering students designed machines and devices related to Lunar Base construction tasks. These include joint projects with Textile Engineering students. Topics studied included lunar environment simulator via drop tower technology, lunar rated fasteners, lunar habitat shelter, design of a lunar surface trenching machine, lunar support system, lunar worksite illumination (daytime), lunar regolith bagging system, sunlight diffusing tent for lunar worksite, service apparatus for lunar launch vehicles, lunar communication/power cables and teleoperated deployment machine, lunar regolith bag collection and emplacement device, soil stabilization mat for lunar launch/landing site, lunar rated fastening systems for robotic implementation, lunar surface cable/conduit and automated deployment system, lunar regolith bagging system, and lunar rated fasteners and fastening systems. A special topics team of five Spring quarter students designed and constructed a remotely controlled crane implement for the SKITTER model.