Dynamical refinement with multipolar electron scattering factors
Status PubMed-not-MEDLINE Jazyk angličtina Země Anglie, Velká Británie Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
2020/39/I/ST4/02904
Narodowe Centrum Nauki
21-44862L
Grantová Agentura České Republiky
PLG/2021/014598
the Polish high-performance computing infrastructure PLGrid
PubMed
38512772
PubMed Central
PMC11067749
DOI
10.1107/s2052252524001763
PII: S2052252524001763
Knihovny.cz E-zdroje
- Klíčová slova
- 3D electron diffraction, dynamical refinement, electron crystallography, microcrystal electron diffraction, multipolar scattering factors, quantum crystallography, transferable aspherical atom model,
- Publikační typ
- časopisecké články MeSH
Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.
Biological and Chemical Research Centre Department of Chemistry University of Warsaw Warsaw Poland
Institute of Physics of the Czech Academy of Sciences Na Slovance 1999 2 182 00 Prague Czechia
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