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The role of aromaticity in the cyclization and polymerization of alkyne-substituted porphyrins on Au(111)

Nature Chemistry (2023)Cite this article

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Abstract

Aromaticity is an established and widely used concept for the prediction of the reactivity of organic molecules. However, its role remains largely unexplored in on-surface chemistry, where the interaction with the substrate can alter the electronic and geometric structure of the adsorbates. Here we investigate how aromaticity affects the reactivity of alkyne-substituted porphyrin molecules in cyclization and coupling reactions on a Au(111) surface. We examine and quantify the regioselectivity in the reactions by scanning tunnelling microscopy and bond-resolved atomic force microscopy at the single-molecule level. Our experiments show a substantially lower reactivity of carbon atoms that are stabilized by the aromatic diaza[18]annulene pathway of free-base porphyrins. The results are corroborated by density functional theory calculations, which show a direct correlation between aromaticity and thermodynamic stability of the reaction products. These insights are helpful to understand, and in turn design, reactions with aromatic species in on-surface chemistry and heterogeneous catalysis.

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Fig. 1: Aromaticity-driven regioselectivity in free-base porphyrins.
Fig. 2: Cyclization and coupling of alkyne-substituted free-base porphyrins on Au(111).
Fig. 3: Regio- and stereoselectivity of cyclization and coupling reactions.
Fig. 4: Correlation between aromaticity and thermodynamical stability.
Fig. 5: Influence of different adsorption positions.
Fig. 6: Reaction kinetics.

Data availability

The data that support the findings are included in this published article (and its supplementary information files). Source data are provided with this paper. Source data for the graphs (Figs. 5 and 6a,b and Supplementary Figs. 9–17), DFT-optimized geometries (used in Figs. 4 and 5, Extended Data Figs. 3 and 4, and Supplementary Figs. 8–17, 20 and 22), and Bader charge analysis data (used in Supplementary Fig. 19) are made available in a zip file. Any additional datasets (STM and AFM data) generated during and/or analysed during the current study are available from the corresponding authors on reasonable request.

Code availability

Apps and libraries used to analyse the data and to generate images were made available in open-source repositories (https://github.com/alexriss/SpmImageTycoon.jl and https://github.com/alexriss/ChemfilesViewer.jl). Any other code generated during the current study is available from the corresponding authors on reasonable request.

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Acknowledgements

This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—453903355, 326785818, under Germany’s Excellence Strategy—EXC 2089/1–390776260 (e-conversion), and a grant from the Irish Research Council (New Foundations, PorOrgMat), and the Guangdong Basic and Applied Basic Research Foundation (grant no. 2019A1515110819). N.C. acknowledges the support from China Scholarship Council (CSC). M.O.S. was supported by the Technical University of Munich–Institute for Advanced Study through a Hans Fischer Senior Fellowship and by Science Foundation Ireland (21/FFP-A/9469). J.B. acknowledges funding from the Swedish Research Council. The computations were enabled by resources provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) and the Swedish National Infrastructure for Computing (SNIC) at the National Supercomputer Centre (NSC), partially funded by the Swedish Research Council through grant agreements no. 2022-06725 and no. 2018-05973. Funding for E.C.-R. was provided by CONACYT-Chihuahua, Mexico (Scholarship 591246). We kindly thank F. Klappenberger for his support during the initial project stage. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Author information

Authors and Affiliations

  1. Physics Department E20, Technical University of Munich, Garching, Germany

    Nan Cao, Eduardo Corral-Rascon, Johannes V. Barth & Alexander Riss

  2. Department of Physics, Chemistry and Biology, IFM, Linköping University, Linköping, Sweden

    Jonas Björk

  3. Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany

    Zhi Chen & Mario Ruben

  4. College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, PR China

    Zhi Chen

  5. Centre Européen de Science Quantique, Institut de Science et d’Ingénierie Supramoléculaires (UMR 7006), CNRS-Université de Strasbourg, Strasbourg, France

    Mario Ruben

  6. Institute of Quantum Materials and Technologies, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany

    Mario Ruben

  7. Institute for Advanced Study (TUM-IAS), Focus Group—Molecular and Interfacial Engineering of Organic Nanosystems, Technical University of Munich, Garching, Germany

    Mathias O. Senge

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Contributions

A.R. conceived the analysis. N.C and A.R. designed the experiments. N.C. performed the experiments and the DFT calculations. E.C.-R. helped with the experiments and interpretation. A.R. supervised the experiments and did the HOMA analysis. J.B. supervised the DFT calculations. Z.C. synthesized the precursors, supervised by M.R. M.O.S. provided insights and guidance for the chemical interpretation. J.V.B. provided materials and methods and supervised the project. N.C. and A.R. wrote the manuscript with help from all other authors.

Corresponding authors

Correspondence to Johannes V. Barth or Alexander Riss.

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Nature Chemistry thanks Nan Jiang 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 Identification of hydrogen tautomers via AFM.

(a-c) AFM images of a chain of three trans-cyclized and one cis-cyclized molecule at different tip-sample distances. The trans-cyclized species show brighter features associated with one pair of nitrogen atoms at opposite sides, as marked by white arrows. (d) The same image as in (c), but with increased contrast. Such bright features connecting one pair of opposing nitrogen atoms were observed in previous work and assigned to iminic nitrogen atoms (Supplementary Fig. 6)19, that is, nitrogen atoms within the pyrrole rings that do not carry internal hydrogens. This assignment corresponds to the 2a-trans2 type. (e) Proposed chemical structure of the chain, consisting of three 2a-trans2 and one 2a-cis molecule. (f),(g) AFM images of an unsubstituted porphyrin molecule adsorbed on Au(111) shows similar features at larger tip-sample heights: a line along the direction of the iminic nitrogen atoms can be seen, marked by the white arrow. (h) Chemical structure of the molecule in (f) and (g). Red arrows mark aminic pyrroles. Scan parameters: Vs = 0 V, constant height. We have investigated 165 trans-cyclized molecules (see also Supplementary Fig. 5), all of which exhibit these particular features, suggesting that (almost) all of the trans-cyclized species are of type 2a-trans2. Further support for this assignment is obtained by tip manipulation experiments (see Extended Data Fig. 2).

Extended Data Fig. 2 Tip-induced cleavage of inner hydrogens.

(a) Application of a voltage pulse (Vs = 3.2 V) close to the center of a trans-cyclized molecule within a chain leads to cleavage of an inner hydrogen atom45,73,74. A substantial contrast change on the lower side can be observed, as marked by filled (before manipulation) and outlined (after manipulation) red arrows. Thus, we deduce that the pyrrole ring at this position was carrying one of the inner hydrogen atoms before the manipulation. This assignment corresponds to a 2a-trans2 type molecule. (b) A similar experiment (with a voltage pulse of Vs = 3.2 V) shows the cleavage of both inner hydrogen atoms, inducing contrast changes at the top and bottom (marked by red arrows). Again, these positions are associated with the pyrroles that carry the inner hydrogen atoms, indicating that this molecule is of type 2a-trans2. We have successfully performed such manipulation experiments on 10 molecules, all of which were confirmed to be of type 2a-trans2. (c) Analogous experiments on unsubstituted porphyrin molecules adsorbed on Au(111). The two inner hydrogens can be cleaved off in two steps, both times associated with contrast changes at the respective hydrogen-carrying pyrrole rings (marked by red arrows). Scan parameters: Vs = 0 V, constant height.

Extended Data Fig. 3 Relaxed geometries of the cyclization products.

Top and side views of relaxed structures of (a) 2a-cis, (b) 2a-trans1 and (c) 2a-trans2 at different adsorption positions, as well as in their free-standing geometry. For each structure, the reaction energies (with respect to the model of the precursor 1a), the adsorption energies, as well as the HOMA indices associated with the aromatic diaza[18]annulene pathway are shown.

Extended Data Fig. 4 Local HOMA indices and relative bond lengths.

The images show the local HOMA indices for the pyrrole rings, as well as the relative bond lengths of each C-C and C-N bond (red for shortened and blue for elongated bond lengths, compared with the ‘optimal’ aromatic bond lengths ‘dopt’). The precursor 1a exhibits an asymmetry, with one pair of two pyrrole rings at opposite ‘corners’ having higher HOMA indices than the other pair. This is in line with the aromatic diaza[18]annulene pathway (see Fig. 1 in the main text) observed in porphyrins75,76,77. The two pairs of carbon atoms with olefinic character outside of the aromatic pathway are marked by gray arrows. The cyclized products also exhibit this twofold symmetry, but there are significant changes in the HOMA indices for the rings. The newly formed five-membered rings lead to a reduction of the HOMA indices of the pyrrole rings that they are attached to. For the structures 2a-cis, 2a-trans1, and 2a-trans2, an additional 22 π-electron circuit exists along all the carbon atoms in the periphery of the molecules. The HOMA indices for these circuits are lower: 0.552 for 2a-cis, 0.464 for 2a-trans1, and 0.540 for 2a-trans2. Furthermore, some of the atoms at the newly formed five-membered rings might be sp3-hybridized (see Supplementary Fig. 7), thus inhibiting conjugation along these 22 π-electron circuits.

Supplementary information

Supplementary Information

Supplementary Methods, Figs. 1–22 (additional experimental and theory data) and References 1–37.

Supplementary Data 1

xyz coordinates of all DFT-optimized structures.

Supplementary Data 2

Source data for Supplementary Fig. 9.

Supplementary Data 3

Source data for Supplementary Fig. 10.

Supplementary Data 4

Source data for Supplementary Fig. 11.

Supplementary Data 5

Source data for Supplementary Fig. 12.

Supplementary Data 6

Source data for Supplementary Fig. 13.

Supplementary Data 7

Source data for Supplementary Fig. 14.

Supplementary Data 8

Source data for Supplementary Fig. 15.

Supplementary Data 9

Source data for Supplementary Fig. 16.

Supplementary Data 10

Source data for Supplementary Fig. 17.

Source data

Source Data Fig. 5

Source data for the graph in Fig. 5.

Source Data Fig. 6

Source data for the graphs in Fig. 6a,b.

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Cao, N., Björk, J., Corral-Rascon, E. et al. The role of aromaticity in the cyclization and polymerization of alkyne-substituted porphyrins on Au(111). Nat. Chem. (2023). https://doi.org/10.1038/s41557-023-01327-6

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  • DOI: https://doi.org/10.1038/s41557-023-01327-6

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