Charge-density distribution in potassium dihydrogen phosphoglycolate – a comparison of phosphate and phosphonate groups

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

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.

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

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.

Charge-density distribution in sodium bis(4-nitrophenyl)phosphate

The electron-density distribution in sodium bis(4-nitrophenyl)phosphate has been analyzed using the multipole refinement of X-ray diffraction data and of theoretical density-functional theory (DFT) calculations. The ester P—O bonds are particularly long and their topological parameters (density at the bond critical point, Laplacian) are lower than for other P—O bonds. Some disagreement between the experimental and theoretical charges of atoms constituting the nitro groups has been observed and the possible reasons are discussed. Weak polarization effects produced by sodium cations may be observed within the phosphate fragment; they are more manifest in the case of the nitro groups.

Charge density distribution of 3-(1-aminoethylidene)-2-methoxy-2-oxo-2,3-dihydro-2λ(5)-benzo[e][1,2]oxaphosphinin-4-one

A combined experimental and theoretical study of one oxaphosphinane derivative was made on the basis of a topological analysis of its electron density distributions. The electron density was determined from a high-resolution X-ray diffraction data set measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using density functional theory (DFT) methods at the B3LYP\6-311++G(3df,3pd) level of approximation. The charge-density distribution and analysis of topological properties revealed that the P-O bond is of the transit closed-shell type. The crystal structure possesses one intra- and several intermolecular hydrogen bonds. They were characterized quantitatively by topological properties using Bader's Atoms in Molecules theory. All hydrogen bonds were classified as weak. Further analysis of the experimental electron density by the source function allowed the intramolecular hydrogen bond to be characterized as an isolated hydrogen bond, in contrast to the resonance-assisted hydrogen bond in related molecules, such as chromone derivatives.

Electron density distribution in tetralithium hypodiphosphate hexahydrate, Li4P2O6·6H2O

Tetralithium hypodiphosphate hexahydrate, Li4P2O6·6H2O, forms a highly symmetrical crystal structure, where hypodiphosphate anions have \bar 3m (D3d) symmetry. Analysis of the charge distribution (experimental and theoretically calculated) shows that the charges of the P atoms are lower than in phosphates and phosphonates, whereas the O charges are similar. Values of both ρc and ∇(2)ρc suggest that the P-P bond is a weak covalent one, while the P-O one is polarized covalent, with topological parameters similar to those of P-O bonds in phosphates or phosphonates. Theoretical calculations show that the hypodiphosphate anion is relatively insensitive to its coordination environment; this is brought about by the vicinity of cationic P atoms. The localization and delocalization indices have been computed and discussed.