Intramolecular Rearrangement Research Articles

Molecular basis of enzymatic nitrogen-nitrogen formation by a family of zinc-binding cupin enzymes

Molecules with a nitrogen-nitrogen (N-N) bond in their structures exhibit various biological activities and other unique properties. A few microbial proteins are recently emerging as dedicated N-N bond forming enzymes in natural product biosynthesis. However, the details of these biochemical processes remain largely unknown. Here, through in vitro biochemical characterization and computational studies, we report the molecular basis of hydrazine bond formation by a family of di-domain enzymes. These enzymes are widespread in bacteria and sometimes naturally exist as two standalone enzymes. We reveal that the methionyl-tRNA synthase-like domain/protein catalyzes ATP-dependent condensation of two amino acids substrates to form a highly unstable ester intermediate, which is subsequently captured by the zinc-binding cupin domain/protein and undergoes redox-neutral intramolecular rearrangement to give the N-N bond containing product. These results provide important mechanistic insights into enzymatic N-N bond formation and should facilitate future development of novel N-N forming biocatalyst.

Accelerated Dissipation of Free and Immobilized Water Facilitating the Intramolecular Dehydration of N-Xylosamine and Conversion Improvement of the Amadori Rearrangement Product of Aspartic Acid-Xylose Reaction.

Compared to the method of aqueous Maillard reaction at atmospheric pressure tandem vacuum concentration, a coupling dehydration method combining spray drying and vacuum drying was used to increase aspartic acid-xylose conversion to the Amadori rearrangement product (ARP). The water activity and moisture states were found as effective indicators to characterize the degree of dehydration of Maillard reaction intermediates and efficient formation of ARP. During the vacuum drying process, the water activity of the product powder decreased significantly. Because the formation of ARP was accompanied by intramolecular dehydration, combining spray drying and vacuum drying increased the proportion of bound water in the vacuum-dried product. Free water was easily dissipated via dehydration, which then converted the immobilized water continuously to free water, and the decreased immobilized water further converted the bound water to immobilized water. The reduction in bound water contributed to the intramolecular dehydration of N-substituted d-xylosamine, which would further be transformed to be the ARP through an intramolecular rearrangement. The yield of ARP was increased from 1.68 to 21.53% after spray drying. The ARP yield was substantially increased up to 77.9% by subsequent vacuum drying.

Unlocking the Friedel-Crafts arylation of primary aliphatic alcohols and epoxides driven by hexafluoroisopropanol

Unlocking the Friedel-Crafts arylation of primary aliphatic alcohols and epoxides driven by hexafluoroisopropanol

Oxidative cleavage of polyunsaturated fatty acid chains via dioxygenation/pseudoperoxidation by 15-lipoxygenase

Aberrant progression of one-electron reduction of fatty acid hydroperoxides in cells is thought to be responsible for cell death, such as ferroptosis caused by reactive carbonyl compounds and hydrocarbon radicals generated through the cleavage of C-C bonds of fatty acid alkoxyl radicals belonging to oxygen-centered radicals. In the present study, we investigated the mechanism underlying the oxidative cleavage of polyunsaturated fatty acid chains by 15-lipoxygenase under anaerobic conditions using soybean 15-lipoxygenase as a model enzyme. The apparent reaction rate constant of lipoxygenase(Fe2+) with 13-hydroperoxyoctadecadienoic acid (13-HpODE) was approximately 7.3 times higher than that with 9-HpODE. The production of 13-oxo-tridecadienoic acid (13-OTA) in this reaction was remarkably inhibited in the presence of a five-membered nitroxyl radical, 3-carbamoyl-2,2,5,5-tetramethyl-3-pyrroline-N-oxyl (CmΔP), which is a specific spin-trapping agent for carbon-centered radicals. The trapped adduct appeared to be a CmΔP adduct with a linoleate epoxyallyl radical, which was derived from the linoleate alkoxyl radical through intramolecular rearrangement at the reaction site on the enzyme. Furthermore, 13-OTA production in the α-linolenate hydroperoxide/lipoxygenase(Fe2+) system was six times higher than that in the linoleate hydroperoxide/lipoxygenase(Fe2+) system. Based on these facts, we hypothesized that under anaerobic conditions, the fatty acid epoxyallyl radical at the reaction site on the enzyme spontaneously degrades into reactive carbonyl compounds and hydrocarbon radicals through the cleavage of C-C bonds. In conclusion, radical scavengers against carbon-centered radicals should inhibit the lipoxygenase-inducing cell death through preventing the cleavage of C-C bond of fatty acid epoxyallyl radicals.

A Selective C-C Bond Cleavage Strategy Promoted by Visible Light.

A new visible-light-promoted reaction between aryldiazoacetates and 1,3-diketones allows good yields and selectivities for C-C bond insertions, leading to the corresponding 1,4-dicarbonyl compounds. This transformation is straightforward and highly practical. It tolerates air and moisture and does not require the use of any metals. Mechanistic investigations support the involvement of a key cyclopropanol intermediate derived from an intramolecular rearrangement.

Intramolecular amination via acid-catalyzed rearrangement of azides: a potent alternative to intermolecular direct electrophilic route.

Although acid-catalyzed intramolecular rearrangement of organic azides is an attractive route to amines, its mechanism and synthetic prospective are still debated. Herein, through computational and experimental studies, we demonstrated that azide intramolecular rearrangement could serve as a potent synthetic route to a sought-after amine functionality including preparation of difficult to access and valuable heterocyclic amines. Using quantum chemical calculations at MP2/aug-cc-pVTZ and B3LYP/aug-cc-pVDZ levels, we discovered that this reaction proceeds via a concerted transition state with nitrogen elimination and alkyl/aryl migration occurring at the same time. Two conformers of protonated azides - syn- and anti- - were shown to precede corresponding transition states. It was shown that the reaction follows Curtin-Hammett scenario as the energy gap required for conformer interconversion was substantially lower than activation barrier of either transition state. Intramolecular amination via azide rearrangement was predicted to be a selective process with migratory aptitude increasing in a row alkyl<Ar-EWG<Ar-EDG (EWG - electron withdrawing group; EDG - electron donating group), which was supported by experimental results. We demonstrated experimentally that organic azides can be generated from stilbenes in situ and selectively undergo rearrangement to corresponding amines in a cascade fashion via amino-dealkenylation reaction.

Obtaining a composite material based on quartz woven filler and pyrolysis matrix of organosilicon resin

The relevance of the study is conditioned by the fact that the most popular and irreplaceable materials that have found wide application in the aerospace industry are composites based on quartz materials. These materials are distinguished by their high mechanical and electrical strength, chemical and corrosion resistance. In this regard, it is of interest to obtain a composite material that combines a low specific gravity, processability of polymers, and thermal stability of ceramics. The aim of this work was to study the effect of the temperature of thermal oxidative destruction of a polymer binder, which is a semi-finished product of a pyrolysis matrix, on the electrophysical parameters of a composite material. The paper investigates a composite material based on woven quartz material with a pyrolysis matrix of an organosilicon binder and functional additives. This composite was considered as a material for creating an electric rocket engine chamber. Thermogravimetric analysis was used to evaluate the effect of the temperature of thermooxidative degradation of the polymer binder on the electro-physical parameters of the obtained material. The tests were carried out according to standard test methods on an Instron 5969 universal testing machine with Bluehill software until the samples failed. In the course of the study, it was found that the processes that occur up to 400°C are mainly associated with the course of the reaction for non-entered functional groups, the telomerisation reaction, intramolecular rearrangement of macromolecules and the removal of low-boiling substances. According to the results of the study, the obtained characteristics of the test material turned out to be suitable for its use in structural elements of electric propulsion engines.

Lectin-Triggered Aggregation of Glyco-Gold Nanoprobes for Activity-based Sensing of Hydrogen Peroxide by the Naked Eye.

The purpose of this study was to develop a colorimetric assay for detecting hydrogen peroxide (H2 O2 ) through a combination of using an aryl boronate (AB) derivative and gold nanoparticles (AuNPs). The unique optical property of AuNPs is applied to design a detection probe. The aggregation of AuNPs could be directly observed as a color change by the naked eye. A mannoside-boronate-sulfide (MBS) ligand was designed that contains an arylboronate (AB), a mannoside, and a thiol group. The thiol group bonds covalently with the surface of AuNPs to obtain MBS@AuNPs. The mannoside moiety recognizes concanavalin A (Con A), a lectin with four carbohydrate recognition sites that can specifically recognize the non-reducing end of an α-D-mannoside or α-D-glucoside structure. The AB structure on MBS first reacts with H2 O2 and then inserts an oxygen atom in the B-H bond, which triggers intramolecular electron rearrangement to cleave the covalent bond, resulting in a MBSt mixture. The MBS or MBSt is then modified to citrate-coated AuNPs (c-AuNPs) to have MBS@AuNPs or MBSt@AuNPs. When the MBS@AuNPs are incubated with Con A, the Con A recognizes multiple mannosides on the surface of the MBS@AuNPs. Subsequently, the MBS@AuNPs aggregate and the solution's color changes from red to purple, but this color change does not occur in the case of MBSt@AuNPs. The phenomenon can be observed by the naked eye.

A Sensitive Fluorescent Probe for Homocysteine/Cysteine in Pure Aqueous Media and Mitochondria

AbstractBiothiols, involving homocysteine (Hcy), cysteine (Cys), and glutathione (GSH), are very important in physiological and pathological processes and play critical roles in the sustainment of the cellular equilibrium. In order to grasp more information about physiological and pathological processes and make new advances in the medical industry, it′s indispensible to develop more useful tools to detect biothiols. Herein, we have successfully prepared a novel mitochondrial homocysteine/cysteine‐selective fluorescent probe. Based on nucleophilic aromatic substitution (SNAr) and intramolecular rearrangement cascade reactions, this fluorescent probe shows not only a mitochondria‐targeting property but also a stable function in pure aqueous media with rapid and sensitive responses toward Hcy/Cys. For one thing, it is able to realize fluorescence imaging of Hcy/Cys in mitochondria. For another, we can acquire information about biothiol‐relevant redox status via this potential probe. We hope this probe will help us to broaden our knowledge about the effects of biothiols especially Hcy/Cys.

Elucidating the Cooperative Roles of Water and Lewis Acid-Base Pairs in Cascade C-C Coupling and Self-Deoxygenation Reactions.

Water plays pivotal roles in tailoring reaction pathways in many important reactions, including cascade C–C bond formation and oxygen elimination. Herein, a kinetic study combined with complementary analyses (DRIFTS, isotopic study, 1H solid-state magic angle spinning nuclear magnetic resonance) and density functional theory (DFT) calculations are performed to elucidate the roles of water in cascade acetone-to-isobutene reactions on a ZnxZryOz mixed metal oxide with balanced Lewis acid–base pairs. Our results reveal that the reaction follows the acetone–diacetone alcohol–isobutene pathway. Isobutene is produced through an intramolecular rearrangement of the eight-membered ring intermediate formed via the adsorption of diacetone alcohol on the Lewis acid–base pairs in the presence of cofed water. OH adspecies, formed by the dissociative adsorption of water on the catalyst surface, were found to distort diacetone alcohol’s hydroxyl functional group toward its carbonyl functional group and facilitate the intramolecular rearrangement of diacetone alcohol to form isobutene. In the absence of water, diacetone alcohol binds strongly to the Lewis acid site, e.g., at a Zr4+ site, via its carbonyl functional group, leading to its dramatic structural distortion and further dehydration reaction to form mesityl oxide as well as subsequent polymerization reactions and the formation of coke. The present results provide insights into the cooperative roles of water and Lewis acid–base pairs in catalytic upgrading of biomass to fuels and chemicals.

Synthesis of 10H‐Indolo[1,2‐a]indole Derivatives via Intramolecular Cycloaddition and H‐Migration

AbstractA novel method for synthesizing 10H‐indolo[1,2‐a]indole derivatives is reported here. All products are prepared by applying the intramolecular cyclization strategy at room temperature. The reaction was realized through I2/ZnI2 catalyzed intramolecular nucleophilic addition, hydrogen migration, and rearrangement procedures. The electronic effect and steric hindrance have a significant influence on the reactivity. Moreover, the synthetic value of 10H‐indolo[1,2‐a]indole was also exemplified by the selective decarboxylation and aromatization.

Developing a dual-site fluorescent probe for simultaneously discriminating Cys/Hcy and GSH, and visualizing metabolism of Cys to SO2

Biothiols as sulfur-containing active substances -play an important physiological and pathological function in organisms, however their specific markers in situ is a big challenging because they have high reactivity, the nature of the short half-life. Among of which due to their similar structure and properties, in particular, the research on their special physiological function is limited. In our study, we designed two biothiol nucleophilic substitution reaction sites in the benzene ring of SBD-Cl. Because of the conjugate effect of Cl, the para-sulfonic acid activated C was inactivated, the nucleophilic substitution of biothiol and Cl occurred, further, the intramolecular rearrangement occurred between the amino and sulfhydryl of Cys/Hcy, and the yellow fluorescence of SBD was released. However, GSH with large structure could not undergo intramolecular rearrangement, so there was no emission of yellow fluorescence, thus, Cys/Hcy and GSH can be detected distingusihly. In the above, adding SO2 can quench the red emission of benzopyrylium. In this way, we visualized the metabolism process from Cys to sulfur dioxide in the mitochondria with the probe. The above metabolic processes were further studied in zebrafish and tissues, and found the probe imaged tissue to a depth of 80 μm.

Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering.

Production of industrially relevant compounds in microbial cell factories can employ either genomes or plasmids as an expression platform. Selection of plasmids as pathway carriers is advantageous for rapid demonstration but poses a challenge of stability. Yarrowia lipolytica has attracted great attention in the past decade for the biosynthesis of chemicals related to fatty acids at titers attractive to industry, and many genetic tools have been developed to explore its oleaginous potential. Our recent studies on the autonomously replicating sequences (ARSs) of nonconventional yeasts revealed that the ARSs from Y. lipolytica showcase a unique structure that includes a previously unannotated sequence (spacer) linking the origin of replication (ORI) and the centromeric (CEN) element and plays a critical role in modulating plasmid behavior. Maintaining a native 645-bp spacer yielded a 2.2-fold increase in gene expression and 1.7-fold higher plasmid stability compared to a more universally employed minimized ARS. Testing the modularity of the ARS sub-elements indicated that plasmid stability exhibits a pronounced cargo dependency. Instability caused both plasmid loss and intramolecular rearrangements. Altogether, our work clarifies the appropriate application of various ARSs for the scientific community and sheds light on a previously unexplored DNA element as a potential target for engineering Y. lipolytica.

On-Surface Synthesis of One-Dimensional Coordination Polymers with Tailored Magnetic Anisotropy.

One-dimensional (1D) metalloporphyrin polymers can exhibit magnetism, depending on the central metal ion and the surrounding ligand field. The possibility of tailoring the magnetic signal in such nanostructures is highly desirable for potential spintronic devices. We present low-temperature (4.2 K) scanning tunneling microscopy and spectroscopy (LT-STM/STS) in combination with high-resolution atomic force microscopy (AFM) and a density functional theory (DFT) study of a two-step synthetic protocol to grow a robust Fe-porphyrin-based 1D polymer on-surface and to tune its magnetic properties. A thermally assisted Ullmann-like coupling reaction of Fe(III)diphenyl-bromine-porphyrin (2BrFeDPP-Cl) on Au(111) in ultra-high vacuum results in long (up to 50 nm) 1D metal-organic wires with regularly distributed magnetic and (electronically) independent porphyrins units, as confirmed by STM images. Thermally controlled C-H bond activation leads to conformational changes in the porphyrin units, which results in molecular planarization steered by 2D surface confinement, as confirmed by high-resolution AFM images. Spin-flip STS images in combination with DFT self-consistent spin-orbit coupling calculations of porphyrin units with different structural conformations reveal that the magnetic anisotropy of the triplet ground state of the central Fe ion units drops down substantially upon intramolecular rearrangements. These results point out to new opportunities for realizing and studying well-defined 1D organic magnets on surfaces and demonstrate the feasibility of tailoring their magnetic properties.

Electrosynthesis of 1,4-bis(diphenylphosphanyl) tetrasulfide via sulfur radical addition as cathode material for rechargeable lithium battery

Organic electrodes are promising as next generation energy storage materials originating from their enormous chemical diversity and electrochemical specificity. Although organic synthesis methods have been extended to a broad range, facile and selective methods are still needed to expose the corners of chemical space. Herein, we report the organopolysulfide, 1,4-bis(diphenylphosphanyl)tetrasulfide, which is synthesized by electrochemical oxidation of diphenyl dithiophosphinic acid featuring the cleavage of a P–S single bond and a sulfur radical addition reaction. Density functional theory proves that the external electric field triggers the intramolecular rearrangement of diphenyl dithiophosphinic acid through dehydrogenation and sulfur migration along the P–S bond axis. Impressively, the Li/bis(diphenylphosphanyl)tetrasulfide cell exhibits the high discharge voltage of 2.9 V and stable cycling performance of 500 cycles with the capacity retention of 74.8%. Detailed characterizations confirm the reversible lithiation/delithiation process. This work demonstrates that electrochemical synthesis offers the approach for the preparation of advanced functional materials.

Distinguishable multi-substance detection based on three-channel NIR fluorescent probe in physiology and pathology of living cells and zebrafish

Mitochondria is the main organelle for the production of reactive sulfur species (RSS), such as homocysteine (Hcy), cysteine (Cys), glutathione (GSH) and sulfur dioxide (SO2). These compounds participate in a large number of physiological processes and play an extremely important role in maintaining the balance of life systems. Abnormal concentration and metabolism are closely related to many diseases. Due to their similarities in chemical properties, it is challenging to develop a single fluorescent probe to distinguish them simultaneously. Here, we synthesized the probe PI-CONBD with three fluorophores, NBD-Cl and benzopyranate as the reaction sites of GSH/Cys/Hcy and SO2, respectively. Three biothiols all could cleavage ether bond to release benzopyrylium and coumarin moiety, which emitted red and blue fluorescence, but Cys/Hcy also could do intramolecular rearrangement after nucleophilic substitution, resulting in yellow fluorescence. Thus the probe can distinguish Cys/Hcy and GSH. Subsequently, only SO2 could quench red fluorescence by adding CC of benzopyrylium. The probe also could localize well in mitochondria by oxonium ion for all kinds of cells. The probe not only could detect above sulfur-containing active substances of intracellular and extracellular but also monitor the level of them under oxidative stress and apoptosis process in living cells and zebrafish.

Rh(II)-catalyzed Denitrogenative Cascade of 1,2,3-Triazolyl Propiolates and Indoles: Access to Butenolide Tethered Homotryptamines.

An efficient Rh(II)-catalyzed denitrogenative reaction of indoles with 1,2,3-triazolyl propiolates has been developed. This methodology provides facile access to butenolide tethered homotryptamines in good to excellent yields under operationally simple conditions and features a broad substrate scope. Overall, the reaction sequence involves the formation of three new bonds (two C-C and one C-O) in a nucleophilic cascade manner. Additionally, an intramolecular rearrangement of these derivatives to thermodynamically more stable butenolides is also demonstrated.

N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement.

The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the FeII-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent FeIV═O species. In the catalytic reaction pathway, the O2 binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the Cε-Nω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.

Dissipation and transformation of the diamide insecticide cyantraniliprole in ornamental snapdragon (Antirrhinum majus)

Dissipation and transformation of cyantraniliprole, a new diamide class of insecticides, were investigated under greenhouse conditions, using snapdragon (Antirrhinum majus) as the model plant. Dissipation of cyantraniliprole in treated leaves was found to be dependent upon application methods (foliar spray versus soil drench) and doses (high versus low dose), with the parent insecticide being the major residue at various sampling points. A high-dose foliar application resulted in pesticide residue of 6.7–23.8 μg/g foliar fresh weight over 8 weeks of treatments, while in soil drench treatment the residue varied from 0.8 to 1.4 μg/g. However, the residue contents were similar between the two application methods at a low application dose. The transformation pathways of cyantraniliprole were primarily intramolecular rearrangements, with IN-J9Z38 being the major metabolite across treatments. Several other metabolites were also identified, some of which were unique to the application methods. Out of total 26 metabolites tentatively identified in this study, 10 metabolites were unique to foliar application, while six metabolites were unique to soil drench. In addition to plant-mediated biotransformation, photodegradation of the parent compound was identified as a potential mechanism in foliar application.

Synthesis of isoxazoles via cyclization of β-fluoro enones with sodium azide

A practical method for the synthesis of 3,5-disubstituted isoxazoles via cyclization of β-fluoro enones with sodium azide was disclosed. Density functional theory (DFT) calculation indicated that both (1) the azirine formation followed by intramolecular rearrangement and (2) direct enolate O-attack via 5-exo-trig cyclization of vinyl azide were possible for the isoxazole formation.