Organic crystal structure refinement from 3D electron diffraction data with application of dynamical theory and more accurate scattering factors

Abstract text (incl. figure legends and references)

In recent years, one can observe spectacular developments in the 3D electron diffraction (3D ED) methods. Practitioners of this method are learning how to improve data collection, among others how to diminish radiation damage and how to deal with dynamical scattering, data processing, and refinement. Currently, available structures from 3D ED reach R-factors even below 10% and resolution around dmin = 0.5 Å. Refinement with a dynamical approach [1] against such data allows for observation of residual density in bonding paths or lone electron pair regions. Therefore, it is possible and profitable to use more sophisticated aspherical models of atomic electrostatic potential instead of the standard independent atom model (IAM).

We have already proposed transferable aspherical atom model (TAAM) refinements against 3D ED data in kinematic approximation [2]. The TAAM was parametrized with the Multipolar Atom Types from Theory and Statistical clustering (MATTS) databank (successor of UBDB2018 [3]). Now TAAM is coupled with dynamical refinement and available in Jana2020 [4]. Here, we present refinements of exemplary organic crystal structures, urea, and α-glycine, with the application of the kinematic approach. Next, we show the refinement of 1-methyluracil crystal structure against dmin = 0.56 Å data with TAAM in the dynamical approach. There is a visible clearing of the residual density maps, also lowering of the maximum and minimum residual values, and a further lowering of R-factors. The combination of various variants of TAAM with the dynamical approach allows us to conclude that quantitative information about electron density distribution due to chemical bonding, the presence of lone electron pairs, partial charges on atoms, and charge density polarization due to intermolecular interactions can be extracted from the 3D ED data (Fig.1). In the future, we will go beyond TAAM and refine the parameters of the multipole model of electron density.

Fig. 1. Residual electrostatic potential maps for dynamical refinements of 1-methyluracil crystal structure with application of IAM (left), TAAM (middle), and periodic TAAM (right) scattering models. Contour level 0.13 eÅ-1, yellow: positive, cyan: negative. Thermal ellipsoids with 50% probability.

References
[1] L. Palatinus, V. Petricek, and C. A. Correa, Acta Crystallogr. A, 71 (2015), 235–244.
[2] B. Gruza, M. L. Chodkiewicz, J. Krzeszczakowska, and P. M. Dominiak, Acta Crystallogr. A, 76 (2020), 92–109.
[3] P. Kumar, B. Gruza, S. A. Bojarowski, P. M. Dominiak, Acta Crystallogr. A, 75 (2019), 398-408.
[4] V. Petrícek, M. Dusek, and L. Palatinus, Zeitschrift für Krist. - Cryst. Mater., 229 (2014), 345–352.

Acknowledgments: This research was funded by National Science Centre, Poland 2020/39/I/ST4/02904 and University of Warsaw IDUB grant BOB-IDUB-622-20/2021 (,,Infrastructure for Cryomicroscopy and Electron Diffraction Core Facility").