Chemical repair of damaged leucine and tryptophane by thiophenols at close to diffusion-controlled rates: Mechanisms and kinetics.

Thiophenols are chemical species with multiple desirable biological properties, including their primary and secondary antioxidant capacity. In this work, the repairing antioxidant activity of eight different thiophenols has been investigated for damaged leucine and tryptophane. The investigation was carried out employing quantum mechanical and transition state methods to calculate the thermodynamic and kinetic data of the reactions involved, while simulating the biological conditions at physiological pH and aqueous and lipidic medium. The analysis of the atomic charges and the spin densities at each of the points on the potential energy surface was the tool that allowed the elucidation of the reaction mechanisms through which thiophenols repair the oxidative damage caused to the amino acids leucine and tryptophan. It was found that thiophenols can repair leucine via a hydrogen atom transfer mechanism in a manner which is similar to the one used by glutathione to repair the carbon-centered radicals of guanosine. In addition, thiophenols can also restore tryptophane, a nitrogen-centered radical, via proton-coupled electron transfer and single electron transfer mechanisms. Moreover, both processes occur at close to diffusion-controlled rates.

Thiophenols, Promising Scavengers of Peroxyl Radicals: Mechanisms and kinetics.

The activity of 12 thiophenols as primary antioxidants in aqueous solution has been studied using density functional theory. Twelve different substituted thiophenols were tested as peroxyl radicals scavengers. Single electron transfer (SET) and formal hydrogen transfer (FHT) were investigated. The SET mechanism was found to be the main mechanism, with rate constants that are close to the diffusion limit, which means that these thiophenolic compounds have the capacity to scavenge peroxyl radicals before they can damage biomolecules. All 12 thiophenolic compounds react faster with methylperoxyl than with hydroperoxyl radicals. In addition, it was found that pH plays an important role in the reactivity of these compounds. © 2019 Wiley Periodicals, Inc.

Indigo adsorption on a silicate surface: a theoretical density functional study.

The applicability of naturally available low-cost and eco-friendly adsorbent materials for the removal of hazardous dyes from aqueous waste is of increasing environmental interest. Among the adsorption treatments available, clays seem to be economically attractive due to their abundance and adsorption capabilities. Indeed, many ancient coloring materials utilized clays mixed with natural dyes (e.g., indigo in Maya Blue). In this work, we performed a quantum-mechanical theoretical study of the adsorption of the indigo molecule onto the (001) surface of a phyllosilicate. Different methods and approaches were applied and compared. We found that the presence of a tetrahedral charge and a sodium counterion significantly increased the adsorption energy of the indigo molecule. The vibrational spectrum of the dye-surface system was also studied, and some interesting shifts in the frequencies of the main vibrational modes of indigo due to its interaction with the surface of the clay mineral were identified.

A theoretical and experimental evaluation of imidazolium-based ionic liquids for atmospheric mercury capture.

In this work, the capacity of three different imidazolium-based ionic liquids (ILs) for atmospheric mercury capture has been evaluated. Theoretical calculations using monomer and dimer models of ILs showed that [BMIM]⁺[SCN]⁻ and [BMIM]⁺[Cl]⁻ ionic liquids capture gaseous Hg°, while [BMIM]⁺[PF6]⁻ shows no ability for this purpose. These findings are supported by experimental data obtained using particle induced X-ray emission (PIXE) trace element analysis. Experimental and theoretical infrared data of the ILs were obtained before and after exposure to Hg. In all cases, no displacement of the bands was observed, indicating that the interaction does not significantly affect the force constants of substrate bonds. This suggests that van der Waals forces are the main forces responsible for mercury capture. Since the anion-absorbate is the driving force of the interaction, the largest charge-volume ratio of [Cl]⁻ could explain the higher affinity for mercury sequestration of the [BMIM]⁺[Cl]⁻ salt.

Molecular description of indigo oxidation mechanisms initiated by OH and OOH radicals.

In this work, we report a quantum chemistry mechanistic study of the hydroxyl (•OH) and hydroperoxyl (•OOH) radicals initiated oxidation of indigo, within the density functional theory framework. All possible hydrogen abstraction and radical addition reaction pathways have been considered. We find that the reaction between a free indigo molecule and an •OH radical occurs mainly through two competing mechanisms: H-abstraction from an NH site and •OH addition to the central C═C double bond. Although the latter is favored, both channels occur, the indigo chromophore group structure is modified, and thus the color is changed. This mechanism adequately accounts for the loss of chromophore in urban air, including indoor air such as in museums and in urban areas. Regarding the reactivity of indigo toward •OOH radicals, only •OOH-addition to the central double bond is thermodynamically feasible. The corresponding transition state free energy value is about 10 kcal/mol larger than the one for the •OH initiated oxidation. Therefore, even considering that the •OOH concentration is considerably larger than the one of •OH, this reaction is not expected to contribute significantly to indigo oxidation under atmospheric conditions.

ROS initiated oxidation of dopamine under oxidative stress conditions in aqueous and lipidic environments.

Dopamine is known to be an efficient antioxidant and to protect neurocytes from oxidative stress by scavenging free radicals. In this work, we have carried out a systematic quantum chemistry and computational kinetics study on the reactivity of dopamine toward hydroxyl (•OH) and hydroperoxyl (•OOH) free radicals in aqueous and lipidic simulated biological environments, within the density functional theory framework. Rate constants and branching ratios for the different paths contributing to the overall reaction, at 298 K, are reported. For the reactivity of dopamine toward hydroxyl radicals, in water at physiological pH, the main mechanism of the reaction is proposed to be the sequential electron proton transfer (SEPT), whereas in the lipidic environment, hydrogen atom transfer (HAT) and radical adduct formation (RAF) pathways contribute almost equally to the total reaction rate. In both environments, dopamine reacts with hydroxyl radicals at a rate that is diffusion-controlled. Reaction with the hydroperoxyl radical is much slower and occurs only by abstraction of any of the phenolic hydrogens. The overall rate coefficients are predicted to be 2.23 × 10(5) and 8.16 × 10(5) M(-1) s(-1), in aqueous and lipidic environment, respectively, which makes dopamine a very good •OOH, and presumably •OOR, radical scavenger.

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.

Theoretical explanation of nonexponential OH decay in reactions with benzene and toluene under pseudo-first-order conditions.

OH radical reactions with benzene and toluene have been studied in the 200-600 K temperature range via the CBS-QB3 quantum chemistry method and conventional transition-state theory. Our study takes into account all possible hydrogen abstraction and OH-addition channels, including ipso addition. Reaction rates have been obtained under pseudo-first-order conditions, with aromatic concentrations in large excess compared to OH concentrations, which is the case in the reported experiments as well as in the atmosphere. The reported results are in excellent agreement with the experimental data and reproduce the discontinuity in the Arrhenius plots in the 300 K < T < 400 K temperature range. They support the suggestion that the observed nonexponential OH decay is caused by the existence of competing addition and abstraction channels and by the decomposition of thermalized OH-aromatic adducts back to reactants. We also find that the low-temperature onset of the nonexponential decay depends on the concentration of the aromatic compounds and that the lower the concentration, the lower the temperature onset. Under atmospheric conditions, nonexponential decay was found to occur in the 275-325 K range, which corresponds to temperatures of importance in tropospheric chemistry. Branching ratios for the different reaction channels are reported. We find that for T > or = 400 K the reaction occurs exclusively by H abstraction. At 298 K, ipso addition contributes 13.0% to the overall OH + toluene reaction, while the major products correspond to ortho addition, which represents 43% of all possible channels.

Theoretical investigation of the OH*-initiated oxidation of benzaldehyde in the troposphere.

A mechanistic and kinetic study of the OH(*)-initiated oxidation of benzaldehyde is carried out using quantum chemical methods and classical transition state theory. We calculate the rate constant for this reaction within the temperature range of 200-350 K at atmospheric pressure. All possible hydrogen abstraction and OH(*) addition channels are considered and branching ratios are obtained. Tunneling corrections are taken into account for abstraction channels, assuming unsymmetrical Eckart barriers. The aldehydic abstraction is by far the most important reaction channel within the entire range of temperatures studied, especially at room temperature and lower-the temperatures relevant to atmospheric chemistry. The relative importance of all the other possible channels increases slightly with temperature. Branching ratios show that addition at the ring and abstraction of an ortho hydrogen contribute about 1% each at about 300 K, while the branching ratio for the main reaction decreases from 99% at 200 K to 93% at 350 K. The results are compared with available experimental measurements.

Theoretical determination of the rate constant for OH hydrogen abstraction from toluene.

The OH abstraction of a hydrogen atom from both the side chain and the ring of toluene has been studied in the range 275-1000 K using quantum chemistry methods. It is found that the best method of calculation is to perform geometry optimization and frequency calculations at the BHandHLYP/6-311++G(d,p) level, followed by CCSD(T) calculations of the optimized structures with the same basis set. Four different reaction paths are considered, corresponding to the side chain and three possible ring hydrogen abstractions, and the branching ratio is determined as a function of temperature. Although negligible at low temperatures, at 1000 K ring-H abstraction is found to contribute 11% to the total abstraction reaction. The calculated rate coefficients agree very well with experimental results. Side chain abstraction is shown to occur through a complex mechanism that includes the reversible formation of a collisionally stabilized reactant complex.

A possible mechanism for furan formation in the tropospheric oxidation of dienes.

The isoprene + OH gas-phase reaction has been widely studied because of its relevance in tropospheric chemistry. However, an unsolved question remains concerning the mechanism for the formation of the observed 3-methylfuran. OH addition to dienes, such as isoprene and butadiene, is assumed to occur only at the external carbon atoms, thus restricting furan formation to a step after addition at C1 and C4. Moreover, cyclization of the carbon chain necessarily involves a cis conformation. In this work, several quantum chemistry methods have been used to model five different reaction paths for furan formation. A mechanism that is highly favored for intermediates that do not undergo collisional stabilization has been identified.

Glycolaldehyde + OH gas phase reaction: a quantum chemistry + CVT/SCT approach.

We present a theoretical study of the mechanism and kinetics of the OH hydrogen abstraction from glycolaldehyde. Optimum geometries, frequencies, and gradients have been computed at the BHandHLYP/6-311++G(d,p) level of theory for all stationary points, as well as for additional points along the minimum energy path (MEP). Energies are obtained by single-point calculations at the above geometries using CCSD(T)/6-311++G(d,p) to produce the potential energy surface. The rate coefficients are calculated for the temperature range 200-500 K by using canonical variational theory (CVT) with small-curvature tunneling (SCT) corrections. Our analysis suggests a stepwise mechanism involving the formation of a reactant complex in the entrance channel and a product complex in the exit channel, for all the modeled paths. The overall agreement between the calculated and experimental kinetic data that are available at 298 K is very good. This agreement supports the reliability of the parameters obtained for the temperature dependence of the glycolaldehyde + OH reaction. The expressions that best describe the studied reaction are k(overall) = 7.76 x 10(-13) e(1328/)(RT) cm(3).molecule(-1).s(-1) and k(overall) = 1.09 x 10(-21)T(3.03) e(3187/)(RT) cm(3) molecule(-1) s(-1), for the Arrhenius and Kooij approaches, respectively. The predicted activation energy is (-1.36 +/- 0.03) kcal/mol, at about 298 K. The agreement between the calculated and experimental branching ratios is better than 10%. The intramolecular hydrogen bond in OO-s-cis glycolaldehyde is found to be responsible for the discrepancies between SAR and experimental rate coefficients.

Mechanism and kinetics of the reaction of OH radicals with glyoxal and methylglyoxal: a quantum chemistry + CVT/SCT approach.

A theoretical study of the mechanism and kinetics of the OH hydrogen abstraction from glyoxal and methylglyoxal is presented. Optimum geometries, frequencies, and gradients have been computed at the BHandHLYP/6-311++G(d,p) level of theory for all the stationary points, as well as for 12 additional points along the minimum energy path (MEP). Energies were obtained by single-point calculations at the above geometries using CCSD(T)/ 6-311++G(d,p) to produce the potential energy surface. The rate coefficients were calculated for the temperature range 200-500 K by using canonical variational theory (CVT) with small-curvature tunneling (SCT) corrections. Our analysis suggests a stepwise mechanism, which involves the formation of a reactant complex. The overall agreement between the calculated and experimental kinetic data is very good. This agreement supports the reliability of the Arrhenius parameters of the glyoxal + OH reaction that are proposed in this work for the first time. The Arrhenius expressions that best describe the studied reactions are k1 = (9.63 +/- 0.23) x l0(-13)exp[(517 +/- 7)/T] and k2 = (3.93 +/- 0.11) x 10(-13)exp[(1060 +/- 8)/T]cm3 molecule(-1)s(-1) for glyoxal and methylglyoxal, respectively.

Ab-initio study of initial atmospheric oxidation reactions of C3 and C4 alkanes.

Second-order, Møller-Plesset (MP2)-unrestricted Hartree-Fock calculations with full geometry optimization in the 6-31G(d, p) basis set were carried out to study the initial atmospheric oxidation reactions of alkanes. All structures in the initial hydrogen abstraction reaction by an OH radical and the subsequent addition of molecular oxygen to the alkyl radical were characterized for alkanes with three and four carbon atoms. The reaction paths for the formation of the peroxyl radicals were obtained and discussed in the light of similarities along series involving primary, secondary, and tertiary hydrogens. A 0.999 correlation was found between the height of our barriers for the OH abstraction of a primary hydrogen atom from alkanes containing one to four carbon atoms and the optimally estimated activation energies for this reaction recently presented. From the slope and the intersection at zero activation energy an equation was obtained that yields scaled values of the activation energies to account for the tunnel effect and for the error due to the basis set and the method employed. We present new results for the abstraction of the less favored primary hydrogens in propane, butane, and isobutane, which should be important at high temperatures. Negative net activation energies were obtained for the addition of molecular oxygen to all the alkyl radicals formed in the first reaction. The structure of the peroxyl radicals is discussed; and very good correlations are observed for similar compounds, regardless of the length of the carbon chain. A revision of some experimental values is suggested. Single point density functional calculations at the MP2 geometries were also performed with the B3LYP functional for comparison. The observed trends are exactly the same for the two methods. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 845-856, 1999.