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The present study was aimed at distinguishing halogen atoms substituted in a molecule of copper-phthalocyanine (CuPc) by high-resolution transmission electron microscopy (HRTEM). The subject was carried out on octabromooctachloro-CuPc and obtained HRTEM images suggested inhomogeneous distribution of bromine and chlorine atoms at 1-, 2-, 3- and 4-substitution positions of CuPc in image contrast. As a result of electron crystallography, the occupancy of bromine atoms at the 1-position (and equally at the 4-position) was found to be 52%, which is slightly higher than for random substitution. This small deviation causes apparent inhomogeneous image contrast of halogen substitution observed in the high-resolution images, as concluded from computer simulation of images. Such potential to detect inhomogeneity in substitution by TEM should be important for the chemical understanding of substitution reactions at the atomic level.

Generally, structures of molecular crystals have imperfections and are therefore rather complex. One kind of imperfection is an expansion of the distance between molecular planes that occurs near a crystal surface. Although such an expansion is often observed in a high-resolution image, it has not been measured quantitatively because of the low signal-to-noise ratio of such images. This problem is due to the sensitivity of molecular crystals to electron doses. Here, we have taken photographs of a crystal surface under high magnification in so far as the dose does not destroy the crystal structure. We have quantitatively measured the distance expansion based on image processing and statistical analysis of many photographs. As a result, we have confirmed that the first and second molecular planes shift towards the outside of a crystal in sub-angstrom order.