Lingxia Jin

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.

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 investigation on exciton-dissociation and charge-recombination processes of PC61BM-PTDPPSe interface.

AbstractDesigning and synthesizing novel electron-donor polymers with the high photovoltaic performances has remained a major challenge and hot issue in organic electronics. In this work, the exciton-dissociation (kdis) and charge-recombination (krec) rates for the PC61BM-PTDPPSe system as a promising polymer-based solar cell candidate have been theoretically investigated by means of density functional theory (DFT) calculations coupled with the non-adiabatic Marcus charge transfer model. Moreover, a series of regression analysis has been carried out to explore the rational structure–property relationship. Results reveal that the PC61BM-PTDPPSe system possesses the large open-circuit voltage (0.77 V), middle-sized exiton binding energy (0.457 eV), and relatively small reorganization energies in exciton-dissociation (0.273 eV) and charge-recombination (0.530 eV) processes. With the Marcus model, the kdis, krec, and the radiative decay rate (ks), are estimated to be 3.167×1011 s−1, 3.767×1010 s−1, and 7.930×108 s−1 respectively in the PC61BM-PTDPPSe interface. Comparably, the kdis is as 1∼3 orders of magnitude larger than the krec and the ks, which indicates a fast and efficient photoinduced exciton-dissociation process in the PC61BM-PTDPPSe interface. Graphical AbstractPTDPPSe is predicted to be a promising electron donor polymer, and the PC61BM-PTDPPSe system is worthy of further device research by experiments.

Modification on C217 by auxiliary acceptor toward efficient sensitiser for dye-sensitised solar cells: a theoretical study

ABSTRACT In this work, to develop efficient organic dye sensitisers, a series of novel donor–acceptor–π–acceptor metal-free dyes were designed based on the C217 dye by means of modifying different auxiliary acceptors, and their photovoltaic performances were theoretically investigated with systematic density functional theory calculations coupled with the incoherent charge-hopping model. Results showed that the designed dyes possess lower highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) levels as well as narrower HOMO–LUMO gaps compared to C217, which indicate their higher light-harvesting efficiency. In addition, using the (TiO2)38 cluster and bidentate bridging model, we predicted that the photoelectric conversion efficiency (PCE) for the C217 dye is as high as 9.92% under air mass (AM) 1.5 illumination (100 mW·cm−2), which is in good agreement with its experimental value (9.60%–9.90%). More interestingly, the cell sensitised by the dye 7 designed in this work exhibits a middle-sized open-circuit voltage of 0.737 V, large short-circuit photocurrent density of 21.16 mAˑcm−2 and a fill factor of 0.801, corresponding to a quite high PCE of 12.49%, denoting the dye 7 is a more promising sensitiser candidate than the C217, and is worth further experimental study.

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*.

Reactivity of 5-carboxycytosine toward addition and hydrogen abstraction by ·OH in acetonitrile: a computational study

Abstract Two distinct mechanisms of -mediated 5-carboxylcytosine (5-caCyt) at the CBS-QB3 approach with polarizable continuum model in acetonitrile have firstly been explored, the addition reaction (paths R1 and R2), the H-atom abstraction reaction (paths R3-R6), respectively. It indicates that the addition of to the C5 = C6 double bond of 5-caCyt remains more favourable than the H-atom abstraction, whether in the gas or aqueous phase. Meanwhile, there is a little difference in the free energy barrier between acetonitrile and water, showing that the solvent has small impact on the reactivity of -mediated 5-caCyt.

Synthesis, Crystal Structure, and Biological Activity of 1,3,5-Thimethyl-2,4,6-tris(3'-methyl-1'-imidazoliomethylene)Benzene Perchlorate

The title compound, C24H33Cl3N6O12(ClO4)3, was synthesized and structurally characterized by elemental analysis, IR, MS, HMR and single crystal X-ray diffraction. The crystals are triclinic, sp. gr. P1, Z = 2. The crystal structure is stabilized by C–H···O hydrogen-bonds forming a three-dimensional network. The preliminary biological test showed that the title compound had anti-Mycobacterium phlei 1180 activity.

A Novel Coordination Polymer Based on Trinuclear Cobalt Building Blocks Cluster: Synthesis, Crystal Structure, and Properties

The title compound {[Co3(μ3-OH)(μ2-H2O)2(H2O)5(BTC)2] · 6H2O}n (H3BTC is a 1,3,5-benzenetricarboxylic acid) was prepared and characterized by single crystal and powder X-ray diffraction, Fourier transform infrared spectroscopy, thermogravimetric and elemental analyses. The single crystal X-ray diffraction reveals that the title compound consists of 1D infinite zigzag chains which were constructed by trinuclear cobalt cluster and BTC3– ligand. Neighbouring above-mentioned 1D infinite zigzag chains are further linked by intermolecular hydrogen bonding to form a 3D supermolecular structure. In addition, the luminescent properties of the title compound were investigated.

Synthesis, Crystal Structure, and Luminescent Properties of Ag(I) Coordination Polymer with Tricarboxylic Acid and Flexible N-donor Ligand

The reaction of AgNO3 with combinations of 1,3-bis(4-pyridyl)propane (bpp) and 1,3,5-benzenetricarboxylic acid (H3btc) in aqueous alcohol/ammonia at room temperature produces crystals of {[Ag6(H2O)2(bpp)6] · (btc)2 · 25H2O}n (Ι). Single crystal X-ray diffraction analysis reveals that the complex Ι consists of 1D infinite cationic chains of [Ag(bpp)]nn+ and [Ag(H2O)(bpp)]nn+ which are further linked into the cation layer of [Ag(bpp)]nn+ by Ag···π interactions. The noncoordinated btc3− serves as template driving surrounding water molecules to aggregate into the anionic water layer. The neighboring anionic water layer and cationic layer were further alternately joined into a 3D sandwich-like framework by hydrogen bonding. In addition, the luminescent properties of Ι were investigated.