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

• Published in: Science China. Chemistry 2012-10, Vol.55 (10), p.2081-2088
• Main Authors: Liang, Juan, Cheng, ShangLi, Hou, JunWei, Xu, ZhenHao, Zhao, Yi-Lei
• Format: Article
• Language: English
• Subjects: Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Crystallography; Hydrogen bonding; Hydrogen bonds; Isomers; Methanol; Molecular dynamics; Quantum mechanics; Rotation; S-亚硝基硫醇; Solvation; Vapor phases; X-射线晶体学; 亚硝基化; 作者; 分子动力学模拟; 气相; 甲醇; 顺式异构体
• ISSN: 1674-7291; 1869-1870
• DOI: 10.1007/s11426-012-4712-9

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.