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Polyyne formation via skeletal rearrangement induced by atomic manipulation


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.

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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.


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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




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, Harry L. Anderson or Leo Gross.

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The authors declare no competing interests.

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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

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Pavliček, N., Gawel, P., Kohn, D.R. et al. Polyyne formation via skeletal rearrangement induced by atomic manipulation. Nature Chem 10, 853–858 (2018).

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