Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mechanism of the Kinugasa Reaction Revisited.

ABSTRACT: The mechanism of the Kinugasa reaction, that is, the copper-catalyzed formation of β-lactams from nitrones and terminal alkynes, is re-evaluated by means of density functional theory calculations and in light of recent experimental findings. Different possible mechanistic scenarios are investigated using phenanthroline as a ligand and triethylamine as a base. The calculations confirm that after an initial two-step cycloaddition promoted by two copper ions, the resulting five-membered ring intermediate can undergo a fast and irreversible cycloreversion to generate an imine and a dicopper-ketenyl intermediate. From there, the reaction can proceed through a nucleophilic attack of a ketenyl copper intermediate on the imine and an intramolecular cyclization, rather than through the previously suggested (2 + 2) Staudinger synthesis.

SUBMITTER: Santoro S

PROVIDER: S-EPMC8389905 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Mechanism of the Kinugasa Reaction Revisited.

Santoro Stefano S Himo Fahmi F

The Journal of organic chemistry 20210713 15

The mechanism of the Kinugasa reaction, that is, the copper-catalyzed formation of β-lactams from nitrones and terminal alkynes, is re-evaluated by means of density functional theory calculations and in light of recent experimental findings. Different possible mechanistic scenarios are investigated using phenanthroline as a ligand and triethylamine as a base. The calculations confirm that after an initial two-step cycloaddition promoted by two copper ions, the resulting five-membered ring interm ...[more]

PMID: 34255506

Similar Datasets

Inhibition and mechanism of HDAC8 revisited.

Project description:Histone deacetylases (HDACs) have found intense interest as drug targets for a variety of diseases, but there is disagreement about basic aspects of the inhibition and mechanism of HDACs. QM/MM calculations of HDAC8 including a large QM region provide a model that is consistent with the available crystal structures and structure-activity relationships of different HDAC inhibitors. The calculations support a spontaneous proton transfer from a hydroxamic acid to an active site histidine upon binding to the zinc. The role of the H142/D176 catalytic dyad as the general base of the reaction is elucidated. The reasons for the disagreements between previous proposals are discussed. The results provide detailed insights into the unique mechanism of HDACs, including the role of the two catalytic dyads and function of the potassium near the active site. They also have important implications for the design of novel inhibitors for a number of HDACs such as the class IIa HDACs.

| S-EPMC4140456 | biostudies-literature

Diffusion- and reaction-limited cluster aggregation revisited.

Project description:We simulated irreversible aggregation of non-interacting particles and of particles interacting via repulsive and attractive potentials explicitly implementing the rotational diffusion of aggregating clusters. Our study confirms that the attraction between particles influences neither the aggregation mechanism nor the structure of the aggregates, which are identical to those of non-interacting particles. In contrast, repulsive particles form more compact aggregates and their fractal dimension and aggregation times increase with the decrease of the temperature. A comparison of the fractal dimensions obtained for non-rotating clusters of non-interacting particles and for rotating clusters of repulsive particles provides an explanation for the conformity of the respective values obtained earlier in the well established model of diffusion-limited cluster aggregation neglecting rotational diffusion and in experiments on colloidal particles.

| S-EPMC6484677 | biostudies-other

Gram-Scale Synthesis of 1,8-Naphthyridines in Water: The Friedlander Reaction Revisited.

Project description:The products of the Friedlander reaction, i.e., 1,8-naphthyridines, have far-reaching impacts in materials science, chemical biology, and medicine. The reported synthetic methodologies elegantly orchestrate the diverse synthetic routes of naphthyridines but require harsh reaction conditions, organic solvents, and expensive metal catalysts. Here, we introduce gram-scale synthesis of 1,8-naphthyridines in water using an inexpensive and biocompatible ionic liquid (IL) as a catalyst. This is the first-ever report on the synthesis of naphthyridines in water. This is a one-step reaction, and the product separation is relatively easy. The choline hydroxide (ChOH) is used as a metal-free, nontoxic, and water-soluble catalyst. In comparison to other catalysts reported in the literature, ChOH has the advantage of forming an additional hydrogen bond with the reactants, which is the vital step for the reaction to happen in water. Density functional theory (DFT) and noncovalent interaction (NCI) plot index analysis provide the plausible reaction mechanism for the catalytic cycle and confirm that hydrogen bonds with the IL catalyst are pivotal to facilitate the reaction. Molecular docking and molecular dynamics (MD) simulations are also performed to demonstrate the potentialities of the newly synthesized products as drugs. Through MD simulations, it was established that the tetrahydropyrido derivative of naphthyridine (10j) binds to the active sites of the ts3 human serotonin transporter (hSERT) (PDB ID: 6AWO) without perturbing the secondary structure, suggesting that 10j can be a potential preclinical drug candidate for hSERT inhibition and depression treatment.

| S-EPMC8320145 | biostudies-literature

Mechanism of RecA-mediated homologous recombination revisited by single molecule nanomanipulation.

Project description:The mechanisms of RecA-mediated three-strand homologous recombination are investigated at the single-molecule level, using magnetic tweezers. Probing the mechanical response of DNA molecules and nucleoprotein filaments in tension and in torsion allows a monitoring of the progression of the exchange in real time, both from the point of view of the RecA-bound single-stranded DNA and from that of the naked double-stranded DNA (dsDNA). We show that strand exchange is able to generate torsion even along a molecule with freely rotating ends. RecA readily depolymerizes during the reaction, a process presenting numerous advantages for the cell's 'protein economy' and for the management of topological constraints. Invasion of an untwisted dsDNA by a nucleoprotein filament leads to an exchanged duplex that remains topologically linked to the exchanged single strand, suggesting multiple initiations of strand exchange on the same molecule. Overall, our results seem to support several important assumptions of the monomer redistribution model.

| S-EPMC1570433 | biostudies-literature

Leptin revisited: its mechanism of action and potential for treating diabetes.

Project description:Since the discovery of leptin in 1994, we now have a better understanding of the cellular and molecular mechanisms underlying its biological effects. In addition to its established anti-obesity effects, leptin exerts antidiabetic actions that are independent of its regulation of body weight and food intake. In particular, leptin can correct diabetes in animal models of type 1 and type 2 diabetes. In addition, long-term leptin replacement therapy improves glycaemic control, insulin sensitivity and plasma triglycerides in patients with severe insulin resistance due to lipodystrophy. These results have spurred enthusiasm for the use of leptin therapy to treat diabetes. Here, we review the current understanding of the glucoregulatory functions of leptin, emphasizing its central mechanisms of action and lessons learned from clinical studies, and discuss possible therapeutic applications of leptin in the treatment of type 1 and type 2 diabetes.

| S-EPMC4019022 | biostudies-literature

Reaction mechanism of Drosophila cryptochrome.

Project description:Cryptochrome (CRY) is a blue-light sensitive flavoprotein that functions as the primary circadian photoreceptor in Drosophila melanogaster. The mechanism by which it transmits the light signal to the core clock circuitry is not known. We conducted in vitro studies on the light-induced conformational change in CRY and its effect on protein-protein interaction and performed in vivo analysis of the lifetime of the signaling state of the protein to gain some insight into the mechanism of phototransduction. We find that exposure of CRY to blue light induces a conformation similar to that of the constitutively active CRY mutant with a C-terminal deletion (CRYΔ). This light-induced conformation has a half-life of ∼15 min in the dark at 25 °C and is characterized by increased affinity to Jetlag E3 ligase. In vivo analysis reveals that in the Drosophila S2 cell line, the signaling state induced by a millisecond light exposure has a half-life of 27 min in the dark at 0 °C during which period it is susceptible to degradation by the ubiquitin-proteasome system. These findings lead to a plausible model for circadian photoreception/phototransduction in Drosophila.

| S-EPMC3021015 | biostudies-literature

Reaction Mechanism of Pd-Catalyzed "CO-Free" Carbonylation Reaction Uncovered by In Situ Spectroscopy: The Formyl Mechanism.

Project description:"CO-free" carbonylation reactions, where synthesis gas (CO/H2 ) is substituted by C1 surrogate molecules like formaldehyde or formic acid, have received widespread attention in homogeneous catalysis lately. Although a broad range of organics is available via this method, still relatively little is known about the precise reaction mechanism. In this work, we used in situ nuclear magnetic resonance (NMR) spectroscopy to unravel the mechanism of the alkoxycarbonylation of alkenes using different surrogate molecules. In contrast to previous hypotheses no carbon monoxide could be found during the reaction. Instead the reaction proceeds via the C-H activation of in situ generated methyl formate. On the basis of quantitative NMR experiments, a kinetic model involving all major intermediates is built which enables the knowledge-driven optimization of the reaction. Finally, a new reaction mechanism is proposed on the basis of in situ observed Pd-hydride, Pd-formyl and Pd-acyl species.

| S-EPMC7898928 | biostudies-literature

Modeling of the RAG reaction mechanism.

Project description:In vertebrate V(D)J recombination, it remains unclear how the RAG complex coordinates its catalytic steps with binding to two distant recombination sites. Here, we test the ability of the plausible reaction schemes to fit observed time courses for RAG nicking and DNA hairpin formation. The reaction schemes with the best fitting capability (1) strongly favor a RAG tetrameric complex over a RAG octameric complex; (2) indicate that once a RAG complex brings two recombination signal sequence (RSS) sites into synapsis, the synaptic complex rarely disassembles; (3) predict that the binding of both RSS sites (synapsis) occurs before catalysis (nicking); and (4) show that the RAG binding properties permit strong distinction between RSS sites within active chromatin versus nonspecific DNA or RSS sites within inactive chromatin. The results provide general insights for synapsis by nuclear proteins as well as more specific testable predictions for the RAG proteins.

| S-EPMC4010234 | biostudies-literature

Coordination polymer structure and revisited hydrogen evolution catalytic mechanism for amorphous molybdenum sulfide.

Project description:Molybdenum sulfides are very attractive noble-metal-free electrocatalysts for the hydrogen evolution reaction (HER) from water. The atomic structure and identity of the catalytically active sites have been well established for crystalline molybdenum disulfide (c-MoS2) but not for amorphous molybdenum sulfide (a-MoSx), which exhibits significantly higher HER activity compared to its crystalline counterpart. Here we show that HER-active a-MoSx, prepared either as nanoparticles or as films, is a molecular-based coordination polymer consisting of discrete [Mo3S13](2-) building blocks. Of the three terminal disulfide (S2(2-)) ligands within these clusters, two are shared to form the polymer chain. The third one remains free and generates molybdenum hydride moieties as the active site under H2 evolution conditions. Such a molecular structure therefore provides a basis for revisiting the mechanism of a-MoSx catalytic activity, as well as explaining some of its special properties such as reductive activation and corrosion. Our findings open up new avenues for the rational optimization of this HER electrocatalyst as an alternative to platinum.

| S-EPMC5495159 | biostudies-literature

Using reaction mechanism to measure enzyme similarity.

Project description:The concept of reaction similarity has been well studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism. We present the first method to give a quantitative measure of the similarity of reactions based upon their explicit mechanisms. Two approaches are presented to measure the similarity between individual steps of mechanisms: a fingerprint-based approach that incorporates relevant information on each mechanistic step; and an approach based only on bond formation, cleavage and changes in order. The overall similarity for two reaction mechanisms is then calculated using the Needleman-Wunsch alignment algorithm. An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanisms. In many cases, mechanism similarity is not reflected by similarity according to the EC system of enzyme classification. In particular, little mechanistic information is conveyed by the class level of the EC system.

| S-EPMC3461574 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data