Polycyclic aromatic hydrocarbons (PAHs) are polluting
agents, produced
naturally or artificially, widely dispersed in the environment and
potentially carcinogenic and immunotoxic to humans and animals, mainly
for marine life. Recently, a tetracationic box-shaped cyclophane (ExBox4+) was synthesized, fully characterized, and revealed to form
host–guest complexes with PAHs in acetonitrile, demonstrating
the potential ability for it to act as a PAHs scavenger. This work
investigates, through Molecular Dynamics (MD) simulations, the binding
affinity between different PAHs and ExBox4+ in different
solvents: chloroform (nonpolar), acetonitrile (polar protic), and
water (polar protic). An alchemical method of simultaneous decoupling-recoupling
(SDR) was used and implemented in a newly developed Python program
called GHOAT, which fully automates the calculation of binding free
energies and invokes the AMBER 2020 simulation package. The results
showed that the affinity between ExBox4+ and PAHs in water
is much larger than in organic media, with free energies between −5
and −20 kcal/mol, being able to act as a PHAs scavenger with
great potential for applications in environmental chemistry such as
soil washing. The results also reveal a significant correlation with
the experimental available ΔG values. The methodology
employed presents itself as an important tool for the in silico determination of binding affinities, not only available for charged
cyclophanes but also extensible to several other HG supramolecular
systems in condensed media, aiding in the rational design of host–guest
systems in a significant way.