Bürgi Hans-Beat
Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Berne, Freiestr. 3, CH-3012 Bern, Switzerland.
Struct Dyn. 2024 Mar 18;11(2):021302. doi: 10.1063/4.0000244. eCollection 2024 Mar.
With the availability of the computer readable information in the Cambridge Structural Database (CSD), wide ranging, largely automated comparisons of fragment, molecular, and crystal structures have become possible. They show that the distributions of interatomic distances, angles, and torsion angles for a given structural fragment occurring in different environments are highly correlated among themselves and with other observables such as spectroscopic signals, reaction and activation energies. The correlations often extend continuously over large ranges of parameter values. They are reminiscent of bond breaking and forming reactions, polyhedral rearrangements, and conformational changes. They map-qualitatively-the regions of the structural parameter space in which molecular dynamics take place, namely, the low energy regions of the respective (free) energy surfaces. The extension and continuous nature of the correlations provides an organizing principle of large groups of structural data and suggests a reconsideration of traditional definitions and descriptions of bonds, "nonbonded" and "noncovalent" interactions in terms of Lewis acids interacting with Lewis bases. These aspects are illustrated with selected examples of historic importance and with some later developments. It seems that the amount of information in the CSD (and other structural databases) and the knowledge on the nature of, and the correlations within, this body of information should allow one-in the near future-to make credible interpolations and possibly predictions of structures and their properties with machine learning methods.
随着剑桥结构数据库(CSD)中计算机可读信息的可得性,对片段、分子和晶体结构进行广泛的、 largely自动化的比较成为可能。这些比较表明,在不同环境中出现的给定结构片段的原子间距离、角度和扭转角的分布彼此之间以及与其他可观测值(如光谱信号、反应和活化能)高度相关。这些相关性通常在大范围的参数值上连续延伸。它们让人联想到键的断裂和形成反应、多面体重排以及构象变化。它们定性地描绘了分子动力学发生的结构参数空间区域,即各自(自由)能量表面的低能量区域。相关性的延伸和连续性为大量结构数据提供了一种组织原则,并建议从路易斯酸与路易斯碱相互作用的角度重新考虑传统的键、“非键”和“非共价”相互作用的定义和描述。这些方面通过具有历史重要性的选定例子以及一些后来的发展进行说明。似乎CSD(以及其他结构数据库)中的信息量以及关于这一信息体系的性质和相关性的知识,应该能让人们在不久的将来,用机器学习方法进行可信的插值,并可能预测结构及其性质。