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Time-resolved imaging and analysis of the electron beam-induced formation of an open-cage metallo-azafullerene

Nature Chemistry volume 15, pages 1444–1451 (2023)Cite this article

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Abstract

The visualization of single-molecule reactions provides crucial insights into chemical processes, and the ability to do so has grown with the advances in high-resolution transmission electron microscopy. There is currently a limited mechanistic understanding of chemical reactions under the electron beam. However, such reactions may enable synthetic methodologies that cannot be accessed by traditional organic chemistry methods. Here we demonstrate the synthetic use of the electron beam, by in-depth single-molecule, atomic-resolution, time-resolved transmission electron microscopy studies, in inducing the formation of a doubly holed fullerene-porphyrin cage structure from a well-defined benzoporphyrin precursor deposited on graphene. Through real-time imaging, we analyse the hybrid’s ability to host up to two Pb atoms, and subsequently probe the dynamics of the Pb–Pb binding motif in this exotic metallo-organic cage structure. Through simulation, we conclude that the secondary electrons, which accumulate in the periphery of the irradiated area, can also initiate chemical reactions. Consequently, designing advanced carbon nanostructures by electron-beam lithography will depend on the understanding and limitations of molecular radiation chemistry.

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Fig. 1: Experimental and computational approach to fullerophyrin FP.
Fig. 2: Electron microscopy analysis of the overall environment of the starting FP.
Fig. 3: Mechanistic insights into beam-induced processes.
Fig. 4: SMART-EM analysis of FP formation.
Fig. 5: Summary of events and electronic characteristics of fullerophyrins.

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The data supporting the findings of this study are available within the paper and its Supplementary Information. Source data are provided with this paper.

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Acknowledgements

This research was supported by the Institute for Basic Science IBS-R026-Y1 (D.L.). K.H. and E.N. acknowledge support from JSPS KAKENHI JP19H05459. K.H. acknowledges support from Japan Science and Technology Agency (CREST JPMJCR20B2). N.J. and K.A. acknowledge support from the Deutsche Forschungsgemeinschaft (DFG, Projektnummer 1828491499, SFB 953). H.H. and D.L. acknowledge support as International Research Fellows from the Japan Society for the Promotion of Science (JSPS). H.H. further thanks the Bavarian Equal Opportunities Sponsorship, Realisierung von Chancengleichheit von Frauen in Forschung und Lehre (FFL), Realization Equal Opportunities for Women in Research and Teaching, for financial support. D.L. thanks the Alexander von Humboldt Foundation for a Feodor–Lynen return fellowship.

Author information

Authors and Affiliations

  1. Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg (FAU), Erlangen, Germany

    Helen Hoelzel & Norbert Jux

  2. Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan

    Helen Hoelzel, Koji Harano, Eiichi Nakamura & Dominik Lungerich

  3. Center for NanoMedicine, Institute for Basic Science (IBS), Seodaemun-gu, Seoul, South Korea

    Sol Lee & Dominik Lungerich

  4. Department of Chemistry, Martin-Luther-University Halle-Wittenberg, Halle, Germany

    Konstantin Yu. Amsharov

  5. Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Japan

    Koji Harano

  6. Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, South Korea

    Dominik Lungerich

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Contributions

D.L. conceptualized the project and wrote the manuscript with feedback from all authors. All authors discussed the results and commented on the manuscript. N.J. and K.Y.A. designed the molecules. H.H. synthesized and characterized the molecules. H.H. and D.L. carried out the TEM experiments. S.L. carried out the STEM/EDS experiments and analysis. D.L. carried out SMART-EM data analysis, DFT calculations and EM simulations. D.L., K.H. and E.N. provided access and maintenance of the TEM. E.N., N.J. and D.L. were responsible for funding acquisition. All authors approved the final version of the manuscript.

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Correspondence to Dominik Lungerich.

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Nature Chemistry thanks Nazario Martin and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Thermochemical comparison of the cyclodehydrogenation reaction of C60H30 to C60 and 1 to FP.

a, Reaction equation for the C60H30 to C60 conversion. b, Relative energies of intermediates for each reaction. c, Energy difference between each reaction intermediate. (DFT: M06-2X/def2-TZVP).

Source data

Extended Data Fig. 2 Characterization of 1M (M = Pt, Pd, Ni) species.

a, UV/Vis analysis in THF at r.t. Spectra are normalized at the absorption maximum of pyrene at 341 nm. b, TEM image of Pt, Pd, and Ni-atom aggregates. c, Low-mag TEM image of single metal atoms from 1M species. d, Time–dependent diffusion of single Pt-atoms. e, Time-dependent diffusion of single Pd-atoms. Arrows indicate the direction of motion.

Source data

Extended Data Fig. 3 Alternative simulations with an outside bound Pb atom instead of an endohedral metal atom.

The surface of the molecule displays the van der Waals surface. In the side view, the graphene is depicted as a CPK model. Scale bar 1 nm.

Extended Data Fig. 4 Simulation analysis of Pb-Pb distance in Pb@(FP-Pb) at various tilting angles.

The measured angle is derived from the static graphene surface and the tilted molecule along the Pb-Pb bond. a, Pb-Pb single bond. b, non-bonded Pb atoms. Scale bar 1 nm.

Extended Data Fig. 5 Secondary knock-on-induced demetallation of complexed Pb atoms through a fast atom flux.

a, Schematic depiction of energy transfer ET from primary electrons to atoms (H, C, N, Pb) and subsequent energy transfer ET’ from the fast moving atoms to Pb atoms, calculated from Eq. 1 and 2. b, Maximum transferred kinetic energy from the primary beam via elastic scattering against the kinetic energy of the primary electrons. c, Maximum transferred kinetic energy from fast atoms to Pb atoms via secondary knock-on energy transfer against the kinetic energy of the primary electrons.

Source data

Extended Data Fig. 6 Additional simulation images of Pb@(FP-Pb) with graphene’s most significant van der Waals surface interactions.

Scale bar 1 nm.

Extended Data Fig. 7 Electronic evaluation of different Pb-, Ge-, and Zn-fullerophyrins.

a, Electrostatic potential map of FP, (FP-M), M@(FP), and M@(FP-M) (color range from −50 to +30 kJ/mol, isovalue 0.002 e/au3 b, Sliced contour plot of the ionization potential of FP, (FP-M), M@(FP), and M@(FP-M) (color range from 7 to 15 eV). Digits indicate natural atomic charge of metal atoms. DFT level: B3LYP-D3/6-311G(2d,p)// ωB97X-D/6-31G(d) for Zn and Ge derivatives, B3LYP-D3/6-31G(d)/LANL2DZ>Kr for Pb-derivatives.

Extended Data Table 1 Expected knock-on-induced events of 1
Full size table

Supplementary information

Supplementary Information

Captions for Supplementary Videos 1–3, synthetic details, description of cross-section calculation, computational details, XYZ coordinates, NMR and MS spectral appendix, text, Figs. 1–36, Tables 1–19 and references.

Supplementary Video 1

Transformation of 1Pb to Pb@(FP-Pb) and Pb@(FP) on graphene. 80 kV, magnification 1,000,000x, texp = 500 ms, drift corrected, bandpass filtered, and contrast corrected. Video displayed at 6 f.p.s., 1-86-frames. The video displays the motion three times faster than the actual recording.

Supplementary Video 2

Decomposition of Pb@(FP) under the electron beam. 80 kV, magnification 1,000,000x, texp = 500 ms, drift corrected, bandpass filtered, and contrast corrected. Video displayed at 12 f.p.s., 87–200 frames. The video displays the motion six times faster than the actual recording.

Supplementary Video 3

Detachment of empty hemi-FP from graphene monolayer. 80 kV, magnification 2,000,000x, texp = 500 ms, drift corrected, bandpass filtered, and contrast corrected. Video displayed at 10 f.p.s., 1–140 frames. The video displays the motion five times faster than the actual recording.

Source data

Source Data Fig. 1

UV–vis spectra, DFT thermochemical calculations.

Source Data Fig. 2

EDS spectrum.

Source Data Fig. 3

Source data Fig. 3.

Source Data Fig. 4

Measured distances and statistical data.

Source Data Fig. 5

Analysis of events; knock-on and ionization cross-sections.

Source Data Extended Data Fig./Table 1

DFT thermochemical calculations.

Source Data Extended Data Fig./Table 2

UV–vis spectra.

Source Data Extended Data Fig./Table 5

Atom flux knock-on energy transfer.

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Hoelzel, H., Lee, S., Amsharov, K.Y. et al. Time-resolved imaging and analysis of the electron beam-induced formation of an open-cage metallo-azafullerene. Nat. Chem. 15, 1444–1451 (2023). https://doi.org/10.1038/s41557-023-01261-7

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