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Theoretical insights into the antiradical activity and copper-catalyzed oxidative damage of mexidol in the physiological environment

Citation

Vo, Quan V.; Hoa, Nguyen Thi; Bay, Mai Van; Mechler, Adam (2022), Theoretical insights into the antiradical activity and copper-catalyzed oxidative damage of mexidol in the physiological environment, Dryad, Dataset, https://doi.org/10.5061/dryad.bzkh18997

Abstract

This dataset contains data from the calculations described in the paper: “Quan V. Vo*, Nguyen Thi Hoa, Mai Van Bay, Adam Mechler, Theoretical insights into the antiradical activity and copper-catalyzed oxidative damage of mexidol in the physiological environment. Royal Society Open Science. 2021.

In this study, the hydroperoxyl radical scavenging activity of MD was studied to establish baseline antioxidant activity, followed by an investigation of the effect of MD on the copper-catalyzed oxidative damage in biological systems, using computational methods. It was found that MD exhibits moderate radical scavenging activity against HOO· in physiological environments. The activity in aqueous solution is defined by the single electron transfer mechanism of the anion state; however in nonpolar environments the formal hydrogen transfer pathway dominates at the O3-H bond. It was also confirmed that MD can chelate Cu (II), forming complexes that are much harder to reduce than free Cu (II): MD chelation completely quenches the Cu (II) reduction by ascorbic acid and suppresses the rate of reduction reaction by O2·- that are the main reductants of Cu (II) in biological environments. Therefore, MD exerts its anti- HO· activity primarily as an OIL-1 inhibitor.

Methods

The dataset was collected during the Gaussian 09 suite of programs at The University of Danang - University of Technology and Education, Vietnam, and La Trobe University, Australia. M06-2X/6-311++G(d,p) model chemistry was used for all calculations. It was demonstrated before that the M06-2X functional is one of the most reliable methods to study thermodynamics and kinetics of radical reactions, particularly in physiological environments. The solvation model density (SMD) method was used for including the effects of water and pentyl ethanoate in the computations. The kinetic calculations were performed following the quantum mechanics-based test for the overall free radical scavenging activity (QM-ORSA) protocol, using the conventional transition state theory (TST) and 1M standard state at 298.15 K.

Usage Notes

The readme file contains the calculation methods (Table S1, SI), the calculated Gibbs free energy of reactions between MD and [Cu(H2O)4]2+ in aqueous solution (Table S2, SI), the calculated BDE, PA, and IE (Table S3), the kinetic data (Table S4, SI), the calculated Gibbs free energy of reactions of the H2A+ with HOO· following the FHT and SET mechanisms in the aqueous solution (Table S5, SI), the Cartesian coordinates of the transition states and complexes (Table S6, SI) and optimized geometries the selected complexes in aqueous solution (Figure 1) in all the studied environments, th draft data and input files. Information on how the calculations were done can also be found in the associated manuscript referenced above.

Funding

The Vietnamese Ministry of Education and Training, Award: B2021-DNA-16