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甘氨酸精氨酸二肽的结构计算和二肽气相最低能构象模型
杨闿祎,杨兵,林子敬*
作者单位E-mail
杨闿祎 中国科学技术大学物理系苏州纳米科技协同创新中心合肥微尺度物质科学国家实验室(筹)合肥 230026  
杨兵 中国科学技术大学物理系苏州纳米科技协同创新中心合肥微尺度物质科学国家实验室(筹)合肥 230026  
林子敬* 中国科学技术大学物理系苏州纳米科技协同创新中心合肥微尺度物质科学国家实验室(筹)合肥 230026 zjlin@ustc.edu.cn 
摘要:
研究了气相下的甘氨酸精氨酸二肽体系.在考虑三种异构体内轴转动时对势能面进行了系统采样.大量的初始构型经PM3、 HF/3-21G*、 BHandHLYP/6-31G*及BHandHLYP/6-311++G**方法逐级优化获取了最终的稳定构型,低能的结构进一步运用BHandHLYP、cam-B3LYP、 B97D及MP2方法在6-311++G(3df,3pd)基组下进行了单点能计算.计算了重要构象的转动常量、偶极矩、垂直电离能、温度分布及红外光谱.最终数据表明,气相GlyArg主要以电中性的状态存在,参考所有的氨基酸及部分二肽的稳定结构特征,结合各类氨基酸的疏水性,归纳出了各种不同二肽的最低能构象是中性或双电性构型的理论模型.
关键词:  势能面  氨基酸  寡肽  构象数据  红外光谱  结构模型
DOI:10.1063/1674-0068/28/cjcp1410197
分类号:
基金项目:
Computational Exploration of Conformations of Glycine-Arginine and a Deduced Model on Global Minimum Configurations of Dipeptides in Gas Phase
Kai-yi Yang,Bing Yang,Zi-jing Lin*
Abstract:
An extensive computational study on the conformations of gaseous dipeptide glycinearginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface (PES) of GlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G*, BHandHLYP/6-31G*, and BHandHLYP/6-311++G** in order to reliably find the low energy conformations. The conformational energies were finally determined with the methods of BHandHLYP, camB3LYP, B97D, and MP2 using the basis set of 6-311++G(3df,3pd). The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.
Key words:  Potential energy surface  Amino acid  Oligopeptide  Conformation data  IR spectrum  Structural model