Isomerization Of Radicals Research Articles

Intramolecular hydrogen atom migration along the backbone of cationic and neutral radical tripeptides and subsequent radical-induced dissociations

Dissociation of peptide radical ions involves competition between charge-induced and radical-induced reactions that can be preceded by isomerization. The isomeric radical cations of the peptide methyl ester [G˙GR-OMe](+) and [GG˙R-OMe](+) provide very similar collision-induced dissociation (CID) spectra, suggesting that isomerization occurs prior to fragmentation. They undergo characteristic radical-induced bond cleavage of the peptide N-terminal amide bond resulting in the y2(+) ion, and of the arginine side-chain's Cα-Cβ bond giving protonated allylguanidine {[CH2[double bond, length as m-dash]CHCH2NHC(NH2)2](+), m/z 100}. The absence of a y2(+) fragment ion in the CID of the radical cationic tripeptide [ACH3G˙R](+) and of an m/z 100 ion in the spectrum of [G˙ACH3R](+) (where ACH3 is an α-aminoisobutyric acid residue, which cannot form an α-carbon-centered radical through hydrogen atom transfer) establishes the importance of hydrogen atom migration along the peptide backbone prior to specific radical-induced fragmentations. Herein we use density functional theory (DFT) at the B3LYP/6-31++G(d,p) level to evaluate the barriers for interconversion between the α-carbon-centered radicals and for dissociation. The radical cations [G˙GR](+) and [GG˙R](+) have their radicals located on the α-carbon atoms of the peptide backbone and their charge densities largely sequestered on the guanidine groups of the side-chain of arginine residues. This is in contrast to the isomeric radical cations of [GGG]˙(+), in which the charge resides necessarily on the peptide backbone. The lower charge densities on the backbones of [G˙GR](+) and [GG˙R](+) result in greater structural flexibility, decreasing the barrier for interconversion between these α-carbon-centered radicals to 36.2 kcal mol(-1) (cf. 44.7 kcal mol(-1) for [GGG]˙(+)). The total absence of charge, assessed by examining intramolecular hydrogen atom transfers among the three α-carbon centers of the isomeric neutral α-carbon-centered triglycine radicals [GGG-H]˙, leads to an additional but slight reduction in enthalpy, to approximately 34 kcal mol(-1).

Confirmed assignments of isomeric dimethylbenzyl radicals generated by corona discharge

The controversial vibronic assignments of isomeric dimethylbenzyl radicals were clearly resolved by using different precursors. By employing corresponding dimethylbenzyl chlorides as precursors, we identified the origins of the vibronic bands of the dimethylbenzyl radicals generated by corona discharge of 1,2,4-trimethylbenzene. From the analysis of the spectra observed from the dimethylbenzyl chlorides in a corona excited supersonic expansion, we revised previous assignments of the 3,4-, 2,4-, and 2,5-dimethylbenzyl radicals. Spectroscopic data of electronic transition and vibrational mode frequencies in the ground electronic state of each isomer were accurately determined by comparing them with those obtained by an ab initio calculation and with the known vibrational data of 1,2,4-trimethylbenzene.

Reactions of OH Radicals with C6–C10 Cycloalkanes in the Presence of NO: Isomerization of C7–C10 Cycloalkoxy Radicals

Rate constants have been measured for the reactions of OH radicals with a series of C(6)-C(10) cycloalkanes and cycloketones at 298 ± 2 K, by a relative rate technique. The measured rate constants (in units of 10(-12) cm(3) molecule(-1) s(-1)) were cycloheptane, 11.0 ± 0.4; cyclooctane, 13.5 ± 0.4; cyclodecane, 15.9 ± 0.5; cyclohexanone, 5.35 ± 0.10; cycloheptanone, 9.57 ± 0.41; cyclooctanone, 15.4 ± 0.7; and cyclodecanone, 20.4 ± 0.8, where the indicated errors are two least-squares standard deviations and do not include uncertainties in the rate constant for the reference compound n-octane. Formation yields of cycloheptanone from cycloheptane (4.2 ± 0.4%), cyclooctanone from cyclooctane (0.85 ± 0.2%), and cyclodecanone from cyclodecane (4.9 ± 0.5%) were also determined by gas chromatography, where the molar yields are in parentheses. Analyses of products by direct air sampling atmospheric pressure ionization mass spectrometry and by combined gas chromatography-mass spectrometry showed, in addition to the cycloketones, the presence of cycloalkyl nitrates, cyclic hydroxyketones, hydroxydicarbonyls, hydroxycarbonyl nitrates, and products attributed to carbonyl nitrates and/or cyclic hydroxynitrates. The observed formation of cyclic hydroxyketones from the cycloheptane, cyclooctane and cyclodecane reactions, with estimated molar yields of 46%, 28%, and 15%, respectively, indicates the occurrence of cycloalkoxy radical isomerization. Potential reaction mechanisms are presented, and rate constants for the various alkoxy radical reactions are derived.

Isomeric Trimethylbenzyl Radicals Produced by Corona Discharge of 1,2,3,5-Tetramethylbenzene

Isomeric trimethylbenzyl radicals were generated and vibronically excited from precursor 1,2,3,5-tetramethylbenzene, isodurene, with a large amount inert carrier gas helium in a corona excited supersonic expansion (CESE) using a pinhole-type glass nozzle. A long-path monochromator was used to record the visible vibronic emission spectra of the jet-cooled benzyl-type radicals in the electronic transition. From the analysis of the spectra, we identified the evidence of the presence of three isomeric trimethylbenzyl radicals in the corona discharge, and obtained the electronic energy and a few vibrational mode frequencies in the ground electronic state for each isomer.

Spectroscopic Identification of Isomeric Trimethylbenzyl Radicals Generated from 1,2,3,4-Tetramethylbenzene

The visible vibronic emission spectrum was recorded from the corona discharge of precursor 1,2,3,4-tetramethylbenzene with a large amount of inert carrier gas helium using a pinhole-type glass nozzle coupled with corona excited supersonic expansion. The spectrum showed a series of vibronic bands in the electronic transition of jet-cooled benzyl-type radicals formed from the precursor in a corona excitation. The analysis confirmed that two isomeric radicals, 2,3,4- and 2,3,6-trimethylbenzyl radicals, were produced as a result of removal of a hydrogen atom from the methyl group at different substitution positions. For each isomeric product, the electronic transition and a few vibrational mode frequencies were determined in the ground electronic state.

Isomerization of dehydrofulvene radicals to the phenyl radical, and application to the growth of polycyclic aromatic hydrocarbons

AbstractIn this work, the isomerization mechanisms of dehydrofulvene radicals to the phenyl radical are described. This study shows, for 6‐dehydrofulvene, a low‐energy isomerization path going through a resonantly stabilized bicyclic system. In a second part, the different established mechanisms are applied to the closing of a second and third aromatic ring. This application highlights the possibility of forming new products, such as 2‐naphthyl radical, and the effect of aromatic cycles on the new mechanisms. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

Theoretical Study of Isomerization and Dissociation Transition States of C3H5O Radical Isomers: Ab Initio Characterization of the Critical Points and Statistical Transition-State Theory Modeling of the Dynamics

I use coupled-cluster theory and a modest basis set, aug-cc-pVDZ, to calculate structures and harmonic vibrational frequencies of local minima and transition states on the C(3)H(5)O potential energy surface. Accurate energies are computed using explicitly correlated coupled-cluster methods and a large basis set, cc-pVQZ-F12, to approach the one-particle basis set limit. My computations characterize eight additional stable radical structures on the global potential energy surface for this system. Additionally, this study encompasses many more isomerization and dissociation pathways, both between previously known intermediates and ones first characterized here. Analysis of the transition states and statistical transition-state theory results shows that energetically small barriers connect many of the alkenol and epoxide intermediates to the straight-chain alkoxy isomers, leading to significant branching to these alkoxy radical intermediates. Facile isomerization to these alkoxy intermediates is significant because the barrier heights leading to H + acrolein and HCO + C(2)H(4) product channels are energetically accessible even at low vibrational energies. The low dissociation barrier heights and loose transition states of these pathways result in unimolecular dissociation as opposed to isomerization to a different C(3)H(5)O intermediate.

DFT studies of N-alkoxyaminyl radicals: ESR parameters, UV–vis absorptions and generations

Although aminoxyl radicals ( RR ′ N O ˙ ) are well-known as organic stable free radicals, the isomeric radicals, N-alkoxyaminyl radicals ( R N ˙ OR ′ ) , are scarcely studied in the area of theoretical study. We carried out the theoretical calculation of the isotropic 14N hyperfine coupling constants ( a N), g-factors, electronic absorbances, and generation mechanisms of N-alkoxyaminyl radicals. For thirty one N-alkoxyaminyl radicals, the PCM-DFT calculation at B3LYP/6-31+G(d,p) could well reproduce the experimental data of a N and g-factors, where R 2 were 0.9796 and 0.9439, respectively. The UV–vis spectra were moderately reproduced by PCM-TD-DFT (PBE0/6-31+G(d,p)), where R 2 was 0.9205. Additionally, the use of a linear scaling procedure precisely reproduced the UV–vis spectrum. The activation Gibbs free energies for the generation of N-alkoxyaminyl radicals and aminoxyl radicals in the competing reactions of nitroso compounds with alkyl radicals were estimated by DFT and coupled cluster calculations. The activation free energies for the generation of N-alkoxyaminyl radicals were estimated to be 9–18 kcal/mol at B3LYP/6-31+G(d,p). The reported product ratios in the competing reactions could be reasonably explained by the differences in the activation free energies.

The Isomerization of Methoxy Radical: Intramolecular Hydrogen Atom Transfer Mediated through Acid Catalysis

The catalytic ability of water, formic acid, and sulfuric acid to facilitate the isomerization of the CH(3)O radical to CH(2)OH has been studied. It is shown that the activation energies for isomerization are 30.2, 25.7, 4.2, and 2.3 kcal mol(-1), respectively, when the reaction is carried out in isolation and with water, formic acid, or sulfuric acid as a catalyst. The formation of a doubly hydrogen bonded transition state is central to lowering the activation energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. The changes in the rate constant for the CH(3)O-to-CH(2)OH isomerization with acid catalysis have also been calculated at 298 K. The largest enhancement in the rate, by over 12 orders of magnitude, is with sulfuric acid. The results of the present study demonstrate the feasibility of acid catalysis of a gas-phase radical isomerization reaction that would otherwise be forbidden.

Tertiary alkoxyl radicals from 3-alkoxythiazole-2(3 H)-thiones

This study deals with the synthesis of tert- O-alkyl thiohydroxamates and their use as tert-alkoxyl radical precursors. tert-Alkoxyl radicals were applied in mechanistic studies to determine rate constants of (i) p-chlorocumyloxyl radical addition to bicyclo[2.2.1]heptene ( k=1×10 7 M −1 s −1), (ii) 2-phenylhex-5-en-2-oxyl radical 5- exo- trig-cyclization ( k cis=3×10 9 s −1, k trans=1×10 9 s −1), and (iii) 2-methyl-5-phenylpent-2-oxyl to 2-hydroxy-2-methyl-5-phenylpent-5-yl radical isomerization (1,5-H-atom shift; k=0.4–1.5×10 8 s −1). The reactions pose key steps in synthesis of 2,2,5-substituted tetrahydrofurans and 2-bromo-3-alkoxybicyclo[2.2.1]heptanes. Stereoselectivity in 5- exo- trig cyclization (2,5-cis) and intermolecular addition ( exo/endo>99:1), originates from torsional strain in transition structures of alkoxyl radical reactions.

Gas-phase ion-molecule reactions using regioselectively generated radical cations to model oxidative damage and probe radical sites in peptides

Collision induced dissociation (CID) of sodiated peptide derivatives containing a nitrate ester functionality was used to regiospecifically generate three isomeric radicals of the model peptide Bz-Ala-Gly-OMe corresponding to radicals formed at: C(α) of the alanine residue [4+Na](+); C(α) of the glycine residue [5+Na](+); and the side chain of alanine [6+Na](+). The ion-molecule reactions of these peptide radicals were examined to model oxidative damage to peptides and to probe whether the radical sites maintain their integrity or whether they isomerise via intramolecular hydrogen atom transfer (HAT). Only [6+Na](+) is reactive towards O(2), forming the peroxyl radical [7+Na](+), which loses O(2), HO˙ and HO(2)˙ under CID. The radical ion [7 + Na](+) abstracts a hydrogen atom from 4-fluorothiophenol to form the hydroperoxide [8+Na](+), which upon CID fragments via the combined loss of HO˙ and CH(2)O. In contrast, all three of the isomeric sodiated radicals react with NO˙ and NO(2)˙ to form adducts. CID of the NO adducts only regenerates the radicals via NO˙ loss, thus providing no structural information. In contrast, CID of the NO(2) adducts gives rise to a range of product ions and the spectra are different for each of the three adducts, suggesting that the isomeric radicals [4+Na](+), [5+Na](+) and [6+Na](+) are produced as discrete species. Finally, CID of the NO(2) adducts was used to probe the rearrangement of the radicals [4+Na](+), [5+Na](+) and [6+Na](+) prior to their reaction with NO(2)˙: [6 + Na](+) rearranges to a mixture of [4+Na](+) and [5+Na](+) while [5+Na](+) rearranges to [4+Na](+).

Oxidation mechanism of diethyl ether: a complex process for a simple molecule

A large number of organic compounds, such as ethers, spontaneously form unstable peroxides through a self-propagating process of autoxidation (peroxidation). Although the hazards of organic peroxides are well known, the oxidation mechanisms of peroxidizable compounds like ethers reported in the literature are vague and often based on old experiments, carried out in very different conditions (e.g. atmospheric, combustion). With the aim to (partially) fill the lack of information, in this paper we present an extensive Density Functional Theory (DFT) study of autoxidation reaction of diethyl ether (DEE), a chemical that is largely used as solvent in laboratories, and which is considered to be responsible for various accidents. The aim of the work is to investigate the most probable reaction paths involved in the autoxidation process and to identify all potential hazardous intermediates, such as peroxides. Beyond the determination of a complex oxidation mechanism for such a simple molecule, our results suggest that the two main reaction channels open in solution are the direct decomposition (β-scission) of DEE radical issued of the initiation step and the isomerization of the peroxy radical formed upon oxygen attack (DEEOO˙). A simple kinetic evaluation of these two competing reaction channels hints that radical isomerization may play an unexpectedly important role in the global DEE oxidation process. Finally industrial hazards could be related to the hydroperoxide formation and accumulation during the chain propagation step. The resulting information may contribute to the understanding of the accidental risks associated with the use of diethyl ether.

Multi-structural thermodynamics of C–H bond dissociation in hexane and isohexane yielding seven isomeric hexyl radicals

The C-H bond dissociation processes of n-hexane and isohexane involve 23 and 13 conformational structures, respectively in the parent molecules and 14-45 conformational structures in each of the seven isomeric products that we studied. Here we use the recently developed multi-structural (MS) thermodynamics method and CCSD(T)-F12a/jul-cc-pVTZ//M06-2X/6-311+G(2df,2p) potential energy surfaces to calculate the enthalpy, entropy, and heat capacity of n-hexane, isohexane, and seven of the possible radical products of dissociation of C-H bonds. We compare our calculations with the limited experimental data and with values obtained by group additivity fits used to extend the experimental data. This work shows that using the MS method involving a full set of structural isomers with density functional geometries, scaled density functional frequencies, and coupled cluster single-point energies can predict thermodynamic functions of complex molecules and bond dissociation reactions with chemical accuracy. The method should be useful to obtain thermodynamic data for complex molecules for which such data has not been measured and to obtain thermodynamic data at temperatures outside the temperature range where measurements are available.

On the intrinsic optical absorptions by tetrathiafulvalene radical cations and isomers

Gas-phase action spectroscopy shows unambiguously that the low-energy absorptions by tetramethylthiotetrathiafulvalene and tetrathianaphthalene cations in solution phase are due to monomers and not π-dimers.

Peroxy radical isomerization in the oxidation of isoprene

We report experimental evidence for the formation of C(5)-hydroperoxyaldehydes (HPALDs) from 1,6-H-shift isomerizations in peroxy radicals formed from the hydroxyl radical (OH) oxidation of 2-methyl-1,3-butadiene (isoprene). At 295 K, the isomerization rate of isoprene peroxy radicals (ISO2•) relative to the rate of reaction of ISO2• + HO2 is k(isom)(295)/(k(ISO2•+HO2)(295)) = (1.2 ± 0.6) x 10(8) mol cm(-3), or k(isom)(295) ≃ 0.002 s(-1). The temperature dependence of this rate was determined through experiments conducted at 295, 310 and 318 K and is well described by k(isom)(T)/(k(ISO2•+HO2)(T)) = 2.0 x 10(21) exp(-9000/T) mol cm(-3). The overall uncertainty in the isomerization rate (relative to k(ISO2•+HO2)) is estimated to be 50%. Peroxy radicals from the oxidation of the fully deuterated isoprene analog isomerize at a rate ∼15 times slower than non-deuterated isoprene. The fraction of isoprene peroxy radicals reacting by 1,6-H-shift isomerization is estimated to be 8-11% globally, with values up to 20% in tropical regions.

Structural comparisons of arachidonic acid-induced radicals formed by prostaglandin H synthase-1 and -2

Cyclooxygenase catalysis by prostaglandin H synthase (PGHS)-1 and -2 involves reaction of a peroxide-induced Tyr385 radical with arachidonic acid (AA) to form an AA radical that reacts with O 2. The potential for isomeric AA radicals and formation of an alternate tyrosyl radical at Tyr504 complicate analysis of radical intermediates. We compared the EPR spectra of PGHS-1 and -2 reacted with peroxide and AA or specifically deuterated AA in anaerobic, single-turnover experiments. With peroxide-treated PGHS-2, the carbon-centered radical observed after AA addition was consistently a pentadienyl radical; a variable wide-singlet (WS) contribution from mixture of Tyr385 and Tyr504 radicals was also present. Analogous reactions with PGHS-1 produced EPR signals consistent with varying proportions of pentadienyl and tyrosyl radicals, and two additional EPR signals. One, insensitive to oxygen exposure, is the narrow singlet tyrosyl radical with clear hyperfine features found previously in inhibitor-pretreated PGHS-1. The second type of EPR signal is a narrow singlet lacking detailed hyperfine features that disappeared upon oxygen exposure. This signal was previously ascribed to an allyl radical, but high field EPR analysis indicated that ~ 90% of the signal originates from a novel tyrosyl radical, with a small contribution from a carbon-centered species. The radical kinetics could be resolved by global analysis of EPR spectra of samples trapped at various times during anaerobic reaction of PGHS-1 with a mixture of peroxide and AA. The improved understanding of the dynamics of AA and tyrosyl radicals in PGHS-1 and -2 will be useful for elucidating details of the cyclooxygenase mechanism, particularly the H-transfer between tyrosyl radical and AA.

Detailed chemical kinetic reaction mechanisms for soy and rapeseed biodiesel fuels

A detailed chemical kinetic reaction mechanism is developed for the five major components of soy biodiesel and rapeseed biodiesel fuels. These components, methyl stearate, methyl oleate, methyl linoleate, methyl linolenate, and methyl palmitate, are large methyl ester molecules, some with carbon carbon double bonds, and kinetic mechanisms for them as a family of fuels have not previously been available. Of particular importance in these mechanisms are models for alkylperoxy radical isomerization reactions in which a C C double bond is embedded in the transition state ring. The resulting kinetic model is validated through comparisons between predicted results and a relatively small experimental literature. The model is also used in simulations of biodiesel oxidation in jet-stirred reactor and intermediate shock tube ignition and oxidation conditions to demonstrate the capabilities and limitations of these mechanisms. Differences in combustion properties between the two biodiesel fuels, derived from soy and rapeseed oils, are traced to the differences in the relative amounts of the same five methyl ester components.

Generation and characterization of distonic dehydrophenoxide radical anions under electrospray and atmospheric pressure chemical ionizations

We have explored the possibilities of generating radical anions under electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) conditions. By using different sets of ortho-, meta-, and para-isomers of nitrobenzoic acids, methylphenols, and nitrophenols, and m-, and p-isomers of hydroxybenzaldehydes and hydroxyacetophenones as the precursor molecules, we have successfully generated the isomeric distonic dehydrophenoxide radical anions (m/z 92) using the ESI process by applying relatively high capillary voltages, the in-source dissociation (ISD) condition. Under the same conditions, the o-hydroxybenzaldehyde and the o-hydroxyacetophenone yielded the even-electron dehydrophenoxide anion (m/z 93) due to the well-known ortho-effect. The distonic phenoxide radical anions at m/z 92 were also generated under APCI-ISD conditions by using m- and p-isomers of nitrobenzaldehydes and nitroacetophenones. While the o-nitrobenzaldehyde and the o-nitroacetophenone mainly yielded the phenoxide anion at m/z 93, due to the ortho-effect. The collision-induced dissociation (CID) experiments of all the anionic precursor molecules formed from either ESI or APCI produced comparable mass spectra as those observed in the ESI-ISD or the APCI-ISD experiments. The radical anions at m/z 92 reacted with CO 2 and O 2 to form the CO 2 adduct and the oxygen atom abstraction product, respectively, revealing the dual-character of the distonic radical anions, the phenide ion and the phenyl radical. Computational studies support the results of the ion-molecule reactions.

Evidence of Molecular Rearrangement in Benzyl-type Radicals

Searching for new molecular radicals which are believed to play an important role as reaction intermediates in aromatic chain reactions, we have applied the technique of corona excited supersonic expansion employing a pinhole-type glass nozzle to obtain the vibronic spectrum from the corona discharge of precursor 3,5-difluorotoluene with a large amount of inert carrier gas helium. An analysis of the observed spectrum revealed that many vibronic bands are from other isomeric difluorobenzyl radicals generated in the jet by migration of the fluorine atom or methylene group to the adjacent position in the 3,5-difluorobenzyl radical. A possible mechanism was proposed for the formation of other isomers by using a bridged cyclic intermediate structure.

Spectroscopic and Computational Studies on the Rearrangement of Ionized [1.1.1]Propellane and Some of its Valence Isomers: The Key Role of Vibronic Coupling

The [1.1.1]propellane radical cation 1(•+), generated by radiolytic oxidation of the parent compound in argon and Freon matrices at low temperatures, undergoes a spontaneous rearrangement to form the distonic 1,1-dimethyleneallene (or 2-vinylideneallyl) radical cation 3(•+) consisting of an allyl radical substituted at the 2-position by a vinyl cation. In similar matrix studies, it is found that the isomeric dimethylenecyclopropane radical cation 2(•+) also rearranges to 3(•+). The unusual molecular and electronic structure of 3(•+) has been established by the results of ESR, UV-vis, and IR spectroscopic measurements in conjunction with detailed theoretical calculations. Also of particular interest is an NIR photoinduced reaction by which 3(•+) is cleanly converted to the vinylidenecyclopropane radical cation 4(•+), a process that can be represented in terms of a single electron transfer from the allyl radical to the vinyl cation followed by allyl cation cyclization. The specificity of this photochemical reaction provides additional strong chemical evidence for the structure of 3(•+). Theoretical calculations reveal the decisive role of vibronic coupling in shaping the potential energy surfaces on which the observed ring-opening reactions take place. Thus vibronic interaction in 1(•+) mixes the (2)A(1)' ground state, characterized by its "non-bonding" 3a(1)' SOMO, with the (2)E'' first excited state resulting in the destabilization of a lateral C-C bond and the initial formation of the methylenebicyclobutyl radical cation 5(•+). The further rearrangement of 5(•+) to 3(•+) occurs via 2(•+) and proceeds through two additional lateral C-C bond cleavages characterized by transition states of extremely low energy, thereby explaining the absence of identifiable intermediates along the reaction pathway. In these consecutive ring-opening rearrangements, the "non-bonding" bridgehead C-C bond in 1(•+) is conserved and ultimately transformed into a normal bond characterized by a shorter C-C bond length. This work provides strong support for the Heilbronner-Wiberg interpretation of the vibrational structure in the photoelectron spectrum of 1 in terms of vibronic coupling.