Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions

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 welldefined 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.

Automated summary

AFICS is a Python 3 tool for analyzing the structural and geometric features of the first coordination sphere of an ion in molecular dynamics simulations. It quantifies the distortion of the coordination geometry compared to uniform polyhedra. This tool was used to analyze the well-defined coordination structure of aqueous Cr3+ and the ambiguous structure of aqueous Eu3+ chelated to ethylenediaminetetraacetic acid.