Crystal structure determination of karibibite, an Fe³⁺arsenite, using electron diffraction tomography

Abstract

The crystal structure of karibibite, Fe33+(As3+O2)4(As23+O5)(OH), from the Urucum mine (Minas Gerais, Brazil), was solved and refined from electron diffraction tomography data [R1 = 18.8% for F > 4σ(F)] and further confirmed by synchrotron X-ray diffraction and density functional theory (DFT) calculations. The mineral is orthorhombic, space group Pnma and unit-cell parameters (synchrotron X-ray diffraction) are a = 7.2558(3), b = 27.992(1), c = 6.5243 (3) Å, V = 1325.10(8) Å3, Z = 4. The crystal structure of karibibbite consists of bands of Fe3+O6 octahedra running along a framed by two chains of AsO3 trigonal pyramids at each side, and along c by As2O5 dimers above and below. Each band is composed of ribbons of three edge-sharing Fe3+O6 octahedra, apex-connected with other ribbons in order to form a kinked band running along a. The atoms As(2) and As(3), each showing trigonal pyramidal coordination by O, share the O(4) atom to form a dimer. In turn, dimers are connected by the O(3) atoms, defining a zig-zag chain of overall (As3+O2)n-n stoichiometry. Each ribbon of (Fe3+O6) octahedra is flanked on both edges by the (As3+O2)n-n chains. The simultaneous presence of arsenite chains and dimers is previously unknown in compounds with As3+. The lone-electron pairs (4s2) of the As(2) and As(3) atoms project into the interlayer located at y = 0 and y = ½, yielding probable weak interactions with the O atoms of the facing (AsO2) chain.The DFT calculations show that the Fe atoms have maximum spin polarization, consistent with the Fe3+ state.

3D Electron Diffraction: The Nanocrystallography Revolution

“…Sketch showing some representative structures solved by 3D ED method for different classes of materials. Starting from the upper left and going anticlockwise: the mineral karibibite, 133 a tunnel (Na,Mn)-oxide for electrolytic applications, 124 the aperiodic structure of SrBi 7 NbO 24 , 122 the extra-large-pore silicoaluminophosphate ITQ-51, 25 the cobat tetraphosphonate MOF Co-CAU-36, 66 the pharma compound carbamazepine-III, 29 the amyloid core of the Sup35 prion protein, 47 and a new monoclinic polymorph of lysozyme. 45 …”

“…For such samples, 3D ED looks like the only technique able to deliver comprehensive structural information. This technique has already allowed the structure determination of several minerals that have been recognized for decades but whose structures were still lacking because no crystal suitable for single-crystal X-ray diffraction actually exists. ,,− Charoite and denisovite embody two emblematic cases which highlight the strengths of the 3D ED method. These extremely complex minerals appear only as submicrometric fibers, typically made of different polytypic sequences stacked one next to the other in areas of few unit cell repetitions.…”

“…82 Moreover, software developed for X-ray crystallography can be also adapted for the analysis of ED data, like DIALS, 99 MOSFLM, 100 and XDS. 41 3D ED intensity data can be subsequently used as kinematical "X-ray-like" input for ab initio structure solution via direct methods, charge flipping, simulated annealing, or 133 a tunnel (Na,Mn)-oxide for electrolytic applications, 124 the aperiodic structure of SrBi 7 NbO 24 , 122 the extra-large-pore silicoaluminophosphate ITQ-51, 25 the cobat tetraphosphonate MOF Co-CAU-36, 66 the pharma compound carbamazepine-III, 29 the amyloid core of the Sup35 prion protein, 47 and a new monoclinic polymorph of lysozyme. molecular replacement in almost all possible kinds of crystalline compounds, both organic and inorganic (Figure 4).…”

Bianchiniite, Ba2(Ti4+V3+)(As2O5)2OF, a new diarsenite mineral from the Monte Arsiccio mine, Apuan Alps, Tuscany, Italy

“…Table 1 lists the minerals characterised by this structural feature. In schneiderhöhnite, Fe 2+ Fe 3+ 3 As 5 O 13 , (As 2 O 5 ) dimers occur along with isolated (AsO 3 ) groups (Hawthorne, 1985; Cooper and Hawthorne, 2016), whereas karibibite displays (As 2 O 5 ) dimers and (AsO 2 ) chains (Colombo et al , 2017).…”

Daliranite, PbHgAs2S5: determination of the incommensurately modulated structure and revision of the chemical formula

“…3D ED methods have been successfully applied in solving new mineral crystal structures. Charoite-90 (Rozhdestvenskaya et al, 2010), charoite-96 (Rozhdestvenskaya et al, 2011), sarrabusite (Gemmi et al, 2012), widenmannite (Plá šil et al, 2014), karibibite (Colombo et al, 2017), denisovite (Rozhdestvenskaya et al, 2017) and a still unnamed mineral with presumed composition (Capitani et al, 2014) are some examples. In experimental petrology 3D ED has been crucial in the identification and structure determination of three new high-pressure phases in the MgO-Al 2 O 3 -SiO 2 -H 2 O system: HAPY (Gemmi et al, 2011), HYSO and 11.5 Å -phase (Gemmi et al, 2016).…”