With the advent of 3D Electron diffraction (3D ED) techniques of data acquisition and processing, electron crystallography has emerged as a powerful technique for achieving accurate structure solutions and refinements at the atomic level [1]. In this study, we selected three samples two inorganic minerals, epidote and natrolite, and one organic, ibuprofen to address specific structural challenges. In both epidote and natrolite, the position of hydrogen atoms was difficult to determine due to the presence of heavier inorganic atoms. Epidote is a solid solution and has a mixed occupancy of Fe and Al in one site to be determined; natrolite being a non-centrosymmetric structure, necessitated the determination of its absolute orientation; ibuprofen is a beam sensitive organic sample that crystallizes in two different enantiomers. For ibuprofen we selected a sample that is enantiopure (S-form) to verify the accurate determination of the absolute structure.
All datasets were collected using a TEM FEI Tecnai G2 20 operating at an accelerating voltage of 200 kV and equipped with a Medipix 3 ASI Cheetah hybrid pixel detector. The data acquisition was performed through both precession-assisted stepwise 3D electron diffraction and continuous rotation 3D ED (Micro ED). Subsequent data processing was conducted using the PETS2[2] software, and the structures were solved and refined using dynamical refinement in JANA2020[3].
All three structures were successfully solved using dynamical refinement, allowing for the precise determination of hydrogen atom positions. In the case of Epidote, the mixed occupancy of Fe and Al was accurately identified. Notably, the dynamical refinement of natrolite revealed a significant 10% difference in R-values between the two absolute orientations, highlighting a pronounced sensitivity to the left- and right-handed structures. For ibuprofen, due to its high beam sensitivity, a low dose cryo 3D ED experimental setup was essential to achieve successful structure resolution. The slight difference in R-values (1.27%) and the Z-score test were critical in determining the absolute configuration of S-ibuprofen, distinguishing it from R-ibuprofen.
3. Petříček, V., Palatinus, L., Plášil, J., Dušek, M. (2023). Z. Krist., 238, 271-282.
This research was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 956099 (NanED – Electron Nanocrystallography – H2020-MSCAITN).