Stereoselective synthesis of a composite knot with nine crossings

Abstract

The simultaneous synthesis of a molecular nine-crossing composite knot that contains three trefoil tangles of the same handedness and a \(9_7^3\) link (a type of cyclic [3]catenane topologically constrained to always have at least three twists within the links) is reported. Both compounds contain high degrees of topological writhe (w= 9), a structural feature of supercoiled DNA. The entwined products are generated from the cyclization of a hexameric Fe(ii) circular helicate by ring-closing olefin metathesis, with the mixture of topological isomers formed as a result of different ligand connectivity patterns. The metal-coordinated composite knot was isolated by crystallization, the topology unambiguously proven by tandem mass spectrometry, with X-ray crystallography confirming that the 324-atom loop crosses itself nine times with matching handedness (all Δ or all Λ) at every metal centre within each molecule. Controlling the connectivity of the ligand end groups on circular metal helicate scaffolds provides an effective synthetic strategy for the stereoselective synthesis of composite knots and other complex molecular topologies.

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Fig. 1: Topologies that result from joining ligand strands with the terminal binding sites coordinated to neighbouring metal ions in a hexameric circular helicate.
Fig. 2: The 12 component (6 × ligand 1; 6 × Fe2+) assembly of the intermediate hexameric circular helicate [Fe616](PF6)12 and the synthesis of the +31#+31#+31 composite knot 2 and \({\mathbf{9}}_{\mathbf{7}}^{\mathbf{3}}\) link 3.
Fig. 3: 1H NMR spectra (600 MHz, 298 K) of molecular knot 2, link 3, building block 1 and their coordination complexes.
Fig. 4: ESI–MS and MS/MS experiments on molecular knot 2 and link 3.
Fig. 5: A 1.8 Å resolution X-ray crystal structure of the +31#+31#+31 composite knot [Fe62](PF6)12, in which parts of the molecule are well resolved (for example, the metal ions and much of the circular helicate), whereas others (in particular the flexible linker chains) needed to be modelled to fit the electron density map in a manner analogous to protein crystallography.

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Acknowledgements

We thank the Engineering and Physical Sciences Research Council (EP/P027067/1) and the European Research Council (Advanced Grant no. 339019) for funding, the Diamond Light Source (UK) for synchrotron beam time on I19 (XR029), the University of Manchester for a President’s Doctoral Scholar Award (to L.Z.) and the Finnish Cultural Foundation for a postdoctoral grant (to P.J.). D.A.L. is a Royal Society Research Professor.

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L.Z., A.J.S., A.L.N., J.-F.L. and P.J. carried out the synthesis and characterization studies. I.J.V.-Y. solved the crystal structure. D.A.L. directed the research. All the authors contributed to the analysis of the results and the writing of the manuscript.

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Correspondence to David A. Leigh.

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Supplementary information

Supplementary information

Experimental methods, synthetic procedures and the characterization details for all new compounds, including the X-ray experimental details

Crystallographic data

CIF for compound [Fe62](PF6)12; CCDC reference: 1565130

Supplementary Video

A video file of the rotating X-ray crystal structure of the composite knot

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Zhang, L., Stephens, A.J., Nussbaumer, A.L. et al. Stereoselective synthesis of a composite knot with nine crossings. Nature Chem 10, 1083–1088 (2018). https://doi.org/10.1038/s41557-018-0124-6

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