A Computational Study of a [2]Rotaxane Molecular Shuttle with All-Atoms Molecular Dynamics and Density Functional...

A rigid H-shaped [2]rotaxane shuttle composed by a mechanically interlocked 24-crown-8(24C8) macrocycle on a thread containing two symmetrical benzimidazole (Bzi) stations bound with a central 2,2'-bipyridyl (Bipy) core is addressed in CH₂Cl₂ solution with all-atoms molecular dynamics simulations. The experimentally observed conformational preferences of the 24C8 ring quantitatively characterizing the free-energy landscape driving its reversible translocation over the synthetic Stop-[Bzi-Bipy-Bzi]-Stop thread at room temperature have been reproduced. Also, this analysis to a translationally inactive form in N,N-dimethylformamide (DMF) dilute solution following the coordination of PtCl₂ to the Bipy chelate site is extended. In this respect, in the presence of PtCl₂, the optimized geometry within the density functional theory (DFT) framework is fully characterized in terms of quantum theory of atoms in molecules (QTAIM) descriptors. Converged DFT wavefunctions in a continuum environment are analytically investigated by means of electron density ρ(r), local electronic energy density, H(r), electron localization function (ELF), and delocalization index δ(X,Y) analysis. The derived picture highlights that the contextual presence of supramolecular contacts confining the 24C8 ring over its primary recognition site, and of a planar square (Bipy)-N₂-Pt^(II)Cl₂ coordination environment parallel to the axle should actually be effective in suppressing the shutting movement as hypothesized via ¹H-nuclear magnetic resonance measurements.