Molecular dynamics simulations on the stability and assembly mechanisms of quadruple and double helical aromatic amide foldamers.

The polymer of 7-amino-8-fluoro-2-quinoline carboxylic acid (abbreviated as QF(n), n denotes polymerization degree, where n = 4 or 8) can form artificial helices that do not exist in nature. The crystal structures of the quadruplex of QF(4) and the duplex of QF(8) (abbreviated as QP_4 and DP_8, respectively) have been unveiled by some researchers recently. In this paper, QP_4 and DP_8 were built based on their crystal structures. Though the quadruplex of QF(8) and the duplex of QF(4) (abbreviated as QP_8 and DP_4, respectively) were not observed in experiments, they were built using molecular modeling tools. The molecular dynamics (MD) method was used to study the stabilities and assembly mechanisms of these helices at different temperatures. In MD simulations, the disassembled QP_4 was observed above 480 K. The results indicate that these oligoamide helices showed slippage of strands to some extent and that double-helical oligoamides act as a basic block in the slippage during the formation of the quadruple-helical structure. DP_4 and QP_4 showed dynamical features with helix-handedness inversion and following slippage of strands at higher temperatures. In addition, the pi-pi conjugations between the different chains are supposed to be responsible for the stability of the helices.