Listyarini Risnita Vicky, Kriesche Bernhard M, Hofer Thomas S
Institute of General, Inorganic and Theoretical Chemistry Center for Chemistry and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria.
Chemistry Education Study Program Sanata Dharma University, Yogyakarta 55282, Indonesia.
J Chem Theory Comput. 2024 Apr 23;20(8):3028-3045. doi: 10.1021/acs.jctc.4c00162. Epub 2024 Apr 10.
The characterization of solvation shells of atoms, ions, and molecules in solution is essential to relate solvation properties to chemical phenomena such as complex formation and reactivity. Different definitions of the first-shell coordination sphere from simulation data can lead to potentially conflicting data on the structural properties and associated ligand exchange dynamics. The definition of a solvation shell is typically based on a given threshold distance determined from the respective solute-solvent pair distribution function () (i.e., GC). Alternatively, a nearest neighbor (NN) assignment based on geometric properties of the coordination complex without the need for a predetermined cutoff criterion, such as the relative angular distance (RAD) or the modified Voronoi (MV) tessellation, can be applied. In this study, the effect of different NN algorithms on the coordination number and ligand exchange dynamics evaluated for a series of monatomic ions in aqueous solution, carbon dioxide in aqueous and dichloromethane solutions, and pure liquid water has been investigated. In the case of the monatomic ions, the RAD approach is superior in achieving a well separated definition of the first solvation layer. In contrast, the MV algorithm provides a better separation of the NNs from a molecular point of view, leading to better results in the case of solvated CO. When analyzing the coordination environment in pure water, the cutoff-based GC framework was found to be the most reliable approach. By comparison of the number of ligand exchange reactions and the associated mean ligand residence times (MRTs) with the properties of the coordination number autocorrelation functions, it is shown that although the average coordination numbers are sensitive to the different definitions of the first solvation shell, highly consistent estimates for the associated MRT of the solvated system are obtained in the majority of cases.
溶液中原子、离子和分子溶剂化壳层的表征对于将溶剂化性质与诸如络合物形成和反应性等化学现象联系起来至关重要。从模拟数据中对第一壳层配位球的不同定义可能导致关于结构性质和相关配体交换动力学的潜在冲突数据。溶剂化壳层的定义通常基于从各自的溶质 - 溶剂对分布函数(即GC)确定的给定阈值距离。或者,可以应用基于配位络合物几何性质的最近邻(NN)分配,而无需预先确定的截止标准,例如相对角距离(RAD)或修正的Voronoi(MV)镶嵌。在本研究中,研究了不同的NN算法对一系列水溶液中的单原子离子、水和二氯甲烷溶液中的二氧化碳以及纯液态水的配位数和配体交换动力学评估的影响。对于单原子离子,RAD方法在实现第一溶剂化层的良好分离定义方面更具优势。相比之下,MV算法从分子角度提供了更好的NN分离,在溶剂化CO的情况下产生更好的结果。在分析纯水的配位环境时,发现基于截止的GC框架是最可靠的方法。通过将配体交换反应的数量和相关的平均配体停留时间(MRT)与配位数自相关函数的性质进行比较,结果表明,尽管平均配位数对第一溶剂化壳层的不同定义敏感,但在大多数情况下,对于溶剂化系统的相关MRT获得了高度一致的估计。