Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions
Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions
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DOI：
10.1021/acs.jcim.3c00294
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发表时间：
2023-04
影响因子：
5.6
通讯作者：
Stuart J. McElhany;Thomas J. Summers;Richard C. Shiery;David C. Cantu
中科院分区：
文献类型：
--
作者：
Stuart J. McElhany;Thomas J. Summers;Richard C. Shiery;David C. Cantu
快速而准确地表征离子的配位结构对于设计配体和量化结构-性质趋势是重要的。在这里，我们介绍了AFICS(分析第一离子配位球)，这是一个用Python3编写的工具，用于在分子动力学模拟过程中分析离子第一配位球的结构和几何特征。AFICS的主要特征是它能够量化坐标几何与均匀多面体相比所经历的变形。这项工作应用该工具包分析了水中Cr3+的明确配位结构以及Eu3+与乙二胺四乙酸络合的更模糊的结构的分子动力学模拟。该工具的目标是分析具有流动或不规则配位结构的离子(例如，f-块元素的溶液结构)，但将其推广到其他系统。
Rapid and accurate approaches to characterizing the coordination structure of an ion are important for designing ligands and quantifying structure-property trends. Here, we introduce AFICS (Analysis of the First Ion Coordination Sphere), a tool written in Python 3 for analyzing the structural and geometric features of the first coordination sphere of an ion over the course of molecular dynamics simulations. The principal feature of AFICS is its ability to quantify the distortion a coordination geometry undergoes compared to uniform polyhedra. This work applies the toolkit to analyze molecular dynamics simulations of the well-defined coordination structure of aqueous Cr3+ along with the more ambiguous structure of aqueous Eu3+ chelated to ethylenediaminetetraacetic acid. The tool is targeted for analyzing ions with fluxional or irregular coordination structures (e.g., solution structures of f-block elements) but is generalized such that it may be applied to other systems.