Metallicious: Automated Force-Field Parameterization of Covalently Bound Metals for Supramolecular Structures

• Published in: Journal of chemical theory and computation Vol. 20; no. 20; pp. 9060 - 9071
• Main Authors: Piskorz, Tomasz K., Lee, Bernadette, Zhan, Shaoqi, Duarte, Fernanda
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 22-10-2024
• Subjects: Charge transfer; Dynamic characteristics; Metal-organic frameworks; Molecular dynamics; Molecular Mechanics; Molecular structure; Parameterization; Quantum mechanics; Simulation
• ISSN: 1549-9618; 1549-9626; 1549-9626
• DOI: 10.1021/acs.jctc.4c00850

Metal ions play a central, functional, and structural role in many molecular structures, from small catalysts to metal–organic frameworks (MOFs) and proteins. Computational studies of these systems typically employ classical or quantum mechanical approaches or a combination of both. Among classical models, only the covalent metal model reproduces both geometries and charge transfer effects but requires time-consuming parameterization, especially for supramolecular systems containing repetitive units. To streamline this process, we introduce metallicious, a Python tool designed for efficient force-field parameterization of supramolecular structures. Metallicious has been tested on diverse systems including supramolecular cages, knots, and MOFs. Our benchmarks demonstrate that parameters accurately reproduce the reference properties obtained from quantum calculations and crystal structures. Molecular dynamics simulations of the generated structures consistently yield stable simulations in explicit solvent, in contrast to similar simulations performed with nonbonded and cationic dummy models. Overall, metallicious facilitates the atomistic modeling of supramolecular systems, key for understanding their dynamic properties and host–guest interactions. The tool is freely available on GitHub (https://github.com/duartegroup/metallicious).