Research Partner of the Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany.
COSMOS-Software, Johann-Griesbach-Str. 26, 07743 Jena, Germany.
Molecules. 2022 Nov 17;27(22):7987. doi: 10.3390/molecules27227987.
To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and J couplings as well.
为了研究士的宁的柔韧性，我们使用取向张量约束的分子动力学模拟（MDOC）进行了研究。张量约束是从核磁共振（NMR）相互作用张量中得出的，例如，从残差偶极耦合（RDC）中得出。将它们用作取向约束时，可以使整个分子和分子部分以低旋转势垒旋转。由于 NMR 参数是在环境温度下测量的，因此取向约束会生成占据整个吉布斯自由能景观的构象。在 MDOC 中，生成的结构不仅受到能量的控制，还受到吉布斯自由能熵项的控制。在士的宁的情况下，表明环构象是被占据的，这在以前的研究中没有讨论过。这些构象的分布不仅与 RDC 一致，而且还满足核奥弗豪瑟效应（NOE）衍生的距离约束和 J 耦合。
