| The equivalent potential of water molecules for electronic structure of lysine |
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| 引用本文： | LI ChunJie,ZHENG HaoPing & WANG XueMei Pohl Institute of Solid State Physics,Tongji University,Shanghai 200092,China. The equivalent potential of water molecules for electronic structure of lysine[J]. 中国科学G辑(英文版), 2007, 50(1): 15-30. DOI: 10.1007/s11433-007-0003-4 |
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| 作者姓名： | LI ChunJie ZHENG HaoPing & WANG XueMei Pohl Institute of Solid State Physics Tongji University Shanghai 200092 China |
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| 作者单位： | LI ChunJie，ZHENG HaoPing & WANG XueMei Pohl Institute of Solid State Physics，Tongji University，Shanghai 200092，China |
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| 基金项目： | 国家自然科学基金;上海市科技发展基金 |
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| 摘 要： | In order to get more reliable electronic structures of proteins in aqueous solution, it is necessary to construct a potential of water molecules for protein’s electronic structure calculation. The lysine is a hydrophilic amino acid. It is positively charged (Lys+) in neutral water solution. The first-principles, all-electron, ab initio calcula-tions, based on the density functional theory, have been performed to construct such an equivalent potential of water molecules for lysine (Lys+). The process consists of three parts. First, the electronic structure of the cluster containing Lys+ and water molecules is calculated. By adjusting the positions of water molecules, the geometric structure of the cluster having minimum total energy is determined. Then, based on the structure, the electronic structure of Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method. Finally, the electronic structure of Lys+ with the potential of dipoles is calculated. The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules. Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained. The major effect of water molecules on lysine’s electronic structure is raising the occupied eigenvalues about 0.5032 eV, and broadening energy gap 89%. The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential.
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| 收稿时间： | 2005-08-08 |
| 修稿时间： | 2006-08-23 |
The equivalent potential of water molecules for electronic structure of lysine |
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| Li ChunJie,Zheng HaoPing,Wang XueMei. The equivalent potential of water molecules for electronic structure of lysine[J]. Science in China(Physics Astronomy), 2007, 50(1): 15-30. DOI: 10.1007/s11433-007-0003-4 |
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| Authors: | Li ChunJie Zheng HaoPing Wang XueMei |
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| Affiliation: | Pohl Institute of Solid State Physics,Tongji University,Shanghai 200092,China |
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| Abstract: | In order to get more reliable electronic structures of proteins in aqueous solution,it is necessary to construct a potential of water molecules for protein's electronic structure calculation.The lysine is a hydrophilic amino acid.It is positively charged(Lys+)in neutral water solution.The first-principles,all-electron,ab initio calcula-tions,based on the density functional theory,have been performed to construct such an equivalent potential of water molecules for lysine(Lys+).The process consists of three parts.First,the electronic structure of the cluster containing Lys+ and water molecules is calculated.By adjusting the positions of water molecules,the geometric structure of the cluster having minimum total energy is determined.Then,based on the structure,the electronic structure of Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding(SCCE)method.Finally,the electronic structure of Lys+ with the potential of dipoles is calculated.The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules.Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained.The major effect of water molecules on lysine's electronic structure is raising the occupied eigenvalues about 0.5032 eV,and broadening energy gap 89%.The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential. |
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| Keywords: | lysine electronic structure water molecule free cluster calculation self-consistent cluster-embedding calculation |
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