Conformational inversion of foldamers has been shown to transmit signals across the lipid membrane. Helicity switching is critical to fulfilling this function. Despite the importance of the conformational inversion, the mechanism that underlies the helicity switching process remains unclear. In the present contribution, a rigid two-tiered stacked architecture (2T) has been investigated at the atomic level using molecular simulations. The architecture consists of two conjugated cores and three flexible side chains. Two- and three-dimensional free-energy landscapes characterizing the isomerization of 2T reveal a four-stage helicity switching process. Four stages involve the flipping of three peripheral aromatic rings in the top tier and rotating of the bottom tier relative to the top one. The highest barrier hampering the transition between right-handed and left-handed helices emerges as the second benzene ring flips. Structural analysis shows that the ring flipping stretches the side chain, which leads to the deformation of conjugated cores, twist of dihedral angles within side chains, and the reorientation of amine moieties attached to chains. By deciphering the intricate mechanism whereby the rigid stacked architecture isomerizes, our understanding of the helicity switching is expected to be improved, helping in turn the construction of novel functional helices.
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