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Supporting Information:
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Substrate-Mediated Electron Tunneling through Molecule-Electrode Interfaces
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Jia-Tao Sun,1 Lan Chen,3* Y. P. Feng,2 A. T. S. Wee,2
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Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
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Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
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Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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1. Technical details
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Experiments:
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The experiments were carried out in a custom-built multi-chamber ultra-high-vacuum (UHV)
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system with base pressure better than 6×10-11 mbar, and housing an Omicron low-temperature
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scanning tunneling microscopy (LT-STM) interfaced to a Nanonis controller (Nanonis,
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Switzerland). Coronene molecules were evaporated from a Knudsen cell onto clean surfaces
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(Ag(111) and HOPG) kept at room temperature. After deposition, the sample was transferred to
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the STM chamber and cooled down to liquid nitrogen temperature (77 K) for STM imaging
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experiments. All STM images were obtained using chemically etched tungsten tips (cleaned by
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cycles of argon ion sputtering at 800-1000 V for about 5-10 min). The bias voltage is tip bias
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which means the electrons tunnel from tip (sample) to sample (tip) when the voltage is
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negative (positive).
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Calculations:
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First-principles calculations were performed within the framework of the local density
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approximation (LDA)1 using the projector-augmented wave (PAW) method2 as implemented in
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Vienna ab-initio Simulation Package (VASP).3 Slab models were used throughout our
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calculations. The computational models containing one coronene molecule on four layers Ag
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atoms are used, where the bottom two layers are fixed during the optimization. A three-layer
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graphite slab model in standard Bernal stacking motif was used for coronene molecular
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adsorption, where the last graphene layer is fixed in the optimization process. The three-layer
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graphene slab is thick enough to simulate the HOPG substrate due to the very weak interaction
S1
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between stacking graphene layers. The structural optimization for coronene molecule on
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HOPG leads to negligible difference in the interlayer separation of graphene layers, which is
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initially set to 3.31 Å. The cutoff energies for plane wave basis set in all calculations are 400
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eV. A vacuum of 17 Å is used to separate the mirror images in the z direction for both cases.
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It is noted that the van der Waals (vdW) interaction has a relatively small and direct effect on
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the electronic structures of the chosen systems.4,5,6 Thus the electronic density of states in
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Figure 2 hold. Then our main conclusion cannot be changed.
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2. Optimized structures and calculated total energy
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In the calculations for coronene molecule on Ag(111) surface, we use the weight center of the
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inner carbon ring as a reference point by taking the advantage of the high symmetry of
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coronene molecule. Four possible adsorption sites, Top, Bridge, FCC and HCP, are shown in
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Fig. S1. The most stable HCP adsorption configuration is marked by red color.
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Figure S1: The optimized structures and total energies of coronene on Ag(111) surface. The
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most stable structure with the minimum energy is mark by red color.
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In the calculations of coronene molecule on HOPG surface, five possible adsorption sites are
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used by taking the same reference point as that on Ag(111) surface. Figure S2 shows the
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optimized structures and the total energies for coronene on HOPG surface.
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S2
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Figure S2: The optimized structures and total energies of coronene on HOPG surface. The first
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and second graphene layer are indicated by red and green color respectively. The most stable
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structure with the minimum energy is mark by red color.
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3. STM simulations
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The tunneling current through the tip-sample nanocontact is the convolution of the density of
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states of STM tip and sample over an energy range following the Bardeen expression as7
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I
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where EF is the Fermi energy, ρ is the density of states, s and t represent the sample and tip
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respectively. Mst is the tunneling matrix element between tip and sample.
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If the tunneling matrix Mst is constant during scanning, the tunneling current is proportional to
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the convolution of the tip DOS and sample DOS as following
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I   s ( EF  eV   ) t ( EF   )d
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In most cases, the tip DOS is constant. Thus the sample DOS can be probed by
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Tersoff-Hamann (T-H) approximation as following8
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dI
  s ( EF  eV   )
dV
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In the T-H approximation, applying a small bias voltage between the tip and the sample yields
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a tunneling current whose density is proportional to the numerical integrations of density of
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states of the sample with respect to the Fermi level. Figure S3 shows the simulated STM
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images for coronene molecule on Ag(111) and HOPG surface by T-H approximation.
4e eV
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 s ( EF  eV   ) t ( EF   ) M st d

 0
eV
0
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Figure S3: The simulated STM image by Tersoff-Hamann approximation for coronene on
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Ag(111) (a) and HOPG (b) surface. The local density of states projected onto the coronene
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molecule and substrate are indicated by red and blue colour respectively.
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It is found that the T-H approximation gives the nearly identical STM topographic images on
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both surfaces. Thus in order to investigate the electron tunneling for same molecule on
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different substrates, Bardeen approximation based on electronic orbital resonant tunneling is
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appropriate. The implementation of Bardeen approximation is based on the code bSKAN.9,10
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4. STM tip
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With respect to the tip calculations, we have used a symmetric pyramidal tungsten cluster
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coupled to the tungsten (110) slab as shown below. The central layer of tungsten atoms is fixed,
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and the other degrees of freedom are completely free upon optimizing the tip model. The
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energy cutoff for the expansion of plane-wave basis set is set to 400 eV.
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Figure S4 The tip model of W(110) slab coupled with a tungsten pyramid.
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References:
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S7. C. J. Chen, Introduction to Scanning Tunneling Microscopy (Oxford University Press,
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Oxford, 1993)
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