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Intra- and intermolecular self-assembly of a 20-nm-wide supramolecular hexagonal grid

An Author Correction to this article was published on 14 May 2020

This article has been updated


For the past three decades, the coordination-driven self-assembly of three-dimensional structures has undergone rapid progress; however, parallel efforts to create large discrete two-dimensional architectures—as opposed to polymers—have met with limited success. The synthesis of metallo-supramolecular systems with well-defined shapes and sizes in the range of 10–100 nm remains challenging. Here we report the construction of a series of giant supramolecular hexagonal grids, with diameters on the order of 20 nm and molecular weights greater than 65 kDa, through a combination of intra- and intermolecular metal-mediated self-assembly steps. The hexagonal intermediates and the resulting self-assembled grid architectures were imaged at submolecular resolution by scanning tunnelling microscopy. Characterization (including by scanning tunnelling spectroscopy) enabled the unambiguous atomic-scale determination of fourteen hexagonal grid isomers.

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Fig. 1: The synthetic strategy of ligand followed by intra- and intermolecular self-assembly of supramolecular hexagonal grids with Fe(ii).
Fig. 2: Mass spectrometry for characterization of the intra- and intermolecular self-assembly processes leading to 5.
Fig. 3: STM imaging of the intra- and intermolecular self-assembled structures on Ag (111) surface.
Fig. 4: Isomeric forms of 5 on substrate and their characterization by STS.

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All data supporting the findings of this study are available in the manuscript or the Supplementary Information.

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  1. He, Y. et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198–201 (2008).

    CAS  PubMed  Google Scholar 

  2. Rappas, M. et al. Structural insights into the activity of enhancer-binding proteins. Science 307, 1972–1975 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Lehn, J.-M. From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry. Chem. Soc. Rev. 36, 151–160 (2007).

    CAS  PubMed  Google Scholar 

  4. Chakrabarty, R., Mukherjee, P. S. & Stang, P. J. Supramolecular coordination: self-assembly of finite two-and three-dimensional ensembles. Chem. Rev. 111, 6810–6918 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Cook, T. R. & Stang, P. J. Recent developments in the preparation and chemistry of metallacycles and metallacages via coordination. Chem. Rev. 115, 7001–7045 (2015).

    CAS  PubMed  Google Scholar 

  6. Chakraborty, S. & Newkome, G. R. Terpyridine-based metallosupramolecular constructs: tailored monomers to precise 2D-motifs and 3D-metallocages. Chem. Soc. Rev. 47, 3991–4016 (2018).

    CAS  PubMed  Google Scholar 

  7. Olenyuk, B., Whiteford, J. A., Fechtenkotter, A. & Stang, P. J. Self-assembly of nanoscale cuboctahedra by coordination chemistry. Nature 398, 796–7799 (1999).

    CAS  PubMed  Google Scholar 

  8. Fujita, D. et al. Self-assembly of tetravalent goldberg polyhedra from 144 small components. Nature 540, 563–566 (2016).

    CAS  PubMed  Google Scholar 

  9. Sun, Q.-F. et al. Self-assembled M24L48 polyhedra and their sharp structural switch upon subtle ligand variation. Science 328, 1144–1147 (2010).

    CAS  PubMed  Google Scholar 

  10. Mal, P., Breiner, B., Rissanen, K. & Nitschke, J. R. White phosphorus is air-stable within a self-assembled tetrahedral capsule. Science 324, 1697–1699 (2009).

    CAS  PubMed  Google Scholar 

  11. Rizzuto, F. J. & Nitschke, J. R. Stereochemical plasticity modulates cooperative binding in a CoII12L6 cuboctahedron. Nat. Chem. 9, 903–908 (2017).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  13. Newkome, G. R. et al. Nanoassembly of a fractal polymer: a molecular “Sierpinski hexagonal gasket”. Science 312, 1782–1785 (2006).

    CAS  PubMed  Google Scholar 

  14. Lewandowski, B. et al. Sequence-specific peptide synthesis by an artificial small-molecule machine. Science 339, 189–193 (2013).

    CAS  PubMed  Google Scholar 

  15. Marcos, V. et al. Allosteric initiation and regulation of catalysis with a molecular knot. Science 352, 1555–1559 (2016).

    CAS  PubMed  Google Scholar 

  16. Danon, J. J. et al. Braiding a molecular knot with eight crossings. Science 355, 159–162 (2017).

    CAS  PubMed  Google Scholar 

  17. Pluth, M. D., Bergman, R. G. & Raymond, K. N. Acid catalysis in basic solution: a supramolecular host promotes orthoformate hydrolysis. Science 316, 85–88 (2007).

    CAS  PubMed  Google Scholar 

  18. McKinlay, R. M., Cave, G. W. V. & Atwood, J. L. Supramolecular blueprint approach to metal-coordinated capsules. Proc. Natl Acad. Sci. USA 102, 5944–5948 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Mohnani, S. & Bonifazi, D. Supramolecular architectures of porphyrins on surfaces: the structural evolution from 1D to 2D to 3D to devices. Coord. Chem. Rev. 254, 2342–2362 (2010).

    CAS  Google Scholar 

  20. Zhang, Z. et al. Supersnowflakes: stepwise self-assembly and dynamic exchange of rhombus star-shaped supramolecules. J. Am. Chem. Soc. 139, 8174–8185 (2017).

    CAS  PubMed  Google Scholar 

  21. Bauer, T. et al. Synthesis of free-standing, monolayered organometallic sheets at the air/water interface. Angew. Chem. Int. Ed. 50, 7879–7884 (2011).

    CAS  Google Scholar 

  22. Zheng, Z. et al. Synthesis of two-dimensional analogues of copolymers by site-to-site transmetalation of organometallic monolayer sheets. J. Am. Chem. Soc. 136, 6103–6110 (2014).

    CAS  PubMed  Google Scholar 

  23. Song, B. et al. Self-assembly of polycyclic supramolecules using linear metal-organic ligands. Nat. Commun. 9, 4575 (2018).

    PubMed  PubMed Central  Google Scholar 

  24. Wang, H. et al. Supramolecular kandinsky circles with high antibacterial activity. Nat. Commun. 9, 1815 (2018).

    PubMed  PubMed Central  Google Scholar 

  25. Sawada, T., Yamagami, M., Ohara, K., Yamaguchi, K. & Fujita, M. Peptide [4]catenane by folding and assembly. Angew. Chem. Int. Ed. 55, 4519–4522 (2016).

    CAS  Google Scholar 

  26. Yamagami, M., Sawada, T. & Fujita, M. Synthetic β-barrel by metal-induced folding and assembly. J. Am. Chem. Soc. 140, 8644–8647 (2018).

    CAS  PubMed  Google Scholar 

  27. Zhang, Y. et al. Simultaneous and coordinated rotational switching of all molecular rotors in a network. Nat. Nanotech. 11, 706–712 (2016).

    Google Scholar 

  28. Lu, X. et al. Probing a hidden world of molecular self-assembly: concentration-dependent, three-dimensional supramolecular interconversions. J. Am. Chem. Soc. 136, 18149–18155 (2014).

    CAS  PubMed  Google Scholar 

  29. Lefter, C. et al. Charge transport and electrical properties of spin crossover materials: towards nanoelectronic and spintronic devices. Magnetochemistry 2, 18 (2016).

  30. Wu, H. & Fuxreiter, M. The structure and dynamics of higher-order assemblies: amyloids, signalosomes, and granules. Cell 165, 1055–1066 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Tompa, P. & Fuxreiter, M. Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions. Trends. Biochem. Sci. 33, 2–8 (2008).

    CAS  PubMed  Google Scholar 

  32. Chan, Y.-T. et al. Self-assembly and traveling wave ion mobility mass spectrometry analysis of hexacadmium macrocycles. J. Am. Chem. Soc. 131, 16395–16397 (2009).

    CAS  PubMed  Google Scholar 

  33. Stejskal, E. O. & Tanner, J. E. Spin diffusion measurements: spin echoes in the presence of a time‐dependent field gradient. J. Chem. Phys. 42, 288–292 (1965).

    CAS  Google Scholar 

  34. Giuseppone, N., Schmitt, J.-L., Allouche, L. & Lehn, J.-M. DOSY NMR experiments as a tool for the analysis of constitutional and motional dynamic processes: implementation for the driven evolution of dynamic combinatorial libraries of helical strands. Angew. Chem. Int. Ed. 47, 2235–2239 (2008).

    CAS  Google Scholar 

  35. Hasegawa, Y. & Avouris, P. Direct observation of standing wave formation at surface steps using scanning tunneling spectroscopy. Phys. Rev. Lett. 71, 1071–1074 (1993).

    CAS  PubMed  Google Scholar 

  36. Li, G., Luican, A. & Andrei, E. Y. Scanning tunneling spectroscopy of graphene on graphite. Phys. Rev. Lett. 102, 176804 (2009).

    PubMed  Google Scholar 

  37. Hess, H. F., Robinson, R. B., Dynes, R. C., Valles, J. M. & Waszczak, J. V. Scanning-tunneling-microscope observation of the abrikosov flux lattice and the density of states near and inside a fluxoid. Phys. Rev. Lett. 62, 214–216 (1989).

    CAS  PubMed  Google Scholar 

  38. Li, Y. et al. Anomalous Kondo resonance mediated by semiconducting graphene nanoribbons in a molecular heterostructure. Nat. Commun. 8, 946 (2017).

    PubMed  PubMed Central  Google Scholar 

  39. Park, J. et al. Coulomb blockade and the Kondo effect in single-atom transistors. Nature 417, 722–725 (2002).

    Google Scholar 

  40. Kresse, G. & Hafner, J. Ab initio molecular-dynamics simulation of the liquid-metal amorphous-semiconductor transition in germanium. Phys. Rev. B 48, 14251–14268 (1994).

    Google Scholar 

  41. Kresse, G. & Furthmuller, J. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput. Mat. Sci. 6, 15–50 (1996).

    CAS  Google Scholar 

  42. Kresse, G. & Furthmuller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B 54, 11169–11186 (1996).

    CAS  Google Scholar 

  43. Anisimov, V. I., Aryasetiawan, F. & Lichtenstein, A. I. First-principles calculations of the electronic structure and spectra of strongly correlated systems: the LDA+U method. J. Phys. Condens. Matter 9, 767–808 (1997).

    CAS  Google Scholar 

  44. Perdew, J. P., Burke, K. & Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865–3868 (1996).

    CAS  PubMed  Google Scholar 

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This research was supported by National Institutes of Health (grant no. R01GM128037 to X.L.). Use of the Center for Nanoscale Materials, an Office of Science user facility, was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract no. DE-AC02-06CH11357. Support from Shanghai University is also gratefully acknowledged. T.R and A.T.N acknowledge the computing resources provided on Bebop, a high-performance computing cluster operated by the Laboratory Computing Resource Center at Argonne National Laboratory. This work was supported in part by the US Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internship (SULI) programme. We also acknowledge partial support through University of South Florida Nexus Initiative (UNI) Award and the Natural Science Foundation of Guangdong Province, China (grant no. 2019A1515011358 to Z.Z.).

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Authors and Affiliations



X.L. and Y.L. conceived and designed the experiments. Z.Z. and Y.L. completed the synthesis. Y.L., B.S., Y.Z., S. W. H and R.T performed STM. Z.Z., X.J. and M.W. conducted NMR. Z.Z. performed MS characterization. T.R. and A.T.N performed DFT calculations. Y.L., B.S., Z.Z., Y.Z., S.W.H, J.L.S., G.R.N. and X.L. analysed the data and wrote the manuscript. All the authors discussed the results and commented on and proofread the manuscript.

Corresponding authors

Correspondence to Yiming Li, Yuan Zhang, Jonathan L. Sessler, Saw Wai Hla or Xiaopeng Li.

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The authors declare no competing interests.

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Supplementary Information

Structures of the species considered in this study; Synthesis and characterization data; computational data; Kondo resonance; Supplementary Schemes 1–6, Figs. 1–97 and references.

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Zhang, Z., Li, Y., Song, B. et al. Intra- and intermolecular self-assembly of a 20-nm-wide supramolecular hexagonal grid. Nat. Chem. 12, 468–474 (2020).

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