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Narrowing down the conformational space with solid-state NMR in crystal structure prediction of linezolid cocrystals
Solid State Nuclear Magnetic Resonance ( IF 3.2 ) Pub Date : 2022-08-08 , DOI: 10.1016/j.ssnmr.2022.101813
Mehrnaz Khalaji 1 , Piotr Paluch 1 , Marek J Potrzebowski 1 , Marta K Dudek 1
Affiliation  

Many solids crystallize as microcrystalline powders, thus precluding the application of single crystal X-Ray diffraction in structural elucidation. In such cases, a joint use of high-resolution solid-state NMR and crystal structure prediction (CSP) calculations can be successful. However, for molecules showing significant conformational freedom, the CSP-NMR protocol can meet serious obstacles, including ambiguities in NMR signal assignment and too wide conformational search space to be covered by computational methods in reasonable time. Here, we demonstrate a possible way of avoiding these obstacles and making as much use of the two methods as possible in difficult circumstances. In a simple case, our experiments led to crystal structure elucidation of a cocrystal of linezolid (LIN), a wide-range antibiotic, with 2,3-dihydroxybenzoic acid, while a significantly more challenging case of a cocrystal of LIN with 2,4-dihydroxybenzoic acid led to the identification of the most probable conformations of LIN inside the crystal. Having four rotatable bonds, some of which can assume many discreet values, LIN molecule poses a challenge in establishing its conformation in a solid phase. In our work, a set of 27 conformations were used in CSP calculations to yield model crystal structures to be examined against experimental solid-state NMR data, leading to a reliable identification of the most probable molecular arrangements.



中文翻译:

用固态核磁共振缩小构象空间在利奈唑胺共晶晶体结构预测中的作用

许多固体结晶为微晶粉末,因此排除了单晶 X 射线衍射在结构解析中的应用。在这种情况下,高分辨率固态 NMR 和晶体结构预测 (CSP) 计算的联合使用可能会成功。然而,对于表现出显着构象自由度的分子,CSP-NMR 协议可能会遇到严重的障碍,包括 NMR 信号分配的模糊性和太宽的构象搜索空间,无法在合理的时间内被计算方法覆盖。在这里,我们展示了一种避免这些障碍的可能方法,并在困难的情况下尽可能多地使用这两种方法。在一个简单的例子中,我们的实验导致了利奈唑胺 (LIN) 的晶体结构阐明,这是一种广谱抗生素,与 2,3-二羟基苯甲酸,而一个更具挑战性的 LIN 与 2,4-二羟基苯甲酸共晶体的案例导致了晶体内部最可能的 LIN 构象的鉴定。LIN 分子有四个可旋转的键,其中一些可以假定许多离散值,因此在建立其固相构象方面提出了挑战。在我们的工作中,在 CSP 计算中使用了一组 27 个构象,以产生模型晶体结构,以根据实验固态 NMR 数据进行检查,从而可靠地识别最可能的分子排列。LIN 分子对在固相中建立其构象提出了挑战。在我们的工作中,在 CSP 计算中使用了一组 27 个构象,以产生模型晶体结构,以根据实验固态 NMR 数据进行检查,从而可靠地识别最可能的分子排列。LIN 分子对在固相中建立其构象提出了挑战。在我们的工作中,在 CSP 计算中使用了一组 27 个构象,以产生模型晶体结构,以根据实验固态 NMR 数据进行检查,从而可靠地识别最可能的分子排列。

更新日期:2022-08-12
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