Ab initio structure determination of kidney stone potassium quadriurate from synchrotron powder diffraction data, a 150 year problem solved

Abstract

a b s t r a c tThe structure of potassium urate, co-crystallized with uric acid K(C 5 H 3 N 4 O 3 )(C 5 H 4 N 4 O 3 ), from human kidney stones, is determined ab initio from synchrotron powder diffraction data, space group P2 1 /c, a ¼ 3.60504(9) Å, b ¼ 19.9293(7) Å, c ¼ 18.4841(6) Å, b ¼ 100.503(2) , Z ¼ 4. Each uric acid molecule is connected to a urate anion through three hydrogen bonds, both molecules are related by a pseudo-inversion center and are randomly distributed in the crystal. Two of the oxygen atoms of the uric acid molecule and two of the urate anions are involved in the potassium coordination forming KO 7 monocapped trigonal prisms sharing their triangular bases, building infinite chains extending along the short a axis. Such a formulation, though controversial, has been claimed to exist since 1862 and named potassium quadriurate. The crystal structure is optimized by energy minimization (DFT) in the solid state, using a hybrid PBE0 functional. The capacity of the urate anion to connect by strong hydrogen bonds to a uric acid molecule has implications concerning the uric acid transport in biological media.

Whitlockite structures in kidney stones indicate infectious origin: a scanning electron microscopy and Synchrotron Radiation investigation

“…With this setup and for each sample, two high angular resolution diagrams recorded in about one hour were summed since sample degradation under the X-ray beam was not significant (Figure 2). Details regarding the experimental set up can be found in reference [69]. To allow for their subsequent superimposition in the same figures, all the collected X-ray diffractograms were first preprocessed using the freely available Graphical User Interface WIN-PLOTR software [70].…”

Scanning electron microscopy—a powerful imaging technique for the clinician

“…A precise identification of the organic [162] and inorganic parts [163] as well as of the trace elements [148,149] has thus to be performed. To attain this goal, in lab characterization techniques [163][164][165] as well as ones related to large scale instruments, such synchrotron radiation [166][167][168][169][170][171][172] or neutron [72,78,103,166,173,174] facilities are needed.…”

Crystal size in μcrystalline pathologies and its clinical implication

“…Moreover calcium phosphate stones containing more than 30% whitlockite are associated with UTI in 81% of cases. Recently, we have performed a set of X-ray scattering experiments using synchrotron radiation as a probe on the CRISTAL beamline of the Soleil synchrotron [103]. Thanks to recent advances [104,105] it was possible to perform a complete Rietveld analysis to obtain crystal sizes of whitlockite in different kidney stones [106].…”