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At least 343 records · Page 19

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function

One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. Here, this process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn 4 CaO 5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn 4 CaO 5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S 0 → S 1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).

59 BASIC BIOLOGICAL SCIENCES↗

Optical sensor employing a refractive index engineered metal oxide material

An optical sensor device includes an optical waveguide portion having a core, the core having a first refractive index, and a functional material layer coupled to the optical fiber portion, the functional material layer being made of a metal oxide material, the functional material layer being structured to have a second refractive index, the second refractive index being less than the first refractive index. The functional material layer may be a nanostructure material comprising the metal oxide material with a plurality of holes or voids formed therein such that the functional material layer is caused to have the second refractive index.

Chen, Peng↗

Oxidation of ZrB2-SiC

In this paper the oxidation behavior of ZrB2-20 vol% SiC is examined. Samples were exposed in stagnant air in a zirconia furnace (Deltech, Inc.) at temperatures of 1327, 1627, and 1927 C for ten ten-minute cycles. Samples were removed from the furnace after one, five, and ten cycles. Oxidized material was characterized by mass change when possible, x-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS). Oxidation kinetics, oxide scale development, and matrix recession were monitored as a function of time and temperature. Oxidation and recession rates of ZrB2 - 20 vol% SiC were adequately modeled by parabolic kinetics. Oxidation rates of this material are rapid, allowing only very short-term application in air or other high oxygen partial pressure environments.

Opila, Elizabeth J.↗

Neural mechanisms in nitric-oxide-deficient hypertension

Nitric oxide is hypothesized to be an inhibitory modulator of central sympathetic nervous outflow, and deficient neuronal nitric oxide production to cause sympathetic overactivity, which then contributes to nitric-oxide-deficient hypertension. The biochemical and neuroanatomical basis for this concept revolves around nitric oxide modulation of glutamatergic neurotransmission within brainstem vasomotor centers. The functional consequence of neuronal nitric oxide in blood pressure regulation is, however, marked by an apparent conflict in the literature. On one hand, conscious animal studies using sympathetic blockade suggest a significant role for neuronal nitric oxide deficiency in the development of nitric-oxide-deficient hypertension, and on the other hand, there is evidence against such a role derived from 'knock-out' mice lacking nitric-oxide synthase 1, the major source of neuronal nitric oxide.

Review, Tutorial↗

[Sources of Methane in the Boreal Region]

In determining the global methane budget the sources of methane must be balanced with the sinks and atmospheric inventory. The approximate contribution of the different methane sources to the budget has been establish showing the major terrestrial inputs as rice, wetlands, bogs, fens, and tundra. Measurements and modeling of production in these sources suggest that temperature, water table height and saturation along with substratum composition are important in controlling methane production and emission. The isotopic budget of 13 C and D/H in methane can be used as a tool to clarify the global budget. This approach has achieved success at constraining the inputs. Studies using the isotopic approach place constraints on global methane production from different sources. Also, the relation between the two biogenic production pathways, acetate fermentation and CO2 reduction, and the effect of substratum composition can be made using isotope measurements shows the relation between the different biogenic, thermogenic and anthropogenic sources of methane as a function of the carbon and hydrogen isotope values for each source and the atmosphere, tropospheric composition. Methane emissions from ponds and fens are a significant source in the methane budget of the boreal region. An initial study in 1993 and 1994 on the isotopic composition of this methane source and the isotopic composition in relation to oxidation of methane at the sediment surface of the ponds or fen was conducted as part of our BOREAS project. The isotopic composition of methane emitted by saturated anoxic sediment is dependent on the sediment composition and geochemistry, but will be influenced by in situ oxidation, in part, a function of rooted plant activity. The influence of oxidation mediated by rooted plant activities on the isotopic composition of methane is not well known and will depend on the plant type, sediment temperature, and numerous other variables. Information on this isotopic composition is important in both understanding the bio-geochemistry of the system and also in determining the regional and global inputs for the methane isotope budget. In determining the destruction of methane for balancing the atmospheric methane budget soil oxidation must be considered.

Source record↗

Engineering Escherichia coli for Urease-Driven Synthesis of Metal Oxide Nanomaterials

The development of functional nanomaterials with controlled morphologies is essential for advancements in medicine, electronics and computing, energy, catalysis, and environmental applications. However, conventional synthesis methods often demand high energy input and pose significant environmental challenges. Urease-based biomineralization presents an efficient, eco-friendly alternative for nanomaterial production under mild conditions. In this study, we engineered Escherichia coli ( E. coli ) to express a urease gene cluster from Sporosarcina pasteurii using CRAGE-Duet technology. The engineered strain successfully synthesized calcium carbonate and calcium phosphate crystals. Expanding the approach, we synthesized metal oxide nanoparticles, including hematite (Fe 2 O 3 ), and nanocrystalline anatase titanium dioxide (TiO 2 ). These nanomaterials were characterized by electron microscopy, demonstrating the potential of E. coli as a sustainable and versatile platform for green nanomaterial synthesis.

bacteria↗

Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae

Bacterial heme nitric oxide/oxygen (H-NOX) domains are nitric oxide (NO) or oxygen sensors. This activity is mediated through binding of the ligand to a heme cofactor. However, H-NOX from Vibrio cholerae (Vc H-NOX) can be easily purified in a heme-free state that is capable of reversibly responding to oxidation, suggesting a heme-independent function as a redox sensor. This occurs by oxidation of Cys residues at a zinc-binding site conserved in a subset of H-NOX homologs. Remarkably, zinc is not lost from the protein upon oxidation, although its ligation environment is significantly altered. Using a combination of computational and experimental approaches, we have characterized localized structural changes that accompany the formation of specific disulfide bonds between Cys residues upon oxidation. Furthermore, the larger-scale structural changes accompanying oxidation appear to mimic those changes observed upon NO binding to the heme-bound form. Thus, Vc H-NOX and its homologs may act as both redox and NO sensors by completely separate mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

Thermoflexus hugenholtzii JAD2 T , the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2 T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2 T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13 C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2 T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2 T using 13 C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13 C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

59 BASIC BIOLOGICAL SCIENCES↗

Electron escape depth variation in thin SiO2 films measured with variable photon energy

A double crystal monochromator at the Stanford Synchrotron Radiation Laboratory is used to study the Si/SiO2 interface, using photon energies of hv = 1950-3700 eV. This photon energy range allows interfaces to be observed through oxide layers 50 A thick or more. Variations in electron escape depth and/or oxide density as a function of distance from the interface are observed over the entire kinetic energy range (100-3600 eV). These differences are attributed to a strained oxide layer near the interface.

Hecht, M. H.↗

Thermal Conductivity of Ultem(TradeMark)/Carbon Nanofiller Blends

In an effort to improve polymer thermal conductivity (TC), Ultem(TradeMark) 1000 was compounded with nano-fillers of carbon allotropes. Ultem(TradeMark) 1000 was selected since it is both solution and melt processable. As-received and modified multiwalled carbon nanotubes (MWCNTs), vapor grown carbon nanofibers (CNF) and expanded graphite (EG) were investigated. MWCNTs were modified by functionalizing the surface through oxidization with concentrated acids, mixing with an alkyl bromide, and addition of alkyl and phosphorus compounds after initial treatment with n-butyl lithium. Functionalization was performed to improve the TC compatibility between the resin and MWCNTs. It was postulated that this may provide an improved interface between the MWCNT and the polymer which would result in enhanced TC. The nano-fillers were mixed with Ultem(TradeMark) 1000 in the melt and in solution at concentrations ranging from 5 to 40 wt%. Ribbons were extruded from the blends to form samples where the nano-fillers were aligned to some degree in the extrusion direction. Samples were also fabricated by compression molding resulting in random orientation of the nano-fillers. Thermal properties of the samples were evaluated by Differential Scanning Calorimetry (DSC) and Thermal Gravimetric Analyzer (TGA). Tensile properties of aligned samples were determined at room temperature. The specimens were cut from the ribbons in the extrusion direction; hence the nano-fillers are somewhat aligned in the direction of stress. Typically it was observed that melt mixed samples exhibited superior mechanical properties compared to solution mixed samples. As expected, increased filler loading led to increased modulus and decreased elongation with respect to the neat polymer. The degree of dispersion and alignment of the nano-fillers was determined by high-resolution scanning electron microscopy (HRSEM). HRSEM of the ribbons revealed that the MWCNTs and CNFs were predominantly aligned in the flow direction. The TC of the samples was measured using a Nanoflash(TradeMark) instrument. Since the MWCNTs and CNF are anisotropic, the TC was expected to be different in the longitudinal (parallel to the nanotube and fiber axis) and transverse (perpendicular to the nanotube and fiber axis) directions. The extruded ribbons provided samples for transverse TC measurements. However, to determine the TC in the longitudinal direction, the ribbons needed to be stacked and molded under 1.7 MPa and 270 C. Samples were then obtained by cutting the molded block with a diamond saw. The largest TC improvement was achieved for aligned samples when the measurement was performed in the direction of MWCNT and CNF alignment (i.e. longitudinal axis). Unaligned samples also showed a significant improvement in TC and may be potentially useful in applications when it is not possible to align the nano-filler. The results of this study will be presented.

Ghose, S.↗

Influencing Bonding Interactions of the Neptunyl (V, VI) Cations with Electron-donating and -withdrawing Groups

Neptunium makes up the largest percentage of minor actinides found in spent nuclear fuel, yet separations of this element have proven difficult due to its rich redox chemistry. Developing new reprocessing techniques should rely on understanding how to control the Np oxidation state and its interactions with different ligands. Designing new ligands for separations requires understanding how to properly tune a system toward a desired trait through functionalization. Emerging technologies for minor actinide separations focus on ligands containing carboxylate or pyridine functional groups, which are desirable due to their high degree of functionalization. So we use DFT calculations to study the interactions of carboxylate and polypyridine ligands with the neptunyl cation [Np(V/VI)O2] +/2+ . A systematic study is performed by varying the electronic properties of the carboxylate and polypyridine ligands through the inclusion of different electron-withdrawing and electron-donating R groups. We focus on how these groups can affect geometric properties, electronic structure, and bonding characterization as a function of the metal oxidation state and ligand character and discuss how these factors can play a role in neptunium ligand design principles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward Long-Life, Ultrahigh-Nickel Layered Oxide Cathodes for Lithium-Ion Batteries: Optimizing the Interphase Chemistry with a Dual-Functional Polymer

Boosting the Ni content in LiMO 2 (M = Ni, Co, Mn, etc.) layered oxides is a promising way to establish high-energydensity, low-cost cathodes, but the poor cathode surface stability is a daunting challenge for their practical viability. Herein, by constructing a dual-functional binder framework with a conductive polymer - polyaniline (PANI), the ultrahigh-Ni layered oxide cathode (LiNi 0.94 Co 0.06 O 2 ) exhibits significantly improved cyclability, with a capacity retention greatly increased from 47% to 81% over 1,000 cycles in full cells. It is demonstrated that the acidic species (e.g. HF) in the electrolyte can be efficiently scavenged through a protonation process of PANI, hence the cathode surface reactivity is greatly suppressed and the rock-salt phase propagation into bulk structure is considerably alleviated. Furthermore, the PANI binder system effectively prevents both the cathode-electrolyte interphase (CEI) and anode-electrolyte interphase (AEI) from degrading to a thick “triple-layer” architecture upon extensive cycling, resulting in more robust, thinner CEI and AEI with regulated interphasial chemistry. Moreover, the delocalized π-conjugated electrons along the backbone of PANI facilitate fast electron transfer and promote rate capability even at low temperatures (-20 °C). Finally, this work sheds light on rational binder engineering for developing high-energy-density lithium-ion batteries with acceptable cycle life.

25 ENERGY STORAGE↗

Investigation of N2 adsorption on Fe3O4(001) using ambient pressure X-ray photoelectron spectroscopy and density functional theory

Reactions on iron oxide surfaces are prevalent in various chemical processes from heterogeneous catalysts to minerals. Nitrogen (N2) is known to dissociate on iron surfaces, a precursor for ammonia production in the Haber–Bosch process, where the dissociation of N2 is the limiting step in the reaction under equilibrium conditions. However, little is known about N2 adsorption on other iron-based materials, such as iron oxide surfaces that are ubiquitous in soils, steel pipelines, and other industrial materials. An atomistic description is reported for the binding of N2 on the Fe3O4(001) surface using first principles calculations with ambient pressure X-ray photoelectron spectroscopy. Two primary adsorption sites are experimentally identified from N2 dissociation on Fe3O4(001). The electronic signatures associated with the valence band region unambiguously show how the electronic structure of magnetite transforms near ambient pressures due to the binding of atomic nitrogen to different surface sites. Overall, the experimental and theoretical results of our study bridge the gap between ultra-high vacuum studies and reaction conditions to provide insight into other nitrogen-based chemistry on iron oxide surfaces that impact the agriculture and energy industries.

Degaga, Gemechis D. (ORCID:0000000205097118)↗

Defect Equilibria from First Principles: From Widegap Oxides to Topological Semimetals

Materials functionality and performance is rarely determined by the ideal crystal alone but is usually affected by formation of imperfections and the solution of impurities. In some applications, such as solar thermochemical hydrogen generation, defect formation is the fundamentally enabling mechanism of the desired functionality. In other cases, such as Cd3As2 topological semimetals, unintentional self-doping presents an obstacle to the access to the unique electronic properties. In either case, a quantitative understanding of the relevant defect mechanism is essential for developing design strategies. This presentation will touch upon numerous aspects in the computational simulation of defect equilibria, including non-equilibrium design strategies, the coupling of solid state and gas-phase reactions, dopant-defect and defect-defect interactions, both attractive and repulsive, the accuracy of total energy functionals and electronic structure methods, and the role of the shape of the density of states for the charge balance condition and Fermi level position, as well as machine-learning prediction of defect energies (1). Specific materials systems include Ga2O3 (2), Cd3As2 (3), and (Sr,Ce)MnO3 (4). (1) M.D. Witman, A. Goyal, T. Ogitsu, A.H. McDaniel, S. Lany, Nat. Comput. Sci. 3, 675 (2023). (2) A. Goyal, A. Zakutayev, V. Stevanovic, S. Lany, J. Appl. Phys. 129, 245704 (2021). (3) C. Brooks, M. van Schilfgaarde, D. Pashov, J.N. Nelson, K. Alberi, D.S. Dessau, S. Lany, Phys. Rev. B 107, 224110 (2023). (4) A. Goyal, M.D. Sanders, R.P. O'Hayre, S. Lany, PRX Energy 3, 013008 (2024).

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,M↗

Local structure of zinc–indium–tin oxide films via grazing-incidence x-ray pair-distribution functions and theoretical methods

A detailed experimental and theoretical study on the local (r ≤ 4.5 Å) atomic structure of amorphous and crystalline zinc–indium–tin oxide (ZITO) thin films using grazing-incidence x-ray Pair-Distribution Functions (PDFs), ab initio Molecular Dynamics (MD), and Empirical Potential Structure Refinement (EPSR) Monte Carlo simulations is presented. High-energy synchrotron x rays, a two-dimensional detector, and different incident angles were used to probe the depth uniformity of five (ZnO) 0.15 (In 2 O 3 ) 0.70 (SnO 2 ) 0.15 films that were deposited via pulsed-laser deposition at growth temperatures (T G ) ranging from 25 to 300 °C. Films deposited at T G ≤ 150 °C were amorphous. The partially crystalline (T G = 200 °C) and fully crystalline (T G = 300 °C) films were highly textured. Both crystalline and amorphous structures were investigated using ab initio MD and EPSR Monte Carlo simulations. The density of the amorphous films determined from the experimental data agreed with MD calculations. Coordination numbers, bond lengths, and distortion for metal–oxygen and for both the edge- and corner-shared In–metal shells up to 4.5 Å obtained from PDF analysis closely agreed with MD and EPSR simulations. There is a pronounced decrease in the edge- and corner-shared In–Zn distances arising from the shorter Zn–O bond length, Zn–O tetrahedral coordination, and In–O–Zn angle in amorphous ZITO compared to its crystalline counterpart. A maximum in electrical mobility was observed for the amorphous film just before crystallization occurred. While the peak is broad, consistent with nearly unchanged overall cation–oxygen coordination in the amorphous films, ESPR results indicate that the tetrahedral coordination follows the conductivity trend.

Grazing Incidence X-ray↗

Tuning Surface Acidity of Mixed Conducting Electrodes: Recovery of Si‐Induced Degradation of Oxygen Exchange Rate and Area Specific Resistance

Abstract Metal oxides are an important class of functional materials, and for many applications, ranging from solid oxide fuel/electrolysis cells, oxygen permeation membranes, and oxygen storage materials to gas sensors (semiconducting and electrolytic) and catalysts, the interaction between the surface and oxygen in the gas phase is central. Ubiquitous Si‐impurities are known to impede this interaction, commonly attributed to the formation of glassy blocking layers on the surface. Here, the surface oxygen exchange coefficient ( k chem ) is examined for Pr 0.1 Ce 0.9 O 2‐δ (PCO), a model mixed ionic electronic conductor, via electrical conductivity relaxation measurements, and the area‐specific resistance (ASR) by electrochemical impedance spectroscopy. It is demonstrated that even low silica levels, introduced by infiltration, depress k chem by a factor 4000, while the ASR increases 40‐fold and we attribute this to its acidity relative to that of PCO. The ability to fully regenerate the poisoned surface by the subsequent addition of basic Ca‐ or Li‐species is further shown. This ability to not only recover Si‐poisoned surfaces by tuning the relative surface acidity of an oxide surface, but subsequently outperform the pre‐poisoned response, promises to extend the operating life of materials and devices for which the catalytic oxygen/solid interface reaction is central.

30 DIRECT ENERGY CONVERSION↗