A particular class of oligomers, known as foldamers, is known to form defined stable secondary structures in solutions. Their applications involve mimicking the structure of biopolymers and forming molecular capsules among others. We use molecular dynamics (MD) to study helical aromatic foldamers with the use of re-parametrized force field to appropriately represent the conformation of helical foldamers. Herein, we present two studies: 1) investigation of molecular capsules formed by pyridine and quinoline foldamer helices and 2) a metadynamics study on aromatic quinoline oligoamide handedness inversion. Our results are in agreement with experimental observations for these helices. The results from our first project reveal ligand binding modes within the capsule, deformations in capsule caused by ligands and two possible mechanisms of ligand entering and leaving the capsule. The results from our second project reveal important atomistic level details of energy pathway for handedness inversion in helical foldamers. Importantly, these studies also show the feasibility of using MD simulations with the proper torsional parameters for investigating both the structure and dynamics of arylamide foldamer.

Molecular dynamics studies of encapsulation and handedness inversion of helical foldamers

248th National Meeting (2014)

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