Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Free Radical Isomerizations in Acetylene Bromoboration Reaction.

ABSTRACT: The experimentally motivated question of the acetylene bromoboration mechanism was addressed in order to suggest possible radical isomerization pathways for the syn-adduct. Addition-elimination mechanisms starting with a bromine radical attack at the "bromine end" or the "boron end" of the C=C bond were considered. Dispersion-corrected DFT and MP2 methods with the SMD solvation model were employed using three all-electron bases as well as the ECP28MWB ansatz. The rate-determining, elimination step had a higher activation energy (12 kcal mol^-1) in case of the "bromine end" attack due to intermediate stabilization at both the MP2 and DFT levels. In case of the "boron end" attack, two modes of C-C bond rotation were followed and striking differences in MP2 vs. DFT potential energy surfaces were observed. Employing MP2, addition was followed by either a 180° rotation through an eclipsed conformation of vicinal bromine atoms or by an opposite rotation avoiding that conformation, with 5 kcal mol^-1 of elimination activation energy. Within B3LYP, the addition and rotation proceeded simultaneously, with a 9 (7) kcal mol^-1 barrier for rotation involving (avoiding) eclipsed conformation of vicinal bromines. For weakly bound complexes, ZPE corrections with MP2 revealed significant artifacts when diffuse bases were included, which must be considered in the Gibbs free energy profile interpretation.

SUBMITTER: Semrad H

PROVIDER: S-EPMC8123272 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Reaction of AdoMet with ThiC generates a backbone free radical.

Project description:ThiC is an [4Fe-4S] cluster protein that catalyzes the formation of 4-amino-5-hydroxymethyl-2-methylpyrimidine. EPR spectroscopic studies demonstrate that, upon interaction with AdoMet, active ThiC from Salmonella enterica generates a persistent free radical on the alpha-carbon of an amino acid residue. The EPR properties of the radical are consistent with any residue other than a Gly or Ala. Exposure to oxygen was accompanied by a fission of the radical-carrying polypeptide chain between the Gly436 and His437 residues in ThiC. Regardless of whether the backbone radical is part of the catalytic machinery, its presence provides evidence that ThiC employs free radical chemistry as expected for radical SAM enzymes.

| S-EPMC2654281 | biostudies-literature

Photocatalytic Reductive Radical-Polar Crossover for a Base-Free Corey-Seebach Reaction.

Project description:A metal-free generation of carbanion nucleophiles is of prime importance in organic synthesis. Herein we report a photocatalytic approach to the Corey-Seebach reaction. The presented method operates under mild redox-neutral and base-free conditions giving the desired product with high functional group tolerance. The reaction is enabled by the combination of photo- and hydrogen atom transfer (HAT) catalysis. This catalytic merger allows a C-H to carbanion activation by the abstraction of a hydrogen atom followed by radical reduction. The generated nucleophilic intermediate is then capable of adding to carbonyl electrophiles. The obtained dithiane can be easily converted to the valuable α-hydroxy carbonyl in a subsequent step. The proposed reaction mechanism is supported by emission quenching, radical-radical homocoupling and deuterium labeling studies as well as by calculated redox-potentials and bond strengths.

| S-EPMC7589390 | biostudies-literature

An Expedient Synthesis of Murrayaquinone A via a Novel Oxidative Free Radical Reaction.

Project description:Murrayaquinones A-D is a group of four bioactive carbazole-1,4-dione natural products isolated from the root bark of the plant Murraya eucrestifolia hayata. Murrayaquinone is synthesized in five steps starting from the commercially available 2,4,5-trimethoxybenzaldehyde with an overall yield of 45%. The novelty of this murrayaquinone synthesis is in the use of a Mn(OAc)3 mediated oxidative radical reaction of a N-benzylaminoquinone derivative with 2-cyclohexen-1-one for the late-stage indole ring construction.

| S-EPMC5935454 | biostudies-literature

EPR spin trapping of an oxalate-derived free radical in the oxalate decarboxylase reaction.

Project description:EPR spin trapping experiments on bacterial oxalate decarboxylase from Bacillus subtilis under turn-over conditions are described. The use of doubly (13)C-labeled oxalate leads to a characteristic splitting of the observed radical adducts using the spin trap N-tert-butyl-α-phenylnitrone linking them directly to the substrate. The radical was identified as the carbon dioxide radical anion which is a key intermediate in the hypothetical reaction mechanism of both decarboxylase and oxidase activities. X-ray crystallography had identified a flexible loop, SENS161-4, which acts as a lid to the putative active site. Site directed mutagenesis of the hinge amino acids, S161 and T165 was explored and showed increased radical trapping yields compared to the wild type. In particular, T165V shows approximately ten times higher radical yields while at the same time its decarboxylase activity was reduced by about a factor of ten. This mutant lacks a critical H-bond between T165 and R92 resulting in compromised control over its radical chemistry allowing the radical intermediate to leak into the surrounding solution.

| S-EPMC3070241 | biostudies-literature

Supplementary data for the quantum chemical calculation of free radical substitution reaction mechanism of camptothecin.

Project description:This data article contains the truncated view of the transition states for methyl radical attacking camptothecin at the site of 9, 10, 11, 12 and 14 in acidic conditions obtained from quantum computation of Gaussian 09 with B3LYP/6-31+G(d,p) level, also the truncated view of transition states for H abstraction by singlet O2 from sites of 9, 10, 11 and 12 of the intermediates of methyl combination with camptothecin and that by triplet O2 from site 9 of the intermediate of methyl combination with camptothecin in acidic condition are included. The corresponding parameters of reaction rate constant calculation for the formation of methyl radical from acetaldehyde, the first and second step of radical substitution of camptothecin under acidic conditions are listed. The data of the basic parameters for the computation of the total energy of the spin-projection of singlet oxygen, and the S2 values for the reactants, transition states and intermediates in the free radical substitution reaction of camptothecin are also included.

| S-EPMC6141799 | biostudies-literature

Free-Radical Polymerization of Acrylic Acid under Extreme Reaction Conditions Mimicking Deep-Sea Hydrothermal Vents.

Project description:Free-radical polymerization with a thermochemical initiator, which usually takes hours to complete, was dramatically accelerated under reaction conditions mimicking the deep-sea hydrothermal vents, where reaction mixtures were only briefly exposed to ultrahigh temperatures under pressure. In tests using acrylic acid and potassium persulfate, poly(acrylic acid) (M n = 2.1 × 104, Đ = 2.73) was obtained in 5.2 s with the monomer conversion of 60.3% in water at 200 °C and 25 MPa without using any catalysts. The process that we call heat-shock-induced polymerization may pave the way for an entirely new strategy in reaction engineering for developing extremely fast, green, and scalable processes for polymer synthesis.

| S-EPMC6641060 | biostudies-literature

From Free-Radical to Radical-Free: A Paradigm Shift in Light-Mediated Biofabrication.

Project description:In recent years, the development of novel photocrosslinking strategies and photoactivatable materials has stimulated widespread use of light-mediated biofabrication techniques. However, despite great progress toward more efficient and biocompatible photochemical strategies, current photoresins still rely on photoinitiators (PIs) producing radical-initiating species to trigger the so-called free-radical crosslinking/polymerization. In the context of bioprinting, where cells are encapsulated in the bioink, the presence of radicals raises concerns of potential cytotoxicity. In this work, a universal, radical-free (RF) photocrosslinking strategy to be used for light-based technologies is presented. Leveraging RF uncaging mechanisms and Michael addition, cell-laden constructs are photocrosslinked by means of one- and two-photon excitation with high biocompatibility. A hydrophilic coumarin-based group is used to cage a universal RF photocrosslinker based on 4-arm-PEG-thiol (PEG4SH). Upon light exposure, thiols are uncaged and react with an alkene counterpart to form a hydrogel. RF photocrosslinker is shown to be highly stable, enabling potential for off-the-shelf products. While PI-based systems cause a strong upregulation of reactive oxygen species (ROS)-associated genes, ROS are not detected in RF photoresins. Finally, optimized RF photoresin is successfully exploited for high resolution two-photon stereolithography (2P-SL) using remarkably low polymer concentration (<1.5%), paving the way for a shift toward radical-free light-based bioprinting.

| S-EPMC10015869 | biostudies-literature

Three-component radical homo Mannich reaction.

Project description:Aliphatic amine, especially tertiary aliphatic amine, is one of the most popular functionalities found in pharmaceutical agents. The Mannich reaction is a classical and widely used transformation for the synthesis of β-amino-carbonyl products. Due to an ionic nature of the mechanism, the Mannich reaction can only use non-enolizable aldehydes as substrates, which significantly limits the further applications of this powerful approach. Here we show, by employing a radical process, we are able to utilize enolizable aldehydes as substrates and develop the three-component radical homo Mannich reaction for the streamlined synthesis of γ-amino-carbonyl compounds. The electrophilic radicals are generated from thiols via the desulfurization process facilitated by visible-light, and then add to the electron-rich double bonds of the in-situ formed enamines to provide the products in a single step. The broad scope, mild conditions, high functional group tolerance, and modularity of this metal-free approach for the synthesis of complex tertiary amine scaffolds will likely be of great utility to chemists in both academia and industry.

| S-EPMC7880990 | biostudies-literature

Selective Radical-Radical Cross-Couplings: Design of a Formal ?-Mannich Reaction.

Project description:A direct ?-coupling of cyclic ketones with imines has been accomplished via the synergistic combination of photoredox catalysis and organocatalysis. Transient ?-enaminyl radicals derived from ketones via enamine and oxidative photoredox catalysis readily combine with persistent ?-amino radicals in a highly selective hetero radical-radical coupling. This novel pathway to ?-aminoketones is predicated upon the use of DABCO as both a base and an electron transfer agent. This protocol also formally allows for the direct synthesis of ?-Mannich products via a chemoselective three-component coupling of aryl aldehydes, amines, and ketones.

| S-EPMC4629778 | biostudies-literature

Free Radical-Mediated Protein Radical Formation in Differentiating Monocytes.

Project description:Free radical-mediated activation of inflammatory macrophages remains ambiguous with its limitation to study within biological systems. U-937 and HL-60 cell lines serve as a well-defined model system known to differentiate into either macrophages or dendritic cells in response to various chemical stimuli linked with reactive oxygen species (ROS) production. Our present work utilizes phorbol 12-myristate-13-acetate (PMA) as a stimulant, and factors such as concentration and incubation time were considered to achieve optimized differentiation conditions. ROS formation likely hydroxyl radical (HO●) was confirmed by electron paramagnetic resonance (EPR) spectroscopy combined with confocal laser scanning microscopy (CLSM). In particular, U-937 cells were utilized further to identify proteins undergoing oxidation by ROS using anti-DMPO (5,5-dimethyl-1-pyrroline N-oxide) antibodies. Additionally, the expression pattern of NADPH Oxidase 4 (NOX4) in relation to induction with PMA was monitored to correlate the pattern of ROS generated. Utilizing macrophages as a model system, findings from the present study provide a valuable source for expanding the knowledge of differentiation and protein expression dynamics.

| S-EPMC8468151 | 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