Skip to main content

Thank you for visiting 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.

Identifying surface reaction intermediates with photoemission tomography


The determination of reaction pathways and the identification of reaction intermediates are key issues in chemistry. Surface reactions are particularly challenging, since many methods of analytical chemistry are inapplicable at surfaces. Recently, atomic force microscopy has been employed to identify surface reaction intermediates. While providing an excellent insight into the molecular backbone structure, atomic force microscopy is less conclusive about the molecular periphery, where adsorbates tend to react with the substrate. Here we show that photoemission tomography is extremely sensitive to the character of the frontier orbitals. Specifically, hydrogen abstraction at the molecular periphery is easily detected, and the precise nature of the reaction intermediates can be determined. This is illustrated with the thermally induced reaction of dibromo-bianthracene to graphene which is shown to proceed via a fully hydrogenated bisanthene intermediate. We anticipate that photoemission tomography will become a powerful companion to other techniques in the study of surface reaction pathways.


Since synthetic organic chemistry emerged in the mid-nineteenth century1, the necessity to correctly identify reaction intermediates and products has led to many techniques and diverse approaches, ranging from classical methods of wet chemistry, including colour reagents and chromatography, to modern variants of nuclear magnetic resonance spectroscopy, to name only a few examples. The applicability of these methods in surface chemistry is often restricted by the specific situation that reactants, intermediates and products remain surface-adsorbed throughout the reaction. This requires the use of surface analytics. But even the rich arsenal of surface science techniques, based for instance on mass spectrometry2,3,4, vibrational5,6 or core level spectroscopies7,8,9 and scanning probe microscopies10,11,12,13,14,15,16,17,18,19,20, does not always allow the authoritative identification of an adsorbed species. For example, it is often difficult to identify the degree of (de-)hydrogenation of a given molecule, as hydrogen is difficult to trace by surface sensitive techniques. Only indirect conclusions can be made from, e.g., the presence or absence of specific vibrational modes in infrared spectroscopy or chemical shifts in core level spectroscopy. Often, however, these data are ambiguous and leave room for interpretation. In contrast, orbitals of molecules, being extremely sensitive to the composition and chemical structure, should allow for unambiguous identification of chemical species.

From this perspective, the momentum-space orbital imaging based on angle-resolved ultraviolet photoemission spectroscopy (ARUPS) is promising. The method of photoemission tomography (PT) developed in the last few years21,22,23,24,25,26 is a combined experimental and theoretical technique in which the results of ARUPS are interpreted in terms of the molecular orbital structure of the electron’s initial state. In a nutshell, a set of maps of the photoelectron intensity distribution in momentum space (k-maps), recorded at energies corresponding to specific molecular emissions, does not only provide a unique fingerprint of the adsorbed species, but allows a straightforward determination of its precise structure. As we will demonstrate, photoemission tomography can thus be employed for the identification of reaction intermediates and can therefore be useful for disentangling surface reaction pathways.

The polymerisation of 10,10′-dibromo-9,9′-bianthracene (DBBA, C28H16Br2) on metal surfaces is used for the on-surface synthesis of graphene nanoribbons27,28,29,30,31 and graphene30,32,33. The reaction is thermally activated and proceeds via dehalogenation and cyclodehydrogenation. On Cu(110), the enhanced chemical reactivity of the surface prevents polymerisation at moderate temperatures (250 °C)32 resulting in a well-defined reaction intermediate, which at higher temperature (>750 °C) transforms into graphene. Based on scanning tunnelling microscopy (STM) and x-ray photoemission spectroscopy (XPS), combined with adsorption energy calculations, a partly dehydrogenated state of bisanthene (Fig. 1) has been suggested32, but the precise nature of this intermediate is debated. The surface reaction of DBBA on Cu(110) is therefore an excellent test case for PT and its ability to identify the exact chemical state of an intermediate of a surface chemical reaction.

Fig. 1

Surface reaction of 10,10′-dibromo-9,9′-bianthracene (DBBA). Dehalogenation and cyclodehydrogenation of DBBA on Cu(110) resulting in bisanthene

Here we apply photoemission tomography to demonstrate the thermally induced chemical reaction of DBBA on Cu(110) and reveal the exact chemical state of the reaction intermediate. We consider three possible reaction intermediates, which only differ in the degree of hydrogenation at the zig-zag edges of the molecule. When comparing their density of states computed within density functional theory with experimental energy distribution curves from ultraviolet photoemission spectroscopy, an assignment of the intermediate cannot be made. Only when taking into account the angular distribution of the photoemitted electrons from the frontier orbitals, both in the experiment and in the simulation, are we able to unambiguously identify the exact chemical state of the intermediate as a chemisorbed, but fully hydrogenated bisanthene (phenanthro(1,10,9,8-opqra)perylene, C28H14) molecule. This demonstrates the outstanding potential of PT in recognising the precise chemical state of molecular adsorbates, especially as far as the chemistry of the molecular periphery is concerned.


Density of states

We have deposited DBBA (Fig. 1) on clean Cu(110) at room temperature and, as a first step, investigated the electronic structure of the as-deposited molecules by conventional ARUPS. Energy distribution curves (EDCs) in the valence band range between the Fermi level and the onset of the Cu d-band emissions are shown in Fig. 2a. At least two adsorbate-related features are discernible, at ~0.15 eV and between 1.0 and 1.5 eV. However, the precise binding energies of these broad features are difficult to determine. Moreover, the anisotropy between the EDCs recorded at the two principal azimuths of the substrate is much weaker than for other organic monolayers on metal (110) surfaces21,22,34. Nevertheless, we will show below that the angular distribution of photoelectrons exhibits a twofold symmetry and thus points to a well-defined orientation of the as-deposited species.

Fig. 2

Valence band of DBBA on Cu(110) before and after annealing at 250 °C. a Energy distribution curves (EDCs) of as-deposited DBBA measured along [001] (blue curve) and [\(\bar 110\)] (red curve) directions of Cu(110). b EDCs after annealing of DBBA at 250 °C measured along [001] direction of Cu(110) (blue curve) and 25° away from [\(\bar 110\)] direction (red curve). For the EDCs, the photoelectron intensity was integrated over the polar angle range of 0° to +85°. c DFT calculations of density of states (DOS) of C28H14, C28H12 and C28H8 on Cu(110). The orange lines show the total DOS, while the black and grey lines display the DOS projected onto the molecule and the π-states of the molecule, respectively. The dotted lines mark energies corresponding to experimental and theoretical k-maps in Figs. 3 and 4

After annealing the sample at 250 °C, the EDCs are clearly modified (Fig. 2b). We now find three molecular emissions, one of them almost completely concealed by the rising flank of the Cu d-electrons. The other two appear as well-defined peaks at 0.5 and 1.15 eV. The anisotropy between the two azimuths is now pronounced, suggesting a high degree of molecular orientation after annealing.

Momentum maps

On the basis of the experimental EDCs, the nature of the molecular emissions, both before and after annealing, remains unclear. We have therefore measured angular photoelectron distributions at the binding energies in question (see Methods, Supplementary Methods and Supplementary Fig. 1). Corresponding momentum maps (or k-maps), which can also be viewed as a momentum-space resolved density of states (DOS), are displayed for the as-deposited molecules at binding energies of 0.15, 0.9 and 1.4 eV (Fig. 3a), and for the annealed molecules at 0.5, 1.15 and 1.9 eV (Fig. 3b).

Fig. 3

Photoelectron distributions. Experimental k-maps of DBBA a before and b after annealing measured at corresponding binding energies (compare dotted lines in Fig. 2a, b). c Theoretical k-maps of LUMO, HOMO and HOMO-1 orbitals of a bisanthene. Corresponding orbitals are shown in insets

For the as-deposited species we observe diffuse patterns that are superimposed on sharp features from Cu sp-band emissions (Fig. 3a). These patterns are twofold symmetric and clearly vary with binding energy, indicating that they must originate from well-defined and distinct molecular orbitals, in spite of the indistinct density of states in Fig. 2a. Both the diffuseness of the momentum maps and the indistinctiveness of the EDCs indicate the co-existence of more than one configuration of the adsorbed species (see Supplementary Note 1, Supplementary Table 1 and Supplementary Figs. 24).

After annealing to 250 °C, the momentum maps appear more defined (Fig. 3b). In agreement with the EDCs in Fig. 2b, this suggests a higher degree of orientation and indicates the presence of only one surface species. Most importantly, however, the changes in the momentum maps prove a significant modification of the orbital structure, indicating that a thermally activated surface reaction to a new species has occurred.

A plausible candidate for this reaction intermediate is bisanthene, which has already been introduced in Fig. 1. We have computed the gas phase electronic structure of bisanthene and simulated the expected angular photoelectron distributions by calculating the Fourier transform of its molecular orbitals21 (see the Methods section). The resulting momentum maps of the lowest unoccupied molecular orbital (LUMO), the highest occupied molecular orbital (HOMO) and the HOMO-1 are depicted in Fig. 3c. They match very well the three measured patterns at 0.5, 1.15 and 1.9 eV, respectively, and thereby give strong evidence that during annealing at 250 °C on Cu(110), DBBA undergoes dehalogenation and cyclodehydrogenation reactions during which the adsorbate planarizes and the π-conjugation expands to the entire fused carbon backbone. The momentum maps in Fig. 3b, c further reveal that, first, bisanthene is oriented along the [\(\bar 110\)] direction of the Cu(110) surface, and second, that bisanthene chemisorbs on Cu(110). The latter is proven by the charge transfer into the formerly unoccupied LUMO, which makes this orbital observable in PT.

Reaction intermediate

Although the agreement between angular photoelectron distributions of gas phase bisanthene and the measured patterns is good, there are deviations, which could in principle point to small modifications of bisanthene, such as (partial) dehydrogenation. Therefore, the exact chemical state of the reaction intermediate is not yet clear.

Focusing on the possibility of edge dehydrogenation, there are in fact two plausible suspects in addition to bisanthene (C28H14, Fig. 4a). These are C28H12 (Fig. 4b) and C28H8 (Fig. 4c). The latter two would form covalent bonds with the Cu surface through dehydrogenated C atoms. Based on STM/XPS and density functional theory (DFT) C28H8 has in fact been suggested as the correct reaction intermediate32 (cf. Supplementary Notes 3 and 4, Supplementary Figs. 8 and 9 for discussion).

Fig. 4

Bisanthene, C28H12 and C28H8 on the Cu(110) surface. ac Chemical structure and df simulated k-maps at three representative binding energies (compare dotted lines in Fig. 3c) for a, d bisanthene C28H14 and partly dehydrogenated b, e C28H12 and c, f C28H8. Grey dashed lines in b, c mark localised chemical bonds of dehydrogenated carbon atom with copper atoms

To shed light on the true nature of the reaction intermediate, we first compare the density of states for the adsorbed C28H14, C28H12 and C28H8 as calculated by DFT and projected onto the molecule (pDOS). At the level of van der Waals-corrected DFT, their relaxed adsorption structures are as follows: bisanthene occupies the short-bridge site on Cu(110), while C28H12 and C28H8 prefer on-top sites. In all three cases the molecules are oriented with their central C-C bond along the [\(\overline {1}1 0\)] direction of the Cu(110) surface (cf. Supplementary Note 2, Supplementary Table 2 and Supplementary Figs. 57 for details). Although the pDOS shown in Fig. 2c contains peaks which can be associated with the states observed in the experimental EDC in Fig. 2b, there is, however, no clear fingerprint which could be used to unambiguously identify the exact nature of the reaction intermediate. Yet, it is interesting to note that the contribution of π-states to the total pDOS gradually decreases from intact bisanthene to C28H8 (Fig. 2c). This is caused by the strong concave distortion of the dehydrogenated bisanthene derivatives, resulting from chemical bonds that form between unsaturated edge carbons and the Cu(110) surface33.

It is reasonable to assume that the strong molecular distortion apparent in the pDOS will modify the corresponding orbital structure significantly. We thus turn again to momentum maps, since these are a direct representation of the orbital structure. Evidently, we need to consider the patterns of the combined adsorbate/substrate system including the local bonds at the edges in order to determine the precise chemical nature of the surface intermediate. We employ here a recently developed extension of PT in which the momentum map simulations are no longer based on gas phase molecular orbitals, but on the wave functions of the (strongly) interacting molecule/metal interface35.

The results of these simulations are depicted in Fig. 4d–f for C28H14/Cu(110), C28H12/Cu(110) and C28H8/Cu(110), respectively. For each chemical species, the simulated momentum maps are shown at three representative binding energies, as indicated by the dotted lines in the pDOS curves of Fig. 2c. We notice profound differences in the momentum maps for the three species, demonstrating a striking sensitivity of PT to the hydrogen saturation of molecular edges. Dehydrogenation alters the patterns and moreover leads to increasingly more diffuse emissions signatures, most likely because the local bonds of the dehydrogenated carbon atoms with the Cu(110) mix substrate states into the molecular wave functions.

The comparison of the simulated momentum maps with the experimental ones (Fig. 3b) allows us to exclude both dehydrogenated species C28H12 and C28H8. We conclude that the fully hydrogenated bisanthene is the sought-after reaction intermediate. The close resemblance of the gas phase simulations (Fig. 3c) with the momentum maps of the adsorbed bisanthene (Fig. 4d) demonstrates that its orbital structure suffers only minor changes upon adsorption, despite the former LUMO being filled and involved in the bonding of the molecule to the metal. A similar robustness of molecular orbitals has been demonstrated for a number of π-bonded systems21,22,23,35.

Reaction energies

Our identification of fully hydrogenated bisanthene as the reaction intermediate is in contrast to Simonov et al. who have identified the dehydrogenated C28H8 as this intermediate32. To resolve this disagreement, we calculate the energetics of forming the three possible intermediates. The adsorption energy, defined as the total energy difference between the combined system and its constituents, turns out to be −5.3, −8.0 and −12.7 eV for C28H14, C28H12 and C28H8, respectively (see Supplementary Note 2 and Supplementary Table 2), and would therefore indicate C28H8 as the most stable intermediate in agreement with Simonov et al. However, this adsorption energy disregards the energy that is necessary to split the carbon-hydrogen bonds. When computing the full chemical reaction energies for the three considered intermediates,

$${\mathrm{C}}_{28}{\mathrm{H}}_{16}{\mathrm{Br}}_2/{\mathrm{Cu}}(110)\left( {\begin{array}{*{20}{l}} { \to {\mathrm{C}}_{28}{\mathrm{H}}_{14}/{\mathrm{Cu}}(110) + 2{\mathrm{Br}}/{\mathrm{Cu}}(110) + 2{\mathrm{H}}/{\mathrm{Cu}}(110)} \hfill & {( - 6.8\,{\mathrm{eV}})} \hfill \\ { \to {\mathrm{C}}_{28}{\mathrm{H}}_{12}/{\mathrm{Cu}}(110) + 2{\mathrm{Br}}/{\mathrm{Cu}}(110) + 4{\mathrm{H}}/{\mathrm{Cu}}(110)} \hfill & {( - 4.1\,{\mathrm{eV}})} \hfill \\ { \to {\mathrm{C}}_{28}{\mathrm{H}}_8/{\mathrm{Cu}}(110) + 2{\mathrm{Br}}/{\mathrm{Cu}}(110) + 8{\mathrm{H}}/{\mathrm{Cu}}(110)} \hfill & {( + 2.0\,{\mathrm{eV}})} \hfill \end{array}} \right.$$

we obtain reaction energies (in parenthesis in Eq. (1)) which demonstrate that the fully hydrogenated bisanthene (C28H14) is the most energetically favourable intermediate in agreement with PT.


The ability of PT to image orbitals makes it particularly sensitive to the exact chemical state of surface reaction species. We demonstrated this for the thermally activated DBBA on Cu(110), where the fully hydrogenated bisanthene (C28H14), with its LUMO occupied by charge transfer from the surface, is identified as the reaction intermediate prior to the formation of graphene at higher annealing temperatures. In contrast to other experimental techniques, PT can differentiate the chemistry of the molecular periphery, i.e., the degree of (de-)hydrogenation, as well as determine the occupation of the frontier orbitals. As photoemission tomography is neither constrained by the need for cryogenic temperatures nor to planar surface species, we envision it to be a complementary companion to atomic force microscopy and other state-of-the-art surface science methods in the study of reaction pathways at surfaces. Its major restrictions are those of vacuum and conductive substrates inherent to ARUPS.


Sample preparation

Sample preparation and ARUPS experiments have been carried out in ultra-high vacuum with a system base pressure in the 10−10 mbar range. The single crystal Cu(110) was cleaned by repeated cycles of Ar+ ion sputtering at 1000 eV followed by annealing at 800 K. 10,10′-dibromo-9,9′-bianthracene (Sigma-Aldrich, CAS number 121848-75-7) was evaporated from a Knudsen type molecular evaporator (Kentax GmbH) at 185 °C onto the Cu(110) surface kept at room temperature (RT). The molecular flux was calibrated using a quartz microbalance to obtain the nominal thickness of the DBBA film of one monolayer. All photoemission experiments were conducted at RT for the cases of as-deposited DBBA/Cu(110) and after several steps of annealing ranging between 250 and 750 °C.

Photoemission experiments

Photoemission was excited with p-polarised light with an incidence angle of 40°, at the Metrology Light Source insertion device beamline36 of the Physikalisch-Technische Bundesanstalt (Berlin, Germany). A photon energy of 35 eV was used, which corresponds to the highest photoemission cross-section in the present experiment. Photoemission data was recorded with the toroidal electron analyser37 over an emission angle range from −85° to +85° (for details see Supplementary Methods). For the presented energy distribution curves, the photoelectron intensity was integrated over the polar angle range of 0° to +85° in selected azimuthal directions. Momentum maps were recorded by measuring the photoelectron intensity in the positive polar angle range for a chosen binding energy and rotating the sample in the azimuthal direction in 1° steps. This results in the full photoelectron distribution in the (kx, ky) plane perpendicular to the sample normal.

Density functional theory calculation

The electronic structure calculations and the simulations of the momentum maps are based on ab initio computations within the framework of density functional theory. We have performed two types of calculations. First, for the isolated (gas phase) bisanthene molecule (C28H14) the NWChem code has been utilised38, and second, for the full molecule/Cu(110) adsorbate system the VASP code was used39,40.

For the calculations of the isolated bisanthene molecule, we employ the generalised gradient approximation (GGA)41 for exchange-correlation effects. The momentum maps of the LUMO, HOMO and HOMO-1 are obtained as Fourier transforms of the respective Kohn-Sham orbitals21.

The electronic structure calculations for DBBA monolayers adsorbed on Cu(110) and monolayers of C28Hx on Cu(110) are performed by a repeated slab approach by using epitaxial matrices of \(\left( {\begin{array}{*{20}{c}} 4 & 0 \\ 1 & 6 \end{array}} \right)\) and \(\left( {\begin{array}{*{20}{c}} 4 & 0 \\ 2 & 5 \end{array}} \right)\), respectively. Using a lattice parameter of aCu = 3.61 Å, the metallic substrate is modelled by five Cu layers where a vacuum layer of at least 15 Å has been added between the slabs to avoid spurious electrical fields42. For each molecule/metal interface, the most favourable adsorption site is determined by testing the four high-symmetry adsorption sites (hollow, top, short bridge and long bridge) and performing local geometry optimisations in which the two topmost Cu-layers and all molecular degrees of freedom are allowed to relax until forces were below 0.01 eV Å−1. The GGA41 is used and van-der-Waals corrections according to the Tkatchenko-Scheffler method are added43,44. Using the projector augmented wave (PAW) method45, a plane-wave cutoff of 500 eV is employed. For k-point sampling, a Monkhorst-Pack grid of 4 × 4 × 1 points is used and a first-order Methfessel-Paxton smearing of 0.1 eV is utilised. Based on the relaxed adsorption geometries, we have computed (projected) densities of states and simulated momentum maps by assuming a damped plane wave as final state as described in more detail in a recent publication35.

Data availability

On request, the experimental data are available from S.S. and the theoretical data from P.P.


  1. 1.

    Yeh, B. J. & Lim, W. A. Synthetic biology: lessons from the history of synthetic organic chemistry. Nat. Chem. Biol. 3, 521–525 (2007).

    CAS  Article  Google Scholar 

  2. 2.

    Borg, H. J. & Niemantsverdriet, J. H. in Catalysis: 11 (eds Spivey, J. J. & Agarwal, S. K.) vol. 11, p. 1–50 (The Royal Society of Chemistry, Cambridge 1994).

  3. 3.

    Brender, P. et al. Characterization of carbon surface chemistry by combined temperature programmed desorption with in situ x-ray photoelectron spectrometry and temperature programmed desorption with mass spectrometry analysis. Anal. Chem. 84, 2147–2153 (2012).

    CAS  Article  Google Scholar 

  4. 4.

    Zhang, W. et al. Monitoring the on-surface synthesis of graphene nanoribbons by mass spectrometry. Anal. Chem. 89, 7485–7492 (2017).

    CAS  Article  Google Scholar 

  5. 5.

    Shen, Y. R. Surface properties probed by second-harmonic and sum-frequency generation. Nature 337, 519–525 (1989).

    ADS  CAS  Article  Google Scholar 

  6. 6.

    Zrimsek, A. B. et al. Single-molecule chemistry with surface- and tip-enhanced raman spectroscopy. Chem. Rev. 117, 7583–7613 (2017).

    CAS  Article  Google Scholar 

  7. 7.

    Siegbahn, K. in Atomic Physics 3 (eds Smith, S. J. & Walters, G. K.) p. 493–522 (Springer US, Boston, MA, 1973).

  8. 8.

    Reinert, F. & Hüfner, S. Photoemission spectroscopy—from early days to recent applications. New J. Phys. 7, 97 (2005).

    ADS  Article  Google Scholar 

  9. 9.

    Nemšák, S. et al. Concentration and chemical-state profiles at heterogeneous interfaces with sub-nm accuracy from standing-wave ambient-pressure photoemission. Nat. Commun. 5, 5441 (2014).

    ADS  Article  Google Scholar 

  10. 10.

    Wintterlin, J., Völkening, S., Janssens, T. V. W., Zambelli, T. & Ertl, G. Atomic and macroscopic reaction rates of a surface-catalyzed reaction. Science 278, 1931–1934 (1997).

    ADS  CAS  Article  Google Scholar 

  11. 11.

    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).

    ADS  CAS  Article  Google Scholar 

  12. 12.

    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).

    ADS  CAS  Article  Google Scholar 

  13. 13.

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

    CAS  Article  Google Scholar 

  14. 14.

    Mohn, F. et al. Reversible bond formation in a gold-atom–organic-molecule complex as a molecular switch. Phys. Rev. Lett. 105, 266102 (2010).

    ADS  Article  Google Scholar 

  15. 15.

    Treier, M. et al. Surface-assisted cyclodehydrogenation provides a synthetic route towards easily processable and chemically tailored nanographenes. Nat. Chem. 3, 61–67 (2010).

    Article  Google Scholar 

  16. 16.

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

    ADS  CAS  Article  Google Scholar 

  17. 17.

    Albrecht, F., Neu, M., Quest, C., Swart, I. & Repp, J. Formation and characterization of a molecule-metal-molecule bridge in real space. J. Am. Chem. Soc. 135, 9200–9203 (2013).

    CAS  Article  Google Scholar 

  18. 18.

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

    ADS  Article  Google Scholar 

  19. 19.

    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).

    ADS  CAS  Article  Google Scholar 

  20. 20.

    Riss, A. et al. Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy. Nat. Chem. 8, 678–683 (2016).

    CAS  Article  Google Scholar 

  21. 21.

    Puschnig, P. et al. Reconstruction of molecular orbital densities from photoemission data. Science 326, 702–706 (2009).

    ADS  CAS  Article  Google Scholar 

  22. 22.

    Puschnig, P. et al. Orbital tomography: deconvoluting photoemission spectra of organic molecules. Phys. Rev. B 84, 235427 (2011).

    ADS  Article  Google Scholar 

  23. 23.

    Lüftner, D. et al. Imaging the wave functions of adsorbed molecules. Proc. Natl Acad. Sci. USA 111, 605–610 (2014).

    ADS  Article  Google Scholar 

  24. 24.

    Wießner, M. et al. Complete determination of molecular orbitals by measurement of phase symmetry and electron density. Nat. Commun. 5, 4156 (2014).

    ADS  Article  Google Scholar 

  25. 25.

    Weiß, S. et al. Exploring three-dimensional orbital imaging with energy-dependent photoemission tomography. Nat. Commun. 6, 8287 (2015).

    ADS  Article  Google Scholar 

  26. 26.

    Puschnig, P. & Ramsey, M. in Encyclopedia of Interfacial Chemistry (ed. Wandelt, K.) p. 380–391 (Elsevier, Oxford, 2018).

  27. 27.

    Cai, J. et al. Atomically precise bottom-up fabrication of graphene nanoribbons. Nature 466, 470–473 (2010).

    ADS  CAS  Article  Google Scholar 

  28. 28.

    Han, P. et al. Bottom-up graphene-nanoribbon fabrication reveals chiral edges and enantioselectivity. ACS Nano 8, 9181–9187 (2014).

    CAS  Article  Google Scholar 

  29. 29.

    Talirz, L., Ruffieux, P. & Fasel, R. On-surface synthesis of atomically precise graphene nanoribbons. Adv. Mater. 28, 6222–6231 (2016).

    CAS  Article  Google Scholar 

  30. 30.

    Simonov, K. A. et al. Effect of substrate chemistry on the bottom-up fabrication of graphene nanoribbons: combined core-level spectroscopy and STM study. J. Phys. Chem. C 118, 12532–12540 (2014).

    CAS  Article  Google Scholar 

  31. 31.

    Packwood, D. M. & Hitosugi, T. Materials informatics for self-assembly of functionalized organic precursors on metal surfaces. Nat. Commun. 9, 2469 (2018).

    ADS  Article  Google Scholar 

  32. 32.

    Simonov, K. A. et al. From graphene nanoribbons on Cu(111) to nanographene on Cu(110): critical role of substrate structure in the bottom-up fabrication strategy. ACS Nano 9, 8997–9011 (2015).

    CAS  Article  Google Scholar 

  33. 33.

    Weiß, S. et al. Dependence of the adsorption height of graphenelike adsorbates on their dimensionality. Phys. Rev. B 98, 075410 (2018).

    ADS  Article  Google Scholar 

  34. 34.

    Koller, G. et al. Intra- and intermolecular band dispersion in an organic crystal. Science 317, 351–355 (2007).

    ADS  CAS  Article  Google Scholar 

  35. 35.

    Lüftner, D. et al. Understanding the photoemission distribution of strongly interacting two-dimensional overlayers. Phys. Rev. B 96, 125402 (2017).

    ADS  Article  Google Scholar 

  36. 36.

    Gottwald, A., Kaser, H. & Kolbe, M. The U125 insertion device beamline at the Metrology Light Source. J. Synchrotron Rad. 26, 535–542 (2019).

    CAS  Article  Google Scholar 

  37. 37.

    Broekman, L. et al. First results from a second generation toroidal electron spectrometer. J. Electron Spectrosc. Relat. Phenom. 144–147, 1001–1004 (2005).

    Article  Google Scholar 

  38. 38.

    Valiev, M. et al. NWchem: a comprehensive and scalable open-source solution for large scale molecular simulations. Comput. Phys. Commun. 181, 1477–1489 (2010).

    ADS  CAS  Article  Google Scholar 

  39. 39.

    Kresse, G. & Hafner, J. Ab initio molecule dynamics for liquid metals. Phys. Rev. B 47, 558–561 (1993).

    ADS  CAS  Article  Google Scholar 

  40. 40.

    Kresse, G. & Joubert, D. From ultrasoft pseudopotentials to the projector augmented-wave method. Phys. Rev. B 59, 1758–1775 (1999).

    ADS  CAS  Article  Google Scholar 

  41. 41.

    Perdew, J. P., Burke, K. & Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865–3868 (1996).

    ADS  CAS  Article  Google Scholar 

  42. 42.

    Neugebauer, J. & Scheffler, M. Adsorbate-substarte and adsorbate-adsorbate interactions of Na and K adlayers on Al(111). Phys. Rev. B 46, 16067–16080 (1992).

    ADS  CAS  Article  Google Scholar 

  43. 43.

    Tkatchenko, A. & Scheffler, M. Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Phys. Rev. Lett. 102, 073005 (2009).

    ADS  Article  Google Scholar 

  44. 44.

    Ruiz, V. G., Liu, W., Zojer, E., Scheffler, M. & Tkatchenko, A. Density-functional theory with screened van der Waals interactions for the modeling of hybrid inorganic-organic systems. Phys. Rev. Lett. 108, 146103 (2012).

    ADS  Article  Google Scholar 

  45. 45.

    Blöchl, P. E. Projector augmented-wave method. Phys. Rev. B 50, 17953–17979 (1994).

    ADS  Article  Google Scholar 

Download references


Financial support from the Austrian Science Fund (FWF) (projects P27649-N20, P27427-N20, I3731) and the Deutsche Forschungsgemeinschaft (DFG) (project Ri 804/8-1 and through the SFB 1083 “Structure and Dynamics of Internal Interfaces”, project A12) is gratefully acknowledged. We thank John Riley (La Trobe University, Australia) for experimental support.

Author information




F.C.B., P.T., M.R., M.G.R., P.P., S.S. and F.S.T. conceived the research. X.Y., L.E., P.H., H.K., G.K., A.G., M.G.R. and S.S. carried out the experiments. X.Y. and S.S. analysed the data. D.L. and P.P. carried out DFT calculations. M.G.R., P.P., S.S. and F.S.T. wrote the paper with contributions from all authors.

Corresponding author

Correspondence to Serguei Soubatch.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information: Nature Communications thanks Nobuo Ueno and other anonymous reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Yang, X., Egger, L., Hurdax, P. et al. Identifying surface reaction intermediates with photoemission tomography. Nat Commun 10, 3189 (2019).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


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