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

Abstract

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.

Elucidating the Structure of the Eu‐EDTA Complex in Solution at Various Protonation States

“…RMSD analysis with AFICS [30] of the classical MD simulations show that the Eu-EDTA complexes have a slight preference for the capped square antiprismatic geometry over the tricapped trigonal prismatic geometry, and that the capped square geometry is not favored, see Table S1.…”

“…Structural analyses were done using the final 10 ns duration of the NVT simulations for each complex. We used the AFICS [30] package to obtain radial distribution functions (RDFs), angle distribution functions (ADFs), and root mean square distances (RMSDs) to ideal geometries.…”

Correction to “Coordination Sphere of Lanthanide Aqua Ions Resolved with Ab Initio Molecular Dynamics and X-ray Absorption Spectroscopy”

“…We recalculated the root-mean-square distances (RMSDs) of the Ln 3+ aqua ion coordinates in simulations to ideal reference geometries using AFICS (Analysis of the First Ion Coordination Sphere), a tool for analyzing the structural and geometric features of the first coordination sphere of an ion over the course of molecular dynamics simulations. AFICS was recently published …”

“…Details on how the RMSD values were calculated appear in ref , and the AFICS script is available for download.…”