Xing-Kang Zhang

Mutations Found in the pncA Gene of Mycobacterium tuberculosis in Clinical Pyrazinamide-resistant Isolates from a Local Region of China

This study was designed to investigate the presence of mutations in the pncA gene, minimum inhibitory concentrations and pyrazinamidase activity of pyrazinamide-resistant Mycobacterium tuberculosis. In total, 47 M. tuberculosis clinical isolates from a local region of China were assayed. Pyrazinamidase activity was measured by pyrazinamide deamination to pyrazinoic acid and ammonia, and a 721 bp region, including the entire pncA open-reading frame, 104 bp of the upstream sequence and 59 bp of the downstream sequence, was determined by DNA sequencing of purified polymerase chain reaction products. Of the 47 isolates resistant to pyrazinamide, 44 lost pyrazinamidase activity and had pncA mutations that occurred mainly near pyrazinamidases active or metal ion binding sites; nine of them have not been reported previously. Three pyrazinamide-resistant isolates carried the wild-type pncA sequence and retained pyrazinamidase activity. These results show the molecular mechanism of pyrazinamide resistance in China and may also contribute towards the prevention of tuberculosis in China.

Triplet excitation transfer between carotenoids in the LH2 complex from photosynthetic bacterium Rhodopseudomonas palustris

We have studied, by means of sub-microsecond time-resolved absorption spectroscopy, the triplet-excited state dynamics of carotenoids (Cars) in the intermediate-light adapted LH2 complex (ML–LH2) from Rhodopseudomonas palustris containing Cars with different numbers of conjugated double bonds. Following pulsed photo-excitation at 590 nm at room temperature, rapid spectral equilibration was observed either as a red shift of the isosbestic wavelength on a time scale of 0.6–1.0 μs, or as a fast decay in the shorter-wavelength side of the Tn←T1 absorption of Cars with a time constant of 0.5–0.8 μs. Two major spectral components assignable to Cars with 11 and 12 conjugated double bonds were identified. The equilibration was not observed in the ML–LH2 at 77 K, or in the LH2 complex from Rhodobacter sphaeroides G1C containing a single type of Car. The unique spectral equilibration was ascribed to temperature-dependent triplet excitation transfer among different Car compositions. The results suggest that Cars of 11 and 12 conjugated bonds, both in close proximity of BChls, may coexist in an α,β-subunit of the ML–LH2 complex.

Studies of the solvent effects on the internal reorganization energy for electron transfer of uracil and its anion with ONIOM

Abstract In this paper, the aqueous adiabatic electron affinity (AEA) of Uracil (U) and internal reorganization energy λ i of the self-exchange electron transfer (ET) reaction between Uracil and Uracil anion radical (U − ) in aqueous solution were studied. The effect of the solvation was studied with the recently developed hybrid quantum molecular chemical method, ONIOM. In all calculations, the geometrical optimization for U and U − was performed at B3LYP/6-31++G(d) level. As for the solvent surroundings, the seven water molecules as the first hydration shell were adopted and treated with B3LYP, PM3 and AMBER methods, namely, ONIOM (B3LYP:B3LYP), ONIOM (B3LYP:PM3) and ONIOM (B3LYP:Amber) methods, respectively. The values of AEA for Uracil, predicted by the above three methods, are small positive ones. The geometrical differences between neutral and anion radical molecules of U originate mainly from those of dihedral angles. According to the corresponding dipole moment values, the excess electron in U − should be trapped dominantly by dipole-bound way. The calculated λ i values by ONIOM (B3LYP:B3LYP) and ONIOM (B3LYP:PM3) are close to each other within 0.89%. The λ i value from ONIOM (B3LYP:Amber) is in agreement with the one from SCRF-CPCM very well. Finally, the calculation results of the detailed geometries and molecular interaction mode effect of U and U − and related water molecules in the hydration shell were discussed.

Theoretical studies on the mechanism of primary electron transfer in the photosynthetic reaction center of Rhodobacter sphaeroides.

The mechanism of the primary electron transfer (ET) process in the photosynthetic reaction center (PRC) of Rhodobacter sphaeroides has been studied with quantum chemistry method of ab initio density functional theory (DFT) (B3LYP/6-31G) based on the optimized X-ray crystallographic structure. The calculation was carried out on different structural levels. The electronic structure of pigment molecules was first studied, and then the influence of the neighboring protein was taken into account at three approximation levels: (a) the surrounding proteins were treated as a homogeneous medium with a uniform dielectric constant (SCRF); (b) both the influence of axial coordination of His to the special pair P and ABChl as, and the hydrogen bonds between related residues and P and also BPhas were included; and (c) the influence of the electronic structure of the protein subunit chains as a whole was studied. The results suggest that: (1) according to the composition of the HOMO and LUMO of P, there might be a charge-separated state of (BChlL+BChlM−) for the excited state of P; (2) to treat the protein surroundings as a homogeneous medium is not sufficient. Different interactions between pigment molecules and related residues play different roles in the ET process; (3) the axial coordination of His to P raises the ELUMO of P greatly, and it is very important for the ET process to occur in the PRC of wild-type bacterium; the axial coordination of His to ABChl as also raises their ELUMO significantly; (4) the hydrogen-bonds between amino acid residues and P and also BPh as depress the ELUMO of the pigment molecules to some extent, which makes the ELUMO of P lower than those of ABChlas, and the ELUMO of BPh aL lower than that of BPh aM. Consequently, the ET process from P to BPh aL does not, according to our calculation model, occur via ABChl aL. The possibility of the ET pathway from P to BPh aL via ABChl aL was discussed; (5) the frontier orbitals of protein subunit chains L and M are localized at the random coil area and the α–helix areas, respectively. Results mentioned above support the fact that the ET process proceeds in favourable circumstances along the branch L.

Density functional investigation on electron‐transfer catalysis of cycloreversion of cyclobutane: Radical anion mechanism

The mechanism of cycloreversion of cyclobutane radical anion (c‐C4H  8− ) has been investigated at the UB3LYP/6‐31++G(d,p) level, and compared with those of neutral c‐C4H8 and c‐C4H  8+ radical cation. Although both c‐C4H  8− and C2H4 are shown to be Rydberg states unstable with respect to electron ejection, the activation barrier for the “rotating” cycloreversion of c‐C4H  8− (37.3 kcal/mol) is lower by about 25.2 kcal/mol than that of c‐C4H8, and even the intervention of tetramethylene radical anion intermediate may reduce the activation barrier for the cycloreversion of c‐C4H8 by about 8.4 kcal/mol, mainly due to stronger electron‐deficiency of intermediate biradical species than close‐shell cyclobutanes. For the cycloreversion for c‐C4H  8− , side isomerization reaction may be efficiently prevented by the low kinetic stability of tetramethylene radical anion intermediate towards dissociation, just different from the radical cation case. Our theoretical results have suggested the possibility of electron‐attachment catalysis of the cycloreversion of some electron‐deficient substituted cyclobutanes.

Theoretical investigation on the reaction of ionized water with ethylene

The mechanism for the reaction of H2O+ with C2H4 has been investigated theoretically at the UCCSD(T)/6-31++G(d,p)//UB3LYP/6-31++G(d,p) level. Two major products (A) H2O+C2H4+ and (B) HO+C2H5+ are shown to be formed through the parallel reactions of charge-transfer and proton-transfer via the respective intermediates of (a) H2O·C2H4+ and (b) HO·HC2H4+. The dissociation of intermediate (c) HOC2H5+ resulting from the 1,3-H-shift of (a), may lead to the minor product (C) HOCH2++CH3. The calculated results agree well with the available experimental data and may be helpful for understanding the chemical behavior of analogous radical cations containing H–O bond.

Spectroscopic study on the photophysical properties of chlorine substituted tetraphenylporphyrin-histidine and its zinc (II) complexes

The photophysical properties ofortho- CI,meta-CI andpara-CI substituted tetraphenylporphyrin-histidine and their zinc (II) complexes have been studied by means of steady-state absorption and fluorescence spectroscopies, as well as time-resolved fluorescence spectroscopy. For the cases of both free-base and zinc complexes, it was found that theortho-chlorine substitution onto the phenyl rings significantly altered the fluorescence quantum yield, the fluorescence lifetime and the ratio between radiative and nonradiative deactivation rates of the porphyrin chromophore, i.e. the photophysical parameters were quite different from those ofmeta- andpara-substituted compounds. On the other hand, however, the introduction of covalently-linked histidine did not exert much effects on the photophysical behavior of the porphyrin chromophore. The results are interpreted in terms of the steric effect and the heavy-atom effect from the chlorine atoms substituted onto the phenyl rings.

Density functional investigations on the (H2O)n·CCH and (H2O)n·HCC complexes (n=1–3)

Abstract The electronic structures and energies of (H2O)n·CCH and (H2O)n·HCC complexes (n=1–3) between CCH and water have been theoretically investigated at the UB3LYP/6-311++G(2df,p)//UB3LYP/6-311G(d,p) level. The complexes with n=2–3 are cyclic structures with homodromic hydrogen-bond chain. The (H2O)n·CCH (n=1–3) complexes show increasing stabilities towards CCH- or H2O-eliminations of 2.3, 5.8 and 7.6 kcal/mol and are energetically more stable than the corresponding (H2O)n·HCC complexes by 0.8, 2.7 and 3.4 kcal/mol, respectively, due to the charge-separation-enhanced hydrogen bonds within (H2O)n·CCH (n=2,3). Strong interactions between CCH and (H2O)2 and (H2O)3 clusters suggest special solvent effects of water on the chemical behavior of unsaturated radicals.

Ultrafast spectroscopy studies on the mechanism of electron transfer and energy conversion in the isolated pseudo ginseng, water hyacinth and spinach chloroplasts

The spectroscopy characteristics and the fluorescence lifetime for the chloroplasts isolated from the pseudo ginseng, water hyacinth and spinach plant leaves have been studied by absorption spectra, low temperature steady-state fluorescence spectroscopy and single photon counting measurement under the same conditions and by the same methods. The similarity of the absorption spectra for the chloroplasts at room temperature suggests that different plants can efficiently absorb light of the same wavelength. The fluorescence decays in PS II measured at the natural QA state for the chloroplasts have been fitted by a three-exponential kinetic model. The three fluorescence lifetimes are 30, 274 and 805 ps for the pseudo ginseng chloroplast; 138, 521 and 1494 ps for the water hyacinth chloroplast; 197, 465 and 1459 ps for the spinach chloroplast, respectively. The slow lifetime fluorescence component is assigned to a collection of associated light harvesting Chl a/b proteins, the fast lifetime component to the reaction center of PS II and the middle lifetime component to the delay fluorescence of recombination of P+ 680 and Pheo-. The excitation energy conversion efficiency(η) in PS II RC is defined and calculated on the basis of the 20 ps electron transfer time constant model, 60%, 87% and 91% for the pseudo ginseng, water hyacinth and spinach chloroplasts, respectively. This interesting result is in unconformity with what is assumed to be 100% efficiency in PS II RC. Our result in this work stands in line with the 20 ps electron transfer time constant in PS II rather sound and the water hyacinth plant grows slower than the spinach plant does as envisaged on the efficiency. But, our results predict that those plants can perform highly efficient transfer of photo-excitation energy from the light-harvesting pigment system to the reaction center (closely to 100%). The conclusion contained in this paper reveals the plant growth characteristics expressed in the primary processes of photosynthesis and a relationship between a plant growing rate and its spectroscopy characteristics and fluorescence lifetimes, namely, the slower a plant grows, the less excitation energy conversation efficiency used might be anticipated.

Investigation on the electronic structural properties associated with the oxidation damage to the telomeric ssDNA

Abstract The oxidation damage to telomeric DNA is closely associated with cellular life-span. In order to obtain the information about the factors related to the oxidation damage of telomeric DNA, electron structure of base stacks and effects of base sequence for telomeric ssDNA units of human, plant, and chlamydomonas were studied with a combined method of quantum and molecular mechanics in this paper. The results showed the following. (i) From the energies of the fragments, it can be seen that telomeric ssDNA sequences are more stable than the corresponding non-telomeric ones. B-type telomeric ssDNAs are more stable than the corresponding A-type ones too. The stability of telomeric DNA fragments is mainly from the contribution of G/G and G/A stacks. The results also showed that the electron correlation energy plays an important role in the stacking systems. (ii) The HOMOs of the series –G 3 AT n – ( n =2–4) are mainly localized at 5′-G(1). The LUMOs of the same series are from the contributions from 5′-T(1) and 5′-T(2). (iii) The E HOMO values increase and E LUMO values decrease with the increase of the number n in –G n – and –G 3 AT n – ( n =1–4) for the same ssDNA type (A or B) and sequence direction (telomere or non-telomere), which results in the decrease of Δ E ( E LUMO − E HOMO ) values with the increase of n . The Δ E values of A-type sequences are always smaller than those of the corresponding B-type ones, which means that the former are more easy to be excited. The E HOMO values of A-type fragments are always higher than those of the corresponding B-type ones so that the former are of more stronger tendency to donate electrons than the cases of the latter. (iv) The different effects of base A, stacked at the 3′terminal and 5′terminal of –GGG–, on frontier orbital energies and components were discussed. (v) These results will be helpful to understand the fact that telomeric DNA prefers B-type conformation at the stationary state to make organism more stable for withstanding reactive oxygen species stress from cell metabolism damage.