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

Abstract

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.

Quantum Crystallography: Current Developments and Future Perspectives

“…The model, starting from free quantum‐physical atoms, allows to “measure” the response of to the formation of molecules (chemical bonds), supramolecular assemblies and crystals, and to other physical stimuli, such as different temperatures, high pressure, light or possibly an external electric field . Parameters of the multipole model are usually refined by a least‐squares fitting against experimental observations.…”

Orbital‐Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions

“…The structural formula and atom labels for DMPU are shown in Scheme 1 and Figure S1. Mention should be made to a few examples of other experimental charge density studies of the uracil derivatives [86–88] …”

“…Mention should be made to a few examples of other experimental charge density studies of the uracil derivatives. [86][87][88]…”

The features of the crystal structure of the layered series hydrates of uridine-5′-monophosphate salts (UMPNax·yH2O)

“…Yet an exception was the crystal structure of potassium uridine-5′-monophosphate salts (UMPK). 21 From Fig. S6, † the coordination of Na gives priority to Na–O (water) for the UMPNa x · y H 2 O hydrates, and the oxygen of water contributes mainly to the coordination sphere of Na ions, and there is not the case that two UMP 2− moieties located in two adjacent layers were linked by the sodium ion coordination interaction.…”