Supplementary Information

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1 Supplementary Information Direct observation of crystal defects in an organic molecular crystals of copper hexachlorophthalocyanine by STEM-EELS Mitsutaka Haruta*, Hiroki Kurata Institute for hemical Research, Kyoto University, Uji, Kyoto , Japan correspondence to: 1

2 1. Materials The crystal structure of 16 -upc is illustrated schematically in Fig. S1(a). The molecules are packed in a base-centered monoclinic structure, with unit-cell dimensions of a = 1.96 nm, b = 2.61 nm, c = nm, and = The molecules are arranged in a herringbone structure where the molecular plane in every second column is parallel to the substrate surface, while the molecular plane in the other columns is tilted 26.5 away from the substrate as shown in Fig. S1(b) 1. High-resolution images were observed along the c-axis by inclining the specimen with respect to the incident electron beam. Therefore, the molecular plane is not perpendicular to the electron beam but tilted at an angle of On the other hand, for molecules observed at the grain boundary, the molecular plane, as indicated by the blue lines, lies parallel to the electron beam. 2

3 N N N N N N N u N N N u N N N N N N N N N N u N a N N N N N N N N N N u N N u N N N N N N N b a Electron beam c Substrate b 26.5 a Figure S1. Schematic illustrations showing (a) molecular arrangement in the a b plane of the monoclinic structure and (b) incident electron direction at the monoclinic 16 -upc crystallite. The plane of the green molecules is parallel to the substrate surface, while that of the blue molecules is parallel to the electron beam direction. The molecular images are obtained with the beam transmitting along the c-axis. 3

4 2. Advantage of LAADF-STEM for organic crystals Figure S2(a) shows schematic ray diagrams of ADF-STEM. Generally, the inner detection angle (θ min ) for HAADF imaging is selected to be more than 50 mrad for inorganic crystal to avoid the elastic scattering electrons. The elastic scattering intensity I BS and thermal diffuse scattering (TDS) I TDS can be expressed respectively as I BS 2 TDS 2 f ( s) exp 2M ( s) and I f ( s) 1 exp 2M ( s) x x x x 25, where s = sin( )/, and f x (s) and exp[-2m x (s)] are the atomic structure factor for the electron and the Debye-Waller factor of each element x, respectively. When the atoms vibrate independently (Einstein model), the temperature factor can be expressed as 2 M x ( s) Bs, where the constant B is related to the lattice vibration amplitude. Figure S2(b) shows the intensity profiles of the elastic scattering and TDS for isolated, N,, u, and Si atoms assuming the Einstein model. The values of constant B for, N, u, and were assumed to be the same as those used in the multislice image simulation for halogenated upc 7 and that for Si was taken as the value for a Si crystal at room temperature 26. Generally, in the case of an atom in an inorganic crystal, the crossover point between the elastic and TDS profiles is found at a scattering angle of around 50 mrad. Therefore, the inner detection angle (θ min ) is usually set to more than 50 mrad in 4

5 order to detect mainly the TDS electrons which are scattered incoherently. On the other hand, since the temperature factor in organic materials is large compared to that in inorganic materials, the crossover point between elastic and TDS profiles is found at a scattering angle of under 20 mrad for each atom. Therefore, because of the large temperature factor in the case of organic materials, the LAADF-STEM method can be used to detect electrons scattered above 30 mrad and almost guarantee collection of only TDS signals, leading to incoherent high-resolution Z-contrast imaging. Figs. S2(c) and (d) show the microdiffraction patterns of Si [110] and 16 upc along the c-axis with a convergence semi-angle of 3.4 mrad. As the lattice constants of 16 -upc are comparatively large, elastically diffracted beams are confined to the lower angular region. Since the high-resolution LAADF-STEM experiments were performed using an electron probe with a convergence semi-angle of 23 mrad to form a fine probe, the inner detection angle was set to 39 mrad in order to avoid the contribution from first-order diffraction. The elastic component was considered to be low in the LAADF images of the 16 -upc crystal under the present experimental conditions. 5

6 Intensity a Objective lens Specimen θ min θ max ADF detector α b 4 TDS Elastic N TDS Elastic 3 TDS Elastic u TDS Elastic 2 Si TDS Elastic 1 LAADF HAADF Scattering angle (mrad) c d Diffracted disk Figure S2. (a) Schematic diagram of ADF-STEM. (b) Intensity profiles of elastic and thermal diffuse scattering (TDS) from isolated, N,, u, and Si atoms under the Einstein model. The Debye-Waller factors for, N, u, and were assumed to be the same as those used in the multislice image simulation for halogenated-upc 1 and that for Si was that for a Si crystal at room temperature 26. The microdiffraction patterns of (c) Si [110] and (d) 16 upc along the c-axis projection with a convergence semi-angle of 3.4 mrad. The inner detection angle (39 mrad) for LAADF imaging is indicated by the white circles. 6

7 3. Effect of spherical aberration corrector in STEM imaging for organic crystals In our previous research 7, only the copper atomic column in each molecular unit was observed directly in the raw image while chlorine atomic columns were visible after noise filtering. This was a critical problem in the high-resolution analysis of non-periodical structures. Increasing the signal-to-noise ratio in the LAADF image by incorporating a spherical aberration (s) corrector, however, not only allowed observation in the raw image of chlorine but also lighter elements. As discussed in our previous research, radiation damage of the specimen has also been an issue. In a previous study using STEM without a s-corrector, the clearest images were observed at 6M-fold magnification with a pixel size of 0.05 nm and a dwell time of 60 s per pixel. The probe current was set to about 5 pa, corresponding to an average electron dose of ca. 12 cm 2, which is smaller than the end-point dose (ca. 35 cm 2 ) for the 16 -upc crystal 24. At magnifications higher than 6 M, the molecular crystal was completely destroyed by electron bombardment. This was because the broad electron probe, with a full-width at half-maximum of about 0.18 nm, leads to unnecessary irradiation when the pixel size in the image was decreased at a higher magnification. In order to achieve a higher resolution in ADF-STEM imaging of organic crystals, any unnecessary irradiation should be minimized by using a finer 7

8 electron probe. The s corrector has improved the size of the electron probe so that it is 1 Å or less in diameter. This improvement in probe size enables observation of an image at a low probe current of about 1 pa, which provides a low-dose observation of about 1.1 cm -2 at 6M-fold magnification with a dwell time of 26.7 s per pixel, leading to a decrease in the unnecessary irradiation and an increase in the signal-to-noise ratio of the STEM image. Therefore, high magnification imaging could be performed even at 25M-fold magnification, corresponding to an average electron dose of ca cm 2, as shown in Figs. 1(d)-(g). The pixel size in 25M-fold magnification images was nm, i.e. the images were over-sampled with 15 pixels per the horizontal u-n atomic distance (0.18 nm) and with 11 pixel per the horizontal - atomic distance (0.14 nm) in the projected plane, which was enough to directly resolve the atomic columns in the molecular unit. In case of the high resolution LAADF image (Fig. 1 (e)), the light elements ( and N) were visible together with the heavier elements ( and u) but not atomically resolved. Fast Fourier transformation (FFT) of the LAADF image indicates that the spatial resolution of the image is 0.18 nm. On the other hands, - columns of the benzene as well as u-n columns of the porphyrin rings were clearly resolved in ABF image, which indicates a spatial resolution better than 0.14 nm. Therefore, we concluded that spatial resolutions of better than 0.18 nm 8

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