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Ab initio simulation of the effect of the potential of water on the electronic structure of arginine

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Abstract

As a part of the task of constructing the equivalent potential of water in order to obtain a reliable electronic structure for a protein, the equivalent potential of water for an arginine molecule was constructed by performing first-principles, all-electron, ab initio calculations. The process consisted of three steps. First, the electronic structure of arginine was calculated using a free cluster calculation. Then, the minimum-energy geometric structure of the system Arg++9H2O was found using free cluster calculations. Then, based on the optimized geometric structure of the Arg++9H2O system, the electronic structure of Arg+ in the potential of water was calculated using the SCCE method. Finally, by performing SCCE calculations, the effect of water on the electronic structure of Arg+ was simulated with dipoles. The results show that the effect of water on the electronic structure of Arg+ is to broaden the energy gap tenfold, and to increase the eight eigenvalues below the HOMO by about 0.0546 Ry on average. The water potential can be accurately simulated using dipoles.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (grant no. 30970694). The work was also supported by the Shanghai Supercomputer Center. The calculations were performed on the supercomputer DAWN 5000A of the Shanghai Supercomputer Center of China.

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  1. Physics Department, Tongji University, Shanghai, 200092, China

    Xingrong Wang & Haoping Zheng

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  1. Xingrong Wang
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  2. Haoping Zheng
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Correspondence to Haoping Zheng.

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Wang, X., Zheng, H. Ab initio simulation of the effect of the potential of water on the electronic structure of arginine. J Mol Model 18, 859–870 (2012). https://doi.org/10.1007/s00894-011-1125-1

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