Tianlei Zhang

The catalytic effects of H2CO3, CH3COOH, HCOOH and H2O on the addition reaction of CH2OO + H2O → CH2(OH)OOH

ABSTRACT The addition reaction of CH2OO + H2O → CH2(OH)OOH without and with X (X = H2CO3, CH3COOH and HCOOH) and H2O was studied at CCSD(T)/6-311+ G(3df,2dp)//B3LYP/6-311+G(2d,2p) level of theory. Our results show that X can catalyse CH2OO + H2O → CH2(OH)OOH reaction both by increasing the number of rings, and by adding the size of the ring in which ring enlargement by COOH moiety of X inserting into CH2OO···H2O is favourable one. Water-assisted CH2OO + H2O → CH2(OH)OOH can occur by H2O moiety of (H2O)2 or the whole (H2O)2 forming cyclic structure with CH2OO, where the latter form is more favourable. Because the concentration of H2CO3 is unknown, the influence of CH3COOH, HCOOH and H2O were calculated within 0–30 km altitude of the Earths atmosphere. The results calculated within 0–5 km altitude show that H2O and HCOOH have obvious effect on enhancing the rate with the enhancement factors are, respectively, 62.47%–77.26% and 0.04%–1.76%. Within 5–30 km altitude, HCOOH has obvious effect on enhancing the title rate with the enhancement factor of 2.69%–98.28%. However, compared with the reaction of CH2OO + HCOOH, the rate of CH2OO···H2O + HCOOH is much slower.

Catalytic effect of water, water dimer, water trimer, HCOOH, H2SO4, CH3CH2COOH and HN(NO2)2 on the isomerisation of HN(NO2)2 to O2NNN(O)OH: a mechanism study

ABSTRACT In this article, the isomerisation mechanisms of HN(NO2)2 to O2NNN(O)OH without and with catalyst X (X = H2O, (H2O)2, (H2O)3, HCOOH, H2SO4, CH3CH2COOH and HN(NO2)2) have been investigated theoretically at the CBS-QB3 level of theory. Our results show that the catalyst X (X = H2O, (H2O)2, (H2O)3, HCOOH, H2SO4 and CH3CH2COOH) shows different positive catalytic effects on reducing the apparent activation energy of the isomerisation reaction processes. Such different catalytic effects are mainly related to the number of hydrogen bonds and the size of the ring structure in X (X = H2O, (H2O)2 and (H2O)3)-assisted transition states, as well as different values of pKa for H2SO4, HCOOH and CH3CH2COOH. Very interesting is also the fact that H2SO4-assisted reaction is the most favourable for the hydrogen transfer from HN(NO2)2 to O2NNN(O)OH, due to the smallest pKa (−3.0) value of H2SO4 than H2O, HCOOH, H2SO4 and CH3CH2COOH, and also because of the largest ∠X•••H•••Y (the angle between the hydrogen bond donor and acceptor) involved in H2SO4-assisted transition state. Compared to the self-catalysis of the isomerisation mechanisms of HN(NO2)2 to O2NNN(O)OH, the apparent activation energy of H2SO4-assisted channel also reduces by 9.6 kcal⋅mol−1, indicating that H2SO4 can affect the isomerisation of HN(NO2)2 to O2NNN(O)OH, most obvious among all the catalysts H2O, (H2O)2, (H2O)3, HCOOH, H2SO4, CH3CH2COOH and HN(NO2)2.

Effects of an acid–alkaline environment on the reactivity of 5-carboxycytosine with hydroxyl radicals

A hydroxyl radical (˙OH) is produced in biological systems by external or endogenous agents. It can damage DNA/RNA by attacking pyrimidine nucleobases through an addition reaction and H-atom abstraction. However, the correlation study for the new cytosine derived DNA modification (5-carboxycytosine, 5-caCyt) remains scarcely existent. Here three distinct groups of mechanisms for 5-caCyt with ˙OH by the CBS-QB3 approach have firstly been explored: the direct reaction (paths R1–R6), acidic (paths R1′–R3′, R5′, R6′), and alkaline (paths R1′′–R5′′)-induced processes. It indicates that the addition of ˙OH to the C5C6 double bond of 5-caCyt is more favourable in neutral, acidic and alkaline conditions, and the ΔGs≠ value of the C5 channel is a little higher than that of the C6 route, which agrees with the tendencies observed experimentally. Moreover, the H5 abstraction in alkaline media might be competitive with the addition reactions, having a ΔGs≠ value of 32.55 kJ mol−1, which is only 17–20 kJ mol−1 more energetic than for the addition reactions. In addition, the ΔGs≠ values of the ˙OH reactions are slightly lower for the neutral or deprotonated systems than for the N3-protonated 5-caCyt, implying that the reaction trends are a little enhanced. Our results give a possible new insight on 5-caCyt in the presence of ˙OH for experimental scientists.

Computational study on the mechanism and kinetics for the reaction between HCHO and HO2

Abstract The reaction mechanism of HCHO with HO2 radical has been studied at CBS-QB3 level of theory. Three direct hydrogen abstraction processes, one double hydrogen transfer mechanism, three cooperative hydrogen abstraction processes, and one additional channel have been identified for HCHO + HO2 reaction. The calculated results indicate that the additional mechanism of HOCH2OO formation as well as the direct hydrogen abstraction process of HOC + H2O2 formations is dominant. Other channels may be negligible due to the high barrier heights. Rate constants and branching ratios have been estimated by means of the conventional transition state theory with zero-curvature tunnelling over the temperature range of 275–1800 K. The calculation shows that the overall rate constant in the temperature of 275–1800 K is mainly dependent on the channel of HOCH2OO formation. The three-parameter expression for the total rate constant is fitted to be cm3 molecule−1 s−1 between 275 and 1800 K.

The multi-channel reaction of the OH radical with 5-hydroxymethylcytosine: a computational study

The hydroxyl radical may attack the new cytosine derivative 5-hydroxymethylcytosine (5-hmCyt) causing DNA oxidative damage, but the study of the related mechanism is still in its infancy. In the present work, two distinct mechanisms have been explored by means of the CBS-QB3 and CBS-QB3/PCM methods, the addition of ˙OH to the nucleophilic C5 (R1) and C6 (R2) atoms and H-abstraction from the N4 (R3 and R4), C7 (R5 and R6), C6 (R7) and O3 (R8) atoms of 5-hmCyt, respectively. The solvent effects of water do not significantly alter the energetics of the addition and abstraction paths compared to those in the gas phase. The ˙OH addition to the C5 and C6 sites of 5-hmCyt is energetically more favorable than to the N3, C4 or O2 sites, and the ΔGs‡ value of the C5 channel is a little lower than that of the C6 route, indicating some amount of regioselectivity, which is in agreement with the conclusions of ˙OH-mediated cytosine reactions reported experimentally and theoretically. The H5 and H6 abstraction reactions are more favorable than other abstractions, which have almost the same energy barriers as those of ˙OH addition to the C5 and C6 sites. Moreover, the energies of the H5 and H6 dehydrogenation products, which formed benzyl-radical-like complexes, are about 62–101 kJ mol−1 higher than those of the adduct radicals, indicating that the H5 and H6 abstractions have a relatively high probability of happening. Accordingly, the proportions of the H5 and H6 dehydrogenation products are large and may be detectable experimentally. These findings hint that the new DNA base (5-hmCyt) is easily damaged when exposed to the surroundings of a hydroxyl radicals environment. Therefore the reduction of free radical production or the addition of some antioxidants should be done in mammalian brain tissues to resist DNA damage. Our results provide some evidence between 5-hmCyt and tumor development for experimental scientists.

Theoretical Study on the Atmospheric Reaction of HS with HO 2 : Mechanism and Rate Constants of the Major Channel

The mechanism for the biradical reaction of HS with HO2 is investigated at the CCSD(T)/6-311++ G(3df,2pd)//B3LYP/6-311+G(2df,2p) level on both the singlet and triplet potential energy surfaces, along with rate constant calculations of the major channel. The results show that there are eight reaction channels involved in the HS + HO2 reaction system. The major channel R1 of the title reaction occurs on the triplet potential energy surfaces, and includes two pathways: Path 1 (R → IM1 → TS1 → P1(O2 + H2S)) and Path 1a 701 Acta Phys. -Chim. Sin. 2016 Vol.32

A computational study on the mechanism and kinetics of the reaction between CH3CH2S and OH

The reaction mechanism of CH3CH2S with OH radicals is studied at the CBS-QB3 level of theory. Five substitution processes and eleven addition–elimination channels are identified for the title reaction. The calculated results indicate that addition–elimination channels CH3CHS + H2O, CH2CH2 + HSOH, CH3CHSO + H2 and CH3CH2SH + O are dominant. Other channels may be negligible due to the high barrier heights. Rate constants and branching ratios are estimated by means of the conventional transition state theory with zero curvature tunnelling over the temperature range of 200–3000 K. The calculation shows that the overall rate constant in the temperature of 200–3000 K is mainly dependent on the channels CH3CHS + H2O, CH2CH2 + HSOH and CH3CH2SH + O. The three-parameter expression for the total rate constant is fitted to be ktotal = 7.42 × 10−21T2.63exp(−772.43/T) cm3 molecule−1 s−1 between 200–3000 K.

Catalytic effect of water, water dimer, HCOOH and H2SO4 on the isomerisation of HON(O)NNO2 to ON(OH)NNO2: a mechanism study

ABSTRACT In this article, we report a theoretical investigation on the role of several catalysts in the isomerisation mechanisms of HON(O)NNO2 to ON(OH)NNO2 by theoretical method of CBS-QB3. The isomerisation reactions with catalyst X (X = H2O, (H2O)2, HCOOH and H2SO4) are multi-hydrogen atom transfer reactions. Compared to the isomerisation mechanisms and rate constant of HON(O)NNO2 to ON(OH)NNO2 without catalysts, incorporation of the catalyst X shows different positive catalytic effects on affecting the reaction processes, with the H2SO4-assisted reaction being the most favourable. Such different catalytic effects are mainly related to the size of the ring structure in X-assisted transition states and the different values of pKa and proton affinities for HCOOH and H2SO4. Besides, compared with the barrier height of the isomerisation process from HON(O)NNO2 to ON(OH)NNO2 with HN(NO2)2 and HON(O)NNO2, the barrier of H2SO4-assisted reaction is lower by 9.3 and 4.5 kcal ·mol−1, meanwhile, the rate constant of H2SO4 catalyzed is larger than water and water dimer–assisted by 3–5 and 2–3 orders of magnitude, respectively. So, H2SO4-assisted reaction is the most favourable.

Computational study of the decomposition mechanisms of ammonium dinitramide in the gas phase

ABSTRACT CBS-QB3 method has been employed to determine the geometries, the vibrational frequencies of the reactants, the products and the transition states involved in intramolecular hydrogen-transfer and decomposition reactions of the free gas-phase H3N···HN(NO2)2 (ADN*). The results show that the intramolecular hydrogen-transfer reaction of ADN* is more feasible than that of HDN. ADN* and its hydrogen-transfer isomers ADN*-IIa,b,c decompose along four channels to form NH3 + HONO + 2NO (PI), ȮH + ṄO3 + N2 + NH3 (PII), ȮH + ṄO2 + N2O + NH3 (PIII), and HNO3 + N2O + NH3 (PIV), respectively. It has been found that the dominant decomposition channels are PI and PIII. The hydrogen-transfer reaction can reduce the barrier of elimination of NO2 and forming N2O reactions in ADN* and HDN. The decomposition of ADN*-IIc to form NO2 and N2O is more feasible than that of the gas-phase HDN. The rate constants (k) of rate-determining step of ADN* show that kPI and kPIII are higher than kPIV and kPII. Compared with HDN-IIc → N2O+ȮH+ṄO2, kPIII of ADN*-IIc is significantly higher than that of kHDN-IIc. These results reveal that NH3 (as a chaperon) has a certain influence on the decomposition mechanisms and kinetics of ADN*.