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A synthetic molecular pentafoil knot

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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.

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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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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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The authors declare no competing financial interests.

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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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