Uric Acid Dihydrate Revisited

(E,E)-1,1'-[1,2-Bis(4-chlorophenyl)ethane-1,2-diyl]bis(phenyldiazene) revisited: threefold configurational disorder of (S,S), (R,R) and (S,R) isomers, a detailed critique

Crystal structures described as concomitant triclinic (I) and monoclinic (II) polymorphs of meso-(E,E)-1,1'-[1,2-bis(4-chlorophenyl)ethane-1,2-diyl]bis(phenyldiazene) [Mohamed et al. (2016). Acta Cryst. C72, 57-62] have been re-investigated. The published model for II was distorted due to forcing the symmetry of space group C2/c on an incomplete structure model. It is shown here to be a likely three-component superposition of S,S and R,R enantiomers with a lesser amount of the meso form. A detailed analysis of how the improbable distortion in the published model aroused suspicion and the subsequent construction of undistorted chemically and crystallographically plausible alternatives having the symmetry of Cc and C2/c is presented. For the sake of completeness, an improved model for the triclinic P-1 structure of the meso isomer I, revised to include a minor disorder component, is also given.

A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model

This paper compares variations on a structure model derived from an X-ray diffraction data set from a solid solution of chalcogenide derivatives of cis-1,2-bis-(di-phenyl-phosphan-yl)ethyl-ene, namely, 1,2-(ethene-1,2-di-yl)bis-(di-phenyl-phoshpine sulfide/selenide), C₂₆H₂₂P₂S_1.13Se_0.87. A sequence of processes are presented to ascertain the composition of the crystal, along with strategies for which aspects of the model to inspect to ensure a chemically and crystallographically realistic structure. Criteria include mis-matches between F _obs ² and F _calc ², plots of |F _obs| vs |F _calc|, residual electron density, checkCIF alerts, pitfalls of the OMIT command used to suppress ill-fitting data, comparative size of displacement ellipsoids, and critical inspection of inter-atomic distances. Since the structure is quite small, solves easily, and presents a number of readily expressible refinement concepts, we feel that it would make a straightforward and concise instructional piece for students learning how to determine if their model provides the best fit for the data and show students how to critically assess their structures.

Crystal structure of the insecticide ethiprole (C13H9Cl2F3N4OS): a case study of whole-mol-ecule configurational disorder

The crystal structure of ethiprole {systematic name: 5-amino-1-[2,6-di-chloro-4-(tri-fluoro-meth-yl)phen-yl]-4-ethane-sulfinyl-1H-imidazole-3-carbo-nitrile}, C₁₃H₉Cl₂F₃N₄OS, a phenyl-pyrazole-based insecticide, is presented. The pyrazole ring carries four substituents: an N-bound 2,6-di-chloro-4-tri-fluoro-methyl-phenyl ring and C-bound amine, ethane-sulfinyl, and cyano groups. The sulfur atom of the ethane-sulfinyl group is trigonal-pyramidal and stereogenic. The structure exhibits whole-mol-ecule configurational disorder due to superposition of enanti-omers. The crystal packing is dominated by strong N-H⋯O and N-H⋯N hydrogen bonds, which form R ⁴ ₄(18) and R ² ₂(12) ring motifs. Since the ethiprole mol-ecule is quite small, and structure solution and refinement were straightforward, the structure presents a convenient instructional example for modelling whole-body disorder of a non-rigid mol-ecule. To this end, a step-by-step overview of the model-building and refinement process is also given. The structure could form the basis of a useful classroom, practical, or workshop-style example.

Unusual shape-preserved pathway of a core-shell phase transition triggered by orientational disorder

The ubiquitous presence of crystal defects provides great potential and opportunities to construct the desired structure (hence with the desired properties) and tailor the synthetic process of crystalline materials. However, little is known about their regulation role in phase transition and crystallization pathways. It was generally thought that a phase transition in solution proceeds predominantly via the solvent-mediated phase-transformation pathway due to energetically high-cost solid-state phase transitions (if any). Herein, we report an unprecedented finding that an orientational disorder defect present in the crystal structure triggers an unusual pathway of a core-shell phase transition with apparent shape-preserved evolution. In the pathway, the solid-state dehydration phase transition occurs inside the crystal prior to its competitive transformation approach mediated by solvent, forming an unconventional core-shell structure. Through a series of combined experimental and computational techniques, we revealed that the presence of crystal defects, introduced by urate tautomerism over the course of crystallization, elevates the metastability of uric acid dihydrate (UAD) crystals and triggers UAD dehydration to the uric acid anhydrate (UAA) phase in the crystal core which precedes with surface dissolution of the shell UAD crystal and recrystallization of the core phase. This unique phase transition could also be related to defect density, which appears to be influenced by the thickness of UAD crystals and crystallization driving force. The discovery of an unusual pathway of the core-shell phase transition suggests that the solid-state phase transition is not necessarily slower than the solvent-mediated phase transformation in solution and provides an alternative approach to constructing the core-shell structure. Moreover, the fundamental role of orientational disorder defects on the phase transition identified in this study demonstrates the feasibility to tailor phase transition and crystallization pathways by strategically importing crystal defects, which has broad applications in crystal engineering.

What roles do alkali metal ions play in the pathological crystallization of uric acid?

Na+ and K+ regulate the crystal growth of uric acid dihydrate by kink blocking and rough growth mechanisms.

Synthesis and crystal structures of 3,6-di-hydroxy-picolinic acid and its labile inter-mediate dipotassium 3-hy-droxy-6-(sulfonato-oxy)pyridine-2-carboxyl-ate monohydrate

A simplified two-step synthesis of 3,6-di-hydroxy-picolinic acid (3-hy-droxy-6-oxo-1,6-di-hydro-pyridine-2-carb-oxy-lic acid), C6H5NO4 (II), an inter-mediate in the metabolism of picolinic acid, is described. The crystal structure of II, along with that of a labile inter-mediate, dipotassium 3-hy-droxy-6-(sulfonato-oxy)pyridine-2-carboxyl-ate monohydrate, 2K+·C6H3NO7S2-·H2O (I), is also described. Compound I comprises a pyridine ring with carboxyl-ate, hydroxyl (connected by an intra-molecular O-H⋯O hydrogen bond), and sulfate groups at the 2-, 3-, and 6-positions, respectively, along with two potassium cations for charge balance and one water mol-ecule of crystallization. These components are connected into a three-dimensional network by O-H⋯O hydrogen bonds arising from the water mol-ecule, C-H⋯O inter-actions and π-π stacking of pyridine rings. In II, the ring nitro-gen atom is protonated, with charge balance provided by the carboxyl-ate group (i.e., a zwitterion). The intra-molecular O-H⋯O hydrogen bond observed in I is preserved in II. Crystals of II have unusual space-group symmetry of type Abm2 in which extended planar networks of O-H⋯O and N-H⋯O hydrogen-bonded mol-ecules form sheets lying parallel to the ac plane, constrained to b = 0.25 (and 0.75). The structure was refined as a 50:50 inversion twin. A minor disorder component was modeled by reflection of the major component across a mirror plane perpendicular to c.

Practical hints and tips for solution of pseudo-merohedric twins: three case studies

Twinning by pseudo-merohedry is a common phenomenon in small-mol-ecule crystallography. In cases where twin-component volume fractions are markedly different, structure solution is often no more difficult than for non-twinned structures of similar complexity. When twin-component volume fractions are similar, however, structure solution can be much more of a problem. This paper presents hints and tips for such cases by means of three worked examples. The first example presents the most common (and simplest) case of a two-component pseudo-ortho-rhom-bic twin. The second example describes structure solution of a reticular threefold pseudo-hexa-gonal twin that benefits from use of an unconventional space-group setting. The third example covers structure solution of a reticular fourfold pseudo-tetra-gonal twin. All three structures are ultimately shown to be monoclinic crystals that twin as a consequence of unit-cell metrics that mimic those of higher symmetry crystal systems.

Urates of colubroid snakes are different from those of boids and pythonids

Uricotelic species, such as squamate reptiles, birds and insects, effectively eliminate nitrogen as uric acid in a solid form commonly called urates. Observations made over a decade suggested that the voided urates produced by colubroids (modern snake species) exhibit remarkable differences from those of boids and pythons (ancient snake species). Here, we compare the urates generated by eight captive snake species fed the same diet. Although all fresh urates were wet at the time of excretion, those produced by modern snakes dried to a powdery solid, whereas those of ancient species dried to a rock-hard mass that was tightly adherent to surfaces. Powder X-ray diffraction and infrared spectroscopy analyses performed on voided urates produced by five modern and three ancient snakes confirmed their underlying chemical and structural differences. Urates excreted by ancient snakes were amorphous uric acid, whereas urates from modern snakes consisted primarily of ammonium acid urate, with some uric acid dihydrate. These compositional differences indicate that snakes have more than one mechanism to manage nitrogenous waste. Why different species use different nitrogen-handling pathways is not yet known, but the answer might be related to key differences in metabolism, physiology or, in the case of ancient snakes, the potential use of urates in social communication.

Thermal Behavior and Phase Transition of Uric Acid and Its Dihydrate Form, the Common Biominerals Uricite and Tinnunculite

Single crystals and powder samples of uric acid and uric acid dihydrate, known as uricite and tinnunculite biominerals, were extracted from renal stones and studied using single-crystal and powder X-ray diffraction (SC and PXRD) at various temperatures, as well as IR spectroscopy. The results of high-temperature PXRD experiments revealed that the structure of uricite is stable up to 380 °C, and then it loses crystallinity. The crystal structure of tinnunculite is relatively stable up to 40 °C, whereas above this temperature, rapid release of H2O molecules occurs followed by the direct transition to uricite phase without intermediate hydration states. SCXRD studies and IR spectroscopy data confirmed the similarity of uricite and tinnunculite crystal structures. SCXRD at low temperatures allowed us to determine the dynamics of the unit cells induced by temperature variations. The thermal behavior of uricite and tinnunculite is essentially anisotropic; the structures not only expand, but also contract with temperature increase. The maximal expansion occurs along the unit cell parameter of 7 Å (b in uricite and a in tinnunculite) as a result of the shifts of chains of H-bonded uric acid molecules and relaxation of the π-stacking forces, the weakest intermolecular interactions in these structures. The strongest contraction in the structure of uricite occurs perpendicular to the (101) plane, which is due to the orthogonalization of the monoclinic angle. The structure of tinnunculite also contracts along the [010] direction, which is mostly due to the stretching mechanism of the uric acid chains. These phase transitions that occur within the range of physiological temperatures emphasize the particular importance of the structural studies within the urate system, due to their importance in terms of human health. The removal of supersaturation in uric acid in urine at the initial stages of stone formation can occur due to the formation of metastable uric acid dihydrate in accordance with the Ostwald rule, which would serve as a nucleus for the subsequent growth of the stone at further formation stages; afterward, it irreversibly dehydrates into anhydrous uric acid.

The culprit of gout: triggering factors and formation of monosodium urate monohydrate

Triggering factors, proposed mechanism and self-sustaining cycle for the crystallization of MSUM and gout.

Solution-mediated phase transformation of uric acid dihydrate

Various crystalline phases of uric acid are frequently identified components of human kidney stones, including anhydrous uric acid (UA) and uric acid dihydrate (UAD).

7,9-Bis(hy-droxy-meth-yl)-7H-purine-2,6,8(1H,3H,9H)trione

The structure of the title uric acid derivative, C₇H₈N₄O₅, from human kidney stones, is characterized by the C and O atoms of one of the two hy­droxy­methyl groups being disordered nearly equally over three different sites. In the crystal, mol­ecules are connected by a three-dimensional hydrogen-bonding scheme though they look stacked in planes nearly parallel to (04).

Uric acid monohydrate—a new urinary calculus phase

In our laboratory more than 100,000 urinary calculi have been analysed since 1972. Amongst this huge sample, 15 specimens originating from a total of eight patients were observed showing similar characteristics but escaping unambiguous identification with any of the substances that have been described so far in urinary concrements. Therefore, the unknown substance was submitted to a more extended analytical regimen. Structural analysis by x-ray crystallography turned out to be most successful, identifying the unknown material as uric acid monohydrate. Uric acid monohydrate crystallizes in the monocline space group P2(1)/c. Within the crystal, uric acid and water molecules form continuous layers by hydrogen bonds. This is in contrast to uric acid in its water free and its dihydrate forms, which both crystallize by forming 3-dimensional networks To the best of our knowledge , the existence of a monohydrate form of uric acid has not been reported so far. Accordingly, this is the first report on uric acid monohydrate as a urinary stone component. The frequency of only 0.015% in our survey indicates that uric acid monohydrate is rarely the main component in concrements, in contrast to uric acid and uric acid dihydrate with frequencies of 10% and 6%, respectively. The infrared spectrum of uric acid monohydrate is very similar to that of the other crystal forms of uric acid. Because of this similarity and its low frequency, uric acid monohydrate may have been overlooked as a component of urinary concrements. X-ray diffraction allows for better differentiation in routine stone analysis. All samples of uric acid monohydrate were found by solid state NMR spectroscopy to be highly contaminated by amorphous material. This material consisted of long aliphatic chains reminiscent of lipids and fatty acids, respectively. Concrements consisting of other forms of uric acid or urate lacked this amorphous component. Therefore, a role of this aliphatic material has to be taken into consideration when discussing the conditions that may favour the rare formation of concrements from uric acid monohydrate. As for as the metabolic situation of the affected patients is concerned, no common peculiarities became evident by a retrospective survey.

Epitaxial relationships between uric acid crystals and mineral surfaces: a factor in urinary stone formation

Uric acid (C5H4N4O3) is one of the final products of purine metabolism. Its concentration balance is maintained in the kidneys, but compromised kidney function can result in its crystallization either in the renal tract or in the interstitial fluid of joints. In physiological deposits, crystalline uric acid is most frequently found either in a protonated state (anhydrous or dihydrate phases) or as a deprotonated urate ion (sodium or ammonium salts). Often these precipitates are found in association with a number of mineral phases (e.g., calcium oxalates, calcium phosphates, and magnesium phosphates). Their frequent and common coexistence suggests that synergistic relationships between these crystalline phases may exist. A comprehensive list of different heterogeneous uric acid/uric acid and uric acid/mineral interfaces that are epitaxially matched was generated with the lattice-matching program EpiCalc. Two hundred twenty-five coincident epitaxial matches and four commensurate epitaxial matches were identified using this screening procedure.

Dyeing uric acid crystals with methylene blue

The growth of anhydrous uric acid (UA) and uric acid dihydrate (UAD) crystals from supersaturated aqueous solutions containing methylene blue, a cationic organic dye, has been investigated. Low concentrations of dye molecules were found to be included in both types of crystal matrixes during the growth process. Incorporation of dye into UA crystals occurs with high specificity, affecting primarily [001] and [201] growth sectors, while UAD crystals grown from solutions of similar dye concentration show inclusion but little specificity. The orientation of the UA-trapped species was determined from polarization data obtained from visible light microspectrometry. To achieve charge neutrality, a second anionic species must also be included with the methylene blue into UA and UAD crystal matrices. Under high pH conditions, crystallization of 1:1 stoichiometric mixtures of methylene blue and urate yields methylene blue hexahydrate (MBU.6(H2O). The crystal structure of MBU.6(H2O) reveals continuous pi-pi stacks of planes of dye cations and urate anions mediated by water molecules. This structure provides an optimal geometry for methylene blue-urate pairs and additional support for the incorporation of these dimers in uric acid single-crystal matrices. The strikingly different inclusion patterns in UA and UAD demonstrate that subtle changes in the crystal surfaces and/or growth dynamics can greatly affect recognition events.