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2018, Vol.91, No.9

1451-1456
Selected Paper

A Theoretical Study on Redox Potential and pKa of [2Fe-2S] Cluster Model from Iron-Sulfur Proteins

Isman Kurniawan ,*1,2Kazutomo Kawaguchi ,1Mitsuo Shoji ,3Toru Matsui ,4Yasuteru Shigeta ,*3 and Hidemi Nagao 1
1Division of Mathematical and Physical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
2School of Computing, Telkom University, Terusan Buah Batu, Bandung, 40257 Indonesia
3Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
4College of Chemistry, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
https://doi.org/10.1246/bcsj.20180116

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Abstract

Iron-sulfur proteins are essential in several biological processes, such as electron transfers in photosystems and respiratory chains. The range of redox potentials of these proteins are so wide that many substrates can interact with them. Thus, the redox potentials of the iron-sulfur proteins are crucial to facilitate the process. This study aims to investigate the redox potential of iron-sulfur proteins with [2Fe-2S] core by using two typical exchange-correlation functionals in density functional theory (DFT), i.e., B3LYP and M06, with and without the diffuse function. Since it involves transition metals, several types of spin approximation were also explored, such as high spin (HS), low spin (LS), approximated spin projection (AP), and J coupling parameter (JC) methods. We found that the diffuse function contributes to improving the accuracy. We also found that M06 functional produced more accurate results than B3LYP. The best result is obtained for AP UM06/6-31++G(d,p) with the absolute error of 0.01 V.

figure

The redox potential and pKa value of iron-sulfur cluster are investigated by density functional theory (DFT). The results are discussed in the relation of calculation method and spin approximation. We found the contribution of DFT functional and diffuse function in improving the accuracy. The method of AP UM06/6-31++G(d,p) produce the best result with the absolute error of 0.01 V.

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