A Computational Study of a [2]Rotaxane Molecular Shuttle with All‐Atoms Molecular Dynamics and Density Functional Theory Simulations in Solution

TL;DR

This paper uses advanced simulations to study the behavior of a molecular shuttle in different solvents and how it interacts with a platinum compound.

Contribution

The study combines all-atoms molecular dynamics and DFT simulations with QTAIM analysis to explain the molecular shuttle's behavior in solution.

Findings

The free-energy landscape of the [2]rotaxane shuttle in CH2Cl2 was accurately reproduced.

Coordination of PtCl2 to the Bipy site suppresses the shuttle movement in DMF solution.

QTAIM and DFT analyses reveal the nature of supramolecular and coordination interactions.

Abstract

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.

A H‐shaped [2]rotaxane is investigated in CH2Cl2 with all‐atoms molecular dynamics simulations combining quantum theory of atoms in molecules (QTAIM) descriptors with density functional theory (DFT) algorithms. Also, the nature of the chemical interactions modulating the formation of a square planar complex following the coordination of a PtCl2 moiety over a 2,2’‐bipyridyl chelate site in N,N‐dimethylformamide (DMF) is fully characterized.© 2026 WILEY‐VCH GmbH

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