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The significance of long-range correction to the hydroperoxyl radical-scavenging reaction of trans-resveratrol and gnetin C.

ABSTRACT: Density functional theory has been gaining popularity for studying the radical scavenging activity of antioxidants. However, only a few studies investigate the importance of calculation methods on the radical-scavenging reactions. In this study, we examined the significance of (i) the long-range correction on the coulombic interaction and (ii) the London dispersion correction to the hydroperoxyl radical-scavenging reaction of trans-resveratrol and gnetin C. We employed B3LYP, CAM-B3LYP, M06-2X exchange-correlation functionals and B3LYP with the D3 version of Grimme's dispersion in the calculations. The results showed that long-range correction on the coulombic interaction had a significant effect on the increase of reaction and activation energies. The increase was in line with the change of hydroperoxyl radical's orientation in the transition state structure. Meanwhile, the London dispersion correction only had a minor effect on the transition state structure, reaction energy and activation energy. Overall, long-range correction on the coulombic interaction had a significant impact on the radical-scavenging reaction.

SUBMITTER: Khoirunisa V

PROVIDER: S-EPMC8074789 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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The significance of long-range correction to the hydroperoxyl radical-scavenging reaction of trans-resveratrol and gnetin C.

Khoirunisa Vera V Rusydi Febdian F Boli Lusia S P LSP Puspitasari Ira I Rachmawati Heni H Dipojono Hermawan K HK

Royal Society open science 20210210 2

Density functional theory has been gaining popularity for studying the radical scavenging activity of antioxidants. However, only a few studies investigate the importance of calculation methods on the radical-scavenging reactions. In this study, we examined the significance of (i) the long-range correction on the coulombic interaction and (ii) the London dispersion correction to the hydroperoxyl radical-scavenging reaction of trans-resveratrol and gnetin C. We employed B3LYP, CAM-B3LYP, M06-2X e ...[more]

PMID: 33972845

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Project description:ContextAntioxidants are known to play a beneficial role in human health. Caffeic acid has been previously recognized as efficient in this context. However, such a capability can be enhanced through structural modification. Thus, 3829 caffeic acid derivatives were computational designed to that purpose by adding functional groups (-OH, -SH, -OCH3, -COOCH3, -F, -CF3, and -N(CH3)(C2H5)) to its framework. Promising candidates were chosen considering drug-like behavior, toxicity, and synthetic accessibility. The best candidates, dCAF-2, dCAF-16, and dCAF-82, were identified by comparison with reference antioxidants. The thermochemistry and kinetics of their reaction with •OOH are provided. The global rate coefficients were estimated to be 1.76 × 109 M-1 s-1, 3.19 × 109 M-1 s-1, and 1.79 × 109 M-1 s-1 in aqueous solution for dCAF-2, dCAF-16, and dCAF-82, respectively. In lipid medium, their total rate coefficients were estimated to be 3.65 × 103 M-1 s-1, 3.73 × 103 M-1 s-1, and 8.63 × 104 M-1 s-1 for dCAF-2, dCAF-16, and dCAF-82, respectively. These values allow predicting the designed caffeic acid derivatives as excellent antioxidants in both environments. The reaction forces for the main reaction path of the dCAF-2, dCAF-16, and dCAF-82 reactions with •OOH were explored.MethodsThree protocols were used: (i) CADMA-Chem (computer-assisted design of multifunctional antioxidants, based on chemical properties) to quantify ADME (absorption, distribution, metabolism, and excretion) properties, toxicity and synthetic accessibility; (ii) eH-DAMA (electron and hydrogen donating ability map) tool, to identify the derivatives expected to behave as the best antioxidants; (iii) QM-ORSA (quantum mechanics-based test for overall free radical scavenging activity), to calculate the rate constants. Electronic structure calculations were performed with Gaussian 09, at the M05-2X/6-311 + g(d,p) level of theory. Both aqueous and lipid environments were considered using the SMD continuous solvation model. Intrinsic reaction coordinate (IRC) calculations, as implemented in Gaussian 09, were used to obtain the reaction force.

Project description:The reaction mechanisms and kinetics of thiophene oxidation reactions initiated by hydroperoxyl radical, and decomposition of the related intermediates and complexes, have been considered herein by using high-level DFT and ab initio calculations. The main energetic parameters of all stationary points of the suggested potential energy surfaces have been computed at the BD(T) and CCSD(T) methods, based on the geometries optimized at the B3LYP/6-311 + g(d,p) level of theory. Rate constants of bimolecular reactions (high-pressure limit rate constants) at temperatures from 300 to 3000 K for the first steps of the title reaction have been obtained through the conventional transition state theory (TST), while the pressure dependent rate constants and the rate constants of the second and other steps have been calculated employing the Rice-Ramsperger-Kassel-Marcus/Master equation (RRKM/ME). The results show that the rate constants of addition to α and β carbons have positive temperature dependence and negative pressure dependence. It is found that the additions of HO2 to the α and β carbons of thiophene in the initial steps of the title reaction are the most favored pathways. Also, the addition to the sulfur atom has a minor contribution. But, all efforts for simulating hydrogen abstraction reactions have been unsuccessful. In this complex oxidation reaction, about 12 different products are obtained, including important isomers such as thiophene-epoxide, thiophene-ol, thiophene-oxide, oxathiane, and thiophenone. The calculated total rate constants for generation of all minimum stationary points show that the addition reactions to the α and β carbons are the fastest among all at temperatures below 1000 K, while the proposed multi-step parallel reactions are more competitive at temperatures above 1200 K. Furthermore, important inter-and intra-molecular interactions for some species have been investigated by two well-known quantum chemistry method, the NBO and AIM analyses. Thermochemical properties such as free energy, enthalpy, internal energy, and entropy for thiophene and hydroperoxyl radical and related species in the simulated reactions have been predicted using a combination of the B3LYP and BD(T) methods.

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The significance of long-range correction to the hydroperoxyl radical-scavenging reaction of trans-resveratrol and gnetin C.

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The significance of long-range correction to the hydroperoxyl radical-scavenging reaction of trans-resveratrol and gnetin C.

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