Notes

Fluorine Marking associated with ortho-Phenylenes in order to Aid Conformational Analysis.
4-Silyl-5,6-dihydropyrans undergo remarkably selective [1,4]-Wittig rearrangements to give silylcyclopropanes in good yields. The selectivity is independent of the silyl group, but it is influenced by the electronic character of the migrating center. Electron-rich and electron-neutral (hetero)aryl groups and aliphatic substituents at the migrating center lead to exclusive [1,4]-migration, whereas electron-deficient aryl groups predominantly afford [1,2]-Wittig products.Global bottom-up mass spectrometry (MS)-based proteomics is widely used for protein identification and quantification to achieve a comprehensive understanding of the composition, structure, and function of the proteome. However, traditional sample preparation methods are time-consuming, typically including overnight tryptic digestion, extensive sample cleanup to remove MS-incompatible surfactants, and offline sample fractionation to reduce proteome complexity prior to online liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Thus, there is a need for a fast, robust, and reproducible method for protein identification and quantification from complex proteomes. Herein, we developed an ultrafast bottom-up proteomics method enabled by Azo, a photocleavable, MS-compatible surfactant that effectively solubilizes proteins and promotes rapid tryptic digestion, combined with the Bruker timsTOF Pro, which enables deeper proteome coverage through trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF) of peptides. We applied this method to analyze the complex human cardiac proteome and identified nearly 4000 protein groups from as little as 1 mg of human heart tissue in a single one-dimensional LC-TIMS-MS/MS run with high reproducibility. Overall, we anticipate this ultrafast, robust, and reproducible bottom-up method empowered by both Azo and the timsTOF Pro will be generally applicable and greatly accelerate the throughput of large-scale quantitative proteomic studies. Raw data are available via the MassIVE repository with identifier MSV000087476.An efficient methodology for synthesis of α-keto acids via oxidation of alkenes using TBHP as oxidant catalyzed by a bifunctional iron nanocomposite has been established. A variety of alkenes with different functional groups were smoothly oxidized into their corresponding α-keto acids in up to 80% yield. Moreover, the bifunctional iron nanocomposite catalyst showed outstanding catalytic stability for successive recycles without appreciable loss of activity.Oxygen is the second-largest-volume industrial gas that is mainly produced using cryogenic air separation. However, the state-of-the-art cryogenic technology thermodynamic efficiency has approached a theoretical limit as near as is practicable. Therefore, there is stimulus to develop an alternative technology for efficient oxygen separation from air. Mixed ionic electronic-conducting (MIEC) ceramic membrane-based oxygen separation technology could become this alternative, but commercialization aspects, including cost, have revealed inadequacies in ceramic membrane materials. Currently, diffusion-bubbling molten oxide membrane-based oxygen separation technology is being developed. It is a potentially disruptive technology that would propose an improvement in oxygen purity and a reduction in capital costs. Bubbles play an important role in ensuring the oxygen mass transfer in diffusion-bubbling membranes. However, there is not sufficient understanding of the bubble dynamics. This understanding is important to be able to control transport properties of these membranes and assess their potential for technological application. The aim of this feature article is to highlight the progress made in developing this understanding and specify the directions for future research.A high yield synthesis of 2-amino-4-pyrrolin-3-ones including 4-pyrrolin-3-one-based amino esters by the NBS- or TfCl-mediated reaction of 3-hydroxypyrroles with amines has been developed. The reaction of 3-hydroxypyrroles with triflyl chloride in the absence of amine affords 2,2'-bi(4-pyrrolin-3-ones) in excellent yields and diastereoselectivity. The relative configuration of stereocenters in these compounds can be changed from (2RS,2'RS) to (2RS,2'SR) by the action of NaH in THF, while the reverse stereoisomerization occurs in the presence of 2,5-lutidine in MeCN. Bi(4-pyrrolin-3-ones) also can be converted to 2-amino-4-pyrrolin-3-ones in excellent yields. Bi(4-pyrrolin-3-ones) and 2-amino-4-pyrrolin-3-ones were evaluated for their antiproliferative activity toward four human tumor cell lines.The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are relevant to the hypothesis being investigated. However, in settings where researchers are interested in a subset of peptides, alternative search and FDR control strategies are needed. Recently, two methods were proposed to address this problem subset-search and all-sub. We show that both methods fail to control the FDR. For subset-search, this failure is due to the presence of "neighbor" peptides, which are defined as irrelevant peptides with a similar precursor mass and fragmentation spectrum as a relevant peptide. Not considering neighbors compromises the FDR estimate because a spectrum generated by an irrelevant peptide can incorrectly match well to a relevant peptide. Therefore, we have developed a new method, "subset-neighbor search" (SNS), that accounts for neighbor peptides. We show evidence that SNS controls the FDR when neighbors are present and that SNS outperforms group-FDR, the only other method that appears to control the FDR relative to a subset of relevant peptides.Protein stability and performance in various natural and artificial systems incorporating many other macromolecules for therapeutic, diagnostic, sensor, and biotechnological applications attract increasing interest with the expansion of these technologies. Here we address the catalytic activity of lysozyme protein (LYZ) in the presence of a polyethylene glycol (PEG) crowder in a broad range of concentrations and temperatures in aqueous solutions of two different molecular mass PEG samples (Mw = 3350 and 10000 g/mol). The phase behavior of PEG-protein solutions is examined by using dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS), while the enzyme denaturing is monitored by using an activity assay (AS) and circular dichroism (CD) spectroscopy. Molecular dynamic (MD) simulations are used to illustrate the effect of PEG concentration on protein stability at high temperatures. The results demonstrate that LYZ residual activity after 1 h incubation at 80 °C is improved from 15% up to 55% with the addition of PEG. The improvement is attributed to two underlying mechanisms. (i) Primarily, the stabilizing effect is due to the suppression of the enzyme aggregation because of the stronger PEG-protein interactions caused by the increased hydrophobicity of PEG and lysozyme at elevated temperatures. (ii) The MD simulations showed that the addition of PEG to some degree stabilizes the secondary structures of the enzyme by delaying unfolding at elevated temperatures. The more pronounced effect is observed with an increase in PEG concentration. This trend is consistent with CD and AS experimental results, where the thermal stability is strengthened with increasing of PEG concentration and molecular mass. The results show that the highest stabilizing effect is approached at the critical overlap concentration of PEG.A fundamental role of pancreatic β-cells to maintain proper blood glucose level is controlled by the Ras superfamily of small GTPases that undergo post-translational modifications, including prenylation. This covalent attachment with either a farnesyl or a geranylgeranyl group controls their localization, activity, and protein-protein interactions. Small GTPases are critical in maintaining glucose homeostasis acting in the pancreas and metabolically active tissues such as skeletal muscles, liver, or adipocytes. Hyperglycemia-induced upregulation of small GTPases suggests that inhibition of these pathways deserves to be considered as a potential therapeutic approach in treating T2D. This Perspective presents how inhibition of various points in the mevalonate pathway might affect protein prenylation and functioning of diabetes-affected tissues and contribute to chronic inflammation involved in diabetes mellitus (T2D) development. We also demonstrate the currently available molecular tools to decipher the mechanisms linking the mevalonate pathway's enzymes and GTPases with diabetes.Calix[4]resorcinarene derivatives such as C-undecylcalix[4]resorcinarene self-assemble into a hexameric capsule-like structure. This structure is expected in any apolar solvent, but we recently found a self-assembled octameric form of resorcinarene in toluene. To understand this unexpected form, we performed small-angle X-ray scattering (SAXS) measurements of the octameric self-assembly. In ab initio shape reconstruction and model fitting of the SAXS profile, a core-shell spherical structure resembling a reverse micelle was found in the octameric self-assembly. The shell and core were composed of alkyl chains and resorcinol moieties, respectively. We also evaluated the temperature dependence of the octameric self-assembly. Above 95 °C, the structure began directly decomposing into unimers, implying the partial cleavage of hydrogen bonds in the octamer core. Meanwhile, below 25 °C, the spherical structure of the octamer partially transformed to a cylindrical structure. This morphological transition could be understood by packing parameter theory, which is often applied to suspected micellar structures.A new type of alkylborate was developed for the purpose of generating radicals via direct photoexcitation. click here These borates were prepared using 2,2'-(pyridine-2,6-diyl)diphenol as a tridentate ligand together with organoboronic acids or potassium trifluoroborates. The ready availability of organoboron compounds is a significant advantage of this direct photoexcitation protocol. The excited states of these borates can also serve as strong reductants, enabling various transformations.Synthetic methodology utilizing two aryne intermediates (i.e., a formal benzdiyne) enables the rapid generation of structurally complex molecules with diverse functionality. This report describes the sequential generation of two ortho-benzyne intermediates for the synthesis of 2,3-disubstituted aryl phosphonates. Aryl phosphonates have proven useful in medicinal chemistry and materials science, and the reported methodology provides a two-step route to functionally dense variants by way of 3-phosphonyl benzyne intermediates. The process begins with regioselective trapping of a 3-trifloxybenzyne intermediate by an O-silyl phosphite in an Abramov-like reaction to bond the strained Csp carbons with phosphorus and silicon. Standard aryne-generating conditions follow to convert the resulting 2-silylphenyl triflate into a 3-phosphonyl benzyne, which readily reacts with numerous aryne trapping reactants to form a variety of 2,3-difunctionalized aryl phosphonate products. DFT computational studies shed light on important mechanistic details and revealed that 3-phosphonyl benzynes are highly polarizable.
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