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 calculations, 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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Supported by the National Natural Science Foundation of China (Grant No. 30470410) and the Science and Technology Development Foundation of Shanghai (Grant No. 03JC14070)
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Li, C., Zheng, H. & Wang, X. The equivalent potential of water molecules for electronic structure of lysine. SCI CHINA SER G 50, 15–30 (2007). https://doi.org/10.1007/s11433-007-0003-4
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DOI: https://doi.org/10.1007/s11433-007-0003-4