Multi-temperature study of potassium uridine-5′-monophosphate: electron density distribution and anharmonic motion modelling

Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials

5 years ago

Multi-temperature study of potassium uridine-5′-monophosphate: electron density distribution and anharmonic motion modelling

Paulina M. Dominiak, Krzysztof Woźniak, Radosław Kamiński, Katarzyna Ślepokura, Matthias J. Gutmann, Katarzyna N. Jarzembska

Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5′-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5′-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH− anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.A multi-temperature high-resolution diffraction study of a biologically important salt potassium uridine monophosphate, K(UMPH), is reported. Anharmonic motion in the uracil moiety was detected and verified by He-temperature X-ray diffraction experiments. The charge density distribution was modelled within the Hansen–Coppens formalism, while anharmonicity was taken into account using Gram–Charlier parameters.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1107/S2052520617005534