Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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

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

Subjects

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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

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.

References

  1. De Oteyza, D. G. et al. Direct imaging of covalent bond structure in single-molecule chemical reactions. Science 340, 1434–1437 (2013).

    Article  CAS  Google Scholar 

  2. Björk, J., Zhang, Y., Klappenberger, F., Barth, J. V. & Stafström, S. Unraveling the mechanism of the covalent coupling between terminal alkynes on a noble metal. J. Phys. Chem. C 118, 3181–3187 (2014).

    Article  Google Scholar 

  3. Di Giovannantonio, M. et al. Insight into organometallic intermediate and its evolution to covalent bonding in surface-confined Ullmann polymerization. ACS Nano 7, 8190–8198 (2013).

    Article  CAS  Google Scholar 

  4. Hla, S.-W., Bartels, L., Meyer, G. & Rieder, K.-H. Inducing all steps of a chemical reaction with the scanning tunneling microscope tip: towards single molecule engineering. Phys. Rev. Lett. 85, 2777–2780 (2000).

    Article  CAS  Google Scholar 

  5. Hulsken, B. et al. Real-time single-molecule imaging of oxidation catalysis at a liquid–solid interface. Nature Nanotech. 2, 285–289 (2007).

    Article  CAS  Google Scholar 

  6. Riss, A. et al. Local electronic and chemical structure of oligo-acetylene derivatives formed through radical cyclizations at a surface. Nano Lett. 14, 2251–2255 (2014).

    Article  CAS  Google Scholar 

  7. Zhou, H. et al. Direct visualization of surface-assisted two-dimensional diyne polycyclotrimerization. J. Am. Chem. Soc. 136, 5567–5570 (2014).

    Article  CAS  Google Scholar 

  8. Sun, Q. et al. On-surface formation of one-dimensional polyphenylene through Bergman cyclization. J. Am. Chem. Soc. 135, 8448–8451 (2013).

    Article  CAS  Google Scholar 

  9. Treier, M. et al. Surface-assisted cyclodehydrogenation provides a synthetic route towards easily processable and chemically tailored nanographenes. Nature Chem. 3, 61–67 (2011).

    Article  CAS  Google Scholar 

  10. Heinrich, B. W. et al. Change of the magnetic coupling of a metal–organic complex with the substrate by a stepwise ligand reaction. Nano Lett. 13, 4840–4843 (2013).

    Article  CAS  Google Scholar 

  11. Dienel, T. et al. Dehalogenation and coupling of a polycyclic hydrocarbon on an atomically thin insulator. ACS Nano 8, 6571–6579 (2014).

    Article  CAS  Google Scholar 

  12. Bartels, L., Meyer, G. & Rieder, K.-H. Controlled vertical manipulation of single CO molecules with the scanning tunneling microscope: a route to chemical contrast. Appl. Phys. Lett. 71, 213–215 (1997).

    Article  CAS  Google Scholar 

  13. Mohn, F., Schuler, B., Gross, L. & Meyer, G. Different tips for high-resolution atomic force microscopy and scanning tunneling microscopy of single molecules. Appl. Phys. Lett. 102, 073109 (2013).

    Article  Google Scholar 

  14. Gross, L., Mohn, F., Moll, N., Liljeroth, P. & Meyer, G. The chemical structure of a molecule resolved by atomic force microscopy. Science 325, 1110–1114 (2009).

    Article  CAS  Google Scholar 

  15. Gross, L. et al. Bond-order discrimination by atomic force microscopy. Science 337, 1326–1329 (2012).

    Article  CAS  Google Scholar 

  16. Gross, L. et al. Organic structure determination using atomic-resolution scanning probe microscopy. Nature Chem. 2, 821–825 (2010).

    Article  CAS  Google Scholar 

  17. Zhang, J. et al. Real-space identification of intermolecular bonding with atomic force microscopy. Science 342, 611–614 (2013).

    Article  CAS  Google Scholar 

  18. Sweetman, A. M. et al.. Mapping the force field of a hydrogen-bonded assembly. Nature Commun. 5, 3931 (2014).

    Article  CAS  Google Scholar 

  19. Hämäläinen, S. K. et al.. Intermolecular contrast in atomic force microscopy images without intermolecular bonds. Phys. Rev. Lett. 113, 186102 (2014).

    Article  Google Scholar 

  20. Hapala, P. et al.. Mechanism of high-resolution STM/AFM imaging with functionalized tips. Phys. Rev. B 90, 085421 (2014).

    Article  Google Scholar 

  21. Kawai, S. et al. Extended halogen bonding between fully fluorinated aromatic molecules. ACS Nano 9, 2574–2583 (2015).

    Article  CAS  Google Scholar 

  22. Zhang, Y.-Q. et al.. Homo-coupling of terminal alkynes on a noble metal surface. Nature Commun. 3, 1286 (2012).

    Article  Google Scholar 

  23. Zhang, X. et al.. Polymerization or cyclic dimerization: solvent dependent homo-coupling of terminal alkynes at HOPG surface. Sci. Rep. 4, 3899 (2014).

    Article  Google Scholar 

  24. Eichhorn, J., Heckl, W. M. & Lackinger, M. On-surface polymerization of 1,4-diethynylbenzene on Cu(111). Chem. Commun. 49, 2900–2902 (2013).

    Article  CAS  Google Scholar 

  25. Gao, H.-Y. et al. Glaser coupling at metal surfaces. Angew. Chem. Int. Ed. 52, 4024–4028 (2013).

    Article  CAS  Google Scholar 

  26. Weymouth, A. J., Hofmann, T. & Giessibl, F. J. Quantifying molecular stiffness and interaction with lateral force microscopy. Science 352, 600–603 (2014).

    Google Scholar 

  27. Boneschanscher, M. P., Hämäläinen, S. K., Liljeroth, P. & Swart, I. Sample corrugation affects the apparent bond lengths in atomic force microscopy. ACS Nano 8, 3006–3014 (2014).

    Article  CAS  Google Scholar 

  28. Hapala, P., Temirov, R., Tautz, F. S. & Jelínek, P. Origin of high-resolution IETS-STM images of organic molecules with functionalized tips. Phys. Rev. Lett. 113, 226101 (2014).

    Article  Google Scholar 

  29. Guo, C., Van Hove, M. A., Ren, X. & Zhao, Y. High-resolution model for noncontact atomic force microscopy with a flexible molecule on the tip apex. J. Phys. Chem. C 119, 1483–1488 (2015).

    Article  CAS  Google Scholar 

  30. Moll, N. et al. Image distortions of a partially fluorinated hydrocarbon molecule in atomic force microscopy with carbon monoxide terminated tips. Nano Lett. 14, 6127–6131 (2014).

    Article  CAS  Google Scholar 

  31. Fabig, S., Haberhauer, G. & Gleiter, R. Dimerization of two alkyne units: model studies, intermediate trapping experiments, and kinetic studies. J. Am. Chem. Soc. 137, 1833–1843 (2015).

    Article  CAS  Google Scholar 

  32. Atkins, P. & de Paula, J. Atkins’ Physical Chemistry (Oxford Univ. Press, 2002).

    Google Scholar 

  33. Reuter, K. & Scheffler, M. First-principles kinetic Monte Carlo simulations for heterogeneous catalysis: application to the CO oxidation at RuO2(110). Phys. Rev. B 73, 045433 (2006).

    Article  Google Scholar 

  34. Stoltze, P. & Nørskov, J. K. in Handbook of Heterogeneous Catalysis (eds Ertl, G., Knozinger, H., Schuth, F. & Weitkamp, J.) 5.2.3 (Wiley-VCH, 2008).

    Google Scholar 

  35. Neurock, M. in ACS Professional Reference Book (eds Dumesic, J. A., Rudd, D. F., Aparicio, L. M., Rekoske, J. E. & Treviño, A. A.) 315 (American Chemical Society, 1993).

    Google Scholar 

  36. Meyer, J. & Reuter, K. Modeling heat dissipation at the nanoscale: an embedding approach for chemical reaction dynamics on metal surfaces. Angew. Chem. Int. Ed. 53, 4721–4724 (2014).

    Article  CAS  Google Scholar 

  37. Ditze, S. et al. On the energetics of conformational switching of molecules at and close to room temperature. J. Am. Chem. Soc. 136, 1609–1616 (2014).

    Article  CAS  Google Scholar 

  38. Marbach, H. & Steinrück, H.-P. Studying the dynamic behaviour of porphyrins as prototype functional molecules by scanning tunnelling microscopy close to room temperature. Chem. Commun. 50, 9034–9048 (2014).

    Article  CAS  Google Scholar 

  39. Eyring, H. The activated complex in chemical reactions. J. Chem. Phys. 3, 107–115 (1935).

    Article  CAS  Google Scholar 

  40. Laidler, K. J. & King, M. C. Development of transition-state theory. J. Phys. Chem. 87, 2657–2664 (1983).

    Article  CAS  Google Scholar 

  41. McQuarrie, D. A. Statistical Mechanics (University Science Books, 2000).

    Google Scholar 

  42. Garcia-Araez, N., Climent, V. & Feliu, J. Separation of temperature effects on double-layer and charge-transfer processes for platinum|solution interphases. Entropy of formation of the double layer and absolute molar entropy of adsorbed hydrogen and OH on Pt(111). J. Phys. Chem. C 113, 19913–19925 (2009).

    Article  CAS  Google Scholar 

  43. Ayala, P. Y. & Schlegel, H. B. Identification and treatment of internal rotation in normal mode vibrational analysis. J. Chem. Phys. 108, 2314–2325 (1998).

    Article  CAS  Google Scholar 

  44. van der Lit, J. et al.. Suppression of electron–vibron coupling in graphene nanoribbons contacted via a single atom. Nature Commun. 4, 2023 (2013).

    Article  Google Scholar 

  45. Giessibl, F. J. Advances in atomic force microscopy. Rev. Mod. Phys. 75, 949–983 (2003).

    Article  CAS  Google Scholar 

  46. Aradi, B., Hourahine, B. & Frauenheim, T. DFTB+, a sparse matrix-based implementation of the DFTB method. J. Phys. Chem. A 111, 5678–5684 (2007).

    Article  CAS  Google Scholar 

  47. Lide, D. R. CRC Handbook of Chemistry and Physics (CRC Taylor & Francis, 2006).

    Google Scholar 

Download references

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.

Author information

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

Authors
  1. Alexander Riss
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alejandro Pérez Paz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sebastian Wickenburg
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hsin-Zon Tsai
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dimas G. De Oteyza
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Aaron J. Bradley
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Miguel M. Ugeda
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Patrick Gorman
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Han Sae Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Michael F. Crommie
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Angel Rubio
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Felix R. Fischer
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary information (PDF 2682 kb)

Supplementary information

Supplementary movie 1 (MP4 3992 kb)

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchem.2506

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing