Reactions of charged phenyl radicals with aliphatic amino acids in the gas phase

Gas-phase reactivity of five differently substituted positively charged phenyl radicals was examined toward six amino acids by using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR). The reactivity of the radicals studied was determined by the electrophilicity of the radical, which can be characterized by the radical's electron affinity (EA). The larger the electron affinity of the radical, the higher the overall reaction rate. In addition to the expected H-atom abstraction, several unprecedented reaction pathways were observed, including NH2 abstraction, SH abstraction, and SCH3 abstraction. These reaction pathways dominate for the most electrophilic radicals, and they may not follow radical but rather nucleophilic addition-elimination mechanisms. Hydrogen abstraction from glycine was also investigated theoretically. The results indicate that hydrogen abstraction from alphaC of glycine is both kinetically and thermodynamically favored over the NH2 group. The ordering of transition state energies for hydrogen abstraction from the alphaC and NH2 groups was found to reflect the radicals' EA ordering.     

Theoretical and experimental investigations on the reactions of positively charged phenyl radicals with aromatic amino acids

The chemical behavior of positively charged phenyl radicals 3-dehydro-N-phenylpyridinium (a), N-(3-dehydro-5-chlorophenyl)pyridinium (b), and N-(3-dehydrophenyl)pyridinium (c) toward L-tyrosine, phenylalanine, and tryptophan was investigated in the gas phase both theoretically by performing molecular orbital calculations and experimentally by using FT/ICR mass spectrometry. All radicals react with phenylalanine and tryptophan nearly at the collision rate. The overall reactivity of the radicals toward tyrosine follows the order a > b > c, which is consistent with the electron affinity (EA) ordering of the radicals. The higher the electrophilicity (or EA) of the radical, the greater the reactivity. As expected, all radicals abstract a hydrogen atom from all of the amino acids. However, the most electrophilic radical a was also found to react with these amino acids via NH2 abstraction. A new reaction observed between radicals a-c and aromatic amino acids is the addition of the radical to the aromatic ring of the amino acid followed by Calpha-Cbeta bond cleavage, which leads to side-chain abstraction by the radical.     

Reactivity of substituted charged phenyl radicals toward components of nucleic acids

Reactions of differently substituted phenyl radicals with components of nucleic acids have been investigated in the gas phase. A positively charged group located meta with respect to the radical site was employed to allow manipulation of the radicals in a Fourier-transform ion cyclotron resonance mass spectrometer. All of these electrophilic radicals react with sugars via exclusive hydrogen atom abstraction, with adenine and uracil almost exclusively via addition (likely at the C8 and C5 carbons, respectively), and with the nucleoside thymidine by hydrogen atom abstraction and addition at C5 in the base moiety (followed by elimination of (*)CH(3)). These findings parallel the reactivity of the phenyl radical with components of nucleic acids in solution, except that the selectivity for addition is different. Like HO(*), the electrophilic charged phenyl radicals appear to favor addition to the C5-end of the C5-C6 double bond of thymine and thymidine, whereas the phenyl radical preferentially adds to C6. The charged phenyl radicals do not predominantly add to thymine, as the neutral phenyl radical and HO(*), but mainly react by hydrogen atom abstraction from the methyl group (some addition to C5 in the base followed by loss of (*)CH(3) also occurs). Adenine appears to be the preferred target among the nucleobases, while uracil is the least favored. A systematic increase in the electrophilicity of the radicals by modification of the radicals' structures was found to facilitate all reactions, but the addition even more than hydrogen atom abstraction. Therefore, the least reactive radicals are most selective toward hydrogen atom abstraction, while the most reactive radicals also efficiently add to the base. Traditional enthalpy arguments do not rationalize the rate variations. Instead, the rates reflect the radicals' electron affinities used as a measure for their ability to polarize the transition state of each reaction.     

Gas‐phase radical–radical recombination reactions of nitroxides with substituted phenyl radicals

Fourier‐transform ion cyclotron resonance mass spectrometry has been used to examine gas‐phase reactions of four different nitroxide free radicals with eight positively charged pyridyl and phenyl radicals (some containing a Cl, F, or CF₃ substituent). All the radicals reacted rapidly (near collision rate) with nitroxides by radical–radical recombination. However, some of the radicals were also able to abstract a hydrogen atom from the nitroxide. The results establish that the efficiency (k_reaction/k_collision) of hydrogen atom abstraction varies with the electrophilicity of the radical, and hence is attributable to polar effects (a lowering of the transition‐state energy by an increase in its polar character). The efficiency of the recombination reaction is not sensitive to substituents, presumably due to a very low reaction barrier. Even so, after radical–radical recombination has occurred, the nitroxide adduct was found to fragment in different ways depending on the structure of the radical. For example, a cationic fragment was eliminated from the adducts of the more electrophilic radicals via oxygen anion abstraction by the radical (i.e., the nitroxide adduct cleaves heterolytically), whereas adducts of the less electrophilic radicals predominantly fragmented via homolytic cleavage (oxygen atom abstraction). Therefore, differences in the product branching ratios were found to be attributable to polar factors. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 36: 216–229 2004     

Substituent effects on the nonradical reactivity of 4-dehydropyridinium cation

Recent studies have shown that the reactivity of the 4-dehydropyridinium cation significantly differs from the reactivities of its isomers toward tetrahydrofuran. While only hydrogen atom abstraction was observed for the 2- and 3-dehydropyridinium cations, nonradical reactions were observed for the 4-isomer. In order to learn more about these reactions, the gas-phase reactivities of the 4-dehydropyridinium cation and several of its derivatives toward tetrahydrofuran were investigated in a Fourier transform ion electron resonance mass spectrometer. Both radical and nonradical reactions were observed for most of these positively charged radicals. The major parameter determining whether nonradical reactions occur was found to be the electron affinity of the radicals--only those with relatively high electron affinities underwent nonradical reactions. The reactivities of the monoradicals are also affected by hydrogen bonding and steric effects.     

An intrinsic radical stability scale from the perspective of bond dissociation enthalpies: a companion to radical electrophilicities

Bond dissociation enthalpies (BDEs) of a large series of molecules of the type A-B, where a series of radicals A ranging from strongly electrophilic to strongly nucleophilic are coupled with a series of 8 radicals (CH2OH, CH3, NF2, H, OCH3, OH, SH, and F) also ranging from electrophilic to nucleophilic, are computed and analyzed using chemical concepts emerging from density functional theory, more specifically the electrophilicities of the individual radical fragments A and B. It is shown that, when introducing the concept of relative radical electrophilicity, an (approximately) intrinsic radical stability scale can be developed, which is in good agreement with previously proposed stability scales. For 47 radicals, the intrinsic stability was estimated from computed BDEs of their combinations with the strongly nucleophilic hydroxymethyl radical, the neutral hydrogen atom, and the strongly electrophilic fluorine atom. Finally, the introduction of an extra term containing enhanced Pauling electronegativities in the model improves the agreement between the computed BDEs and the ones estimated from the model, resulting in a mean absolute deviation of 16.4 kJ mol(-1). This final model was also tested against 82 experimental values. In this case, a mean absolute deviation of 15.3 kJ mol(-1) was found. The obtained sequences for the radical stabilities are rationalized using computed spin densities for the radical systems.     

Computational Study on the Attack of .OH Radicals on Aromatic Amino Acids

The attack of hydroxyl radicals on aromatic amino acid side chains, namely phenylalanine, tyrosine, and tryptophan, have been studied by using density functional theory. Two reaction mechanisms were considered: 1) Addition reactions onto the aromatic ring atoms and 2) hydrogen abstraction from all of the possible atoms on the side chains. The thermodynamics and kinetics of the attack of a maximum of two hydroxyl radicals were studied, considering the effect of different protein environments at two different dielectric values (4 and 80). The obtained theoretical results explain how the radical attacks take place and provide new insight into the reasons for the experimentally observed preferential mechanism. These results indicate that, even though the attack of the first ^.OH radical on an aliphatic C atom is energetically favored, the larger delocalization and concomitant stabilization that are obtained by attack on the aromatic side chain prevail. Thus, the obtained theoretical results are in agreement with the experimental evidence that the aromatic side chain is the main target for radical attack and show that the first ^.OH radical is added onto the aromatic ring, whereas a second radical abstracts a hydrogen atom from the same position to obtain the oxidized product. Moreover, the results indicate that the reaction can be favored in the buried region of the protein.     

Reactions of carbamyl radicals: intramolecular hydrogen abstraction reactions

ω-Phenylalkyl-N-methylcarbarnyl radicals undergo intermolecular addition to 3,3-dinethylbut-l-ene in preference to intramolecular hydrogen abstraction. Methyl N-(ω-phenylalkyl) carbanyl radicals and methyl N-pentylcarbamyi radicals readily abstract hydrogen through a six membered transition state or a seven membered transition state if the hydrogen is beniylic. The selectivities are interpreted in terms of the electrophilicity of the radical and the stereo-electronic requirements of hydrogen abstraction reactions.     

Intramolecular hydrogen abstraction promoted by amidyl radicals. Evidence for electronic factors in the nucleophilic cyclization of ambident amides to oxocarbenium ions

A tandem 1,5-hydrogen atom transfer/radical oxidation/nucleophilic cyclization mechanism is proposed for the intramolecular hydrogen abstraction reaction promoted for primary carboxamidyl radicals. The electron-withdrawing capacity of the C-5 substituent can switch the reaction to give exclusively bicyclic spirolactams (6-oxa-1-azaspiro[4.5]decan-2-one) when R(1) = H or spirolactones (1,6-dioxaspiro[4.5]decan-2-one) when R(1) = OAc. With a substituent of medium polarity (R(1) = OMe), a mixture of lactones and lactams is formed.     

Direct comparison of solution and gas-phase reactions of the three distonic isomers of the pyridine radical cation with methanol

To directly compare the reactivity of positively charged carbon-centered aromatic σ-radicals toward methanol in solution and in the gas phase, the 2-, 3-, and 4-dehydropyridinium cations (distonic isomers of the pyridine radical cation) were generated by ultraviolet photolysis of the corresponding iodo precursors in a mixture of water and methanol at varying pH. The reaction mixtures were analyzed by using liquid chromatography/mass spectrometry. Hydrogen atom abstraction was the only reaction observed for the 3- and 4-dehydropyridinium cations (and pyridines) in solution. This also was the major reaction observed earlier in the gas phase. Depending on the pH, the hydrogen atom can be abstracted from different molecules (i.e., methanol or water) and from different sites (in methanol) by the 3- and 4-dehydropyridinium cations/pyridines in solution. In the pH range 1-4, the methyl group of methanol is the main hydrogen atom donor site for both 3- and 4-dehydropyridinium cations (just like in the gas phase). At higher pH, the hydroxyl groups of water and methanol also act as hydrogen atom donors. This finding is rationalized by a greater abundance of the unprotonated radicals that preferentially abstract hydrogen atoms from the polar hydroxyl groups. The percentage yield of hydrogen atom abstraction by these radicals was found to increase with lowering the pH in the pH range 1.0-3.2. This pH effect is rationalized by polar effects: the lower the pH, the greater the fraction of protonated (more polar) radicals in the solution. This finding is consistent with previous results obtained in the gas phase and suggests that gas-phase studies can be used to predict solution reactivity, but only as long as the same reactive species is studied in both experiments. This was found not to be the case for the 2-iodopyridinium cation. Photolysis of this precursor in solution resulted in the formation of two major addition products, 2-hydroxy- and 2-methoxypyridinium cations, in addition to the hydrogen atom abstraction product. These addition products were not observed in the earlier gas-phase studies on 2-dehydropyridinium cation. Their observation in solution is explained by the formation of another reactive intermediate, the 2-pyridylcation, upon photolysis of 2-iodopyridinium cation (and 2-iodopyridine). The same intermediate was observed in the gas phase but it was removed before examining the reactions of the desired radical, 2-dehydropyridinium cation (which cannot be done in solution).     

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.     

The selectivity of charged phenyl radicals in hydrogen atom abstraction reactions with isopropanol

The vertical electron affinity is demonstrated to be a key factor in controlling the selectivity of charged phenyl radicals in hydrogen atom abstraction from isopropanol in the gas phase. The measurement of the total reaction efficiencies (hydrogen and/or deuterium atom abstraction) for unlabeled and partially deuterium-labeled isopropanol, and the branching ratios of hydrogen and deuterium atom abstraction, by using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, allowed the determination of the selectivity for each site in the unlabeled isopropanol. Examination of hydrogen atom abstraction from isopropanol by eight structurally different radicals revealed that the preferred site is the CH group. The selectivity of the charged phenyl radicals correlates with the radical's vertical electron affinity and the reaction efficiency. The smaller the vertical electron affinity of a radical, the lower its reactivity, and the greater the preference for the thermodynamically favored CH group over the CH3 group or the OH group. As the vertical electron affinity increases from 4.87 to 6.28 eV, the primary kinetic isotope effects decrease from 2.9 to 1.3 for the CD group, and the mixture of primary and alpha-secondary kinetic isotopes decreases from 6.0 to 2.4 for the CD3 group.     

Design of radical-resistant amino acid residues: a combined theoretical and experimental investigation

Ab initio calculations have been used to design radical-resistant amino acid residues. Optimized structures of free and protected amino acids and their corresponding alpha-carbon-centered radicals were determined with B3-LYP/6-31G(d). Single-point RMP2/6-31G(d) calculations on these structures were then used to obtain radical stabilization energies, to examine the effect of steric repulsion between the side chains and amide carbonyl groups on the stability of alpha-carbon-centered peptide radicals. Relative to glycine, the destabilization for alanine and valine residues was found to be approximately 9 and 18 kJ mol(-1), respectively, which correlates with the reactivity of analogous amino acid residues in peptides toward hydrogen atom abstraction in conventional free radical reactions. To design amino acid residues that would resist radical reactions, strategies by which the steric effects could be magnified were considered. This resulted in the identification of tert-leucine and 3,3,3-trifluoroalanine as suitable molecules. With these amino acid residues, the destabilization of the alpha-carbon-centered radicals relative to that of glycine is increased substantially to approximately 36 and 41 kJ mol(-1), respectively. The theoretical predictions have been supported by experimental observations: a tert-leucine derivative was shown to be very slow to react with N-bromosuccinimide, while the corresponding trifluoroalanine derivative was found to be inert.     

Reductive tert-Butylation of Anils by tert-Butylmercury Halides(1)

tert-Butyl radicals add to the carbon atom of benzylideneanilines to form anilino radicals, which are protonated in the presence of PTSA or NH(4)(+) in Me(2)SO. Reduction of the resulting aniline radical cations occurs readily by the ate complex, t-BuHgI(2)(-). In the absence of a proton donor, t-BuHgI will also transfer a hydrogen atom to the anilino radical to give the reductive alkylation product. Protonation can promote a free radical chain process involving electron transfer by substrate activation and/or by increasing the electron affinity of the intermediate radicals. Since the adduct radicals formed from benzylideneanilines are more easily protonated than the parent Schiff bases, PTSA but not NH(4)(+) demonstrates substrate activation, although both proton donors promote the free radical reaction.     

Model Calculations of Radiation-Induced Damage in 1-Methyluracil:9-Ethyladenine

Detailed EPR and ENDOR experiments on the cocrystalline complex of 1-methyluracil:9-Ethyladenine (MUEA) have revealed that the major radiation-induced products observed at 10 K on MU are: MUEA1, a radical formed by net hydrogen abstraction from the N1-CH₃ methyl group, MUEA2, the MU radical anion, and MUEA3, the C5 H-addition radical. The following four products were observed on the adenine moiety at 10 K, MUEA4, the N3 protonated adenine anion, MUEA5, the native adenine cation, MUEA6, the amino deprotonated adenine cation, and MUEA7, the C8 H-addition radical formed by net H-addition to C8 of the adenine base. The geometries, energetics, and hyperfine properties of all possible radicals of MU and EA, the native anions and cations, as well as radicals formed via net hydrogen atom abstraction (deprotonated cations) or addition (protonated anions) were investigated theoretically. All systems were optimized using the hybrid Hartree–Fock–density functional theory functional B3LYP, in conjunction with the 6-31G(d,p) basis set of Pople and co-workers. Calculations of the anisotropic hyperfine couplings for all the radicals observed in MUEA are presented and are shown to compare favorably with the experimentally measured hyperfine couplings. The calculated ionizations potentials indicate that EA would be the preferred oxidation site. In MUEA, both the adenine cation and its N4-deprotonated derivative were observed. The calculated electron affinities indicate that MU would be the preferred reduction site. In MUEA radical, MUEA2 is a uracil reduction product, however the protonation state of this radical could not be determined experimentally. Calculations suggest that MUEA2 is actually the C4=O protonated anion.     

Hydrogen atom abstraction reactions from tertiary amines by benzyloxyl and cumyloxyl radicals: influence of structure on the rate-determining formation of a hydrogen-bonded prereaction complex

A time-resolved kinetic study on the hydrogen atom abstraction reactions from a series of tertiary amines by the cumyloxyl (CumO(?)) and benzyloxyl (BnO(?)) radicals was carried out. With the sterically hindered triisobutylamine, comparable hydrogen atom abstraction rate constants (k(H)) were measured for the two radicals (k(H)(BnO(?))/k(H)(CumO(?)) = 2.8), and the reactions were described as direct hydrogen atom abstractions. With the other amines, increases in k(H)(BnO(?))/k(H)(CumO(?)) ratios of 13 to 2027 times were observed. k(H) approaches the diffusion limit in the reactions between BnO(?) and unhindered cyclic and bicyiclic amines, whereas a decrease in reactivity is observed with acyclic amines and with the hindered cyclic amine 1,2,2,6,6-pentamethylpiperidine. These results provide additional support to our hypothesis that the reaction proceeds through the rate-determining formation of a C-H/N hydrogen-bonded prereaction complex between the benzyloxyl α-C-H and the nitrogen lone pair wherein hydrogen atom abstraction occurs, and demonstrate the important role of amine structure on the overall reaction mechanism. Additional mechanistic information in support of this picture is obtained from the study of the reactions of the amines with a deuterated benzyloxyl radical (PhCD(2)O(?), BnO(?)-d(2)) and the 3,5-di-tert-butylbenzyloxyl radical.     

Photolysis of 1-alkylcycloalkanols in the presence of (diacetoxyiodo)benzene and I2. Intramolecular selectivity in the beta-scission reactions of the intermediate 1-alkylcycloalkoxyl radicals

The C-C beta-scission reactions of 1-alkylcycloalkoxyl radicals, generated photochemically by visible light irradiation of CH2Cl2 solutions containing the parent 1-alkylcycloalkanols, (diacetoxy)iodobenzene (DIB), and I2, have been investigated through the analysis of the reaction products. The 1-alkylcycloalkoxyl radicals undergo competition between ring opening and C-alkyl bond cleavage as a function of ring size and of the nature of the alkyl substituent. With the 1-propylcycloheptoxyl, 1-propylcyclooctoxyl,and 1-phenylcyclooctoxyl radicals, formation of products deriving from an intramolecular 1,5-hydrogen atom abstraction reaction from the cycloalkane ring has also been observed. The results are discussed in terms of release of ring strain associated to ring opening, stability of the alkyl radical formed by C-alkyl cleavage, and with cycloheptoxyl and cyclooctoxyl radicals, also in terms of the possibility of achieving a favorable geometry for intramolecular hydrogen atom abstraction.     

Photosensitization by phenylalanine of carboxylic acids, amides, and peptides in frozen aqueous solution

Abstract— In order to elucidate the mechanism of the photosensitization of proteins and peptides by aromatic amino acids, the behaviour of aliphatic carboxylic acids and amides upon irradiation in frozen aqueous solution in the presence of phenylalanine (l-Phe) has been studied by EPR spectroscopy. EPR signals are much stronger when acids or amides are irradiated in the presence of l-Phe, showing that they are photosensitized by the aromatic amino acid. The species observed are either alkyl radicals, or radicals formed by abstraction of a hydrogen atom from a molecule of acid or arnide. A mechanism is proposed which involves the capture by carboxyl or amide carbonyl groups of hydrated electrons released by the photo-excited l-Phe, followed by the splitting of the resulting anion free radical with the formation of alkyl radicals, and transfer reactions leading to more stable free radicals. In peptides, which are also photosensitized by l-Phe, electrons are captured preferably by the carboxylic carbonyl groups.     

Electron super-rich radicals in the gas phase. A neutralization-reionization mass spectrometric and ab initio/RRKM study of diaminohydroxymethyl and triaminomethyl radicals

Diaminohydroxymethyl (1) and triaminomethyl (2) radicals were generated by femtosecond collisional electron transfer to their corresponding cations (1+ and 2+, respectively) and characterized by neutralization-reionization mass spectrometry and ab initio/RRKM calculations at correlated levels of theory up to CCSD(T)/aug-cc-pVTZ. Ion 1+ was generated by gas-phase protonation of urea which was predicted to occur preferentially at the carbonyl oxygen with the 298 K proton affinity that was calculated as PA = 875 kJ mol-1. Upon formation, radical 1 gains vibrational excitation through Franck-Condon effects and rapidly dissociates by loss of a hydrogen atom, so that no survivor ions are observed after reionization. Two conformers of 1, syn-1 and anti-1, were found computationally as local energy minima that interconverted rapidly by inversion at one of the amine groups with a <7 kJ mol-1 barrier. The lowest energy dissociation of radical 1 was loss of the hydroxyl hydrogen atom from anti-1 with ETS = 65 kJ mol-1. The other dissociation pathways of 1 were a hydroxyl hydrogen migration to an amine group followed by dissociation to H2N-C=O* and NH3. Ion 2+ was generated by protonation of gas-phase guanidine with a PA = 985 kJ mol-1. Electron transfer to 2+ was accompanied by large Franck-Condon effects that caused complete dissociation of radical 2 by loss of an H atom on the experimental time scale of 4 mus. Radicals 1 and 2 were calculated to have extremely low ionization energies, 4.75 and 4.29 eV, respectively, which belong to the lowest among organic molecules and bracket the ionization energy of atomic potassium (4.34 eV). The stabilities of amino group containing methyl radicals, *CH2NH2, *CH(NH2)2, and 2, were calculated from isodesmic hydrogen atom exchange with methane. The pi-donating NH2 groups were found to increase the stability of the substituted methyl radicals, but the stabilities did not correlate with the radical ionization energies.     

Synchrotron photoionization measurements of OH-initiated cyclohexene oxidation: ring-preserving products in OH + cyclohexene and hydroxycyclohexyl + O2 reactions

Earlier synchrotron photoionization mass spectrometry experiments suggested a prominent ring-opening channel in the OH-initiated oxidation of cyclohexene, based on comparison of product photoionization spectra with calculated spectra of possible isomers. The present work re-examines the OH + cyclohexene reaction, measuring the isomeric products of OH-initiated oxidation of partially and fully deuterated cyclohexene. In particular, the directly measured photoionization spectrum of 2-cyclohexen-1-ol differs substantially from the previously calculated Franck-Condon envelope, and the product spectrum can be fit with no contribution from ring-opening. Measurements of H(2)O(2) photolysis in the presence of C(6)D(10) establish that the addition-elimination product incorporates the hydrogen atom from the hydroxyl radical reactant and loses a hydrogen (a D atom in this case) from the ring. Investigation of OH + cyclohexene-4,4,5,5-d(4) confirms this result and allows mass discrimination of different abstraction pathways. Products of 2-hydroxycyclohexyl-d(10) reaction with O(2) are observed upon adding a large excess of O(2) to the OH + C(6)D(10) system.