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Car-Parinello molecular dynamics simulations of thionitroxide and S-nitrosothiol in the gas phase, methanol, and water—A theoretical study of S-nitrosylation

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  • Special Topic Physical Organic Chemistry in China
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Abstract

A dilemma about whether thionitroxide radical (RSNHO) or S-nitrosothiol (RSNO) is observed in protein S-nitrosylation has arisen recently. To illustrate the effect of chemical environment on these structures, this paper presents quantum mechanical molecular dynamics of thionitroxide, and cis- and trans-S-nitrosothiols in the gas phase, methanol, and water. By using Car-Parrinello molecular dynamics (CPMD), we have observed that there is free rotation about the S-N bond at 300 K in thionitroxide, but no such rotation is observed for S-nitrosothiol. The C-S-N-O torsion angle distribution in thionitroxide is significantly dependent upon the surrounding environment, leading to either gauche-, cis-, or trans-conformation. In the case of S-nitrosothiol the C-S-N-O plane is twisted slightly by 5°–15° in the cis-isomer, while the periplanar structure is well-retained in the trans-isomer. The calculated results are in agreement with the X-ray crystallographic data of small molecular RSNO species. Interestingly, for both compounds, the CPMD simulations show that solvation can cause a decrease in the S-N bond length. Moreover, the oxygen atom of thionitroxide is found to be a good hydrogen-bond acceptor, forming an oxyanionhole-like hydrogen bonding network.

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Authors and Affiliations

  1. State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China

    Juan Liang, ShangLi Cheng, JunWei Hou, ZhenHao Xu & Yi-Lei Zhao

  2. Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China

    ZhenHao Xu & Yi-Lei Zhao

  3. MOE Laboratory of Scientific and Engineering Computing, Shanghai Jiao Tong University, Shanghai, 200240, China

    Yi-Lei Zhao

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  1. Juan Liang
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  2. ShangLi Cheng
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  3. JunWei Hou
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  4. ZhenHao Xu
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  5. Yi-Lei Zhao
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Correspondence to Yi-Lei Zhao.

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Liang, J., Cheng, S., Hou, J. et al. Car-Parinello molecular dynamics simulations of thionitroxide and S-nitrosothiol in the gas phase, methanol, and water—A theoretical study of S-nitrosylation. Sci. China Chem. 55, 2081–2088 (2012). https://doi.org/10.1007/s11426-012-4712-9

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  • DOI: https://doi.org/10.1007/s11426-012-4712-9

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