PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent

23 May 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

We introduce PyConSolv, a freely available python package that automates the generation of conformers of metal and non-metal containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal, only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing the AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of pre-parametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open-source and free of charge.

Keywords

Conformer Generation
Conformer
Transition-Metal Complex
Automation
MCPB
Explicit Solvent

Supplementary materials

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Supporting Information
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Contains details about calculation settings, parametrized solvents, additional information related to case studies.
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