Case study: Polydiacetylene crystal^[1]

True molecular resolution in tapping-mode atomic force microscopy study of polydiacetylene crystal using HRC probe. Images of the bc plane of the crystal, which were obtained at ambient conditions, reproduce the crystallographic molecular arrangement. The image features directly correspond to the edges of the individual side groups of the polymer chains, which form the crystal surface. The molecular-size defects have been observed on this surface as an additional proof of the true molecular resolution.

Tapping mode height AFM images obtained with HRC probe on the bc plane of the polydiacetylene crystal are shown in Figs. 1(a)–1(c). Images exhibit a well-defined pattern with the bottom-to-top rows. Two white arrows in (a), (b), and (c) indicate two molecular-size (3–5 Å) defects, whose positions are changing due to thermal drift. These images reproduce the molecular arrangement in the bc plane, where most elevated F, H, and C atoms are forming rows in the b direction. The crystallographic orientation of the side groups alternates in the neighboring rows separated by 0.705 nm (half of the c parameter). Bright spots along the rows, which are clearly seen in Fig. 1(b) and less pronounced in Fig. 1(c), can be assigned to individual side groups of the polymer. The spacings along the rows in the filtered images [Figs. 1(d) and 1(e)] are ~0.66 nm and ~0.36 nm with their average close to the b parameter. When the conventional Si probe (radius ~10 nm) is applied, tapping-mode image of the bc plane shows a rough striped pattern (a continuous strip is seen instead of two rows, the strips are separated by 1.4 nm) with a few 2–3 nm defects, Fig. 2. The molecular rows within the unit cell are resolved only in the images obtained with HRC probe.

Fig. 1 Tapping mode height AFM images obtained with the HRC probe on the bc plane of the polydiacetylene crystal. The contrast in the images in (a), (b), and (c) reflects the height corrugations in the 0–0.6 nm scale. The power spectra of the images in (b) and (c), which were obtained in the 2D FFT procedure, are shown in the top right corners of these images. The 2D FFT filtering led to the periodical patterns in (d) and (e), which were obtained from the images (b) and (c), respectively.

Fig. 2 Tapping mode height AFM images obtained with conventional Si probe on the bc plane of the polydiacetylene crystal. The contrast in the images reflects the height corrugations in the 0–0.3 nm scale.

Measurements were performed with a Dimension 5000 (Veeco Instruments) scanning probe microscope.

Images were kindly given by Dr. D. Klinov (Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences).

^[1] D. Klinov and S. Magonov, True molecular resolution in tapping-mode atomic force microscopy with high-resolution probes, Appl. Phys. Lett. 84 (14), 2697–9 (2004)