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Structures and Stability of Complexes Ca+ -RNA Nucleic Acid Bases
Zhang Xingchu1,2, Hu Yihua*3, Fang Yun3, Chen Li3, Wu Hua3, Wang Xiaojuan3
1.Faculty of Applied Physics, Guangdong University of Technology, Guangzhou 510090;2.Department of Electrochanical Engineering, College of Science and Trade, Guangzhou University, Guangzhou 511442;3.Faculty of Applied Physics,Guangdong University of Technology, Guangzhou 510090
Abstract:
Gas-phase metal ion affinities and optimized structures of RNA nucleic acid bases for the Ca+ were determined at a density functional level employing the hybrid B3LYP exchange correlation potential in connection with the 6-311+G(2df,2p) basis set. All the molecular complexes, obtained by the interaction between several low-lying tautomers of RNA nucleic acid and Ca+ on the different binding sites, were considered. For Cytosine, the most stable complex was obtained starting from the most stable tautomer of the free nucleic acid base tautomers. As to thymine, the bond energy of the ion with the most stable tautomer of the free nucleic acid base is the weakest among the three tautomer’s complexes, and that of the ion with least stable tautomer of the free nucleic acid base is the strongest . Uracil is similar to thymine. The two kinds of relation, bond energy and total energy for the complex, are in disagreement, as the metal affinities of RNA bases for the Ca+ depend on binding sites, and total energy of complex (Ca+-RNA base) relies on all atoms and their relative positions in the complex.
Key words:  DFT, RNA, Pyrimidine, Stability, Metal ion affinity
FundProject:
复合物Ca+-RNA碱基的结构与稳定性
张兴初,胡义华*,方允,陈丽,武华,王小涓
1.广东工业大学,应用物理学院,广州,510090;2.广州大学科技贸易技术学院机电系,广州,511442
摘要:
用密度泛函理论(DFT)中的杂化密度泛函B3LYP方法,在6-311+G(2df,2p)基组水平上,确定了RNA碱基与Ca+的气相金属离子亲和能和复合物的优化结构.通过考虑Ca+作用于RNA碱基互变异构体的不同位置,获得了所有稳定的复合物.对于胞核嘧啶,最稳定的复合物起源于最稳定的分子互变异构体;对于胸腺嘧啶,最稳定的分子互变异构体形成的复合物的键能最小,而最不稳定的互变异构体形成的复合物键能最强;尿嘧啶的情形与胸腺嘧啶相似.在互变异构体复合物中,键能是依赖于金属离子成键的位置,而总能量取决于全部的原子和
关键词:  DFT  RNA  嘧啶  金属离子亲和能  稳定性
DOI:10.1088/1674-0068/18/4/537-540
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