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At least 181 records · Page 10

First-principles insights into Si substitution effects in Sm 2 (Fe,Si) 17 C x magnet

The partial substitution of Fe by Si enhances the phase stability of Sm 2 Fe 17 C x magnets with x > 1.0. Here, we elucidate the Si-substitution scheme and its impact on phase stability and magnetic properties in Sm 2 (Fe,Si) 17 C 3 from first-principles calculations and chemical bonding analysis. The calculated substitution energies for Si at various Fe sites are negative, indicating improved phase stability. Si preferentially substitutes Fe atoms at the 9d site in Sm 2 (Fe,Si) 17 C 3 while it tends to enter the Fe 18h site in Sm 2 (Fe,Si) 17 . This difference in site preference is attributed to the distinct chemical environments surrounding the Fe (Si) sites in the two compounds. Si substitution favors the formation of Sm–Si bonds while minimizing the Si–C and Si–Si interactions. Crystal orbital Hamilton populations and crystal orbital bond index calculations indicate that the partial replacement of Fe with Si strengthens the chemical bonding of Sm–Fe 3 (18f) and Sm–Fe 4 (18h) and improves overall phase stability in Sm 2 (Fe,Si) 17 C 3 . Beyond the dilution effect, Si substitution also reduces the magnetic moments of neighboring Fe atoms, a phenomenon linked to the strong Fe–Si bonding. These findings highlight the dual role of Si in modifying both the structural and magnetic characteristics of Sm 2 Fe 17 -based magnetic compounds.

Chemical bonding↗

Enhanced Phase Stability of Sm 2 (Fe, Al) 17 C x

Aluminum doping can improve the phase stability of metastable compound Sm 2 Fe 17 C x with a high carbon content (x > 1.5). We investigated the preferential site substitution of Al, chemical bonding, and structural stability in Sm 2 (Fe,Al) 17 C 3 using first-principle calculations. Our results reveal a strong correlation between the preferential substitution of Fe by Al and the atomic site chemical environment, which affects the overall phase stability. Specifically, Al preferentially occupies the 9d site in Sm 2 (Fe,Al) 17 C 3 . At the same time, Al prefers the site 6c in its parent phase Sm 2 (Fe,Al) 17 . Partial replacement of Fe with Al leads to a more negative formation energy, indicating enhanced thermodynamic stability. Crystal Orbital Hamilton Population (COHP) and Crystal Orbital Bond Index (COBI) analysis suggest that insertion of carbon weakens the bonding strength of Sm-Fe (18f) and Sm-Fe (18h), resulting in metastability of Sm 2 Fe 17 C x . Doping Al strengthens Al-Fe, Al-Sm, Sm-Fe (18f, 18h) and Fe–C bonding in Sm 2 (Fe,Al) 17 C 3 , as revealed by calculated COHP and COBI. These effects contribute to improved phase stability in the Al-doped 2:17 interstitial compound.

chemical bonding↗

Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor

We recently demonstrated that inhibitor binding reorganizes the oxyanion loop of a monomeric catalytic domain of SARS CoV-2 main protease (MPro) from an unwound (E) to a wound (active, E*) conformation, independent of dimerization. Here we assess the effect of the flanking N-terminal residues, to imitate the MPro precursor prior to its autoprocessing, on conformational equilibria rendering stability and inhibitor binding. Thermal denaturation (T m ) of C145A mutant, unlike H41A, increases by 6.8 °C, relative to wild-type mature dimer. An inactivating H41A mutation to maintain a miniprecursor containing TSAVL[Q or E] of the flanking nsp4 sequence in an intact form [ (-6) MPro H41A and (-6*) MPro H41A , respectively], and its corresponding mature MPro H41A were systematically examined. While the H41A mutation exerts negligible effect on T m and dimer dissociation constant (K dimer ) of MPro H41A , relative to the wild type MPro, both miniprecursors show a 4–5 °C decrease in T m and > 85-fold increase in K dimer as compared to MPro H41A . The K d for the binding of the covalent inhibitor GC373 to (-6*) MPro H41A increases ~12-fold, relative to MPro H41A , concomitant with its dimerization. While the inhibitor-free dimer exhibits a state in transit from E to E* with a conformational asymmetry of the protomers’ oxyanion loops and helical domains, inhibitor binding restores the asymmetry to mature-like oxyanion loop conformations (E*) but not of the helical domains. Finally, disorder of the terminal residues 1–2 and 302–306 observed in both structures suggest that N-terminal autoprocessing is tightly coupled to the E-E* equilibrium and stable dimer formation.

59 BASIC BIOLOGICAL SCIENCES↗

The Kinetic Consequences of Water on Catalytic Methane Pyrolysis

Hydrogen production from biomass and natural gas has emerged as a prominent research area in response to the growing demand for energy from alternative sources that minimize CO 2 emissions. In this study, we investigate the impact of water, which is present in and generated from biomass-derived streams, on carbon nanotube (CNT) growth and hydrogen production during methane decomposition using Ni–Mo/MgO as a catalyst. We reveal here that the role of water on CNT growth is highly complex; its effect depends on the stage of growth at which the water is incorporated. When water is introduced at the beginning of methane decomposition ( t = 0 h), methane conversion rates are negatively impacted. We hypothesize that water inhibits the significant phase changes the Ni–Mo/MgO catalyst undergoes during catalyst carburization. In contrast, the incorporation of a small percentage of water after a stabilization period ( t = 3 h) results in methane conversion rate enhancements that scale with the introduced water partial pressure as water selectively reacts with amorphous carbon deposits that lead to catalyst deactivation, thus prolonging the lifetime of some of the most active sites. Moreover, water incorporation after stabilization significantly reduces the apparent activation energy. Density Functional Theory (DFT) calculations reveal that water preferentially interacts with carbon fragments on the catalyst surface to remove carbon deposits with a barrier lower than that required for methane activation, further supporting its role in cleaning active sites on the catalyst surface. Characterization of the resulting carbon nanotubes reveals the formation of more graphitic materials produced in the presence of water, highlighting the impact of water on nanotube properties. These results provide clarity toward the many ways in which water, or cofeeding of biomass-derived materials, may impact catalytic methane pyrolysis rates.

carbon nanotubes↗

Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography

Abstract Wetlands store 20–30% of the world’s soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.

Environmental Sciences & Ecology↗

Observations of the Marine Atmospheric Boundary Layer’s Response to a Solar Eclipse

The atmospheric response to the solar eclipse of 8 April 2024 in North America is investigated with a specific focus on the marine atmospheric boundary layer (MABL). We leverage measurements collected during the Third Wind Forecast Improvement Project (WFIP3), including Doppler lidars, sonic anemometers, and thermodynamic profiler data to investigate the atmospheric response across sites that experienced partial eclipse conditions with nearly 90% obscuration. Using these measurements, we examine eclipse-induced changes in key meteorological parameters, such as temperature, wind speed, and turbulent fluxes. Most previous eclipse studies have been conducted over land, whereas this study provides new observations for both coastal and marine environments, offering additional insight into eclipse-driven variability in the MABL. The findings confirm a notable decrease in downwelling shortwave radiation during the eclipse, which results in rapid cooling of surface air. The temperature reduction ranges from $1.2^\circ \text {C}$ to $1.4^\circ \text {C}$ in coastal regions and from $0.3^\circ \text {C}$ to $0.5^\circ \text {C}$ over the ocean. This analysis suggests that the MABL’s higher thermal inertia compared to coastal regions moderates the temperature decrease during the eclipse. Wind speed exhibits a more complex behavior, as it is influenced by both the MABL and preexisting synoptic conditions. Although a reduction in wind speed is observable up to approximately 140 m above ground level (AGL) at more inland sites, at other locations closer to the coast, this reduction is constrained to the lowest 100 m AGL. Turbulence parameters retrieved from sonic anemometers, such as turbulence kinetic energy, turbulent heat flux, and friction velocity, decrease during the eclipse at coastal sites, accompanied by a brief transition of atmospheric stability from unstable to neutral or weakly stable conditions. For the open-ocean sites, the variability in turbulence statistics and atmospheric stability is minimal during the occurrence of the eclipse.

16 TIDAL AND WAVE POWER↗

Structural snapshots of human DNA polymerase μ engaged on a DNA double-strand break

Genomic integrity is threatened by cytotoxic DNA double-strand breaks (DSBs), which must be resolved efficiently to prevent sequence loss, chromosomal rearrangements/translocations, or cell death. Polymerase μ (Polμ) participates in DSB repair via the nonhomologous end-joining (NHEJ) pathway, by filling small sequence gaps in broken ends to create substrates ultimately ligatable by DNA Ligase IV. Here we present structures of human Polμ engaging a DSB substrate. Synapsis is mediated solely by Polμ, facilitated by single-nucleotide homology at the break site, wherein both ends of the discontinuous template strand are stabilized by a hydrogen bonding network. The active site in the quaternary Pol μ complex is poised for catalysis and nucleotide incoporation proceeds in crystallo. These structures demonstrate that Polμ may address complementary DSB substrates during NHEJ in a manner indistinguishable from single-strand breaks.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring Trends on Coupling Mechanisms toward C 3 Product Formation in CO (2) R

Challenges in improving catalysts for electrochemical CO 2 reduction require a clear understanding of the reaction mechanisms that lead to products of higher value. Here, we use density functional theory (DFT) to determine the most competitive coupling mechanisms leading to C 3 products on Cu(100) and Cu(511). We exhaustively consider surface coupling pathways between CO* and different C 2 intermediates. On Cu(100), CO* coupling with acetaldehyde was identified as a notable step for C 3 product formation. On Cu(511), local field stabilizations enable an additional coupling step between HCCH* and CO*. This suggests that there is more than one possible pathway toward forming C 3 intermediates. Our simulations show that much like C 2 formation, C 3 formation prefers stepped surfaces with (100)-like sites and that local field stabilization can play a pivotal role in certain coupling steps.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Selective reduction in epitaxial SrFe 0.5 Co 0.5 O 2.5 and its reversibility

Oxygen-vacancy engineering in transition metal oxides enables programmable functionalities by modulating the valence states and local coordination of constituents. Here, we report the selective reduction of cobalt ions in epitaxial SrFe 0.5 Co 0.5 O 2.5 thin films under reducing gas environments, while iron ions remain unchanged. X-ray absorption spectroscopy reveals an absorption edge shift of 1.65 eV in the Co L-edge upon reduction, and multiplet simulations estimate a decrease in the average Co valence from Co 2.91+ to Co 2.00+ . This site- and element-specific reduction leads to the formation of a structurally distinct oxygen-deficient phase stabilized by oxygen vacancies at tetrahedral sites, as confirmed by density functional theory. Optical spectroscopy reveals an increase in the bandgap from 2.47 eV to 3.04 eV, accompanied by enhanced transparency. Furthermore, simultaneous in situ diffraction and transport measurements confirm fully reversible redox-driven transitions among three phases: reduced defective perovskite, brownmillerite, and oxygen-rich perovskite phases. These findings demonstrate that selective redox control in multi-cation oxides enables the realization of chemically and functionally distinct oxygen-deficient phases.

Fuel cells↗

Regulating Catalytic Properties and Thermal Stability of Pt and PtCo Intermetallic Fuel-Cell Catalysts via Strong Coupling Effects between Single-Metal Site-Rich Carbon and Pt

Developing low platinum-group-metal (PGM) catalysts for the oxygen reduction reaction (ORR) in proton-exchange membrane fuel cells (PEMFCs) for heavy-duty vehicles (HDVs) remains a great challenge due to the highly demanded power density and long-term durability. Here, this work explores the possible synergistic effect between single Mn site-rich carbon (Mn SA -NC) and Pt nanoparticles, aiming to improve intrinsic activity and stability of PGM catalysts. Density functional theory (DFT) calculations predicted a strong coupling effect between Pt and MnN 4 sites in the carbon support, strengthening their interactions to immobilize Pt nanoparticles during the ORR. The adjacent MnN 4 sites weaken oxygen adsorption at Pt to enhance intrinsic activity. Well-dispersed Pt (2.1 nm) and ordered L1 2 -Pt 3 Co nanoparticles (3.3 nm) were retained on the Mn SA -NC support after indispensable high-temperature annealing up to 800 °C, suggesting enhanced thermal stability. Both PGM catalysts were thoroughly studied in membrane electrode assemblies (MEAs), showing compelling performance and durability. The Pt@Mn SA -NC catalyst achieved a mass activity (MA) of 0.63 A mg Pt –1 at 0.9 V iR-free and maintained 78% of its initial performance after a 30,000-cycle accelerated stress test (AST). The L1 2 -Pt 3 Co@Mn SA -NC catalyst accomplished a much higher MA of 0.91 A mg Pt –1 and a current density of 1.63 A cm –2 at 0.7 V under traditional light-duty vehicle (LDV) H 2 –air conditions (150 kPa abs and 0.10 mg Pt cm –2 ). Furthermore, the same catalyst in an HDV MEA (250 kPa abs and 0.20 mg Pt cm –2 ) delivered 1.75 A cm –2 at 0.7 V, only losing 18% performance after 90,000 cycles of the AST, demonstrating great potential to meet the DOE targets.

25 ENERGY STORAGE↗

Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-γ-semialdehyde Dehydrogenase

The proline catabolic pathway consisting of proline dehydrogenase (PRODH) and L-glutamate-γ-semialdehyde (GSAL) dehydrogenase (GSALDH) catalyzes the four-electron oxidation of L-proline to L-glutamate. Chemical probes to these enzymes are of interest for their role in cancer and inherited metabolic disease. Here, we report the results of a crystallographic fragment-screening campaign targeting both enzymes. A unique aspect of our approach is the screening of both enzymes simultaneously using crystals of the bifunctional PRODH-GSALDH enzyme, proline utilization A (PutA). A 288-fragment library from Zenobia was screened in crystallo in cocktails of six fragments. Validation X-ray crystallography with individual fragments identified seven crystal hits distributed in the PRODH active site, GSALDH aldehyde substrate-binding site, and GSALDH NAD+ adenine-binding site. The fragment bound in the PRODH active site, 4-methoxybenzyl alcohol, is structurally distinct from all known PRODH inhibitors as it lacks an anionic anchor and stabilizes open conformations of the active site, motivating the study of eighteen analogs. In total, thirteen crystal structures with resolutions ranging from 1.32 Å to 1.80 Å were determined, resolving the poses and interactions of seven fragments from the Zenobia library and five analogs of 4-methoxybenzyl alcohol. These results expand the chemical space of probes targeting proline catabolic enzymes and provide new structural information for further inhibitor development.

Biochemistry & Molecular Biology↗

In-situ monitoring of atomically dispersed Pt sites supported on OMS-2 during CO 2 activation

Atomically dispersed catalysts have drawn great interest lately, as they showcase a high density of active sites, selectivity, and high turnover frequencies in oxidation chemistry due to labile oxygen activation. In contrast, the applications of these catalysts have lagged in reduction reactions due to the ambiguity caused by the sintering and restructuring of active sites. To bridge this gap, the evolution of Pt 4+ isomorphically substituted into an octahedral molecular sieve structure (OMS-2) under reductive conditions was correlatively characterized using multiple in-situ analytical techniques such as ambient pressure X-ray photoelectron spectroscopy, environmental transmission electron microscopy, and solid-state nuclear magnetic resonance. The surface dynamics of the Pt single atoms were revealed during the Reverse Water Gas Shift (RWGS) reaction, where the active sites were identified as two-coordinated platinum single atoms. Under reaction, we show nonbinding atoms adjacent to the single atoms restructured the motif of the single atoms to Pt 2+ via ion mobility of potassium, increasing the activation energy by 25.6 kJ/mol. Here, this work also highlights the potential for increased stability of the single atom sites via isomorphic substitution of the metal oxide support, since the Pt-OMS-2 catalyst retained activity for about 33 h before deactivation, after which nanoparticles were observed in TEM images. This work offers a new perspective in single atom synthesis using the metal oxide as the host for the single atom site, instead of adatoms on the surface

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessment of InSAR Seasonal Movements at Bayou Choctaw SPR Site

Ground deformation is important to monitor for the ongoing safety and stability of underground caverns. Implementing InSAR technology to monitor site-wide surface deformation at the Strategic Petroleum Reserve has revealed seasonal ground movements at Bayou Choctaw in Louisiana. The cyclic, seasonal pattern shows soil shrinkage during the spring and summer months and soil expansion during the fall and winter months. Prior to this report, no in-depth investigation was conducted to explain this seasonal phenomenon. However, the ground movement is believed to be near-surface and not geological due to the relatively insignificant movement between years. To better understand seasonality movements, soil properties, land cover, and climatic conditions are assessed to relate near-surface water and soil interactions. The soil, land, and climatic properties all contribute to seasonal ground movement, and vegetation cover and the soil's water capacity contribute to the spatial variability of InSAR seasonal measurements at Bayou Choctaw.

02 PETROLEUM↗

Cation Adaptive Structures Based on Manganese Cyanide Prussian Blue Analogues: Application of Powder Diffraction Data to Solve Complex, Unprecedented Stoichiometries and New Structure Types

Abstract A Mn(II) salt and A + CN − under anaerobic conditions react to form 2‐D and 3‐D extended structured compounds of A m Mn II n (CN) m+2n stoichiometry. Here, the creation and characterization of this large family of compounds, for example AMn II 3 (CN) 7 , A 2 Mn II 3 (CN) 8 , A 2 Mn II 5 (CN) 12 , A 3 Mn II 5 (CN) 13 , and A 2 Mn II [Mn II (CN) 6 ], where A represents alkali and tetraalkylammonium cations, is reviewed. Cs 2 Mn II [Mn II (CN) 6 ] has the typical Prussian blue face centered cubic unit cell. However, the other alkali salts are monoclinic or rhombohedral. This is in accord with smaller alkali cation radii creating void space that is minimized by increasing the van der Waals stabilization energy by reducing ∠Mn−N≡C, which, strengthens the magnetic coupling and increases the magnetic ordering temperatures. This is attributed to the non‐rigidity of the framework structure due the significant ionic character associated with the high‐spin Mn II sites. For larger tetraalkylammonium cations, the high‐spin Mn sites lack sufficient electrostatic A + ⋅⋅⋅NC stabilization and form unexpected 4‐ and 5‐coordinated Mn sites within a flexible, extended framework around the cation; hence, the size, shape, and charge of the cation dictate the unprecedented stoichio‐metry and unpredictable cation adaptive structures. Antiferromagnetic coupling between adjacent Mn II sites leads to ferrimagnetic ordering, but in some cases antiferromagnetic coupling of ferrimagnetic layers are compensated and synthetic antiferromagnets are observed. The magnetic ordering temperatures for ferrimagnetic A 2 Mn II [Mn II (CN) 6 ] with both octahedral high‐ and low‐spin Mn II sites increase with decreasing ∠Mn−N≡C. The crystal structures for all of the extended structured materials were obtained by powder diffraction.

Chemistry↗

Methanol tolerance of atomically dispersed single metal site catalysts: mechanistic understanding and high-performance direct methanol fuel cells

Proton-exchange membrane fuel cells (PEMFCs) and direct methanol fuel cells (DMFCs) are promising power sources from portable electronic devices to vehicles. The high-cost issue of these low-temperature fuel cells can be primarily addressed by using platinum-group metal (PGM)-free oxygen reduction reaction (ORR) catalysts, in particular atomically dispersed metal–nitrogen–carbon (M–N–C, M = Fe, Co, Mn). Furthermore, a significant advantage of M–N–C catalysts is their superior methanol tolerance over Pt, which can mitigate the methanol cross-over effect and offer great potential of using a higher concentration of methanol in DMFCs. In this work, we investigated the ORR catalytic properties of M–N–C catalysts in methanol-containing acidic electrolytes via experiments and density functional theory (DFT) calculations. FeN 4 sites demonstrated the highest methanol tolerance ability when compared to metal-free pyridinic N, CoN 4 , and MnN 4 active sites. The methanol adsorption on MN 4 sites is even strengthened when electrode potentials are applied during the ORR. The negative influence of methanol adsorption becomes significant for methanol concentrations higher than 2.0 M. However, the methanol adsorption does not affect the 4e - ORR pathway or chemically destroy the FeN 4 sites. The understanding of the methanol-induced ORR activity loss guides the design of promising M–N–C cathode catalyst in DMFCs. Accordingly, we developed a dual-metal site Fe/Co–N–C catalyst through a combined chemical-doping and adsorption strategy. Instead of generating a possible synergistic effect, the introduced Co atoms in the first doping step act as “scissors” for Zn removal in metal–organic frameworks (MOFs), which is crucial for modifying the porosity of the catalyst and providing more defects for stabilizing the active FeN 4 sites generated in the second adsorption step. The Fe/Co–N–C catalyst significantly improved the ORR catalytic activity and delivered remarkably enhanced peak power densities (i.e., 502 and 135 mW cm -2 ) under H 2 –air and methanol–air conditions, respectively, representing the best performance for both types of fuel cells. Notably, the fundamental understanding of methanol tolerance, along with the encouraging DMFC performance, will open an avenue for the potential application of atomically dispersed M–N–C catalysts in other direct alcohol or ammonia fuel cells.

25 ENERGY STORAGE↗

Directed Synthesis of Gold Nanoparticle Superstructures Using Self-Assembling Peptoids Containing Metal-Bonding N-Heterocyclic Carbenes

N-Heterocyclic carbene (NHC) ligands, with strong metal-binding affinity, offer a robust platform for constructing organic–inorganic nanohybrids with high stability and tunable properties. However, achieving precise structural control in a simple manner remains challenging. Here, we report a one-pot synthesis of nanohybrids using self-assembling peptoids functionalized with histidine-2-ylidene, which simultaneously enable peptoid assembly and NHC–metal binding. Histidine-2-ylidene-functionalized peptoids were designed to self-assemble and provide NHC binding sites, while AuNPs served as the inorganic component due to NHCs’ strong affinity for gold surfaces. The resulting peptoid-NHC@AuNPs form well-defined vesicles that are characterized by UV–vis spectroscopy, X-ray photoelectron spectroscopy, and electron microscopy. Importantly, the vesicle size and morphology can be tuned via the peptoid sequence or environmental conditions. Further experiments highlight the crucial role of the NHC sites in the formation and stabilization of these nanohybrids. This modular strategy offers a versatile route to fabricating functional NHC-based nanohybrids for potential applications in sensing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗