Abstract
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- 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 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.
| Original language | English |
|---|---|
| Article number | 124902 |
| Journal | Journal of Chemical Physics |
| Volume | 131 |
| Issue number | 12 |
| DOIs | |
| Publication status | Published - 2009 |
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ASJC Scopus subject areas
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry
Cite this
Single-molecule pulling and the folding of donor-acceptor oligorotaxanes : Phenomenology and interpretation. / Franco, Ignacio; Schatz, George C; Ratner, Mark A.
In: Journal of Chemical Physics, Vol. 131, No. 12, 124902, 2009.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Single-molecule pulling and the folding of donor-acceptor oligorotaxanes
T2 - Phenomenology and interpretation
AU - Franco, Ignacio
AU - Schatz, George C
AU - Ratner, Mark A
PY - 2009
Y1 - 2009
N2 - 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- 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 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.
AB - 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- 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 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.
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U2 - 10.1063/1.3223729
DO - 10.1063/1.3223729
M3 - Article
VL - 131
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 12
M1 - 124902
ER -