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Chemical Structure Imaging of a Single Molecule by Atomic Force Microscopy at Room Temperature


Chemical Structure Imaging of a Single Molecule by Atomic Force Microscopy at Room Temperature

Kota Iwata et al. Nat Commun.


Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)-(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule.


Figure 1
Figure 1. A single PTCDA molecule adsorbed on the Si(111)-(7 × 7) surface.
(a) An STM image at Vs=+500 mV. Scale bar, 1 nm. The five arrows indicate stripes corresponding to a molecular orbital. (b) Schematic view of the arrangement of a PTCDA molecule adsorbed onto the surface over a corner-hole site.
Figure 2
Figure 2. Chemical structure imaging of single molecule by AFM at room temperature.
(a) Constant-height AFM image of a single PTCDA molecule adsorbed on the Si(111)-(7 × 7) surface. The acquisition parameters were f0=158,586.6 Hz, k=31.9 N/m, A=138 Å, Vs=Vc.p.d.=130 mV, and Q=22,000. The scan speed was 3 nm s-1. Scale bar, 0.5 nm. (b) Calculated map of electron density cut along a plane parallel to the surface. (c,d) Top and side views of the optimized configuration of the PTCDA molecule adsorbed at a corner-hole site of the Si(111)-(7 × 7) surface.
Figure 3
Figure 3. Tip identification by force measurements.
(a,b) Δf(z) curves measured over the centre of the PTCDA molecules (blue), corner adatoms (red) and corner holes (gray) using (a) a reactive tip and (b) an inert tip. Fitting curves for the long-range force contributions are shown by the dotted curves. The acquisition parameters were (a) f0=165,371.4 Hz, k=37.6 N m−1, A=133 Å, Vs=Vc.p.d.=−280 mV and Q=23,000, (b) f0=156,719.7 Hz, k=29.6 N m−1, A=201 Å, Vs=Vc.p.d.=−350 mV and Q=25,000. Corresponding AFM images are shown in the insets. Scale bar, 1 nm. (c,d) F(z) curves over the centre of the PTCDA molecules (blue) and corner adatoms (red), converted from the short-range part of the ΔF(z) curves from a and b. The F(z)curves over the H adsorbed on Si adatoms (green) and Si adatoms (orange) from our previous study are also shown. The tip models identified are shown in the insets.
Figure 4
Figure 4. Theoretical force and frequency shift curves.
(a) Theoretical F(z) curves over the centre of a PTCDA (light blue) and a corner adatom (orange). The model of an Si dimer tip shown in Fig. 3c is used. The corresponding experimental curves from Fig. 3c are shown: F(z) on PTCDA (blue) and Si adatom (red). The Van der Waals (vdW) force is taken into account for the calculations on the molecule. The theoretically derived maximum attractive force is around −0.29 nN, which matches the value obtained experimentally. Since the attractive force in the F(z) calculated without the vdW contribution is too small to reproduce the experimental results (not shown), the vdW interaction force dominates the attractive force on the molecule. (b) Theoretical F(z) curves over the centre of a PTCDA (blue), a carbon atom (green) and an oxygen atom (red). (c) A model of the PTCDA molecule showing the three sites used for the force calculations. (d) Δf(z) curves converted from the F(z) curves shown in b. For the conversion, we used the same parameters as used for the experiments shown in Fig. 3a.

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