Functionally rigid and degenerate molecular shuttles

Il Yoon, Diego Benítez, Yan Li Zhao, Ognjen Š Miljanić, Soo Young Kim, Ekaterina Tkatchouk, Ken C.F. Leung, Saeed I. Khan, William A. Goddard, J. Fraser Stoddart

Research output: Contribution to journalArticle

38 Scopus citations


The preparation and dynamic behavior of two functionally rigid and degenerate [2]rotaxanes (1·4PF6 and 2·4PF6) in which a π-electron deficient tetracationic cyclophane, cyclobis(para-quat-p-phenylene) (CBPQT4+) ring, shuttles back and forth between two π-electron-rich naphthalene (NP) stations by making the passage along an ethynyl-phenylene-(PH)-ethynyl or buta-diyne rod, are described. The [2]rotaxanes were synthesized by using the clipping approach to template-directed synthesis, and were characterized by NMR spectroscopic and mass spectrometry analyses. 1H NMR spectra of both [2]rotaxanes show evidence for the formation of mechanically interlocked structures, resulting in the upfield shifts of the resonances for key protons on the dumbbell-shaped components. In particular, the signals for the peri protons on the NP units in the dumbbell-shaped components experienced significant upfield shifts at low temperatures, just as has been observed in the flexible [2]rotaxanes. Interestingly, the resonances for the same protons did not exhibit a significant upfield shift at 298 K, but rather only a modest shift. This phenomenon arises from the much reduced binding of the ethynylNP unit compared to the 1,5-dioxy-NP unit. This effect, in turn, increases the shuttling rate when compared to the 1,5-dioxy-NP-based rotaxane systems investigated previously. The kinetic and thermodynamic data of the shuttling behavior of the CBPQT4+ ring between the NP units were obtained by variable-temperature NMR spectroscopy and using the coalescence method to calculate the free energies of activation (δGc=) of 9.6 and 10.3 kcal mor-1 for 1·4PF6 and 2·4PF6, respectively, probed by using the rotaxane's α-bipyridinium protons. The solid-state structure of the free dumbbell-shaped compound (3) shows the fully rigid ethynyl-PH-ethynyl linker with a length (8.1 Å) twice as long as that (3.8 Å) of the butadiyne linker. Full-atomistic simulations were carried out with the DREIDING force field (FF) to probe the degenerate molecular shuttling processes, and afforded shuttling energy barriers (ΔG = 10.4 kcal mol -1 for 1·4PF6 and 2·4PF6) that are in good agreement with the experimental values (ΔGc = 9.6 and 10.3 kcal mor-1 for 1·4PF 6 and 2·4PF6, respectively, probed by using their α-bipyridinium protons).

Original languageEnglish (US)
Pages (from-to)1115-1122
Number of pages8
JournalChemistry - A European Journal
Issue number5
StatePublished - Jan 19 2009


  • Molecular modeling
  • Molecular shuttles
  • Rotaxanes
  • Self-assembly
  • Template-directed synthesis

ASJC Scopus subject areas

  • Catalysis
  • Organic Chemistry

Fingerprint Dive into the research topics of 'Functionally rigid and degenerate molecular shuttles'. Together they form a unique fingerprint.

  • Cite this

    Yoon, I., Benítez, D., Zhao, Y. L., Miljanić, O. Š., Kim, S. Y., Tkatchouk, E., Leung, K. C. F., Khan, S. I., Goddard, W. A., & Stoddart, J. F. (2009). Functionally rigid and degenerate molecular shuttles. Chemistry - A European Journal, 15(5), 1115-1122.