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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基金项目: | supported by the National High-Tech R&DProgram of China “863” (2012AA020403);the National Basic Research Program of China “973” (2012CB72100);Shanghai Municipal Council of Science and Technology (10PJ1405200);the Specialized Research Fund for the Doctoral Program of Higher Education (Z1025507);Shanghai Municipal Education Commission (Oriental Professorial Scholarship 0900000171);the National Natural Science Foundation of China (30821005) |
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摘 要: | 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 s-ignificantly 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 oxyanion-hole-like hydrogen bonding network.
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关 键 词: | quantum mechanical molecular dynamics S-nitrosylation thionitroxide S-nitrosothiol solvent effect |
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