Co-reporter:Lingxia Jin;Mengdan Lv;Mengting Zhao;Rui Wang;Caibin Zhao;Jiufu Lu;Ling Wang;Yawen Wei
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 48) pp:32741-32741
Publication Date(Web):2017/12/13
DOI:10.1039/C7CP90270K
Correction for ‘Formic acid catalyzed isomerization of protonated cytosine: a lower barrier reaction for tautomer production of potential biological importance’ by Lingxia Jin et al., Phys. Chem. Chem. Phys., 2017, 19, 13515–13523.
Co-reporter:Qiangli Zhao;Fengyi Liu;Weina Wang;Chunying Li;Jian Lü
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 23) pp:15073-15083
Publication Date(Web):2017/06/14
DOI:10.1039/C7CP00869D
The reactions of four hydroxyl-substituted alkylperoxy (RO2) radicals with four stabilized Criegee intermediates (SCIs) were investigated. Due to the existence of various reactive sites in both RO2 and SCI, various reaction modes were obtained. By adjusting the relative orientation of the two components of the reactants, different pathways were predicted. The addition of RO2 radical terminal oxygen atom to SCI carbonyl carbon is a favorable reaction mode. For RO2 radicals, increasing the number of methyl substituents in β-carbon will promote the addition reaction. Carbonyl oxides with hydrogen atoms as substituents in the anti-position react faster than the corresponding carbonyl oxides with hydrogen atom substituents in the syn-position. Thus, the reaction barrier can be “tuned” by the substitution of alkyl groups. The analysis of the transition states have revealed that there were correlations between the reaction barrier heights, NPA charges and electron spin population of the terminal oxygen of RO2, as well as between the interatomic distances of O–C in transition states. As the oligomers formed by the sequential addition of SCIs to RO2 radicals are the common components of secondary organic aerosols, the investigation was able to contribute to understand the formation of SOA.
Co-reporter:Lingxia Jin;Mengdan Lv;Mengting Zhao;Rui Wang;Caibin Zhao;Jiufu Lu;Ling Wang;Yawen Wei
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 21) pp:13515-13523
Publication Date(Web):2017/05/31
DOI:10.1039/C7CP01008G
Tautomerism in nucleotide bases is one of the possible mechanisms of DNA mutation. In spite of numerous studies on the structure and energy of protonated cytosine tautomers, little information is available on the process of their intra- and intermolecular tautomerizations. The catalytic ability of H2O, HCOOH, and the HCOOH⋯H2O group to facilitate the tautomerism of the Cyt2t+ to CytN3+ isomer has been studied. It is shown that the activation free energies of tautomerism in the gas phase are 161.17, 58.96, 26.06, and 15.69 kJ mol−1, respectively, when the reaction is carried out in the absence and presence of H2O, HCOOH, or the HCOOH⋯H2O group. The formation of a doubly hydrogen bonded transition state is central to lowering the activation free energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of intramolecular tautomerization, the isomerization of the Cyt2t+ to CytN3+ isomer remains unfavorable, and the HCOOH and HCOOH⋯H2O group mediated mechanisms are still more favorable. Meanwhile, conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants. The rate constant with Wigner tunneling correction for direct tautomerization is obviously smaller than that of HCOOH-mediated tautomerization, which is the most plausible mechanism. Finally, another important finding is that the product complex (CytN3+⋯HCOOH) is in the rapid tautomeric equilibrium with the reaction complex (Cyt2t+⋯HCOOH) (τ99.9% = 3.84 × 10−12 s), which is implemented by the mechanism of the concerted synchronous double proton transfer. Its lifetime of the formed CytN3+⋯HCOOH complex (τ = 8.33 × 10−9 s) is almost one order of magnitude larger than the time required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication (several ns), which is further dissociated into the CytN3+ and HCOOH monomers. The results of the present study demonstrate the feasibility of acid catalysis for DNA base isomerization reactions that would otherwise be forbidden.
Co-reporter:Qiangli Zhao, Weina Wang, Fengyi Liu, Jian Lü, Wenliang Wang
Atmospheric Environment 2017 Volume 166(Volume 166) pp:
Publication Date(Web):1 October 2017
DOI:10.1016/j.atmosenv.2017.07.008
•The effects from the structures of the reactants are analyzed.•The preferred path for the formation of oligomeric hydroxyalkyl hydroperoxide is investigated.•The reaction process and constituents of the oligomers can be regulated by temperature and reactants.To better understand the formation mechanism of oligomeric hydroxyalkyl hydroperoxides HOROO(SCI)nH composed of stabilized Criegee intermediate (SCI) as a chain unit, the reactions of SCI with hydroxyalkyl hydroperoxides (HOROOH) and hydroxyalkylperoxy radical (HORO2) as well as HO2 radical were investigated. For the reactions of HORO2 + SCI, two preferred pathways involving a SCI insertion in HOROOH hydroperoxide bond can be found, and the formation of HOROO(SCI)H is the dominant pathway in the reaction of HOCH2(CH3)2COOH + (CH3)2COO. The structures of the HORO2, HOROOH as well as the SCIs play a crucial role in determining the reactivity of the oligomerization. Both the reactions of HORO2 + SCI + HO2 and HOROOH + SCI could be the source of the processors to the formation of secondary organic aerosol (SOA). But from the point of free energy barriers, the formation of HOROO(SCI)H prefers to follow the mechanism involving initiation by the reaction of a HORO2 and a SCI, sequential addition of SCIs, and termination by reaction with the HO2 radical. The rate coefficients show negative temperature dependence and vary in different systems depending on the reactants. The reaction process and constituents of the products can be regulated by temperature and reactants.A comparison between two formation mechanisms for the oligomeric hydroxyalkyl hydroperoxides.Download high-res image (161KB)Download full-size image
Co-reporter:Lingxia Jin, Caibin Zhao, Cunfang Liu, Suotian Min, Tianlei Zhang, Zhiyin Wang, Wenliang Wang and Qiang Zhang
RSC Advances 2016 vol. 6(Issue 16) pp:13349-13357
Publication Date(Web):22 Jan 2016
DOI:10.1039/C5RA24293B
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.
Co-reporter:Weina Wang
The Journal of Physical Chemistry C 2016 Volume 120(Issue 5) pp:2655-2666
Publication Date(Web):January 11, 2016
DOI:10.1021/acs.jpcc.5b09790
Trimethylacetic acid (TMAA) adsorption on stoichiometric and oxygen-deficient CeO2(111) surfaces was investigated using density functional theory that accounts for the on-site Coulomb interaction via a Hubbard term (DFT+U) and long-range dispersion correction. Both the molecular state and dissociative state (TMAA → TMA– + H+) were identified on stoichiometric and oxygen-deficient CeO2(111) surfaces. For the stoichiometric surface, two thermodynamically favorable configurations with adsorption energies of the order of −30 kcal/mol are identified; one is a molecule adsorption state, and the other one is a dissociative state. For the oxygen-deficient surface, dissociative states are more favorable than molecular states. The most favorable configuration is the dissociative adsorption of TMAA with the adsorption energy of the order of −77 kcal/mol. The dissociated TMA moiety takes the position of oxygen vacancy, forming three Ce–O bonds. The signature vibrational frequencies for these thermodynamically stable structures are reported as well as their electronic structures. The effects of long-range dispersion interactions are found to be negligible for geometries but important for adsorption energies.
Co-reporter:Qiangli Zhao, Wenliang Wang, Chen Zhang, Zhongjie Du and Jianguo Mi
Physical Chemistry Chemical Physics 2015 vol. 17(Issue 39) pp:26338-26345
Publication Date(Web):14 Sep 2015
DOI:10.1039/C5CP03915K
The microstructures of diblock copolymer/particle composites confined in slitpores have been investigated using a density functional theory approach. It has been shown that, under the condition of confinement, particles display different distributions near the solid surfaces, in the microdomains of two blocks, and at the microphase interfaces. The final dispersion depends on the balance between the enthalpic contribution arising from the particle–segment attraction as well as the entropy-driven depletion attraction induced by the polymer conformation and the confinement environment. For the systems in which particles weakly attract one block but repel another block, particle dispersion can be enhanced by the increasing confinement effect, and the enhancement becomes more obvious as the size asymmetries of particles and two blocks increase. If the attraction increases, however, particle dispersion declines as the confinement effect increases.
Co-reporter:Tianlei Zhang, Rui Wang, Hao Chen, Suotian Min, Zhiyin Wang, Caibin Zhao, Qiong Xu, Lingxia Jin, Wenliang Wang and Zhuqing Wang
Physical Chemistry Chemical Physics 2015 vol. 17(Issue 22) pp:15046-15055
Publication Date(Web):06 May 2015
DOI:10.1039/C5CP00968E
The effect of a single water molecule on the HO2 + NO2 hydrogen abstraction reaction has been investigated by employing B3LYP and CCSD(T) theoretical approaches with the aug-cc-pVTZ basis set. The reaction without water has three types of reaction channels on both singlet and triplet potential energy surfaces, depending on how the HO2 radical approaches NO2. These correspond to the formation of trans-HONO + O2, cis-HONO + O2 and HNO2 + O2. Our calculated results show that triplet reaction channels are favorable and their total rate constant, at 298 K, is 2.01 × 10−15 cm3 molecule−1 s−1, which is in good agreement with experimental values. A single water molecule affects each one of these triplet reaction channels in the three different reactions of H2O⋯HO2 + NO2, HO2⋯H2O + NO2 and NO2⋯H2O + HO2, depending on the way the water interacts. Interestingly, the water molecule in these reactions not only acts as a catalyst giving the same products as the naked reaction, but also as a reactant giving the product of HONO2 + H2O2. The total rate constant of the H2O⋯HO2 + NO2 reaction is estimated to be slower than the naked reaction by 6 orders of magnitude at 298 K. However, the total rate constants of the HO2⋯H2O + NO2 and NO2⋯H2O + HO2 reactions are faster than the naked reaction by 4 and 3 orders of magnitude at 298 K, respectively. Their total effective rate constant is predicted to be 1.2 times that of the corresponding total rate constant without water at 298 K, which is in agreement with the prediction reported by Li et al. (science, 2014, 344, 292–296).
Co-reporter:Long Chen, Zhifang Gao, Weina Wang, Fengyi Liu, Jian Lü, Wenliang Wang
Computational and Theoretical Chemistry 2015 Volume 1063() pp:10-18
Publication Date(Web):1 July 2015
DOI:10.1016/j.comptc.2015.04.001
•The detailed mechanism includes reversible intramolecular H atom transfer and beta CC bond scission.•All investigated decomposition pathways are endothermic, while the isomerization processes are exothermic.•The rate coefficients of each elementary reaction are calculated with conventional transition state theory.A detailed theoretical investigation on the thermal decomposition and isomerization of 3-Me-1-heptyl radical is performed at the ab initio CBS-QB3 level of theory. The calculation reveals that the detailed reaction mechanisms of 3-Me-1-heptyl radical mainly incorporate reversible intramolecular hydrogen atom transfer and the beta-site CC bond scission. The standard reaction enthalpies (ΔrH2980) and enthalpies of formation (ΔfH2980) are determined at the CBS-QB3 level of theory. All investigated decomposition reactions are generally endothermic, while most of the isomerization processes are exothermic. Among the hydrogen atom transfer processes, the 1,3- and 1,2-hydrogen atom migration (R5 and R6, respectively) are prohibited due to their high isomerization barriers, while the 1,6-(R2) and 1,5-hydrogen atom transfer (R3) are kinetically accessible (owing to their low ring strains in the cyclic transition states). Compared with the 1,5-hydrogen atom shift for the n-heptyl radical, the methyl-substitution increases the rate coefficient by a factor of about 3.0. The product distributions are predicted at different temperatures on the basis of the steady-state approximation (SSA). The ultimate and dominant products majorly include ethylene (C2H4), propylene (C3H6), 1-butylene (1-C4H8) and 2-hexene (2-C6H12) over the temperature range of 500–2500 K.The mole percent of 4-Me-1-C6H11 + CH3, 1-C4H8 + C3H6 + CH3, 2C3H6 + C2H5 and 3-C7H14 + CH3 pass through a turning point with an increase in temperature, and the maximum values are 38.50% (at 900 K), 22.33% (at 1350 K), 14.53% (at 1150 K), and 10.63% (at 650 K), respectively.
Co-reporter:Lin Guan;Rong Shao;Fengyi Liu;Shiwei Yin
Journal of Molecular Modeling 2015 Volume 21( Issue 5) pp:
Publication Date(Web):2015 May
DOI:10.1007/s00894-015-2677-2
The nitrogen doping and phenyl substitution effects on the geometries, molecular stacking character, electronic, and charge transport properties of tetrabenzoheptacene (TTBH) have been investigated by means of density functional theory (DFT) calculation and incoherent charge hopping model. Our results indicate that the nitrogen doping (TTH) at the 6,8,15,17 positions improves its stability in air and the ability of electron injection and in the meantime slightly changes the molecular stacking due to the C-H···N interaction. For both TTBH and TTH, large hole transport mobility (μh) and electron transport mobility (μe), which are on the same order of magnitude, are given rise by their dense displaced π-stacking in crystal. Comparatively, the phenyl substitution (Ph-TTBH) at the 6,8,15,17 positions adopts a non-planar conformation, adverse to close packing and therefore leads to smaller electron/hole transport mobility (μ) than those of TTBH and TTH. The calculations suggest TTBH and TTH are promising candidates for excellent ambipolar OFET materials.
Co-reporter:Lingxia Jin, Lu Wang, Caiying Zhang, Wenliang Wang, Suotian Min and Daodao Hu
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 30) pp:16264-16277
Publication Date(Web):08 May 2014
DOI:10.1039/C4CP00387J
Cytosine (Cyt) can be converted to 5-methylcytosine (5-MeCyt) in CpG sequences of DNA. Conventional bisulfite sequencing can discriminate Cyt from 5-MeCyt, however inappropriate conversion of 5-MeCyt to thymine and a failure to convert Cyt to uracil always occur when Cyt and 5-MeCyt are treated with bisulfite, which would lead to erroneous estimates of DNA methylation densities. Here, the direct hydrolytic deamination of cis (paths A–C) and trans (paths A′–C′) 5-MeCytN3+-SO3− isomers with bisulfite have been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energies (ΔGs-a≠) of the cis and trans 5-MeCytN3+-SO3− isomers’ paths exhibit no obvious differences, implying both isomers may make an equal contribution to the hydrolytic deamination of 5-MeCyt under bisulfite conditions. It is greatly expected that these results could aid experimental scientists to explore new methods to avoid the formation of the deaminated reactants (5-MeCytN3+-SO3−). Meanwhile, the HSO3−-induced direct hydrolytic deamination of cis and trans 5-MeCytN3+-SO3− isomers is represented by paths A and A′, respectively, and has been further explored in the presence of two water molecules. It was found that the contribution of two water molecules renders the HSO3−-induced direct hydrolytic deamination of cis and trans 5-MeCytN3+-SO3− isomers by paths A and A′ favourable. In addition, the ΔGs-a≠ values (85.74–85.34 kJ mol−1) of the rate-limiting steps of the two water-mediated paths A and A′ are very close to that of the theoretical value for CytN3+-SO3− (88.18 kJ mol−1), implying that the free barrier gap between Cyt and 5-MeCyt is very small under bisulfite conditions. This further suggests that bisulfite sequencing technology may be easily influenced by the external environment.
Co-reporter:Lingxia Jin, Wenliang Wang, Daodao Hu and Jian Lü
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 8) pp:3573-3585
Publication Date(Web):16 Dec 2013
DOI:10.1039/C3CP54266A
5-Methylcytosine (5-MeCyt) can be converted to 5-hydroxymethylcytosine (5-hmCyt) in mammalian DNA by the ten-eleven translocation enzymes. The conventional bisulfite sequencing cannot discriminate 5-hmCyt from 5-MeCyt, whereas the oxidation products of 5-hmCyt, 5-carboxycytosine (5-caCyt) and 5-formylcytosine (5-fCyt) enable them to be identified in bisulfite sequencing. This mechanism likely involves the decarboxylation of 5-caCyt and deformylation of 5-fCyt to cytosine (Cyt) before deamination. Another possibility could be a direct bisulfite-induced deamination reaction followed by decarboxylation and deformylation. Here the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− (paths A and B) and 5-O+fCytN3+–SO3− (paths C and D) has been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energy (ΔGs≠ = 54.16 kJ mol−1) of the direct hydrolytic deamination of 5-caCytN3+–SO3− path A is much lower than the ΔGs≠ of CytN3+–SO3− (100.91 kJ mol−1) under bisulfite conditions, implying that 5-caCyt may firstly involve a process of deamination. Meanwhile, the ΔGs≠ (103.84 kJ mol−1) of the HSO3−-induced direct hydrolytic deamination of 5-O+fCytN3+–SO3− path C is in close proximity to our previous theoretical data for CytN3+–SO3−, indicating that the deamination of 5-fCyt is also likely to occur in the presence of bisulfite. Meanwhile, the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− path A and 5-O+fCytN3+–SO3− path C is represented and has been further explored in the presence of one and two water molecules. The results show that both in the gas and aqueous phases, the participation of one and two water molecules makes the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− path A unfavorable, whereas the contribution of one and two water molecules facilitates the HSO3−-induced direct hydrolytic deamination of 5-O+fCytN3+–SO3− path C.
Co-reporter:Tianlei Zhang, Rui Wang, Liting Zhou, Zhiyin Wang, Qiong Xu, Suotian Min and Wenliang Wang
RSC Advances 2014 vol. 4(Issue 108) pp:62835-62843
Publication Date(Web):13 Nov 2014
DOI:10.1039/C4RA07780F
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.
Co-reporter:Tianlei Zhang, Rui Wang, Wenliang Wang, Suotian Min, Qiong Xu, Zhiyin Wang, Caibin Zhao, Zhuqing Wang
Computational and Theoretical Chemistry 2014 Volume 1045() pp:135-144
Publication Date(Web):1 October 2014
DOI:10.1016/j.comptc.2014.06.020
•Singlet water-catalyzed reaction of HO2···H2O + HO2 was considered.•Three different reactions were reported for two water-catalyzed reaction.•The positive water effect comes mainly from the contribution of one water molecule.Second-order perturbation theory and transition state theory rate constant calculations have been performed to gain insight into the effect of one and two water molecules on the process of 3O2 formation from the HO2 + HO2 reaction that is proposed to be important in atmospheric chemistry. Based on the reaction of H2O⋯HO2 + HO2 investigated by Zhu and Lin (2002), a comprehensive mechanism for a single water-catalyzed the title reaction was suggested in which the additional reactions of HO2⋯H2O + HO2 were also not neglected, with barrier heights between 1.10 and 1.79 kcal mol−1, and the estimated reaction rate constants 1–2 orders-of-magnitude larger than the naked reaction estimates. At 298 K the total enhancement factor of the reactions of H2O⋯HO2 + HO2 and HO2⋯H2O + HO2 is up to ∼5.70%. The question whether two water molecules will affect 3O2 formation in the HO2 + HO2 reaction was investigated by studying the reactions of H2O⋯HO2 + H2O⋯HO2, H2O⋯HO2 + HO2⋯H2O and HO2⋯(H2O)2 + HO2. The results show that the reaction occurring through the H2O⋯HO2 + HO2⋯H2O reactants is dominant. However, its effective rate constant within the temperature range of 216.7–298.2 K is much smaller than that with a water molecule, showing that the positive water effect for the title reaction mainly comes from one water molecule.Graphical abstract
Co-reporter:Lingxia Jin, Wenliang Wang, Daodao Hu and Jian Lü
Physical Chemistry Chemical Physics 2013 vol. 15(Issue 23) pp:9034-9042
Publication Date(Web):16 Apr 2013
DOI:10.1039/C3CP51275D
The induced ability of bisulfite to facilitate the hydrolytic deamination of the protonated cytosine-SO3− has been studied at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level and CBS-QB3 approach, respectively. In the gas phase, two distinct groups of mechanisms were explored, the direct hydrolytic deamination (path A) and HSO3−-induced hydrolytic deamination (paths B–D), and it indicates that the direct hydrolytic deamination of protonated cytosine-SO3− (path A) is unlikely because of the high activation free energy involved in the rate-limiting step, whereas the presence of bisulfite (paths B–D) significantly contributes to decreasing the activation free energy. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of path A, the direct hydrolysis reaction remains unfavorable and the HSO3−-induced mechanism is still more favorable, which is in agreement with previous experimental data. The pseudo-first-order rate constant (k′) for direct hydrolysis is obviously smaller than that of HSO3−-induced hydrolytic deamination, which is the most plausible mechanism, where the calculated the k′ (1.99–3.81 × 10−5 s−1) is in close proximity to the experimentally determined the pseudo-first-order rate constant (26.2 × 10−5 s−1). Furthermore, the results also manifest that there is a positive correlation between the k′ and temperature, and the ratio of reaction rates between direct hydrolysis reaction and HSO3−-induced hydrolytic deamination increases with the increase of the bisulfite concentration at a given temperature.
Co-reporter:Caibin Zhao, Wenliang Wang, Shiwei Yin and Yan Ma
New Journal of Chemistry 2013 vol. 37(Issue 9) pp:2925-2934
Publication Date(Web):03 Jul 2013
DOI:10.1039/C3NJ00561E
Electronic, optical, and charge transport properties of 7,8,15,16-tetraazaterrylene (TAT) and its three tetrasubstituted derivatives with the electron-attracting substituent have been studied theoretically using density functional theory (DFT) calculations coupled with the incoherent charge-hopping model. The calculated results reveal that the introduction of electron-attracting substituents, which does not break down the planar skeleton of TAT core, can stabilize the extended π-system and then improve the electron injection efficiency as well as the ambient stability. Based on TAT single-crystal structure, the predicted 3D-average electron mobility reaches as high as 3.404 × 10−2 cm2 V−1 s−1 at 300 K, but the hole mobility is only 6.516 × 10−4 cm2 V−1 s−1, which indicates that TAT single crystal may be a promising candidate as n-channel materials. The simulation of the angle-resolved electron mobility shows that TAT single-crystal possesses a remarkably anisotropic electron-conducting behaviour, and the maximum electron mobility is found to be along the crystallographic a-axis direction. In addition, the calculated reorganization energies and electronic coupling values show that the three TAT derivates (4F-TAT, 4Cl-TAT, and 4CN-TAT) designed in this work may well be potential n-channel materials with the high electron mobility. TD-DFT B3LYP/6-311G(d,p) calculations reveal the most relevant electronic transitions for the studied compounds present the π → π* character and the strongest absorption and emission peaks are dominated by the transitions of HOMO → LUMO. The introduction of electron-withdrawing substituents red-shifts the maximal absorption and emission wavelengths.
Co-reporter:Cao Jia;Tianlei Zhang;Loujun Gao;Feng Fu;Danjun Wang
Chinese Journal of Chemistry 2013 Volume 31( Issue 10) pp:1341-1347
Publication Date(Web):
DOI:10.1002/cjoc.201300410
Abstract
The isomerization of CH3S(OH)CH2 to CH3S(O)CH3 in the absence and presence of water has been investigated at the G3XMP2//B3LYP/6-311+G(2df,p) level. The naked isomerization, the reaction without water, gives the high barrier height (21.56 kcal·mol−1). Three models are constructed to describe the water influence on the isomerization, that is, water molecules are the catalyst and the microsolvation, and water molecules act as the catalyst and microsolvation simultaneously. Our results show that the isomerization barrier heights of CH3S(OH)CH2 to CH3S(O)CH3 are reduced by 12.32, 11.04, and 7.80 kcal·mol−1, respectively, when one, two, and three water molecules are performed as catalyst, in contrast to the naked isomerization. Moreover, the rate constants of the isomerization are calculated using the transition state theory with the Wigner tunneling correction over the temperature range of 240–425 K. We find that the rate constant of a single water molecule as the catalyst is 1.58 times larger than the naked isomerization at 325 K, whereas it is slower by 6 orders of magnitude when water molecule serves as the microsolvation at 325 K, compared to naked reaction. So the water-catalyzed isomerization of CH3S(OH)CH2 to CH3S(O)CH3 is predicted to be the key role in lowering the activation energy. The isomerization involving water molecules acting as microsolvation is unfavorable under atmospheric conditions.
Co-reporter:Long Chen, Tianlei Zhang, Chunying Li, Weina Wang, Jian Lü, Wenliang Wang
Computational and Theoretical Chemistry 2013 Volume 1026() pp:38-45
Publication Date(Web):15 December 2013
DOI:10.1016/j.comptc.2013.10.004
•H-atom abstraction reactions are energetically favored over other types of reactions.•Alkyl radicals are easier isomerize to form resonance stabilized allylic radicals.•The products of MCH thermal decomposition are some molecules like CH4, C2H4, etc.The thermal decomposition of methylcyclohexane (MCH) has been investigated at the CBS-QB3 and CCSD level of theory. The pyrolysis of MCH follows a radical chain mechanism, which mainly includes the C–C bond scission, H-atom abstraction, secondary and biradical reactions. Thermodynamic data for selected species involved in this study are computed at the CBS-QB3 level. The rate constants for all elementary reactions are also evaluated with conventional transition state theory (TST) in the temperature range of 298–2000 K, where Eckart method is adopted to correct the quantum mechanical tunneling effect. The rate constants are reasonable agreement with experimental measurements and previous theoretical reports. Furthermore, the final products of MCH thermal decomposition are methane (CH4), ethylene (C2H4), propylene (C3H6), 1,3-butadiene (1,3-C4H6), isoprene (C5H8) and 1,3-pentadiene (1,3-C5H8). The main goal of this work is to give an exhaustive description of the MCH thermal decomposition by means of high level quantum chemical methods and provide a reliable reference for thermodynamic and kinetic information.Five different kinds of H-atom abstraction barrier of MCH by CH3 radical is found to increase in the order of TS2 < TS3 ≈ TS4 ≈ TS5 < TS1, indicating that the tertiary H-atom abstraction channel is energetically favored over the primary and secondary channels.
Co-reporter:Lingxia Jin, Wenliang Wang, Daodao Hu, and Suotian Min
The Journal of Physical Chemistry B 2013 Volume 117(Issue 1) pp:3-12
Publication Date(Web):December 5, 2012
DOI:10.1021/jp304282z
The mechanism for the effects of protonation and C5 methylation on the electrophilic addition reaction of Cyt has been explored by means of CBS-QB3 and CBS-QB3/PCM methods. In the gas phase, three paths, two protonated paths (N3 and O2 protonated paths B and C) as well as one neutral path (path A), were mainly discussed, and the calculated results indicate that the reaction of the HSO3– group with neutral Cyt is unlikely because of its high activation free energy, whereas O2-protonated path (path C) is the most likely to occur. In the aqueous phase, path B is the most feasible mechanism to account for the fact that the activation free energy of path B decreases compared with the corresponding path in the gas phase, whereas those of paths A and C increase. The main striking results are that the HSO3– group directly interacts with the C5═C6 bond rather than the N3═C4 bond and that the C5 methylation, compared with Cyt, by decreasing values of global electrophilicity index manifests that C5 methylation forms are less electrophilic power as well as by decreasing values of NPA charges on C5 site of the intermediates make the trend of addition reaction weaken, which is in agreement with the experimental observation that the rate of 5-MeCyt reaction is approximately 2 orders of magnitude slower than that of Cyt in the presence of bisulfite. Apart from cis and trans isomers, the rare third isomer where both the CH3 and SO3 occupy axial positions has been first found in the reactions of neutral and protonated 5-MeCyt with the HSO3– group. Furthermore, the transformation of the third isomer from the cis isomer can occur easily.
Co-reporter:Chunmei Zhao;Chunrong Li;Yan Ma;Caibin Zhao
Chinese Journal of Chemistry 2012 Volume 30( Issue 10) pp:2501-2508
Publication Date(Web):
DOI:10.1002/cjoc.201200444
Abstract
A series of combinations of thiophene and vinyl/butadiene were investigated by ab initio and DFT methods to explore their electronic structures and charge transfer properties. The results show that increasing thiophene ring and vinyl number is a rational strategy to raise the HOMO energy levels and lower the LUMO energy levels. Moving the vinyl from the periphery to the core has the slight effect on the HOMO and LUMO energy levels. Furthermore, replacing the middle vinyl and end-capped vinyl of 3b (T5V4) with the butadiene can lower LUMO energy levels and then facilitate the electron injection. Above all, the close hole and electron reorganization energies (λh and λe) are observed from these compounds. However, the λes are smaller than their respective λhs in some compounds, which is relatively rare in organic materials. Especially, the promising ambipolar material 3c (T5B4) is recommended theoretically for possessing the equivalent minimum λh (0.24 eV) and λe (0.24 eV). The absorption wavelengths exhibit red shifts with the increasing of the thiophene ring and the vinyl number under the same configuration, which correspond to the reverse order of ΔEH-L and Eg. The linear relationships are found between experimental lowest singlet excited energies (Eexp) with theoretical values ΔEH-L and Eg.
Co-reporter:Tianlei Zhang, Guona Li, Wenliang Wang, Yongmei Du, Chunying Li, Jian Lü
Computational and Theoretical Chemistry 2012 Volume 991() pp:13-21
Publication Date(Web):1 July 2012
DOI:10.1016/j.comptc.2012.03.016
The formations of CHFO, 1O2, O3 and 3O2 in CH2FO2 + HO2 and CH2FO2 + HO2⋅H2O reaction are studied by employing the quantum chemical calculations with B3LYP and CCSD(T) theoretical methods, canonical variational transition (CVT) state theory with small curvature tunneling (SCT) correction. The calculated results show that the formations of CHFO and 3O2 are main products in the naked reaction of CH2FO2 + HO2. When water is added, the formations of CHFO and O3 are main products in CH2FO2 + HO2⋅H2O reaction. Moreover, the calculated rate constants for the title reaction without and with a water molecule show that, although the single water molecule plays a positive catalytic effect on enhancing the rate for CHFO and O3 formation, in humid conditions the effective rate of CH2FO2 + HO2 reaction will changes little with respect to dry conditions.Graphical abstractHighlights► Mechanism and kinetic for title reaction without and with a water molecule are calculated. ► Preferred process is different in the catalytic and non-catalytic condition. ► Water molecule has different catalytic effect on different formations. ► In humid conditions the effective rate of title reaction will change little with respect to dry conditions.
Co-reporter:Yue Zhang, Wei Zhang, Tianlei Zhang, Wenxin Tian, Wenliang Wang
Computational and Theoretical Chemistry 2012 Volume 994() pp:65-72
Publication Date(Web):15 August 2012
DOI:10.1016/j.comptc.2012.06.016
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.Graphical abstractHighlights► The reaction mechanism of C2H5S with HO2 was studied using DFT and CC approaches. ► The reaction scheme was designed on the basis of Mulliken atomic spin densities. ► Eleven singlet and triplet reaction channels for the title reaction were explored. ► The addition–elimination R4 and direct hydrogen abstraction reaction R5 are likely competitive.
Co-reporter:Pei Zhang, Wenliang Wang, Tianlei Zhang, Long Chen, Yongmei Du, Chunying Li, and Jian Lü
The Journal of Physical Chemistry A 2012 Volume 116(Issue 18) pp:4610-4620
Publication Date(Web):April 11, 2012
DOI:10.1021/jp301308u
Oxygen-to-oxygen coupling, direct H-abstraction and oxygen-to-(α)carbon nucleophilic substitution processes have been investigated for both the singlet and triplet self-reaction of C2H5O2 radicals at the CCSD(T)/cc-pVDZ//B3LYP/6-311G(2d,2p) level to evaluate the reaction mechanisms, possible products and rate constants. The calculated results show that the title reaction mainly occurs through the singlet oxygen-to-oxygen coupling mechanism with the formation of entrance tetroxide intermediates, and the most dominant product is C2H5O + HO2 + CH3CHO (P5) generated in channel R5. Beginning from the radical products of 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 favorable because of lower barrier heights. The calculated rate constants of channel R5 between 200 and 295 K are almost independent of the temperature, which is in agreement with the experimental report. With regard to the final products distribution, CH3CHO, C2H5OH, C2H5OOH, H2O2, and 3O2 are predicted to be major, whereas C2H5OOC2H5 should be in minor amount.
Co-reporter:Tianlei Zhang, Wenliang Wang, Pei Zhang, Jian Lü and Yue Zhang
Physical Chemistry Chemical Physics 2011 vol. 13(Issue 46) pp:20794-20805
Publication Date(Web):17 Oct 2011
DOI:10.1039/C1CP21563A
The gas-phase hydrogen abstraction reactions of CH3O2 and HO2 with HO2 in the presence and absence of a single water molecule have been studied at the CCSD(T)/6-311++G(3d,2p)//B3LYP/6-311G(2d,2p) level of theory. The calculated results show that the process for O3 formation is much faster than that for 1O2 and 3O2 formation in the water-catalyzed CH3O2 + HO2 reaction. This is different from the results for the non-catalytic reaction of CH3O2 + HO2, in which almost only the process for 3O2 formation takes place. Unlike CH3O2 + HO2 reaction in which the preferred process is different in the catalytic and non-catalytic conditions, the channel for 3O2 formation is the dominant in both catalytic and non-catalytic HO2 + HO2 reactions. Furthermore, the calculated total CVT/SCT rate constants for water-catalyzed and non-catalytic title reactions show that the water molecule doesn't contribute to the rate of CH3O2 + HO2 reaction though the channel for O3 formation in this water-catalyzed reaction is more kinetically favorable than its non-catalytic process. Meanwhile, the water molecule plays an important positive role in increasing the rate of HO2 + HO2 reaction. These results are in good agreement with available experiments.
Co-reporter:Jia Cao;Yue Zhang;Weina Wang
Theoretical Chemistry Accounts 2011 Volume 129( Issue 6) pp:771-780
Publication Date(Web):2011 August
DOI:10.1007/s00214-011-0934-8
The reaction mechanism of CH3SCH2CH3 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 (CH2SCH2CH3 + H2O) and P2 (CH3SCHCH3 + H2O) are major products during 200–900 K. The three-parameter expressions for the total rate constant is fitted to be \( k_{\text{total}} = 1.45 \times 10^{ - 21} T^{3.24} \exp ( - 1384.54/T) \) cm3 molecule−1 s−1 from 200 to 900 K.
Co-reporter:Ni Wei; Dr. Wenliang Wang;Shiwei Yin;Song Du ;Weina Wang
Chinese Journal of Chemistry 2010 Volume 28( Issue 10) pp:1907-1914
Publication Date(Web):
DOI:10.1002/cjoc.201090318
Abstract
The relationships between electronic structures and spectra properties are investigated by DFT/TDDFT for terthiophene derivatives, BMA-3T (tri-aryl amine end-capped terthiophene), BBA-3T (tri-aryl amine and tri-aryl boron end-capped terthiophene) and BPB-3T (tri-aryl boron end-capped terthiophene). The calculated results show that BMA-3T, BBA-3T and BPB-3T have higher HOMO energy level and lower ionization potentials (IPs) than 3T. BMA-3T has good hole injection ability and hole-transport property as reported in experiment. The designed molecule of BBA-3T and BPB-3T own lower LUMO level and higher electron affinities (EAs) than BMA-3T, which facilitate electron injection and improve their electron-transport properties. Surprisingly, BPB-3T has preferable charge equilibrium property since its hole reorganization energy (λh) is close to electron reorganization energy (λe). The ΔE (HOMO−LUMO) and Eg of these three derivatives are narrower compared to 3T, and the absorption as well as emission spectrum exhibited red-shifts.
Co-reporter:Hongjiang Ren;Weina Wang;Ni Wei
Chinese Journal of Chemistry 2010 Volume 28( Issue 6) pp:1027-1033
Publication Date(Web):
DOI:10.1002/cjoc.201090161
Abstract
The tautomerization reaction mechanism has been reported between N7(H) and N9(H) of isolated and monohydrated 2,6-dithiopurine using B3LYP/6-311+G(d,p). The isodensity polarized continuum model (IPCM) in the self-consistent reaction field (SCRF) method is employed to account for the solvent effect of water on the tautomerization reaction activation energies. The results show that the two pathways P(1) (via the carbene intermediate I1) and P(2) (via the sp3-hybrid intermediate I2) are found in intramolecular proton transfer, and each pathway is composed by two primary steps. The calculated activation energy barriers of the rate-determining steps in isolated 2,6-dithiopurine N7(H)N9(H) tautomerism are 308.2 and 220.0 kJ·mol−1 in the two pathways, respectively. Interestingly, in one-water molecule catalyst, it dramatically lowers the N7(H)N9(H) energy barriers by the concerted double proton transfer mechanism in P(1), favoring the formation of 2,6-dithiopurine N9(H). However, the single proton transfer mechanism assisted with out-of-plane water in the first step of P(2) increases the activation energy barrier from 220.0 to 232.3 kJ·mol−1, while the second step is the out-of-plane concerted double proton transfer mechanism, indicating that they will be less preferable for proton transfer. Additionally, the results also show that all the pathways are put into the aqueous solution, and the activation energy barriers have no significant changes. Therefore, the long-range electrostatic effect of bulk solvent has no significant impact on proton transfer reactions and the interaction with explicit water molecules will significantly influence proton transfer reactions.
Co-reporter:Long TANG;Feng FU;Dongsheng LI;Yapan WU;Xiaoming GAO;Xiaogang YANG
Chinese Journal of Chemistry 2009 Volume 27( Issue 2) pp:273-280
Publication Date(Web):
DOI:10.1002/cjoc.200990044
Abstract
By changing auxiliary ligands, two new Cu(II) complexes, [Cu(mal)(tap)(H2O)]n (1) and [Cu2(mal)2(bpym)2(H2O)2]·2H2O (2) (mal=maleate, tap=1,4,5,8-tetraazaphenanthrene, bpym=2,2′-bipyrimidine), have been synthesized and structurally characterized by X-ray single-crystal diffraction. Complex 1 shows a 1D arch-shaped coordination polymer chain, further, the dimensionality is extended to a 3D supramolecular architecture through hydrogen-bonding and aromatic π-π stacking interactions. Complex 2 features a 2-fold interpenetrated 3D3D supramolecular architecture with 6-connected α-Po (46) topology. According to the crystal structures, the full geometry optimizations of complexes 1 and 2 were carried out by using hybrid DFT methods at B3LYP/6-31G(d) level. Meantime, the DFT-BS approach was applied to study the magnetic coupling behavior for the two complexes, and the result reveals that the calculated exchange coupling constants J were in good agreement with the experimental data. Both 1 and 2 showed almost the same antiferromagnetic behavior.
Co-reporter:Shihong Dong, Wenliang Wang, Shiwei Yin, Chunying Li, Jian Lu
Synthetic Metals 2009 Volume 159(5–6) pp:385-390
Publication Date(Web):March 2009
DOI:10.1016/j.synthmet.2008.10.012
Electronic structures and spectroscopic properties of tris(8-hydroxyquinoline) aluminum (Alq3) and its difluorinated derivatives are studied by using ab initio and DFT methods. The B3LYP and CIS methods have been used to optimize the ground- and excited-state geometries, respectively. Absorption and emission spectra are also calculated by using the time-dependent density functional theory (TD-DFT) based on the ground- and excited-state geometries. We have found that for difluorinated Alq3 the substituents cause energy lowering in the energy levels of the lowest unoccupied molecular orbitals (LUMO) and the electron affinity (EA) increase, which facilitates injection of the electron carrier from the metal electrode. By comparing with the non-substituted Alq3, 5,6-difluoro-substituted (2) and 5,7-difluoro-substituted Alq3 (3) undergo slight red-shift in the spectra, while the 6,7-difluoro-substituted Alq3 (4) shows blue-shift. In view of the electronic reorganization energy (λe), the complexes 2 and 4 are potential materials for electron injection and transport. In addition, the results reveal that important blue luminescence materials can be obtained by applying strong electron-withdrawing substituents at the 6,7-positions of phenoxide.The emission and absorption electronic spectra of Alq3 and its difluorinated derivatives are calculated by using time-dependent density functional theory (TD-DFT) methods. The results provide insights on obtaining important blue luminescence materials by attaching strong electron-withdrawing difluoro-substituents at the 6,7-positions of the phenoxide group.
Co-reporter:Wenliang Wang, Shihong Dong, ShiWei Yin, Jianming Yang, Jian Lu
Journal of Molecular Structure: THEOCHEM 2008 Volume 867(1–3) pp:116-121
Publication Date(Web):30 October 2008
DOI:10.1016/j.theochem.2008.07.035
The structure and electronic properties of 5- and 6-coordinated Al complexes Alq2R (6-coordinated Al complexes: R = q(8-hydroxyquinoline); 5-coordinated Al complexes: R = OH, P (phenolate) and B (phenylphenolate)) were investigated theoretically by means of quantum mechanical calculations based on density functional theory (DFT) and time-dependent DFT (TD-DFT) using the B3LYP functional. Geometry optimizations of the complexes were performed for the ground state (S0) and the lowest exited stated (S1, calculated using the configuration interaction singles (CIS) method). The second ligand (R) of 5-coordinated Al complexes is found to be important contributors in the geometry structure and the charge transport properties of the complexes. In addition, the second ligands substitutes in 5-coordinated Al complexes also noticeable affect the vertical ionizations (VIPs), which will be expected to be used as selective hole-block materials to increase the efficiency and lifetime of the OLED. The nature and the energy of the first singlet-singlet electronic transitions have been obtained from TD-DFT, and radiative lifetimes were calculated as well. As for tuning the spectra properties, it is indicated that the electron-withdrawing methyl at 4-position of quinoline in either 5- or 6-coordinated Al complexes would be more efficient to get blue-light materials, and could obviously affect the radiative lifetimes.
Co-reporter:Yan Liu, Wenliang Wang, Weina Wang, Kehe Su, Yue Zhang
Journal of Molecular Structure: THEOCHEM 2008 Volume 866(1–3) pp:46-51
Publication Date(Web):15 October 2008
DOI:10.1016/j.theochem.2008.07.002
The reaction pathways of CH3S and ClO radicals on the singlet potential energy surface have been investigated theoretically by QCISD(T)/6-311 + G(2df,p)//B3LYP/6-311 + G(3df,3pd) method. The calculated results show that the reactants will firstly associate into the energy-rich adducts CH3SClO and CH3SOCl with barrierless processes. Then, the adducts undergo disassociation (combined with hydrogen migration) or isomerization process to produce main products HOCl, CH2S and CH3S(O)Cl. The (ClO)CH2(SH), HCl, CH2SO, SO and CH3Cl species are found to be the minor products via different channels. Natural bond orbital analyses indicate that the sulfur atom of CH3S radical prefers to attack the oxygen atom rather than the chlorine atom of ClO in the initial association process.
Co-reporter:Wenliang Wang, Lingxia Jin, Weina Wang, Jian Lu, Jianming Yang
Chemical Physics Letters 2007 Volume 444(4–6) pp:359-365
Publication Date(Web):27 August 2007
DOI:10.1016/j.cplett.2007.07.055
All the possible addition and hydrogen abstraction reactions of OH radical with 5-methylcytosine (5-MeC) have been investigated at B3LYP/6-31++G(d,p)//B3LYP/6-31G(d,p)+ZPE level. The results indicate that OH radical may form complexes with 5-MeC, and the reaction is assumed to occur from these complexes. The estimated activation energies corresponding to addition reactions at N3, C4, C5 and C6 sites of the 5-MeC are 80.96, 63.41, 0.00 and 0.30 kJ/mol, respectively. The order of stability of adducts is P4(C6) > P3(C5) > P2(C4) > P1(N3). The activation energies corresponding to the H9, H10, H11, and H14 abstraction reactions from the 5-MeC are all small, and the stabilization of the products is P8(H14) > P6(H10) > P5(H9) > P7(H11).All the addition and hydrogen abstraction reactions of OH radical with 5-methylcytosine (5-MeC) have been investigated by DFT methods. The results indicate that the preferred addition sites of OH radical to 5-MeC are at C5 and C6 and the H14 of methyl group abstraction reaction of 5-MeC by OH radical to produce P8 should be the dominant process. For the activation energies of OH radical addition to C5 and C6 cites of 5-MeC are very small, and the potential energy profiles along the reaction coordination is very flat around the transition structure.
Co-reporter:Tianlei Zhang, Wenliang Wang, Pei Zhang, Jian Lü and Yue Zhang
Physical Chemistry Chemical Physics 2011 - vol. 13(Issue 46) pp:NaN20805-20805
Publication Date(Web):2011/10/17
DOI:10.1039/C1CP21563A
The gas-phase hydrogen abstraction reactions of CH3O2 and HO2 with HO2 in the presence and absence of a single water molecule have been studied at the CCSD(T)/6-311++G(3d,2p)//B3LYP/6-311G(2d,2p) level of theory. The calculated results show that the process for O3 formation is much faster than that for 1O2 and 3O2 formation in the water-catalyzed CH3O2 + HO2 reaction. This is different from the results for the non-catalytic reaction of CH3O2 + HO2, in which almost only the process for 3O2 formation takes place. Unlike CH3O2 + HO2 reaction in which the preferred process is different in the catalytic and non-catalytic conditions, the channel for 3O2 formation is the dominant in both catalytic and non-catalytic HO2 + HO2 reactions. Furthermore, the calculated total CVT/SCT rate constants for water-catalyzed and non-catalytic title reactions show that the water molecule doesn't contribute to the rate of CH3O2 + HO2 reaction though the channel for O3 formation in this water-catalyzed reaction is more kinetically favorable than its non-catalytic process. Meanwhile, the water molecule plays an important positive role in increasing the rate of HO2 + HO2 reaction. These results are in good agreement with available experiments.
Co-reporter:Lingxia Jin, Wenliang Wang, Daodao Hu and Jian Lü
Physical Chemistry Chemical Physics 2013 - vol. 15(Issue 23) pp:NaN9042-9042
Publication Date(Web):2013/04/16
DOI:10.1039/C3CP51275D
The induced ability of bisulfite to facilitate the hydrolytic deamination of the protonated cytosine-SO3− has been studied at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level and CBS-QB3 approach, respectively. In the gas phase, two distinct groups of mechanisms were explored, the direct hydrolytic deamination (path A) and HSO3−-induced hydrolytic deamination (paths B–D), and it indicates that the direct hydrolytic deamination of protonated cytosine-SO3− (path A) is unlikely because of the high activation free energy involved in the rate-limiting step, whereas the presence of bisulfite (paths B–D) significantly contributes to decreasing the activation free energy. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of path A, the direct hydrolysis reaction remains unfavorable and the HSO3−-induced mechanism is still more favorable, which is in agreement with previous experimental data. The pseudo-first-order rate constant (k′) for direct hydrolysis is obviously smaller than that of HSO3−-induced hydrolytic deamination, which is the most plausible mechanism, where the calculated the k′ (1.99–3.81 × 10−5 s−1) is in close proximity to the experimentally determined the pseudo-first-order rate constant (26.2 × 10−5 s−1). Furthermore, the results also manifest that there is a positive correlation between the k′ and temperature, and the ratio of reaction rates between direct hydrolysis reaction and HSO3−-induced hydrolytic deamination increases with the increase of the bisulfite concentration at a given temperature.
Co-reporter:Qiangli Zhao, Fengyi Liu, Weina Wang, Chunying Li, Jian Lü and Wenliang Wang
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 23) pp:NaN15083-15083
Publication Date(Web):2017/05/16
DOI:10.1039/C7CP00869D
The reactions of four hydroxyl-substituted alkylperoxy (RO2) radicals with four stabilized Criegee intermediates (SCIs) were investigated. Due to the existence of various reactive sites in both RO2 and SCI, various reaction modes were obtained. By adjusting the relative orientation of the two components of the reactants, different pathways were predicted. The addition of RO2 radical terminal oxygen atom to SCI carbonyl carbon is a favorable reaction mode. For RO2 radicals, increasing the number of methyl substituents in β-carbon will promote the addition reaction. Carbonyl oxides with hydrogen atoms as substituents in the anti-position react faster than the corresponding carbonyl oxides with hydrogen atom substituents in the syn-position. Thus, the reaction barrier can be “tuned” by the substitution of alkyl groups. The analysis of the transition states have revealed that there were correlations between the reaction barrier heights, NPA charges and electron spin population of the terminal oxygen of RO2, as well as between the interatomic distances of O–C in transition states. As the oligomers formed by the sequential addition of SCIs to RO2 radicals are the common components of secondary organic aerosols, the investigation was able to contribute to understand the formation of SOA.
Co-reporter:Lingxia Jin, Mengdan Lv, Mengting Zhao, Rui Wang, Caibin Zhao, Jiufu Lu, Ling Wang, Wenliang Wang and Yawen Wei
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 21) pp:NaN13523-13523
Publication Date(Web):2017/04/26
DOI:10.1039/C7CP01008G
Tautomerism in nucleotide bases is one of the possible mechanisms of DNA mutation. In spite of numerous studies on the structure and energy of protonated cytosine tautomers, little information is available on the process of their intra- and intermolecular tautomerizations. The catalytic ability of H2O, HCOOH, and the HCOOH⋯H2O group to facilitate the tautomerism of the Cyt2t+ to CytN3+ isomer has been studied. It is shown that the activation free energies of tautomerism in the gas phase are 161.17, 58.96, 26.06, and 15.69 kJ mol−1, respectively, when the reaction is carried out in the absence and presence of H2O, HCOOH, or the HCOOH⋯H2O group. The formation of a doubly hydrogen bonded transition state is central to lowering the activation free energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of intramolecular tautomerization, the isomerization of the Cyt2t+ to CytN3+ isomer remains unfavorable, and the HCOOH and HCOOH⋯H2O group mediated mechanisms are still more favorable. Meanwhile, conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants. The rate constant with Wigner tunneling correction for direct tautomerization is obviously smaller than that of HCOOH-mediated tautomerization, which is the most plausible mechanism. Finally, another important finding is that the product complex (CytN3+⋯HCOOH) is in the rapid tautomeric equilibrium with the reaction complex (Cyt2t+⋯HCOOH) (τ99.9% = 3.84 × 10−12 s), which is implemented by the mechanism of the concerted synchronous double proton transfer. Its lifetime of the formed CytN3+⋯HCOOH complex (τ = 8.33 × 10−9 s) is almost one order of magnitude larger than the time required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication (several ns), which is further dissociated into the CytN3+ and HCOOH monomers. The results of the present study demonstrate the feasibility of acid catalysis for DNA base isomerization reactions that would otherwise be forbidden.
Co-reporter:Lingxia Jin, Wenliang Wang, Daodao Hu and Jian Lü
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 8) pp:NaN3585-3585
Publication Date(Web):2013/12/16
DOI:10.1039/C3CP54266A
5-Methylcytosine (5-MeCyt) can be converted to 5-hydroxymethylcytosine (5-hmCyt) in mammalian DNA by the ten-eleven translocation enzymes. The conventional bisulfite sequencing cannot discriminate 5-hmCyt from 5-MeCyt, whereas the oxidation products of 5-hmCyt, 5-carboxycytosine (5-caCyt) and 5-formylcytosine (5-fCyt) enable them to be identified in bisulfite sequencing. This mechanism likely involves the decarboxylation of 5-caCyt and deformylation of 5-fCyt to cytosine (Cyt) before deamination. Another possibility could be a direct bisulfite-induced deamination reaction followed by decarboxylation and deformylation. Here the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− (paths A and B) and 5-O+fCytN3+–SO3− (paths C and D) has been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energy (ΔGs≠ = 54.16 kJ mol−1) of the direct hydrolytic deamination of 5-caCytN3+–SO3− path A is much lower than the ΔGs≠ of CytN3+–SO3− (100.91 kJ mol−1) under bisulfite conditions, implying that 5-caCyt may firstly involve a process of deamination. Meanwhile, the ΔGs≠ (103.84 kJ mol−1) of the HSO3−-induced direct hydrolytic deamination of 5-O+fCytN3+–SO3− path C is in close proximity to our previous theoretical data for CytN3+–SO3−, indicating that the deamination of 5-fCyt is also likely to occur in the presence of bisulfite. Meanwhile, the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− path A and 5-O+fCytN3+–SO3− path C is represented and has been further explored in the presence of one and two water molecules. The results show that both in the gas and aqueous phases, the participation of one and two water molecules makes the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− path A unfavorable, whereas the contribution of one and two water molecules facilitates the HSO3−-induced direct hydrolytic deamination of 5-O+fCytN3+–SO3− path C.
Co-reporter:Qiangli Zhao, Wenliang Wang, Chen Zhang, Zhongjie Du and Jianguo Mi
Physical Chemistry Chemical Physics 2015 - vol. 17(Issue 39) pp:NaN26345-26345
Publication Date(Web):2015/09/14
DOI:10.1039/C5CP03915K
The microstructures of diblock copolymer/particle composites confined in slitpores have been investigated using a density functional theory approach. It has been shown that, under the condition of confinement, particles display different distributions near the solid surfaces, in the microdomains of two blocks, and at the microphase interfaces. The final dispersion depends on the balance between the enthalpic contribution arising from the particle–segment attraction as well as the entropy-driven depletion attraction induced by the polymer conformation and the confinement environment. For the systems in which particles weakly attract one block but repel another block, particle dispersion can be enhanced by the increasing confinement effect, and the enhancement becomes more obvious as the size asymmetries of particles and two blocks increase. If the attraction increases, however, particle dispersion declines as the confinement effect increases.
Co-reporter:Lingxia Jin, Lu Wang, Caiying Zhang, Wenliang Wang, Suotian Min and Daodao Hu
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 30) pp:NaN16277-16277
Publication Date(Web):2014/05/08
DOI:10.1039/C4CP00387J
Cytosine (Cyt) can be converted to 5-methylcytosine (5-MeCyt) in CpG sequences of DNA. Conventional bisulfite sequencing can discriminate Cyt from 5-MeCyt, however inappropriate conversion of 5-MeCyt to thymine and a failure to convert Cyt to uracil always occur when Cyt and 5-MeCyt are treated with bisulfite, which would lead to erroneous estimates of DNA methylation densities. Here, the direct hydrolytic deamination of cis (paths A–C) and trans (paths A′–C′) 5-MeCytN3+-SO3− isomers with bisulfite have been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energies (ΔGs-a≠) of the cis and trans 5-MeCytN3+-SO3− isomers’ paths exhibit no obvious differences, implying both isomers may make an equal contribution to the hydrolytic deamination of 5-MeCyt under bisulfite conditions. It is greatly expected that these results could aid experimental scientists to explore new methods to avoid the formation of the deaminated reactants (5-MeCytN3+-SO3−). Meanwhile, the HSO3−-induced direct hydrolytic deamination of cis and trans 5-MeCytN3+-SO3− isomers is represented by paths A and A′, respectively, and has been further explored in the presence of two water molecules. It was found that the contribution of two water molecules renders the HSO3−-induced direct hydrolytic deamination of cis and trans 5-MeCytN3+-SO3− isomers by paths A and A′ favourable. In addition, the ΔGs-a≠ values (85.74–85.34 kJ mol−1) of the rate-limiting steps of the two water-mediated paths A and A′ are very close to that of the theoretical value for CytN3+-SO3− (88.18 kJ mol−1), implying that the free barrier gap between Cyt and 5-MeCyt is very small under bisulfite conditions. This further suggests that bisulfite sequencing technology may be easily influenced by the external environment.
Co-reporter:Tianlei Zhang, Rui Wang, Hao Chen, Suotian Min, Zhiyin Wang, Caibin Zhao, Qiong Xu, Lingxia Jin, Wenliang Wang and Zhuqing Wang
Physical Chemistry Chemical Physics 2015 - vol. 17(Issue 22) pp:NaN15055-15055
Publication Date(Web):2015/05/06
DOI:10.1039/C5CP00968E
The effect of a single water molecule on the HO2 + NO2 hydrogen abstraction reaction has been investigated by employing B3LYP and CCSD(T) theoretical approaches with the aug-cc-pVTZ basis set. The reaction without water has three types of reaction channels on both singlet and triplet potential energy surfaces, depending on how the HO2 radical approaches NO2. These correspond to the formation of trans-HONO + O2, cis-HONO + O2 and HNO2 + O2. Our calculated results show that triplet reaction channels are favorable and their total rate constant, at 298 K, is 2.01 × 10−15 cm3 molecule−1 s−1, which is in good agreement with experimental values. A single water molecule affects each one of these triplet reaction channels in the three different reactions of H2O⋯HO2 + NO2, HO2⋯H2O + NO2 and NO2⋯H2O + HO2, depending on the way the water interacts. Interestingly, the water molecule in these reactions not only acts as a catalyst giving the same products as the naked reaction, but also as a reactant giving the product of HONO2 + H2O2. The total rate constant of the H2O⋯HO2 + NO2 reaction is estimated to be slower than the naked reaction by 6 orders of magnitude at 298 K. However, the total rate constants of the HO2⋯H2O + NO2 and NO2⋯H2O + HO2 reactions are faster than the naked reaction by 4 and 3 orders of magnitude at 298 K, respectively. Their total effective rate constant is predicted to be 1.2 times that of the corresponding total rate constant without water at 298 K, which is in agreement with the prediction reported by Li et al. (science, 2014, 344, 292–296).
![Propanedioic acid, 2-[[4-(dimethylamino)phenyl]methylene]-, 1,3-dimethyl ester](/data/chemimg/1951300/72955-45-4.png)
![Propanedioic acid, 2-[[4-(dimethylamino)phenyl]methylene]-, 1,3-dimethyl ester](/data/chemimg/1951300/72955-45-4_b.png)
