Dynamics simulation of the interaction between serine and water.
Dynamics simulation of the interaction between serine and water.
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DOI：
10.1063/1.4807004
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发表时间：
2013-05
期刊：
影响因子：
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通讯作者：
Yang Liu;Peng Zhang;Ying‐Bo Lu;Shenghao Han;Hui Yu
中科院分区：
文献类型：
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作者：
Yang Liu;Peng Zhang;Ying‐Bo Lu;Shenghao Han;Hui Yu
采用第一性原理密度泛函理论（DFT），模拟了丝氨酸水合动力学的中子散射谱。实验数据分析表明，解离的H2O分子更可能与一水合丝氨酸中的-OH基团形成氢键（H-键），并且在更高的水合水平下容易转变为-NH3（+）基团[P. Zhang，Y. Zhang，S. H.汉角，澳-地W.扬河，巴西-地C.福特和J. C. Li，J.Phys.Chem.A110，5000（2006）]。我们在两个位置设置1：1的水合化合物，发现H2O可以被优化以分别与-OH和-NH3（+）形成H-键。当模拟的-OH···H2O和-NH 3（+）···H2O的声子信号按3：1比例相加时，计算谱与实验结果吻合较好，特别是-OH···H2O的423 cm（-1）峰和-NH 3（+）···H2O的367 cm（-1）峰与真实的谱相互补充。我们证实了H2O可能会破坏分子间的-OH键，形成新的结构，并且随着丝氨酸骨架的变形，H2O更多地与-NH3（+）侧形成更强的氢键，表明丝氨酸水合过程的灵活动力学机制。
Using the first principles density functional theory (DFT), we simulated the neutron scattering spectra of the hydration dynamics of serine. Experimental data analyses have shown that dissociative H2O molecules were more likely to form hydrogen bonds (H-bonds) with an -OH group in monohydrated serine and easily shift to a -NH3 (+) group at a higher hydration level [P. Zhang, Y. Zhang, S. H. Han, Q. W. Yan, R. C. Ford, and J. C. Li, J. Phys. Chem. A 110, 5000 (2006)]. We set the 1:1 ratio hydrated compounds at the two positions and found that the H2O could be optimized to form H-bonds with -OH and -NH3 (+) separately. When the simulated phonon signals of the -OH···H2O and -NH3(+)···H2O combinations were summed on a 3:1 scale, the calculating spectra were in good agreement with the experimental results, especially for the peak at 423 cm(-1) of the -OH···H2O combination and the peak at 367 cm(-1) of the -NH3(+)···H2O combination, which mutually complemented the real spectrum. We confirm that H2O may break the intermolecular H-bonds of the interlaced binding -OH to form a new structure, and that with the skeleton deformation of serine, H2O forms stronger H-bonds more often with the -NH3 (+) side indicating the flexible dynamic mechanism of the serine hydration process.