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Single-molecule tautomerization tracking through space- and time-resolved fluorescence spectroscopy


Tautomerization, the interconversion between two constitutional molecular isomers, is ubiquitous in nature1, plays a major role in chemistry2 and is perceived as an ideal switch function for emerging molecular-scale devices3. Within free-base porphyrin4, porphycene5 or phthalocyanine6, this process involves the concerted or sequential hopping of the two inner hydrogen atoms between equivalent nitrogen sites of the molecular cavity. Electronic and vibronic changes6 that result from this NH tautomerization, as well as details of the switching mechanism, were extensively studied with optical spectroscopies, even with single-molecule sensitivity7. The influence of atomic-scale variations of the molecular environment and submolecular spatial resolution of the tautomerization could only be investigated using scanning probe microscopes3,8,9,10,11, at the expense of detailed information provided by optical spectroscopies. Here, we combine these two approaches, scanning tunnelling microscopy (STM) and fluorescence spectroscopy12,13,14,15, to study the tautomerization within individual free-base phthalocyanine (H2Pc) molecules deposited on a NaCl-covered Ag(111) single-crystal surface. STM-induced fluorescence (STM-F) spectra exhibit duplicate features that we assign to the emission of the two molecular tautomers. We support this interpretation by comparing hyper-resolved fluorescence maps15,16,17,18(HRFMs) of the different spectral contributions with simulations that account for the interaction between molecular excitons and picocavity plasmons19. We identify the orientation of the molecular optical dipoles, determine the vibronic fingerprint of the tautomers and probe the influence of minute changes in their atomic-scale environment. Time-correlated fluorescence measurements allow us to monitor the tautomerization events and to associate the proton dynamics to a switching two-level system. Finally, optical spectra acquired with the tip located at a nanometre-scale distance from the molecule show that the tautomerization reaction occurs even when the tunnelling current does not pass through the molecule. Together with other observations, this remote excitation indicates that the excited state of the molecule is involved in the tautomerization reaction path.

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Fig. 1: STM-F spectroscopy of individual H2Pc molecules.
Fig. 2: Highly resolved fluorescence mapping of a single H2Pc molecule.
Fig. 3: Tautomerization dynamics revealed by spectrally filtered time-correlated fluorescence.
Fig. 4: Excited-state mediated tautomerization reaction.

Data availability

The data that support the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request.


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The authors thank V. Speisser for technical support and A. Boeglin and Andrei Borissov for fruitful discussions. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 771850). The Agence National de la Recherche (project SMALL’LED no. ANR-14-CE26-0016-01), the Labex NIE (Contract no. ANR-11-LABX-0058_NIE) and the International Center for Frontier Research in Chemistry (FRC) are acknowledged for financial support. R.S.-M. and H.B. acknowledge GENCI-CINES (Project no. A0060907459) and the Pôle HPC and Equipex Equip@Meso at the University of Strasbourg. T.N. and J.A. acknowledge the project FIS2016-80174-P from the Spanish Ministry of Science, and project ELKARTEK KK-2018/00001 from the Basque Government, as well as grant IT1164-19 from the Basque Government for consolidated groups at the university.

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Authors and Affiliations



B.D. and G.S. conceived, designed and performed the experiments. B.D., M.R., F.S. and G.S. analysed the experimental data. T.N. and J.A. conceived and performed the simulations of the HRFM maps. R.S.-M. and H.B. performed the density functional theory calculations of the H2Pc under strain. L.E.P.L. and S.B. performed and analysed the Raman spectra. All the authors discussed the results and contributed to the redaction of the paper.

Corresponding author

Correspondence to Guillaume Schull.

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The authors declare no competing interests.

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Peer review information Nature Nanotechnology thanks Takashi Kumagai 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 Experimental and DFT calculated images of the HOMO and LUMO of \({{\rm{H}}}_{2} \)Pc.

a) Chemical structure of free-base phthalocyanine (\({{\rm{H}}}_{2} \)Pc). DFT calculations (see S5 for details) of the HOMO (b) and LUMO (c) of \({{\rm{H}}}_{2} \)Pc, and experimental STM images (d, e, 3 \(\times \) 3 nm\({}^{2} \), \(I \) = 10 pA) of the same molecular orbitals. This figure corresponds to Fig. S1 of the Supplementary Information.

Extended Data Fig. 2 Spectral split and adsorption site of \({{\rm{H}}}_{2} \)Pc on NaCl.

STM-F spectra acquired at \(V \) = \(- \)2.5 V, \(I \) = 200 pA, acquisition time t = 300 s for the three different \({{\rm{H}}}_{2} \)Pc molecules. The spectrum labeled type 1 is similar to the one reported in14. STM images (20 \(\times \) 14.2 nm\({}^{2} \), \(V \) = \(- \)2.5 V) of the three type of \({{\rm{H}}}_{2} \)Pc molecules with (b) a silver terminated tip and (c) a CO terminated tip. The blue lines in (c) are aligned with chlorine atomic rows. This figure corresponds to Fig. S2 of the Supplementary Information.

Extended Data Fig. 3 Effect of the NaCl/Ag(111) Moiré pattern on the electronic and fluorescent properties of adsorbed \({{\rm{H}}}_{2} \)Pc molecules.

a) STM image (20 \(\times \) 20 m\({}^{2} \), \(V \) = \(- \)2.5 V) of four \({{\rm{H}}}_{2} \)Pc molecules. The position of the atomically resolved STM image in inset (10 \(\times \) 10 nm\({}^{2} \), \(V \) = \(- \)100 mV) has been precisely adjusted with respect to the larger STM image. (b) STM-F spectra acquired at \(V \) = \(- \)2.5 V, \(I \) = 200 pA, acquisition time t = 120 s on the 4 molecules imaged in (a). (c) d\(I \)//d\(V \) spectra acquired on the four molecules imaged in (a). (d) Same STM image as in (a) with an overlaid superstructure of gray lines that follow the linear Moiré pattern. This figure corresponds to Fig. S3 of the Supplementary Information.

Extended Data Fig. 4 Calculated photon maps as a function of tip height and tunneling current background.

(a) Local density of states of the HOMO of the \({{\rm{H}}}_{2} \)Pc molecule, (b,c) LDOS of the HOMO for larger distances \(z \) > \({z}_{0} \) from the plane of the molecule (defined by \(z \) = 0) propagated until \({z}_{1} \) = \({z}_{0} \) + 0. 2 nm in (b) and \({z}_{2} \) = \({z}_{0} \) + 0.5 nm in (c). (di) Show normalized photon maps [as given by Eq. (S8)] using the LDOS given in (c) for different values of the background current \({I}_{{\rm{BG}}} \) (specified via \({{\rm{C}}}_{{\rm{eff}}} \)) for (df) \({{\rm{Q}}}_{{\rm{x}}} \), and (gi) \({{\rm{Q}}}_{{\rm{y}}} \), respectively. The maps (d) and (g) calculated assuming \({{\rm{C}}}_{{\rm{eff}}} \) = 0 are maps of \(| {{\rm{g}}}_{{\rm{Q}}}{| }^{2} \) as the pumping efficiency \({\eta }_{{\rm{exc}}} \) (r) is identically equal to one in this case. When \({{\rm{C}}}_{{\rm{eff}}}\ne 0 \), i.e., a background is considered, the originally smooth broad lobes of the exciton immediately split into smaller lobes as seen in (e, f, h, i). This splitting emerges for \({{\rm{C}}}_{{\rm{eff}}} \) as small as 0.01 [as shown in (e, h)]. This figure corresponds to Fig. S4 of the Supplementary Information.

Extended Data Fig. 5 Vibronic signature of the two tautomers.

Vibronic signature of the two tautomers probed by STM-F. We recorded the vibronic spectrum18 associated to each tautomer. To this end we excited the molecule with the tip located at positions marked by blue and red dots in (a), resulting in the preferential emission of one or the other of the tautomers. The obtained vibronic spectra (b) can be understood as fingerprints of the molecule in a given environment18. As a reference, we also provide a Raman spectrum obtained on a macroscopic crystal of \({{\rm{H}}}_{2} \)Pc molecules. The vibronic spectrum of tautomer 2 and the Raman spectrum are extremely similar suggesting that tautomer 2 is weakly affected by its adsorption site. The spectrum of tautomer 1, however, reveals important differences, that can hardly be reconciled with the sole modification of the electronic structure of the molecule, but rather indicates modifications of its geometry. This figure corresponds to Fig. S6 of the Supplementary Information.

Extended Data Fig. 6 Ratio of the time spent in each tautomer as a function of tip position.

Ratio \(\alpha ={\tau }_{2}/{\tau }_{1} \) of the time spent by the molecule in tautomer 2 and tautomer 1 configurations as a function of the tip position. (a) STM image of the molecule (\(V \) = \(- \)2.5 V; \(I \) = 10 pA). (b) Chemical structure of the two tautomers. (c) Ratio α of the time spent by the molecule in tautomer 2 and tautomer 1 configurations for the different tip positions marked in (a). These values are determined based on 5 s long photon traces recorded simultaneously on APD1 and APD2 at a tunneling current \(I \) = 100 pA and a bias \(V \) = \(- \)2.5 V following the procedure described in27. Except for position 7, the molecule spends always a longer time in the most stable tautomer 2 configuration. The error bars are estimated by accounting for the standard deviation of the averaged light intensity in the bright and dark states of the APD1 and APD2 time traces and the error on the linear fit applied to the correlation functions in logarithmic scale. This figure corresponds to Fig. S9 of the Supplementary Information.

Extended Data Fig. 7 Electronic and STM-F data on free-base Naphthalocyanine.

a) Sketch of the naphthalocyanine molecule (\({{\rm{H}}}_{2} \)Nc). (b) d\(I \)/d\(V \) spectrum acquired on a single molecule adsorbed on 3 layers of NaCl on Ag(111). Inset : STM images (3.5 \(\times \) 3.5 nm\({}^{2} \)) of the HOMO (\(V \) = \(- \)1.9 V; \(I \) = 10 pA) and LUMO (\(V \) = 0.7 V; \(I \) = 10 pA). (c) STM-F spectra (\(V \) = \(- \)2.2 V; \(I \) = 50 pA; acquisition time : t = 180 s) acquired with the STM tip located at the positions identified in (b). This figure corresponds to Fig. S11 of Supplementary Information.

Extended Data Fig. 8 \({{\rm{H}}}_{2} \)Pc vs \({{\rm{N}}}_{2} \)Pc tautomerization onset.

(a) Comparison between STM-F spectrum of \({{\rm{H}}}_{2} \)Pc (top spectrum :\(V \) = \(- \)2.5 V; \(I \) = 100 pA; acquisition time t = 120 s) and \({{\rm{H}}}_{2} \)Nc (bottom spectrum : \(V \) = -2.2 V; \(I \) = 50 pA; acquisition time t = 180 s). (b, c) At-distance (\(\approx \)1.2 nm) STM-F spectra as a function of voltage for \({{\rm{H}}}_{2} \)Pc and \({{\rm{H}}}_{2} \)Nc (\(I \) = 600 pA; acquisition time t = 180 s). A vertical offset is used for clarity. (d, e) Current-time traces (vertically offset for clarity) as a function of voltage for \({{\rm{H}}}_{2} \)Pc and \({{\rm{H}}}_{2} \)Nc. An initial setpoint of \(I \) = 10 pA is used for all traces. The tautomerization voltage onset is very close to the optical gap in both cases, supporting an excited-state mediated tautomerization mechanism. This figure corresponds to Fig. S12 of the Supplementary Information.

Supplementary information

Supplementary Information

Supplementary Figs. 1–13, discussions, Table 1 and refs. 1–49.

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Doppagne, B., Neuman, T., Soria-Martinez, R. et al. Single-molecule tautomerization tracking through space- and time-resolved fluorescence spectroscopy. Nat. Nanotechnol. 15, 207–211 (2020).

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