Theoretical Studies on the Hydrolysis Mechanism of N-(2-oxo-1,2-dihydro-pyrimidinyl) Formamide

Theoretical insight into the degradation of p-nitrophenol by OH radicals synergized with other active oxidants in aqueous solution

The degradation of p-nitrophenol (p-NP) based on OH radicals (HO^∙), HO₂ radicals (HO₂^∙) and O₂ in aqueous solution was investigated using theoretical computational methods. The complete degradation mechanisms of reaction between p-NP and HO^∙ were explored by density functional theory (DFT) methods. The 4-nitrophenoxy radicals and 1,2-dihydroxy-4-nitrocylohexadienyl radicals are confirmed to be major intermediates of the HO^∙-initiated reactions in aqueous phase, which consistent with experimental results. The chemical structures of some products (2,4-dihydroxycyclohexa-2,4-dien-1-one and 4-nitrocyclohexa-3,5-diene-1,2-dione) which were not identified in the experiment are determined. New favorable formation channels for some intermediates were found. The primary reactions initiated by HO^∙ or HO₂^∙ with p-NP reveals that HO^∙-initiated degradation is the dominant reaction. HO₂^∙ and O₂ can enhance the degradation extent of p-NP in further reactions. Rate constants of the elementary reactions and overall rate constants were calculated. In addition, the HO^∙-initiated primary reactions in a water box of 500 water molecules were studied using Monte Carlo simulation. All the OH-addition reactions are barrierless and highly feasible. The observed dynamic reaction process is similar to the DFT calculation prediction. Furthermore, the eco-toxicity evaluation shows that important products are harmless or harmful to aquatic organisms, and are much less toxic than p-NP.

Mechanism of Phosphine-Catalyzed Novel Rearrangement of Vinylcyclopropylketone to Cycloheptenone: A DFT Study

The title reaction is theoretically investigated in detail using density functional theory. Three possible routes starting from keto- or enol-type vinylcyclopropylketone are considered in this work. Results indicate that phosphine catalyst would first attack at the three-membered ring (C3 position) rather than the terminal of alkene (C1 position) in vinylcyclopropylketone. It is found that the two-stage mechanism would be responsible for the title reaction. The first stage is the S_N2-type ring-opening of the keto-type vinylcyclopropylketone with phosphine catalyst. After the proton-transfer tautomerisms in the zwitterionic intermediates, the second stage is associated with the 7-endo-trig S_N2'-type ring closure of keto- or enol-type zwitterions to furnish seven-membered cyclic products and recover the catalyst. Moreover, it turns out that 7-endo-trig S_N2'-type ring closure would be highly asynchronous and could be well described as an addition/elimination process where the ring closure already finishes before the cleavage of the C-P bond. Computational results provide a deep insight into experimental observations.

Theoretical insight into the Au(i)-catalyzed hydration of halo-substituted propargyl acetate: dynamic water-assisted mechanism

Three possible hydration pathways, including 1,5-exo-dig cycloaddition, 1,6-endo-dig cycloaddition, and direct water attack, have been considered and investigated by using DFT method and the cluster-continuum solvent model.

THE MECHANISM OF ACID-CATALYZED DECARBOXYLATION OF PYRROLE-2-CARBOXYLIC ACID: INSIGHTS FROM CLUSTER-CONTINUUM MODEL CALCULATIONS

The decarboxylation of pyrrole-2-carboxylic acid comprises the addition of water to the carboxyl group and the C–C bond cleavage leading to the protonated carbonic acid. Herein possible concerted and stepwise mechanisms for the C-protonated and O-protonated pathways were extensively investigated by using the cluster-continuum model. The calculated results indicate that the initial hydration or the nucleophilic attack of water at the carbonyl group of both C- and O-protonated derivatives is the rate-determining step for the overall reaction, and the O-protonated pathway will dominate the whole reaction. The predicted activation Gibbs energies for the overall reaction initialized by the O-protonated species fall in the range of 83.3 ∼ 123.0 kJ/mol, showing good agreement with experimental values of 91.6 ∼ 101.3 kJ/mol. On the basis of extensive calculations, the remarkable dependence of the predicted mechanisms and thermodynamic values on the number of explicit water molecules in the cluster-continuum model was discussed.

Acid-catalyzed reactions of twisted amides in water solution: competition between hydration and hydrolysis

The acid-catalyzed reactions of twisted amides in water solution were investigated by using cluster-continuum model calculations. In contrast to the previous widely suggested concerted hydration of the C=O group, our calculations show that the reaction proceeds in a practically stepwise manner, and that the hydration and hydrolysis channels of the C-N bond compete. The Eigen ion (H(3)O(+)) is the key species involved in the reaction, and it modulates the hydration and hydrolysis reaction pathways. The phenyl substitution in the twisted amide not only activates the N-CO bond, but also stabilizes the hydrolysis product through n(N)→π(phenyl) delocalization, leading exclusively to the hydrolysis product of the ring-opened carboxylic acid. Generally, the twisted amides are more active than the planar amides, and such a rate acceleration results mainly from the increase in exothermicity in the first N-protonation step; the second step of the nucleophilic attack is less affected by the twisting of the amide bond. The present results show good agreement with the available experimental observations.

Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol

The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.