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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Computational calculations at B3LYP/CC-PVDZ level were employed in the study of tautomers of Thioguanine (TG) in the gas phase and selected solvents such as benzene , tetrahydrofuran (THF), methanol, Dimethyl sulfoxide (DMSO) and water using PCM model. All tautomers are optimized at this level. In addition, stability of the tautomers in different solvents shows interesting results. In the gas phase, benzene and THF, TG1 form is more stable than the other forms but in polarisable solvents (methanol, DMSO and water) TG5 is the most stabilized form. Variation of dipole moments and NBO charges on atoms in the solvents were studied.

Water as an important assistant can alter the reactivity of atmospheric species. This project is designed to investigate the impact of a single water molecule on the atmospheric reactions of aromatic compounds that have not been attended to comprehensively. In the first part, the atmospheric oxidation mechanisms of thiophene initiated by hydroperoxyl radical through a multiwell-multichannel potential energy surface were studied to have useful information about the chemistry of the considered reaction. It was verified that for the thiophene plus HO2 reaction, the addition mechanism is dominant the same as other aromatic compounds. Due to the importance of the subject and the presence of water molecules in the atmosphere with a high concentration that we know as relative humidity, and also the lack of insight into the influence of water on the reactions of aromatic compounds with active atmospheric species, herein, the effect of a single water molecule on the addition pathways of the title reaction is evaluated. In another word, this research explores how water can change the occurrence of reactions of aromatic compounds in the atmosphere. For this, the presence of one water molecule is simulated by higher-level calculations (BD(T) method) through the main interactions with the stationary points of the most probable pathways. The results show that the mechanism of the reaction with water is more complicated than the bare reaction due to the formation of the ring-like structures. Also, water molecule decreases the relative energies of all addition pathways. Moreover, atoms in molecule theory (AIM) along with the kinetic study by the transition state (TST) and the Rice–Ramsperger–Kassel–Marcus (RRKM) theories demonstrate that the overall interactions of a path determine how the rate of that path changes. In this regard, our results establish that the interactions of water with HO2 (thiophene) in the initial complex 1WHA (1WTA or 1WTB) are stronger (weaker) than the sum of its interactions in transition states. Also, for the water-assisted pathways, the ratio of the partition function of the transition state to the partition functions of the reactants is similar to the respective bare reaction. Therefore, the reaction rates of the bare pathways are more than the water-assisted paths that include the 1WHA complex and are less than the paths that involve the 1WTA and 1WTB complexes.