X-ray crystal analysis of the substrates of aconitase. VI. The structures of sodium and lithium dihydrogen citrates

Structures of disodium hydrogen citrate monohydrate, Na2HC6H5O7(H2O), and diammonium sodium citrate, (NH4)2NaC6H5O7, from powder diffraction data

The crystal structures of disodium hydrogen citrate monohydrate and di­ammonium sodium citrate have been solved and refined using laboratory X-ray powder diffraction data and optimized using density functional techniques.

The crystal structures of disodium hydrogen citrate monohydrate, Na₂HC₆H₅O₇(H₂O), and di­ammonium sodium citrate, (NH₄)₂NaC₆H₅O₇, have been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. In NaHC₆H₅O₇(H₂O), the NaO₆ coordination polyhedra share edges, forming zigzag layers lying parallel to the bc plane. The hydro­phobic methyl­ene groups occupy the inter­layer spaces. The carb­oxy­lic acid group makes a strong charge-assisted hydrogen bond to the central carboxyl­ate group. The hydroxyl group makes an intra­molecular hydrogen bond to an ionized terminal carboxyl­ate oxygen atom. Each hydrogen atom of the water mol­ecule acts as a donor, to a terminal carboxyl­ate and the hydroxyl group. Both the Na substructure and the hydrogen bonding differ from those of the known phase Na₂HC₆H₅O₇(H₂O)_1.5. In (NH₄)₂NaC₆H₅O₇, the NaO₆ coordination octa­hedra share corners, making double zigzag chains propagating along the b-axis direction. Each hydrogen atom of the ammonium ions acts as a donor in a discrete N—H⋯O hydrogen bond. The hydroxyl group forms an intra­molecular O—H⋯O hydrogen bond to a terminal carboxyl­ate oxygen atom.

A mixed molecular salt of lithium and sodium breaks the Hume-Rothery rules for solid solutions

Despite the difference in size and chemistry, lithium and sodium form a solid solution as isoorotate salt. Such behaviour, which represents an exception to the Hume-Rothery rules, can be exploited in the preparation of novel lithium drugs.

Crystal structures of alkali metal (Group 1) citrate salts

The crystal structures of 16 new alkali metal citrates were determined using powder and/or single crystal techniques. These structures and 12 previously determined citrate structures were optimized using density functional techniques. The central portion of a citrate ion is fairly rigid, while the conformations of the terminal carboxylate groups exhibit no preferences. The citrate–metal bonding is ionic. Trends in metal–citrate coordination are noted. The energy of an O—H...O hydrogen bond is proportional to the square root of the H...acceptor Mulliken overlap population, and a correlation between the hydrogen bond energy and the H...acceptor distance was developed:E(kJ mol−1) = 137.5 (5) − 45.7 (8) (H...A, Å). The hydrogen bond contribution to the crystal energy ranges from 62.815 to 627.6 kJ mol−1 citrate−1and comprises ∼5 to 30% of the crystal energy. The general order of ionization of the three carboxylic acid groups of citric acid is: central, terminal, terminal, although there are a few exceptions. Comparisons of the refined and DFT-optimized structures indicate that crystal structures determined using powder diffraction data may not be as accurate as single-crystal structures.

A second polymorph of sodium di-hydrogen citrate, NaH2C6H5O7: structure solution from powder diffraction data and DFT comparison

The crystal structure of a second polymorph of sodium di-hydrogen citrate, Na(+)·H2C6H5O7 (-), has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The powder pattern of the commercial sample used in this study did not match that corresponding to the known crystal structure [Glusker et al. (1965). Acta Cryst. 19, 561-572; refcode NAHCIT]. In this polymorph, the [NaO7] coordination polyhedra form edge-sharing chains propagating along the a axis, while in NAHCIT the octa-hedral [NaO6] groups form edge-sharing pairs bridged by two hy-droxy groups. The most notable difference is that in this polymorph one of the terminal carboxyl groups is deprotonated, while in NAHCIT the central carboxyl-ate group is deprotonated, as is more typical.

Structural characterization of a ternary Fe(III)-U(VI)-citrate complex

Citric acid, a naturally occurring hydroxycarboxylic acid, forms bidentate, tridentate, dinuclear, or polymeric species, depending on the metal. In the presence of iron and uranium a ternary Fe: U: citric acid complex is formed. We determined the molecular structure of the ternary complex in both the aqueous and solid phase. Fourier transform infrared spectroscopy (FTIR) showed the presence of uni- and bi-dentate bonding of the citric acid to the metals, and the involvement of the α-hydroxyl group. Analysis of molecular fragments generated from time-of-flight secondary ion mass spectroscopy (TOF-SIMS) confirmed the bonding of terminal carboxylate groups of citric acid to uranium and iron. Extended X-ray absorption fine structure (EXAFS) analysis revealed the dinuclear nature of the Fe bonding to citrate and mononuclear uranium species with citrate. Coordination of a sodium atom to the iron was also noted. The proposed empirical formula for the complex is [NaFe2(μ-O)(μ-citrato)(OH)2(H2O)(C6H4O7)bis(UO2)(C6H5O7)]7-. The structure consists of a dinuclear ferric ion core coordinated through an oxy (μ-O) and a carboxylate (μ-citrato) group of citric acid. The mononuclear uranyl ions are coordinated in bidentate fashion to the central carboxylate groups of citric acid and tridentate coordinated to citric acid.

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase

The crystal structure of M4 apo-lactate dehydrogenase from the spiny dogfish (Squalus acanthius) was initially refined by a constrained-restrained, and subsequently restrained, least-squares technique. The final structure contained 286 water molecules and two sulfate ions per subunit and gave an R-factor of 0.202 for difraction data between 8.0 and 2.0 A resolution. The upper limit for the co-ordinate accuracy of the atoms was estimated to be 0.25 A. The elements of secondary structure of the refined protein have not changed from those described previously, except for the appearance of a one-and-a-half turn 3(10) helix immediately after beta J. There is also a short segment of 3(10) helix between beta C and beta D in the part of the chain that connects the two beta alpha beta alpha beta units of the six-stranded parallel sheet (residues Tyr83 to Ala87). Examination of the interactions among the different elements of secondary structure by means of a surface accessibility algorithm supports the four structural clusters in the subunit. The first of the two sulfate ions is in the active site and occupies a cavity near the essential His195. Its nearest protein ligands are Arg171, Asp168 and Asn140. The second sulfate ion is located near the P-axis subunit interface. It is liganded by His188 and Arg173. These two residues are conserved in bacterial lactate dehydrogenase and form part of the fructose 1,6-bisphosphate effector binding site. Two other data sets in which one (collected at pH 7.8) or both (collected at pH 6.0) sulfate ions were replaced by citrate ions were also analyzed. Five cycles of refinement with respect to the pH 6.0 data (25 to 2.8 A resolution) resulted in an R value of 0.191. Only water molecules occupy the subunit boundary anion binding site at pH 7.8. The amino acid sequence was found to be in poor agreement with (2Fobs-Fcalc) electron density maps for the peptide between residues 207 and 211. The original sequence WNALKE was replaced by NVASIK. The essential His195 is hydrogen bonded to Asp168 on one side and Asn140 on the other. The latter residue is part of a turn that contains the only cis peptide bond of the structure at Pro141. The "flexible loop" (residues 97 to 123), which folds down over the active center in ternary complexes of the enzyme with substrate and coenzyme, has a well-defined structure. Analysis of the environment of Tyr237 suggests how its chemical modification inhibits the enzyme.