Single-molecule pulling and the folding of donor-acceptor oligorotaxanes

Phenomenology and interpretation

Research output: Contribution to journalArticle

25 Citations (Scopus)

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 languageEnglish
Article number124902
JournalJournal of Chemical Physics
Volume131
Issue number12
DOIs
Publication statusPublished - 2009

Fingerprint

pulling
phenomenology
folding
Force measurement
Molecules
molecules
Microscopes
Thermodynamics
Paraquat
Mechanical stability
Polyethers
Oligomers
Isotherms
Molecular dynamics
Atomic force microscopy
Entropy
Phase transitions
Experiments
Spectroscopy
Computer simulation

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

@article{94187abe0d55458f9a9abcd96d27a1f9,
title = "Single-molecule pulling and the folding of donor-acceptor oligorotaxanes: Phenomenology and interpretation",
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.",
author = "Ignacio Franco and Schatz, {George C} and Ratner, {Mark A}",
year = "2009",
doi = "10.1063/1.3223729",
language = "English",
volume = "131",
journal = "Journal of Chemical Physics",
issn = "0021-9606",
publisher = "American Institute of Physics Publising LLC",
number = "12",

}

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.

UR - http://www.scopus.com/inward/record.url?scp=70349616636&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70349616636&partnerID=8YFLogxK

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 -