Hydrogen bonding system in euchroite, Cu₂(AsO₄)(OH)(H₂O)₃: low-temperature crystal-structure refinement and solid-state density functional theory modeling

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• 作者：Sergey V. Krivovichev ; Andrey A. Zolotarev ; Igor V. Pekov
• 关键词：Euchroite ; Hydrous copper arsenate ; Mineral ; Crystal structure ; X ; ray diffraction ; Hydrogen bonding ; Density functional theory ; L’ubietová
• 刊名：Mineralogy and Petrology
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：110
• 期：6
• 页码：877-883
• 全文大小：1,034 KB
• 刊物类别：Earth and Environmental Science
• 刊物主题：Earth sciences
  Mineralogy
  Geochemistry
  
• 出版者：Springer Wien
• ISSN：1438-1168
• 卷排序：110

文摘

Hydrogen bonding in euchroite has been studied by means of low-temperature single-crystal X-ray diffraction (XRD) and solid-state density functional theory (DFT) calculations. The mineral is orthorhombic, P2₁2₁2₁, a = 10.0350(8), b = 10.4794(8), c = 6.1075(5) Å, V = 642.27(9) Å3, and Z = 4. The structure has been refined to R₁ = 0.036 for 2436 unique observed reflections with |F_o| ≥ 4σ_F. DFT calculations were performed with the CRYSTAL14 software package. The basic features of the crystal structure of euchroite are the same as described by previous authors. There are two symmetrically-independent Cu sites octahedrally coordinated by O atoms. The CuO₆ octahedra are strongly distorted containing four short (1.927–2.012 Å) and two long (2.360–2.797 Å) bonds each, in agreement with the expected Jahn-Teller distortion of an octahedrally-coordinated Cu2+ cation. There is one symmetrically-independent As site that is tetrahedrally coordinated by four O atoms to form an arsenate oxyanion, AsO₄3−. The structure is based upon chains of edge-sharing CuO₆ octahedra running parallel to [001]. The chains are linked by AsO₄ tetrahedra into a three-dimensional framework, which is stabilized by hydrogen bonds formed from OH and H₂O groups. The coordinates of H atoms determined by single-crystal X-ray diffraction and those calculated using DFT are very similar. The distance Δ between experimental and theoretical H positions does not exceed 0.250 Å, except for the H72 site, for which Δ = 0.609 Å. The hydrogen bonding scheme in euchroite is rather complex and involves a combination of relatively strong two-center hydrogen bonds as well as few three-center (bifurcated) hydrogen bonds. The largest difference between the XRD and DFT results involves the H72 atom of the H₂O7 molecule and can be assigned to the effect of temperature, which favors a strong linear hydrogen bond at 0 K (calculated) and a bifurcated three-center bond at 100 K (measured). The Cu-H₂O configurations are bent for the H₂O7 and H₂O6 groups and are almost planar for the H₂O8 groups.