Polyyne formation via skeletal rearrangement induced by atomic manipulation

Abstract

Rearrangements that change the connectivity of a carbon skeleton are often useful in synthesis, but it can be difficult to follow their mechanisms. Scanning probe microscopy can be used to manipulate a skeletal rearrangement at the single-molecule level, while monitoring the geometry of reactants, intermediates and final products with atomic resolution. We studied the reductive rearrangement of 1,1-dibromo alkenes to polyynes on a NaCl surface at 5 K, a reaction that resembles the Fritsch–Buttenberg–Wiechell rearrangement. Voltage pulses were used to cleave one C–Br bond, forming a radical, then to cleave the remaining C–Br bond, triggering the rearrangement. These experiments provide structural insight into the bromo-vinyl radical intermediates, showing that the C=C–Br unit is nonlinear. Long polyynes, up to the octayne Ph–(C≡C)8–Ph, have been prepared in this way. The control of skeletal rearrangements opens a new window on carbon-rich materials and extends the toolbox for molecular synthesis by atom manipulation.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: FBW rearrangement.
Fig. 2: On-surface reactions studied in this work.
Fig. 3: On-surface reaction to generate triyne 5 from precursor 5(Br2) on bilayer NaCl on Cu(111).
Fig. 4: On-surface reaction to generate hexayne 7 from precursor 7(Br4).
Fig. 5: Characterization of polyynes 5–8 on NaCl using AFM, STM and STS.

References

  1. 1.

    Schrettl, S. et al. Functional carbon nanosheets prepared from hexayne amphiphile monolayers at room temperature. Nat. Chem. 6, 468–476 (2014).

    Article  CAS  PubMed  Google Scholar 

  2. 2.

    Wang, C. et al. Oligoyne single molecule wires. J. Am. Chem. Soc. 131, 15647–15654 (2009).

    Article  CAS  PubMed  Google Scholar 

  3. 3.

    Eisler, S. et al. Polyynes as a model for carbyne: synthesis, physical properties, and nonlinear optical response. J. Am. Chem. Soc. 127, 2666–2676 (2005).

    Article  CAS  PubMed  Google Scholar 

  4. 4.

    Diederich, F. Carbon scaffolding: building acetylenic all-carbon and carbon-rich compounds. Nature 369, 199–207 (1994).

    Article  CAS  Google Scholar 

  5. 5.

    Tykwinski, R. R. Carbyne: the molecular approach. Chem. Rec. 15, 1060–1074 (2015).

    Article  CAS  PubMed  Google Scholar 

  6. 6.

    Hoye, R. H., Baire, B., Niu, D., Willoughby, P. H. & Woods, B. P. The hexadehydro-Diels–Alder reaction. Nature 490, 208–212 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Chalifoux, W. A. & Tykwinski, R. R. Synthesis of polyynes to model the sp-carbon allotrope carbyne. Nat. Chem. 2, 967–971 (2010).

    Article  CAS  PubMed  Google Scholar 

  8. 8.

    Stahl, J. et al. sp Carbon chains surrounded by sp 3 carbon double helices: a class of molecules that are accessible by self-assembly and models for ‘insulated’ molecular-scale devices. Angew. Chem. Int. Ed. 41, 1871–1876 (2002).

    Article  CAS  Google Scholar 

  9. 9.

    Movsisyan, L. D. et al. Polyyne rotaxanes: stabilization by encapsulation. J. Am. Chem. Soc. 138, 1366–1376 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Diederich, F. et al. All-carbon molecules: evidence for the generation of cyclo[18]carbon from a stable organic precursor. Science 245, 1088–1090 (1989).

    Article  CAS  PubMed  Google Scholar 

  11. 11.

    Fritsch, P. IV. Ueber die Darstellung von Diphenylacetaldehyd und eine neue Synthese von Tolanderivaten. Liebigs Ann. Chem. 279, 319–323 (1894).

    Article  Google Scholar 

  12. 12.

    Buttenberg, W. P. Condensation des Dichloracetals mit Phenol und Toluol. Liebigs Ann. Chem. 279, 324–337 (1894).

    Article  Google Scholar 

  13. 13.

    Wiechell, H. Condensation des Dichloracetals mit Anisol und Phenetol. Liebigs Ann. Chem. 279, 337–344 (1894).

    Article  Google Scholar 

  14. 14.

    Jahnke, E. & Tykwinski, R. R. The Fritsch–Buttenberg–Wiechell rearrangement: modern applications for an old reaction. Chem. Commun. 46, 3235–3249 (2010).

    Article  CAS  Google Scholar 

  15. 15.

    Corey, E. J. & Fuchs, P. L. A synthetic method for formyl→ethynyl conversion (RCHO→RC≡CH or RC≡CR’). Tetrahedron Lett. 13, 3769–3772 (1972).

    Article  Google Scholar 

  16. 16.

    Eisler, S. & Tykwinski, R. R. Migrating alkynes in vinylidene carbenoids: an unprecedented route to polyynes. J. Am. Chem. Soc. 122, 10736–10737 (2000).

    Article  CAS  Google Scholar 

  17. 17.

    Luu, T., Morisaki, Y., Cunningham, N. & Tykwinski, R. R. One-pot formation and derivatization of di- and triynes based on the Fritsch–Buttenberg–Wiechell rearrangement. J. Org. Chem. 72, 9622–9629 (2007).

    Article  CAS  PubMed  Google Scholar 

  18. 18.

    Stang, P. J. Unsaturated carbenes. Chem. Rev. 78, 383–405 (1978).

    Article  CAS  Google Scholar 

  19. 19.

    Knorr, R. Alkylidenecarbenes, alkylidenecarbenoids, and competing species: which is responsible for vinylic nucleophilic substitution, [1+2] cycloadditions, 1,5-CH insertions, and the Fritsch–Buttenberg–Wiechell rearrangement? Chem. Rev. 104, 3795–3849 (2004).

    Article  CAS  PubMed  Google Scholar 

  20. 20.

    Pritchard, J. G. & Bothner-By, A. A. Base-initiated dehydrohalogenation and rearrangement of 1-halo-2,2-diphenylethylenes in t-butyl alcohol. The effect of deuterated solvent. J. Phys. Chem. 64, 1271–1277 (1960).

    Article  CAS  Google Scholar 

  21. 21.

    Kunishima, M., Hioki, K., Ohara, T. & Tani, S. Generation of alkylidenecarbenes from 1,1-dibromoalk-1-enes by the reaction with samarium diiodide in hexamethylphosphoric triamide-benzene. J. Chem. Soc., Chem. Commun. 219–220 (1992).

  22. 22.

    Umeda, R., Yuasa, T., Anahara, N. & Nishiyama, Y. Fritsch–Buttenberg–Wiechell rearrangement to alkynes from gem-dihaloalkenes with lanthanum metal. J. Organomet. Chem. 696, 1916–1919 (2011).

    Article  CAS  Google Scholar 

  23. 23.

    Binnig, G. & Rohrer, H. Scanning tunneling microscopy—from birth to adolescence. Angew. Chem. Int. Ed. Engl. 26, 606–614 (1987).

    Article  Google Scholar 

  24. 24.

    Eigler, D. M. & Schweizer, E. K. Positioning single atoms with a scanning tunnelling microscope. Nature 344, 524–526 (1990).

    Article  CAS  Google Scholar 

  25. 25.

    Gross, L., Mohn, F., Moll, N., Liljeroth, P. & Meyer, G. The chemical structure of a molecule resolved by atomic force microscopy. Science 325, 1110–1114 (2009).

    Article  CAS  PubMed  Google Scholar 

  26. 26.

    Gross, L. et al. Organic structure determination using atomic-resolution scanning probe microscopy. Nat. Chem. 2, 821–825 (2010).

    Article  CAS  PubMed  Google Scholar 

  27. 27.

    de Oteyza, D. G. et al. Direct imaging of covalent bond structure in single-molecule chemical reactions. Science 340, 1434–1437 (2013).

    Article  CAS  PubMed  Google Scholar 

  28. 28.

    Ruffieux, P. et al. On-surface synthesis of graphene nanoribbons with zigzag edge topology. Nature 531, 489–493 (2016).

    Article  CAS  Google Scholar 

  29. 29.

    He, Y. et al. Fusing tetrapyrroles to graphene edges by surface-assisted covalent coupling. Nat. Chem. 9, 33–38 (2016).

    PubMed  Google Scholar 

  30. 30.

    Sun, Q. et al. Bottom-up synthesis of metalated carbyne. J. Am. Chem. Soc. 138, 1106–1109 (2016).

    Article  CAS  PubMed  Google Scholar 

  31. 31.

    Kawai, S. et al. Thermal control of sequential on-surface transformation of a hydrocarbon molecule on a copper surface. Nat. Commun. 7, 12711 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Riss, A. et al. Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy. Nat. Chem. 8, 678–683 (2016).

    Article  CAS  PubMed  Google Scholar 

  33. 33.

    Stetsovych, O. et al. From helical to planar chirality by on-surface chemistry. Nat. Chem. 9, 213–218 (2017).

    Article  CAS  PubMed  Google Scholar 

  34. 34.

    Shiotari, A. et al. Strain-induced skeletal rearrangement of a polycyclic aromatic hydrocarbon on a copper surface. Nat. Commun. 8, 16089 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Sun, Q. et al. On-surface formation of cumulene by dehalogenative homocoupling of alkenyl gem-dibromides. Angew. Chem. Int. Ed. 56, 12165–12169 (2017).

    Article  CAS  Google Scholar 

  36. 36.

    Hla, S.-W., Bartels, L., Meyer, G. & Rieder, K.-H. Inducing all steps of a chemical reaction with the scanning tunneling microscope tip: towards single molecule engineering. Phys. Rev. Lett. 85, 2777–2780 (2000).

    Article  CAS  PubMed  Google Scholar 

  37. 37.

    Pavliček, N. et al. On-surface generation and imaging of arynes by atomic force microscopy. Nat. Chem. 7, 623–628 (2015).

    Article  CAS  PubMed  Google Scholar 

  38. 38.

    Schuler, B. et al. Reversible Bergman cyclization by atomic manipulation. Nat. Chem. 8, 220–224 (2016).

    Article  CAS  PubMed  Google Scholar 

  39. 39.

    Pavliček, N. et al. Generation and characterization of a meta-aryne on Cu and NaCl surfaces. ACS Nano 11, 10768–10773 (2017).

    Article  CAS  PubMed  Google Scholar 

  40. 40.

    Pavliček, N. et al. Synthesis and characterization of triangulene. Nat. Nanotech. 12, 308–311 (2017).

    Article  CAS  Google Scholar 

  41. 41.

    Repp, J., Meyer, G., Stojković, S. M., Gourdon, A. & Joachim, C. Molecules on insulating films: scanning-tunneling microscopy imaging of individual molecular orbitals. Phys. Rev. Lett. 94, 026803 (2005).

    Article  CAS  PubMed  Google Scholar 

  42. 42.

    Giessibl, F. J. High-speed force sensor for force microscopy and profilometry utilizing a quartz tuning fork. Appl. Phys. Lett. 73, 3956–3958 (1998).

    Article  CAS  Google Scholar 

  43. 43.

    Mohn, F., Schuler, B., Gross, L. & Meyer, G. Different tips for high-resolution atomic force microscopy and scanning tunneling microscopy of single molecules. Appl. Phys. Lett. 102, 073109 (2013).

    Article  CAS  Google Scholar 

  44. 44.

    Schendel, V. et al. Remotely controlled isomer selective molecular switching. Nano Lett. 16, 93–97 (2015).

    Article  CAS  PubMed  Google Scholar 

  45. 45.

    Ladenthin, J. N. et al. Hot carrier-induced tautomerization within a single porphycene molecule on Cu(111). ACS Nano 9, 7287–7295 (2015).

    Article  CAS  PubMed  Google Scholar 

  46. 46.

    Schuler, B. et al. Adsorption geometry determination of single molecules by atomic force microscopy. Phys. Rev. Lett. 111, 106103 (2013).

    Article  CAS  PubMed  Google Scholar 

  47. 47.

    Moore, K. A., Vidaurri-Martinez, J. S. & Thamattoor, D. M. The benzylidenecarbene–phenylacetylene rearrangement: an experimental and computational study. J. Am. Chem. Soc. 134, 20037–20040 (2012).

    Article  CAS  PubMed  Google Scholar 

  48. 48.

    Galli, C., Guarnieri, A., Koch, H., Mencarelli, P. & Rappoport, Z. Effect of substituents on the structure of the vinyl radical: calculations and experiments. J. Org. Chem. 62, 4072–4077 (1997).

    Article  CAS  Google Scholar 

  49. 49.

    Zhu, C., Duarte, L. & Khriachtchev, L. Matrix-isolation and computational study of H2CCCl and H2CCBr radicals. J. Chem. Phys. 145, 074312 (2016).

    Article  CAS  PubMed  Google Scholar 

  50. 50.

    Albrecht, T. R., Grütter, P., Horne, D. & Rugar, D. Frequency modulation detection using high-Q cantilevers for enhanced force microscope sensitivity. J. Appl. Phys. 69, 668–673 (1991).

    Article  Google Scholar 

Download references

Acknowledgements

The research leading to these results received funding from ERC Advanced Grants CEMAS (agreement no. 291194) and CoSuN (320969), ERC Consolidator Grant AMSEL (682144) and EU project PAMS (610446). P.G. acknowledges receipt of Postdoc.Mobility fellowships from the Swiss National Science Foundation. Y.X. was supported by the EPSRC Centre for Doctoral Training in Synthesis for Biology and Medicine (EP/L015838/1) and by a University of Oxford Clarendon Fund Scholarship. The authors acknowledge use of the Oxford Advanced Research Computing (ARC) facility to carry out computational work (doi: 10.5281/zenodo.22558). The authors thank R.S. Paton and I. Gruebner for discussions on computational studies and A.L. Thompson for help with X-ray crystal structure refinements.

Author information

Affiliations

Authors

Contributions

P.G. conceived the project. N.P., Z.M., G.M. and L.G. performed the STM/AFM experiments and analysis. P.G. and D.R.K. performed the organic synthesis. Y.X. measured and solved X-ray crystal structures. H.L.A. contributed to the design of the study. All authors analysed the results and contributed to the manuscript.

Corresponding authors

Correspondence to Przemyslaw Gawel or Harry L. Anderson or Leo Gross.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary information

Supplementary details about the synthesis and analysis of dibromoolefins, crystallographic information and extensive information on computational studies and additional surface experiments

Crystallographic data

CIF for compound 6Br4; CCDC reference: 1567547

Crystallographic data

Structure factors for compound 6Br4; CCDC reference: 1567547

Crystallographic data

CIF for compound 7Br4; CCDC reference: 1567546

Crystallographic data

Structure factors for compound 7Br4; CCDC reference: 1567546

Crystallographic data

CIF for compound 8Br4; CCDC reference: 1567548

Crystallographic data

Structure factors for compound 8Br4; CCDC reference: 1567548

Calculated Cartesian coordinates

Cartesian coordinates of geometries for all calculated structures

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Pavliček, N., Gawel, P., Kohn, D.R. et al. Polyyne formation via skeletal rearrangement induced by atomic manipulation. Nature Chem 10, 853–858 (2018). https://doi.org/10.1038/s41557-018-0067-y

Download citation

Further reading