Research Mentor(s)
Dr. Andreas Riemann
Description
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.
Document Type
Event
Start Date
May 2022
End Date
May 2022
Location
Carver Gym (Bellingham, Wash.)
Department
CSE - Physics and Astronomy
Genre/Form
student projects; posters
Type
Image
Rights
Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this document for commercial purposes, or for financial gain, shall not be allowed without the author’s written permission.
Language
English
Format
application/pdf
Effect of partial atomic charges on molecular adsorption to a substrate using Molecular Mechanics
Carver Gym (Bellingham, Wash.)
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.