On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors.

Autor: Pacoste L; Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden., Ignat'ev VM; Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland., Dominiak PM; Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland., Zou X; Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
Jazyk: angličtina
Zdroj: IUCrJ [IUCrJ] 2024 Sep 01; Vol. 11 (Pt 5), pp. 878-890. Date of Electronic Publication: 2024 Sep 01.
DOI: 10.1107/S2052252524006730
Abstrakt: This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal-organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe-O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe 3+ has a lower scattering amplitude than the Fe 3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R 1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R 1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe 3+ ), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R 1 reductions occurred in the low-resolution region (8.65-2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00-0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal-organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED.
(open access.)
Databáze: MEDLINE
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