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A synthetic molecular pentafoil knot

Nature Chemistry volume 4, pages 15–20 (2012)Cite this article

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Abstract

Knots are being discovered with increasing frequency in both biological and synthetic macromolecules and have been fundamental topological targets for chemical synthesis for the past two decades. Here, we report on the synthesis of the most complex non-DNA molecular knot prepared to date: the self-assembly of five bis-aldehyde and five bis-amine building blocks about five metal cations and one chloride anion to form a 160-atom-loop molecular pentafoil knot (five crossing points). The structure and topology of the knot is established by NMR spectroscopy, mass spectrometry and X-ray crystallography, revealing a symmetrical closed-loop double helicate with the chloride anion held at the centre of the pentafoil knot by ten CH···Cl– hydrogen bonds. The one-pot self-assembly reaction features an exceptional number of different design elements—some well precedented and others less well known within the context of directing the formation of (supra)molecular species. We anticipate that the strategies and tactics used here can be applied to the rational synthesis of other higher-order interlocked molecular architectures.

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Figure 1: Chloride-template assembly of pentameric iron(II) cyclic double helicates [3a–g]Cl(PF6)9.
Figure 2: Partial 1H NMR spectra (500 MHz, CD3CN, 298 K) of cyclic double helicates and the chloride-complexed and ‘empty cavity’ pentafoil knot.
Figure 3: Synthesis of molecular pentafoil knot [6]Cl(PF6)9 and ‘empty cavity’ pentafoil knot [6](PF6)10.
Figure 4: X-ray crystal structure of molecular pentafoil knot [6]Cl(PF6)9.

References

  1. Wasserman, S. A. & Cozzarelli, N. R. Biochemical topology: applications to DNA recombination and replication. Science 232, 951–960 (1986).

    Article  CAS  Google Scholar 

  2. Taylor, W. R. A deeply knotted protein structure and how it might fold. Nature 406, 916–919 (2000).

    Article  CAS  Google Scholar 

  3. Taylor, W. R. & Lin, K. Protein knots: a tangled problem. Nature 421, 25 (2003).

    Article  CAS  Google Scholar 

  4. Wagner, J. R., Brunzelle, J. S., Forest, K. T. & Vierstra, R. D. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438, 325–331 (2005).

    Article  CAS  Google Scholar 

  5. Taylor, W. R. Protein knots and fold complexity: some new twists. Comput. Biol. Chem. 31, 151–162 (2007).

    Article  CAS  Google Scholar 

  6. Saitta, A. M., Soper, P. D., Wasserman, E. & Klein, M. L. Influence of a knot on the strength of a polymer strand. Nature 399, 46–48 (1999).

    Article  CAS  Google Scholar 

  7. Arai, Y. et al. Tying a molecular knot with optical tweezers. Nature 399, 446–448 (1999).

    Article  CAS  Google Scholar 

  8. Menasco, W. W. & Thistlethwaite, M. B. (eds) Handbook of Knot Theory (Elsevier, 2005).

  9. Fenlon, E. E. Open problems in chemical topology. Eur. J. Org. Chem. 5023–5035 (2008).

    Article  Google Scholar 

  10. Beves, J. E., Blight, B. A., Campbell, C. J., Leigh, D. A. & McBurney, R. T. Strategies and tactics for the metal-directed synthesis of rotaxanes, knots, catenanes, and higher order links. Angew. Chem. Int. Ed. 50, 9260–9327 (2011).

    Article  CAS  Google Scholar 

  11. Alexander, J. W. & Briggs, G. B. On types of knotted curves. Ann. Math. 28, 562–586 (1926–1927).

  12. Adams, C. C. The Knot Book (American Mathematical Society, 2004).

  13. Dietrich-Buchecker, C. O. & Sauvage, J-P. A synthetic molecular trefoil knot. Angew. Chem. Int. Ed. Engl. 28, 189–192 (1989).

    Article  Google Scholar 

  14. Piguet, C., Bernardinelli, G. & Hopfgartner, G. Helicates as versatile supramolecular complexes. Chem. Rev. 97, 2005–2062 (1997).

    Article  CAS  Google Scholar 

  15. Ashton, P. R. et al. Molecular meccano 27. A template-directed synthesis of a molecular trefoil knot. Liebigs Ann. Recueil 2485–2494 (1997).

    Article  Google Scholar 

  16. Rapenne, G., Dietrich-Buchecker, C. & Sauvage, J-P. Copper(I)- or iron(II)-templated synthesis of molecular knots containing two tetrahedral or octahedral coordination sites. J. Am. Chem. Soc. 121, 994–1001 (1999).

    Article  CAS  Google Scholar 

  17. Safarowsky, O., Nieger, M., Fröhlich. R. & Vögtle, F. A molecular knot with twelve amide groups—one-step synthesis, crystal structure, chirality. Angew. Chem. Int. Ed. 39, 1616–1618 (2000).

    Article  CAS  Google Scholar 

  18. Lukin, O. & Vögtle, F. Knotting and threading of molecules: chemistry and chirality of molecular knots and their assemblies. Angew. Chem. Int. Ed. 44, 1456–1477 (2005).

    Article  CAS  Google Scholar 

  19. Feigel, M., Ladberg, R., Engels, S., Herbst-Irmer, R. & Fröhlich, R. A trefoil knot made of amino acids and steroids. Angew. Chem. Int. Ed. 45, 5698–5702 (2006).

    Article  CAS  Google Scholar 

  20. Fenlon, E. E. & Ito, B. R. The thread & cut method: syntheses of molecular knot precursors. Eur. J. Org. Chem. 3065–3068 (2008).

  21. Guo, J., Mayers, P. C., Breault, G. A. & Hunter, C. A. Synthesis of a molecular trefoil knot by folding and closing on an octahedral coordination template. Nature Chem. 2, 218–222 (2010).

    Article  CAS  Google Scholar 

  22. Barran, P. E. et al. Active metal template synthesis of a molecular trefoil knot. Angew. Chem. Int. Ed. http://dx.doi.org/10.1002/anie.201105012 (2011).

  23. Carina, R. F., Dietrich-Buchecker, C. & Sauvage, J-P. Molecular composite knots. J. Am. Chem. Soc. 118, 9110–9116 (1996).

    Article  CAS  Google Scholar 

  24. Fujita, M., Ibukuro, F., Hagihara, H. & Ogura, K. Quantitative self-assembly of a [2]catenane from two preformed molecular rings. Nature 367, 720–723 (1994).

    Article  CAS  Google Scholar 

  25. Wang, L., Vysotsky, M. O., Bogdan, A., Bolte, M. & Böhmer, V. Multiple catenanes derived from calix[4]arenes. Science 304, 1312–1314 (2004).

    Article  CAS  Google Scholar 

  26. Lam, R. T. S. et al. Amplification of acetylcholine-binding catenanes from dynamic combinatorial libraries. Science 308, 667–669 (2005).

    Article  CAS  Google Scholar 

  27. Ronson, T. K. et al. Stellated polyhedral assembly of a topologically complicated Pd4L4 ‘Solomon cube’. Nature Chem. 1, 212–216 (2009).

    Article  CAS  Google Scholar 

  28. Hasell, T. et al. Triply interlocked covalent organic cages. Nature Chem. 2, 750–755 (2010).

    Article  CAS  Google Scholar 

  29. Chichak, K. S. et al. Molecular Borromean rings. Science 304, 1308–1312 (2004).

    Article  CAS  Google Scholar 

  30. Dietrich-Buchecker, C., Colasson, B., Jouvenot, D. & Sauvage, J-P. Synthesis of multi-1,10-phenanthroline ligands with 1,3-phenylene linkers and their lithium complexes. Chem. Eur. J. 11, 4374–4386 (2005).

    Article  CAS  Google Scholar 

  31. Hasenknopf, B., Lehn, J-M., Kneisel, B. O., Baum, G. & Fenske, D. Self-assembly of a circular double helicate. Angew. Chem. Int. Ed. Engl. 35, 1838–1840 (1996).

    Article  CAS  Google Scholar 

  32. Hasenknopf, B. et al. Self-assembly of tetra- and hexanuclear circular helicates. J. Am. Chem. Soc. 119, 10956–10962 (1997).

    Article  CAS  Google Scholar 

  33. Hasenknopf, B., Lehn, J-M., Boumediene, N., Leize, E. & Van Dorsselaer, A. Kinetic and thermodynamic control in self-assembly: sequential formation of linear and circular helicates. Angew. Chem. Int. Ed. 37, 3265–3268 (1998).

    Article  CAS  Google Scholar 

  34. Leigh, D. A., Lusby, P. J., Teat, S. J., Wilson, A. J. & Wong, J. K. Y. Benzylic imine catenates: readily accessible octahedral analogues of the Sauvage catenates. Angew. Chem. Int. Ed. 40, 1538–1543 (2001).

    Article  CAS  Google Scholar 

  35. Hogg, L. et al. A simple general ligand system for assembling octahedral metal–rotaxane complexes. Angew. Chem. Int. Ed. 43, 1218–1221 (2004).

    CAS  Google Scholar 

  36. Hutin, M., Schalley, C. A., Bernardinelli, G. & Nitschke, J. R. Helicate, macrocycle, or catenate: dynamic topological control over subcomponent self-assembly. Chem. Eur. J. 12, 4069–4076 (2006).

    Article  CAS  Google Scholar 

  37. Price, J. R. et al. Copper(I)-templated synthesis of a 2,2′-bipyridine derived [2]catenane: synthetic, modelling, and X-ray studies. Aust. J. Chem. 62, 1014–1019 (2009).

    Article  CAS  Google Scholar 

  38. Murcko, M. A. & DiPaola, R. A. Ab initio molecular orbital conformational analysis of prototypical organic systems. 1. Ethylene glycol and 1,2-dimethoxyethane. J. Am. Chem. Soc. 114, 10010–10018 (1992).

    Article  CAS  Google Scholar 

  39. Ohsawa, Y., DeArmond, M. K., Hanck, K. W. & Moreland, C. G. A proton NMR study of reduced paramagnetic tris(2,2′-bipyridine) complexes of iron(II), ruthenium(II) and osmium(II). J. Am. Chem. Soc. 107, 5383–5386 (1985).

    Article  CAS  Google Scholar 

  40. Mamula, O., von Zelewsky, A. & Bernardinelli, G. Completely stereospecific self-assembly of a circular helicate. Angew. Chem. Int. Ed. 37, 290–293 (1998).

    Article  CAS  Google Scholar 

  41. Krämer, R., Lehn, J-M. & Marquis-Rigault, A. Self-recognition in helicate self-assembly: spontaneous formation of helical metal complexes from mixtures of ligands and metal ions. Proc. Natl Acad. Sci. USA 90, 5394–5398 (1993).

    Article  Google Scholar 

  42. Albrecht, M. ‘Let's twist again’—double-stranded, triple-stranded, and circular helicates. Chem. Rev. 101, 3457–3497 (2001).

    Article  CAS  Google Scholar 

  43. Nitschke, J. R. Construction, substitution, and sorting of metallo-organic structures via subcomponent self-assembly. Acc. Chem. Res. 40, 103–112 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank the Diamond Light Source (UK) for synchrotron beamtime on I19 (XR029), the Engineering and Physical Sciences Research Council (EPSRC) National Crystallography Service for data collection, and the EPSRC National Mass Spectrometry Service Centre (Swansea, UK) and C.L. Mackay (SIRCAMS, University of Edinburgh) for high-resolution mass spectrometry. J.E.B. and D.S. are Swiss National Science Foundation postdoctoral fellows. This research was funded by the EPSRC and the Academy of Finland (K.R., projects 212588 and 218325).

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Authors and Affiliations

  1. School of Chemistry, University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK

    Jean-François Ayme, Jonathon E. Beves, David A. Leigh, Roy T. McBurney & David Schultz

  2. Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, 40014 JYU, Finland

    Kari Rissanen

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  1. Jean-François Ayme
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Contributions

J-F.A., J.E.B., R.T.M. and D.S. carried out the synthesis and characterization studies, helped plan the experiments, and participated in the preparation of the manuscript. K.R. solved the crystal structure. D.A.L. helped plan the experiments and prepare the manuscript.

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Correspondence to David A. Leigh.

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Crystallographic data for compound 6 (CIF 117 kb)

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Ayme, JF., Beves, J., Leigh, D. et al. A synthetic molecular pentafoil knot. Nature Chem 4, 15–20 (2012). https://doi.org/10.1038/nchem.1193

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