DNA碱基(对)及其Zn2+复合物对CO2,N2,H2小分子的吸附

doi:10.7503/cjcu20140137

摘要/Abstract

摘要：

用M062X/6-31+G^*方法探讨了腺嘌呤(A)、胸腺嘧啶(T)、鸟嘌呤(G)、胞嘧啶(C)及其碱基对(AT, GC)以及Zn²⁺复合物(AAA-Zn²⁺, AAT-Zn²⁺和GGC-Zn²⁺)对混合小分子H₂, N₂, CO₂的吸附情况, 系统研究了其相互作用模式及吸附强度, 预测了常见混合气体分子与碱基(对)及复合物的吸附位置. 研究表明, CO₂倾向于以氢键的形式结合到碱基(对)的氨基氢或亚氨基氢上, 而N₂和H₂分子则倾向于结合到这些碱基(对)的平面π电子上, 以堆垛的形式存在. 根据吸附强度大小, 预测了由这些碱基为骨架合成的金属有机骨架(MOF)吸附材料对小分子的选择性吸附顺序为H₂<N₂<CO₂. 研究表明, 以AT对结合金属Zn²⁺为节点的纯天然碱基对构成的MOF要比实验合成的AA碱基对与Zn²⁺结合的MOF具备更好的吸附和分离性能.

关键词: 碱基对-Zn2+复合物, M062X方法, 吸附, 氢键, 小分子, 金属有机骨架材料

Abstract:

As an intriguing material building block for microporous metal-organic framework(MOF) materials, DNA base(pair) holds usually rigid-ring structures, multiple metal coordination sites, biological compatibility, and molecular recognition as well as self-assembling characteristics that could ultimately translate into interesting material properties. In the present paper, guanine G, cytosine C, adenine A, thymine T, and their pairs GC/AT as well as their Zn²⁺ complexes were selected as models to study their potential behavior of building block to adsorb mixed small molecules H₂, N₂, CO₂ by employing M062X/6-31+G^* method. The interaction modes and strengths as well as potential binding sites were predicted. These results reveal that CO₂ prefers H-bonding to the amino hydrogen(s) or/and imino hydrogen(s) of these bases(pairs), whereas both H₂ and N₂ prefer being adsorbed over the base ring with a π-stacking interaction mode. A comparison for the binding energies of these different small molecules shows that AT is the more potential building block of MOF material than GC and AA, and will adsorb these small molecules hierarchically according to the following order: H₂ < N₂ < CO₂. The result offers theoretical predictions and direction for the experimental synthesis of such MOF materials built by these different base-pair building blocks.

Key words: Base pair-Zn2+ complex, M062X method, Adsorption, Hydrogen bond, Small molecule, Metal-organic framework(MOF) material

中图分类号:

O641

TrendMD:

师帅, 黄曦明, 艾洪奇. DNA碱基(对)及其Zn²⁺复合物对CO₂,N₂,H₂小分子的吸附. 高等学校化学学报, 2014, 35(7): 1492.

SHI Shuai, HUANG Ximing, AI Hongqi. Mechanism Studies on Adsorption of DNA Bases and Base Pair-Zn²⁺ mplexes for CO₂, N₂ and $H 2 †$ . Chem. J. Chinese Universities, 2014, 35(7): 1492.

图/表 6

参考文献 23

[1]	Wu Y., Yang B. H., Li M., Chemistry Online, 2011, 74(9), 1—7
	(吴云, 杨本宏, 李萌. 化学通报, 2011, 74(9), 1—7)
[2]	Yang Q. Y., Liu D. H., Zhong C. L., Acta Chimica Sinca, 2009, 60(4), 805—818
	(阳庆元, 刘大欢, 仲崇立. 化工学报, 2009, 60(4), 805—818)
[3]	Metz B., Davidson O., de Coninck H., Loos M., Meyer L., Cambridge University Press, New York, 2005, 3—15
[4]	Tin P. S., Chung T. S., Ind. Eng. Chem. Res., 2004, 43, 6476—6483
[5]	Lin H., Van Wagner E., Freeman B. D., Toy L. G., Gupta R. P., Science, 2006, 311, 639—642
[6]	Cui Y., Kita H., Okamoto K., J. Mater. Chem., 2004, 14, 924—932
[7]	Farha O. K., Eryazici I., Jeong N. C., Hauser B. G., Wilmer C. E., Sarjeant A. A., Snurr R. Q., Nguyen S. T., Yazaydin A. O., Hupp J. T., J. Am. Chem. Soc., 2012, 134, 15016—15021
[8]	James S. L., Chem. Soc. Rev., 2003, 32, 276—288
[9]	Li J. R., Kuppler R. J., Zhou H. C., Chem. Soc. Rev., 2009, 38, 1477—1504
[10]	Li J. R., Sculley J., Zhou H. C., Chem. Rev., 2012, 112, 869—932
[11]	Kitagawa S., Kitaura R., Noro S. I., Angew. Chem., 2004, 116, 2388—2430
[12]	Kitagawa S., Kitaura R., Noro S. I., Angew. Chem. Int. Ed., 2004, 43, 2334—2375
[13]	An J., Fiorella R. P., Geib S. J., Rosi N. L., J. Am. Chem. Soc., 2009, 131, 8401—8403
[14]	Sivakova S., Rowan S., J. Chem. Soc. Rev., 2005, 34, 9—21
[15]	Vogiatzis K. D., Mavrandonakis A., Klopper W., Froudakis G. E., Chem. Phys. Chem., 2009, 10, 374—383
[16]	Hongqi A., Jinpeng C., Chong Z., J. Phys. Chem. B, 2012, 116, 13624—13636
[17]	Zhao Y., Truhlar D. G., Acc. Chem. Res., 2008, 41, 157—167
[18]	Srinivasadesikan V., Sahu P. K., Lee S. L., J. Phys. Chem. B, 2012, 116, 11173—11179
[19]	Fang H., Kim Y., J. Chem. Theory Comput., 2011, 7, 642—657
[20]	Zhao Y., Truhlar D. G., J. Phys. Chem., 2006, 110, 5121—5129
[21]	Boys S. F., Bernardi F., Mol. Phys., 1970, 19, 553—566
[22]	Frisch M.J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Scalmani G., Barone V., Mennucci B., Petersson G. A., Nakatsuji H., Caricato M., Li X., Hratchian H. P., Izmaylov A. F., Bloino J., Zheng G., Sonnenberg J. L., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Vreven T., Montgomery J. A. Jr., Peralta J. E., Ogliaro F., Bearpark M., Heyd J. J., Brothers E., Kudin K. N., Staroverov V. N., Kobayashi R., Normand J., Raghavachari K., Rendell A., Burant J. C., Iyengar S. S., Tomasi J., Cossi M., Rega N., Millam J. M., Klene M., Knox J. E., Cross J. B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R. E., Yazyev O., Austin A. J., Cammi R., Pomelli C., Ochterski J. W., Martin R. L., Morokuma K., Zakrzewski V. G., Voth G. A., Salvador P., Dannenberg J. J., Dapprich S., Daniels A. D., Farkas O., Foresman J. B., Ortiz J. V., Cioslowski J., Fox D. J., Gaussian 09, Revision A.02, Gaussian Inc.,Wallingford CT, 2009
[23]	Mishra B. K., Arey J. S., Sathyamurthy N., J. Phys. Chem. A, 2010, 114, 9606—9616
	(Ed.: Y, Z)

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
C-H₂1	-5.9	0.014	G-H₂1	-6.6	0.014	GC-H₂1	-6.4	0.014
C-H₂2	-5.5	0.014	G-H₂2	-6.4	0.014	GC-H₂2	-6.2	0.014
C-H₂3	-5.4	0.014	G-H₂3	-6.3	0.014	GC-H₂3	-6.0	0.014
C-H₂4	-4.8	0.015	G-H₂4	-6.2	0.014	GC-H₂4	-5.6	0.022
C-H₂5	-2.5	0.015	G-H₂5	-6.2	0.014
			G-H₂6	-5.8	0.014
			G-H₂7	-2.7	0.014

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
C-H₂1	-5.9	0.014	G-H₂1	-6.6	0.014	GC-H₂1	-6.4	0.014
C-H₂2	-5.5	0.014	G-H₂2	-6.4	0.014	GC-H₂2	-6.2	0.014
C-H₂3	-5.4	0.014	G-H₂3	-6.3	0.014	GC-H₂3	-6.0	0.014
C-H₂4	-4.8	0.015	G-H₂4	-6.2	0.014	GC-H₂4	-5.6	0.022
C-H₂5	-2.5	0.015	G-H₂5	-6.2	0.014
			G-H₂6	-5.8	0.014
			G-H₂7	-2.7	0.014

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
A-H₂1	-6.1	0.014	T-H₂1	-5.5	0.014	AT-H₂1	-5.4	0.014
A-H₂2	-6.1	0.014	T-H₂2	-5.5	0.014	AT-H₂2	-4.6	0.014
A-H₂3	-6.0	0.014	T-H₂3	-5.3	0.014	AT-H₂3	-4.6	0.014
A-H₂4	-5.8	0.014	T-H₂4	-1.5	0.014	AT-H₂4	-3.6	0.014
A-H₂5	-5.6	0.014
A-H₂6	-5.6	0.014
A-H₂7	-4.2	0.014

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
A-H₂1	-6.1	0.014	T-H₂1	-5.5	0.014	AT-H₂1	-5.4	0.014
A-H₂2	-6.1	0.014	T-H₂2	-5.5	0.014	AT-H₂2	-4.6	0.014
A-H₂3	-6.0	0.014	T-H₂3	-5.3	0.014	AT-H₂3	-4.6	0.014
A-H₂4	-5.8	0.014	T-H₂4	-1.5	0.014	AT-H₂4	-3.6	0.014
A-H₂5	-5.6	0.014
A-H₂6	-5.6	0.014
A-H₂7	-4.2	0.014

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
AAA-Zn²⁺-H₂1	-6.6	0.014	AAT-Zn²⁺-H₂1	-6.6	0.014	GGC-Zn²⁺-H₂1	-8.6	0.014
AAA-Zn²⁺-H₂2	-6.2	0.014	AAT-Zn²⁺-H₂2	-6.5	0.014	GGC-Zn²⁺-H₂2	-8.6	0.014
AAA-Zn²⁺-H₂3	-6.0	0.014	AAT-Zn²⁺-H₂3	-6.4	0.014	GGC-Zn²⁺-H₂3	-6.8	0.014
AAA-Zn²⁺-H₂4	-5.6	0.014	AAT-Zn²⁺-H₂4	-6.4	0.014	GGC-Zn²⁺-H₂4	-6.2	0.014
AAA-Zn²⁺-H₂5	-2.8	0.014	AAT-Zn²⁺-H₂5	-5.9	0.014	GGC-Zn²⁺-H₂5	-5.9	0.014
			AAT-Zn²⁺-H₂6	-2.0	0.014	GGC-Zn²⁺-H₂6	-4.7	0.014
						GGC-Zn²⁺-H₂7	-3.9	0.014

DNA碱基(对)及其Zn²⁺复合物对CO₂,N₂,H₂小分子的吸附

Mechanism Studies on Adsorption of DNA Bases and Base Pair-Zn²⁺ mplexes for CO₂, N₂ and $H 2 †$

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 6

参考文献 23

相关文章 15

编辑推荐

Metrics

本文评价

[1]	郇歆宇赖淦强黄悦杨财广. 化学干预N⁶-甲基腺嘌呤修饰的研究进展[J]. 高等学校化学学报, 2022, 43(Album-4): 20220340.
[2]	李玉龙, 谢发婷, 管燕, 刘嘉丽, 张贵群, 姚超, 杨通, 杨云慧, 胡蓉. 基于银离子与DNA相互作用的比率型电化学传感器用于银离子的检测[J]. 高等学校化学学报, 2022, 43(8): 20220202.
[3]	姜宏斌, 代文臣, 张娆, 徐晓晨, 陈捷, 杨光, 杨凤林. Co₃O₄/UiO-66@α-Al₂O₃陶瓷膜对VOCs废气的分离催化性能[J]. 高等学校化学学报, 2022, 43(6): 20220025.
[4]	戴卫, 侯华, 王宝山. 七氟异丁腈负离子结构与反应活性的理论研究[J]. 高等学校化学学报, 2022, 43(6): 20220044.
[5]	郝宏蕾, 孟繁雨, 李若钰, 李迎秋, 贾明君, 张文祥, 袁晓玲. 生物质基氮掺杂多孔炭材料的制备及对水中亚甲基蓝的吸附性能[J]. 高等学校化学学报, 2022, 43(6): 20220055.
[6]	闵婧, 王力彦. 利用三中心氢键限制芳酰胺构象的核磁共振氢谱分析[J]. 高等学校化学学报, 2022, 43(6): 20220084.
[7]	鲁聪, 李振华, 刘金露, 华佳, 李光华, 施展, 冯守华. 一种新的镧系金属有机骨架材料的合成、结构及荧光检测性质[J]. 高等学校化学学报, 2022, 43(6): 20220037.
[8]	张勇, 许俊, 鲍雨, 崔树勋. 非极性有机溶剂对分子内氢键弱化程度的单分子力谱定量研究[J]. 高等学校化学学报, 2022, 43(4): 20210863.
[9]	王红宁, 黄丽, 清江, 马腾洲, 蒋伟, 黄维秋, 陈若愚. 香蒲基生物炭的活化及对VOCs吸附的应用[J]. 高等学校化学学报, 2022, 43(4): 20210824.
[10]	崔韶丽, 张维佳, 邵学广, 蔡文生. 自由能计算揭示苏氨酸对抗冻蛋白与冰晶结合能力的影响[J]. 高等学校化学学报, 2022, 43(3): 20210838.
[11]	陈潇禄, 袁珍闫, 仲迎春, 任浩. 机械球磨制备三苯胺基PAF-106s及C2烃吸附性质[J]. 高等学校化学学报, 2022, 43(3): 20210771.
[12]	孟祥龙, 杨歌, 郭海玲, 刘晨光, 柴永明, 王纯正, 郭永梅. 纳米分子筛的合成及硫化氢吸附性能[J]. 高等学校化学学报, 2022, 43(3): 20210687.
[13]	胡波, 朱昊辰. 双层氧化石墨烯纳米体系中受限水的介电常数[J]. 高等学校化学学报, 2022, 43(2): 20210614.
[14]	靳科研, 白璞, 李小龙, 张佳楠, 闫文付. 新型Mg-Al吸附剂去除压水堆核电厂废水中高浓度硼[J]. 高等学校化学学报, 2022, 43(2): 20210516.
[15]	谭乐见, 仲宣树, 王锦, 刘宗建, 张爱英, 叶霖, 冯增国. β-环糊精的低临界溶解温度现象及其在有序纳米孔道片晶制备中的应用[J]. 高等学校化学学报, 2022, 43(11): 20220405.