An Asymmetric Mechanism in a Symmetric Molecular Machine

01 April 2020, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


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.


Free energy calculations
Molecular Dynamics
Molecular Machines
Supramolecular Chemistry


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