留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

三-(五氟苯基)咔咯锰配合物与DNA碱基的相互作用理论研究

李皎 徐艳 许旋 徐志广

李皎, 徐艳, 许旋, 徐志广. 三-(五氟苯基)咔咯锰配合物与DNA碱基的相互作用理论研究[J]. 华南师范大学学报(自然科学版), 2021, 53(1): 23-28. doi: 10.6054/j.jscnun.2021004
引用本文: 李皎, 徐艳, 许旋, 徐志广. 三-(五氟苯基)咔咯锰配合物与DNA碱基的相互作用理论研究[J]. 华南师范大学学报(自然科学版), 2021, 53(1): 23-28. doi: 10.6054/j.jscnun.2021004
LI Jiao, XU Yan, XU Xuan, XU Zhiguang. A Theoretical Study of the Interaction between Tris(pentafluorophenyl)corrole Mn(Ⅲ) and DNA Bases[J]. Journal of South China normal University (Natural Science Edition), 2021, 53(1): 23-28. doi: 10.6054/j.jscnun.2021004
Citation: LI Jiao, XU Yan, XU Xuan, XU Zhiguang. A Theoretical Study of the Interaction between Tris(pentafluorophenyl)corrole Mn(Ⅲ) and DNA Bases[J]. Journal of South China normal University (Natural Science Edition), 2021, 53(1): 23-28. doi: 10.6054/j.jscnun.2021004

三-(五氟苯基)咔咯锰配合物与DNA碱基的相互作用理论研究

doi: 10.6054/j.jscnun.2021004
基金项目: 

国家自然科学基金项目 21671068

广东省自然科学基金项目 S2012010008763

详细信息
    通讯作者:

    徐志广,Email: chzgxu@scnu.edu.cn

  • 中图分类号: O641

A Theoretical Study of the Interaction between Tris(pentafluorophenyl)corrole Mn(Ⅲ) and DNA Bases

  • 摘要: 采用DFT/B3LYP方法对三-(五氟苯基)咔咯锰配合物(TPFC)Mn(Ⅲ)与DNA的4种碱基以及碱基对的轴向配位性质进行了理论研究. 计算结果表明:以相同碱基的不同原子作为配位原子时,与(TPFC)Mn(Ⅲ)的配位能力不同,其中氧原子的配位能力强;(TPFC)Mn(Ⅲ)主要以插入的方式与A=T和C≡G碱基对结合;无论是插入结合,还是外部结合,A=T碱基对中A的配位能力强于T,C≡G碱基对中G的配位能力强于C.
  • 图  1  A、C、G、T和(TPFC)Mn(Ⅲ)(L)的分子结构

    注:L为A、T、C、G.

    Figure  1.  The molecular structure of A, C, G, T and (TPFC)Mn(Ⅲ)(L)

    图  2  (TPFC) Mn(Ⅲ)(L)的优化几何结构

    Figure  2.  The optimized geometric structures of (TPFC)Mn(Ⅲ)(L)

    图  3  (TPFC) Mn(Ⅲ)(A=T)和(TPFC)Mn(Ⅲ)(C≡G)的分子结构

    注:L为A=T或C≡G;L1和L2分别为A、T(或C、G).

    Figure  3.  The molecular structures of (TPFC)Mn(Ⅲ)(A=T) and (TPFC)Mn(Ⅲ)(C≡G)

    图  4  (TPFC) Mn(Ⅲ)与DNA碱基对的优化几何结构

    Figure  4.  The optimized geometric structures of (TPFC)Mn(Ⅲ) and base pairs in the DNA

    表  1  (TPFC) Mn(Ⅲ)(L)的部分几何结构参数和结合能

    Table  1.   The selected geometrical parameters and binding energy of (TPFC)Mn(Ⅲ)(L)

    项目 模型分子
    GN1 GN2 GO3 AN1 AN2 AN3 CN1 CO2 TO1 TO2
    dMn4N/nm 0.027 6 0.024 4 0.030 3 0.028 2 0.029 1 0.029 2 0.025 1 0.032 7 0.029 2 0.029 3
    dMnL/nm 0.238 7 0.247 2 0.219 7 0.238 3 0.236 7 0.232 1 0.245 9 0.217 3 0.224 4 0.224 0
    ΔE/(kJ·mol-1) -41.89 -36.17 -57.77 -43.07 -43.40 -45.19 -40.45 -68.39 -52.58 -55.15
    注:dMn4N为Mn原子与(TPFC)Mn(Ⅲ)中心平面环的距离;dMnL为Mn原子与L的配位键长.
    下载: 导出CSV

    表  2  (TPFC) Mn(Ⅲ)(L)的NPA电荷和韦伯键级

    Table  2.   The NPA charge and Wiberg bond Index (WI) of (TPFC)Mn(Ⅲ)(L)

    项目 模型分子
    GN1 GN2 GO3 AN1 AN2 AN3 CN1 CO2 TO1 TO2
    ΔQL 0.166 0.120 0.167 0.134 0.136 0.151 0.178 0.183 0.133 0.178
    WIMn-L 0.108 0.100 0.127 0.111 0.112 0.116 0.106 0.135 0.121 0.124
    注:WIMn-L为配位原子和Mn原子之间的韦伯键级;ΔQL为碱基与(TPFC)Mn(Ⅲ)配位前后电荷的变化量(碱基与(TPFC)Mn(Ⅲ)配位前电荷为0).
    下载: 导出CSV

    表  3  (TPFC) Mn(Ⅲ)(L)的二级微扰稳定化能

    Table  3.   The second-order perturbation stabilition energy of (TPFC)Mn(Ⅲ)(L)

    配合物 轨道 配体NBO 受体NBO E(2)/ (kJ·mol-1) ΣE(2)/ (kJ·mol-1)
    GN1 α LP(N) LP*(Mn) 27.61 103.97
    β LP(N) LP*(Mn) 76.36
    GN2 α LP(N) LP*(Mn) 28.37 82.34
    β LP(N) LP*(Mn) 53.97
    GO3 α LP(O) LP*(Mn) 36.32 167.82
    β LP(O) LP*(Mn) 83.76
    LP(O) BD*(O—Mn) 47.74
    AN1 α LP(N) LP*(Mn) 31.59 116.19
    β LP(N) LP*(Mn) 84.60
    AN2 α LP(N) LP*(Mn) 31.88 118.24
    β LP(N) LP*(Mn) 86.36
    AN3 α LP(N) LP*(Mn) 33.93 124.64
    β LP(N) LP*(Mn) 90.71
    CN1 α LP(N) LP*(Mn) 31.55 96.91
    β LP(N) LP*(Mn) 65.06
    CO2 α LP(O) LP*(Mn) 43.47 186.98
    β LP(O) LP*(Mn) 143.51
    TO1 α LP(O) LP*(Mn) 33.89 136.69
    β LP(O) LP*(Mn) 102.80
    TO2 α LP(O) LP*(Mn) 34.98 141.21
    β LP(O) LP*(Mn) 106.23
    下载: 导出CSV

    表  4  (TPFC) Mn(Ⅲ)(A=T)的部分几何结构参数和结合能

    Table  4.   The selected geometrical parameters and binding energy of (TPFC)Mn(Ⅲ)(A=T)

    项目 模型分子
    AT1 AT2 AT3 AT4 AT5 AT6
    dMn—O/nm 0.232 1 0.261 3 0.264 1
    dMn—N/nm 0.245 8 0.238 7 0.253 2 0.256 4
    ΔE/(kJ·mol-1) -3.65 12.72 -16.64 30.03 -56.72 -46.08
    注:dMnO为Mn原子与O原子的配位键长;dMnN为Mn原子与咔咯平面环上4个N原子之间的平均距离.
    下载: 导出CSV

    表  5  (TPFC) Mn(Ⅲ)(C≡G)的部分几何结构参数和结合能

    Table  5.   The selected geometrical parameters and binding energy of (TPFC)Mn(Ⅲ)(C≡G)

    项目 模型分子
    GC1 GC2 GC3 GC4 GC5 GC6
    dMn—O/nm 0.220 4 0.220 2 0.221 1
    dMn—N/nm 0.243 9 0.243 4
    ΔE/(kJ·mol-1) -71.31 -68.73 -45.87 -50.76 -61.13 23.23
    下载: 导出CSV

    表  6  (TPFC) Mn(Ⅲ)(A=T)和(TPFC)Mn(Ⅲ)(C≡G)的NPA电荷

    Table  6.   The NPA charge of (TPFC)Mn(Ⅲ)(A=T) and (TPFC)Mn(Ⅲ)(C≡G)

    项目 模型分子
    AT1 AT3 AT5 GC1 GC4 GC5
    ΔQL 0.137 0.146 0.241 0.156 0.200 0.214
    QA/QG 0.036 0.175 0.149 0.137 0.005 0.003
    ΔQAQG 0.017 0.156 0.130 0.192 0.060 0.058
    QT/QC 0.101 -0.029 0.092 0.019 0.195 0.211
    ΔQTQC 0.120 -0.010 0.111 -0.036 0.140 0.156
    注:ΔQL、ΔQA、ΔQG、ΔQT和ΔQC分别代表碱基对、碱基A、G、T和C配位前后的电荷变化量.
    下载: 导出CSV
  • [1] SONG Y, WU Q, YANG P, et al. DNA Binding and cleavage activity of Ni(Ⅱ) complex with all-trans retinoic acid[J]. Journal of Inorganic Biochemistry, 2006, 100(10): 1685-1691. doi: 10.1016/j.jinorgbio.2006.06.001
    [2] GUROVA K. New hopes from old drugs: revisiting DNA-binding small molecules as anticancer agents[J]. Future Oncology, 2009, 5(10): 1685-1704. doi: 10.2217/fon.09.127
    [3] ZHENG X H, CHEN H Y, TONG M L, et al. Platinum squares with high selectivity and affinity for human telomeric G-quadruplexes[J]. Chemical Communications, 2012, 48 (61): 7607-7609. doi: 10.1039/c2cc32942e
    [4] DONG X, WANG X, LIN M, et al. Promotive effect of the platinum moiety on the DNA cleavage activity of copper-based artificial nucleases[J]. Inorganic Chemisty, 2010, 49 (5): 2541-2549. doi: 10.1021/ic100001x
    [5] JOYNER J C, REICHFIELD J, COWAN J A. Factors influencing the DNA nuclease activity of iron, cobalt, nickel, and copper chelates[J]. Journal of the American Chemical Society, 2011, 133(39): 15613-15626. doi: 10.1021/ja2052599
    [6] SANGEETHAGOWDA K R, MATHEW B B, SUDHAMANI C N, et al. Mechanism of DNA binding and cleavage[J]. Journal of Biomedicine and Biotechnology, 2014, 2(1): 1-9. http://www.sciepub.com/reference/31151
    [7] GERSHMAN Z, GOLDBERG I, GROSS Z. DNA binding and catalytic properties of positively charged corroles[J]. Angewandte Chemie(International Edition), 2007, 46(23): 4320-4324. doi: 10.1002/anie.200700757
    [8] 王家敏, 史蕾, 刘海洋. 咔咯及其金属配合物与DNA的作用和抗肿瘤活性[J]. 化学进展, 2015, 27(6): 755-762. https://www.cnki.com.cn/Article/CJFDTOTAL-HXJZ201506011.htm

    WANG J M, SHI L, LIU H Y. The interaction of corrole and its metal complex with DNA and their anti-tumor activity[J]. Progress in Chemistry, 2015, 27(6): 755-762. https://www.cnki.com.cn/Article/CJFDTOTAL-HXJZ201506011.htm
    [9] FIEL R J. Porphyrin-Nucleic acid interactions: a review[J]. Journal of Biomolecular Structure & Dynamics, 1989, 6(6): 1259-1274.
    [10] VAISHNAVI E, RENGANATHAN R. "Turn-on-off-on" fluorescence switching of quantum. dots-cationic porphyrin nanohybrid: a sensor for DNA[J]. Analyst, 2013, 139(1): 225-234. http://europepmc.org/abstract/med/24187682
    [11] GHOSH S, UCER K B, JR D'AGOSTINO R, et al. Non-covalent assembly of meso-tetra-4-pyridyl porphine with single-stranded DNA to form nano-sized complexes with hydrophobicity-dependent DNA release and anti-tumor activity[J]. Nanomed-Nanotechnol, 2014, 10(2): 451-461. doi: 10.1016/j.nano.2013.07.019
    [12] ETHIRAJAN M, CHEN Y, JOSHI P, et al. The role of porphyrin chemistry in tumor imaging and photodynamic therapy[J]. Chemical Society Reviews, 2010, 40(1): 340-362. doi: 10.1002/chin.201117269/full
    [13] LANG K, MOSINGER J, WAGNEROVA D M, et al. Photophysical properties of porphyrinoid sensitizers non-covalently bound to host molecules; models for photodynamic therapy[J]. Coordination Chemistry Reviews, 2004, 248(3): 321-350. http://www.sciencedirect.com/science/article/pii/S0010854504000293
    [14] SHI L, LIU H Y, SI L P, et al. The heavy atom effect on photocleavage of DNA by mono-hydroxyl halogenated corroles[J]. Chinese Chemical Letters, 2010, 21(3): 373-375. doi: 10.1016/j.cclet.2009.11.027
    [15] 刘海洋, 刘兰英, 张雷, 等. 锰(Ⅲ)Corrole配合物催化DNA氧化断裂[J]. 高等学校化学学报, 2007, 28(9): 1628-1630. doi: 10.3321/j.issn:0251-0790.2007.09.031

    LIU H Y, LIU L Y, ZHANG L, et al. Oxidative DNA cleavage catalyzed by Mn(Ⅲ) corrole[J]. Chemistry Journal of Chinese universities, 2007, 28(9): 1628-1630. doi: 10.3321/j.issn:0251-0790.2007.09.031
    [16] LU J, LIU H Y, SHI L, et al. DNA cleavage mediated by water-soluble manganese corrole[J]. Chinese Chemical Letters, 2011, 22(1): 101-104. doi: 10.1016/j.cclet.2010.09.005
    [17] 徐艳, 章小慧, 徐志广, 等. 取代基和配体的负离子效应对(TPFC)Mn(V)O轴向配位作用的影响[J]. 华南师范大学学报(自然科学版), 2019, 51(1): 28-34. doi: 10.6054/j.jscnun.2019006

    XU Y, ZHANG X H, XU Z G, et al. Effects of substituents and anionic ligands for axial coordination of manganese(Ⅴ)-oxo corrole complex[J]. Journal of South China Normal University(Natural Science Edition), 2019, 51(1): 28-34. doi: 10.6054/j.jscnun.2019006
    [18] GONG L Z, XU Z G, XU X, et al. Axial coordination behavior of corrole MnⅢ and MnVO complexes with N-based ligands[J]. Acta Physico-Chimica Sinica, 2014, 30 (2), 265-272. doi: 10.3866/PKU.WHXB201312181
    [19] HE J, XU Z G, XU X, et al. Reactivity of (oxo)manganese(V) corroles in one-electron redox state: insights from conceptual DFT and transition state calculations[J]. Journal of Porphyrins and Phthalocyanines, 2013, 17: 1196-1203. doi: 10.1142/S1088424613500971
    [20] MULLIKEN R S. Electronic population analysis on lcaomo molecular wave functions[J]. The Journal of Chemical Physics, 1955, 23(10): 1833-1840. doi: 10.1063/1.1740588
    [21] REED A E, CURTISS L A, WEINHOLD F. Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint[J]. Chemical Reviews, 1988, 88: 899-926. doi: 10.1021/cr00088a005
    [22] FRISCH M J, TRUCKS G W, SCHLEGEI H B, et al. Gaussian 03, Revision A.01[CP]. Pittsburgh: Gaussian Inc., 2003.
  • 加载中
图(4) / 表(6)
计量
  • 文章访问数:  314
  • HTML全文浏览量:  91
  • PDF下载量:  26
  • 被引次数: 0
出版历程
  • 收稿日期:  2020-02-23
  • 网络出版日期:  2021-03-24
  • 刊出日期:  2021-02-25

目录

    /

    返回文章
    返回