A DFT study on the addition and abstraction reactions of thiourea with hydroxyl radical

A theoretical study of the addition of CH2OO to hydroxymethyl hydroperoxide and its implications on SO3 formation in the atmosphere

The reaction of hydroxymethyl hydroperoxide (HMHP, HOCH₂OOH) with the simplest Criegee intermediate, CH₂OO, has been examined using quantum chemical methods with transition state theory. Geometry optimization and IRC calculations were performed using the M06-2X, MN15-L, and B2PLYP-D3 functionals in conjunction with the aug-cc-pVTZ basis set. Single point energy calculations using QCISD(T) and BD(T) with the same basis set have been performed to determine the energy of reactants, reactive complexes, transition states, and products. Rate coefficients have been obtained using variational transition state theory. The addition of CH₂OO on the three different oxygen atoms in HMHP has been considered and the ether oxide forming channel, CH₂OO + HOCH₂OOH → HOCH₂O(O)CH₂OOH (channel 2), is the most favorable. The best computed standard enthalpy of reaction (ΔH) and zero-point corrected barrier height are -20.02 and -6.33 kcal mol^-1, respectively. The reaction barrier is negative and our results suggest that both the inner and outer transition states contribute to the corresponding overall reactive flux in the tropospheric temperature range (220 K to 320 K). A two-transition state model has been used to obtain reliable rate coefficients at the high-pressure limit. The pressure-dependent rate coefficient calculations using the SS-QRRK theory have shown that this channel is pressure-dependent. Moreover, our investigation has shown that the ether oxide formed may rapidly react with SO₂ at 298 K to form SO₃, which can, in turn, react with water to form atmospheric H₂SO₄. A similar calculation has been conducted for the reaction of HMHP with OH, suggesting that the titled reaction may be a significant sink of HMHP. Therefore, the reaction between CH₂OO and HOCH₂OOH could be an indirect source for generating atmospheric H₂SO₄, which is crucial to the formation of clouds, and it might relieve global warming.

Hydroxyl radical scavenging activity of melatonin and its related indolamines

The hydroxyl radical (•OH) scavenging activities of Melatonin, an endogenously produced neurohormone and its related indolamines like N-acetyl tryptophan (NAT) and N-acetyl serotonin (NAS) have been investigated using density functional theory. The mechanism involves 4 steps: initial radical addition to position-3 of the indole ring, keto-amine to enol-imine tautomerization, cyclisation, and finally, addition of a second •OH leading to a cyclic end product. Incorporation of an explicit water molecule in tautomerization step leads to a significant reduction in the barrier of this step, so that the subsequent cyclisation step becomes rate-limiting. In agreement with the very high reactivity of •OH, the initial and final addition of •OH to indolamine are found to be barrierless. Radical adduct formed in the initial step was found to be very stable due to the extensive conjugation present in the substrate. Our calculations show that melatonin is the most effective radical scavenger among the three molecules chosen. NAS was found to exhibit antiradical property comparable to that of melatonin. In contrast to the general observation of reduced antioxidant activity of tryptophan, a non-natural derivative of tryptophan used here (NAT) is found to have good radical scavenging activity. This work further implies that non-natural derivatives of indolamines might as well be useful in the detoxification of free radicals as they exhibit almost comparable antioxidant efficiency as that of melatonin.

Mechanism and kinetics of diuron oxidation by hydroxyl radical addition reaction

Diuron is a phenyl urea herbicide used to control weeds in agricultural lands. The degradation of diuron in the atmosphere takes place dominantly via reaction with OH radicals. In this work, the OH addition reaction of diuron has been studied by using density functional theory methods M06-2X, ωB97X-D and MPWB1K with 6-31G(d,p) basis set. The calculated thermochemical parameters show that OH addition reaction occurs favourably at C₂ position of diuron. The rate constant is calculated for the favourable initial reaction pathway by using canonical variational transition state theory with small curvature tunnelling (SCT) correction over the temperature range of 200-1000 K. The reaction of initially formed diuron-OH adduct intermediate with O₂ leads to the formation of peroxy radical intermediate. The reaction of peroxy radical intermediate with HO₂ and NO_x (x = 1, 2) radicals is studied in detail. The results obtained from time-dependent density functional theory (TDDFT) calculations show that the intermediates and products formed from oxidation of diuron can be easily photolyzed in the sunlight. This study provides thermodynamical and kinetic data for the atmospheric oxidation of diuron by OH radical addition reaction and demonstrates the atmospheric chemistry of diuron and its derivatives.

A DFT mechanistic, thermodynamic and kinetic study on the reaction of 1, 3, 5-trihydroxybenzene and 2, 4, 6-trihydroxyacetophenone with •OOH in different media

A theoretical investigation on the reactions of 1, 3, 5-trihydroxybenzene (PG) and 2, 4, 6-trihydroxyacetophenone (ACPG) with •OOH has been performed with the aim of elucidating the peroxyl radical scavenging properties of PG and its acylated derivative. The study has considered the hydrogen atom transfer (HAT), the single electron transfer-proton transfer and the sequential proton loss-electron transfer mechanisms and determined the geometric, energetic and electronic properties of the reaction species as well as the kinetic parameters for the HAT mechanism. DFT/M06-2X, DFT/MPW1K and DFT/BHHLYP calculation methods have been utilized in combination with the 6-311++G(3df, 2p) basis set. The DFT methods were benchmarked using the CBS-QB3 method. Thermodynamic parameters such as bond dissociation enthalpy (BDE) and ionization energy suggest that the thermodynamically preferred mechanism is the HAT mechanism. The geometric, electronic and energetic parameters suggest that the preferred site for the abstraction of the free phenolic H atom in ACPG is the ortho position. Spin density and branching ratio values indicate that the most stable and preferable product formed is for the reaction of ACPG [Formula: see text] •OOH at the ortho position. The estimated rate constants obtained indicate that the reaction of ACPG [Formula: see text] •OOH is kinetically preferred to the reaction of PG [Formula: see text] •OOH, which is in agreement with experimental findings.

A DFT mechanistic and kinetic study on the reaction of phloroglucinol with •OH in different media: Hydrogen atom transfer versus oxidation

A theoretical study on the reaction of phloroglucinol with •OH has been performed with the aim of elucidating the geometric, energetic and kinetic properties of the reaction as well as identifying the preferred reaction pathway. Three reaction mechanisms have been considered, namely, direct hydrogen atom abstraction, addition–elimination mechanism in the absence and in the presence of a base catalyst and oxidation mechanism in the absence and in the presence of O2. The study has been performed using the DFT/M06[Formula: see text]2X, DFT/BHHLYP and DFT/MPW1K methods in conjunction with either the 6-31++G(d,p) or the 6-311++G(3df,2p) basis set. The energetic parameters are influenced by the type of function utilized and the media in which the calculation is done. The direct hydrogen abstraction mechanism provides the smallest branching ratio with respect to the •OH addition mechanisms. The PG + •OH reaction under atmospheric conditions saturated with O2 would predominantly form tetrahydroxybenzene; the predominant product within the biological system would largely depend on physiological conditions; under pH [Formula: see text] 7 and with oxygen dissolved within the biological system, the preferred product would be tetrahydroxybenzene; however, if the reaction takes place in some part of the biological system where the pH [Formula: see text] 7, the preferred product would be the phenoxyl radical.