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Unveiling the full reaction path of the Suzuki–Miyaura cross-coupling in a single-molecule junction

Nature Nanotechnology volume 16, pages 1214–1223 (2021)Cite this article

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Abstract

Conventional analytic techniques that measure ensemble averages and static disorder provide essential knowledge of the reaction mechanisms of organic and organometallic reactions. However, single-molecule junctions enable the in situ, label-free and non-destructive sensing of molecular reaction processes at the single-event level with an excellent temporal resolution. Here we deciphered the mechanism of Pd-catalysed Suzuki–Miyaura coupling by means of a high-resolution single-molecule platform. Through molecular engineering, we covalently integrated a single molecule Pd catalyst into nanogapped graphene point electrodes. We detected sequential electrical signals that originated from oxidative addition/ligand exchange, pretransmetallation, transmetallation and reductive elimination in a periodic pattern. Our analysis shows that the transmetallation is the rate-determining step of the catalytic cycle and clarifies the controversial transmetallation mechanism. Furthermore, we determined the kinetic and thermodynamic constants of each elementary step and the overall catalytic timescale of this Suzuki–Miyaura coupling. Our work establishes the single-molecule platform as a detection technology for catalytic organochemistry that can monitor transition-metal-catalysed reactions in real time.

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Fig. 1: Design of a single-molecule catalyst device.
Fig. 2: Preparation and characterization of a single-molecule catalyst device.
Fig. 3: Electrical characterization and signal attribution of the single-molecule Suzuki–Miyaura cross-coupling reaction.
Fig. 4: Intermediate-controlled experiments.
Fig. 5: Theoretical potential energy surface calculation of the single-molecule Suzuki–Miyaura cross-coupling reaction.
Fig. 6: Dynamic characterization of a single-molecule Suzuki–Miyaura cross-coupling reaction.

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Data availability

The datasets used in this work are available online from the Zenodo repository at https://doi.org/10.5281/zenodo.4903414. Source data are provided with this paper.

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Acknowledgements

We acknowledge primary financial support from the National Key R&D Program of China (2017YFA0204901), the National Natural Science Foundation of China (21727806, 21933001 and 21772003) and the Tencent Foundation through the XPLORER PRIZE. The research at UCLA was supported by the US National Science Foundation (CHE 1764328). S.Z. and Z.L. appreciate the support from the High-Performance Computing Platform of the Center for Life Science at Peking University.

Author information

Author notes

  1. These authors contributed equally: Chen Yang, Lei Zhang, Chenxi Lu.

Authors and Affiliations

  1. Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China

    Chen Yang, Shuyao Zhou, Yu Li, Zhirong Liu & Xuefeng Guo

  2. Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, P. R. China

    Lei Zhang & Fanyang Mo

  3. Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA

    Chenxi Lu, Yanwei Li & K. N. Houk

  4. Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, P. R. China

    Xingxing Li & Jinlong Yang

  5. Environment Research Institute, Shandong University, Qingdao, P. R. China

    Yanwei Li

  6. Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA

    Yang Yang

  7. Center of Single-Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, P. R. China

    Xuefeng Guo

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Contributions

X.G., F.M. and K.N.H. conceived and designed the experiments. C.Y., L.Z. and Yu Li fabricated the devices and performed the device measurements. L.Z. carried out the molecular synthesis. C.L., S.Z., X.L., Yanwei Li, Z.L. and J.Y. built and analysed the theoretical model and performed the quantum transport calculations. X.G., F.M., K.N.H., Y.Y., C.Y. and L.Z. analysed the data and wrote the paper. All the authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to K. N. Houk, Fanyang Mo or Xuefeng Guo.

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Peer review information Nature Nanotechnology thanks Nadim Darwish, Albert Poater and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Sections 1–16, Figs. 1–39 and Tables 1–5.

Supplementary Data 1

Supplementary source data and original figures including compounds 1–3, Scheme 1, Figs. 1–39 and Tables 1–5.

Supplementary Video 1

Highly correlated fluorescent and current signals of the single-molecule catalyst site during the Suzuki–Miyaura cross-coupling.

Source data

Source Data Fig. 1

Original NMR data.

Source Data Fig. 2

Statistical source data and original figures.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 6

Statistical source data.

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Yang, C., Zhang, L., Lu, C. et al. Unveiling the full reaction path of the Suzuki–Miyaura cross-coupling in a single-molecule junction. Nat. Nanotechnol. 16, 1214–1223 (2021). https://doi.org/10.1038/s41565-021-00959-4

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