Anharmonic RRKM Calculation for the Dissociation of (H2O)2H+ and Its Deuterated Species (D2O)2D+

Deprotonation of Guanine Radical Cation G•+ Mediated by the Protonated Water Cluster

Proton transfer is regarded as a fundamental process in chemical reactions of DNA molecules and continues to be an active research theme due to the connection with charge transport and oxidation damage of DNA. For the guanine radical cation (G^•+) derived from one-electron oxidation, experiments suggest a facile proton transfer within the G^•+:C base pair, and a rapid deprotonation from N1 in free base or single-strand DNA. To address the deprotonation mechanism, we perform a thorough investigation on deprotonation of G^•+ in free G base by combining density functional theory (DFT) and laser flash photolysis spectroscopy. Experimentally, kinetics of deprotonation is monitored at temperatures varying from 280 to 298 K, from which the activation energy of 15.1 ± 1.5 kJ/mol is determined for the first time. Theoretically, four solvation models incorporating explicit waters and the polarized continuum model (PCM), i.e., 3H₂O-PCM, 4H₂O-PCM, 5H₂O-PCM, and 7H₂O-PCM models are used to calculate deprotonation potential energy profile, and the barriers of 5.5, 13.4, 14.4, and 13.7 kJ/mol are obtained, respectively. It is shown that at least four explicit waters are required for properly simulating the deprotonation reaction, where the participation of protonated water cluster plays key roles in facilitating the proton release from G^•+.

Anharmonic effect of the unimolecular dissociation of Glycerol to Glycidol

The unimolecular dissociation rate constants of the dehydration of Glycerol to Glycidol were calculated at the MP2/6–311G(d,p) level using the Rice–Ramsperger–Kassel–Marcus (RRKM) theory. The anharmonic effect of the reactions was examined by comparing the rate constants at temperatures (700–3000[Formula: see text]K) of the canonical case and total energies (25654–53089[Formula: see text]cm[Formula: see text]) of the microcanonical system. The calculations showed that high temperatures are required for the reaction to proceed. As the temperatures and total energies increased, the rate of reactions increased. However, the growth rate of the unimolecular dissociation rate constants was high and slower both in the canonical and microcanonical systems. Comparative analysis showed that the anharmonic effect was most significant for the reaction [Formula: see text] and least significant for the reaction [Formula: see text]. The anharmonic effect became more significant as the temperatures and total energies increased. Compared with the microcanonical situation, the anharmonic effect of the canonical system was more pronounced.

Calculation of anharmonic effect on the dissociation of ethylene glycol

The unimolecular dissociation rate constants of ethylene glycol were examined using the MP2/6-311[Formula: see text]G(d,p) method based on the Rice–Ramsperger–Kassel–Marcus (RRKM) theory. The effect of anharmonicity on the dissociation rate constants was evaluated at 500–4000[Formula: see text]K temperatures of the canonical system and 25,182–50,235[Formula: see text]cm[Formula: see text] total energies of the microcanonical system. The comparison of the results showed that the H2O elimination reaction played a critical role in the decomposition processes of ethylene glycol. The results of the rate constant calculations indicated that the H2O elimination reaction dominated at low temperatures, whereas the direct C–C bond dissociation reaction (CH2OHCH2OH [Formula: see text] CH2OH[Formula: see text][Formula: see text][Formula: see text]CH2OH) dominated at high temperatures. For channel 1, CH2OH[Formula: see text][Formula: see text][Formula: see text]CH2OH, the anharmonic effect of the canonical system was not observed, while it became more obvious with the increasing total energies in the microcanonical system. For channels 2–5, CH3CHO[Formula: see text][Formula: see text][Formula: see text]H2O, CH2CHOH[Formula: see text][Formula: see text][Formula: see text]H2O, CH3OH[Formula: see text][Formula: see text][Formula: see text]CHOH, and CH2OHCHO[Formula: see text][Formula: see text][Formula: see text]H2, the anharmonic effect of canonical and microcanonical systems became more obvious with increasing temperatures and total energies. The comparison showed that, for channels 1 and 4, C–C bond dissociation and the anharmonic effect of the microcanonical system were more evident, whereas the anharmonic effect of the canonical system was more predominant for channels 2 (CH3CHO[Formula: see text][Formula: see text][Formula: see text]H2O), 3 (CH2CHOH[Formula: see text][Formula: see text][Formula: see text]H2O), and 5 (CH2OHCHO[Formula: see text][Formula: see text][Formula: see text]H2).

Anharmonic Rice-Ramsperger-Kassel-Marcus (RRKM) and product branching ratio calculations for the partially deuterated protonated water dimers: dissociation and isomerization

Partially deuterated protonated water dimers, H2O·H(+)·D2O, H2O·D(+)·HDO, and HDO·H(+)·HDO, as important intermediates of isotopic labeled reaction of H3O(+) + D2O, undergo direct dissociation and indirect dissociation, i.e., isomerization before the dissociation. With Rice-Ramsperger-Kassel-Marcus theory and ab initio calculations, we have computed their dissociation and isomerization rate constants separately under the harmonic and anharmonic oscillator models. On the basis of the dissociation and isomerization rate constants, branching ratios of two primary products, [HD2O(+)]∕[H2DO(+)], are predicted under various kinetics models with the harmonic or anharmonic approximation included. The feasible kinetics model accounting for experimental results is shown to include anharmonic effect in describing dissociation, while adopting harmonic approximation for isomerization. Thus, the anharmonic effect is found to play important roles affecting the dissociation reaction, while isomerization rates are shown to be insensitive to whether the anharmonic or harmonic oscillator model is being applied.

Apparent stoichiometry of water in proton hydration and proton dehydration reactions in CH3CN/H2O solutions

Gradual solvation of protons by water is observed in liquids by mixing strong mineral acids with various amounts of water in acetonitrile solutions, a process which promotes rapid dissociation of the acids in these solutions. The stoichiometry of the reaction XH(+) + n(H(2)O) = X + (H(2)O)(n)H(+) was studied for strong mineral acids (negatively charged X, X = ClO(4)¯, Cl¯, Br¯, I¯, CF(3)SO(3)¯) and for strong cationic acids (uncharged X, X = R*NH(2), H(2)O). We have found by direct quantitative analysis preference of n = 2 over n = 1 for both groups of proton transfer reactions at relatively low water concentrations in acetonitrile. At high water concentrations, we have found that larger water solvates must also be involved in the solvation of the proton while the spectral features already observed for n = 2, H(+)(H(2)O)(2), remain almost unchanged at large n values up to at least 10 M of water.