13C chemical shifts and 1JCH coupling constants of cytidine at different χ dihedrals based on DFT calculations
13C chemical shifts and 1JCH coupling constants of cytidine at different χ dihedrals based on DFT calculations
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DOI：
10.1002/ejoc.200500878
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发表时间：
2006-04-28
影响因子：
2.8
通讯作者：
Reinscheid, Uwe M.
中科院分区：
文献类型：
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作者：
Fischer, Joerg T.;Reinscheid, Uwe M.
胞苷的分子动力学模拟再现了占主导地位的E-3-内型，即糖的所谓North构象和chi = -120度的反碱基方向。作为几何优化的起始结构，通过DFT [泛函：B3 LYP，基组：6- 31 G（d，p）]计算C-13化学位移和（1）J偶合常数。由于第一次没有使用最小结构模型，因此除了不包括溶剂依赖性外，无需进一步近似即可解释结果。研究了糖苷扭转角的影响。C-13化学位移与北构象的糖独立的基础方向时，使用经验推导的坐标分析。然而，（1）J（CH）耦合常数和C-13化学位移清楚地显示了对糖苷扭转的依赖性，这使得能够识别chi。（1）J（CH）分析表明，糖皱褶不是（1）J（C1'H1'）的主要决定因素。相反，基础方向引起了重大变化，最大差异为14 Hz。另外，（1）J（C2'H2'）、（1）J（C3'H3'）和（1）J（C4'H4'）受到可用于分配chi的糖苷扭转的不同影响。静电和空间位阻效应的分析表明，一个孤立的观点是不能解释所有的NMR光谱数据，但提供了一些有用的想法。通过空间效应解释了C_3 ′上较高的电荷和（1）J（C_6H_6）偶合常数。取决于糖苷扭转，碱基非平面性显著改变。结果清楚地表明，对于核糖核苷酸，C-13化学位移和（1）J（CH）偶合常数也依赖于碱基取向，这在过去是有疑问的。
A molecular dynamic simulation of cytidine reproduced the dominating E-3-endo, the so-called North conformation of the sugar and the anti base orientation with chi = -120 degrees. Taken as starting structures for a geometry optimisation, C-13 chemical shifts and (1)J coupling constants were calculated by DFT [functional: B3LYP, basis set: 6-31G(d,p)]. As for the first time no minimal structural model was used, the results can be interpreted without further approximations except solvent dependence which was not included. The influence of the glycosidic torsion angle was studied. The C-13 chemical shifts correlated with a North conformation of the sugar independent of the base orientation when using an empirically derived coordinate analysis. However, the (1)J(CH) coupling constants and C-13 chemical shifts clearly showed a dependence on the glycosidic torsion which enables the identification of chi. The (1)J(CH) analysis showed that the sugar pucker is not the major determinant for (1)J(C1'H1'). Instead, the base orientation caused major changes, with a maximal difference of 14 Hz. Additionally, (1)J(C2'H2'), (1)J(C3'H3'), and (1)J(C4'H4') are differently influenced by the glycosidic torsion which can be exploited for assigning chi. Analysis of electrostatic and steric effects showed that an isolated view is not able to explain all NMR spectroscopic data but gives some useful ideas. A higher charge on C3' and the (1)J(C6H6) coupling constants were explained by through-space effects. Depending on the glycosidic torsion, the base non-planarity changes substantially. The results clearly show that also for ribonucleotides C-13 chemical shifts and (1)J(CH) coupling constants are dependent on the base orientation which was questioned in the past.