Helical oligomer organization derived from multiple three-center H-bonds has attracted special interest in foldamer design, leading to crescent shaped and helical staircase structures. However, important structural features of such structures have remained unknown. Hydrogen bonding (H-bonding) has been used as a highly effective means to restrict the conformational freedom and introduce curvature into the foldamer backbone. Therefore, obtaining a quantitative description of the involved molecular interactions at an atomistic level provides a platform for novel foldamer applications, and new directions in biomedical research.We present molecular dynamics studies on various groups of helical aromatic oligoamides with intramolecular H-bonding substituents at the ortho position. These simulations are based on standard and modified GAFF parameters, previously developed in the group. We evaluate several possible conformations of the helical oligomers, their relative stabilities, and relevant intramolecular interactions such as H-bonding. We find that the presence of three-center, shared H-bonds is crucial for the appearance of helical conformations.

Building helical aromatic oligoamide foldamers

244th National Meeting (2012)

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