Determination of hydroxyl radical photoproduction rates in natural waters.

The photochemical formation rates of hydroxyl radicals (OH radicals) in river water and seawater were determined by a simple, rapid and sensitive benzene probe method, in which phenol formed by the reaction between benzene and photochemically-generated OH radicals was analyzed by on-line preconcentration HPLC. The OH radical formation rates from well-known OH radical sources, such as nitrate, nitrite and hydrogen peroxide, were in good agreement with those reported previously. River water samples containing high concentrations of nitrate and nitrite were found to show high OH radical formation rates. Ten to 80% of the OH radical formation in river water and seawater was due to the photolysis of nitrate and nitrite, but OH radical formation from hydrogen peroxide was negligible. The OH radical formation from unknown sources other than nitrate, nitrite and hydrogen peroxide was strongly correlated to the amount of fluorescent matter.     

Radical cyclisation reactions with indoles

Several radical cyclisation reactions involving indoles are described. Most notably, we have shown that radical additions to C3 of an indole are frequently facile. A dichotomy in the course of radical cyclisation reactions to C2 of the indole has also been exposed wherein 6-endo-trig cyclisations are propagated by the loss of a hydrogen atom from C2 while 5-exo-trig cyclisations are propagated by hydrogen atom abstraction at C3 from tributyltin hydride. Cyclisations involving the addition of indolyl radical intermediates to arenes have also been demonstrated.     

Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical

Hydrogen abstraction from the C1' and C2' positions of deoxyadenosine by a neighbouring uracil-5-yl radical in the 5'-AU*-3' DNA sequence is explored using DFT. This hydrogen abstraction is the first step in a sequence leading to single or double strand break in DNA. The uracil-5-yl radical can be the result of photolysis or low-energy electron (LEE) attachment. If the radical is produced by photolysis the neighbouring adenine will become a cation radical and if it is produced by LEE the adenine will remain neutral. The hydrogen abstraction reactions for both cases were investigated. It is concluded that it is possible for the uracil-5-yl to abstract hydrogen from C1' and C2'. When adenine is neutral there is a preference for the C1' site and when the adenine is a radical cation the C2' site is the preferred. If adenine is positively charged, the rate-limiting step when abstracting hydrogen from C1' is the formation of an intermediate crosslink between uracil and adenine. This crosslink might be avoided in dsDNA, making C1' the preferred site for abstraction.     

Reactivity and selectivity of charged phenyl radicals toward amino acids in a Fourier transform ion cyclotron resonance mass spectrometer

The reactivity of 10 charged phenyl radicals toward several amino acids was examined in the gas phase in a dual-cell Fourier transform ion cyclotron resonance mass spectrometer. All radicals abstract a hydrogen atom from the amino acids, as expected. The most electrophilic radicals (with the greatest calculated vertical electron affinities (EA) at the radical site) also react with these amino acids via NH(2) abstraction (a nonradical nucleophilic addition-elimination reaction). Both the radical (hydrogen atom abstraction) and nonradical (NH(2) abstraction) reaction efficiencies were found to increase with the electrophilicity (EA) of the radical. However, NH(2) abstraction is more strongly influenced by EA. In contrast to an earlier report, the ionization energies of the amino acids do not appear to play a general reactivity-controlling role. Studies using several partially deuterium-labeled amino acids revealed that abstraction of a hydrogen atom from the α-carbon is only preferred for glycine; for the other amino acids, a hydrogen atom is preferentially abstracted from the side chain. The electrophilicity of the radicals does not appear to have a major influence on the site from which the hydrogen atom is abstracted. Hence, the regioselectivity of hydrogen atom abstraction appears to be independent of the structure of the radical but dependent on the structure of the amino acid. Surprisingly, abstraction of two hydrogen atoms was observed for the N-(3-nitro-5-dehydrophenyl)pyridinium radical, indicating that substituents on the radical not only influence the EA of the radical but also can be involved in the reaction. In disagreement with an earlier report, proline was found to display several unprecedented reaction pathways that likely do not proceed via a radical mechanism but rather by a nucleophilic addition-elimination mechanism. Both NH(2) and (15)NH(2) groups were abstracted from lysine labeled with (15)N on the side chain, indicating that NH(2) abstraction occurs both from the amino terminus and from the side chain. Quantum chemical calculations were employed to obtain insights into some of the reaction mechanisms.     

Radical addition of alkyl halides to formaldehyde in the presence of cyanoborohydride as a radical mediator. A new protocol for hydroxymethylation reaction

Hydroxymethylation of alkyl halides was achieved using paraformaldehyde as a radical C1 synthon in the presence of tetrabutylammonium cyanoborohydride as a hydrogen source. The reaction proceeds via a radical chain mechanism involving an alkyl radical addition to formaldehyde to form an alkoxy radical, which abstracts hydrogen from a hydroborate anion.     

CIDNP study of the photochemistry of 1-acetylindole-2,3-dione

CIDNP is a convenient means to study reactionsvia radical pairs, which provides a way to distinguishthe reactions via radical pairs from the reactions in-volving exciplexes and short-chain biradicals[1]. Het-erocyclic compounds with different electron wit…     

Revisiting the Mechanism of the Anaerobic Coproporphyrinogen III Oxidase HemN

HemN is a radical S‐adenosyl‐l ‐methionine (SAM) enzyme that catalyzes the oxidative decarboxylation of coproporphyrinogen III to produce protoporphyrinogen IX, an intermediate in heme biosynthesis. HemN binds two SAM molecules in the active site, but how these two SAMs are utilized for the sequential decarboxylation of the two propionate groups of coproporphyrinogen III remains largely elusive. Provided here is evidence showing that in HemN catalysis a SAM serves as a hydrogen relay which mediates a radical‐based hydrogen transfer from the propionate to the 5′‐deoxyadenosyl (dAdo) radical generated from another SAM in the active site. Also observed was an unexpected shunt product resulting from trapping of the SAM‐based methylene radical by the vinyl moiety of the mono‐decarboxylated intermediate, harderoporphyrinogen. These results suggest a major revision of the HemN mechanism and reveal a new paradigm of the radical‐mediated hydrogen transfer in radical SAM enzymology.     

A furoindoline synthesis by remote radical functionalization

The preliminary results of an investigation toward a synthesis of furoindolines from 3-(2-hydroxyethyl)indolines by remote radical functionalization are described. Using an oxidative radical cyclization, it was discovered that the intramolecular hydrogen abstraction was only successful when the resulting radical (and hence carbocation) was resonance stabilized by adjacent tertiary amine and phenyl groups. The successful cyclization affords diastereomeric furoindolines, one of which contains a highly strained trans-fused 5,5-ring system. This furoindoline synthesis contains a rare example of an alkoxy radical promoted hydrogen atom transfer of a proton attached to a nitrogen-substituted carbon.     

On the possibility of the detachment of hydrogen as a result of electron capture by a Broensted center on zeolites

The structure and reactivity of the radical anion center in ZSM-5 zeolite were studied by the density functional theory method. It was shown that the interaction of the hydrogen zeolite form with adsorbed olefins and aromatic hydrocarbons could be accompanied by electron transfer from hydrocarbon molecules to the Broensted acid center with the formation of a radical anion fragment. The radical anion fragment formed is unstable, which contributes to the probability of the exothermic process (ΔE = ?21 kcal/mol) of atomic hydrogen detachment with the activation energy not exceeding 10–12 kcal/mol. The atomic hydrogen split off can initiate hydrocarbon transformations, and such a radical anion center can play the role of a catalytic activity carrier on acid zeolites.     

Radical para-benzoic acid derivatives: transmission of ferromagnetic interactions through hydrogen bonds at long distances

Investigation of the transmission of magnetic interactions through hydrogen bonds has been carried out for two different benzoic acid derivatives which bear either a tert-butyl nitroxide (NOA) or a poly(chloro)triphenylmethyl (PTMA) radical moiety. In the solid state, both radical acids formed dimer aggregates by the complementary association of two carboxylic groups though hydrogen bonding. This association ensured that atoms with most spin density are separated from one another by more than 15 A. Thus, no competing through-space magnetic exchange interactions are expected in these dimers and, hence, they provide good models to investigate whether noncovalent hydrogen bonds play a role in the long-range transmission of magnetic interactions. The nature of the magnetic exchange interaction and their strengths within similar dimer aggregates in solution was assessed by electron spin resonance (ESR) spectroscopy. In the case of radical NOA, low-temperature ESR experiments showed a weak ferromagnetic interaction between the two radicals in the dimer aggregates (which have the same geometry as in the solid state). In contrast, the corresponding solution ESR study performed with radical PTMA did not lead to any conclusive results, as aggregates were formed by noncovalent interactions other than hydrogen bonds. However, the bulkiness of the poly(chloro)triphenylmethyl radical prevented interdimer contacts in the solid state between regions of high spin density. Hence, solid-state measurements of the alpha phase of PTMA radical provided evidence of the intradimer interaction to confirm the transmission of a weak ferromagnetic interaction through the carboxylic acid bridges, as found for the NOA radical. Moreover, crystallization of the PTMA radical in presence of ethanol to form the beta phase of PTMA radical prevented the dimer formation; this resulted in the suppression of this interaction and provides further evidence of the magnetic exchange mechanism through noncovalent hydrogen bonds at long distances.     

Time-resolved FT-EPR study of photoreduction of duroquinone by triethylamine in methanol

Using time resolved Fourier transform EPR spectroscopy the photoreduction of duroquinone by triethylamine in methanol solution was investigated. It is found that the spin-polarized (CIDEP) duroquinone triplet deactivates by electron transfer from triethylamine generating duroquinone radical anion and amine radical cation, and by hydrogen transfer from the solvent generating durosemiquinone radical and hydroxymethyl radical, respectively. All radicals are observed at different conditions and are spin-polarized by triplet mechanism and partially by ST₀ radical pair mechanism. The time dependence of FT-EPR intensities of radical cation and radical anion on the amine concentration is investigated in the range of 1 to 100 mM triethylamine. The contribution of the triplet mechanism to the spin polarization of radicals changes with different triethylamine concentrations. The durosemiquinone radical is found to be transformed into duroquinone radical anion in the presence of triethylamine in the solution. CIDNP experiments indicate that the hydrogen back transfer between the durosemiquinone radical and hydroxymethyl radical pair has a significant influence on the time behaviour of duroquinone radical anion. The intensity of triethylamine radical cation is found to be decreased with the increase of triethylamine concentration, which is interpreted that the triethylamine radical cation is deprotonated by the amine. Based on the FT-EPR results, a new complete mechanism is proposed.     

Hydrogen-atom abstraction from the adenine-uracil base pair

The hydrogen-abstracted radicals from the adenine-uracil (AU) base pair have been studied at the B3LYP/DZP++ level of theory. The A(N9)-U and A-U(N1) radicals, which correspond to hydrogen-atom abstraction at the adenine N9 and uracil N1 atoms, respectively, were predicted to be the two lowest-lying among the nine (AU-H) radicals studied in this study. The removal of the amino hydrogen of the adenine moiety that forms a hydrogen bond with the uracil O4 atom in the AU pair resulted in radical A(N6a)-U, which has the smallest base-pair dissociation energy, 5.9 kcal mol(-1). This radical is more likely to dissociate into the two isolated bases than to recover the hydrogen bond with the O4 atom through N6-H bond rotation along the C6-N6 bond. In general, the radicals generated by C-H bond breaking were higher in energy than those arising from N-H bond cleavage, because the unpaired electrons in the carbon-centered radicals were mainly localized on the carbon atom from which the hydrogen atom was removed. However, the highest-lying radical was found to arise from removal of the N3 hydrogen of uracil. The most remarkable structural feature of this radical is a very short C-H...O distance of 2.094 A, consistent with a substantial hydrogen bond. Although this radical lost the N1...H-N3 hydrogen bond between the two bases, its dissociation energy was predicted to be 12.9 kcal mol(-1), similar to that of the intact AU base pair. This is due to the transfer of electron density from the adenine N1 atom to the uracil N3 atom.     

Radical conversion and migration in electron capture dissociation

Electron capture dissociation (ECD) is an important analytical technique which is used frequently in proteomics experiments to reveal information about both primary sequence and post-translational modifications. Although the utility of ECD is unquestioned, the underlying chemistry which leads to the observed fragmentation is still under debate. Backbone dissociation is frequently the exclusive focus when mechanistic questions about ECD are posed, despite the fact that numerous other abundant dissociation channels exist. Herein, the focus is shifted to side chain loss and other dissociation channels which offer clues about the underlying mechanism(s). It is found that the initially formed hydrogen abundant radicals in ECD can convert quickly to hydrogen deficient radicals via a variety of pathways. Dissociation which occurs subsequent to this conversion is mediated by hydrogen deficient radical chemistry, which has been the subject of extensive study in experiments which are independent from ECD. Statistical analysis of fragments observed in ECD is in excellent agreement with predictions made by an understanding of hydrogen deficient radical chemistry. Furthermore, hydrogen deficient radical mediated dissociation likely contributes to observed ECD fragmentation patterns in unexpected ways, such as the selective dissociation observed at disulfide bonds. Many aspects of dissociation observed in ECD are easily reproduced in well-controlled experiments examining hydrogen deficient radicals generated by non-ECD methods. All of these observations indicate that when considering the means by which electron capture leads to dissociation, hydrogen deficient radical chemistry must be given careful consideration.     

Homolytic reductive alkylation of methylvinyl ketone with ethers by Ti(III) decomposition of t-butyl hydroperoxide

Reductive alkylatin of methylvinylketone has been accomplished by hydrogen abstraction from cyclic ethers with the redox couple: t-butyl hydroperoxide-titanous chloride. A redox radical mechanism is proposed and the selectivity of the hydrogen abstraction by t-butoxy radicals and reduction of α-ketoalkyl radical by titanous ions is discussed.     

Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues

Radical S‐adenosyl‐l ‐methionine (SAM) enzymes utilize a [4Fe‐4S] cluster to bind SAM and reductively cleave its carbon–sulfur bond to produce a highly reactive 5′‐deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical‐based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical‐based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside‐containing compounds by using radical SAM‐dependent reactions.     

Thiyl radical-mediated cleavage of allylic C-N bonds: scope, limitations, and theoretical support to the mechanism

Thiols mediate the radical isomerization of allylic amines into enamines. The reaction results in the cleavage of the allylic C-N bond, after treatment with aqueous HCl. The mechanism involves the abstraction of an allylic hydrogen alpha to nitrogen by thiyl radical, followed by a return hydrogen transfer from the thiol to the carbon gamma to nitrogen in the intermediate allylic radical. The scope and limitations of the reaction with respect to the nature of the thiol, to the structure of the allylic chain, and to the nature of the substituents at nitrogen were investigated. The experimental results were interpreted on the ground of DFT calculations of the C-Halpha BDE in the starting allylic amines, and of the C-Hgamma BDE in the resulting enamines. The efficiency of the initial hydrogen transfer is the first requirement for the reaction to proceed. A balance must be found between the S-H BDE and the two above-mentioned C-H BDEs. The incidence of stereoelectronic factors was analyzed through NBO calculations performed on the optimized geometries of the starting allylic amines. Additional calculations of the transition structures and subsequent tracing of the reaction profiles were performed for the abstraction of Halpha from both the allyl and the prenyl derivatives by p-TolS(*). The latter allowed us to estimate the rate constant for the abstraction of hydrogen by thiyl radical from an N-prenylamine and an N-allylamine.     

Mechanistic insights on how hydroquinone disarms OH and OOH radicals

Phenol derivatives are distinguished as successful free radical scavengers. We present a detailed analysis of hydroxyl hydrogen abstraction from hydroquinone by hydroxyl and hydroperoxyl radical with emphasis on changes that take place in the vicinity of the transition state. Quantum theory of atoms in molecules is employed to elucidate the sequence of positive and negative charge transfer by studying selected properties of the three key atoms (the transferring hydrogen, the donor atom, and the acceptor atom) along intrinsic reaction path. The presented results imply that in both reactions, which are examples of proton coupled electron transfer, proton, and electron get simultaneously transferred to the radical oxygen atom. The fact that the hydrogen's charge and volume do not monotonously change in the vicinity of the transition state in the product valley results from the adjacency of the proton and the electron to the donor and the acceptor oxygen atoms. Obtaining a detailed understanding of mechanisms by which free radicals are disarmed is of paramount importance given the effects of those highly reactive species on biological systems. A comprehensive analysis of hydroxyl hydrogen abstraction from hydroquinone by hydroxyl and hydroperoxyl radicals, based on changes of selected electronic properties of the three most relevant atoms (hydrogen donor, hydrogen acceptor, and the hydrogen itself), along the reaction coordinate, can be obtained by first‐principles calculations.     

Oxygen-dependent DNA damage amplification involving 5,6-dihydrothymidin-5-yl in a structurally minimal system.

5,6-Dihydrothymidin-5-yl (1) was independently generated in a dinucleotide from a phenyl selenide precursor (4). Under free radical chain propagation conditions, the products resulting from hydrogen atom donation and radical-pair reaction are the major observed products in the absence of O(2). The stereoselectivity of the trapping process is dependent on the structure of the hydrogen atom donor. No evidence for internucleotidyl hydrogen atom abstraction by 1 was detected. The tandem lesion (17) resulting from hydrogen atom abstraction from the C1' position of the adjacent 2'-deoxyuridine by the peroxyl radical derived from 1 (3) is observed under aerobic conditions. The structure of this product is confirmed by independent synthesis and its transformation into a second independently synthesized product (24). Internucleotidyl hydrogen atom abstraction is effected selectively by the 5S-diastereomer of the peroxyl radical. The formation of dinucleotide 17 provides further support for the novel O(2)-dependent DNA damage amplification mechanism involving 1 reported previously (Greenberg, M. M.; et al. J. Am. Chem. Soc. 1997, 119, 1828).     

The capacity of an α-nitroalkyl radical for hydrogen abstraction

Photochemical decomposition of 2-iodo-2-nitroadamantane in several hydrogen donating solvents, gives rise to formation of α-nitroalkyl radicals. Such ambident radicals can abstract hydrogen from the solvent via oxygen, resulting in a nitronic acid which decomposes exlusively into adamantanone. Alternately the abstraction can take place via carbon to give 2-nitroadamantane. The product distribution is strongly influenced by electron-withdrawing substituents in the hydrogen donor. The oxidation products derived from the solvent have been detected. All the experiments point towards a minor stabilisation of a carbon radical by a nitro group. INDO-calculations on the nitromethyl radical are in good agreement with this lack of stabilization.     

Mechanism of the hydrogen transfer from the OH group to oxygen-centered radicals: proton-coupled electron-transfer versus radical hydrogen abstraction

High-level ab initio electronic structure calculations have been carried out with respect to the intermolecular hydrogen-transfer reaction HCOOH+.OH-->HCOO.+H(2)O and the intramolecular hydrogen-transfer reaction .OOCH2OH-->HOOCH(2)O.. In both cases we found that the hydrogen atom transfer can take place via two different transition structures. The lowest energy transition structure involves a proton transfer coupled to an electron transfer from the ROH species to the radical, whereas the higher energy transition structure corresponds to the conventional radical hydrogen atom abstraction. An analysis of the atomic spin population, computed within the framework of the topological theory of atoms in molecules, suggests that the triplet repulsion between the unpaired electrons located on the oxygen atoms that undergo hydrogen exchange must be much higher in the transition structure for the radical hydrogen abstraction than that for the proton-coupled electron-transfer mechanism. It is suggested that, in the gas phase, hydrogen atom transfer from the OH group to oxygen-centered radicals occurs by the proton-coupled electron-transfer mechanism when this pathway is accessible.