What is it about?

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.

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Why is it important?

We focused on this synthetic supramolecular assembly since driven by the curiosity of addressing the nature of the chemical interactions opening up the fascinating possibility of modulating translocation mechanisms of interlocked macrocycles via metal cations. The modification of rotaxane structures through metal complexation and selective electrochemical reduction represents an intriguing perspective to enhance the functionalities of molecular machines and devices operating in liquid environments. The proposed computational scenario at room-temperature conditions provides a reproduction of the conformational preferences of the 24C8 ring along the Stop-[Bzi-Bipy-Bzi]-Stop molecular axis. Moreover, the real time shuttling kinetic arising from the free-energy landscape driving the reversible translocation of the macrocycle over the Stop-[Bzi-Bipy-Bzi]-Stop thread is also well reproduced (ΔG‡ of 15.1 versus 11.2 kcal mol−1) with an umbrella sampling method. Further analyses suggest that a labile supramolecular aggregate can be appreciated at the middle point along the shuttling movement connecting the ether ring with the central Bipy unit. Also, we extended our combined C-PCM/DFT+QTAIM analysis to a translationally inactive form in DMF following the coordination of a PtCl2 moiety to the Bipy chelate site. From these data, we obtain that the contextual presence of supramolecular contacts confining the 24C8 ring over its primary recognition site, and, of a planar square (Bipy)-N2-Pt2+Cl2 complex parallel to the axle and held together by covalent chemical bonds should be actually effective in suppressing the shuttling movement as hypothesized via 1 H-NMR measurements.

Perspectives

The proposed work suggests once again that theoretical modeling can be useful for obtaining—in a computationally affordable and relatively accurate way—analytical information finely modulating the conformational shaping of molecular machines and devices of a certain complexity. Consequently, we expect that these investigation methods will become part of a more general protocol that will enable the identification of molecular systems for advanced nanotechnological applications with progressively higher efficiency and functionalities.

Dr Costantino Zazza
Universita degli Studi della Tuscia

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This page is a summary of: A Computational Study of a [2]Rotaxane Molecular Shuttle with All‐Atoms Molecular Dynamics and Density Functional Theory Simulations in Solution, ChemPhysChem, November 2025, Wiley,
DOI: 10.1002/cphc.202500660.
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