中国物理B ›› 2009, Vol. 18 ›› Issue (5): 1968-1978.doi: 10.1088/1674-1056/18/5/040

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Simulation of water potential for the electronic structureof serine

王兴荣, 郑浩平   

  1. Pohl Institute of Solid State Physics, Tongji University, Shanghai 200092, China
  • 收稿日期:2008-07-28 出版日期:2009-05-20 发布日期:2009-05-20
  • 基金资助:
    Project supported by the National Natural Science Foundation of China (Grant No 30470410) and the Science and Technology Development Foundation of Shanghai, China (Grant No 03JC14070).

Simulation of water potential for the electronic structure of serine

Wang Xing-Rong(王兴荣) and Zheng Hao-Ping(郑浩平)   

  1. Pohl Institute of Solid State Physics, Tongji University, Shanghai 200092, China
  • Received:2008-07-28 Online:2009-05-20 Published:2009-05-20
  • Supported by:
    Project supported by the National Natural Science Foundation of China (Grant No 30470410) and the Science and Technology Development Foundation of Shanghai, China (Grant No 03JC14070).

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摘要： First-principles, all-electron, \textit{ab initio} calculations have been performed to construct an equivalent water potential for the electronic structure of serine (Ser) in solution. The calculation is composed of three steps. The first step is to search for the configuration of the Ser + NH2O system with a minimum energy. The second step is to calculate the electronic structure of Ser with the water molecule potential via the self-consistent cluster-embedding method (SCCE), based on the result obtained in the first step. The last step is to calculate the electronic structure of Ser with the dipole potential after replacing the water molecules with dipoles. The results show that the occupied states of Ser are raised by about 0.017~Ry on average due to the effect of water. The water effect can be successfully simulated by using the dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method.

关键词: serine, electronic structure, water, self-consistent cluster-embedding calculation

Abstract: First-principles, all-electron, ab initio calculations have been performed to construct an equivalent water potential for the electronic structure of serine (Ser) in solution. The calculation is composed of three steps. The first step is to search for the configuration of the Ser + nH2O system with a minimum energy. The second step is to calculate the electronic structure of Ser with the water molecule potential via the self-consistent cluster-embedding method (SCCE), based on the result obtained in the first step. The last step is to calculate the electronic structure of Ser with the dipole potential after replacing the water molecules with dipoles. The results show that the occupied states of Ser are raised by about 0.017~Ry on average due to the effect of water. The water effect can be successfully simulated by using the dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method.

Key words: serine, electronic structure, water, self-consistent cluster-embedding calculation

中图分类号:  (Properties of solutions of macromolecules)

  • 87.15.N-
87.15.B- (Structure of biomolecules) 87.14.E- (Proteins) 36.20.Kd (Electronic structure and spectra)