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

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

李皎^{1, 2},
徐艳¹,
许旋¹,
徐志广^1, ,

1.
华南师范大学化学学院//教育部环境理论化学重点实验室, 广州 510006
2.
珠峰实验学校, 珠海 519000

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
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- PDF下载量: 28
- 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

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

LI Jiao^{1, 2},
XU Yan¹,
XU Xuan¹,
XU Zhiguang^{1
, ,}

1.
MOE Key Laboratory of Theoretical Chemistry of Environment//School of Chemistry, South China Normal University Guangzhou 510006, China
2.
Zhufeng Shiyan School, Zhuhai 519000, China

摘要

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.
- 密度泛函理论 /
- 咔咯锰(III)配合物 /
- 轴向配位
Abstract: The axial coordination between Tris(pentafluorophenyl)corrole (TPFC)Mn(Ⅲ) and DNA bases was studied with the DFT/B3LYP method. The results showed that different coordination atoms of the same base led to different degrees of coordination binding with (TPFC)Mn(Ⅲ). The O atoms exhibited stronger coordination binding ability than the N atoms. The interaction between (TPFC)Mn(Ⅲ) and A = T or C≡G base pairs of DNA occurred mainly through intercalation mode. Whether intercalation or external binding, the coordination ability of adenine (A) or guanine (G) was stronger than that of thymine (T) or cytosine (C) for A≡T or C≡G base pair.
- density functional theory /
- manganese corrole /
- axial coordination

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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)

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图 2 (TPFC) Mn(Ⅲ)(L)的优化几何结构

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

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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)

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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

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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
项目	GN1	GN2	GO3	AN1	AN2	AN3	CN1	CO2	TO1	TO2
d_Mn_—₄_N/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
d_Mn_—_L/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：d_Mn_—_4N为Mn原子与(TPFC)Mn(Ⅲ)中心平面环的距离；d_Mn_—_L为Mn原子与L的配位键长.

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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
项目	GN1	GN2	GO3	AN1	AN2	AN3	CN1	CO2	TO1	TO2
ΔQ_L	0.166	0.120	0.167	0.134	0.136	0.151	0.178	0.183	0.133	0.178
WI_Mn_-L	0.108	0.100	0.127	0.111	0.112	0.116	0.106	0.135	0.121	0.124
注：WI_Mn_-L为配位原子和Mn原子之间的韦伯键级；ΔQ_L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).

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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

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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
项目	AT1	AT2	AT3	AT4	AT5	AT6
d_Mn_—O/nm	0.232 1	—	—	—	0.261 3	0.264 1
d_Mn_—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：d_Mn_—_O为Mn原子与O原子的配位键长；d_Mn_—_N为Mn原子与咔咯平面环上4个N原子之间的平均距离.

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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
项目	GC1	GC2	GC3	GC4	GC5	GC6
d_Mn_—O/nm	0.220 4	0.220 2	—	—	0.221 1	—
d_Mn_—N/nm	—	—	0.243 9	0.243 4	—	—
ΔE/(kJ·mol^-1)	-71.31	-68.73	-45.87	-50.76	-61.13	23.23

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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
项目	AT1	AT3	AT5	GC1	GC4	GC5
ΔQ_L	0.137	0.146	0.241	0.156	0.200	0.214
Q_A/Q_G	0.036	0.175	0.149	0.137	0.005	0.003
ΔQ_A/ΔQ_G	0.017	0.156	0.130	0.192	0.060	0.058
Q_T/Q_C	0.101	-0.029	0.092	0.019	0.195	0.211
ΔQ_T/ΔQ_C	0.120	-0.010	0.111	-0.036	0.140	0.156
注：ΔQ_L、ΔQ_A、ΔQ_G、ΔQ_T和ΔQ_C分别代表碱基对、碱基A、G、T和C配位前后的电荷变化量.

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