The true nature of rotary movements in rotaxanes

Chemical Science
Peng LiuWensheng Cai

Abstract

Disentangling the different movements observed in rotaxanes is critical to characterize their function as molecular and biological motors. How to achieve unidirectional rotation is an important question for successful construction of a highly efficient molecular motor. The motions within a rotaxane composed of a benzylic amide ring threaded on a fumaramide moiety were investigated employing atomistic molecular dynamics simulations. The free-energy profiles describing the rotational process of the ring about the thread were determined from multi-microsecond simulations. Comparing the theoretical free-energy barriers with their experimental counterpart, the syn-anti isomerization of the amide bond within the ring was ruled out. The free-energy barriers arise in fact from the disruption of hydrogen bonds between the ring and the thread. Transition path analysis reveals that complete description of the reaction coordinate requires another collective variable. The free-energy landscape spanned by the two variables characterizing the coupled rotational and shuttling processes of the ring in the rotaxane was mapped. The calculated free-energy barrier, amounting to 9.3 kcal mol-1, agrees well with experiment. Further analysis shows tha...Continue Reading

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Citations

Nov 14, 2018·Physical Chemistry Chemical Physics : PCCP·Peng LiuXiaoyao Tan
Jun 4, 2020·Physical Chemistry Chemical Physics : PCCP·Peng LiuDonghai Mei
Oct 4, 2017·Chemical Science·Haohao FuWensheng Cai
Mar 26, 2021·The Journal of Physical Chemistry Letters·Florian E Blanc, Marco Cecchini
Nov 5, 2019·Accounts of Chemical Research·Haohao FuChristophe Chipot
Apr 21, 2017·The Journal of Physical Chemistry. B·Abhishek Singharoy, Christophe Chipot
Dec 23, 2021·Chemical Communications : Chem Comm·Matthew M SartinTahei Tahara
Dec 25, 2021·Physical Chemistry Chemical Physics : PCCP·Haohao FuWensheng Cai

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Methods Mentioned

BETA
NMR

Software Mentioned

NAMD
RESPA
VMD

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