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Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale

Nature Protocols volume 18, pages 1958–1978 (2023)Cite this article

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Abstract

The ability to measure the behavior of a single molecule during a reaction implies the detection of inherent dynamic and static disordered states, which may not be represented when measuring ensemble averages. Here, we describe the building of devices with graphene–molecule–graphene single-molecule junctions integrated into an electrical circuit. These devices are simple to build and are stable, showing tolerance to mechanical changes, solution environment and voltage stimulation. The design of a conductive channel based on a single molecule enables single-molecule detection and is sensitive to variations in physical properties and chemical structures of the detected molecules. The on-chip setup of single-molecule junctions further offers complementary metal–oxide–semiconductor (CMOS) compatibility, enabling logic functions in circuit elements, as well as deciphering of reaction intermediates. We detail the experimental procedure to prepare graphene transistor arrays as a basis for single-molecule junctions and the preparation of nanogapped carboxyl-terminal graphene electrodes by using electron-beam lithography and oxygen plasma etching. We describe the basic design of a molecular bridge with desired functions and terminals to form covalent bonds with electrode arrays, via a chemical reaction, to construct stably integrated single-molecule devices with a yield of 30−50% per chip. The immobilization of the single molecules is then characterized by using inelastic electron tunneling spectra, single-molecule imaging and fluorescent spectra. The whole protocol can be implemented within 2 weeks and requires users trained in using ultra-clean laboratory facilities and the aforementioned instrumentation.

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Fig. 1: Schematic illustrations of potential applications using single-molecule devices.
Fig. 2: A comparison of different single-molecule junctions.
Fig. 3: Preparation of graphene FETs.
Fig. 4: Preparation of single-molecule devices.
Fig. 5: Schematic diagram of the characterization system for single-molecule devices.

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Data availability

The main data discussed in this protocol are available in the supporting primary research paper46. The raw datasets are too large to be publicly shared but are available for research purposes from the corresponding author upon reasonable request.

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Acknowledgements

We acknowledge primary financial support from the National Key R&D Program of China (2021YFA1200101 and 2022YFE0128700), the National Natural Science Foundation of China (22150013, 21727806 and 21933001), the Tencent Foundation through the XPLORER PRIZE “Frontiers Science Center for New Organic Matter” at Nankai University (63181206) and the Natural Science Foundation of Beijing (2222009).

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  1. These authors contributed equally: Chen Yang, Caiyao Yang.

Authors and Affiliations

  1. Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Centre, College of Chemistry and Molecular Engineering, Peking University, Beijing, People’s Republic of China

    Chen Yang, Caiyao Yang, Yilin Guo, Jianfei Feng & Xuefeng Guo

  2. Centre of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, People’s Republic of China

    Xuefeng Guo

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Contributions

Chen Yang, Caiyao Yang and X.G. designed and created the figures. Chen Yang, Caiyao Yang, Y.G. and J.F. performed the experiments and wrote the manuscript. X.G. supervised the research and edited the manuscript.

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Correspondence to Xuefeng Guo.

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Key references using this protocol

Jia, C. et al. Science 352, 1443−1445 (2016): https://doi.org/10.1126/science.aaf6298

Yang, C. et al. Nat. Nanotechnol. 16, 1214−1223 (2021): https://doi.org/10.1038/s41565-021-00959-4

Yang, C. et al. Sci. Adv. 7, eabf0689 (2021): https://doi.org/10.1126/sciadv.abf0689

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Yang, C., Yang, C., Guo, Y. et al. Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale. Nat Protoc 18, 1958–1978 (2023). https://doi.org/10.1038/s41596-023-00822-x

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