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TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

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dc.abstract.enHydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X - H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X - H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorGruza, Barbara
dc.contributor.authorDominiak, Paulina
dc.contributor.authorChodkiewicz, Michal Leszek
dc.contributor.authorKumar, Prashant
dc.contributor.authorJha, Kunal
dc.date.accessioned2024-01-26T09:30:21Z
dc.date.available2024-01-26T09:30:21Z
dc.date.issued2020
dc.description.financePublikacja bezkosztowa
dc.description.number3
dc.description.volume76
dc.identifier.doi10.1107/S2052520620002917
dc.identifier.issn2052-5206
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/121490
dc.identifier.weblinkhttp://journals.iucr.org/b/issues/2020/03/00/px5019/px5019.pdf
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofActa Crystallographica Section B: Structural Science, Crystal Engineering and Materials
dc.relation.pages296-306
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.subject.enaspherical scattering factors
dc.subject.enDiSCaMB
dc.subject.enHAR
dc.subject.enIAM
dc.subject.enquantum crystallography
dc.subject.enstructure refinement
dc.subject.enTAAM
dc.titleTAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data
dc.typeJournalArticle
dspace.entity.typePublication