Hong-Xing Zhang

Jilin University, Yung-chi, Jilin Sheng, China

Are you Hong-Xing Zhang?

Claim your profile

Publications (176)398.22 Total impact

  • Hong-Qiang Xia, Jian Wang, Fu-Quan Bai, Hong-Xing Zhang
    Dyes and Pigments 01/2015; 113:87–95. · 3.53 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Human serotonin N-acetyltransferase (hAANAT), included in the melatonin biosynthesis, plays a pivotal role in the regulation of the biological clock and the daily rhythm. In this research, a reliable model of hAANAT was first constructed by the homology modelling method. Then the inhibition mode of two representative rhodanine-based inhibitors was explored by molecular dynamics simulations and energy analyses. The results show that the inhibitor class could share a similar inhibition mechanism in which the carboxyl moiety is positioned in the Ac-CoA binding region while the other end spans the serotonin binding pocket. The interaction between the inhibitor's carboxyl and the enzyme seems to be more important according to the decomposition of binding free energy. Based on the proposed inhibition mode, the inhibitor's improvement was carried out to obtain a more potent compound. The newly designed inhibitor, with the larger binding free energy, exhibits the stronger interaction with the related residues of the enzyme by the added chemical groups. This work will shed light on the inhibition mechanism of the rhodanine-based inhibitors and promote the development of a new drug targeting hAANAT.
    Molecular Simulation 12/2014; 40(15). · 1.06 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The molecular aggregation structure of 5,5’-Bis(naphthalen-2-yl)-2,2’-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational Frequencies of BOXD-NP were also calculated with B3LYP/6-311+G** method, which showed great consistence with the experimental observations and make the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π* state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, M062x functional was applied in the construction of the potential energy surface. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that the PES have great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding.
    RSC Advances 10/2014; · 3.71 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: D-A-π-A dyes have exhibited several excellent advantages including optimized energy levels, distinct improvement of photovoltaic performance and stability. By modulating the auxiliary acceptor and acceptor unit, the efficiency of D-A-π-A dyes based dye-sensitized solar cells can be further improved. Based on density functional theory methods, sixteen dimethoxyl-substituted triphenylamine based D-A-π-A dyes composed of different acceptor and auxiliary acceptor groups were designed, and other four referenced homologous D-π-A dyes were also involved to compare in this work. The properties of all the dyes, including intramolecular charge transfer, lighting harvesting efficiency, kinetic of electron injection, and vertical dipole moment, have been investigated theoretically to screen out the dyes which would produce high efficiency. Then the interaction between the selected dyes and the electron acceptor in electrolyte was discussed to reveal the interfacial charge recombination process. In comparison with other dyes, TNA4 would be a promising candidate for its better performance on key parameters and achieving a balance between competing factors. Compared with cyanoacrylic acid, 2-(1, 1-dicyanomethylene) rhodanine group can serve as an excellent acceptor for future DSSCs applications.
    RSC Advances 10/2014; · 3.71 Impact Factor
  • Li Li, Fu-Quan Bai, Hong-Xing Zhang
    [Show abstract] [Hide abstract]
    ABSTRACT: When adding two azobenzene chromophores on a dithienylethene molecule, the irradiation at 450nm can effectively arouse the cycloreversion reaction of the ring-closed dithienylethene. We investigated the frontier molecular orbitals and absorption properties of such series of molecules and inferred the mechanism of the ring-opening reaction. The 450nm light sensed by the side azobenzene groups can excite the whole molecule to a high excited state, and through electronic transition and energy transfer the active electron may centre on the dithienylethene ring part, then the ring-opening happens. While for the ring-open form, the energy of the 450nm light is not high enough to promote the electron to the exact molecular orbital occupying the central dithienylethene ring, so it cannot cause the ring-closing reaction.
    Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy 09/2014; 137C:987-994. · 1.98 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The anaerobic metabolism of CCl4 by P450 enzymes was investigated using quantum chemical calculations. It was found that under anaerobic conditions, the substrate CCl4 might undergo one or two subsequent one-electron reductions to generate different reactive metabolites, trichloromethyl radical (˙CCl3) and dichlorocarbene (:CCl2) respectively. Meanwhile, it was the reduced ferrous haem complex rather than the unreduced ferric haem complex that could directly achieve such reductions. Based on the formation of the former reactive metabolite, a further one-electron reduction could take place with the assistance of a proton to yield the latter reactive species, i.e., a further reductive dechloridation of ˙CCl3 could take place via a novel SE3 mechanism. In addition, the ˙CCl3 species was capable of binding covalently to the meso-carbon atom of the prosthetic group, leading to the suicidal destruction of P450 enzymes. Whereas the :CCl2 species was involved in the CCl4-dependent reversible P450 inhibition as its hydrolysis product, CO, but was not significantly involved in the CCl4-dependent irreversible P450 destruction. It is obvious that the reductive metabolism of CCl4 to reactive intermediates by P450 enzymes is an essential prerequisite for its toxicity.
    Dalton Transactions 08/2014; · 3.81 Impact Factor
  • Hong-qiang Xia, Jie Chen, Fu-quan Bai, Hong-xing Zhang
    [Show abstract] [Hide abstract]
    ABSTRACT: The density functional theory (DFT) and time-dependent DFT (TD-DFT) approaches have been applied to obtain the optimized geometries, electronic structures, molecular orbitals and absorption spectra of a series of meso-substituted zinc porphyrin analogs with phenyl and thiophene groups as the π bridging unit and cyanoacrylic acid as the acceptor unit. The results showed that the introduction of thiophene group increases the orbital splitting and changes the absorption spectra properties significantly. It is indicated that when there is only one thiophene group included in the π bridge, the oscillator strength of B absorption band is much stronger. The increasing length of thiophene chain just changes the scope of specific absorption enhancement. The effect of attaching an additional electron-donating group diphenylamine instead of phenyl to the porphyrin core also has been shown. It is found that the diphenylamine group reduces the band gap, and leads to facile intramolecular charge transfer from diphenylamine and porphyrin ring unit to acceptor unit. These kinds of zinc porphyrin analogs have the LUMO energy close to the conduction band of TiO2 and more red-shifted absorption spectrum compared with phenyl substituted analogs.
    Journal of Porphyrins and Phthalocyanines 06/2014; 18(05). · 1.43 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Monometallic (UO2)(X)2(L)3 (L = pyridine (py), X = F (1), Cl (2), Br (3) and I (4); L = tetrahydrofuran (thf), X = Cl (5); L = pyrrole (pl), X = Cl (6)) as well as bimetallic [(UO2)(μ2-X)(X)(L)2]2 (L = py, X = F (7), Cl (8), Br (9) and I (10); L = thf, X = Cl (11); L = pl, X = Cl (12); μ 2 = doubly bridged) were examined using relativistic density functional theory. With changing from F, Cl, Br to I irregardless of in mono- or bis-uranyl complexes, bond lengths of U = O were calculated to be decreasing, resulting from strengthening of axial U = O bonds while weakening equatorial X → U coordination. This is further evidenced by calculated bond orders of U = O and stretching vibrational frequencies. A similar situation was is found in 2, 5 and 6 as well as in 8, 11 and 12, where N/O ligands are varied but the chlorine atoms are retained. The present study reveals that all these complexes have U(f)-character low-lying unoccupied orbitals, and their π*(U = O) antibonds are located on higher-energy orbitals. Complex 1 was calculated to show σ(U = O) bonding character for HOMO, and pyridine-character for other occupied orbitals; the fluorine ligand occurs in a relatively low-energy region. In contrast, the π(p) characters of heavier halogen atoms significantly contribute to most frontier molecular orbitals of 2, 3 and 4. Unlike this electronic feature of 2, complexes 5 and 6 exhibit mainly thf and pyrrole characters, respectively, for their high-lying occupied orbitals. Electronic structures of bisuranyl complexes 7-12, albeit a little more complicated, are revealed to be similar to those of the corresponding monouranyl complexes. Finally, energies of formation reactions of the above complexes were calculated and compared with available experimental results.
    Journal of Molecular Modeling 06/2014; 20(6):2305. · 1.98 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Fosfomycin resistance kinases FomA, one of the key enzymes responsible for bacterial resistances to fosfomycin, has gained much attention recently due to the raising public concern for multi-drug resistant bacteria. Using molecular docking followed by molecular dynamics simulations, our group illustrated the process of fosfomycin induced conformational change of FomA. The detailed roles of the catalytic residues (Lys18, His58 and Thr210) during the formation of the enzyme-substrate complex were shown in our research. The organization functions of Gly53, Gly54, Ile61 and Leu75 were also highlighted. Furthermore, the cation-π interaction between Arg62 and Trp207 was observed and speculated to play an auxiliary role in the conformation change process of the enzyme. This detailed molecular level illustration of the formation of FomA·ATP·Mg·Fosfomycin complex could provide insight for both anti-biotic discovery and improvement of fosfomycin in the future.
    Journal of Molecular Modeling 05/2014; 20(5):2236. · 1.98 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In order to understand the binding mechanism between Barrier-to-autointegration factor (BAF) and DNA, two DNA:BAF complexes with wild type (WT) BAF and its Gly25Glu point mutate type (MT) were generated by molecular docking on the basis of the crystal structures of BAF (PDB code: 2ODG, chain A) and DNA (PDB code: 2BZF, chain B and C). Then, molecular dynamics (MD) simulations were performed on the two docked structures, as well as BAF (WT) and BAF (MT). The results show that monomer BAF is more flexible than BAF in DNA:BAF complex, suggesting that DNA is effective to stabilize conformation of BAF, which is in good agreement with the experimental results. Besides, the mutated Glu25 in DNA:BAF (MT) can change the BAF conformation to some extent. With deeper investigation on the DNA:BAF structures, the hydrogen bonds are found to make great contribution to the interaction between DNA and BAF. The hydrogen bonds in DNA:BAF (MT) are fewer than those in DNA:BAF (WT), indicating that the Gly25Glu mutation in BAF has an important effect on the hydrogen bonds in the DNA:BAF complex. Besides, the binding free energy in DNA:BAF (MT) is also higher than that in DNA:BAF (WT). It results from the influence of Glu25 side chain on the orientation of Lys6 and Lys33 in the interface between DNA and BAF. The binding free energy of Lys72, another key residue, decreases a lot in DNA:BAF (MT) anomalously. The decreasing energy causes the destruction of hydrophobic pocket in the binding site between DNA and BAF (MT). Our results are helpful for further experimental investigations.
    Journal of Molecular Modeling 05/2014; 20(5):2246. · 1.98 Impact Factor
  • Ling Li, Zeng-xia Zhao, Hong-xing Zhang
    [Show abstract] [Hide abstract]
    ABSTRACT: The electronic spectra of HNCSe were studied by performing multireference ab initio calculations at CASPT2 level of theory taking into account spin-orbit (SO) coupling. Our highly accurate calculation indicated that theoretically determined geometric parameters and harmonic vibrational frequencies for the ground state X1A′ are consistent with observed experimental data. We present the oscillator strengths, electronic and structural changes accompanying the excitation process. The bonding characteristics in the low-lying excited states were analyzed on the basis of the valence molecular orbitals (MOs). And the excited states of HNCSe exist in the complex of Se and HNC radical pair. According to our calculations, the ground-state of HNCSe+ is linear, and the value of the ionization potential of HNCSe has been found. The existence of bound excited anion states has been found for the first time in HNCSe-.
    Journal of Theoretical and Computational Chemistry 04/2014; 13(02). · 0.52 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In this study, surface pressure-area isotherms for N-stearoyldopamine (DOPA) and 4-stearylcatechol (ST) monolayers are obtained by means of molecular dynamics simulations and compared to experimental isotherms. The difference between DOPA and ST is an amide group, which is present in the alkyl tails of DOPA molecules. We find a large difference between the isotherms for DOPA and ST monolayers. Upon using TIP4P/2005 for water and OPLS force fields for the organic material and a relatively large system size, the simulated results are found to be consistent with experiments. With molecular dynamics simulations, the configurations of molecules in the monolayers can be directly analyzed. When the surface pressure is high, a regular molecular orientation is observed for ST molecules, whereas regular orientations are only observed in local domains for DOPA molecules. The differences between DOPA and ST monolayers are attributed to the amide groups in DOPA molecules, which are useful for both steric effects and the formation of hydrogen bonds in the DOPA monolayers. This study clearly demonstrates that hydrogen bonds, due to the presence of the amide group in DOPA, are the cause of the disorder in its Langmuir monolayers. Thus, the conclusion may be helpful in making ordered organic monolayers in the future.
    Physical Chemistry Chemical Physics 04/2014; · 4.20 Impact Factor
  • Wei Li, Jian Wang, Jie Chen, Fu-Quan Bai, Hong-Xing Zhang
    [Show abstract] [Hide abstract]
    ABSTRACT: DSSCs have been extensively investigated in the past decade, and the search for more efficient dyes for DSSCs remains challenging. In this work we discuss the influences of elongating π-spacers and rigidifying dithiophene on the performance of dithiafulvenyl (DTF)-based organic dyes using density functional theory (DFT) and time-dependent DFT methods. We show that systematically elongating the π-spacer of the DTF-2P dye by increasing the number of thiophene groups tends to red-shift the absorption peak and broaden the absorption range, thus improving the light-harvesting efficiency of DTF-2P-T and DTF-2P-2T. Furthermore, among the three dyes, DTF-2P-T would have the best performance because it performs nicely on the key parameters including the electron injection driving force (D), the light-harvesting efficiency (LHE), and the shift of the TiO2 conduction band (ΔEcb). In particular, DTF-2P-2T has a larger LHE despite the smaller D and ΔEcb compared with DTF-2P-T. Having realized the great merits of modification on π-spacers, afterwards, we designed a novel dye by rigidifying the dithiophene moiety of DTF-2P-2T. The resulting dye is proven to be very promising to challenge the conversion efficiency 8.29% of DTF-2P-T due to the improved ΔEcb and LHE. Our theoretical studies are expected to provide valuable insights into the molecular design of novel DTF-based dyes for the optimization of DSSC.
    Physical Chemistry Chemical Physics 04/2014; · 4.20 Impact Factor
  • Ang-yang Yu, Hong-xing Zhang
    03/2014; 112(7).
  • Mo Xie, Jie Chen, Fu-Quan Bai, Wei Wei, Hong-Xing Zhang
    [Show abstract] [Hide abstract]
    ABSTRACT: We report a DFT study of interaction between the Ru complex sensitizer [Ru(dcbpy)2(NCS)2: dcbpy=4,4'-dicarboxy-2,2'-bipyridy] (N3) and iodide ion under the influence of different deprotonation situations. There are two kinds of interaction mechanisms: iodide ion interacts with metal-center Ru atom or carboxyl, derived from the natural charge distribution analysis. The calculation indicated that there were several stable intermedium forms in different deprotonation degree. The stability of these intermedium forms would be perturbed gradually while the number of eliminated protons increased. It can be predicted that in the initial period of absorption and injection as well as the dissolve process where the deprotonation was demanded, the dye will not attacked by the iodide ion in solution extensively. Additionally, dye with more carboxyls will reduce the activity of redox reaction and more obstacles are required to be overcome before or during the redox reaction. The comparison of natural charge between isolate N3 and N3 with iodide ion intermedium (N3I(-)) showed the iodide ion attacking made the charge contribute on N3 molecule more negative, nevertheless the N3I(-) still has ability to attract another iodide ion. The attacking of iodide ion will also influence the electronic transition and absorption properties through the analysis of the frontier molecular orbitals and the densities of states. The results reported in this paper give us the guidance to carry out the further investigations about the dye regeneration process.
    The Journal of Physical Chemistry A 03/2014; · 2.77 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Transthyretin (TTR) dissociation and aggregation appear to cause several amyloid diseases. TTR dimer is an important intermediate that is hard to be observed from the biological experiments. To date, the molecular origin and the structural motifs for TTR dimer dissociation, as well as the unfolding process have not been rationalized at atomic resolution. To this end, we have investigated the effect of low pH and mutation L55P on stability as well as the unfolding pathway of TTR dimer using constant pH molecular dynamics simulations. The result shows that acidic environment results in loose TTR dimer structure. Mutation L55P causes the disruption of strand D and makes the CE-loop very flexible. In acidic conditions, dimeric L55P mutant exhibits notable conformation changes and an evident trend to separate. Our work shows that the movements of strand C and the loops nearby are the beginning of the unfolding process. In addition, hydrogen bond network at the interface of the two monomers plays a part in stabilizing TTR dimer. The dynamic investigation on TTR dimer provides important insights into the structure-function relationships of TTR, and rationalizes the structural origin for the tendency of unfolding and changes of structure that occur upon introduction of mutation and pH along the TTR dimer dissociation and unfolding process.
    Biophysical chemistry 03/2014; 189C:8-15. · 2.28 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In the current contribution, we present a critical study of the theoretical protocol used for the determination of the electronic spectra properties of luminescent cyclometalated iridium(III) complex, [Ir(III)(ppy)2H2dcbpy](+) (where, ppy = 2-phenylpyridine, H2dcbpy = 2,2'-bipyridine-4,4'-dicarboxylic acid), considered as a representative example of the various problems related to the prediction of electronic spectra of transition metal complex. The choice of the exchange-correlation functional is crucial for the validity of the conclusions that would be drawn from the numerical results. The influence of the exchange-correlation on geometry parameter and absorption/emission band, the role of solvent effects on time-dependent density function theory (TD-DFT) calculations, as well as the importance of the chosen proper procedure to optimize triplet excited geometry, have been thus examined in detail. From the obtained results, some general conclusions and guidelines are presented: i) PBE0 functional is the most accurate in prediction of ground state geometry; ii) the well-established B3LYP, B3P86, PBE0, and X3LYP have similar accuracy in calculation of absorption spectrum; and iii) the hybrid approach TD-DFT//CIS gives out excellent agreement in the evaluation of triplet excitation energy.
    Journal of Molecular Modeling 03/2014; 20(3):2108. · 1.98 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Self-healing materials should take effect immediately following crack generation in principle, but the speed of autonomic recovery of mechanical properties through either extrinsic or intrinsic healing strategy reported so far is not that fast. Mostly, a couple of hours are taken for reaching steady state or maximum healing. To obviously accelerate the healing process, the authors of this work make use of antimony pentafluoride as instant hardener of epoxy, and successfully encapsulate the highly active antimony pentafluoride-ethanol complex in terms of hollow silica spheres. Accordingly, self-healing agent based on microencapsulated antimony pentafluoride-ethanol complex and epoxy monomer is developed. Epoxy material with the embedded healant capsules can thus be healed within a few seconds, as demonstrated by impact and fatigue tests. It is believed that the outcome presented here might help to move the self-healing technique closer to practical application, especially when the engineering significance of epoxy material is concerned.
    ACS Applied Materials & Interfaces 02/2014; · 5.90 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Filoviruses often cause terrible infectious disease which has not been successfully dealt with pharmacologically. All filoviruses encode a unique protein termed VP35 which can mask doubled-stranded RNA to deactivate interferon. The interface of VP35-dsRNA would be a feasible target for structure-based antiviral agent design. To explore the essence of VP35-dsRNA interaction, molecular dynamics simulation combined with MM-GBSA calculations were performed on Marburg virus VP35-dsRNA complex and several mutational complexes. The energetic analysis indicates that nonpolar interactions provide the main driving force for the binding process. Although the intermolecular electrostatic interactions play important roles in VP35-dsRNA interaction, the whole polar interactions are unfavorable for binding which result in a low binding affinity. Compared with wild type VP35, the studied mutants F228A, R271A and K298A have obviously reduced binding free energies with dsRNA reflecting in the reduction of polar or nonpolar interactions. The results also indicate that the loss of binding affinity for one dsRNA strand would abolish the total binding affinity. Three important residues Arg271, Arg294 and Lys298 which makes the largest contribution for binding in VP35 lose their binding affinity significantly in mutants. The uncovering of VP35-dsRNA recognition mechanism will provide some insights for development of antiviral drug.
    Biopolymers 01/2014; · 2.88 Impact Factor
  • Wen-Ting Chu, Qing-Chuan Zheng, Hong-Xing Zhang
    [Show abstract] [Hide abstract]
    ABSTRACT: Bisphosphoglycerate mutase (BPGM) is a multi-activity enzyme. Its main function is to synthesize the 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. This enzyme can also catalyze the 2,3-bisphosphoglycerate to the 3-phosphoglycerate. In this study, the reaction mechanisms of both the phosphatase and the synthase activities of human bisphosphoglycerate mutase were theoretically calculated by using the quantum mechanics/molecular mechanics method based on the metadynamics and umbrella sampling simulations. The simulation results not only show the free energy curve of the phosphatase and the synthase reactions, but also reveal the important role of some residues in the active site. Additionally, the energy barriers of the two reactions indicate that the activity of the synthase in human bisphosphoglycerate mutase is much higher than that of the phosphatase. The estimated reaction barriers are consistent with the experimental data. Therefore, our work can give important information to understand the catalytic mechanism of the bisphosphoglycerate mutase family.
    Physical Chemistry Chemical Physics 01/2014; · 4.20 Impact Factor

Publication Stats

429 Citations
398.22 Total Impact Points

Institutions

  • 2003–2014
    • Jilin University
      • • State Key Lab of Theoretical and Computational Chemistry
      • • College of Chemistry
      Yung-chi, Jilin Sheng, China
  • 2012
    • Virginia Commonwealth University
      • Department of Physiology and Biophysics
      Richmond, VA, United States
  • 2003–2011
    • Heilongjiang University
      • School of Chemistry and Materials Science
      Harbin, Heilongjiang Sheng, China