Real-space crystal structure analysis by low-dose focal-series TEM imaging of organic materials with near-atomic resolution

Structural analysis of beam-sensitive materials by transmission electron microscopy (TEM) represents a significant challenge, as high resolution TEM (HRTEM) requires high electron doses that limits its applicability to stable inorganic materials. Beam sensitive materials, such as organic crystals (of key importance in pharmaceuticals, organic electronics, and biology) must be imaged under low dose conditions, leading to problematic contrast interpretation and the loss of fine structural details. Here, we describe HRTEM imaging of organic crystalline materials with near-atomic resolution of up to 1.6 Å that enabled the real-space study of crystal structures, as well as observation of co-existing polymorphs, crystal defects, and atoms. This is made possible by a low-dose focal series reconstruction (LD-FSR) methodology developed by us, which provides HRTEM images where contrast reflects true object structure and can be performed on contemporary cryo-EM instruments available to many research institutions. We imaged copper phthalocyanine (CuPc), perchlorinated analogue of CuPc, and indigo crystalline films. In the case of indigo crystals, we were able to observe co-existing polymorphs and individual atoms (carbonyl oxygen). In the case of CuPc, we observed several polymorphs, including a new one, for which we elucidated the crystal structure based on direct in-focus imaging, accomplishing real-space crystal structure elucidation. Direct structural analysis of beam sensitive materials with high resolution that enables the real-space study of crystals can be transformative for structural science of organic materials.