Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Thiyl free radicals and the oxidation of ferrocytochrome c. Direct observation of coupled hydrogen-atom- and electron-transfer reactions.

ABSTRACT: Absolute rate constants for the reaction of ferrocytochrome c with the thiyl radicals derived from cysteine, GSH, penicillamine and N-(2-mercaptopropionyl)glycine were measured by using the technique of pulse radiolysis. The reaction is believed to occur through a one-electron-transfer process, in agreement with the hypothesis that thiols may act as catalysts linking hydrogen-atom- and electron-transfer reactions.

SUBMITTER: Forni LG

PROVIDER: S-EPMC1147505 | biostudies-other | 1986 Dec

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Thiyl and phenoxyl free radicals and NADH. Direct observation of one-electron oxidation.

Project description:Absolute rate constants for the reaction of NADH with thiyl free radicals derived from various sulphur-containing compounds of biological significance were measured by using the technique of pulse radiolysis. These and related reactions with phenoxyl free radicals are believed to occur through one-electron-transfer processes. Further evidence comes from studies with deuterated NADH. The results support the possibility that, in biochemical systems, thiols may act as catalysts linking hydrogen-atom and electron-transfer reactions.

| S-EPMC1147504 | biostudies-other

Intramolecular hydrogen transfer reactions of thiyl radicals from glutathione: formation of carbon-centered radical at Glu, Cys, and Gly.

Project description:Glutathione thiyl radicals (GS(•)) were generated in H(2)O and D(2)O by either exposure of GSH to AAPH, photoirradiation of GSH in the presence of acetone, or photoirradiation of GSSG. Detailed interpretation of the fragmentation pathways of deuterated GSH and GSH derivatives during mass spectrometry analysis allowed us to demonstrate that reversible intramolecular H-atom transfer reactions between GS(•) and C-H bonds at Cys[(?)C], Cys[(?)C], and Gly[(?)C] are possible.

| S-EPMC3736831 | biostudies-literature

Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography.

Project description:The 1.1 ?, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O?H…? interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C?H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 ? ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.

| S-EPMC3458323 | biostudies-literature

Reversible hydrogen transfer reactions of cysteine thiyl radicals in peptides: the conversion of cysteine into dehydroalanine and alanine, and of alanine into dehydroalanine.

Project description:The photodissociation of disulfide bonds in model peptides containing Ala and Ala-d(3) generates a series of photoproducts following the generation of a CysS(•) thiyl radical pair. These photoproducts include transformations of Cys to dehydroalanine (Dha) and Ala, as well as Ala to Dha. Intramolecular Michael addition of an intact Cys with a photolytically generated Dha results in the formation of cyclic thioethers. The conversion of Cys into Dha likely involves a 1,3-H-shift from the Cys (?)C-H bond to the thiyl radical, followed by elimination of HS(•). The conversion of Dha into Ala most likely involves hydrated electrons, which are generated through the photolysis of Cys, the photoproduct of disulfide photolysis. Prior to stable product formation, CysS(•) radicals engage in reversible hydrogen transfer reactions with (?)C-H and (?)C-H bonds of the surrounding amino acids. Especially for the (?)C-H bonds of Ala, such hydrogen transfer reactions are unexpected on the basis of thermodynamic grounds; however, the replacement of deuterons in Ala-d(3) by hydrogens in H(2)O provides strong experimental evidence for such reactions.

| S-EPMC3736842 | biostudies-literature

Stereoselective additions of thiyl radicals to terminal ynamides.

Project description:Two complementary sets of conditions for radical additions of thiols to terminal ynamides are described. The use of 1 equiv of thiol affords the cis-beta-thioenamide adducts in rapid fashion (10 min) and good dr, whereas employing excess thiol and longer reaction times favors the trans products.

| S-EPMC2878391 | biostudies-literature

Kinetics of hydrogen atom abstraction from substrate by an active site thiyl radical in ribonucleotide reductase.

Project description:Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides in all organisms. Active E. coli class Ia RNR is an ?2?2 complex that undergoes reversible, long-range proton-coupled electron transfer (PCET) over a pathway of redox active amino acids (?-Y122 ? [?-W48] ? ?-Y356 ? ?-Y731 ? ?-Y730 ? ?-C439) that spans ?35 Å. To unmask PCET kinetics from rate-limiting conformational changes, we prepared a photochemical RNR containing a [Re(I)] photooxidant site-specifically incorporated at position 355 ([Re]-?2), adjacent to PCET pathway residue Y356 in ?. [Re]-?2 was further modified by replacing Y356 with 2,3,5-trifluorotyrosine to enable photochemical generation and spectroscopic observation of chemically competent tyrosyl radical(s). Using transient absorption spectroscopy, we compare the kinetics of Y· decay in the presence of substrate and wt-?2, Y731F-?2 ,or C439S-?2, as well as with 3'-[(2)H]-substrate and wt-?2. We find that only in the presence of wt-?2 and the unlabeled substrate do we observe an enhanced rate of radical decay indicative of forward radical propagation. This observation reveals that cleavage of the 3'-C-H bond of substrate by the transiently formed C439· thiyl radical is rate-limiting in forward PCET through ? and has allowed calculation of a lower bound for the rate constant associated with this step of (1.4 ± 0.4) × 10(4) s(-1). Prompting radical propagation with light has enabled observation of PCET events heretofore inaccessible, revealing active site chemistry at the heart of RNR catalysis.

| S-EPMC4244835 | biostudies-literature

Chemical Kinetics of Hydrogen Atom Abstraction from Propargyl Sites by Hydrogen and Hydroxy Radicals.

Project description:Hydrogen atom abstraction from propargyl C-H sites of alkynes plays a critical role in determining the reactivity of alkyne molecules and understanding the formation of soot precursors. This work reports a systematic theoretical study on the reaction mechanisms and rate constants for hydrogen abstraction reactions by hydrogen and hydroxy radicals from a series of alkyne molecules with different structural propargyl C-H atoms. Geometry optimizations and frequency calculations for all species are performed at M06-2X/cc-pVTZ level of theory and the hindered internal rotations are also treated at this level. The high-level W1BD and CCSD(T)/CBS theoretical calculations are used as a benchmark for a series of DFT calculations toward the selection of accurate DFT functionals for large reaction systems in this work. Based on the quantum chemistry calculations, rate constants are computed using the canonical transition state theory with tunneling correction and the treatment of internal rotations. The effects of the structure and reaction site on the energy barriers and rate constants are examined systematically. To the best of our knowledge, this work provides the first systematic study for one of the key initiation abstraction reactions for compounds containing propargyl hydrogen atoms.

| S-EPMC6650822 | biostudies-other

Catalytic Synthesis of Indolines by Hydrogen Atom Transfer to Cobalt(III)-Carbene Radicals.

Project description:We report a new method for the synthesis of indolines from o-aminobenzylidine N-tosylhydrazones proceeding through a cobalt(III)-carbene radical intermediate. This methodology employs the use of inexpensive commercially available reagents and allows for the transformation of easily derivatized benzaldehyde-derived precursors to functionalized indoline products. This transformation takes advantage of the known propensity of radicals to undergo rapid intramolecular 1,5-hydrogen atom transfer (1,5-HAT) to form more stabilized radical intermediates. Computational investigations using density functional theory identify remarkably low barriers for 1,5-HAT and subsequent radical rebound displacement, providing support for the proposed mechanism. We explore the effect of a variety of nitrogen substituents, and highlight the importance of adequate resonance stabilization of radical intermediates to the success of the transformation. Furthermore, we evaluate the steric and electronic effects of substituents on the aniline ring. This transformation is the first reported example of the synthesis of nitrogen-containing heterocycles from cobalt(III)-carbene radical precursors.

| S-EPMC5915749 | biostudies-literature

Mechanisms for Hydrogen-Atom Abstraction by Mononuclear Copper(III) Cores: Hydrogen-Atom Transfer or Concerted Proton-Coupled Electron Transfer?

Project description:In a possibly biomimetic fashion, formally copper(III)-oxygen complexes LCu(III)-OH (1) and LCu(III)-OOCm (2) (L2- = N,N'-bis(2,6-diisopropylphenyl)-2,6-pyridinedicarboxamide, Cm = ?,?-dimethylbenzyl) have been shown to activate X-H bonds (X = C, O). Herein, we demonstrate similar X-H bond activation by a formally Cu(III) complex supported by the same dicarboxamido ligand, LCu(III)-O2CAr1 (3, Ar1 = meta-chlorophenyl), and we compare its reactivity to that of 1 and 2. Kinetic measurements revealed a second order reaction with distinct differences in the rates: 1 reacts the fastest in the presence of O-H or C-H based substrates, followed by 3, which is followed by (unreactive) 2. The difference in reactivity is attributed to both a varying oxidizing ability of the studied complexes and to a variation in X-H bond functionalization mechanisms, which in these cases are characterized as either a hydrogen-atom transfer (HAT) or a concerted proton-coupled electron transfer (cPCET). Select theoretical tools have been employed to distinguish these two cases, both of which generally focus on whether the electron (e-) and proton (H+) travel "together" as a true H atom, (HAT), or whether the H+ and e- are transferred in concert, but travel between different donor/acceptor centers (cPCET). In this work, we reveal that both mechanisms are active for X-H bond activation by 1-3, with interesting variations as a function of substrate and copper functionality.

| S-EPMC7197025 | biostudies-literature

Direct observation and catalytic role of mediator atom in 2D materials.

Project description:The structural transformations of graphene defects have been extensively researched through aberration-corrected transmission electron microscopy (AC-TEM) and theoretical calculations. For a long time, a core concept in understanding the structural evolution of graphene defects has been the Stone-Thrower-Wales (STW)-type bond rotation. In this study, we show that undercoordinated atoms induce bond formation and breaking, with much lower energy barriers than the STW-type bond rotation. We refer to them as mediator atoms due to their mediating role in the breaking and forming of bonds. Here, we report the direct observation of mediator atoms in graphene defect structures using AC-TEM and annular dark-field scanning TEM (ADF-STEM) and explain their catalytic role by tight-binding molecular dynamics (TBMD) simulations and image simulations based on density functional theory (DFT) calculations. The study of mediator atoms will pave a new way for understanding not only defect transformation but also the growth mechanisms in two-dimensional materials.

| S-EPMC7286694 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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