Jhenny F. Galan, Zhiwei Liu, Jodian Brown, Whelton A Miller, and Vojislava Pophristic. University of the Sciences in Philadelphia, Philadelphia, PA
Hydrogen bonding is known to play an important role in biological secondary structures, such as alpha-helices and beta-sheets. In synthetic foldamers, which mimic naturally occurring polymers, the same principles that govern the conformations of biofoldamers are used. In this study, we investigate the intramolecular hydrogen-bonding ability of different model aromatic amides and its effect on the conformational distributions of the aromatic oligomers. We have developed a systematic scheme using a combination of quantum mechanics and molecular dynamics simulations to estimate the strengths of hydrogen bonds and their effect on the conformational distributions of the aromatic oligomers. In addition, we modified the GAFF (general AMBER force field) parameters for this class of compounds and applied them in the molecular dynamics simulations. This study is aimed to provide further insights in the design of aromatic foldamers.