The thermodynamic driving force in the folding of a class of oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy by atomic force microscopy experiments. The oligorotaxanes consist of cyclobis(paraquat--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 versus 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 versus 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 folding. In addition, an analogy between the single-molecule folding/unfolding events driven by the atomic force microscope (AFM) tip and the thermodynamic theory of first-order phase transitions is discussed. General conditions (on the molecule and the AFM cantilever) for the emergence of mechanical instabilities and blinks in the force measurements in equilibrium isometric pulling experiments are also 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.
Skip Nav Destination
Article navigation
28 September 2009
Research Article|
September 23 2009
Single-molecule pulling and the folding of donor-acceptor oligorotaxanes: Phenomenology and interpretation
Ignacio Franco;
Ignacio Franco
a)
Department of Chemistry,
Northwestern University
, Evanston, Illinois 60208-3113, USA
Search for other works by this author on:
George C. Schatz;
George C. Schatz
Department of Chemistry,
Northwestern University
, Evanston, Illinois 60208-3113, USA
Search for other works by this author on:
Mark A. Ratner
Mark A. Ratner
Department of Chemistry,
Northwestern University
, Evanston, Illinois 60208-3113, USA
Search for other works by this author on:
a)
Electronic mail: ifranco@chem.northwestern.edu.
J. Chem. Phys. 131, 124902 (2009)
Article history
Received:
July 02 2009
Accepted:
August 17 2009
Citation
Ignacio Franco, George C. Schatz, Mark A. Ratner; Single-molecule pulling and the folding of donor-acceptor oligorotaxanes: Phenomenology and interpretation. J. Chem. Phys. 28 September 2009; 131 (12): 124902. https://doi.org/10.1063/1.3223729
Download citation file:
Sign in
Don't already have an account? Register
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Pay-Per-View Access
$40.00
Citing articles via
A theory of pitch for the hydrodynamic properties of molecules, helices, and achiral swimmers at low Reynolds number
Anderson D. S. Duraes, J. Daniel Gezelter
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
Electronic structure simulations in the cloud computing environment
Eric J. Bylaska, Ajay Panyala, et al.
Related Content
Immobilized reagent disodium salt of 1, 8-dioxynaphthalene-3,6-disulfonic acids for the determination of chromium ions
AIP Conference Proceedings (June 2022)
Possible performance improvement in [2]catenane molecular electronic switches
Appl. Phys. Lett. (April 2006)
Effect of mechanical load on the shuttling operation of molecular muscles
Appl. Phys. Lett. (June 2009)
A chromophoric switch based on pseudorotaxanes
J. Chem. Phys. (February 2007)