Effect of partial atomic charges on molecular adsorption to a substrate using Molecular Mechanics

Molecular Mechanics (MM) calculations use partial atomic charges to optimize adsorption geometries and energies. Fixing the charges outside of the program allows for the use of less computational power, which contrasts with calculating atomic charges during each iteration via quantum mechanics. MM offers several force fields that, when combined with differing charge schemes, allows the comparison of adsorption geometries and energies across various conformers. Within the MM application, the molecular conformers were adsorbed to an NaCl substrate. Additionally, the substrate had several variations of polarity. The results show that despite using different charge schemes, the stable conformers maintained similar adsorption configurations independent of the force field used. As expected, the adsorption energies increased following the increase in polarity of the substrate. Additionally, these stable conformers adsorbed in a configuration that was noticeably parallel to the substrate. However, less stable conformers did not adsorb consistently across different charge schemes. Although adsorption geometries and energies depend on conformer stability, partial atomic charges appear to have a limited effect.