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Blanc_Cecchini_asymmetric_submission1.pdf (7.41 MB)

An Asymmetric Mechanism in a Symmetric Molecular Machine

submitted on 31.03.2020 and posted on 01.04.2020 by Florian Blanc, Marco Cecchini
The design of molecular architectures exhibiting functional motions is a promising area for disruptive technological development. Towards this goal, rotaxanes and catenanes, which undergo relative motions of their sub-units in response to external stimuli, are prime candidates. Here, we report on the computational analysis of the contraction/extension of a bistable [c2]-daisy chain rotaxane. Using free energy calculations and transition path optimizations, we explore the free energy landscape governing the functional motions of a prototypical molecular machine with atomic resolution.
The calculations reveal a sequential mechanism for contraction/extension in which the asynchronous gliding of each ring is preferred over the concerted movement suggested by chemical intuition. Analysis of the underlying free energy surface indicates that dissymmetric gliding is favored because it entails crossings of much smaller barriers.
Our findings illustrate an important design principle for molecular machines, namely that efficient exploitation of thermal fluctuations may be realized by breaking down the large-scale functional motions into smaller steps.


Email Address of Submitting Author


Max Planck Institute of Biophysics



ORCID For Submitting Author


Declaration of Conflict of Interest

The authors declare no conflict of interest.

Version Notes

First submitted version to Angew. Chem.