Physics – Condensed Matter – Statistical Mechanics
Scientific paper
2009-08-16
Physics
Condensed Matter
Statistical Mechanics
42 pages, 17 figures, accepted to the Journal of Chemical Physics
Scientific paper
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.
Franco Ignacio
Ratner Mark A.
Schatz George C.
No associations
LandOfFree
AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-704400