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The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy

Science  28 Aug 2009:
Vol. 325, Issue 5944, pp. 1110-1114
DOI: 10.1126/science.1176210

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  1. Fig. 1

    STM and AFM imaging of pentacene on Cu(111). (A) Ball-and-stick model of the pentacene molecule. (B) Constant-current STM and (C and D) constant-height AFM images of pentacene acquired with a CO-modified tip. Imaging parameters are as follows: (B) set point I = 110 pA, V = 170 mV; (C) tip height z = –0.1 Å [with respect to the STM set point above Cu(111)], oscillation amplitude A = 0.2 Å; and (D) z = 0.0 Å, A = 0.8 Å. The asymmetry in the molecular imaging in (D) (showing a “shadow” only on the left side of the molecules) is probably caused by asymmetric adsorption geometry of the CO molecule at the tip apex.

  2. Fig. 2

    Constant-height AFM images of pentacene on NaCl(2ML)/Cu(111) using different tip modifications (16). (A) Ag tip, z = –0.7 Å, A = 0.6 Å; (B) CO tip, z = +1.3 Å, A = 0.7 Å; (C) Cl tip, z = –1.0 Å, A = 0.7 Å; and (D) pentacene tip, z = +0.6 Å, A = 0.5 Å. The z values are given with respect to a STM set point of I = 2 pA, V = 200 mV above the NaCl(2 ML)/Cu(111) substrate.

  3. Fig. 3

    Maps of measured frequency shift Δf (A) and extracted vertical force Fz (B) at different tip heights z. Corresponding line profiles of Δf (C) and Fz (D) along the long molecular axis. The data shown are part of a complete three-dimensional force field that has been measured in a box of 25 Å by 12.5 Å by 13 Å above a pentacene molecule (16). The z values are given with respect to a STM set point of I = 2 pA, V = 200 mV above the NaCl(2 ML)/Cu(111) substrate.

  4. Fig. 4

    Calculated energy map (A) for a CO-pentacene distance of d = 4.5 Å. Calculated line profiles of the energy (B), the vertical force (C), and Δf (D) above the long molecular axis for different molecular distances. Calculated (E) and measured (F) force-distance curves above different molecular sites: central hollow site (blue), C-C bond of central ring on long molecular axis (red), C atom of central ring on short molecular axis (green), and H atom on short axis (orange). The inset in (E) shows a measured Δf map with the different molecular sites indicated. In the experimental data, the force components that arise from the metal tip behind the CO molecule have been subtracted (16, 29).