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The simulation of NMR data of flexible molecules: sagittamide A as an example for MD simulations with orientational constraints.
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2020-07-08 , DOI: 10.1039/d0cp01905d Ulrich Sternberg 1 , Pavleta Tzvetkova 2 , Claudia Muhle-Goll 2
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2020-07-08 , DOI: 10.1039/d0cp01905d Ulrich Sternberg 1 , Pavleta Tzvetkova 2 , Claudia Muhle-Goll 2
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The recently developed MDOC (Molecular Dynamics with Orientational Constraints) simulation is applied for the first time to a fully flexible molecule. MDOC simulations aim to single out the naturally existing configuration of molecules and to elucidate conformer populations. The performance of the method was first demonstrated on a well-studied test case, the five-membered ring lactone (α-methylene-γ-butyrolactone). In the case of sagittamide A, one-bond 1H–13C residual dipolar couplings (RDC) are used as orientational constraints that reorient the molecule or parts of it. In addition, NOE distances and 3J scalar couplings are used as constraints. Five possible configurations of sagittamide A (labelled a to e) are considered. One experimental RDC value per flexible unit was available and this was not sufficient to single out one valid configuration. The problem could be solved by including NOE distances as well as 3J couplings as complementary constraints into the MDOC simulations. In accordance with former investigations, we confirmed the configuration a for the natural product. A detailed analysis of conformers of the central chain of 6 chiral carbon atoms could be given by inspecting the MDOC trajectory. The relative abundance of these conformers is crucial in fulfilling all three sets of constraints.
中文翻译：
柔性分子的NMR数据模拟：矢状酰胺A作为具有方向约束的MD模拟的示例。
最近开发的MDOC（具有方向约束的分子动力学）模拟首次应用于完全柔性的分子。MDOC模拟旨在找出分子的自然存在构型，并阐明构象体群体。该方法的性能首先在经过充分研究的测试用例五元环内酯（α-亚甲基-γ-丁内酯）上得到证明。在矢状酰胺A的情况下，单键1 H– 13 C残留的偶极偶合（RDC）被用作重新定向分子或分子部分的方向约束。此外，NOE距离和3 J标量耦合用作约束。考虑了矢状酰胺A的五种可能的构型（标记为a至e）。每个弹性单元有一个实验性RDC值，这不足以挑选出一种有效的配置。通过将NOE距离以及3 J耦合作为补充约束纳入MDOC仿真中，可以解决该问题。根据先前的调查，我们确认了天然产品的配置a。可以通过检查MDOC轨迹来详细分析6个手性碳原子的中心链构象。这些符合者的相对丰富度对于满足所有三组约束至关重要。
更新日期：2020-08-05
中文翻译：
柔性分子的NMR数据模拟：矢状酰胺A作为具有方向约束的MD模拟的示例。
最近开发的MDOC（具有方向约束的分子动力学）模拟首次应用于完全柔性的分子。MDOC模拟旨在找出分子的自然存在构型，并阐明构象体群体。该方法的性能首先在经过充分研究的测试用例五元环内酯（α-亚甲基-γ-丁内酯）上得到证明。在矢状酰胺A的情况下，单键1 H– 13 C残留的偶极偶合（RDC）被用作重新定向分子或分子部分的方向约束。此外，NOE距离和3 J标量耦合用作约束。考虑了矢状酰胺A的五种可能的构型（标记为a至e）。每个弹性单元有一个实验性RDC值，这不足以挑选出一种有效的配置。通过将NOE距离以及3 J耦合作为补充约束纳入MDOC仿真中，可以解决该问题。根据先前的调查，我们确认了天然产品的配置a。可以通过检查MDOC轨迹来详细分析6个手性碳原子的中心链构象。这些符合者的相对丰富度对于满足所有三组约束至关重要。
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