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关于通过团簇中分子计算的限制来模拟无序晶体结构,以及区分静态和动态无序。

On modelling disordered crystal structures through restraints from molecule-in-cluster computations, and distinguishing static and dynamic disorder.

作者信息

Dittrich Birger

机构信息

Novartis Campus, Novartis Pharma AG, Postfach, Basel, CH-4002, Switzerland.

Mathematisch-Naturwissen-schaftliche Fakultät, Universität Zürich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland.

出版信息

IUCrJ. 2021 Feb 18;8(Pt 2):305-318. doi: 10.1107/S2052252521000531. eCollection 2021 Mar 1.

Abstract

Distinguishing disorder into static and dynamic based on multi-temperature X-ray or neutron diffraction experiments is the current state of the art, but is only descriptive, not predictive. Here, several disordered structures are revisited from the Cambridge Crystallographic Data Center 'drug subset', the Cambridge Structural Database and own earlier work, where experimental intensities of Bragg diffraction data were available. Using the molecule-in-cluster approach, structures with distinguishable conformations were optimized separately, as extracted from available or generated disorder models of the respective disordered crystal structures. Re-combining these 'archetype structures' by restraining positional and constraining displacement parameters for conventional least-squares refinement, based on the optimized geometries, then often achieves a superior fit to the experimental diffraction data compared with relying on experimental information alone. It also simplifies and standardizes disorder refinement. Ten example structures were analysed. It is observed that energy differences between separate disorder conformations are usually within a small energy window of ( = crystallization temperature). Further computations classify disorder into static or dynamic, using single experiments performed at one single temperature, and this was achieved for propionamide.

摘要

基于多温度X射线或中子衍射实验将无序分为静态和动态是当前的技术水平,但这只是描述性的,而非预测性的。在此,从剑桥晶体学数据中心“药物子集”、剑桥结构数据库以及本人早期工作中重新审视了几种无序结构,这些工作中都有布拉格衍射数据的实验强度。使用簇中分子方法,从各自无序晶体结构的可用或生成的无序模型中提取具有可区分构象的结构并分别进行优化。基于优化后的几何结构,通过限制位置参数和约束位移参数进行传统最小二乘法精修,将这些“原型结构”重新组合,相较于仅依靠实验信息,这样通常能更好地拟合实验衍射数据。这也简化并规范了无序精修。分析了十个示例结构。观察到单独的无序构象之间的能量差异通常在一个较小的能量窗口内(=结晶温度)。通过在一个单一温度下进行的单次实验,进一步的计算将无序分为静态或动态,丙酰胺的情况就是如此。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af33/7924241/a1adc67387fc/m-08-00305-fig1.jpg

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