Class Of Substrates Research Articles

Classification of Lakebed Geologic Substrate in Autonomously Collected Benthic Imagery Using Machine Learning

Mapping benthic habitats with bathymetric, acoustic, and spectral data requires georeferenced ground-truth information about habitat types and characteristics. New technologies like autonomous underwater vehicles (AUVs) collect tens of thousands of images per mission making image-based ground truthing particularly attractive. Two types of machine learning (ML) models, random forest (RF) and deep neural network (DNN), were tested to determine whether ML models could serve as an accurate substitute for manual classification of AUV images for substrate type interpretation. RF models were trained to predict substrate class as a function of texture, edge, and intensity metrics (i.e., features) calculated for each image. Models were tested using a manually classified image dataset with 9-, 6-, and 2-class schemes based on the Coastal and Marine Ecological Classification Standard (CMECS). Results suggest that both RF and DNN models achieve comparable accuracies, with the 9-class models being least accurate (~73–78%) and the 2-class models being the most accurate (~95–96%). However, the DNN models were more efficient to train and apply because they did not require feature estimation before training or classification. Integrating ML models into benthic habitat mapping process can improve our ability to efficiently and accurately ground-truth large areas of benthic habitat using AUV or similar images.

Multicomponent Synthesis of α-Branched Amines via a Zinc-Mediated Carbonyl Alkylative Amination Reaction.

Methods for the synthesis of α-branched alkylamines are important due to their ubiquity in biologically active molecules. Despite the development of many methods for amine preparation, C(sp3)-rich nitrogen-containing compounds continue to pose challenges for synthesis. While carbonyl reductive amination (CRA) between ketones and alkylamines is the cornerstone method for α-branched alkylamine synthesis, it is sometimes limited by the sterically demanding condensation step between dialkyl ketones and amines and the more restricted availability of ketones compared to aldehydes. We recently reported a "higher-order" variant of this transformation, carbonyl alkylative amination (CAA), which utilized a halogen atom transfer (XAT)-mediated radical mechanism, enabling the streamlined synthesis of complex α-branched alkylamines. Despite the efficacy of this visible-light-driven approach, it displayed scalability issues, and competitive reductive amination was a problem for certain substrate classes, limiting applicability. Here, we report a change in the reaction regime that expands the CAA platform through the realization of an extremely broad zinc-mediated CAA reaction. This new strategy enabled elimination of competitive CRA, simplified purification, and improved reaction scope. Furthermore, this new reaction harnessed carboxylic acid derivatives as alkyl donors and facilitated the synthesis of α-trialkyl tertiary amines, which cannot be accessed via CRA. This Zn-mediated CAA reaction can be carried out at a variety of scales, from a 10 μmol setup in microtiter plates enabling high-throughput experimentation, to the gram-scale synthesis of medicinally-relevant compounds. We believe that this transformation enables robust, efficient, and economical access to α-branched alkylamines and provides a viable alternative to the current benchmark methods.

Enzymatic and Chemo–catalytic Redox Deracemization: Recent Progress

AbstractThe precise synthesis of chiral small molecules is a core research area in chemical science. Deracemization, an appealing technology that converts racemate to its single enantiomer with the same constitution in theoretical 100 % yield, appears as a straightforward and efficient strategy in asymmetric synthesis. A cascading redox sequence was the most employed approach to drive deracemization through destroy and recreate the stereocenter in a given molecule. This review mainly focuses on the progress of redox deracemization driven by respective biocatalysis and chemo–catalysis. In particular, each section will be subdivided according to the action modes, the respective substrate classes and perspectives on future development.

Direct Heterocycle C-H Alkenylation via Dual Catalysis Using a Palladacycle Precatalyst: Multifactor Optimization and Scope Exploration Enabled by High-Throughput Experimentation.

One of the major challenges in developing catalytic methods for C-C bond formation is the identification of generally applicable reaction conditions, particularly if multiple substrate structural classes are involved. Pd-catalyzed direct arylation reactions are powerful transformations that enable direct functionalization of C-H bonds; however, the corresponding direct alkenylation reactions, using vinyl (pseudo) halide electrophiles, are less well developed. Inspired by process development efforts toward GSK3368715, an investigational active pharmaceutical ingredient, we report that a Pd(II) palladacycle derived from tri-tert-butylphosphine and Pd(OAc)2 is an effective single-component precatalyst for a variety of direct alkenylation reactions. High-throughput experimentation identified optimal solvent/base combinations for a variety of HetAr-H substrate classes undergoing C-H activation without the need for cocatalysts or stoichiometric silver bases (e.g., Ag2CO3). We propose this reaction proceeds via a dual cooperative catalytic mechanism, where in situ-generated Pd(0) supports a canonical Pd(0)/(II) cross-coupling cycle and the palladacycle effects C-H activation via CMD in a redox-neutral cycle. In all, 192 substrate combinations were tested with a hit rate of approximately 40% and 24 isolated examples. Importantly, this method was applied to prepare a key intermediate in the synthesis of GSK3368715 on multigram scale.

Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback.

Methane (CH4) and nitrous oxide (N2O) are major greenhouse gases that are predominantly generated by microbial activities in anoxic environments. N2O inhibition of methanogenesis has been reported, but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth yield and kinetic measurements and showed that micromolar concentrations of N2O suppress the growth of methanogens and CH4 production from major methanogenic substrate classes. Acetoclastic methanogenesis, estimated to account for two-thirds of the annual 1 billion metric tons of biogenic CH4, was most sensitive to N2O, with inhibitory constants (KI) in the range of 18-25μM, followed by hydrogenotrophic (KI, 60-90μM) and methylotrophic (KI, 110-130μM) methanogenesis. Dissolved N2O concentrations exceeding these KI values are not uncommon in managed (i.e. fertilized soils and wastewater treatment plants) and unmanaged ecosystems. Future greenhouse gas emissions remain uncertain, particularly from critical zone environments (e.g. thawing permafrost) with large amounts of stored nitrogenous and carbonaceous materials that are experiencing unprecedented warming. Incorporating relevant feedback effects, such as the significant N2O inhibition on methanogenesis, can refine climate models and improve predictive capabilities.

Jamming on convex deformable surfaces.

Jamming is a fundamental transition that governs the behavior of particulate media, including sand, foams and dense suspensions. Upon compression, such media change from freely flowing to a disordered, marginally stable solid that exhibits non-Hookean elasticity. While the jamming process is well established for fixed geometries, the nature and dynamics of jamming for a diverse class of soft materials and deformable substrates, including emulsions and biological matter, remains unknown. Here we propose a new scenario, metric jamming, where rigidification occurs on a surface that has been deformed from its ground state. Unlike classical jamming processes that exhibit discrete mechanical transitions, surprisingly we find that metric jammed states possess mechanical properties continuously tunable between those of classically jammed and conventional elastic media. The compact and curved geometry significantly alters the vibrational spectra of the structures relative to jamming in flat Euclidean space, and metric jammed systems also possess new types of vibrational mode that couple particle and shape degrees of freedom. Our work provides a theoretical framework that unifies our understanding of solidification processes that take place on deformable media and lays the groundwork to exploit jamming for the control and stabilization of shape in self-assembly processes.

Liquid-assisted mechanochemical synthesis of thioamide building blocks with the Lawesson reagent: ex situ monitoring and detection of intermediate polymorphs

Thioamidation of various classes of carboxamide substrates with Lawesson's reagent under liquid-assisted mechanical activation for the synthesis of relevant building blocks is described.

A C-H functionalization approach to diverse nitrogenous scaffolds through conjugate addition of catalytic allyliron nucleophiles.

Cyclopentadienyliron(ii) dicarbonyl complexes capable of coordinating to and enhancing the acidity of a range of unsaturated substrates have emerged as a new class of base-metal derived catalysts for C-H functionalization. In this manuscript, the iron-catalyzed C-H functionalization of allylic C(sp3)-H bonds using nitrogen containing α,β-unsaturated carbonyl compounds as coupling partners is reported. Employing a cationic cyclopentadienyliron dicarbonyl complex, this redox neutral process converts simple alkenes into allylic anion equivalents for 1,4-addition into maleimides, acyclic α,β-unsaturated imides, and vinylogous amides. The judicious pairing of pyridine and alkylamine bases with Lewis acid additives allowed each of these classes of substrates to be successfully employed, allowing for the formation of a diverse collection of cyclic and acyclic nitrogen-containing compounds featuring C-C unsaturation. The resulting Michael adducts can be further transformed into a variety of useful scaffolds such as allylated pyrroles, pyrrolidines, and carbocyclic acids.

Expedient radical phosphonylations via ligand to metal charge transfer on bismuth.

Bismuth, in spite of its low cost and low toxicity, has found limited application in organic synthesis. Although the photoactivity of Bi(iii) salts has been well studied, this has not been effectively exploited in photocatalysis. To date, only a single report exists for the Bi-based photocatalysis, wherein carbon centered radicals were generated using ligand to metal charge transfer (LMCT) on bismuth. In this regard, expanding the horizon of bismuth LMCT catalysis for the generation of heteroatom centered radicals, we hereby report an efficient radical phosphonylation using BiCl3 as the LMCT catalyst. Phosphonyl radicals generated via visible-light induced LMCT of BiCl3 were subjected to a variety of transformations like alkylation, amination, alkynylation and cascade cyclizations. The catalytic system tolerated a wide range of substrate classes, delivering excellent yields of the scaffolds. The reactions were scalable and required low catalytic loading of bismuth. Detailed mechanistic studies were carried out to probe the reaction mechanism. Diverse radical phosphonylations leading to the formation of sp3-C-P, sp2-C-P, sp-C-P, and P-N bonds in the current work present the candidacy of bismuth as a versatile photocatalyst for small molecule activation.

Monolayer Organic Crystals for Ultrahigh Performance Molecular Diodes.

Molecular diodes are of considerable interest for the increasing technical demands of device miniaturization. However, the molecular diode performance remains contact-limited, which represents a major challenge for the advancement of rectification ratio and conductance. Here, it is demonstrated that high-quality ultrathin organic semiconductors can be grown on several classes of metal substrates via solution-shearing epitaxy, with a well-controlled number of layers and monolayer single crystal over 1mm. The crystals are atomically smooth and pinhole-free, providing a native interface for high-performance monolayer molecular diodes. As a result, the monolayer molecular diodes show record-high rectification ratio up to 5 × 108 , ideality factor close to unity, aggressive unit conductance over 103 S cm-2 , ultrahigh breakdown electric field, excellent electrical stability, and well-defined contact interface. Large-area monolayer molecular diode arrays with 100% yield and excellent uniformity in the diode metrics are further fabricated. These results suggest that monolayer molecular crystals have great potential to build reliable, high-performance molecular diodes and deeply understand their intrinsic electronic behavior.

A type VII-secreted lipase toxin with reverse domain arrangement

The type VII protein secretion system (T7SS) is found in many Gram-positive bacteria and in pathogenic mycobacteria. All T7SS substrate proteins described to date share a common helical domain architecture at the N-terminus that typically interacts with other helical partner proteins, forming a composite signal sequence for targeting to the T7SS. The C-terminal domains are functionally diverse and in Gram-positive bacteria such as Staphylococcus aureus often specify toxic anti-bacterial activity. Here we describe the first example of a class of T7 substrate, TslA, that has a reverse domain organisation. TslA is widely found across Bacillota including Staphylococcus, Enterococcus and Listeria. We show that the S. aureus TslA N-terminal domain is a phospholipase A with anti-staphylococcal activity that is neutralised by the immunity lipoprotein TilA. Two small helical partner proteins, TlaA1 and TlaA2 are essential for T7-dependent secretion of TslA and at least one of these interacts with the TslA C-terminal domain to form a helical stack. Cryo-EM analysis of purified TslA complexes indicate that they share structural similarity with canonical T7 substrates. Our findings suggest that the T7SS has the capacity to recognise a secretion signal present at either end of a substrate.

Genetic and enzymatic characterization of Amy13E from Cellvibrio japonicus reclassifies it as a cyclodextrinase also capable of α-diglucoside degradation.

Cyclodextrinases are carbohydrate-active enzymes involved in the linearization of circular amylose oligosaccharides. Primarily thought to function as part of starch metabolism, there have been previous reports of bacterial cyclodextrinases also having additional enzymatic activities on linear malto-oligosaccharides. This substrate class also includes environmentally rare α-diglucosides such as kojibiose (α-1,2), nigerose (α-1,3), and isomaltose (α-1,6), all of which have valuable properties as prebiotics or low-glycemic index sweeteners. Previous genome sequencing of three Cellvibrio japonicus strains adapted to utilize these α-diglucosides identified multiple, but uncharacterized, mutations in each strain. One of the mutations identified was in the amy13E gene, which was annotated to encode a neopullulanase. In this report, we functionally characterized this gene and determined that it in fact encodes a cyclodextrinase with additional activities on α-diglucosides. Deletion analysis of amy13E found that this gene was essential for kojibiose and isomaltose metabolism in C. japonicus. Interestingly, a Δamy13E mutant was not deficient for cyclodextrin or pullulan utilization in C. japonicus; however, heterologous expression of the gene in E. coli was sufficient for cyclodextrin-dependent growth. Biochemical analyses found that CjAmy13E cleaved multiple substrates but preferred cyclodextrins and maltose, but had no activity on pullulan. Our characterization of the CjAmy13E cyclodextrinase is useful for refining functional enzyme predictions in related bacteria and for engineering enzymes for biotechnology or biomedical applications.IMPORTANCEUnderstanding the bacterial metabolism of cyclodextrins and rare α-diglucosides is increasingly important, as these sugars are becoming prevalent in the foods, supplements, and medicines humans consume that subsequently feed the human gut microbiome. Our analysis of a cyclomaltodextrinase with an expanded substrate range is significant because it broadens the potential applications of the GH13 family of carbohydrate active enzymes (CAZymes) in biotechnology and biomedicine. Specifically, this study provides a workflow for the discovery and characterization of novel activities in bacteria that possess a high number of CAZymes that otherwise would be missed due to complications with functional redundancy. Furthermore, this study provides a model from which predictions can be made why certain bacteria in crowded niches are able to robustly utilize rare carbon sources, possibly to gain a competitive growth advantage.

Moisture-Assisted Hydroboration of Nitriles and Conversion Thereof to N-Heterocyles and N-Containing Derivatives.

The recent revelation of hidden-borane catalysis has revolutionized the field of catalytic hydroboration in organic synthesis. Many nucleophilic reaction promoters, previously believed to be the catalysts, in fact primarily facilitated the formation of borane (BH3), which subsequently acted as the true catalyst. This revelation prompted us to explore the untapped potential of these unexpected transformations, with a view to simplify hydroboration using more cost-effective and environmentally friendly nucleophilic precatalysts. Via computational studies, we were able to identify that water can actually undertake that role. Herein, we report a study on the simple hydroboration of nitriles, a notoriously challenging yet synthetically valuable class of substrates, using nothing more than moisture as an activating agent. This moisture-assisted nitrile hydroboration process can seamlessly integrate with a range of downstream transformations in a one-pot fashion to produce valuable N-containing products such as symmetrical imines, thioureas, and bis(alcohol)amines as well as N-heterocycles such as pyrroles, pyridines, pyridinium salts, 2-iminothiazolines, and carbazoles.

The generation of detergent-insoluble clipped fragments from an ERAD substrate in mammalian cells

Proteostasis ensures the proper synthesis, folding, and trafficking of proteins and is required for cellular and organellar homeostasis. This network also oversees protein quality control within the cell and prevents accumulation of aberrant proteins, which can lead to cellular dysfunction and disease. For example, protein aggregates irreversibly disrupt proteostasis and can exert gain-of-function toxic effects. Although this process has been examined in detail for cytosolic proteins, how endoplasmic reticulum (ER)-tethered, aggregation-prone proteins are handled is ill-defined. To determine how a membrane protein with a cytoplasmic aggregation-prone domain is routed for ER-associated degradation (ERAD), we analyzed a new model substrate, TM-Ubc9ts. In yeast, we previously showed that TM-Ubc9ts ERAD requires Hsp104, which is absent in higher cells. In transient and stable HEK293 cells, we now report that TM-Ubc9ts degradation is largely proteasome-dependent, especially at elevated temperatures. In contrast to yeast, clipped TM-Ubc9ts polypeptides, which are stabilized upon proteasome inhibition, accumulate and are insoluble at elevated temperatures. TM-Ubc9ts cleavage is independent of the intramembrane protease RHBDL4, which clips other classes of ERAD substrates. These studies highlight an unappreciated mechanism underlying the degradation of aggregation-prone substrates in the ER and invite further work on other proteases that contribute to ERAD.

Rhodium(III)-Catalyzed C–H Activation in Indole: A Comprehensive Report (2017–2022)

AbstractIn the realm of synthetic organic chemistry, the catalysis of directed C–H activation by transition metals is an outstanding and efficient method for the synthesis of natural products, organic materials, and fundamental organic building blocks. Notably, this strategy has experienced remarkable advances in recent years, particularly in its application to various substrate classes, including the essential indole scaffold. Indole is a highly sought-after target in organic chemistry. The significance of indole extends beyond its use in total synthesis and drug discovery. It also serves as an important tool in the development of pharmaceutical agents, agrochemicals, and materials. By targeting indole, synthetic chemists can access a wide range of bioactive compounds, which opens new avenues for drug development and chemical biology research. The synthesis of structurally varied indoles has been greatly aided by the development of a comprehensive toolkit made possible by the use of C–H activation as a versatile functionalization platform. This review highlights the latest breakthroughs in rhodium-catalyzed C–H activation at the C2, C4, and C7 positions of the indole scaffold. These developments represent significant progress in the field and hold promising potential for further advances in the synthesis of indole-based compounds.1 Introduction2 The Development of Rhodium-Catalyzed C–H Activation3 General Mechanistic Introduction to Rh(III)-Catalyzed C–H Activation4 Direct C–H Functionalization of Indoles4.1 C2 Activation of Indoles4.2 C4 Activation of Indoles4.3 Dual C–H Activation Strategy4.4 C7 Activation of Indoles5 Conclusion

Protein arginine methyltransferase 1, a major regulator of biological processes.

Protein arginine methyltransferase 1 (PRMT1) is a major type I arginine methyltransferase that catalyzes the formation of monomethyl and asymmetric dimethylarginine in protein substrates. It was first identified to asymmetrically methylate histone H4 at the third arginine residue forming the H4R3me2a active histone mark. However, several protein substrates are now identified as being methylated by PRMT1. As a result of its association with diverse classes of substrates, PRMT1 regulates several biological processes like chromatin dynamics, transcription, RNA processing, and signal transduction. The review provides an overview of PRMT1 structure, biochemical features, specificity, regulation, and role in cellular functions. We discuss the genomic distribution of PRMT1 and its association with tRNA genes. Further, we explore the different substrates of PRMT1 involved in splicing. In the end, we discuss the proteins that interact with PRMT1 and their downstream effects in diseased states.

Effect of Fe–N–Cs as Catalytic Active Support for Platinum towards ORR in Acidic Environment

Metal-nitrogen-carbon (M–N–C) compounds such as Fe–N–Cs are currently the most promising platinum group metal free catalysts for oxygen reduction in acidic environment. Regarding the overriding goal of reducing PEMFC production costs by reducing the platinum content, the use of Fe–N–Cs as catalytic active support for low Pt amounts is investigated in this study. Activity and stability of Pt in different contents on a commercial Fe–N–C is compared to Pt on a typical carbon black. Pt nanoparticles are well-distributed on both support substrate classes. Although the electrochemical surface and mass activity of Pt is lower on Fe–N–C compared to carbon black, the Fe–N–C has a contribution to total ORR activity depending on the Pt/Fe–N–C ratio, which is quantified. In the low Pt content case of 1 wt%, the ORR activity is increased by factor of two in presence of Fe–N–C. This boosting effect on ORR activity is important for future strategies to lower the Pt content in PEMFCs.

ATP-dependent transporters: emerging players at the crossroads of immunity and metabolism.

Nearly 50 ATP-binding cassette (ABC) transporters are encoded by mammalian genomes. These transporters are characterized by conserved nucleotide-binding and hydrolysis (i.e., ATPase) domains, and power directional transport of diverse substrate classes - ions, small molecule metabolites, xenobiotics, hydrophobic drugs, and even polypeptides - into or out of cells or subcellular organelles. Although immunological functions of ABC transporters are only beginning to be unraveled, emerging literature suggests these proteins have under-appreciated roles in the development and function of T lymphocytes, including many of the key effector, memory and regulatory subsets that arise during responses to infection, inflammation or cancers. One transporter in particular, MDR1 (Multidrug resistance-1; encoded by the ABCB1 locus in humans), has taken center stage as a novel player in immune regulation. Although MDR1 remains widely viewed as a simple drug efflux pump in tumor cells, recent evidence suggests that this transporter fills key endogenous roles in enforcing metabolic fitness of activated CD4 and CD8 T cells. Here, we summarize current understanding of the physiological functions of ABC transporters in immune regulation, with a focus on the anti-oxidant functions of MDR1 that may shape both the magnitude and repertoires of antigen-specific effector and memory T cell compartments. While much remains to be learned about the functions of ABC transporters in immunobiology, it is already clear that they represent fertile new ground, both for the definition of novel immunometabolic pathways, and for the discovery of new drug targets that could be leveraged to optimize immune responses to vaccines and cancer immunotherapies.

Synthesis of Complex Diarylamines through a Ring-Opening Difunctionalization Strategy.

The diarylation and skeletal diversification of unstrained cyclic amines was exploited to expand and modify the favorable properties of this important substrate class with pivotal roles in drug discovery. Cyclic amines were employed in the synthesis of a novel class of amino-substituted diaryliodonium salts, which were converted to highly functionalized diarylamines through an atom-efficient one-pot N-arylation/ring opening reaction with external nucleophiles. The reaction proceeds through in situ formation of a diarylammonium intermediate that undergoes a nucleophilic ring opening by cleavage of the strong C-N bond. A wide variety of diarylamines was obtained through introduction of two different aryl groups of varied electronics, and the retained iodo-substituent enables downfield diversifications of the products. More than 20 nucleophiles, including amines, phenols, carboxylic acids, thiols and halides, were alkylated with high functional group tolerance, and the strategy proved efficient also in in late-stage functionalization of natural products and pharmaceuticals.

Synthesis of Complex Diarylamines through a Ring‐Opening Difunctionalization Strategy**

AbstractThe diarylation and skeletal diversification of unstrained cyclic amines was exploited to expand and modify the favorable properties of this important substrate class with pivotal roles in drug discovery. Cyclic amines were employed in the synthesis of a novel class of amino‐substituted diaryliodonium salts, which were converted to highly functionalized diarylamines through an atom‐efficient one‐pot N‐arylation/ring opening reaction with external nucleophiles. The reaction proceeds through in situ formation of a diarylammonium intermediate that undergoes a nucleophilic ring opening by cleavage of the strong C−N bond. A wide variety of diarylamines was obtained through introduction of two different aryl groups of varied electronics, and the retained iodo‐substituent enables downfield diversifications of the products. More than 20 nucleophiles, including amines, phenols, carboxylic acids, thiols and halides, were alkylated with high functional group tolerance, and the strategy proved efficient also in in late‐stage functionalization of natural products and pharmaceuticals.