Charge-density distribution in hydrogen methylphosphonates of calcium and lithium

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.

Understanding Nitrilotris(methylenephosphonic acid) reactions with ferric hydroxide

Phosphonate compounds are used in a wide variety of industrial and agricultural applications, and are commonly found in surface and ground waters. Adsorption to ferric hydroxide can have a significant effect on the transport and fate of phosphonate compounds in the environment. This research used density functional theory modeling to investigate the adsorption mechanisms of nitrilotris(methylenephosphonic acid) (NTMP) on ferric hydroxide. Standard Gibbs free energies of reaction (ΔG_r^o) and reaction activation barriers (E_a) were calculated for different possible adsorption mechanisms. Physical adsorption of NTMP to ferric hydroxide was promoted by negative charge assisted hydrogen bonding, and had ΔG_r^o ranging from -2.7 to -7.4 kcal/mol. NTMP was found to form three different types of inner sphere complexes, monodentate, bidentate mononuclear and bidentate binuclear. For the monodentate complexes, ΔG_r^o ranged from -8.0 to -13.7 kcal/mol, for the bidentate complexes ΔG_r^o ranged from -15.3 to -28.9 kcal/mol. Complexation with Ca²⁺ decreased the energy for physical adsorption but increased the binding energies for mono- and bidentate complexes. Complexation with Ca²⁺ also allowed formation of a tridentate ternary surface complex, whereby the Ca²⁺ ion formed a bridge between three FeO^- and three PO^- groups. Physical adsorption had E_a = 0, but mono- and bidentate complex formation had E_a values ranging from 36 to 53 kcal/mol. Formation of tridentate ternary surface complexes involving Ca²⁺ had the lowest activation barriers of 8 and 10 kcal/mol. The different activation barriers for different modes of adsorption may explain previous experimental observations of unusual kinetic behavior for adsorption and desorption of NTMP.

Synthesis and characterization of new barium methylphosphonates

Eight new barium methylphosphonates were prepared and described. In dependence on pH, either barium hydrogen methylphosphonates or barium methylphosphonates can be formed. In the case of barium methylphosphonates, BaCH₃PO₃·3H₂O crystallizes from the solution at room temperature and BaCH₃PO₃·H₂O at a temperature above 65 °C. On heating, these hydrates form two anhydrous barium methylphosphonates (α-BaCH₃PO₃ and β-BaCH₃PO₃) with the same composition but with a different structure. In a basic environment, barium hydrogen methylphosphonate monohydrate, Ba(CH₃PO₃H)₂·H₂O, transforms to BaCH₃PO₃·3H₂O through an intermediate with the formula Ba₂(CH₃PO₃H)₂(CH₃PO₃)·4H₂O. The reverse reaction, that is the reaction of BaCH₃PO₃·3H₂O with methylphosphonic acid, proceeds to the intermediate only and hydrogen methylphosphonate is not formed. Acidic Ba(CH₃PO₃H)₂·H₂O is able to interact with basic amines and form stable intercalates with them. Structures of β-BaCH₃PO₃ (P2₁/c, a = 8.4501(6) Å, b = 7.2555(7) Å, c = 7.4604(8) Å, β = 99.837(8)°, Z = 4) and BaCH₃PO₃·H₂O (P2₁/c, a = 20.5077(5) Å, b = 7.2175(2) Å, c = 7.4909(3) Å, β = 95.522(3)°, Z = 8) were solved from powder X-ray diffraction data. Both compounds are layered, and the layers are formed of two sheets of Ba atoms connected through oxygen atoms of the phosphonate groups. The methyl groups point towards the interlayer space. In the case of BaCH₃PO₃·H₂O, the molecules of water are coordinated to the Ba atoms and are placed in the interlayer space among the methyl groups.

Stoichiometry of lanthanide(iii) complexes with tripodal aminophosphonic ligands – a new solution to an old problem

The [Eu(NP₂py)₂]⁵⁻ complex crystallized as a [C(NH₂)₃]₅[Eu(NP₂py)₂]·12 compound. However, the formation of the [Ln(NP₂py)₂]^5– species in aqueous solution starts at pH as high as 8.

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.

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

Analysis of the experimental and theoretical charge-density distribution in potassium dihydrogen phosphoglycolate has been performed. The P—O bonds in the phosphate group are more polarized and the P atom is more positively charged than in phosphonate groups. The P—O bonds belong to a transit closed-shell (or polar covalent) class, while the ester C—O bond is a covalent (or shared-shell) bond. The coordination of potassium exerts a small effect on the phosphate group, whereas more pronounced changes, e.g. concerning the ellipticities of the C—O bonds, may be observed. The profiles of Laplacians and ellipticities give more insight in the polarization of the bonds.