C12 is a long-chain ligand which binds to a protein (QscR) found in <i>Pseudomonas aeruginosa</i>. Binding of the C12 ligand to the protein contributes to the development of a biofilm on the lungs of patients with cystic fibrosis. This project used quantum mechanical calculations to parameterize C12. The results of these calculations were compared to standard values generated from SwissParam, which uses averaged values of bond and angle force constants and energies. The results showed an average absolute deviation of 6.8% for bond lengths and average atomic bond angle rigidity deviation of 99.3%. Relaxed energy scans on a selection of dihedrals were used to create potential energy surfaces for comparison with the classical mechanically derived surfaces of the same dihedrals. There were significant and substantial differences between the surfaces for all of the sampled dihedrals. The quantum mechanical results showed C12 to be less symmetric and more rigid than previously predicted by classical parameterization. While quantum mechanical calculations are far more costly and time consuming than calculations performed using classical mechanics, they provide a much more individualized depiction of the C12 ligand.

Comparison of quantum mechanical and standard molecular dynamics parameters for the C12 ligand

2019 Spring National Meeting

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