Showing papers on "Substrate (chemistry) published in 2021"

Mechanism and dynamics of fatty acid photodecarboxylase

Abstract: Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.

Highly Sensitive and Reproducible SERS Substrates Based on Ordered Micropyramid Array and Silver Nanoparticles.

Abstract: The construction of a highly sensitive and reproducible surface-enhanced Raman scattering (SERS) substrate is the key factor that restricts its practical application. In this paper, a three-dimensional (3D) SERS substrate based on ordered micropyramid array and silver nanoparticles (MPA/AgNPs 3D-SERS) was constructed using the roll-to-plate embossing technology and a hydrothermal method, which provided an efficient and low-cost preparation process for the SERS substrate. Using rhodamine 6G (R6G) as a probe molecule, the performance of an MPA/AgNP 3D-SERS substrate was studied in detail, whose minimum detection limit was 10-12 M and the enhancement factor was calculated as 8.8 × 109, indicating its high sensitivity. In addition, the minimum relative standard deviation (RSD) for the MPA/AgNP 3D-SERS substrate was calculated as 4.99%, and SERS performance basically had no loss after 12 days of placement, which indicated that the prepared SERS substrate had excellent stability and repeatability. At last, the thiram detection application of the MPA/AgNP 3D-SERS substrate was also investigated. The results showed that the minimum detection limit was 1 × 10-7 M, and quantitative analysis of pesticide residues could be realized. This research could provide useful guidance for the efficient and low-cost fabrication of highly sensitive and reproducible SERS substrates.

Exclusive and ultrasensitive detection of formaldehyde at room temperature using a flexible and monolithic chemiresistive sensor.

Abstract: Formaldehyde, a probable carcinogen, is a ubiquitous indoor pollutant, but its highly selective detection has been a long-standing challenge. Herein, a chemiresistive sensor that can detect ppb-level formaldehyde in an exclusive manner at room temperature is designed. The TiO2 sensor exhibits under UV illumination highly selective detection of formaldehyde and ethanol with negligible cross-responses to other indoor pollutants. The coating of a mixed matrix membrane (MMM) composed of zeolitic imidazole framework (ZIF-7) nanoparticles and polymers on TiO2 sensing films removed ethanol interference completely by molecular sieving, enabling an ultrahigh selectivity (response ratio > 50) and response (resistance ratio > 1,100) to 5 ppm formaldehyde at room temperature. Furthermore, a monolithic and flexible sensor is fabricated successfully using a TiO2 film sandwiched between a flexible polyethylene terephthalate substrate and MMM overlayer. Our work provides a strategy to achieve exclusive selectivity and high response to formaldehyde, demonstrating the promising potential of flexible gas sensors for indoor air monitoring. Formaldehyde, a probable carcinogen, is a ubiquitous indoor pollutant, but its ultraselective detection has been a long-standing challenge. Here, the authors develop a chemiresistive sensor that can detect ppb-level formaldehyde in an exclusive manner at room temperature.

Enzyme-like Supramolecular Iridium Catalysis Enabling C−H Bond Borylation of Pyridines with meta-Selectivity

Abstract: The use of secondary interactions between substrates and catalysts is a promising strategy to discover selective transition metal catalysts for atom-economy C-H bond functionalization. The most powerful catalysts are found via trial-and-error screening due to the low association constants between the substrate and the catalyst in which small stereo-electronic modifications within them can lead to very different reactivities. To circumvent these limitations and to increase the level of reactivity prediction in these important reactions, we report herein a supramolecular catalyst harnessing Zn⋅⋅⋅N interactions that binds to pyridine-like substrates as tight as it can be found in some enzymes. The distance and spatial geometry between the active site and the substrate binding site is ideal to target unprecedented meta-selective iridium-catalyzed C-H bond borylations with enzymatic Michaelis-Menten kinetics, besides unique substrate selectivity and dormant reactivity patterns.

Comparative study on crystallographic orientation, precipitation, phase transformation and mechanical response of Ni-rich NiTi alloy fabricated by WAAM at elevated substrate heating temperatures

Abstract: In this investigation, a Ni-rich NiTi alloy was in-situ deposited with different substrate heating temperatures and the evolution of crystallographic orientation, precipitation, phase transformation, and mechanical responses were evaluated. The experimental results indicated that with the increment of substrate heating temperature from 150 °C to 350 °C, the average B2 grain size and the high angle grain boundaries (HAGBs) gradually increased from 53.44 μm to 85.38 μm and 53.6%–62.4%, respectively. The crystallographic texture exhibited a dominant, strong (001) orientation with comparatively weak (111) and (101) orientations in all conditions and the intensity of {100} increased slightly as the substrate heating temperature increased. Moreover, Ni4Ti3 precipitates with an inhomogeneous size distribution were identified within the B2 NiTi matrix. Increasing the substrate heating temperature coarsened the Ni4Ti3 precipitates. All the phase transformation temperatures increased when the substrate heating temperature increased, indicating that the martensitic transformation is more likely to occur. As the substrate heating temperature increased from 150 °C to 350 °C, the yield stress and ultimate tensile stress decreased from 683.9 to 513.1 MPa and 855.2 to 743.8 MPa, respectively, and the ductility decreased from 6.90% to 6.13%. In addition, a remarkable eir, poor recovery ratio and a broad stress hysteresis were obtained during the initial deformation of the cyclic loading-unloading tension. The highest recoverable strain (ere), recovery ratio and elastic energy storage efficiency (ƞ) were obtained in samples processed with the lowest substrate heating temperature. These findings provide useful references concerning process optimization in fabricating Ni-rich NiTi components by WAAM with acceptable microstructure and mechanical properties.

Comparative Biochemistry of Four Polyester (PET) Hydrolases

Abstract: The potential of bioprocessing in a circular plastic economy has strongly stimulated research into the enzymatic degradation of different synthetic polymers. Particular interest has been devoted to the commonly used polyester, poly(ethylene terephthalate) (PET), and a number of PET hydrolases have been described. However, a kinetic framework for comparisons of PET hydrolases (or other plastic-degrading enzymes) acting on the insoluble substrate has not been established. Herein, we propose such a framework, which we have tested against kinetic measurements for four PET hydrolases. The analysis provided values of kcat and KM , as well as an apparent specificity constant in the conventional units of M-1 s-1 . These parameters, together with experimental values for the number of enzyme attack sites on the PET surface, enabled comparative analyses. A variant of the PET hydrolase from Ideonella sakaiensis was the most efficient enzyme at ambient conditions; it relied on a high kcat rather than a low KM . Moreover, both soluble and insoluble PET fragments were consistently hydrolyzed much faster than intact PET. This suggests that interactions between polymer strands slow down PET degradation, whereas the chemical steps of catalysis and the low accessibility associated with solid substrate were less important for the overall rate. Finally, the investigated enzymes showed a remarkable substrate affinity, and reached half the saturation rate on PET when the concentration of attack sites in the suspension was only about 50 nM. We propose that this is linked to nonspecific adsorption, which promotes the nearness of enzyme and attack sites.

Substrate inhibition by the blockage of product release and its control by tunnel engineering

Abstract: Substrate inhibition is the most common deviation from Michaelis-Menten kinetics, occurring in approximately 25% of known enzymes. It is generally attributed to the formation of an unproductive enzyme-substrate complex after the simultaneous binding of two or more substrate molecules to the active site. Here, we show that a single point mutation (L177W) in the haloalkane dehalogenase LinB causes strong substrate inhibition. Surprisingly, a global kinetic analysis suggested that this inhibition is caused by binding of the substrate to the enzyme-product complex. Molecular dynamics simulations clarified the details of this unusual mechanism of substrate inhibition: Markov state models indicated that the substrate prevents the exit of the halide product by direct blockage and/or restricting conformational flexibility. The contributions of three residues forming the possible substrate inhibition site (W140A, F143L and I211L) to the observed inhibition were studied by mutagenesis. An unusual synergy giving rise to high catalytic efficiency and reduced substrate inhibition was observed between residues L177W and I211L, which are located in different access tunnels of the protein. These results show that substrate inhibition can be caused by substrate binding to the enzyme-product complex and can be controlled rationally by targeted amino acid substitutions in enzyme access tunnels.

Mediator-Enabled Electrocatalysis with Ligandless Copper for Anaerobic Chan-Lam Coupling Reactions.

Abstract: Simple copper salts serve as catalysts to effect C-X bond-forming reactions in some of the most utilized transformations in synthesis, including the oxidative coupling of aryl boronic acids and amines. However, these Chan-Lam coupling reactions have historically relied on chemical oxidants that limit their applicability beyond small-scale synthesis. Despite the success of replacing strong chemical oxidants with electrochemistry for a variety of metal-catalyzed processes, electrooxidative reactions with ligandless copper catalysts are plagued by slow electron-transfer kinetics, irreversible copper plating, and competitive substrate oxidation. Herein, we report the implementation of substoichiometric quantities of redox mediators to address limitations to Cu-catalyzed electrosynthesis. Mechanistic studies reveal that mediators serve multiple roles by (i) rapidly oxidizing low-valent Cu intermediates, (ii) stripping Cu metal from the cathode to regenerate the catalyst and reveal the active Pt surface for proton reduction, and (iii) providing anodic overcharge protection to prevent substrate oxidation. This strategy is applied to Chan-Lam coupling of aryl-, heteroaryl-, and alkylamines with arylboronic acids in the absence of chemical oxidants. Couplings under these electrochemical conditions occur with higher yields and shorter reaction times than conventional reactions in air and provide complementary substrate reactivity.

Oxidative additions of alkynyl/vinyl iodides to gold and gold-catalyzed vinylation reactions triggered by the MeDalphos ligand

Abstract: The hemilabile Ad2P(o-C6H4)NMe2 ligand promotes fast, quantitative and irreversible oxidative addition of alkynyl and vinyl iodides to gold. The reaction is general. It works with a broad range of substrates of various electronic bias and steric demand, and proceeds with complete retention of stereochemistry from Z and E vinyl iodides. Both alkynyl and vinyl iodides react faster than aryl iodides. The elementary step is amenable to catalysis. Oxidative addition of vinyl iodides to gold and π-activation of alkenols (and N-alkenyl amines) at gold have been combined to achieve hetero-vinylation reactions. A number of functionalized heterocycles, i.e. tetrahydrofuranes, tetrahydropyranes, oxepanes and pyrrolidines were obtained thereby (24 examples, 87% average yield). Taking advantage of the chemoselectivity for vinyl iodides over aryl iodides, sequential transformations involving first a hetero-vinylation step and then a C–N coupling, a C–C coupling or an heteroarylation were achieved from a vinyl/aryl bis-iodide substrate.

Bound oxygen-atom transfer endows peroxidase-mimic M-N-C with high substrate selectivity

Abstract: Advances in nanoscience have stimulated the wide exploration of nanozymes as alternatives to enzymes. Nonetheless, nanozymes often catalyze multiple reactions and are not specialized to a specific substrate, restricting their broad application. Here, we report that the substrate selectivity of the peroxidase-mimic M-N-C can be significantly altered via forming bound intermediates with variable interactions with substrates according to the type of metal. Taking two essential reactions in chemical sensing as an example, Fe-N-C and Co-N-C showed opposite catalytic selectivity for the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) and 3-aminophthalhydrazide (luminol), respectively, by factors of up to 200-fold. It was revealed that specific transition metal-N coordination was the origin of the selective activation of H2O2 forming critically bound oxygen intermediates (M[double bond, length as m-dash]O) for oxygen-atom transfer and the consequent oxidization of substrates. Notably, owing to the embedded ligands in the rigid graphitic framework, surprisingly, the selectivity of M-N-C was even superior to that of commonly used horseradish peroxidase (HRP).

Microbial Fuel Cell: Recent Developments in Organic Substrate Use and Bacterial Electrode Interaction

Abstract: A new bioelectrochemical approach based on metabolic activities inoculated bacteria, and the microbial fuel cell (MFC) acts as biocatalysts for the natural conversion to energy of organic substrates. Among several factors, the organic substrate is the most critical challenge in MFC, which requires long-term stability. The utilization of unstable organic substrate directly affects the MFC performance, such as low energy generation. Similarly, the interaction and effect of the electrode with organic substrate are well discussed. The electrode-bacterial interaction is also another aspect after organic substrate in order to ensure the MFC performance. The conclusion is based on this literature view; the electrode content is also a significant challenge for MFCs with organic substrates in realistic applications. The current review discusses several commercial aspects of MFCs and their potential prospects. A durable organic substrate with an efficient electron transfer medium (anode electrode) is the modern necessity for this approach.

A sensitive colorimetric sensor based on one-pot preparation of h-Fe3O4@ppy with high peroxidase-like activity for determination of glutathione and H2O2

Abstract: At present, artificial mimic enzyme has become a powerful substitute for natural enzyme. In particular, the biosensors based on nano-enzymes have been the focus of current research. Herein, a novel magnetic ternary nanocomposite hemin-Fe3O4@polypyrrole (h-Fe3O4@ppy) was synthesized by chemical oxidation polymerization. The results showed that the h-Fe3O4@ppy had stronger peroxidase activity than Fe3O4 nanoparticles (Fe3O4 NPs) and h-ppy NPs, and was indicated by Michaelis-Menten constant (Km) and maximum initial velocity (Vmax). Therefore, we used h-Fe3O4@ppy catalyzing H2O2 to oxidize the chromogenic substrate TMB, and built Hydrogen peroxide (H2O2) and Glutathione (GSH) colorimetric biosensors with the help of signal intrinsic exponential amplification and easy operation. The controllable catalysis was realized by h-Fe3O4@ppy which was prone to separation. The method of removing h-Fe3O4@ppy by magnetic separation effectively eliminated the effect of residual catalysis when terminating the reaction. The sensor was then applied to the determination of GSH in biological samples from acute coronary syndrome patients. The linear ranges of H2O2 and GSH were 0.2–100 μM and 0.5–80 μM, respectively. The detection limits of H2O2 and GSH are 0.18 μM and 0.15 μM, respectively. This research not only proposes a new type of nanoenzyme, but also shows the multiple advantages of magnetic nano-enzymes for the construction of biosensors.

Selective Photodimerization in a Cyclodextrin Metal-Organic Framework.

Abstract: For the most part, enzymes contain one active site wherein they catalyze in a serial manner chemical reactions between substrates both efficiently and rapidly. Imagine if a situation could be created within a chiral porous crystal containing trillions of active sites where substrates can reside in vast numbers before being converted in parallel into products. Here, we report how it is possible to incorporate 1-anthracenecarboxylate (1-AC-) as a substrate into a γ-cyclodextrin-containing metal-organic framework (CD-MOF-1), where the metals are K+ cations, prior to carrying out [4+4] photodimerizations between pairs of substrate molecules, affording selectively one of four possible regioisomers. One of the high-yielding regioisomers exhibits optical activity as a result of the presence of an 8:1 ratio of the two enantiomers following separation by high-performance liquid chromatography. The solid-state superstructure of 1-anthracenecarboxylate potassium salt (1-ACK), which is co-crystallized with γ-cyclodextrin, reveals that pairs of substrate molecules are not only packed inside tunnels between spherical cavities present in CD-MOF-1, but also stabilized-in addition to hydrogen-bonding to the C-2 and C-3 hydroxyl groups on the d-glucopyranosyl residues present in the γ-cyclodextrin tori-by combinations of hydrophobic and electrostatic interactions between the carboxyl groups in 1-AC- and four K+ cations on the waistline between the two γ-cyclodextrin tori in the tunnels. These non-covalent bonding interactions result in preferred co-conformations that account for the highly regio- and enantioselective [4+4] cycloaddition during photoirradiation. Theoretical calculations, in conjunction with crystallography, support the regio- and stereochemical outcome of the photodimerization.

Mechanism of substrate transport and inhibition of the human LAT1-4F2hc amino acid transporter.

Abstract: LAT1 (SLC7A5) is one of the representative light chain proteins of heteromeric amino acid transporters, forming a heterodimer with its heavy chain partner 4F2hc (SLC3A2). LAT1 is overexpressed in many types of tumors and mediates the transfer of drugs and hormones across the blood-brain barrier. Thus, LAT1 is considered as a drug target for cancer treatment and may be exploited for drug delivery into the brain. Here, we synthesized three potent inhibitors of human LAT1, which inhibit transport of leucine with IC50 values between 100 and 250 nM, and solved the cryo-EM structures of the corresponding LAT1-4F2hc complexes with these inhibitors bound at resolution of up to 2.7 or 2.8 A. The protein assumes an outward-facing occluded conformation, with the inhibitors bound in the classical substrate binding pocket, but with their tails wedged between the substrate binding site and TM10 of LAT1. We also solved the complex structure of LAT1-4F2hc with 3,5-diiodo-l-tyrosine (Diiodo-Tyr) at 3.4 A overall resolution, which revealed a different inhibition mechanism and might represent an intermediate conformation between the outward-facing occluded state mentioned above and the outward-open state. To our knowledge, this is the first time that the outward-facing conformation is revealed for the HAT family. Our results unveil more important insights into the working mechanisms of HATs and provide a structural basis for future drug design.

Protease Biosensor by Conversion of a Homogeneous Assay into a Surface-Tethered Electrochemical Analysis Based on Streptavidin–Biotin Interactions

Abstract: This work proposed a new sensing strategy for protease detection by converting a homogeneous assay into a surface-tethered electrochemical analysis. Streptavidin (SA), a tetramer protein, was used as the sensing unit based on the SA-biotin coupling chemistry. Caspase-3 was used as the model analyte, and a biotinylated peptide with a sequence of biotin-GDEVDGK-biotin was designed as the substrate. Specifically, the peptide substrate could induce an assembly of SA to form (SA-biotin-GDEVDGK-biotin)n aggregates through SA-biotin interactions, which was confirmed by atomic force microscopy (AFM). The peptide substrate-induced assembly of SA was facilely initiated on an electrode-liquid surface by modification of the electrode with SA. The in situ formation of (SA-biotin-GDEVDGK-biotin)n aggregates created an insulating layer, thus limiting the electron transfer of ferricyanide. Once the peptide substrate was cleaved into two shorter fragments (biotin-GDEVD and GK-biotin) by caspase-3, the resulting products would compete with biotin-GDEVDGK-biotin to bind SA proteins immobilized on the electrode surface and distributed in a solution, thus preventing the in situ formation of (SA-biotin-GDEVDGK-biotin)n assemblies. With the simple principle of the substrate-induced assembly of SA, a dual-signal amplification was achieved with improved sensitivity. Taking advantage of high sensitivity, simple principle, and easy operation, this method can be augmented to design various surface-tethered biosensors for practical applications.