Cargando…

The true nature of rotary movements in rotaxanes

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Liu, Peng, Shao, Xueguang, Chipot, Christophe, Cai, Wensheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Royal Society of Chemistry 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090524/
https://www.ncbi.nlm.nih.gov/pubmed/30155010
http://dx.doi.org/10.1039/c5sc03022f
_version_ 1783347207583301632
author Liu, Peng
Shao, Xueguang
Chipot, Christophe
Cai, Wensheng
author_facet Liu, Peng
Shao, Xueguang
Chipot, Christophe
Cai, Wensheng
author_sort Liu, Peng
collection PubMed
description 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 that shuttling is coupled with the isomerization of the ring, which is not limited to a simplistic chair-to-chair transition. This work provides a cogent example that contrary to chemical intuition, molecular motion can result from complex, entangled movements requiring for their accurate description careful modeling of the underlying reaction coordinate. The methodology described here can be used to evaluate the different components of the multifaceted motion in rotaxanes, and constitutes a robust tool for the rational design of molecular machines.
format Online
Article
Text
id pubmed-6090524
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Royal Society of Chemistry
record_format MEDLINE/PubMed
spelling pubmed-60905242018-08-28 The true nature of rotary movements in rotaxanes Liu, Peng Shao, Xueguang Chipot, Christophe Cai, Wensheng Chem Sci Chemistry 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 that shuttling is coupled with the isomerization of the ring, which is not limited to a simplistic chair-to-chair transition. This work provides a cogent example that contrary to chemical intuition, molecular motion can result from complex, entangled movements requiring for their accurate description careful modeling of the underlying reaction coordinate. The methodology described here can be used to evaluate the different components of the multifaceted motion in rotaxanes, and constitutes a robust tool for the rational design of molecular machines. Royal Society of Chemistry 2016-01-01 2015-10-13 /pmc/articles/PMC6090524/ /pubmed/30155010 http://dx.doi.org/10.1039/c5sc03022f Text en This journal is © The Royal Society of Chemistry 2016 http://creativecommons.org/licenses/by/3.0/ This article is freely available. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence (CC BY 3.0)
spellingShingle Chemistry
Liu, Peng
Shao, Xueguang
Chipot, Christophe
Cai, Wensheng
The true nature of rotary movements in rotaxanes
title The true nature of rotary movements in rotaxanes
title_full The true nature of rotary movements in rotaxanes
title_fullStr The true nature of rotary movements in rotaxanes
title_full_unstemmed The true nature of rotary movements in rotaxanes
title_short The true nature of rotary movements in rotaxanes
title_sort true nature of rotary movements in rotaxanes
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090524/
https://www.ncbi.nlm.nih.gov/pubmed/30155010
http://dx.doi.org/10.1039/c5sc03022f
work_keys_str_mv AT liupeng thetruenatureofrotarymovementsinrotaxanes
AT shaoxueguang thetruenatureofrotarymovementsinrotaxanes
AT chipotchristophe thetruenatureofrotarymovementsinrotaxanes
AT caiwensheng thetruenatureofrotarymovementsinrotaxanes
AT liupeng truenatureofrotarymovementsinrotaxanes
AT shaoxueguang truenatureofrotarymovementsinrotaxanes
AT chipotchristophe truenatureofrotarymovementsinrotaxanes
AT caiwensheng truenatureofrotarymovementsinrotaxanes