From GROMACS Molecular Dynamics Simulations to Electronic Absorption Spectra: A Tutorial for Small Molecules in Organic Solvents

Abstract

Classical molecular dynamics is a theoretical method useful for investigating noncovalent intermolecular interactions and conformational flexibility, enabling the simulation of processes such as aggregation/dissolution and adsorption. Molecular dynamics and quantum chemistry are increasingly introduced in chemistry curricula, yet students may encounter difficulties when translating theoretical concepts into robust simulation protocols, particularly outside biomolecular systems. Here, we present a tutorial designed to guide students through the preparation, execution, and analysis of the simulations of small organic molecules in nonaqueous solvents, followed by the calculation of ultraviolet–visible (UV–vis) absorption spectra using time-dependent density functional theory. This tutorial focuses on several practical issues: obtaining force-field parameters, building simulation cells, selecting ensembles, and interpreting critical simulation parameters. Custom solvent models are validated against reference density and radial distribution functions, demonstrating how selected observables can be used to assess simulation reliability. We illustrate the usefulness of molecular dynamics by showing that molecular flexibility and solvent interactions broaden the UV–vis absorption band of indigo in chloroform. This contribution is intended as a hands-on educational resource for upper-level undergraduate and graduate students enrolled in physical chemistry and computational chemistry courses, as well as for Ph.D. students working in chemistry, physics, or material science, who are approaching molecular simulations. To support dissemination, we have released a ready-to-use package on GitHub that includes solvent boxes and all the necessary files and data for incorporating new molecules into GROMACS simulations: https://github.com/cippee/SolventSafari-for-GROMACS.