Charge density distribution and theoretical analysis of low and high energy phosphate esters

Mermer, Adrian; Lis, Tadeusz; Starynowicz, Przemysław

doi:10.1039/c5ra12605c

Cited by 1 publication

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References 60 publications

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“…We note here that to make the 300 K charge density model reasonable, the P v parameter for the potassium centre was restrained to the value of 6.3 e with = 0.01 (based on the results from the lower-temperature data sets). For more details see also the supporting information (Moss et al, 1995;Souhassou et al, 1995;Espinosa et al, 1996;Yufit et al, 2000;Janicki & Starynowicz, 2010;Mermer & Starynowicz, 2011, 2012Mermer et al, 2015;Kinzhybalo et al, 2013;Starynowicz & Lis, 2014;Volkov et al, 2016). Despite the very low residual density extreme values obtained for models at all temperatures and satisfactory Rfactors (considering non-trivial description of the potassium and phosphorus atoms), careful inspection of the residual density for 100, 200 and 300 K data sets revealed some systematic effects within the uracil fragment.…”

Section: Structure Solution and Refinementmentioning

confidence: 99%

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

Jarzembska

Ślepokura

Kamiński

et al. 2017

Acta Crystallogr Sect B

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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.

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Section: Structure Solution and Refinementmentioning

confidence: 99%

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

Jarzembska

Ślepokura

Kamiński

et al. 2017

Acta Crystallogr Sect B

View full text Add to dashboard Cite

show abstract

Charge density distribution and theoretical analysis of low and high energy phosphate esters

Abstract: There is a strict relation between the energy of hydrolysis of phosphate esters and the extent of interactions between the p ester oxygen lone pair and the antibonding orbitals of the rest of the molecule. Its impact on experimental charge density distribution is analyzed.

Cited by 1 publication

References 60 publications

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

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

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