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.     

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.     

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.     

Characterization of transient species in laser photolysis of aromatic amino acids using acetone as photosensitizer

The photochemical processes of aromatic amino acids were investigated in aqueous solution using acetone as photosensitizer by KrF (248 nm) laser flash photolysis. Laser-induced transient species were characterized according to kinetic analysis and quenching experiments. The intermediates recorded were assigned to the excited triplet state of tryptophan, the radicals of tryptophan and tyrosine. The excited triplet state of tryptophan produced via a triplet-triplet excitation transfer and the radicals arising from electron transfer reaction has been identified. Neither electron transfer nor energy transfer between triplet acetone and phenylalanine can occur in photolysis of phenylalanine aqueous solution which contains acetone. Furthermore, triplet acetone-induced radical transformation: Trp/N-Tyr→Trp-Tyr/O was observed directly in photolysis of dipeptide (Trp-Tyr) aqueous solution containing acetone, and the transformation resulting from intramolecular electron transfer was suggested.     

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.     

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.     

Reactions of an aromatic σ,σ-biradical with amino acids and dipeptides in the gas phase

Gas-phase reactivity of a positively charged aromatic σ,σ-biradical (N-methyl-6,8-didehydroquinolinium) was examined toward six aliphatic amino acids and 15 dipeptides by using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) and laser-induced acoustic desorption (LIAD). While previous studies have revealed that H-atom and NH₂ abstractions dominate the reactions of related monoradicals with aliphatic amino acids and small peptides, several additional, unprecedented reaction pathways were observed for the reactions of the biradical. For amino acids, these are 2H-atom abstraction, H₂O abstraction, addition — CO₂, addition — HCOOH, and formation of a stable adduct. The biradical reacts with aliphatic dipeptides similarly as with aliphatic amino acids, but undergoes also one additional reaction pathway, addition/C-terminal amino acid elimination (addition — CO — NHCHR_C). These reactions are initiated by H-atom abstraction by the biradical from the amino acid or peptide, or nucleophilic addition of an NH₂ or a HO group of the amino acid or peptide at the radical site at C-6 in the biradical. Reactions of the unquenched C-8 radical site then yield the products not observed for related monoradicals. The biradical reacts with aromatic dipeptides with an aromatic ring in N-terminus (i.e., Tyr-Leu, Phe-Val, and Phe-Pro) similarly as with aliphatic dipeptides. However, for those aromatic dipeptides that contain an aromatic ring in the C-terminus (i.e., Leu-Tyr and Ala-Phe), one additional pathway, addition/N-terminal amino acid elimination (addition — CO — NHCHR_N), was observed. This reaction is likely initiated by radical addition of the biradical at the aromatic ring in the C-terminus. Related monoradicals add to aromatic amino acids and small peptides, which is followed by Cα-Cβ bond cleavage, resulting in side-chain abstraction by the radical. For biradicals, with one unquenched radical site after the initial addition, the reaction ultimately results in the loss of the N-terminal amino acid. Similar to monoradicals, the C-S bond in amino acids and dipeptides was found to be especially susceptible to biradical attack.     

Gas-phase reactivity of charged pi-type biradicals

Four pi,pi-biradicals, 2,6-dimethylenepyridinium and the novel isomers N-(3-methylenephenyl)-3-methylenepyridinium, N-phenyl-3,5-dimethylenepyridinium, and N-(3,5-dimethylenephenyl)pyridinium ions, were generated and structurally characterized in a Fourier transform ion cyclotron resonance mass spectrometer. Their gas-phase reactivity toward various reagents was compared to that of the corresponding monoradicals, 2-methylenepyridinium, N-phenyl-3-methylenepyridinium, and N-(3-methylenephenyl)pyridinium ions. The biradicals reactivity was found to reflect their predicted multiplicity. The 2,6-dimethylenepyridinium ion, the only biradical in this study predicted to have a closed-shell singlet ground state, reacts significantly faster than the other biradicals, which are predicted to have triplet ground states. In fact, this biradical reacts at a higher rate than the analogous monoradical, which suggests that to avoid the costly uncoupling of its unpaired electrons, the biradical favors ionic mechanisms over barriered radical pathways. In contrast, the second-order reaction rate constants of the isomeric biradicals with triplet ground states are well approximated by those of the analogous monoradicals, although the final reaction products are sometimes different. This difference arises from rapid radical-radical recombination of the initial monoradical reaction products. The overall reactivity toward the hydrogen-atom donors benzeneselenol and tributylgermanium hydride is significantly greater for the radicals with the charged site in the same ring system as the radical site. This finding indicates that polar effects play an important role in controlling the reactivity of pi,pi-biradicals, just as has been demonstrated for sigma,sigma-biradicals.     

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.     

Interaction of 4-nitroquinoline-1-oxide with indole derivatives and some related biomolecules: a study with magnetic field

Laser flash photolysis and an external magnetic field have been used for the study of the interaction of 4-nitroquinoline-1-oxide (4NQO) with some indole derivatives, amino acids, tyrosine and tryptophan, and model proteins, lysozyme and bovine serum albumin. In an aprotic medium, photoinduced electron transfer (PET) from indoles to 4NQO is accompanied by proton transfer from the indole moieties irrespective of the substitution at the N-1 position. For 1,2-dimethylindole, however, proton abstraction is hindered possibly due to steric effects. In a protic medium, obviously proton transfer is possible from the medium and is the dominating reaction following PET. The effect of an external magnetic field is very small for all the systems studied. This is attributed to a competition between geminate proton abstraction by the 4NQO radical anion from the partner radical cation and escape of the 4NQO radical anion to the medium followed by proton transfer. The latter process is more predominant, and the former one, which produces a small population of geminate spin-correlated radical pairs, leads to a minor field effect. Another interesting observation is the affinity of 4NQO toward the tryptophan residues in a protein environment. It is seen that PET takes place preferably from the tryptophan residues rather than from the tyrosine residues.     

ESI／MS of N-（O, O-Diisopropyl） Phosphoryl Aromatic Amino Acids and their Stability Investigation Using HPLC／UV／ESI／MS

The full scan ESI/MS and ESI/MS^2 of N-(O, O-diisopropyl) phosphoryl aromatic amino acids (DIPPAAAs), N-(O, O-diisopropyl) phosphoryl phenylalanine, N-(O, O-diisopropyl)phosphoryl tryptophan and N-(O, O-diisopropyl) phosphoryl tyrosine, were obtained. The specific ions for them were found. Their stability in the LC mobile phase was investigated using developed HPLC/UV/ESI/MS and the results demonstrated that the DIPPAAAs were stable in the mobile phase (5 mmol/L NH4Ac-MeCN (80:20,v/v, pH7.5) within 48 h.     

Theoretical and experimental investigations on the chemical reactions of positively charged phenyl radicals with cytosine and 1-methylcytosine

The chemical behavior of positively charged phenyl radicals toward cytosine, 1-methylcytosine, and some pyrimidine analogues in the gas phase was investigated both theoretically by performing molecular orbital calculations and experimentally by using FT/ICR mass spectrometry. The phenyl radicals react with cytosine and 1-methylcytosine predominately by hydrogen abstraction and addition. For cytosine, the preferred site for hydrogen abstraction appears to be the amino group, and addition occurs preferentially at the N3 and N1 positions of the keto and enol tautomeric forms, respectively. For 1-methylcytosine, the methyl group is the thermodynamically favored site for hydrogen abstraction and N3 for addition. Possible structures and formation mechanisms are suggested for two unknown product ions formed upon the reaction of cytosine with the 3-dehydro-N-phenylpyridinium radical cation.     

Perturbations of aromatic amino acids are associated with iron cluster assembly in ribonucleotide reductase

The β2 subunit of class Ia ribonucleotide reductases (RNR) contains an antiferromagnetically coupled μ-oxo bridged diiron cluster and a tyrosyl radical (Y122?). In this study, an ultraviolet resonance Raman (UVRR) difference technique describes the structural changes induced by the assembly of the iron cluster and by the reduction of the tyrosyl radical. Spectral contributions from aromatic amino acids are observed through UV resonance enhancement at 229 nm. Vibrational bands are assigned by comparison to histidine, phenylalanine, tyrosine, tryptophan, and 3-methylindole model compound data and by isotopic labeling of histidine in the β2 subunit. Reduction of the tyrosyl radical reveals Y122? Raman bands at 1499 and 1556 cm(-1) and Y122 Raman bands at 1170, 1199, and 1608 cm(-1). There is little perturbation of other aromatic amino acids when Y122? is reduced. Assembly of the iron cluster is shown to be accompanied by deprotonation of histidine. A p(2)H titration study supports the assignment of an elevated pK for the histidine. In addition, structural perturbations of tyrosine and tryptophan are detected. For tryptophan, comparison to model compound data suggests an increase in hydrogen bonding and a change in conformation when the iron cluster is removed. pH and (2)H(2)O studies imply that the perturbed tryptophan is in a low dielectric environment that is close to the metal center and protected from solvent exchange. Tyrosine contributions are attributed to a conformational or hydrogen-bonding change. In summary, our work shows that electrostatic and conformational perturbations of aromatic amino acids are associated with metal cluster assembly in RNR. These conformational changes may contribute to the allosteric effects, which regulate metal binding.     

Study on the interaction mechanism between aromatic amino acids and quercetin

In this paper, we selected quercetin and aromatic amino acids (tryptophan, tyrosine, phenylalanine) as the research objects to investigate the change rules in the reaction process. The thermodynamic functions (Ka, ΔG, and ΔS) of the interactions between quercetin and aromatic amino acids (tryptophan, tyrosine, phenylalanine) were measured by isothermal titration calorimetry. The values of binding constant (Ka) reached maximum at 25°C; the entropies and Gibbs free energies were both negative at different temperatures. The kinetic parameters of quercetin and amino acids in the interaction process was determined by microcalorimetry. The results inferred that the driving force of the reaction was hydrogen bond or van der Waals force.     

THE PHOTOREDUCTION OF FLAVINS BY AMINO ACIDS AND EDTA. A CONTINUOUS AND FLASH PHOTOLYSIS STUDY

Abstract— Primary and secondary photochemical processes in oxygen-free aqueous solution have been characterised for FMN alone and in the presence of EDTA and four amino acids using nanosecond and microsecond flash photolysis and continuous photolysis techniques. The relative contributions of oneelectron and two-electron (group or hydride transfer) reactions to the deactivation of the triplet has been determined by comparing the radical concentration (560 nm) with the bleaching of the ground state (446 nm). It was concluded that one-electron reactions (hydrogen atom or electron abstraction) are the major mode of reactivity of the flavin triplet state with all the suhstrates studied.
The nature of the reactions of the flavin semiquinone radical have been studied quantitatively by microsecond flash photolysis. These secondary reactions consist of either a 'back reaction' between the flavin and substrate radicals (tryptophan or glycyl-tyrosine) or the transfer of a second electron (or hydrogen atom) from the substrate radical to the flavin radical (EDTA, methionine and possibly cysteine) to form reduced flavin and oxidised substrate. From a comparison of the quantum yields of formation of reduced flavin using 'flash' and continuous irradiation, an additional pathway for the decay of the flavin radical is suggested to occur at low light intensities in the presence of glycyl-tyrosine or histidine.     

The solid-phase Zincke reaction: preparation of omega-hydroxy pyridinium salts in the search for CFTR activation

A study of structural modifications of MPB-07 was undertaken as part of a synthetic program aimed at discovering small molecules with CFTR activation potential. Solid-phase synthesis techniques were used to prepare derivatives of MPB-07 employing the Zincke reaction for the construction of aromatic, quaternary ammonium salts such as those found in 2 or 3. In this transformation, primary amines react with highly electrophilic N-2,4-dinitrophenylpyridinium (DNP) salt 4 to afford pyridinium salt 8 with release of 2,4-dinitroaniline 6. Thus, the reaction of 1-(2,4-dinitrophenyl)pyridinium salts with various polymer-bound amino ethers, followed by cleavage from the resin, delivers the desired salts in good yield and high purity.     

Generation and reactivity toward oxygen of carbon-centered radicals containing indane,indene, and fluorenyl moieties

Resonance-stabilized radicals containing indane, indene, and fluorenyl moieties exhibit attenuated reactivity toward oxygen. Rate constants of approximately 10(5) M(-1) s(-1) were observed for the most stabilized radicals. The dependence of k(OX) (rate constant for radical trapping by oxygen) on the corresponding bond dissociation energies revealed that stereoelectronic effects are more important than steric effects in determining the low radical reactivity with oxygen. Scavenging by the nitroxide TEMPO was also examined, and revealed that in this case steric effects are more important than in the case of oxygen. The rate constants for the hydrogen abstraction by cumyloxyl and tert-butoxyl radicals generated thermally and photochemically have been determined in benzene, and were in the range of ca. (1-13) x 10(6) M(-1) s(-1), showing that benzylic stabilization has a modest effect on substrate reactivity as a hydrogen donor toward alkoxyl radicals.     

The formation of the stable radicals .CH2CN, CH3.CHCN and .CH2CH2CN from the anions -CH2CN, CH3-CHCN and -CH2CH2CN in the gas phase. A joint experimental and theoretical study

Franck-Condon one-electron oxidation of the stable anions -CH2CN, CH3-CHCN and -CH2CH2CN (in the collision cell of a reverse-sector mass spectrometer) produce the radicals .CH2CN, CH3.CHCN and .CH2CH2CN, which neither rearrange nor decompose during the microsecond duration of the neutralisation-reionisation experiment. Acetonitrile (CH3CN) and propionitrile (CH3CH2CN) are known interstellar molecules and radical abstraction of these could produce energised .CH2CN and CH3.CHCN, which might react with NH2. (a known interstellar radical) on interstellar dust or ice surfaces to form NH2CH2CN and NH2CH(CH3)CN, precursors of the amino acids glycine and alanine.     

Reactions of psoralen radical cations with biological substrates

The reactions of several psoralen and coumarin radical cations with biological substrates such as nucleotides, amino acids and alkenes that serve as models for unsaturated fatty acids have been examined. The radical cations were generated by laser photoionization of the parent psoralen or coumarin in aqueous buffer in most cases. Easily oxidized substrates such as tyrosine, tryptophan and guanosine monophosphate react with the 8-methoxypsoralen and several methoxy-substituted coumarin radical cations with rate constants in excess of 2 x 10(9) M-1 s-1. In each case reaction occurs via electron transfer, as demonstrated by the observation of quencher-derived radical cations or radicals by transient absorption spectroscopy. For other substrates such as histidine, methionine and adenosine monophosphate the measured rate constants are significantly slower and vary with the oxidation potential of both the parent psoralen or coumarin and the quencher, again indicative of electron transfer reactivity. Most of the alkenes studied also react with the psoralen or coumarin radical cations via electron transfer, although there is some evidence for addition for linoleic acid. Product studies carried out using both lamp and laser irradiation in the presence of deoxyguanosine as a radical cation trap lead to the formation of characteristic base-derived Type-I (electron transfer) products. This lends support to our previous hypothesis that photoionization occurs via a monophotonic process and is thus relevant to conditions used in clinical phototherapeutic applications of psoralens. The results demonstrate the relevance of electron transfer chemistry to the use of psoralens and related compounds as photoactivated drugs.     

Direct and sensitized photoinitiated cationic polymerization using pyridinium salts

Results of polymerization and laser flash photolysis studies concerning the direct and indirect photoinitiation of cationic polymerizations using N-alkoxy pyridinium and N-alkoxy quinolinium salts are presented. The indirect action can be based on (a) the generation of carbocations via the oxidation of photochemically produced free radicals and (b) the generation of radical cations via the reaction of electronically excited sensitizers with pyridinium or quinolinium ions. With respect to (a) substituted vinyl bromides were found be an effective source of oxidizable free radicals (vinyl radicals), and regarding (b) singlet or triplet excited states of thioxanthone, anthracene, perylene and phenothiazine, which, in the ground state, strongly absorb light in the 300 to 400 nm range, were found to react rapidly with pyridinium salts.