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Updated: Jul 17, 2026

Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules
Published on: April 25, 2025
A minimalist [2]rotaxane with orthogonal Li+ and F- binding sites and differential fluorescence response
Hazem Amarne1, Eyad A Younes2,3, Fatemeh Salami3
1Department of Chemistry, Faculty of Science, The University of Jordan Amman 11942 Jordan h.amarne@ju.edu.jo.
Abstract:
A minimalist [2]rotaxane, comprising a benzimidazole-dimesitylborane axle mechanically interlocked with a crown ether macrocycle, was designed and synthesized as a dual-responsive heteroditopic receptor. Single-crystal X-ray diffraction unambiguously confirmed the interlocked architecture, revealing hydrogen-bonding interactions between the imidazolyl N-H donor and the crown ether oxygen atoms. 1H NMR binding studies demonstrated that the rotaxane binds Li+ ions at a cooperative binding pocket formed by the crown ether and the imidazole unit, while F- ions bind selectively at the Lewis acidic boron center via formation of a stable fluoroborate species under a slow-exchange regime. Competition experiments established that Li+ binding thermodynamically prevails over F- binding, leading to quantitative displacement of fluoride upon addition of a lithium salt. Density functional theory (DFT) and molecular dynamics (MD) calculations were performed to further examine the 1 : 1 binding complexes for both ionic guests. Fluorescence spectroscopy revealed markedly distinct signal responses: Li+ binding induced a 4.6-fold fluorescence enhancement at 456 nm attributable to rigidification of the molecular framework, whereas F- binding resulted in appreciable quenching observed upon addition of a stoichiometric amount of F- ion. Importantly, subsequent addition of Li+ to the pre-formed [1 + F-] adduct restored the fluorescence. The mutual exclusivity of the two binding events and the differential fluorescence outputs render this rotaxane a functional prototype for molecular logic operations, demonstrating that sophisticated dual responsiveness can be realized within a structurally concise mechanically interlocked framework.

