Hong-Xing Zhang

Jilin University, Yung-chi, Jilin Sheng, China

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Publications (232)607.5 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Cytochrome P450 (CYP) 3A7 plays a crucial role in the biotransformation of the metabolized endogenous and exogenous steroids. To compare the metabolic capabilities of CYP3A7-ligands complexes, three endogenous ligands were selected, namely, dehydroepiandrosterone (DHEA), estrone and estradiol. In this study, a three-dimensional model of CYP3A7 was constructed by homology modeling using the crystal structure of CYP3A4 as the template and refined by molecular dynamics simulation (MD). The docking method was adopted, combined with MD simulation and the Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) method, to probe the ligand selectivity of CYP3A7. These results demonstrate that DHEA has the highest binding affinity, and the results of the binding free energy were in accordance with the experimental conclusion that estrone is better than estradiol. Moreover, several key residues responsible for substrate specificity were identified on the enzyme. Arg372 may be the most important residue as the low interaction energies and the existence of hydrogen bond with DHEA throughout simulation. In addition, a cluster of Phe residues provides a hydrophobic environment to stabilize ligands. The present study provides insights into the structural features of CYP3A7, which could contribute to further understanding of related protein structures and dynamics.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1054884 · 2.98 Impact Factor
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    ABSTRACT: The molecular aggregation structure of three D-A cocrystal complexes based on substituted distyrylbenzenes (DSB) was studied by density functional theory calculation. The influence of molecular stacking on molecular interactions, frontier molecular orbitals, charge transport and photophysical properties have been investigated in depth, by comparison of D1-A1, D2-A2 and D2-A2’ pairs with different substituents in D and A monomers. Our results provide not only better understanding of the relationship of D-A configuration and electrical/optical properties, but also the theoretical prediction of novel organic semiconductor materials for the mixed-stack D−A charge-transfer crystal. In particular, the charge-transfer complexes of D1-A1 have been demonstrated as good ambipolar material, while the complexes of D2-A2 and D2-A2’ should conduct as better n-type organic semiconductor materials.
    RSC Advances 05/2015; 5(59). DOI:10.1039/C5RA06497J · 3.71 Impact Factor
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    Mo Xie, Jian Wang, Fu-Quan Bai, Li Hao, Hong-Xing Zhang
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    ABSTRACT: Dye regeneration was a key process to influence lifetime and open-circuit voltage of dye-sensitized solar cells. In order to explore the mechanism of dye regeneration, the intermediate forms of this reaction were searched by first principle calculations in this study. The possible intermediat forms were obtained by analyzing the reactivity of four organic dyes with different donors and two electrolyte ions (I- and Br-). Then camparing their structures,interaction energy and reaction free energy, most appropraite intermediate forms were screened out. Throughout the comparison between I- and Br-, we found that Br-/Br3- could be a good redox couple if the redox potential matched with the energy gap of dye. In particular, steric-hindrance was likely the most infuential factor in determining the intermediate forms. It is suggested that triphenylamine homologues as donor groups may both interact with electrolyte easily and accordingly keep off the electrolyte from semiconductor effectively.
    Dyes and Pigments 04/2015; 120. DOI:10.1016/j.dyepig.2015.03.026 · 3.47 Impact Factor
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    ABSTRACT: Ruthenium(II) complexes, as the dye sensitizer in the solar cell system, has attracted great interests. In the present study, based on the ruthenium(II) complex N749, new sensitizers have been designed theoretically to increase the stability and the efficiency of dye-sensitized solar cell (DSSC). By investigating the ground state geometries, electronic structures, and spectroscopic properties by density functional theory (DFT) and time-dependent DFT, the orbital components and absorption transition have been obtained. The effect of tripyrrin ligand in the designed new sensitizers can be demonstrated from our results. The results show that the absorption spectra are systematically broadened and red-shifted with the increase sizes of the pyrrole ligands. The important unoccupied orbitals referred to charge transfer are mainly from di/tripyrrin derivative groups. Consequently, the charge transfer to the di/tripyrrin derivative groups has been strengthened. According to our study, the di/tripyrrin derivative ligand is more efficient than the NCS− ligand in absorbing visible light. The calculation results also indicate that the electronic structures of the N749 derived sensitizers are significantly influenced by the different substituted positions of the thienyl groups on di/tripyrrin ligands. Thus, the efficiency of DSSCs would be different. Our research predicted that the Ru(II) complexes containing 5,10-(2-thienyl)-4,6,9,11-tripyrrin ligand may enhance the visible light absorption of DSSC. This is in accordance with the corresponding experiment. These results are expected to assist the molecular design for new dyes in future DSSCs.
    Theoretical Chemistry Accounts 04/2015; 134(4-4):1-14. DOI:10.1007/s00214-015-1645-3 · 2.14 Impact Factor
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    ABSTRACT: The dye sensitizers play an important role in dye-sensitized solar cell (DSSC). Owing to the synthetic challenge and cost of precious metal-complex dyes, increasing researches have been focused on the organic molecule dyes, porphyrin and light metal porphyrins dyes. In this paper, three natural porphyrin derivatives as dyes with TiO2 nanoparticulate model are studied theoretically using density functional theory (DFT) approaches to explore their spectroscopic properties and application future in DSSC. The detailed orbital components and absorption transitions of thses porphyrin derivatives are analyzed from the calculated results. Key parameters of the short-circuit current density (Jsc) including light harvesting efficiency (LHE), electron injection driving force (ΔGinject) and nonlinear optical properties (NLO) were discussed. In addition, the calculated values of open circuit photovoltage (Voc) for these dyes were also presented. The tetrapyrrole macrocycle of porphyrin with central metals Mg or Zn can enrich the absorption strength greatly. Our research reveals that the Zn-porphyrin sensitizer can be used as potential sensitizer for DSSCs due to its best electronic and optical properties and good photovoltaic parameters. This study is expected to understand natural dye sensitizers and assist the molecular design of new dyes for the further DSSC improvement.
    RSC Advances 03/2015; 5(42). DOI:10.1039/C4RA17080F · 3.71 Impact Factor
  • Dong Shen, Chuipeng Kong, Ran Jia, Peng Fu, Hong-Xing Zhang
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    ABSTRACT: The global minimum structures of Mgn clusters have been determined using the so-called "kick method". With the improved DFT method of B3PW91 functional and Grimme's dispersion correction, a series of the most stable structure of Mgn have been found and a novel Mg9 structure has been located. Subsequently, the chemisorption of hydrogen onto Mg clusters was systemically studied. Considering the average adsorption energies and the ratio of Mg and H, we developed a function that can describe the relation between average adsorption energy and number of Mg and H atoms. Our result may be helpful in developing further to other gas chemisorption material.
    The Journal of Physical Chemistry A 03/2015; 119(15). DOI:10.1021/acs.jpca.5b01474 · 2.78 Impact Factor
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    ABSTRACT: In this work, the effect of regulated host and auxiliary ligand π-conjugation on photophysical properties of a series of Ir(III) carbene complexes are examined by using the start-of-the-art theoretical methods. According to our results, all of the lowest-lying and strongest absorptions can be assigned as a mixed ligand-to-ligand/metal-to-ligand charge transfer (LLCT/MLCT) character, but the different ways of the introduced phenyl have a great effect on the absorption wavelength variation. In addition, the charge transfer characters of lowest-lying emission have some minute differences. What is more, when the extension of π-conjugation is broken, the emission wavelength can be effectively retained due to the similar emission charge transfer related electronic density distribution of occupied molecular orbital and unoccupied molecular orbital. However, the larger π-conjugation can give rise to the remarkably blue-shifted emission. This blue-shifted emission can be attributed to the alteration of transition character from intense interaction between nearly degenerated unoccupied molecular orbitals. Through the evaluation of the spin-orbit coupling (SOC) effect, we can gain the deeply understanding concerning the radiative decay rate processes. These results reveal that the larger π-conjugation can also lead to the higher quantum efficiency due to the larger radiative decay and smaller nonradiative decay rate. Our theoretical studies highlight the role of π-conjugation of host and auxiliary ligand, thus, can pave the way for the design of novel and efficient blue phosphorescence materials.
    Physical Chemistry Chemical Physics 03/2015; 17(15). DOI:10.1039/C5CP00211G · 4.20 Impact Factor
  • Zhi-Xiang Zhang, Fu-Quan Bai, Li Li, Hong-Xing Zhang
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    ABSTRACT: Density functional theory (DFT) calculations are utilized to analyze a novel S,S-dioxide diarylethene of which, contrary to general ones, ring-closing happens under visible light (436 nm) and ring-opening arises in ultraviolet light (365 nm). The asymmetrical structure and the oxidized S atoms alter the continuity and switch method of the conjugation system between the two isomers. The role and position of the substituent affects the intramolecular electron transfer during reaction and results in changes in conversion ratio and quantum yield. Based on the diarylethene, we designed new dyads in which ring-closing and -opening of the two diarylethene parts in one molecule proceed simultaneously under a single wavelength. The photocyclization on one section of the molecule does not limit but facilitate the photocycloreversion on the other section.
    New Journal of Chemistry 03/2015; 39(3). DOI:10.1039/C4NJ01471E · 3.16 Impact Factor
  • Li Li, Fu-Quan Bai, Hong-Xing Zhang
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    ABSTRACT: The ring-closing reaction occurs at the lowest singlet excited state commonly when the open-form dithienylethene is irradiated at about 300 nm. And connecting the dithienylethene and platinum-terpyridyl segment to be a complex through an ethynyl linker or an ethynyl-ether linker, a lower-energy light at 425 nm can also arouse this ring-closing reaction. Through the calculation of the energy levels, we propose the ring-closing process as follows. The light absorbed by the platinum-terpyridyl unit excites the molecule to a singlet excited state. Meanwhile, this electronic state of the molecule transfers to the lowest triplet excited state through intersystem crossing and internal conversion. When absorbs energy from the environment, this state goes up to a higher triplet state around the dithienylethene part, where the ring-closing reaction takes place. Moreover, different patterns of linkers bring about different efficiency of the reaction. And a direct shared linker may facilitate the ring-closing process. In addition, the conjugated linker also causes the maximum wavelength of the complex red shift, because the energy gap between the involved frontier molecular orbitals becomes lower.
    The Journal of Physical Chemistry A 03/2015; 119(12). DOI:10.1021/jp412562j · 2.78 Impact Factor
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    Hong-Qiang Xia, Jian Wang, Fu-Quan Bai, Hong-Xing Zhang
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    ABSTRACT: A series of organic donor-pi-acceptor dyes with difference in pi spacer have been designed and investigated theoretically as sensitizers for application in dye-sensitized solar cells. Density functional theory and time-dependent density functional theory calculations reveal how the additional electron-withdrawing diketopyrrolopyrrole unit and pi spacer order influence the physical properties of the dyes, including spectral response, light harvesting efficiency, and electron injection rate. The results show that auxiliary acceptor leads to the greatly red-shifted of the charge-transfer absorption band. Meanwhile, the number and sort order of thiophene groups can significantly tune the orbital energy levels and change the electronic transition processes. The thiophene groups locating between triphenylamine and diketopyrrolopyrrole units would conduce to the light absorption and electron injection efficiency. The results also suggest that the donor-acceptor-pi-acceptor type dyes have indirect electron injection mode compared with the direct mode in the dyes without containing diketopyrrolopyrrole.
    Dyes and Pigments 02/2015; 113:87–95. DOI:10.1016/j.dyepig.2014.07.033 · 3.47 Impact Factor
  • Lin Chen, Qing-Chuan Zheng, Hong-Xing Zhang
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    ABSTRACT: A novel, highly conserved chromatin protein, Cren7 is involved in regulating essential cellular processes such as transcription, replication and repair. Although mutations in the DNA-binding loop of Cren7 destabilize the structure and reduce DNA-binding activity, the details are not very clear. Focused on the specific Cren7-dsDNA complex ( PDB code 3LWI), we applied molecular dynamics (MD) simulations and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation to explore the structural and dynamic effects of W26A, L28A, and K53A mutations in comparison to the wild-type protein. The energetic analysis indicated that the intermolecular van der Waals interaction and the nonpolar solvation term play an important role in the binding process of Cren7 and dsDNA. Compared with the wild type Cren7, all the studied mutants W26A, L28A, and K53A have obvious reduced binding free energies with dsDNA in the reduction of the polar and/or nonpolar interactions. These results further elucidated the previous experiments to comprehensive understanding the Cren7- DNA interaction. Our work also would provide support to understand the interactions of proteins with nucleic acids.
    Physical Chemistry Chemical Physics 01/2015; 17(8). DOI:10.1039/C4CP05413J · 4.20 Impact Factor
  • Theoretical Chemistry Accounts 01/2015; 134(4):1-14. · 2.14 Impact Factor
  • Theoretical Chemistry Accounts 01/2015; 134(4):1-14. · 2.14 Impact Factor
  • Theoretical Chemistry Accounts 01/2015; 134(4):1-14. · 2.14 Impact Factor
  • Theoretical Chemistry Accounts 01/2015; 134(4):1-14. · 2.14 Impact Factor
  • Theoretical Chemistry Accounts 01/2015; 134(4):1-14. · 2.14 Impact Factor
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    ABSTRACT: The interaction between barrier-to-autointegration factor dimer (BAF2) and LEM domain of emerin (Em(LEM)) was studied by molecular simulation methods. Nonspecific fragment of double-strand DNA molecule was docked with each chain of BAF2 by ZDOCK program. The model of DNA2:BAF2:Em(LEM) was thus constructed. The mutant Gly25Glu of BAF2 was manually constructed to explore the detailed effect of the mutation on the binding of BAF2 and Em(LEM). It has been experimentally suggested that point mutation Gly25Glu can disturb the binding between BAF2 and Em(LEM). Then, molecular dynamics (MD) simulations were performed on DNA2:BAF2(WT):Em(LEM) and DNA2:BAF2(MT):Em(LEM) complexes. 30 ns trajectories revealed that the trajectory fluctuations of MT complex are more violent than that of the WT complex. Further, the binding free energy analysis showed that the electronegative residues Asp57, Glu61 and Asp65 from chain A, glu36 from chain B of BAF2 mainly contribute to interact with Em(LEM). Besides, a stable pi-pi stack between trp62 and phe39 from BAF2(WT) chain B is destroyed by Glu25 in BAF2(MT). As a result, trp62 forms an interaction with glu25, and phe39 converts to strengthen affinity to Em(LEM). On the other hand, Trp62 from chain A also forms a strong interaction with MT Glu25. Thus, with the docking of DNA, BAF2(MT) has higher affinity with Em(LEM) than BAF2(WT).
    Computational Biology and Chemistry 12/2014; 53. DOI:10.1016/j.compbiolchem.2014.09.007 · 1.60 Impact Factor
  • Xi Chen, Chui-Peng Kong, Fu-Quan Bai, Hong-Xing Zhang
    Journal of Physical Organic Chemistry 12/2014; 27(12):973-980. DOI:10.1002/poc.3384 · 1.23 Impact Factor
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    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). DOI:10.1080/08927022.2013.854894 · 1.12 Impact Factor
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    ABSTRACT: Uranyl complexes, [(UO2)(py)F4]2– (1a, py = pyridine), [(UO2)(py)3(cis-F)2] (1a′), [(UO2)(py)5]2+ (1a″), [(UO2)(bpy)F3]– (2a, bpy = 2,2′-bipyridine), [(UO2)(tpy)F2] (3a, tpy = 2,2′:6′2″-terpyridine) and [(UO2)(qpy)F]+ (4a, qpy = 2,2′:6′,2″:6″,2‴-quaterpyridine) have been examined using scalar relativistic density functional theory (DFT). It is shown that both increasing the monopyridyl number (from 1a to 1a′ and 1a″) and extending the pyridyl conjugation (from 1a to 2a, 3a and 4a) are capable of tuning electronic structures of uranyl complexes. Unlike those of 1a, for instance, 4a is featured with π(qpy) character of HOMO and HOMO-1, and its σ(U=O) bond is greatly stabilized to form HOMO-2; and more π∗(qpy)-type orbitals insert between U(f)-based and π∗(U=O) unfilled orbitals. For comparison, four-fold uranyl complexes with one less equatorial fluorine ligand ([(UO2)(py)F3]– (1b), [(UO2)(bpy)F2] (2b), [(UO2)(tpy)F]+ (3b) and [(UO2)(qpy)]2+ (4b)) were calculated. Both thermodynamic and geometrical results suggest that polypyridyl (such as bpy, tpy and qpy) dioxouranium complexes favor five-coordinated mode in the equatorial plane, whereas four-fold is preferred by the single-pyridyl complex.
    Computational and Theoretical Chemistry 11/2014; DOI:10.1016/j.comptc.2014.11.008 · 1.37 Impact Factor

Publication Stats

1k Citations
607.50 Total Impact Points


  • 2002–2015
    • Jilin University
      • State Key Lab of Theoretical and Computational Chemistry
      Yung-chi, Jilin Sheng, China
  • 2012
    • Harbin Institute of Technology at Weihai
      Wei-hai-shih, Shandong Sheng, China
  • 2006
    • Heilongjiang University
      • School of Chemistry and Materials Science
      Harbin, Heilongjiang Sheng, China
  • 2004
    • Northeast Normal University
      Hsin-ching, Jilin Sheng, China
  • 2003
    • The University of Hong Kong
      • Department of Chemistry
      Hong Kong, Hong Kong