Formation and characterization of a. molecule-metal-molecule bridge in real space SUPPORTING INFORMATION

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1 Formation and characterization of a molecule-metal-molecule bridge in real space SUPPORTING INFORMATION Florian Albrecht,, Mathias Neu, Christina Quest, Ingmar Swart,, and Jascha Repp Institute of Experimental and Applied Physics, University of Regensburg, Regensburg, Germany Florian.Albrecht@physik.uni-regensburg.de Site-determination of the phenazine monomer and the complex Figure S1 shows the determination of the adsorption site for phenazine monomers and a phenazine-gold-phenazine complex from constant-current STM images. Using individual gold anions as markers the positions of chlorine ions in the NaCl lattice are determined as indicated by the grid in Figure S1 a. 1 Individual phenazine molecules adsorb along polar rows of the NaCl lattice with their center located at chlorine bridge sites. In Figure S1 b an individual phenazine molecule serves as marker to determine the adsorption site of a phenazine-gold-phenazine complex. The grid shows again the positions of chlorine ions. The phenazine molecules within the complex have an equivalent adsorption site as the individual molecule. The adsorption site of the gold atom changes upon complex formation from ontop To whom correspondence should be addressed Institute of Experimental and Applied Physics, University of Regensburg, Regensburg, Germany Current address: Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, P. O. Box 80000, 3508 TA Utrecht, the Netherlands S1

2 a b c 10 Å 30 Å + Na - Cl c Figure 30 Å S1: Site determination for phenazine monomers and phenazine-goldphenazine complex from constant current STM images. a, Individual gold anions indicate position of Cl atoms in the salt lattice. Phenazine monomers adsorb with their centers at Cl bridge sites (I = 3.5 pa, V = 0.4 V). b, Using a monomer as marker, the adsorption site of a phenazine-gold-phenazine complex is determined. (I = 1.0 pa, V = 0.4 V) In a and b the grids indicate the position of Cl ions. c, Schematic drawing of of the adsorption site of monomer and complex (oriented like in b). Sodium and chlorine ions are represented as indicated in the model. Only the top-most layer of NaCl is shown. chlorine to chlorine bridge site. Figure S1 c shows a model of the adsorption sites as deduced from Figure S1 b. DFT calculations and basic orbital models Figure S2 shows experimental constant-height di/dv maps, DFT-calculated orbital contours, orbital structures rationalized in our basic model in top-view of the complex as well as cross sections through the DFT calculated complex orbitals. The experimental images are the same as in the main text. The gold atom in the complex is assumed to be closer to the surface than the molecular plane of the phenazines. Note that, the frontier orbitals of the phenazine belonging to the delocalized π-system have a nodal plane coinciding with the molecular plane. In the case of the HOMO the phenazine's orbitals below the molecular plane are assumed to couple in-phase to the gold 6s-state and have therefore the opposite sign when looking from top. Hence, the STM image of the bonding HOMO shows a depression at the position of the gold atom. In the case of the LUMO+1, the out of phase coupling below the molecular plane leads to an in-phase coupling above. As a consequence, the STM S2

3 image of the LUMO+1 does not show a depression at the center of the complex. This picture is qualitatively conrmed by cross sections through DFT-calculated orbitals (see bottom row of Figure S2), which are discussed in more detail further below. HOMO LUMO LUMO+1 experimental di/dv LUMO+1 orbital models orbital models DFT LUMO HOMO DFT cross sections Figure S2: Comparison of experimental orbital images, DFT-calculated orbital contours, orbital models in top view, and cross sections through the DFTcalculated orbitals of the phenazine-gold-phenazine complex. Top row, Constant height di/dv maps of HOMO, LUMO and LUMO+1; Second row, Low-density contours of DFT calculated orbitals; Third row, Top view of corresponding orbital schemes as derived from our basic model. Bottom row, cross sections through the DFT calculated orbital densities in the plane spanned by the gold and nitrogen atoms (indicated by dotted lines in the second row). White crosses indicate the positions of the gold and nitrogen atoms. The nodal plane directly at the gold atom in the case of HOMO and LUMO+1 is due to the outermost change of sign of the gold 6s orbital. The density scale is logarithmic. We performed DFT calculations on isolated Au-phenazine complexes, using the ADF2012 package. 2 Image processing was performed using Avogadro. 3 The calculations employed the PBE0 exchange-correlation functional, in combination with all-electron basis sets of TZ2P quality for all atoms (ZORA/TZ2P for Au). First, the geometry of the phenazine molecules S3

4 was optimized. Increasing the basis set to QZ4P did not result in signicant changes in the energetic spacing of the orbitals (see table S1). These calculations conrm that the LUMO is non-degenerate and well-separated in energy from any other molecular orbitals, which is important to justify the applicability of our basic model considering only the phenazine's LUMO. In addition, the results are used for plotting the orbital density contours of Figure 2 b of the main text. Table S1: Electronic level spacing of a free phenazine monomer as calculated in DFT using basis sets as indicated. Level spacing DZP TZ2P QZ4P LUMO to LUMO ev 1.76 ev 1.78 ev HOMO to LUMO 4.01 ev 3.99 ev 3.98 ev The calculations of the complexes were done in xed geometry with both molecules positioned in the same plane. The relaxed structure of the monomer was taken as input for the two molecules in the complex. We varied both the molecule - molecule distance (from 14 Å to 8 Å center-to-center) and the vertical oset of the Au atom w.r.t. the plane of the molecules (from 0 Å to 1.3 Å). In all cases we found that the HOMO, LUMO, and LUMO+1 of the complex are derived from the LUMO of the phenazine molecules and the Au 6s state. For example, these orbitals of the complex with a molecule - molecule spacing of 9 Å and a vertical oset of the Au atom of 1.1 Å are shown in the second row in Figure S2. The cross sections through the DFT-calculated orbitals conrm the picture that the depression in the HOMO image at the gold atom arises from two close lying nodal planes, even though the gold 6s state couples in phase to the phenazine's LUMOs. As discussed in the main text, this is a result of the gold atom being closer to the surface than the two phenazine molecules, where it couples to the lower part of their orbitals. Things are slightly complicated by the fact that the phenazine's LUMOs have an additional sign change (cf. Fig. 2b). However, this does not aect the basic picture of the proposed electronic coupling scheme. A quantitative agreement with the experiment cannot be expected since the substrate S4

5 was not taken into account. We nd best agreement between the experimental images and calculated orbital contours for a molecule spacing of 9 Å, whereas the experimentally determined distance was only 8 Å. We attribute this disagreement to neglecting the substrate in the calculations. Most importantly, the DFT calculations support the applicability of our basic model, which in turn provides insight into the electronic coupling inside the complex. (a) Au vertically displaced by 0.5 Å negatively charged complex (b) Au vertically displaced by 1.1 Å negatively charged complex (c) Au vertically displaced by 1.1 Å positively charged complex Energy (ev) 0.0 Energy (ev) 0.0 Energy (ev) Å 9Å 10Å Å Figure S3: DFT calculated orbital energies for dierent geometries and charge states of the phenazine-gold-phenazine complex. (a) and (b), Energies of frontier orbitals for anionic complex for geometries as indicated; (c), Molecular energy levels for cationic complex; The center to center distance of the phenazine molecules is indicated below each panel. 8.5Å 9Å Å 8.5Å 9Å DFT calculations may also provide some insight into the electronic coupling strength inside the complex as a function of two geometrical parameters, namely the phenazine spacing (center-to-center) and the vertical oset of the gold atom with respect to the molecular plane. Figure S3 shows the energetic level schemes for dierent geometries and charge states of the complex. For the anionic state, which we have in our experiments, the level spacing varies by a couple of tenths of ev as a function of both geometrical parameters (cf. Figure S3 a and b). This indicates a considerable electronic coupling between the constituents of the complex formed and is in line with our experimental observations. To shed light on the nature of the energy splitting of states, we additionally performed DFT calculations for the complex in a cationic state. Interestingly, in the case of 8.5 and 9Å S5

6 molecular spacing the LUMO+1 and LUMO+2 (which correspond to LUMO and LUMO+1 of the anionic complex) are nearly degenerate ( E = 13 mev and 3 mev for 8.5 and 9Å molecular spacing, respectively). Hence, the much larger splitting in the anionic case has to be partially due to Coulomb repulsion between the HOMO and the LUMO+1 state. However, for the distance of 8Å corresponding to the geometry as is deduced from the experiment, a considerable splitting of LUMO+1 and LUMO+2 is also observed for the cationic complex. Also for the energetic level alignment we do not expect a quantitative agreement with the experiment since the substrate was not taken into account. References (1) J. Repp, G. Meyer, F. Olsson, M. Persson, Science 2004, 305, 493. (2) G. te Velde, F. M. Bickelhaupt, E. J. Baerends, C. Fonseca Guerra, S. J. A. van Gisbergen, J. G. Snijders, T. Ziegler, J. Comp. Chem. 2001, 22, 931. (3) Avogadro: An open-source molecular builder and visualization tool. Version S6