Conformational analysis and UV/Vis spectroscopic properties of a rotaxane-based molecular machine in acetonitrile dilute solution: when simulations meet experiments

A reduced form of a synthetic hydrogen-assembled molecular shuttle for nano-technological applications has been investigated by molecular dynamics simulations and density functional theory calculations. It is composed by a benzylic amide macrocycle mechanically locked onto a thread in acetonitrile s...

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Bibliographic Details
Published in:Physical chemistry chemical physics : PCCP 2011-01, Vol.13 (6), p.2342-2349
Main Authors: MANCINI, Giordano, ZAZZA, Costantino, ASCHI, Massimiliano, SANNA, Nico
Format: Article
Language:English
Subjects:
Acetonitrile
Acetonitriles - chemistry
Anions
Chemistry
Electrochemistry
Exact sciences and technology
General and physical chemistry
Hydrogen Bonding
Models, Molecular
Molecular Conformation
Molecular dynamics
Molecular Dynamics Simulation
Nanostructure
Reduction
Rotaxanes - chemistry
Sampling
Simulation
Solutions
Spectrophotometry, Ultraviolet
Spectroscopy
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Summary:A reduced form of a synthetic hydrogen-assembled molecular shuttle for nano-technological applications has been investigated by molecular dynamics simulations and density functional theory calculations. It is composed by a benzylic amide macrocycle mechanically locked onto a thread in acetonitrile solution. Classical sampling indicates, in agreement with experimental findings, that in equilibrium condition at 298 K the macrocycle and the naphthalimide radical anion moiety within the thread strongly interact forming four strong OCN-H-O=CNR hydrogen bonds. Simulations also revealed that the geometry of the supramolecular assembly reversibly oscillates between unfolded and folded conformations, with the latter characterized by an electrostatic hook involving the succinamide end group and the macrocycle itself. Finally, the simulated UV-Vis absorption spectra for free and complexed reduced naphthalimide quantitatively confirm that the transient spectroscopic change experimentally used as a probe for monitoring the translational motion of the macrocycle, from succinamide to naphthalimide stations, accompanying the selective electrochemical reduction.
ISSN:1463-9076
1463-9084
DOI:10.1039/c0cp01773f