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Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy

Nature Chemistry volume 8, pages 678–683 (2016)Cite this article

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Abstract

Chemical transformations at the interface between solid/liquid or solid/gaseous phases of matter lie at the heart of key industrial-scale manufacturing processes. A comprehensive study of the molecular energetics and conformational dynamics that underlie these transformations is often limited to ensemble-averaging analytical techniques. Here we report the detailed investigation of a surface-catalysed cross-coupling and sequential cyclization cascade of 1,2-bis(2-ethynyl phenyl)ethyne on Ag(100). Using non-contact atomic force microscopy, we imaged the single-bond-resolved chemical structure of transient metastable intermediates. Theoretical simulations indicate that the kinetic stabilization of experimentally observable intermediates is determined not only by the potential-energy landscape, but also by selective energy dissipation to the substrate and entropic changes associated with key transformations along the reaction pathway. The microscopic insights gained here pave the way for the rational design and control of complex organic reactions at the surface of heterogeneous catalysts.

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Figure 1: Experimental observation of transient intermediates in a stepwise bimolecular enediyne coupling and cyclization cascade.
Figure 2: Calculated energy diagram for the stepwise enediyne coupling and cyclization cascade.
Figure 3: Calculated temperature-dependent relative concentrations of reactant, intermediates and product determined by solving kinetic rate equations for the reaction pathway from 1 to 4c.
Figure 4: Dissipation of the chemical energy at different intermediate reaction steps as calculated by MD DFTB simulations.

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Acknowledgements

Research supported by the US Department of Energy, Office of Basic Energy Sciences Nanomachine Program under contract No. DE-AC02-05CH11231 (STM and nc-AFM instrumentation development, AFM imaging), the Office of Naval Research BRC Program (molecular synthesis, characterization and STM imaging), the European Research Council Advanced Grant DYNamo No. ERC-2010-AdG-267374 (computer resources and support), Spanish Grant No. FIS2013-46159-C3-1-P (MD calculations) and Grupos Consolidados UPV/EHU del Gobierno Vasco No. IT-578-13 (DFTB calculations). A.Ri. acknowledges fellowship support from the Austrian Science Fund (FWF) No. J3026-N16. A.P.P. acknowledges fellowship support from the Ayuda para la Especialización de Personal Investigador del Vicerrectorado de Investigación de la UPV/EHU-2013. A.Ru. acknowledges fellowship support from the Miller Institute for Basic Research in Science of the University of California at Berkeley (Miller Visiting Research Professor program). We thank P. Jelínek and P. Hapala for their help with the nc-AFM simulations and D. J. Mowbray for useful discussions.

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Author notes

  1. Alexander Riss

    Present address: Present address: Department of Physics E20, Technical University Munich, James-Franck-Straße 1, 85748 Garching, Germany,

Authors and Affiliations

  1. Department of Physics, University of California, Berkeley, 94720, California, USA

    Alexander Riss, Sebastian Wickenburg, Hsin-Zon Tsai, Aaron J. Bradley, Miguel M. Ugeda, Han Sae Jung & Michael F. Crommie

  2. Institute of Applied Physics, Vienna University of Technology, Wien, 1040, Austria

    Alexander Riss

  3. Nano-Bio Spectroscopy Group and ETSF, Universidad del País Vasco, San Sebastián, 20018, Spain

    Alejandro Pérez Paz & Angel Rubio

  4. Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, California, USA

    Sebastian Wickenburg, Michael F. Crommie & Felix R. Fischer

  5. Donostia International Physics Center, San Sebastián, 20018, Spain

    Dimas G. De Oteyza

  6. Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain

    Dimas G. De Oteyza & Miguel M. Ugeda

  7. Centro de Física de Materiales CSIC/UPV-EHU-Materials Physics Center, San Sebastián, 20018, Spain

    Dimas G. De Oteyza

  8. CIC nanoGUNE, San Sebastián, 20018, Spain

    Miguel M. Ugeda

  9. Department of Chemistry, University of California, Berkeley, 94720, California, USA

    Patrick Gorman, Han Sae Jung & Felix R. Fischer

  10. Kavli Energy NanoSciences Institute at the University of California Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, 94720, California, USA

    Michael F. Crommie & Felix R. Fischer

  11. Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, 22761, Germany

    Angel Rubio

  12. Center for Free-electron Laser Science (CFEL), Luruper Chaussee 149, Hamburg, 22761, Germany

    Angel Rubio

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Contributions

A.Ri., A.P.P. and S.W. contributed equally to this work. A.Ri. and S.W. conceived the research and designed the experiments. A.Ri., S.W. and H.-Z.T. performed the nc-AFM experiments. A.Ri. was responsible for the kinetic simulations and wrote the first draft of the manuscript. A.P.P. conducted the theoretical calculations. A.J.B., H.S.J. and M.M.U. helped with the experiments. D.G.O. helped with the interpretation of the experimental and theoretical results. A.Ru. supervised the theoretical calculations and helped with the interpretation. P.G. and F.F. were responsible for molecular design. P.G. was responsible for synthesis. F.F. helped with the interpretation of the experimental results. M.F.C. supervised the experimental measurements, and helped with the design of the study and the interpretation of the results. All the authors discussed the results and helped in writing the manuscript.

Corresponding authors

Correspondence to Alexander Riss, Michael F. Crommie, Angel Rubio or Felix R. Fischer.

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Riss, A., Paz, A., Wickenburg, S. et al. Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy. Nature Chem 8, 678–683 (2016). https://doi.org/10.1038/nchem.2506

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