Order and Disorder in Calcium Oxalate Monohydrate: Insights from First-Principles Calculations

Abstract

Calcium oxalate minerals are broadly present in nature. They form through biogenic, geogenic, and pathogenic processes that lead to different pseudopolymorphs. Being the most common solid phase in human nephrolithiasis, calcium oxalate monohydrate (COM) in particular has been the focus of much investigation. It exists in several crystalline forms, two of which appear to be of biological and medical relevance: the low-and hightemperature forms (COM-LT and COM-HT, respectively). While there is broad consensus on the ordered structure of COM-LT, which possesses the P2 1 /n space group symmetry, for COM-HT controversy remains. Experimental results suggest that there is a certain degree of structural disorder in the high-temperature form. However, the exact character of disorder in COM-HT is yet an open question. Here, we examine the effect of the disorder of water molecules on the structure of COM using first-principles calculations based on dispersion-augmented density functional theory. Such calculations allow for controlled examination of specific disorder features and their effect on crystal structure and stability. On the basis of our first-principles analysis, we suggest that in COM-HT each water dimer site is randomly occupied by any of four water dimer arrangements present in COM-LT, leading to statistical 2/m point symmetry at each site and a statistical I2/m space group symmetry.

A novel multinuclear solid state NMR approach for the characterization of kidney stones

“…From one synthetic sample to the other, δiso( 1 H) may slightly vary under DUMBO conditions (~ 0.3 ppm). Such a variation is attributed to some disorder of the water molecules which can be present in the COM crystallographic structure (Shepelenko, 2019). (c).…”

“…νrot > 30 kHz. This point is of prime importance as calcium oxalate structures may undergo subtle structural modifications upon heating (Deganello, 1981;Shepelenko, 2019) -see also https://doi.org/10.5194/mr-2021-38…”

Opportunities given by density functional theory in pathological calcifications

“…This resulted in the understanding that more attention should be paid to the stone morphology, rather than the spectra in these specific cases. Further on this less ordered form of COM, which had already been proposed in some experimental studies, DFT studies were needed to fully unravel the involvement of the structural water molecules in the structure and the related symmetry of the crystal [49].…”

A novel multinuclear solid-state NMR approach for the characterization of kidney stones

“…Nevertheless, the following four main experimental approaches have been successfully developed during the last few years: (i) using large volume rotors (7 mm; ∼ 400 mg of sample) at high magnetic field (20 T), under moderate MAS (∼ 5 kHz) and implementing DFS (double frequency sweep) excitation scheme (Sect. 6); (ii) using much smaller rotors (3.2 mm; ∼ 20 mg of sample at ultra-high magnetic field (35.2 T) and under moderate/fast MAS (∼ 18 kHz); (iii) using dynamic nuclear polarization (DNP) to strongly enhance the 43 Ca polarization, usually in the indirect mode (from 1 H to 43 Ca); (iv) using labeling in 43 Ca (starting from an enriched calcite precursor; Laurencin et al, 2021;Smith, 2020;Laurencin and Smith, 2013). Here, we follow the approach in (i), which is by far the easiest to implement in most NMR facilities worldwide (as long as a low γ probe is available).…”

“…The study of KSs is presently at the heart of a concerted multidisciplinary axis of research involving physicians, physical chemists and spectroscopists (Bazin et al, 2016). Nevertheless, the nucleation and growth of KSs remains largely unknown, and the associated mechanism is based mainly on assumption and incomplete evidence; hence, more thorough and wide-ranging structural investigations are still required (Sherer et al, 2018;. The growth of KSs is clearly a multifactorial problem, with their chemical composition and morphology presenting considerable variability due to the extreme complexity of the in vivo reaction media in which they are formed.…”