New Journal of Chemistry (1998-Present) 2017 vol. 41(Issue 10) pp:3829-3845
Publication Date(Web):2017/05/15
DOI:10.1039/C6NJ03980D
The antioxidant and pro-oxidant behavior of 3-hydroxyanthranilic acid was investigated using density functional theory. In the absence of metal ions 3-hydroxyanthranilic acid acts as an excellent antioxidant by scavenging free radicals. It was found to be an excellent peroxyl radical scavenger in both lipid and aqueous solution, reacting with ˙OOH faster than Trolox. Moreover, the gathered kinetic data support the idea that 3-hydroxyanthranilic acid significantly contributes to the antioxidant activity usually attributed to tryptophan. In contrast, in the presence of metal ions (at physiological pH) it exhibits pro-oxidant behavior. This behavior arises from the Cu(II) reducing ability of the anionic fractions of this compound, which would contribute to producing Cu(I) and consequently promote ˙OH production via the Fenton reaction. Accordingly, the environmental factor identified to be crucial for ruling the dual behavior of 3-hydroxyanthranilic acid is the presence of metal ions. In addition, the pH is also predicted to influence the pro-oxidant effects of this compound.
A set of 19 melatonin analogues, intended to be better antioxidants than the parent molecule, have been computationally designed. Eight of them were planned to have good primary antioxidant capacity (AOC), i.e., being good free radical scavengers. Seven of them were designed for their secondary AOC, being able to inhibit ˙OH production by acting as metal ion chelators. Based on their predicted behavior for the intended functions, four multifunctional melatonin analogues were proposed. They were found to be among the best peroxyl radical scavengers identified so far, in aqueous solution, at physiological pH. They were also found to be capable of turning off Cu(II) reduction by O2˙− and Asc−, thus fully inhibiting the associated ˙OH production. Two of them, namely the IIcD and IbG analogues, were identified as the ones with the best multifunctional AOC. They both fulfill the Lipinski's and Ghose's rules for orally active drugs. However, IIcD has been chosen as the best prospect for possible application based on potential toxicity and synthetic accessibility estimations. Hopefully, these results might provide motivation for further investigations on the subject, and the synthesis of this compound, so its potential role as protector against oxidative stress – and the associated health issues – could be experimentally confirmed or refuted.
Co-reporter:Misaela Francisco-Marquez, Mario Aguilar-Fernández, Annia Galano
Computational and Theoretical Chemistry 2016 Volume 1077() pp:18-24
Publication Date(Web):1 February 2016
DOI:10.1016/j.comptc.2015.09.025
•Anthranilic acid is an excellent secondary antioxidant, through metal chelation.•It is efficient for sequestering Cu(II) ions from not too strong reductants.•It is able of fully preventing oxidation by Cu(II)–ascorbate mixtures as oxidant.•It is efficient for deactivating OH immediately after formation by Fenton-like reactions.•It is proposed as a proper OH-inactivating ligand.The protection exerted by anthranilic acid against oxidative stress was investigated using the Density Functional Theory. It was found to be a rather poor primary antioxidant, not efficient as a peroxyl radical scavenger, albeit it may be able of scavenging other, more reactive, free radicals. On the contrary, it was found to be an excellent secondary antioxidant, through metal chelation. Anthranilic acid is proposed to be a proper OH-inactivating ligand, with ways of action that depend on the strength of the reductant. It is able of chelating Cu(II) ions and fully prevent them from reduction by not too strong reductants such as the ascorbate ion. Accordingly, it is predicted to behave as an efficient antioxidant for in vitro experiments using Cu(II)–ascorbate mixtures as oxidant. On the other hand, anthranilic acid is able of downgrading the production of OH in biological systems, where stronger reductants such as the superoxide radical anion are present, but only partially. However, under such conditions it would be efficient for deactivating this radical as it is formed through Fenton-like reactions. Accordingly, anthranilic would be an efficient protector against the OH associated oxidative stress through its secondary antioxidant activity.
Co-reporter:Misaela Francisco-Marquez and Annia Galano
The Journal of Physical Chemistry C 2016 Volume 120(Issue 42) pp:24476-24481
Publication Date(Web):October 10, 2016
DOI:10.1021/acs.jpcc.6b08641
The potential ability of single-walled silicon–carbon nanotubes (SWSiCNTs) as CO2 scavengers was investigated using density functional theory calculations and (5,5) SWSiCNT models with 2%, 33%, and 50% Si. It was found that while the reactions between CO2 and pristine C tubes are endergonic, Si-doped materials have exergonic adsorption routes. It was also found that 50–50 Si–C composition is not required for the SWSiCNTs to be able to sequester CO2, which seems to be relevant because this is the maximum Si–C proportion allowed to maintain the SWSiCNT stability. The modeled SWSiCNTs are predicted to be selective to CO2 over N2, which is a critical feature for materials with potential applications for CO2 capture. The rate constants for the SWSiCNT reactions with CO2 were found to be around 105 M–1 s–1, which suggests that they are fast enough to ensure efficient CO2 capture at room temperature. In addition, for the SWSiCNT with 33% Si, the possibility of multiple CO2 adsorption was also investigated (up to seven CO2 molecules). It was found that all the consecutive reactions are significantly exergonic, which indicates that one SWSiCNT is able to sequester several CO2 equivalents. These findings suggest that SWSiCNT-based materials are promising candidates for selectively, and efficiently, sequestering CO2 molecules, in particular, SWSiCNTs with intermediate (2–33%) Si amounts.
Co-reporter:Yenny Villuendas-Rey, Juan Raul Alvarez-Idaboy, and Annia Galano
Journal of Chemical Information and Modeling 2015 Volume 55(Issue 12) pp:2552-2561
Publication Date(Web):December 1, 2015
DOI:10.1021/acs.jcim.5b00513
The protection exerted by 3,5-dihydroxy-4-methoxybenzyl alcohol (DHMBA), a phenolic compound recently isolated from the Pacific oyster, against oxidative stress (OS) is investigated using the density functional theory. Our results indicate that DHMBA is an outstanding peroxyl radical scavenger, being about 15 times and 4 orders of magnitude better than Trolox for that purpose in lipid and aqueous media, respectively. It was also found to react faster with HOO• than other known antioxidants such as resveratrol and ascorbic acid. DHMBA is also predicted to be able to sequester Cu(II) ions, consequently inhibiting the OS induced by Cu(II)–ascorbate mixtures and downgrading the •OH production via the Haber-Weiss reaction. However, it is proposed that DHMBA is more efficient as a primary antioxidant (free radical scavenger), than as a secondary antioxidant (metal ion chelator). In addition, it was found that DHMBA can be efficiently regenerated in aqueous solution, at physiological pH. Such regeneration is expected to contribute to increase the antioxidant protection exerted by DHMBA. These results suggest that probably synthetic routes for this compound should be pursued, because albeit its abundance in nature is rather low, its antioxidant activity is exceptional.
Co-reporter:Ruslán Álvarez-Diduk, Annia Galano, Dun Xian Tan, and Russel J. Reiter
The Journal of Physical Chemistry B 2015 Volume 119(Issue 27) pp:8535-8543
Publication Date(Web):June 16, 2015
DOI:10.1021/acs.jpcb.5b04920
The protection exerted by N-acetylserotonin (NAS) and 6-hydroxymelatonin (6OHM) against oxidative stress was investigated using the density functional theory. It was found that these compounds are better peroxyl radical scavengers than melatonin itself, Trolox, caffeine, or genistein both in lipid and aqueous solutions. The related kinetic data is provided for the first time. The solvent polarity influences not only the absolute reactivity of NAS and 6OHM toward peroxyl radicals, but also their relative scavenging activity. In addition, they both fully inhibit the oxidative effects of copper-ascorbate mixtures, and •OH production via the Haber–Weiss reaction, albeit the effects on the later are only partial. On the basis of comparisons with other melatonin-related compounds, it is proposed that the role of NAS and 6OHM on the overall protection exerted by melatonin against oxidative stress is mainly related to their free radical scavenging activities. Moreover, they increase such protection. The role of the phenol moiety on such activity is demonstrated.
The Journal of Physical Chemistry B 2015 Volume 119(Issue 8) pp:3479-3491
Publication Date(Web):February 3, 2015
DOI:10.1021/acs.jpcb.5b00052
Density functional theory was used to investigate the potential role of neurotransmitters adrenaline and noradrenaline regarding oxidative stress. It is predicted that they can be efficient as free radical scavengers both in lipid and aqueous media, with the main reaction mechanism being the hydrogen transfer and the sequential proton loss electron transfer, respectively. Despite the polarity of the environment, adrenaline and noradrenaline react with •OOH faster than Trolox, which suggests that they are better peroxyl radical scavengers than the reference compound. Both catecholamines are also proposed to be capable of efficiently inhibiting the oxidative stress induced by copper(II)–ascorbate mixtures, and the •OH production via Haber–Weiss reaction, albeit the effects on the later are only partial. They exert such beneficial effects by sequestering Cu(II) ions. In summary, these catecholamines can be capable of reducing oxidative stress, by scavenging free radicals and by sequestering metal ions. However, at the same time they might lose their functions in the process due to the associated structural modifications. Consequently, adrenaline and noradrenaline can be considered as both protectors and molecular targets of oxidative stress. Fortunately, under the proper conditions, both catecholamines can be regenerated to their original form so their functions are restored.
Journal of Molecular Modeling 2015 Volume 21( Issue 8) pp:
Publication Date(Web):2015 August
DOI:10.1007/s00894-015-2758-2
Free-radical scavenging by tryptophan and eight of its metabolites through electron transfer was investigated in aqueous solution at physiological pH, using density functional theory and the Marcus theory. A test set of 30 free radicals was employed. Thermochemical and kinetic data on the corresponding reactions are provided here for the first time. Two different pathways were found to be the most important: sequential proton loss electron transfer (SPLET) and sequential double proton loss electron transfer (SdPLET). Based on kinetic analyses, it is predicted that the tryptophan metabolites kynurenic acid and xanthurenic acid are the best free-radical scavengers among the tested compounds; they were estimated to be at least 24 and 12 times more efficient than Trolox for scavenging •OOH. These findings are in line with previous reports suggesting that the antioxidant activity that has been attributed to tryptophan is actually due to its metabolites, and they demonstrate the particular importance of phenolic metabolites to such activity.
Co-reporter:Adriana Pérez-González, Annia Galano and Juan Raúl Alvarez-Idaboy
New Journal of Chemistry 2014 vol. 38(Issue 6) pp:2639-2652
Publication Date(Web):18 Mar 2014
DOI:10.1039/C4NJ00071D
The free radical scavenging activity of dihydroxybenzoic acids (DHBA) has been studied in non-polar and aqueous solutions, using the Density Functional Theory. It was found that the environment plays an important role in the free radical scavenging activity of DHBA. The hydrogen transfer (HT) from the phenolic OH was identified as the main mechanism of reaction in non-polar media, while the single electron transfer (SET) from the di-anions is proposed as the mechanism contributing the most to the peroxyl scavenging activity of DHBA in aqueous solution, at physiological pH. Two key structural features are associated with the reactivity of DHBA towards peroxyl radicals, via HT. The OH from which the H is transferred should be: (i) in the meta position with respect to the carboxyl group; and (ii) in the para or ortho position with respect to the other hydroxyl group. Regarding SET, the key factors are the formation of the di-anion, and its molar fraction at the anticipated pH. DHBA are predicted to be versatile scavengers in aqueous solution, capable of efficiently scavenging a wide variety of free radicals via SET. In addition, 25-DHBA, 34-DHBA and 23-DHBA were found to be among the best peroxyl radical scavengers identified so far, in aqueous solution, at physiological pH.
Co-reporter:Adriana Pérez-González, Annia Galano, and J. V. Ortiz
The Journal of Physical Chemistry A 2014 Volume 118(Issue 31) pp:6125-6131
Publication Date(Web):July 18, 2014
DOI:10.1021/jp505276n
The performance of several direct and indirect computational strategies for the calculation of the first ionization energies (IEs) of free radicals and adiabatic detachment energies of their anions has been tested using experimental data as references. The outer valence Green’s function and the partial third-order approximations, which are based on electron propagator theory, have been identified as the most accurate. They were in turn used to estimate the IEs of a large set of free radicals for which these data have not been previously reported. The calculated data also have been used to assess the possible oxidation of nucleosides by these radicals, as well as the potential, antioxidant-protection effects of phenol, catechol, ascorbic acid, and Trolox in their neutral and deprotonated forms, via electron transfer.
Co-reporter:Claudia Zavala-Oseguera, Annia Galano, and Gabriel Merino
The Journal of Physical Chemistry A 2014 Volume 118(Issue 36) pp:7776-7781
Publication Date(Web):August 21, 2014
DOI:10.1021/jp507244s
Carbaryl is released into the atmosphere as a spray drift immediately following the application. In order to evaluate its fate in the atmosphere, a computational study on the kinetics of the OH radical reaction with carbaryl is presented. Different reaction paths are studied at the M05-2X/6-311++G(d,p) level. A complex mechanism involving the formation of a stable reactant complex is proposed and the temperature dependence of the rate coefficients is studied in the 280–650 K temperature range. The principal degradation path is the hydroxyl radical addition to naphthalene, but hydrogen abstractions from the methyl group are identified as a secondary significant path. The rate coefficients, computed using the conventional transition state theory, reproduce quite well the scarce experimental data available.
Co-reporter:Jorge Rafael León-Carmona, Juan Raúl Alvarez-Idaboy and Annia Galano
Physical Chemistry Chemical Physics 2012 vol. 14(Issue 36) pp:12534-12543
Publication Date(Web):26 Mar 2012
DOI:10.1039/C2CP40651A
The peroxyl radical scavenging activity of four hydroxycinnamic acid derivatives (HCAD) has been studied in non-polar and aqueous solutions, using the density functional theory. The studied HCAD are: ferulic acid (4-hydroxy-3-methoxycinnamic acid), p-coumaric acid (trans-4-hydroxycinnamic acid), caffeic acid (3,4-dihydroxycinnamic acid), and dihydrocaffeic acid (3-(3,4-dihydroxyphenyl)-2-propionic acid). It was found that the polarity of the environment plays an important role in the relative efficiency of these compounds as peroxyl scavengers. It was also found that in aqueous solution the pH is a key factor for the overall reactivity of HCAD towards peroxyl radicals, for their relative antioxidant capacity, and for the relative importance of the different mechanisms of reaction. The H transfer from the phenolic OH has been identified as the main mechanism of reaction in non-polar media and in aqueous solution at acid pHs. On the other hand, the single electron transfer mechanism from the phenoxide anion is proposed to be the one contributing the most to the overall peroxyl scavenging activity of HCAD in aqueous solution at physiological pH (7.4). This process is also predicted to be a key factor in the reactivity of these compounds towards a large variety of free radicals.
Co-reporter:Adriana Pérez-González and Annia Galano
The Journal of Physical Chemistry B 2012 Volume 116(Issue 3) pp:1180-1188
Publication Date(Web):December 21, 2011
DOI:10.1021/jp209930y
The single electron transfer (SET) reactions from the neutral and anionic forms of 27 edaravone derivatives to 11 free radicals have been studied using density functional theory and the Marcus theory. All of the studied compounds were found to be able to efficiently scavenge at least some of the studied radicals. More than half of them were found to be excellent free radical scavengers, via SET, under physiological conditions. Their SET reactions with all the studied radicals were found to have rate constants ranging from 106 to 109 M–1 s–1 (diffusion limited). Therefore, they are predicted to be versatile scavengers, able to deactivate free radicals of different nature. Functionalizing the R1 and R3 sites of the pyrazol-5-one ring with the NO group is not recommended for edaravone derivatives designed as free radical scavengers through the SET mechanism. In general, this family of compounds was found to be exceptionally good for scavenging free radicals by transferring one electron. Moreover they are predicted to be outstanding scavengers, even if they would only react by SET. In addition, the acid–base equilibrium was found to play an important role in their activity.
Co-reporter:Annia Galano, Jorge Rafael León-Carmona, and Juan Raúl Alvarez-Idaboy
The Journal of Physical Chemistry B 2012 Volume 116(Issue 24) pp:7129-7137
Publication Date(Web):May 30, 2012
DOI:10.1021/jp302810w
The peroxyl radical scavenging activity of five guaiacol derivatives (GD) has been studied in nonpolar and aqueous solutions, using the density functional theory. The studied GD are guaiacol, vanillin, vanillic alcohol, vanillic acid, and eugenol. It was found that the environment plays an important role in the peroxyl scavenging activity of these compounds. They were all found to react faster in aqueous solution than in nonpolar media. The order of reactivity in nonpolar environments was found to be vanillic alcohol > eugenol > guaiacol > vanillin > vanillic acid, while, in aqueous solution, at physiological pH, it becomes vanillic acid > vanillic alcohol > guaiacol ≈ eugenol > vanillin. It was also found that in aqueous solution as the pH increases so does the reactivity of GD toward peroxyl radicals. The environment also has important effects on the relative importance of the hydrogen transfer (HT) and the sequential proton electron transfer (SPET) mechanisms, which are the ones relevant to the peroxyl radical scavenging activity of GD. The HT from the phenolic OH was identified as the main scavenging process in nonpolar media, and in aqueous solution at pH ≤ 4. On the other hand, SPET is proposed to be the one contributing the most to the overall peroxyl scavenging activity of GD in aqueous solution at pH ≥ 6.
The free radical scavenging activity of protocatechuic acid has been studied in aqueous and lipid solutions, using the density functional theory. It was found to be a moderately good protector in non-polar environments (lipid), while in aqueous solution it is predicted to be an excellent peroxyl radical scavenger. In such media, the pH has an important role in the free radical scavenging activity of protocatechuic acid. At physiological pH, after the first peroxyl radical is scavenged, and in the presence of a good electron-donor species, such as the superoxide radical anion, the latter is consumed and protocatechuic acid is regenerated. This means that, under such conditions, it has the ability of scavenging several radical equivalents, two per cycle. An equivalent cyclic process can be assumed as possible also for other scavengers with the catechol moiety. If this assumption is confirmed, the role of compounds with a catechol moiety as free radical scavengers might be even more important that what has been assumed so far.
Physical Chemistry Chemical Physics 2011 vol. 13(Issue 15) pp:7178-7188
Publication Date(Web):15 Mar 2011
DOI:10.1039/C0CP02801K
The reactions of melatonin (MLT) with hydroxyl and several peroxyl radicals have been studied using the Density Functional Theory, specifically the M05-2X functional. Five mechanisms of reaction have been considered: radical adduct formation (RAF), Hydrogen atom transfer (HAT), single electron transfer (SET), sequential electron proton transfer (SEPT) and proton coupled electron transfer (PCET). It has been found that MLT reacts with OH radicals in a diffusion-limited way, regardless of the polarity of the environment, which indicates that MLT is an excellent OH radical scavenger. The calculated values of the overall rate coefficient of MLT + ˙OH reaction in benzene and water solutions are 2.23 × 1010 and 1.85 × 1010 M−1 s−1, respectively. MLT is also predicted to be a very good ˙OOCCl3 scavenger but rather ineffective for scavenging less reactive peroxyl radicals, such as alkenyl peroxyl radicals and ˙OOH. Therefore it is concluded that the protective effect of MLT against lipid peroxidation does not take place by directly trapping peroxyl radicals, but rather by scavenging more reactive species, such as ˙OH, which can initiate the degradation process. Branching ratios for the different channels of reaction are reported for the first time. In aqueous solutions SEPT was found to be the main mechanism for the MLT + ˙OH reaction, accounting for about 44.1% of the overall reactivity of MLT towards this radical. The good agreement between the calculated and the available experimental data, on the studied processes, supports the reliability of the results presented in this work.
Co-reporter:Adriana Pérez-González and Annia Galano
The Journal of Physical Chemistry B 2011 Volume 115(Issue 5) pp:1306-1314
Publication Date(Web):December 29, 2010
DOI:10.1021/jp110400t
The reactions of OH radicals with the neutral and anionic forms of Edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one, EDA) have been studied using Density Functional Theory. Different mechanisms and reaction sites have been considered. The overall rate constant was found to be diffusion-limited (1.35 × 1010 M−1 s−1, in aqueous solution), and in excellent agreement with the experimental results. Therefore, the present work supports previous evidence that EDA is an excellent •OH scavenger. The anionic form of EDA is predicted to react 8.6 times faster than its neutral form. The preponderant mechanism was found to be different depending on the form of EDA reacting with the radical. For the anionic form, the single electron transfer mechanism was found to be the one contributing the most to the overall reactivity toward •OH (∼ 44%), closely followed by radical adduct formation (∼40%). For the neutral form, the latter was found to be the main mechanism, with contributions larger than 98%, regardless of the polarity of the environment. For the global reactivity of EDA toward OH radicals, at physiological pH, the main mechanism of reaction is proposed to be the sequential electron proton transfer. A detailed analysis of the UV−vis spectra is also provided. The excellent agreement with the available experimental data supports the reliability of the new information provided in the present work.
Co-reporter:Jorge Rafael León-Carmona and Annia Galano
The Journal of Physical Chemistry B 2011 Volume 115(Issue 15) pp:4538-4546
Publication Date(Web):March 25, 2011
DOI:10.1021/jp201383y
The reactions of caffeine (CAF) with different reactive oxygen species (ROS) have been studied using density functional theory. Five mechanisms of reaction have been considered, namely, radical adduct formation (RAF), hydrogen atom transfer (HAT), single electron transfer (SET), sequential electron proton transfer (SEPT), and proton coupled electron transfer (PCET). The SET, SEPT, and PCET mechanisms have been ruled out for the reactions of CAF with •OH, O2•−, ROO•, and RO• radicals. It was found that caffeine is inefficient for directly scavenging O2•− and •OOCH3 radicals and most likely other alkyl peroxyl radicals. The overall reactivity of CAF toward •OH was found to be diffusion-controlled, regardless of the polarity of the environment, supporting the excellent •OH scavenging activity of CAF. On the other hand, it is predicted to be a modest scavenger of •OCH3, and probably of other alkoxyl radicals, and a poor scavenger of HOO•. RAF has been identified as the main mechanism involved in the direct ROS scavenging activity of CAF. The excellent agreement with the available experimental data supports the reliability of the present calculations.
Co-reporter:Adriana Pérez-González and Annia Galano
The Journal of Physical Chemistry B 2011 Volume 115(Issue 34) pp:10375-10384
Publication Date(Web):July 28, 2011
DOI:10.1021/jp2047163
The electron-donating capability (EDC) and the ease of deprotonation (ED) of 26 edaravone derivatives have been evaluated. Their first ionization energies have been used to assess their EDC. Four different approaches to obtain vertical ionization energies were tested, using a set of structurally related compounds. Those based on the electron propagator theory (EPT) were identified as the best ones. In particular, the partial third order (P3) approximation led to the lowest mean unsigned error (MUE = 0.10 eV). Two descriptors were used to evaluate ED: the proton affinity (PA) and the pKa. It was found that pKa values are better descriptors than PA values. Ideal candidates to perform as efficiently as, or even better than, edaravone itself are proposed. The recommendations were based on the simultaneous analyses of EDC and ED, and they should be particularly valid when the electron transfer mechanism plays an important role in the antioxidant activity of the studied compounds.
Co-reporter:Perla D. Maldonado, J. Raúl Alvarez-Idaboy, Adriana Aguilar-González, Alfonso Lira-Rocha, Helgi Jung-Cook, Omar Noel Medina-Campos, José Pedraza-Chaverrí, and Annia Galano
The Journal of Physical Chemistry B 2011 Volume 115(Issue 45) pp:13408-13417
Publication Date(Web):October 13, 2011
DOI:10.1021/jp208233f
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—CH2—CH═CH2) 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•.
Co-reporter:Jorge Rafael León-Carmona and Annia Galano
The Journal of Physical Chemistry B 2011 Volume 115(Issue 51) pp:15430-15438
Publication Date(Web):November 18, 2011
DOI:10.1021/jp209776x
The reactions of uric and 1-methyluric acids in nonpolar environments, as well as those of the corresponding urate anions in aqueous solution, with •OH, •OCH3, •OOH, and •OOCH3 have been studied using the density functional theory. Different mechanisms of reactions have been taken into account, and their relative importance on the antiradical activity of these compounds is analyzed. Both uric and methyluric acids are better scavengers in aqueous solution than in nonpolar media, which indicates that the urate anions are the most active species. The free radical scavenging activity of the studied compounds was found to be excellent for •OH, and very good for •OCH3. In addition, 1-methyluric acid is predicted to moderately protect against peroxyl oxidation, while the protective effects of uric acid against these particular species are not expected to be significant. In addition, 1-methyluric acid was found to be a better radical scavenger than its precursor, caffeine, suggesting that the antiradical activity of the latter might be explained by the action of its metabolites, rather than by its direct activity.
The potential role of carbon nanotubes (CNTs) as free-radical scavengers is still an emerging area of research. So far some promising results have been reported strongly suggesting that CNTs can be very efficient for that task. The implications of such a valuable property for applications aimed at biomedical and environmental uses are encouraging. There are still abundant open questions related to the possible use of CNTs for scavenging free radicals. Thus much more work needs to be devoted to this fascinating topic. In this mini review the progress made so far is reviewed and some future perspectives are provided.
Co-reporter:Misaela Francisco-Marquez, Annia Galano and Ana Martínez
The Journal of Physical Chemistry C 2010 Volume 114(Issue 14) pp:6363-6370
Publication Date(Web):March 22, 2010
DOI:10.1021/jp100065t
Density functional theory calculations have been used to model the efficiency of carboxylated single-walled carbon nanotubes (SWCNT) to act as free radical scavengers, relative to that of their corresponding nonfunctionalized partners. The exergonicity of the reactions between carboxylated SWCNTs and the studied free radicals was found to be dependent on the site of functionalization as well as on the site of reaction. The major conclusion from this work is that carboxylated SWCNTs are at least as good, or even better, free radical scavengers than their nonfunctionalized partners. It is proposed that the presence of −COOH groups would increase the free radical scavenging activity of SWCNTs, provided that the coverage occurs in such an amount that there is enough free space on the walls for the reactions to take place. The reliability of the calculations reported in the present work has been tested by comparison with different levels of theory.
Co-reporter:Annia Galano, Misaela Francisco-Marquez and Ana Martínez
The Journal of Physical Chemistry C 2010 Volume 114(Issue 18) pp:8302-8308
Publication Date(Web):April 2, 2010
DOI:10.1021/jp101544u
The effect of point defects on the free-radical scavenging activity of armchair and zigzag single-walled carbon nanotubes (SWCNTs), through a radical adduct formation mechanism, has been studied using density functional theory calculations. SWCNTs with different vacancy (V), adatom (AA), and Stone−Wales (SW) defects have been considered, as well as their pristine partners. All the studied reactions were found to be significantly exothermic and exergonic, which supports their viability. The presence of point defects in the carbon lattice of SWCNTs is predicted to increase their free-radical scavenging activity. The AA and V point defects, involving C atoms with dangling bonds, are expected to cause a larger increase on the SWCNTs’ reactivity toward free radicals than the SW and vacancy defects without C atoms with dangling bonds. The studied Stone−Wales point defect shows the largest site-dependent effect on the free-radical scavenging activity of SWCNTs. The presence of nonpolar environments is not expected to change the proposed trends. Characteristic infrared bands in the 3300 and 900−1100 cm−1 regions have been assigned to the νO−H and νC−O vibrations of the OH radical adducts.
The Journal of Physical Chemistry C 2010 Volume 114(Issue 18) pp:8184-8191
Publication Date(Web):April 16, 2010
DOI:10.1021/jp100168q
The scavenging activity of ultrashort single-walled carbon nanotubes (US-SWCNTs) is analyzed in this work considering the electron transfer mechanism. Such processes have been modeled using density functional theory for a wide variety of US-SWCNTs and free radicals. Different structures with diverse diameters and helicities (armchair and zigzag) have been considered. In addition, US-SWCNTs with three different kinds of defects and carboxylic functionalized US-SWCNTs have been taken into account. It stands out that ultrashort zigzag nanotubes are better electron acceptors and also slightly better electron donors than their corresponding armchair partners. Pristine zigzag nanotubes were found to be better electron donors and worse electron acceptors than carboxylated US-SWCNTs. The electron donor capability of carboxylated armchair nanotubes is equivalent to that of the pristine US-SWCNT, while they are better electron acceptors than the nonfunctionalized tubes. Our results indicate that neither the length nor the defects have a significant effect on the free radical scavenger capacity of the US-SWCNTs, when reacting through the electron transfer mechanism. The electron transfer reaction mechanism depends on the characteristics of the free radical and on the nature of the nanotubes.
It is well known that free radicals are responsible for oxidative stress and cause numerous health disorders. As a result, the study of molecules that can scavenge free radicals is significant. One of the most important classes of free radical scavengers are carotenoids (CAR). In this work, the effectiveness of the CAR in terms of the radical adduct formation (RAF) reaction is studied using density functional theory calculations (in polar and non-polar environments). The reactions between four CAR [β-carotene (BC), zeaxanthin (ZEA), canthaxanthin (CANTA) and astaxanthin (ASTA)] with eight different radicals (•OH, •OOH, •CH3, •O–CH3, •OO–CH3, •SH, •O–CH2–CH=CH2, and •OO–CH2–CH=CH2), as well as substantial further reactions involved in the radical chain propagation, are analyzed. According to our results, the RAF reactions are controlled to a larger extent by the nature of the free radical than by the particular CAR they are reacting with. Thermochemistry calculations predict that each CAR molecule is able to scavenge at least two free radicals, which would lead to the termination of the radical chain process. Epoxy and diepoxy CAR species can be formed, being epoxy molecules as good free radical scavengers as their parent CAR. ASTA and CANTA are predicted to be less reactive, when reacting through RAF mechanism, than BC and ZEA.
Co-reporter:Annia Galano, Norma A. Macías-Ruvalcaba, Omar Noel Medina Campos and José Pedraza-Chaverri
The Journal of Physical Chemistry B 2010 Volume 114(Issue 19) pp:6625-6635
Publication Date(Web):April 26, 2010
DOI:10.1021/jp912001c
The antioxidant nordihydroguaiaretic acid (NDGA) is a plant phenolic lignan originally isolated from the creosote bush (Larrea tridentata). It has been shown that NDGA scavenges efficiently hydroxyl radicals (•OH). In the present paper the mechanism by which NDGA scavenges •OH is addressed performing a combined experimental and theoretical investigation. We found that NDGA protects, in a concentration-dependent way, bovine serum albumin and DNA from the damage induced by •OH generated by the Fenton reaction. In addition, the NDGA + •OH reaction is predicted to be diffusion-controlled. The first step of this reaction is proposed to occur mainly by a sequential electron proton transfer from NDGA to •OH generating a neutral radical of NDGA, which after a second oxidation step gives a diradical that after a cascade sequential complex reaction produces a cyclic compound. This cyclic product is predicted to have a UV−vis spectrum very similar to that of NDGA, making its identification by this technique very difficult. The electrochemical studies performed in water support the formation of a cyclic compound (C2) as the main product of the reaction. It is concluded that NDGA can scavenge at least two •OH.
The effect of the inclusion of counterpoise corrections (CP) on the accuracy of interaction energies has been studied for different systems accounting for (1) intermolecular interactions, (2) intramolecular interactions and (3) chemical reactions. To minimize the error associated with the method of choice, the energy calculations were performed using CCSD(T) in all the cases. The values obtained using aug-cc-pVXZ basis sets are compared to CBS-extrapolated values. It has been concluded that at least for the tested systems CP corrections systematically leads to results that differ from the CBS-extrapolated ones to a larger extension than the uncorrected ones. Accordingly, from a practical point of view, we do not recommend the inclusion of such corrections in the calculation of interaction energies, except for CBS extrapolations. The best way of dealing with basis set superposition error (BSSE) is not to use CP corrections, but to make a computational effort for increasing the basis set. This approach does not eliminate BSSE but significantly decreases it, and more importantly it proportionally decreases all the errors arising from the basis set truncation.
Co-reporter:Annia Galano, J. Raul Alvarez-Idaboy and Misaela Francisco-Márquez
The Journal of Physical Chemistry A 2010 Volume 114(Issue 28) pp:7525-7536
Publication Date(Web):June 24, 2010
DOI:10.1021/jp103575f
A theoretical study on the mechanism and branching ratios of the gas phase reactions of hydroxyl radicals with a series of hydroxy ethers is presented. This is the first report on branching ratios for these reactions. The studied hydroxy ethers are: methoxy-methanol (MM), ethoxy-methanol (EM), 1-methoxy-ethanol (1ME), 2-methoxy-ethanol (2ME), and 2-ethoxy-ethanol (2EE). All the possible H abstraction channels have been modeled, involving the rupture of C−H and O−H bonds. The H abstractions from the alcohol group were found to be almost negligible for all the studied systems. The role of H bond interactions in the transition states (TS) is discussed, as well as the importance of the location of the reaction site with respect to the alcohol and the ether functional groups. TSs with seven-member ring-like structures were found to lead to stronger H bond interactions than TSs with six- and five-member ring-like structures, with the latter leading to the weakest interactions. Kinetic calculations have been performed within the 250−440 K temperature range. Rate coefficients for the reactions of •OH with MM, EM, and 1ME are reported here for the first time. Nonlinear Arrhenius plots were found for all the overall reactions. Negative activation energies at room temperature are proposed for the •OH reactions with EM, 2ME, and 2EE. The excellent agreement with the scarce experimental data available supports the reliability of the data reported here for the first time.
Co-reporter:Annia Galano, Marcela Narciso-Lopez and Misaela Francisco-Marquez
The Journal of Physical Chemistry A 2010 Volume 114(Issue 18) pp:5796-5809
Publication Date(Web):April 16, 2010
DOI:10.1021/jp101157b
Water complexes involving methanol, ethanol, formaldehyde, formic acid, acetone, ammonia, acetylene, ethylene, chloroethene, trichloroethene, 1,1,1-trichloroethane, hydroxyl radical, and hydroperoxyl radical have been studied. Enthalpies, entropies, and Gibbs free energies of association have been estimated, as well as the concentrations of the complexes under lower-troposphere conditions. The influence of the relative air humidity on the complexation processes has been analyzed. The association processes yielding water complexes of methanol, ethanol, formic acid, ammonia, acetone, hydroxyl radical, and hydroperoxyl radical were found to be more exothermic than that of the water dimer. General trends for the reactivity of the studied water complexes, compared to those of the corresponding free species, are proposed based on global reactivity indexes. The previously reported increased reactivity of the •OOH self-reaction, when there is water present, has been explained. The IR spectra of the complexes have been analyzed and compared with those of the free species.
Thermodynamic and kinetic calculations have been used to reinterpret the UV−vis data related to the OH radical oxidation of guanosine. The main channel of reaction (70−75%) is proposed to be the formation of a guanosine radical cation followed by deprotonation. It accounts for both the absorbance decay at ∼620 nm and the build-up at ∼300 nm. A secondary channel yielding the G8OH adduct was found to contribute to the overall reaction by 12% at least.
Co-reporter:Claudia Zavala-Oseguera and Annia Galano
Journal of Chemical Theory and Computation 2009 Volume 5(Issue 5) pp:1295-1303
Publication Date(Web):April 17, 2009
DOI:10.1021/ct9000679
Different paths of reaction have been modeled, at high level of theory, accounting for the possible atmospheric fate of methyl N-methylcarbamate (MMC). The OH hydrogen abstractions from the methyl groups are predicted to account for almost 100% of the MMC + OH gas-phase reaction. The H abstraction from the methyl group at the N side of MMC was found to be the main path of reaction, with contributions to the overall reaction from 96% at 260 K to 89.2% at 400 K. Hydrogen abstractions from the other methyl group were identified as a secondary, but significant path. The Arrhenius activation energy, in the temperature range 260−400 K, was found to be close to zero, but slightly negative. The proposed value is (−0.10 ± 0.02) kcal/mol. The excellent agreement with the scarce experimental data available supports the reliability of the data reported here for the first time. Different IVTST-M-H/G schemes were tested for dynamic calculations. According to our results, including the Hessians and gradients, as few as four nonstationary points along the MEP is sufficient to achieve an excellent accuracy, provided that the data for these few points were obtained from high-quality levels of theory.
Co-reporter:Annia Galano, Ruslán Álvarez-Diduk, María Teresa Ramírez-Silva, Georgina Alarcón-Ángeles, Alberto Rojas-Hernández
Chemical Physics 2009 Volume 363(1–3) pp:13-23
Publication Date(Web):18 September 2009
DOI:10.1016/j.chemphys.2009.07.003
Abstract
Density functional theory is used to study the antioxidant mechanism of curcumin. Five different mechanisms are considered: single electron transfer (SET), radical adduct formation (RAF), H atom transfer from neutral curcumin (HAT), H atom transfer from deprotonated curcumin (HAT-D), and sequential proton loss electron transfer (SPLET). The influence of the environment is investigated for polar and non-polar surroundings. The apparent contradictions among previous experimental results are explained by the role of the nature of the reacting free radical on the relative importance of the above mentioned mechanism. It is proposed that the curcumin + DPPH reaction actually takes place mainly through the SPLET mechanism, while the reaction with OCH3, and likely with other alkoxyl radicals, is governed by the HAT mechanism. Branching ratios for the OCH3 + curcumin reaction are reported for the first time. The calculated overall rate constants for this reaction are 1.16 × 1010 (benzene) and 5.52 × 109 (water) L mol−1 s−1. The role of phenolic groups on the antioxidant activity of curcumin has been experimentally confirmed.
Co-reporter:Claudia Zavala-Oseguera, Juan R. Alvarez-Idaboy, Gabriel Merino and Annia Galano
The Journal of Physical Chemistry A 2009 Volume 113(Issue 50) pp:13913-13920
Publication Date(Web):November 12, 2009
DOI:10.1021/jp906144d
A theoretical study of the mechanism and kinetics of the OH radical reactions with aliphatic ethers is presented. Several methods were evaluated using the 6-311++G(d,p) basis set, with dimethyl ether as a test molecule. On the basis of the dimethyl ether results, the M05−2X functional was selected for the rest of the calculations. All the possible H abstraction paths have been modeled, and the importance of differentiating among H atoms bonded to the same C atom, according to their orientation with respect to the O atom in the ether, is analyzed. The rate coefficients are calculated using interpolated variational transition-state theory by mapping (IVTST-M), within the IVTST-M-4/4 scheme, in conjunction with small-curvature tunneling (SCT) corrections. The discussion is focused on the 280−400 K temperature range, but additional information is provided for an extended range (280−2000 K). Our analysis suggests a stepwise mechanism involving the formation of H bonded complexes in the entrance and exit channels. The vicinity of the O atom was found to increase the relative site reactivity. In fact, it was found to influence reactivity to a larger extent than the nature of the carbon site (primary, secondary, or tertiary). The overall agreement between the calculated and the available experimental data is very good and supports the reliability of the rate coefficients and the branching ratios proposed here for the first time. It also supports the performance of the M05−2X functional and the IVTST-M-4/4 scheme for kinetic calculations.
The Journal of Physical Chemistry C 2009 Volume 113(Issue 43) pp:18487-18491
Publication Date(Web):October 7, 2009
DOI:10.1021/jp904646q
Density functional theory calculations have been used to model the influence of diameter, length, and chirality of single-walled carbon nanotubes (SWCNT) on their free radical scavenging activity. SWCNTs with wide distributions of different diameter, length, and chirality are proposed to have good free radical scavenging activity in the gas phase and in nonpolar environments. Therefore, they can be used as free radical traps with potential application in environmental and biological systems. In general, thinner tubes are expected to have better antiradical activities. However, the curvature of the tubes seems to modify the antiradical activity of armchair nanotubes. Therefore, for wide distributions of tube diameter, the zigzag SWCNTs are expected to be more efficient for free radical scavenging purposes than the armchair ones. The length of the tubes only has a minor influence on the free radical trapping efficiency of SWCNTs. From the results reported in this work, thin and zigzag nanotubes are recommended as those with the best antiradical activity, regardless of their length.
Co-reporter:Annia Galano and Misaela Francisco-Marquez
The Journal of Physical Chemistry B 2009 Volume 113(Issue 49) pp:16077-16081
Publication Date(Web):November 11, 2009
DOI:10.1021/jp907906h
The OOH radical reactions with allicin and its Cope elimination products (2-propenesulfenic acid and thioacrolein) in aqueous solution have been studied. The CBS-QB3 quantum chemistry method has been used, with geometries and frequencies at BHandHLYP/6-311++G(d,p) level and conventional transition state theory. 2-Propenesulfenic acid is predicted to be over 1000 times more reactive toward OOH radical than allicin (2.60 × 107 vs 7.38 × 103 L mol−1 s−1, at 298 K). Accordingly, our results strongly support the novel suggestion by Vaidya et al. (Angew. Chem., Int. Ed. 2009, 48, 157) that the active ingredient responsible for the free radical scavenging activity of garlic is actually 2-propenesulfenic acid and not allicin. In addition, direct reaction branching ratios and product distribution for the three studied reactions are proposed for the first time.
Co-reporter:Misaela Francisco-Marquez and Annia Galano
The Journal of Physical Chemistry B 2009 Volume 113(Issue 14) pp:4947-4952
Publication Date(Web):March 19, 2009
DOI:10.1021/jp900118f
Density functional theory has been used to model the OH reaction with Gly-Met-Gly and Gly-Nle-Gly tripeptides. The first one is predicted to be about 100 times faster than the second one. Therefore, if a methionine fragment is replaced by norleucine, the overall reactivity of the peptide toward free radicals is expected to be significantly reduced, which is in agreement with previous experimental findings. Since the most reactive sites were found to be located in the central backbone for Nle and in the terminal fragment of the side chain for Met, this decrease is expected to be even more critical for large-sized free radicals. The S atom seems to activate not only those alkyl sites next to it but also those located an odd number of bonds apart. In addition the viability of different paths explaining the formation of methionine sulfoxide has been tested, and it is proposed that this process involves the formation of R−SO radical and formaldehyde. The results from the present work offer an explanation to the role of sulfur atom on the reactivity of methionine toward free radicals. They also support the preponderant role of Met35 on the development of the Alzheimer disease.
Co-reporter:Annia Galano and Misaela Francisco-Marquez
The Journal of Physical Chemistry B 2009 Volume 113(Issue 32) pp:11338-11345
Publication Date(Web):July 22, 2009
DOI:10.1021/jp904061q
The relative free radical scavenging activity of β-carotene, lycopene, and torulene toward OOH radicals has been studied using density functional theory. Hydrogen atom transfer (HAT) and radical adduct formation (RAF) mechanisms have been considered. All the possible reaction sites have been included in the modeling, and detailed branching ratios are reported for the first time. The reactions of hydrocarbon carotenoids (Car) with peroxyl radicals, in both polar and nonpolar environments, are predicted to proceed via RAF mechanism, with contributions higher than 98% to the overall OOH + Car reactions. Lycopene and torulene were found to be more reactive than β-carotene. In nonpolar environments the reactivity of the studied carotenoids toward peroxyl radical follows the trend LYC > TOR > BC, whereas in aqueous solutions it is TOR > LYC > BC. OOH adducts are predicted to be formed mainly at the terminal sites of the conjugated polyene chains. The main addition sites were found to be C5 for β-carotene and lycopene and C30 for torulene. The general agreement between the calculated magnitudes and the available experimental data supports the predictions from this work.
Co-reporter:Ana Martínez, Rubicelia Vargas and Annia Galano
The Journal of Physical Chemistry B 2009 Volume 113(Issue 35) pp:12113-12120
Publication Date(Web):July 30, 2009
DOI:10.1021/jp903958h
Oxidative stress is related to the development of a large number of health disorders. Therefore, the study of molecular systems capable of preventing its onset by fighting free radicals is a crucial area of research. Carotenoids are one of the most efficient families of compounds fulfilling this purpose. In the present work, the free-radical-scavenger efficiency, expressed as the one-electron-donating capability, of different carotenoids has been studied using density functional theory. A large number of free radicals were considered, as well as environments of different polarity. A new donor−acceptor map is proposed that allows a rapid evaluation of full electron-transfer processes. Its efficiency for predicting the feasibility of electron transfer (ET) between carotenoids and free radicals was tested and validated through comparison with the corresponding Gibbs free energies of reaction. Our results demonstrate that ET reactions between carotenoids and free radicals are strongly influenced by the nature of the latter. Moreover, it is proposed that the electron affinity (EA) of the reacting free radical has an important effect on the viability of these reactions. The reactions were found to become exergonic when the EA of the free radical involved reaches a value of ∼5 eV.
Density functional theory has been used to model the reaction of OH with L-phenylalanine, as a free molecule and in the Gly-Phe-Gly peptide. The influence of the environment has been investigated using water and benzene as models for polar and non-polar surroundings, in addition to gas phase calculations. Different paths of reaction have been considered, involving H abstractions and addition reactions, with global contributions to the overall reaction around 10% and 90% respectively when Phe is in its free form. The ortho-adducts (o-tyrosine) were found to be the major products of the Phe + OH reaction, for all the modeled environments and especially in water solutions. The reactivity of phenylalanine towards OH radical attacks is predicted to be higher in its peptidic form, compared to the free molecule. The peptidic environment also changes the sites’ reactivity, and for the Gly-Phe-Gly + OH reaction H abstraction becomes the major path of reaction. The good agreement found between the calculated and the available experimental data supports the methodology used in this work, as well as the data reported here for the first time.
Chemical Physics 2008 Volume 345(Issue 1) pp:87-94
Publication Date(Web):3 April 2008
DOI:10.1016/j.chemphys.2008.01.040
Abstract
Adsorption processes of thiophene and benzothiophene on pristine carbon nanotubes (CNTs), and on CNTs doped with Si or Ge, have been modeled with Density Functional. This is the first study on the chemical reactivity of such doped tubes. The calculated data suggest that the presence of silicon or germanium atoms in CNTs increases their reactivity toward thiophene, and benzothiophene. The adsorption of these species on pristine CNTs seems very unlikely to occur, while the addition products involving doped CNTs were found to be very stable, with respect to the isolated reactants, in terms of Gibbs free energy. Several of these adsorption processes were found to be significantly exergonic (ΔG < 0) in non-polar liquid phase. The results reported in this work suggest that Si and Ge defects on CNTs increase their reactivity toward unsaturated species, and could make them useful in the removal processes of aromatic sulfur compounds from oil-hydrocarbons. However, according to our results, CNTs doped with Si atoms are expected to be more efficient as aromatic sulfur compounds scavengers than those doped with Ge. These results also suggest that the presence of silicon and germanium atoms in the CNTs structures enhances their reactivity toward nucleophilic molecules, compared to pristine carbon nanotubes.
The mechanism of the oxidation of acetylene, in the presence of O2 and NOx, has been studied. Different levels of theory have been tested for the first step of the mechanism: the acetylene + OH radical reaction. Based on these results the meta-hybrid functional MPWB1K has been chosen for modeling all the other steps involved in the oxidation of acetylene. Different reaction paths have been considered and the one leading to glyoxal formation and OH regeneration is predicted to be the main channel, independently of the presence of NOx. Two different mechanisms were modeled to account for formic acid formation, both of them involving cyclic intermediates. According to the computed activation free energies, the three-membered intermediate seems to be more likely to occur than the four-membered one. However, reaction barriers are very high and only a very small proportion of formic acid is expected to be formed through such intermediates. In the presence of NOx, considered in this work for the first time, the main product of the tropospheric oxidation of acetylene is also expected to be glyoxal.
The Journal of Physical Chemistry C 2008 Volume 112(Issue 24) pp:8922-8927
Publication Date(Web):May 27, 2008
DOI:10.1021/jp801379g
Density functional theory calculations have been used to model the potential ability of single-walled carbon nanotubes (SWCNT) to act as free-radical scavengers. The reactions of a (5,5) SWCNT fragment with six different radicals have been studied, and for hydroxyl radical, which is the most reactive and dangerous from all of the studied set, up to four additions were modeled. Energetic considerations show that, once a first radical is attached to the nanotube, further additions are increasingly feasible, suggesting that SWCNTs can act as free-radical sponges. For reactions with OH radicals, subsequent additions are expected to lead to products where the OHs are distributed in groups rather than regularly spread on the nanotube. Because nanotubes with none or an even number of OH groups attached are stable (nonradical) species that can be used for other purposes, their properties were analyzed in terms of global reactivity indexes and density of states (DOS). The results from these analyses suggest that, by controlling the proportion of OH on the nanotubes, their properties can be manipulated.
The ability of antifreeze glycoproteins to inhibit clathrate-hydrate formation is studied using DFT. A 512 cavity, dodecahedral (H2O)20, and the AATA peptide are used to model the inhibitor–clathrate interaction. The presence of AATA in the vicinity of the water cavities not only leads to the formation of complexes, with different peptide/cavity ratios, but also to the deformation of the cavity and to the elongation of several of the hydrogen bonds responsible for keeping the dodecahedral (H2O)20 together. The complexes are formed through hydrogen bonding between the peptides and the water cavities. The glycoproteins are expected to anchor onto the clathrate surface, blocking the access of new water molecules and preventing the incipient crystals from growing. They are also expected to weaken the clathrate structure. Amide IR bands are associated with the complexes’ formation. They are significantly red-shifted in the hydrogen-bonded systems compared to isolated AATA. The amide A band is the most sensitive to hydrogen bonding. In addition a distinctive band around 3100 cm−1 is proposed for the identification of clathrate–peptide hydrogen-bonded complexes.
Co-reporter:E. Torres-García, A. Galano, G. Rodriguez-Gattorno
Journal of Catalysis (15 August 2011) Volume 282(Issue 1) pp:201-208
Publication Date(Web):15 August 2011
DOI:10.1016/j.jcat.2011.06.010
An experimental and theoretical study on the relationships between oxidative reactivity, thermochemical viability, and structural requirement of the activity sites in oxidative desulfurization (ODS) process has been performed. A series of aromatic sulfur compounds and peroxo-metallate complexes of WOx–ZrO2 with different structures have been studied. The models chosen for mimicking the catalyst correspond to surface densities of ∼7 W nm−2. The results indicate that the ODS takes place in two consecutive stages: (i) the formation of sulfoxide and (ii) the formation of sulfone. However, a detailed analysis suggests that these stages occur in two separated steps, (a) addition and (b) elimination, involving the formation of intermediate adducts and that the elimination of sulfoxide from the site surface is the rate-determining step. The results also reveal that the thermochemical feasibility of the studied reactions depends on both: the local structure of the WOx–ZrO2 surface and on the nature of the aromatic sulfur compound. It was found that the reactions involving dibenzothiophene (DBT) and 4,6-dimethyldibenzothiophene (46DMDBT) are the most favored reactions, while the reaction of thiophene (Th) is the least favored. Therefore, highly substituted dibenzothiophenes are the most readily oxidized species, which is in agreement with experimental evidence. An explanation to the different reactivity shown by sulfur compounds, during ODS processes, is provided.Graphical abstractThe experimental-theoretical study reveal that the oxidative desulfurization (ODS) process takes place in two stages, the formation of sulfoxide and the formation of sulfone and that each stage occur in two independent steps, addition (1a and 2a) and elimination (1b and 2b), involving the formation of intermediate adducts. The values of the Gibbs free energy of activation show that the barriers of the addition steps are significantly lower than those of the elimination steps, supporting the hypothesis that the elimination is the rate-determining step of the ODS process.Download high-res image (56KB)Download full-size imageHighlights► Thermochemical viability of oxidative desulfurization (ODS) reactions. ► Surface peroxo-metallate complexes of WOx–ZrO2 were modeled. ► Oxidative reactivity of sulfur compounds was established. ► Reactivity indexes provide an explanation to the thermochemical feasibility.
Density functional theory has been used to model the reaction of OH with L-phenylalanine, as a free molecule and in the Gly-Phe-Gly peptide. The influence of the environment has been investigated using water and benzene as models for polar and non-polar surroundings, in addition to gas phase calculations. Different paths of reaction have been considered, involving H abstractions and addition reactions, with global contributions to the overall reaction around 10% and 90% respectively when Phe is in its free form. The ortho-adducts (o-tyrosine) were found to be the major products of the Phe + OH reaction, for all the modeled environments and especially in water solutions. The reactivity of phenylalanine towards OH radical attacks is predicted to be higher in its peptidic form, compared to the free molecule. The peptidic environment also changes the sites’ reactivity, and for the Gly-Phe-Gly + OH reaction H abstraction becomes the major path of reaction. The good agreement found between the calculated and the available experimental data supports the methodology used in this work, as well as the data reported here for the first time.
Co-reporter:Jorge Rafael León-Carmona, Juan Raúl Alvarez-Idaboy and Annia Galano
Physical Chemistry Chemical Physics 2012 - vol. 14(Issue 36) pp:NaN12543-12543
Publication Date(Web):2012/03/26
DOI:10.1039/C2CP40651A
The peroxyl radical scavenging activity of four hydroxycinnamic acid derivatives (HCAD) has been studied in non-polar and aqueous solutions, using the density functional theory. The studied HCAD are: ferulic acid (4-hydroxy-3-methoxycinnamic acid), p-coumaric acid (trans-4-hydroxycinnamic acid), caffeic acid (3,4-dihydroxycinnamic acid), and dihydrocaffeic acid (3-(3,4-dihydroxyphenyl)-2-propionic acid). It was found that the polarity of the environment plays an important role in the relative efficiency of these compounds as peroxyl scavengers. It was also found that in aqueous solution the pH is a key factor for the overall reactivity of HCAD towards peroxyl radicals, for their relative antioxidant capacity, and for the relative importance of the different mechanisms of reaction. The H transfer from the phenolic OH has been identified as the main mechanism of reaction in non-polar media and in aqueous solution at acid pHs. On the other hand, the single electron transfer mechanism from the phenoxide anion is proposed to be the one contributing the most to the overall peroxyl scavenging activity of HCAD in aqueous solution at physiological pH (7.4). This process is also predicted to be a key factor in the reactivity of these compounds towards a large variety of free radicals.
Physical Chemistry Chemical Physics 2011 - vol. 13(Issue 15) pp:NaN7188-7188
Publication Date(Web):2011/03/15
DOI:10.1039/C0CP02801K
The reactions of melatonin (MLT) with hydroxyl and several peroxyl radicals have been studied using the Density Functional Theory, specifically the M05-2X functional. Five mechanisms of reaction have been considered: radical adduct formation (RAF), Hydrogen atom transfer (HAT), single electron transfer (SET), sequential electron proton transfer (SEPT) and proton coupled electron transfer (PCET). It has been found that MLT reacts with OH radicals in a diffusion-limited way, regardless of the polarity of the environment, which indicates that MLT is an excellent OH radical scavenger. The calculated values of the overall rate coefficient of MLT + ˙OH reaction in benzene and water solutions are 2.23 × 1010 and 1.85 × 1010 M−1 s−1, respectively. MLT is also predicted to be a very good ˙OOCCl3 scavenger but rather ineffective for scavenging less reactive peroxyl radicals, such as alkenyl peroxyl radicals and ˙OOH. Therefore it is concluded that the protective effect of MLT against lipid peroxidation does not take place by directly trapping peroxyl radicals, but rather by scavenging more reactive species, such as ˙OH, which can initiate the degradation process. Branching ratios for the different channels of reaction are reported for the first time. In aqueous solutions SEPT was found to be the main mechanism for the MLT + ˙OH reaction, accounting for about 44.1% of the overall reactivity of MLT towards this radical. The good agreement between the calculated and the available experimental data, on the studied processes, supports the reliability of the results presented in this work.
