Deciphering the helicity switching mechanism: a case study of the rigid three-tiered stacked architecture
writer：Peng Liu*, Yingzhe Liu, Xihui Bian,Xiaoyao Tan
keywords：Switching mechanism, Molecular dynamics simulations, Free–energy calculations
source：期刊
specific source：Physical Chemistry Chemical Physics, 2018, 20 (45), 28881-28885
Issue time：2018年
Understanding the switching mechanism of helical architectures is critical in characterizing their function of biological systems and molecular devices. Helical inversion of a three-tiered stacked architecture designed by Scott Hartley was investigated by employing molecular dynamics simulations combined with free–energy calculations. Two dimensional free–energy landscape characterizing the spinning processes of the top and bottom tiers around z axis was determined using the extended adaptive biasing force method. Free–energy barrier in the least free–energy pathway is estimated to be 17.5 kcal/mol, in excellent agreement with experimental measurements. Further analysis reveals that the barrier was is caused by geometric deformation, weakening of π-π stacking between aromatic rings, and re-orientation of partially polarized amine moieties. The present contribution takes a step toward understanding the helical inversion mechanism involving involved in the working process of artificial membrane massagers and other chemical systems with helicity.