Theoretical Study of the Reactivity and Selectivity of Various Free Radicals with Cysteine Residues.

Radicals in biochemical environments can lead to protein damage. Theoretical studies can help us to understand the observed radical selectivity. In this work, the kinetics and thermodynamics of the hydrogen-transfer (HT) and single-electron transfer (SET) reactions between a cysteine derivative and 17 free radicals of biological significance have been theoretically investigated in aqueous and lipid media. With the exception of the reaction with •OCCl3, all SET reactions in aqueous medium have rate constants in the diffusion-limited regime. The γ site of cysteine was found to be the most reactive for the HT reactions with all the radicals, with rate constants in the diffusion limit for •OH, •OCHCl2, and •OCCl3. The HT reactions from the α and γ positions have very similar ΔG° values and even though the ß position is the least thermodynamically favored, when the HT from ß is exergonic it is a more reactive site than α. The results obtained confirm that the Bell-Evans-Polanyi principle does not apply to the reactions between amino acid residues and free radicals and that reactivity comparisons demand proper kinetic calculations.

Radical-trapping and preventive antioxidant effects of 2-hydroxymelatonin and 4-hydroxymelatonin: Contributions to the melatonin protection against oxidative stress.

BACKGROUND: Melatonin is well known for its antioxidant capacity, which has been attributed to the combined protective effects of the parent molecule and its metabolites. However, the potential role of 2-hydroxymelatonin (2OHM) and 4-hydroxymelatonin (4OHM) in such protection has not been previously investigated. METHODS: The calculations were performed using the Density Functional Theory, with the M05-2X and M05 functionals, the 6-311+G(d,p) basis set and the solvation model based on density (SMD). RESULTS: 4OHM shows excellent antioxidant activity via radical-trapping, reacting with peroxyl radicals faster than Trolox and melatonin. 4OHM can be moderately efficient as a preventing antioxidant by inhibiting Cu(II). This effect would lower the Cu(I) availability, which is the redox state required for the OH to be formed, via Fenton-like reactions. 4OHM turns off the oxidant effects of copper-ascorbate mixtures. The presence of a phenolic group was identified as the key structural feature in the antioxidant activity of 4OHM. On the other hand, 2OHM does not present a phenolic group, despite its formal name. Its keto tautomer was identified as the most abundant one (~100%). This may explain the relative low antioxidant protection of 2OHM. CONCLUSIONS: 4OHM significantly contributes to the overall antioxidant activity exhibited by melatonin, while the effects of 2OHM in this context are predicted to be only minor. This low reactivity might justify the relatively large abundance of 2OHM in biological systems. GENERAL SIGNIFICANCE: Hydroxylated melatonin metabolites, such as 4OHM, may play an important role in the protective effects of melatonin against oxidative stress.

Lipoic acid and dihydrolipoic acid. A comprehensive theoretical study of their antioxidant activity supported by available experimental kinetic data.

The free radical scavenging activity of lipoic acid (LA) and dihydrolipoic acid (DHLA) has been studied in nonpolar and aqueous solutions, using the density functional theory and several oxygen centered radicals. It was found that lipoic acid is capable of scavenging only very reactive radicals, while the dehydrogenated form is an excellent scavenger via a hydrogen transfer mechanism. The environment plays an important role in the free radical scavenging activity of DHLA because in water it is deprotonated, and this enhances its activity. In particular, the reaction rate constant of DHLA in water with an HOO(•) radical is close to the diffusion limit. This has been explained on the basis of the strong H-bonding interactions found in the transition state, which involve the carboxylate moiety, and it might have implications for other biological systems in which this group is present.

Acid-catalyzed nucleophilic additions to carbonyl groups: is the accepted mechanism the rule or an exception?

The transesterification reaction, and in particular the methanolysis of ethyl acetate with sulfuric acid as catalyst, is used as a model reaction to study the acid-catalyzed nucleophilic addition to a carbonyl group. Continuum solvation methods (SMD and IEF-PCM) and the MPWB1K functional are used. The reaction mechanism is studied in methanol and in acetonitrile as solvents. Our results indicate that the acid-catalyzed addition mechanism is stepwise, and the transition state (TS) is a contact ion-pair. The counteranion of the acid catalyst remains in the reaction site playing an important role in the TS of this reaction. Changes in the reaction kinetics and the ionic/nonionic nature of the TS with the ionizing ability of the solvent and the strength of the acid catalyst are explored. Additional calculations at the CBS-Q3 level of theory reinforce the conclusions of this paper. The results obtained allow the generalization of important ideas regarding the mechanism of the nucleophilic addition to carbonyl groups.

Antioxidant activity of trans-resveratrol toward hydroxyl and hydroperoxyl radicals: a quantum chemical and computational kinetics study.

In this work, we have carried out a systematic study of the antioxidant activity of trans-resveratrol toward hydroxyl ((•)OH) and hydroperoxyl ((•)OOH) radicals in aqueous simulated media using density functional quantum chemistry and computational kinetics methods. All possible mechanisms have been considered: hydrogen atom transfer (HAT), proton-coupled electron transfer (PCET), sequential electron proton transfer (SEPT), and radical adduct formation (RAF). Rate constants have been calculated using conventional transition state theory in conjunction with the Collins-Kimball theory. Branching ratios for the different paths contributing to the overall reaction, at 298 K, are reported. For the global reactivity of trans-resveratrol toward (•)OH radicals, in water at physiological pH, the main mechanism of reaction is proposed to be the sequential electron proton transfer (SEPT). However, we show that trans-resveratrol always reacts with (•)OH radicals at a rate that is diffusion-controlled, independent of the reaction pathway. This explains why trans-resveratrol is an excellent but very unselective (•)OH radical scavenger that provides antioxidant protection to the cell. Reaction between trans-resveratrol and the hydroperoxyl radical occurs only by phenolic hydrogen abstraction. The total rate coefficient is predicted to be 1.42 × 10(5) M(-1) s(-1), which is much smaller than the ones for reactions of trans-resveratrol with (•)OH radicals, but still important. Since the (•)OOH half-life time is several orders larger than the one of the (•)OH radical, it should contribute significantly to trans-resveratrol oxidation in aqueous biological media. Thus, trans-resveratrol may act as an efficient (•)OOH, and also presumably (•)OOR, radical scavenger.

Role of allyl group in the hydroxyl and peroxyl radical scavenging activity of S-allylcysteine.

S-Allylcysteine (SAC) is the most abundant compound in aged garlic extracts, and its antioxidant properties have been demonstrated. It is known that SAC is able to scavenge different reactive species including hydroxyl radical (•OH), although its potential ability to scavenge peroxyl radical (ROO•) has not been explored. In this work the ability of SAC to scavenge ROO• was evaluated, as well as the role of the allyl group (-S-CH(2)-CH═CH(2)) in its free radical scavenging activity. Two derived compounds of SAC were prepared: S-benzylcysteine (SBC) and S-propylcysteine (SPC). Their abilities to scavenge •OH and ROO• were measured. A computational analysis was performed to elucidate the mechanism by which these compounds scavenge •OH and ROO•. SAC was able to scavenge •OH and ROO•, in a concentration-dependent way. Such activity was significantly ameliorated when the allyl group was replaced by benzyl or propyl groups. It was shown for the first time that SAC is able to scavenge ROO•.

Mechanism and kinetics of the water-assisted formic acid + OH reaction under tropospheric conditions.

In this work, we have revisited the mechanism of the formic acid + OH radical reaction assisted by a single water molecule. Density functional methods are employed in conjunction with large basis sets to explore the potential energy surface of this radical-molecule reaction. Computational kinetics calculations in a pseudo-second-order mechanism have been performed, taking into account average atmospheric water concentrations and temperatures. We have used this method recently to study the single water molecule assisted H-abstraction by OH radicals (Iuga, C.; Alvarez-Idaboy, J. R.; Reyes, L.; Vivier-Bunge, A. J. Phys. Chem. Lett. 2010, 1, 3112; Iuga, C.; Alvarez-Idaboy, J. R.; Vivier-Bunge, A. Chem. Phys. Lett. 2010, 501, 11; Iuga, C.; Alvarez-Idaboy, J. R.; Vivier-Bunge, A. Theor. Chem. Acc. 2011, 129, 209), and we showed that the initial water complexation step is essential in the rate constant calculation. In the formic acid reaction with OH radicals, we find that the water-acid complex concentration is small but relevant under atmospheric conditions, and it could in principle be large enough to produce a measurable increase in the overall rate constant. However, the water-assisted process occurs according to a formyl hydrogen abstraction, rather than abstraction of carboxylic hydrogen as in the water-free case. As a result, the overall reaction rate constant is considerably smaller. Products are different in the water-free and water-assisted processes.

Mechanism and kinetics studies on the antioxidant activity of sinapinic acid.

The OOH radical scavenging activity of sinapinic acid (HSA) has been studied in aqueous and lipid solutions, using the Density Functional Theory. HSA is predicted to react about 32.6 times faster in aqueous solution than in lipid media. The overall rate coefficients are predicted to be 5.39 × 10(5) and 1.66 × 10(4) M(-1) s(-1), respectively. Branching ratios for the different channels of reaction are also reported for the first time, as well as the UV-Vis spectra of the main products of reaction. It was found that the reactivity of sinapinic acid towards OOH radicals takes place almost exclusively by H atom transfer from its phenolic moiety. However it was found to react via SET, at diffusion-limit controlled rate constants, with ˙OH, ˙OCCl(3) and ˙OOCCl(3) radicals. It was found that the polarity of the environment and the deprotonation of HSA in aqueous solution, both increase the reactivity of this compound towards peroxyl radicals.