Practical Synthesis of N -Formylmethionylated Peptidyl-tRNA Mimics
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Distinguishing Potassium Channel Resting State Conformations in Live Cells with Environment-Sensitive Fluorescence
Ion channels are polymorphic membrane proteins whose high-resolution structures offer images of individual conformations, giving us starting points for identifying the complex and transient allosteric changes that give rise to channel physiology. Here, we report live-cell imaging of voltage-dependent structural changes of voltage-gated Kv2.1 channels using peptidyl tarantula toxins labeled with an environment-sensitive fluorophore, whose spectral shifts enable identification of voltage-dependent conformation changes in the resting voltage sensing domain (VSD) of the channel. We synthesize a new environment-sensitive, far-red fluorophore, julolidine phenoxazone (JP) azide, and conjugate it to tarantula toxin GxTX to characterize Kv2.1 VSD allostery during membrane depolarization. JP has an inherent response to the polarity of its immediate surroundings, offering site-specific structural insight into each channel conformation. Using voltage-clamp spectroscopy to collect emission spectra as a function of membrane potential, we find that they vary with toxin labeling site, the presence of Kv2 channels, and changes in membrane potential. With a high-affinity conjugate in which the fluorophore itself interacts closely with the channel, the emission shift midpoint is 50 mV more negative than the Kv2.1 gating current midpoint. This suggests that substantial conformational changes at the toxin-channel interface are associated with early gating charge transitions and these are not concerted with VSD motions at more depolarized potentials. These fluorescent probes enable study of conformational changes that can be correlated with electrophysiology, putting channel structures and models into a context of live-cell membranes and physiological states.
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Electrochemical Synthesis and Investigation of Stoichiometric, Phase-Pure CoSb 2 O 6 and MnSb 2 O 6 Electrodes for the Oxygen Evolution Reaction in Acidic Media
The electrochemical oxidation of water to oxygen gas is the primary counter reaction to the formation of hydrogen gas via water splitting. In acidic media, the only well-established and active oxygen evolution catalysts are expensive noble metal oxides such as IrO x and RuO x , necessitating the development of practical oxygen evolution catalysts that are stable in acidic media. In this study, we prepared stoichiometric, phase-pure CoSb 2 O 6 and MnSb 2 O 6 electrodes using electrochemical synthesis and investigated their ability to oxidize water in 0.5 M H 2 SO 4 (pH 0.3). In addition, their stabilities during the oxygen evolution reaction (OER) were carefully examined by comparing their morphologies, crystallinities, compositions, and surface compositions before and after the OER. The chlorine evolution reaction on CoSb 2 O 6 and MnSb 2 O 6 in acidic media was also examined so that their performances can be compared with previously reported non-stoichiometric CoSb 2 O 6 and MnSb 2 O 6 electrodes. The electrochemical properties and stabilities of stoichiometric, phase-pure CoSb 2 O 6 and MnSb 2 O 6 reported in this study can provide useful insights into the development and understanding of acid-stable, non-noble metal oxide-based OER catalysts.
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TALSPEAK-based separation of the trivalent actinides from rare earth elements using LN resin
The separation of 241 Am, 244 Cm and 249 Cf from rare earth elements using LN resin and lactate buffer solutions with diethylenetriaminepentaacetic acid is described with numerous columns studies. The elutions are based on TALSPEAK liquid–liquid extraction chemistry, and provide high yield (> 90%), rapid, simple separations of the trivalent actinides from the lanthanides, which is often challenging due to similarities in chemical behavior among the trivalent f-block elements. Further, all three actinides can be separated from rare earth elements, including from massless fission product samples and samples with small amounts (~ 1–5 mg) of stable lanthanides. Separations with no detectable overlap between the actinide and lanthanide elutions is possible with massless samples, and in samples with mass high separation factors can be achieved (Am/Eu: 171; Am/La: 10 6 ).
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Environmental and Energy Research at the Texas Center for Advanced Scientific Computing and Modeling (CASCaM)
The funding enabled the creation of the (University of North) Texas Center for Advanced Scientific Computing and Modeling (CASCaM). Due to its success, CASCaM has continued to grow beyond the initial team focused on the biological and environmental research discussed herein, with investments by the University of North Texas in new faculty and researchers who contribute to CASCaM research. CASCaM is now a sustainable effort, with researchers across multiple fields including chemistry, physics, biology, mechanical engineering, materials science, and other fields, with multiple researchers engaged in a broad variety of research, including other DOE projects. Over 20 PI’s and ~100 researchers are engaged in CASCaM research. The overall goal of the research effort was to provide greater understanding about carbon capture, storage, and utilization. As part of this effort, the development of computational methods and identification of novel strategies to support the CO2 and CO studies were necessary. Three primary themes were investigated: carbon dioxide and CO catalysis; protein- and amino acid-based strategies towards carbon dioxide capture, storage, and utilization; and, finally, the methodology improvements for modeling carbon dioxide chemistry
54 ENVIRONMENTAL SCIENCES↗
Strategies toward the Synthesis of Advanced Functional Sorbent Performance for Uranium Uptake from Seawater
A polymer fiber-based adsorbent (AF1) composed of acrylonitrile and itaconic acid functional groups was synthesized by a radiation-induced graft polymerization technique onto hollow-gear shaped polyethylene (PE) fibers. Investigation of the optimum reaction parameters for the conversion of grafted cyano moieties into amidoxime groups was conducted by the reaction with hydroxylamine at different temperatures and periods in a variety of aqueous and organic solvents. The 13 C CP/MAS spectra of amidoximated AF1 adsorbent fibers from water–methanol and dimethyl sulfoxide (DMSO) revealed that both the cyclic imide dioxime and open-chain amidoxime were formed through the reaction. The conversion from amidoxime to imide dioxime was found to occur slowly and gradually with the increasing reaction time. The quicker diffusion of DMSO as compared to that of water–methanol, in the grafted trunk PE fiber, resulted in faster kinetics of the amidoximation reaction. The uranium adsorption capacity of the amidoximated AF1 samples was determined after (i) 24 h contact with sodium-based brine spiked with uranium and (ii) 56 days of exposure to filtered seawater (Sequim Bay, WA, USA) in flow-through columns. Finally, the uranium extraction performance of the adsorbents after exposure to filtered seawater was consistent with the laboratory screening results, and the amidoximated AF1 samples (in DMSO at 70 °C for 3 h) exhibited the highest 56 day uranium adsorption capacity (5.04 ± 0.15 g U/kg-ads) with faster adsorption kinetics compared to the pristine AF1 adsorbents.
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Molecular dynamics study of carbon dioxide and nitrogen selectivity through poly[bis((methoxyethoxy)ethoxy)phosphazene] (MEEP) membrane
Here, a molecular dynamics simulation model was developed to comprehensively understand carbon dioxide over nitrogen (CO 2 /N 2 ) selectivity through polyphosphazene-based membrane comprising of poly[bis((methoxyethoxy)ethoxy)phosphazene] (MEEP) selective layer at the molecular level. The effects of temperature, pressure, and initial feed gas composition on the CO 2 transport on a polymer membrane were studied. The computed free energy and density profile of the permeating gas mixture exhibited that CO 2 molecules express higher interactions with the membrane than N 2 molecules, resulting in higher CO 2 /N 2 selectivity. Statistical analysis of gas molecules (CO 2 , water (H 2 O), and N 2 ) transportation suggested that hydro- and CO 2 -philic functional groups in the membrane significantly impact CO 2 permeability and CO 2 /N 2 selectivity. This study suggested that Lewis acid–base and hydrogen bonding combinations contribute to CO 2 permeation and CO 2 /N 2 selectivity. An equal CO 2 /N 2 selectivity was observed with and without water vapor in the feed gas suggesting that water does not hinder CO 2 transport through the membrane.
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Development of sulfonated carbon-based solid-acid catalysts derived from biorefinery residues and biomass ash for xylan hydrolysis
In this study, biorefinery residues and biomass ash were used to develop sulfonated carbon-based solid-acid catalysts to enhance xylan hydrolysis. Here, metals extracted from the biomass ash were impregnated into a carbon support prepared from biorefinery residues to synthesize sulfonated ash-impregnated carbon-based catalyst. Metals present in the ash most probably are responsible for the increased acid density in the catalyst. Using this catalyst, 11.4 % xylose yield was produced, an increase of 171 % over the yield obtained from a catalyst without ash impregnation. Using a xylan-to-catalyst ratio of 1:2, 72.9 % xylose yield was obtained, comparable to using 0.5 wt% sulfuric acid under the same reaction condition. Moreover, this catalyst significantly inhibited xylose dehydration, only forming 11.3 % furfural compared to that generated using dilute acid. Hence, these results show the potential for using biomass ash as a metal source to increase the number of acid sites in solid-acid catalysts used for biomass pretreatment.
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A numerical examination of the effect of sulfide dissolution on silicate weathering
Silicate weathering regulates climate on geological time scales as a net, climate-sensitive sink of atmospheric CO 2 . On the other hand, sulfuric acid produced through sulfide dissolution affects silicate weathering, diminishing its effectiveness as a climate regulator based on evidence from river chemistry. This study takes a theoretical approach to quantitatively examine the effect of sulfide dissolution, coupling a one-dimensional model of pyrite weathering to that of albite transformation to kaolinite. The coupled model reveals that when the reaction front of sulfide is deeper than that of silicates reacting with CO 2 , the silicate-weathering feedback on climate is not directly affected by sulfide dissolution, but only indirectly through oceanic processes such as reverse weathering and carbonate deposition. In turn, when sulfide dissolution occurs within zones of CO 2 -silicate reactions close to the surface, the feedback between climate and silicate weathering can be significantly weakened because sulfuric acid competes effectively with carbonic acid in mineral dissolution. As the depth of the sulfide reaction front can be changed by variations in water table depth, the latter feedback weakening could have occurred in concert with climate-change-driven water table fluctuations, amplifying atmospheric CO 2 variations during the Phanerozoic.
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Quick-and-Easy Validation of Protein–Ligand Binding Models Using Fragment-Based Semiempirical Quantum Chemistry
Electronic structure calculations in enzymes converge very slowly with respect to the size of the model region that is described using quantum mechanics (QM), requiring hundreds of atoms to obtain converged results and exhibiting substantial sensitivity (at least in smaller models) to which amino acids are included in the QM region. As such, there is considerable interest in developing automated procedures to construct a QM model region based on well-defined criteria. However, testing such procedures is burdensome due to the cost of large-scale electronic structure calculations. Here, we show that semiempirical methods can be used as alternatives to density functional theory (DFT) to assess convergence in sequences of models generated by various automated protocols. The cost of these convergence tests is reduced even further by means of a many-body expansion. We use this approach to examine convergence (with respect to model size) of protein–ligand binding energies. Fragment-based semiempirical calculations afford well-converged interaction energies in a tiny fraction of the cost required for DFT calculations. Two-body interactions between the ligand and single-residue amino acid fragments afford a low-cost way to construct a “QM-informed” enzyme model of reduced size, furnishing an automatable active-site model-building procedure. This provides a streamlined, user-friendly approach for constructing ligand binding-site models that needs neither a priori information nor manual adjustments. Extension to model-building for thermochemical calculations should be straightforward.
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Capture of volatile RuO 4 from oxidized simulated used nuclear fuel solutions
Ruthenium is a challenging fission product in used nuclear fuel (UNF) reprocessing due to its complex redox chemistry, variable speciation in nitric acid, partial extractability, and volatility. This work presents a strategy for Ru removal based on the volatilization of RuO 4 using the strong oxidant sodium bismuthate, followed by RuO 2 deposition onto various substrates. Among the materials tested, polymer-based substrates such as polyolefin wax film (Parafilm®), exhibited superior performance, achieving up to near-quantitative Ru removal from solution. After dissolution of the substrate, 99.6% of the Ru was recovered as RuO 2 . The deposition mechanism onto the polyolefin wax film involves both physisorption and chemical reaction through oxidative cleavage of olefinic bonds within the polymer. In contrast, on inorganic substrates such as Al foil, RuO 4 undergoes incomplete surface adsorption and reduction, as confirmed by FTIR and XPS analyses. This approach remains effective under conditions of simulated oxidation of UNF solutions, selectively removing Ru while leaving other fission products in solution. As a result, capture of RuO 4 offers a practical and efficient strategy for ruthenium decontamination and recovery, offering a route for integration into existing UNF reprocessing flowsheets to enhance overall process safety and performance.
Ruthenium↗
Water Promotion (or Inhibition) of Condensation Reactions Depends on Exposed Cerium Oxide Catalyst Facets
Nanoparticles with well-defined facets enable quantitative correlations between surface features and catalytic activity. In this work, we explore the role of geometric and acid–base properties in the mechanism of aldol condensation catalyzed by ceria nanoshapes. In the crucial C–C coupling step, the two carbonyl adsorbates are bound to two adjacent cations. On the CeO 2 (110) plane, all atoms lie on the same layer, favoring the interaction between adsorbates and facilitating the bimolecular C–C coupling. Thus, the initial unimolecular deprotonation is rate-limiting. In contrast, the (100) and (111) planes have an open structure with O on the top layer and Ce on the layer below. The former O layer interferes between adsorbates linked to Ce sites, making the C–C coupling rate-limiting. Water helps in overcoming this spatial hindrance by remote bond polarization via H-bonds. Therefore, water promotion is only observed on those planes for which the bimolecular step is rate-limiting.
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Predicting the chemical space of fungal polyketides by phylogeny-based bioinformatics analysis of polyketide synthase-nonribosomal peptide synthetase and its modification enzymes
Fungal polyketide synthase (PKS)–nonribosomal peptide synthetase (NRPS) hybrids are key enzymes for synthesizing structurally diverse hybrid natural products (NPs) with characteristic biological activities. Predicting their chemical space is of particular importance in the field of natural product chemistry. However, the unexplored programming rule of the PKS module has prevented prediction of its chemical structure based on amino acid sequences. Here, we conducted a phylogenetic analysis of 884 PKS–NRPS hybrids and a modification enzyme analysis of the corresponding biosynthetic gene cluster, revealing a hidden relationship between its genealogy and core structures. This unexpected result allowed us to predict 18 biosynthetic gene cluster (BGC) groups producing known carbon skeletons (number of BGCs; 489) and 11 uncharacterized BGC groups (171). The limited number of carbon skeletons suggests that fungi tend to select PK skeletons for survival during their evolution. The possible involvement of a horizontal gene transfer event leading to the diverse distribution of PKS–NRPS genes among fungal species is also proposed. This study provides insight into the chemical space of fungal PKs and the distribution of their biosynthetic gene clusters.
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Adsorption, Orientation, and Speciation of Amino Acids at Air–Aqueous Interfaces for the Direct Air Capture of CO 2
Amino acids make up a promising family of molecules capable of direct air capture (DAC) of CO 2 from the atmosphere. Under alkaline conditions, CO 2 reacts with the anionic form of an amino acid to produce carbamates and deactivated zwitterionic amino acids. The presence of the various species of amino acids and reactive intermediates can have a significant effect on DAC chemistry, the role of which is poorly understood. In this study, all-atom molecular dynamics (MD) based computational simulations and vibrational sum frequency generation (vSFG) spectroscopy studies were conducted to understand the role of competitive interactions at the air–aqueous interface in the context of DAC. We find that the presence of potassium bicarbonate ions, in combination with the anionic and zwitterionic forms of amino acids, induces concentration and charge gradients at the interface, generating a layered molecular arrangement that changes under pre- and post-DAC conditions. In parallel, an enhancement in the surface activity of both anionic and zwitterionic forms of amino acids is observed, which is attributed to enhanced interfacial stability and favorable intermolecular interactions between the adsorbed amino acids in their anionic and zwitterionic forms. The collective influence of these competitive interactions, along with the resulting interfacial heterogeneity, may in turn affect subsequent capture reactions and associated rates. Finally, these effects underscore the need to consider dynamic changes in interfacial chemical makeup to enhance DAC efficiency and to develop successful negative emission and storage technologies.
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Alloy selective optical sorting of mixed post-consumer aluminum scrap streams
Shredded post-consumer non-ferrous scrap stream, also known as Zorba, contains a mixture of cast and wrought aluminum pieces with very different compositions. Cast Al pieces, with their high Si, Cu and Fe content, are a major contaminant in wrought scrap fraction, which results in downcycling of the mixed cast + wrought scrap into non-structural cast Al alloys and parts. Here, in this paper, we introduce a chemical treatment method to color-code scrap aluminum pieces by alloy family and demonstrate low-cost optical sorting of cast from wrought pieces to upgrade the scrap stream. We utilized non-acidic chemical solutions that react with (i.e., etch) the scrap pieces to produce colors based on the Al alloy chemistry of a given piece. Cast pieces with high Si and Cu fractions turned black, whereas the much leaner wrought pieces remained unreacted. We showed > 95% sorting efficiency of mixed cast and wrought pieces using a repurposed low-cost optical sorter originally designed for food sorting. We also colored wrought Al pieces by alloy families, such as 5xxx and 6xxx, using a two-step chemical etching technique, which has the potential to create a circular supply chain in which wrought aluminum alloys are sorted from the mixed scrap stream and recycled back to high-value wrought products such as sheets, extrusions, and forgings with minimal contamination from cast scrap.
Aluminum↗
Photoenzymatic Catalysis in a New Light: Gluconobacter “Ene”-Reductase Conjugates Possessing High-Energy Reactivity with Tunable Low-Energy Excitation
Non-natural light-driven enzymatic reactivity was recently developed to perform the highly stereoselective reactions required for pharmaceutical synthesis. However, photoenzymes require high-intensity light to function because of the poor absorption properties of their photoactive intermediates. Inspired by the modular architecture of photosynthesis, we designed a conjugate composed of a covalently linked photoenzyme and a light antenna to separate light capture from catalysis. Spectroscopic characterization of the conjugate showed the presence of efficient energy transfer from the light-harvesting components to the photoenzyme. In the presence of energy transfer, a ~4-fold increase in product yield was observed for intramolecular hydroalkylation of alkenes, and reactivity was enabled for intermolecular hydroalkylation of alkenes. As a result, these improvements establish the power of incorporating nature’s design into non-natural photoenzymatic catalysis.
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Assessment of two benzylation strategies for the analysis of nerve-agent derived ethyl- and pinacolyl methyl phosphonic acids in sandy loam soil by GC–MS
Despite their prohibition by the Chemical Weapons Convention, nerve agents (NAs) remain in use against military and civilian targets. Due to their high reactivity, NAs readily degrade to phosphonic acids, making them important markers in the inspection of areas of presumed NA use. In this work, we assess the use of benzylation to modify ethyl- and pinacolyl methylphosphonic acids, degradation products of VX and Soman respectively, for their efficient detection in a soil matrix at ~10 and ~1 μg/g using GC–MS. The soil matrix, Sandy Loam (SL), was chosen for its ubiquitous nature, complex composition with silica particles embedded in clay, and low organic content. In this study, we demonstrate that benzylation via benzyl bromide yields a LOD = 25.6 ng/mL for benzylated-EMPA and LOD = 30.1 ng/mL for benzylated-PMPA. This is superior to the use of p-methoxybenzyl trichloroacetimidate in providing stable phosphonic acid ester derivatives for analysis. A base-modified procedure for p-methoxybenzylation was explored in this study yielding a LOD = 29.1 ng/mL for p-methoxybenzylated-EMPA and LOD = 39.8 ng/mL for p-methoxybenzylated-PMPA. Both benzylation pathways (benzyl bromide and p-methoxybenzyl trichloroacetimidate) can be used to yield phosphonic acid derivatives that provide further confirmation of these Soman and VX degradation products in soil samples in investigative scenarios. The work herein represents the first application of benzylation methods for the analysis of these NA markers in the acidic, silicon-based SL soil.
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