AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation

TL;DR

This study uses molecular dynamics simulations of AFM experiments to understand the thermodynamics and mechanics of oligorotaxane folding, revealing energetic favorability, entropic penalties, and conditions for mechanical instabilities.

Contribution

It provides a detailed analysis of the folding mechanism of donor-acceptor oligorotaxanes through simulations, linking force spectroscopy data to thermodynamic and mechanical insights.

Findings

Folding is energetically favored but entropically penalized.

Force-extension curves show unstable regions with force blinks.

Mechanical stability relates to force fluctuations and phase transition analogy.

Abstract

The thermodynamic driving force in the self-assembly of the secondary structure of a class of donor-acceptor oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy AFM experiments. The oligorotaxanes consist of cyclobis(paraquat-\emph{p}-phenylene) rings threaded onto an oligomer of 1,5-dioxynaphthalenes linked by polyethers. The simulations are performed in a high dielectric medium using MM3 as the force field. The resulting force vs. extension isotherms show a mechanically unstable region in which the molecule unfolds and, for selected extensions, blinks in the force measurements between a high-force and a low-force regime. From the force vs. extension data the molecular potential of mean force is reconstructed using the weighted histogram analysis method and decomposed into energetic and entropic contributions. The simulations indicate that the folding of the oligorotaxanes is energetically favored but entropically penalized, with the energetic contributions overcoming the entropy penalty and effectively driving the self-assembly. In addition, an analogy between the single-molecule folding/unfolding events driven by the AFM tip and the thermodynamic theory of first-order phase transitions is discussed and general conditions, on the molecule and the cantilever, for the emergence of mechanical instabilities and blinks in the force measurements in equilibrium isometric pulling experiments are presented. In particular, it is shown that the mechanical stability properties observed during the extension are intimately related to the fluctuations in the force measurements.