Theoretical simulations of noncontact atomic force microscopy of 5-(4-methylthiophenyl)-10,15,20-tris(3,5-di-t-butylphenyl)porphyrin molecules on a graphene sheet

For the interpretation of noncontact atomic force microscopy (NC-AFM) images of large organic molecules on a substrate, the effect of the sliding movement and deformation of the molecules caused by the tip should be properly taken into account. In the present work, we attempted to clarify this problem by taking a case study of NC-AFM for a 5-(4-methylthiophenyl)-10,15,20-tris(3,5-di-t-butylphenyl)porphyrin molecule (MSTBPP) on a graphene sheet with a fullerene $\left({\text{C}}_{60}\right)$ molecule tip or an octane $\left({\text{C}}_8{\text{H}}_{18}\right)$ molecule tip. Theoretical simulations and detailed interpretation of NC-AFM images for these systems are presented. When the MSTBPP molecule is fixed on a substrate surface, simulated images in attractive force regions are similar to an experimental image. When the molecule is not fixed or simulated in a repulsive force region, the atomic force microscopy image is difficult to observe because of the translational and deformation movements of the molecule. On the other hand, a significant energy dissipation can be seen. The motion of the molecule also depends on the volume and the shape of the tips.

Figure 1

(Color online) The front (a) and the bottom (b) views of the fullerene tip. The front (c), the top (d), and the bottom (e) views of the octane tip. Blue-colored atoms are the lowest, which means the closest atom to a sample molecule. Green-colored hydrogen atoms of the octane tip are fixed for model (ii).

Figure 2

(Color online) The MSTBPP molecule on a graphene sheet and the scan area. The scan direction is bottom-to-top in the $y$ direction and alternates left-to-right and right-to-left in the $x$ direction.

Figure 3

(Color online) A ${\text{CH}}_2$ (in a dotted line circle) is artificially inserted. All atoms are fixed for model (i). A sulfur atom (in circles) is fixed for model (ii). All atoms are free for model (iii).

Figure 4

H-a and h-b are the tip heights of (a) the initial straight structure and (b) a deformed structure of the octane tip, respectively. H-c is not the tip height for the deformed tip.

Figure 5

(Color online) Motion and parameters of NC-AFM.

Figure 6

The simulated topographical images of model (i) of the MSTBPP molecule by the molecular tips. The frequency shift value for (a) fullerene is $-2.0\text{Hz}$, for (b) octane is $-0.5\text{Hz}$, for (c) fullerene is 2.0 Hz, and for (d) octane is 2.0 Hz.

Figure 7

(Color online) The simulated topographical images of model (ii) of the MSTBPP molecule by the molecular tips. The frequency shift value for (a) fullerene is $-2.0\text{Hz}$, for (b) octane is $-0.5\text{Hz}$, for (c) fullerene is 2.0 Hz, and for (d) octane is 2.0 Hz.

Figure 8

(Color online) Locations and structures of the MSTBPP molecules (a), (b), and (c) at scan positions 1, 2, and 3 indicated in Fig. 7a, respectively.

Figure 9

The simulated energy dissipation images of model (ii) of the MSTBPP molecule by the molecular tips. The frequency shift value for (a) fullerene is $-2.0\text{Hz}$, for (b) octane is $-0.5\text{Hz}$, for (c) fullerene is 2.0 Hz, and for (d) octane is 2.0 Hz.

Figure 10

The initial straight structure (a) and a typical deformed structure (b) of the octane tip.

Figure 11

(Color online) The simulated topographical images of model (iii) of the MSTBPP molecule by the molecular tips. The frequency shift value for (a) fullerene is $-2.0\text{Hz}$, for (b) octane is $-0.5\text{Hz}$, for (c) fullerene is 2.0 Hz, and for (d) octane is 2.0 Hz.

Figure 12

(Color online) Force-distance curves of (a) the force in $z$ direction and (b) the forces in the $x$ and $y$ directions for both the downward and upward motions in the tip oscillation at the scan position indicated by the circle drawn in Fig. 11a.

Figure 13

(Color online) Locations and structures of the MSTBPP molecule when the tip moves down to the heights of (a) $8.4\text{Å}$ and (b) $8.2\text{Å}$ in a tip oscillation at the scan position indicated by the circle drawn in Fig. 11a.

Figure 14

The simulated energy dissipation images of model (iii) of the MSTBPP molecule by the molecular tips. The frequency shift value for (a) fullerene is $-2.0\text{Hz}$, for (b) octane is $-0.5\text{Hz}$, for (c) fullerene is 2.0 Hz, and for (d) octane is 2.0 Hz.

Figure 15

(Color online) Locations and structures of the MSTBPP molecule, (a) and (b), at the scan position indicated by the circle drawn in Fig. 11d before and after the tip is closest to the molecule in a tip oscillation.