Ab initio structure determination and structure refinement of mAra
This protocol is extracted from research article:
A nanocrystalline monoclinic CaCO3 precursor of metastable aragonite
Sci Adv, Dec 12, 2018; DOI: 10.1126/sciadv.aau6178

The ab initio structure determination resulted in a model in which five atoms (three C and two O) were missing compared to the expected stoichiometry for aragonite. We refined this model using SHELXL and obtained an overall agreement R value of 0.4908 (table S2). Using restraints (SADI on C–O distances and FLAT for CO3 triangles), we placed the missing C and O atoms into the model and refined it. The all-atoms model refinement resulted in an overall R value of 0.3861, which was lower than that of the missing-atoms model. For both models, the thermal factors were positive and scattered in a reasonable range (table S4).

The missing-atoms model contained Ca in six- to ninefold coordination, whereas the coordination number of all Ca atoms was nine in the all-atoms mAra model (Fig. 4). The Ca–O bond distances for this refined model were shown in table S5. The cif structure data of missing and all atoms and the measured hkl file were reported in data files S3 to S5.

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