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Hydroxyl radical (•OH) damages DNA/RNA by attacking pyrimidine nucleobases through the addition reaction and H-atom abstraction. It may attack on the new cytosine derivative (5-formylCytosine [5-fCyt]) causing DNA oxidative damage, whereas the study of the related mechanism is still in its infancy. In the present work, 2 distinct mechanisms of •OH-mediated 5-fCyt at the complete basis set methods (CBS-QB3) and CBS-QB3/polarized continuum model approaches have firstly been explored, the addition reaction (paths R1 ~ R3) and the abstraction reaction (paths R4 ~ R6), respectively, and it shows that the addition of •OH to the C5═C6 double bond of 5-fCyt is more favourable than other reactions, indicating that the •OH addition to the C5 and C6 atoms have relatively high probability to happen. The proportion of the C5 and C6 adducts is large and may be detectable experimentally, which is in agreement with the conclusions of •OH-mediated cytosine reaction reported experimentally and theoretically. These hint that the new DNA base (5-fCyt) is easily damaged when exposed the surrounding of •OH environment. Therefore, the reducing free radical production or the addition of some antioxidants should be taken in embryonic stem cells to resistance DNA damage. Our results provide some evidences between 5-fCyt and tumor development for the experimental scientists. [ABSTRACT FROM AUTHOR]

Abstract: The mechanism of the reaction of the radical C2H5S with the radical HO2 has been investigated theoretically by means of the density functional theory (DFT) and coupled cluster theory (CC). The geometries of all the stationary points and the selected points along the potential energy surfaces for the reaction of C2H5S with HO2 were optimized at the B3LYP/6-311G(2d,p) level of theory. The harmonic vibrational frequencies of all the stationary points were calculated at the above same level of theory. The single point energies were further refined at the CCSD(T)/aug-cc-pVDZ level of theory based on the B3LYP/6-311G(2d,p) optimized geometries. Eight possible reaction pathways including eleven reaction channels on both the singlet and triplet potential energy profiles for the title reaction were explored. The calculated results indicated that Path R4, the formation of the products C2H5SO+OH on the singlet potential energy profile, is likely to be the most favorable channel among Path R1∼4, and Path R5, hydrogen abstraction of HO2 by the S atom of CH3CH2S, is the most favorable among Path R5∼8 on the triplet potential energy profile. The major products of the reaction may be C2H5SH, 3O2, C2H5SO and OH. [Copyright &y& Elsevier]

The reaction mechanism of CHSCHCH with OH radical is studied at the CCSD(T)/6-311+G(3df,p)//MP2/6-31+G(2d,p) level of theory. Three hydrogen abstraction channels, one substitution process and five addition-elimination channels are identified in the title reaction. The result shows hydrogen abstraction is dominant. Substitution process and addition-elimination reactions may be negligible because of the high barrier heights. Enthalpies of formation [ $$ \Updelta_{f} H_{(298.15{\text{K}})}^{o} $$] of the reactants and products are evaluated at the CBS-QB3, G3 and G3MP2 levels of theory, respectively. It is found that the calculated enthalpies of formation by the aforementioned three methods are in consistent with the available experimental data. Rate constants and branching ratios are estimated by means of the conventional transition state theory with the Wigner tunneling correction over the temperature range of 200-900 K. The calculation shows that the formations of P1 (CHSCHCH + HO) and P2 (CHSCHCH + HO) are major products during 200-900 K. The three-parameter expressions for the total rate constant is fitted to be $$ k_{\text{total}} = 1.45 \times 10^{ - 21} T^{3.24} \exp ( - 1384.54/T) $$ cm molecule s from 200 to 900 K. [ABSTRACT FROM AUTHOR]

Abstract: The hydrogen and oxygen abstraction mechanism for the radical–radical reaction of CH3S with HOO has been investigated at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-311+G(d,p) level of theory on both the singlet and triplet potential energy profiles. Four hydrogen abstraction channels and one oxygen abstraction process are found for the title reaction. The calculations indicate that the triplet potential energy profile is much lower than the singlet energetically. Two hydrogen abstraction channels Rc, Rd and one oxygen abstraction process Re are identified on the triplet potential energy profile. Channel Rc, formation of CH3SH+ 3O2, is the most favorable. Furthermore, the rate constants of channel Rc in a temperature range 200–800K are calculated by means of the canonical variational transition state theory with small-curvature tunneling correction. The fitted three-parameter expression for k CVT/SCT of the major pathway is k CVT/SCT =2.80×10−39 T 7.49exp(6071/T)cm3 molecule−1 s−1 and it shows a negative dependence in the calculated temperature range. [ABSTRACT FROM AUTHOR]

Oxygen-to-oxygen coupling, direct H-abstraction and oxygen-to-(α)carbonnucleophilic substitution processes have been investigated for boththe singlet and triplet self-reaction of C2H5O2radicals at the CCSD(T)/cc-pVDZ//B3LYP/6-311G(2d,2p)level to evaluate the reaction mechanisms, possible products and rateconstants. The calculated results show that the title reaction mainlyoccurs through the singlet oxygen-to-oxygen coupling mechanism withthe formation of entrance tetroxide intermediates, and the most dominantproduct is C2H5O + HO2+ CH3CHO (P5) generated in channel R5. Beginning from the radical productsof P5 (C2H5O, HO2) and reactant (C2H5O2), five secondary reactions HO2+ HO2(a), HO2+ C2H5O (b), C2H5O + C2H5O (c), HO2+ C2H5O2(d),and C2H5O + C2H5O2(e) mainly proceed on the triplet potential energy surface.Among these reactions, (a), (b), and (d) are kinetically favorablebecause of lower barrier heights. The calculated rate constants ofchannel R5 between 200 and 295 K are almost independent of the temperature,which is in agreement with the experimental report. With regard tothe final products distribution, CH3CHO, C2H5OH, C2H5OOH, H2O2, and 3O2are predicted to be major, whereasC2H5OOC2H5should be inminor amount. [ABSTRACT FROM AUTHOR]