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Acta Crystallographica Section B



Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials publishes scientific articles related to the structural science of compounds and materials in the widest sense. Knowledge of the arrangements of atoms, including their



Published: 2018-02-01

 



Microporous crystal structure of labuntsovite-Fe and high-pressure behavior up to 23 GPa

2018-01-06

Labuntsovite-Fe, an Fe-dominant member of the labuntsovite subgroup, was first discovered in the Khibiny alkaline massif on Mt Kukisvumchorr [Khomyakov et al. (2001). Zap. Vseross. Mineral. Oba, 130, 36–45]. However, no data are published about the crystal structure of this mineral. Labuntsovite-Fe from a peralkaline pegmatite located on Mt Nyorkpakhk, in the Khibiny alkaline complex, Kola Peninsula, Russia, has been investigated by means of electron microprobe analyses, single-crystal X-ray structure refinement, and IR and Raman spectroscopies. Monoclinic unit-cell parameters of labuntsovite-Fe are: a = 14.2584 (4), b = 13.7541 (6), c = 7.7770 (2) Å, β = 116.893 (3)°; V = 1360.22 (9) Å3; space group C2/m. The structure was refined to final R1 = 0.0467, wR2 = 0.0715 for 3202 reflections [I > 3σ(I)]. The refined crystal chemical formula is (Z = 2): Na2K2Ba0.7[(Fe0.5Ti0.1Mg0.05)(H2O)1.3]{[Ti2(Ti1.9Nb0.1)(O,OH)4][Si4O12]2}·4H2O. The high-pressure in situ single-crystal X-ray diffraction study of the labuntsovite-Fe has been carried out in a diamond anvil cell. The labuntsovite-type structure is stable up to 23 GPa and phase transitions are not observed. Calculations using the BM3 equation of state resulted in the bulk modulus K = 72 (2) GPa, K′0 = 3.7 (2) and V0 = 1363 (2) Å3. Compressing of the heteropolyhedral zeolite-like framework leads to the deformation of main structural units. Octahedral rods show the gradual increase of distortion and the wave-like character of rods becomes more distinct. Rod deformations result in the distortion of the silicon–oxygen ring which is not equal in different directions. Structural channels are characterized by a different ellipticity–pressure relationship: the cross-section of the largest channel I and channel II demonstrates the stability of the geometrical characteristics which practically do not depend on pressure: ∊channel I ≃ 0.85 (4) (cross-section is rather regular) and ∊channel II ≃ 0.52 (2) within the whole pressure range. However, channel III is characterized by the increasing of ellipticity with pressure (∊ = 0.40 → 0.10).



X-ray, dielectric, piezoelectric and optical analyses of a new nonlinear optical 8-hydroxyquinolinium hydrogen squarate crystal

2018-01-09

The 1:1 complex of 8-hydroxyquinoline with squaric acid has been characterized using single-crystal X-ray diffraction, UV–vis spectroscopy, density functional theory (DFT) calculations, and photoluminescence, dielectric, piezoelectric and second-harmonic generation (SHG) studies. The title compound (8-hydroxyquinolinium hydrogen squarate; HQS) contains one protonated 8-hydroxyquinoline cation (C9H8NO+) and one hydrogen squarate mono-anion (C4HO4−). All the intermolecular hydrogen-bonding interactions present in the HQS crystal structure are analyzed by three-dimensional molecular Hirshfeld surface analysis and their relative contributions are determined from two-dimensional fingerprint plots. The structure of C9H8NO+·C4HO4− molecular complex has been optimized at the DFT/B3LYP/6-31G(d,p) level. The UV–vis spectroscopic data calculated by time-dependent density functional theory are compared with the experimental data. The LUMO+1, LUMO, HOMO and HOMO−1 energy values, their shapes and energy gaps are calculated using the B3LYP/6-31G(d,p) level of theory. The HQS material exhibits high SHG output (2.6 times of that of potassium dihydrogen phosphate), high photoluminescence emission centred at 474 nm and a piezoelectric charge coefficient of 3 pC N−1. Henceforth, HQS can serve as an alternative potential candidate for multifunctional nonlinear optically active and piezoelectric crystals.



The crystal structure of cesbronite, Cu3TeO4(OH)4: a novel sheet tellurate topology

2018-01-09

The crystal structure of cesbronite has been determined using single-crystal X-ray diffraction and supported by electron-microprobe analysis, powder diffraction and Raman spectroscopy. Cesbronite is orthorhombic, space group Cmcm, with a = 2.93172 (16), b = 11.8414 (6), c = 8.6047 (4) Å and V = 298.72 (3) Å3. The chemical formula of cesbronite has been revised to CuII3TeVIO4(OH)4 from CuII5(TeIVO3)2(OH)6·2H2O. This change has been accepted by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association, Proposal 17-C. The previously reported oxidation state of tellurium has been shown to be incorrect; the crystal structure, bond valence studies and charge balance clearly show tellurium to be hexavalent. The crystal structure of cesbronite is formed from corrugated sheets of edge-sharing CuO6 and (Cu0.5Te0.5)O6 octahedra. The structure determined here is an average structure that has underlying ordering of Cu and Te at one of the two metal sites, designated as M, which has an occupancy Cu0.5Te0.5. This averaging probably arises from an absence of correlation between adjacent polyhedral sheets, as there are two different hydrogen-bonding configurations linking sheets that are related by a ½a offset. Randomised stacking of these two configurations results in the superposition of Cu and Te and leads to the Cu0.5Te0.5 occupancy of the M site in the average structure. Bond-valence analysis is used to choose the most probable Cu/Te ordering scheme and also to identify protonation sites (OH). The chosen ordering scheme and its associated OH sites are shown to be consistent with the revised chemical formula.



Supramolecular heterosynthon assemblies of ortho-phenylenediamine with substituted aromatic carboxylic acids

2018-01-09

Co-crystallization experiments conducted between ortho-phenylenediamine (OPDA) and five substituted aromatic acids (phthalic acid, salicylic acid, 4-hydroxybenzoic acid, 4-nitrobenzoic acid and 3,5-dinitrobenzoic acid) reveal the formation of supramolecular networks constructed from acid–base heterosynthons of ortho-phenylenediammonium cations with respective aromatic anions. All of these coformers are generally regarded as safe (GRAS) molecules. The five reported crystal structures are sustained predominantly by intermolecular N+−H...O−, N—H...O− and N—H...O hydrogen-bonding interactions; in addition intramolecular O—H...O and intermolecular O—H...O, O—H...O− and C—H...O interactions contribute to the formation of various networks. Five 1:1 salts [NH2C6H4NH3]+·[COOHC6H4COO]− (1); [NH2C6H4NH3]+·[OHC6H4COO]− (2); [{NH2C6H4NH2}2·{OHC6H4COOH}2·{NH2C6H4NH3}+2·{OHC6H4COO}−2] (OPDPHB) (3); [NH2C6H4NH3]+·[NO2C6H4COO]− (4) and [NH2C6H4NH3]+·[(NO2)2C6H4COO]− (5) were isolated as single crystals by the slow evaporation method and were characterized using spectroscopic and X-ray crystallographic techniques. X-ray diffraction studies confirmed the formation of salts. The pKa difference between the amine and respective acid favours the transfer of a proton from the acid to the amine, which leads to the formation of the anion and the cation. The interactions between these ions resulted in a stable heterosynthon in each case. The asymmetric units of salts (1), (2), (4) and (5) contain one anion and one cation each, but salt (3) consists of two anions, two cations and two neutral species in its asymmetric unit. A polymorph of salt (3) was also isolated from the crystallization of the ground material from liquid-assisted grinding [{NH2C6H4NH2}·{NH2C6H4NH3}+·{OHC6H4COO}−] (OPDPHB 3P). The polymorph crystallized in the monoclinic non-centrosymmetric space group P21. The liquid-assisted grinding experiments using a 1:1 ratio also revealed the formation of the expected salts, except salt (3), where this product matches with polymorph (OPDPHB 3P).



Using structural mimics for accessing and exploring structural landscapes of poorly soluble molecular solids

2018-01-18

The importance of using structural mimics for mapping out the structural landscape of a poorly soluble active pharmaceutical ingredient was investigated using erlotinib as an example. A mimic was synthesized by preserving the main molecular functionalities responsible for creating the most probable structural arrangements in the solid state. Calculated molecular electrostatic potentials on both erlotinib and the mimic showed very comparable values indicating that the latter would be able to form hydrogen bonds of similar probability and strength as those of erlotinib. In order to establish the binding preference in co-crystallization experiments, the mimic molecule was co-crystallized with US Food and Drug Administration approved dicarboxylic acids. The crystal structures of the mimic and of four co-crystals thereof were obtained. The mimic forms hydrogen bonds in a way that closely resembles those found in the crystal structure of erlotinib. The four co-crystals display self-consistent hydrogen-bond interactions. Thermal and solubility data for the co-crystals demonstrate that by making systematic and controllable changes to the solid forms of the mimic, it is also possible to alter the behaviour and properties of the new solid forms. The use of a suitable structural mimic can allow for a systematic structural examination of a compound that is otherwise not amenable to such investigations by facilitating the elucidation and mapping out of a closely related structural landscape.



Bond-length distributions for ions bonded to oxygen: results for the lanthanides and actinides and discussion of the f-block contraction

2018-01-12

Bond-length distributions have been examined for 84 configurations of the lanthanide ions and 22 configurations of the actinide ions bonded to oxygen, for 1317 coordination polyhedra and 10 700 bond distances for the lanthanide ions, and 671 coordination polyhedra and 4754 bond distances for the actinide ions. A linear correlation between mean bond length and coordination number is observed for the trivalent lanthanides ions bonded to O2−. The lanthanide contraction for the trivalent lanthanide ions bonded to O2− is shown to vary as a function of coordination number, and to diminish in scale with an increasing coordination number. The decrease in mean bond length from La3+ to Lu3+ is 0.25 Å for coordination number (CN) 6 (9.8%), 0.22 Å for CN 7 (8.7%), 0.21 Å for CN 8 (8.0%), 0.21 Å for CN 9 (8.2%) and 0.18 Å for CN 10 (6.9%). The crystal chemistry of Np5+ and Np6+ is shown to be very similar to that of U6+ when bonded to O2−, but differs for Np7+.



Bond-length distributions for ions bonded to oxygen: metalloids and post-transition metals

2018-01-12

Bond-length distributions have been examined for 33 configurations of the metalloid ions and 56 configurations of the post-transition metal ions bonded to oxygen, for 5279 coordination polyhedra and 21 761 bond distances for the metalloid ions, and 1821 coordination polyhedra and 10 723 bond distances for the post-transition metal ions. For the metalloid and post-transition elements with lone-pair electrons, the more common oxidation state between n versus n+2 is n for Sn, Te, Tl, Pb and Bi and n+2 for As and Sb. There is no correlation between bond-valence sum and coordination number for cations with stereoactive lone-pair electrons when including secondary bonds, and both intermediate states of lone-pair stereoactivity and inert lone pairs may occur for any coordination number > [4]. Variations in mean bond length are ∼0.06–0.09 Å for strongly bonded oxyanions of metalloid and post-transition metal ions, and ∼0.1–0.3 Å for ions showing lone-pair stereoactivity. Bond-length distortion is confirmed to be a leading cause of variation in mean bond lengths for ions with stereoactive lone-pair electrons. For strongly bonded cations (i.e. oxyanions), the causes of mean bond-length variation are unclear; the most plausible cause of mean bond-length variation for these ions is the effect of structure type, i.e. stress resulting from the inability of a structure to adopt its characteristic a priori bond lengths.



Bond-length distributions for ions bonded to oxygen: results for the non-metals and discussion of lone-pair stereoactivity and the polymerization of PO4

2018-01-13

Bond-length distributions are examined for three configurations of the H+ ion, 16 configurations of the group 14–16 non-metal ions and seven configurations of the group 17 ions bonded to oxygen, for 223 coordination polyhedra and 452 bond distances for the H+ ion, 5957 coordination polyhedra and 22 784 bond distances for the group 14–16 non-metal ions, and 248 coordination polyhedra and 1394 bond distances for the group 17 non-metal ions. H...O and O—H + H...O distances correlate with O...O distance (R2 = 0.94 and 0.96): H...O = 1.273 × O...O – 1.717 Å; O—H + H...O = 1.068 × O...O – 0.170 Å. These equations may be used to locate the hydrogen atom more accurately in a structure refined by X-ray diffraction. For non-metal elements that occur with lone-pair electrons, the most observed state between the n versus n+2 oxidation state is that of highest oxidation state for period 3 cations, and lowest oxidation state for period 4 and 5 cations when bonded to O2−. Observed O—X—O bond angles indicate that the period 3 non-metal ions P3+, S4+, Cl3+ and Cl5+ are lone-pair seteroactive when bonded to O2−, even though they do not form secondary bonds. There is no strong correlation between the degree of lone-pair stereoactivity and coordination number when including secondary bonds. There is no correlation between lone-pair stereoactivity and bond-valence sum at the central cation. In synthetic compounds, PO4 polymerizes via one or two bridging oxygen atoms, but not by three. Partitioning our PO4 dataset shows that multi-modality in the distribution of bond lengths is caused by the different bond-valence constraints that arise for Obr = 0, 1 and 2. For strongly bonded cations, i.e. oxyanions, the most probable cause of mean bond length variation is the effect of structure type, i.e. stress induced by the inability of a structure to follow its a priori bond lengths. For ions with stereoactive lone-pair electrons, the most probable cause of variation is bond-length distortion.



A novel representative in the rare family of trivanadates, KMn2V3O10: synthesis, crystal structure and magnetic properties

2018-01-17

Potassium dimanganese trivanadate, KMn2V3O10, was synthesized hydrothermally and its crystal structure was determined from single-crystal X-ray diffraction data. The novel phase crystallizes with triclinic symmetry in space group P\bar 1 with unit-cell parameters of a = 6.912 (5), b = 6.993 (5), c = 9.656 (5) Å, α = 101.858 (5), β = 102.627 (5), γ = 100.669 (5)°, Z = 2 and V = 432.6 (5) Å3. Its structure is built from tetramers of MnO6 octahedra sharing edges and trimers of VO4 tetrahedra sharing vertices. These main structural fragments are linked in a three-dimensional framework with channels occupied by potassium ions. The transformation of this structure to that of interconnected NaCa3Mn(V3O10)(V2O7) is discussed. The title compound orders antiferromagnetically at TN = 8.2 K due to the magnetic exchange interactions between tetramers of Mn octahedra through VO4 tetrahedra. First-principles calculations show the magnetic couplings via Mn—O—Mn and Mn—O—V—O—Mn pathways.



Crystal structure refinements of tetragonal (OH,F)-rich spessartine and henritermierite garnets

2018-01-30

Cubic garnet (space group Ia\overline 3 d) has the general formula X3Y2Z3O12, where X, Y and Z are cation sites. In the tetragonal garnet (space group I41/acd), the corresponding cation sites are X1 and X2, Y, and Z1 and Z2. In both space groups only the Y site is the same. The crystal chemistry of a tetragonal (OH,F)-rich spessartine sample from Tongbei, near Yunxiao, Fujian Province, China, with composition X(Mn2.82Fe^{2+}_{0.14}Ca0.04)Σ3Y{Al1.95Fe^{3+}_{0.05}}Σ2Z[(SiO4)2.61(O4H4)0.28(F4)0.11]Σ3 (Sps94Alm5Grs1) was studied with single-crystal X-ray diffraction and space group I41/acd. The deviation of the unit-cell parameters from cubic symmetry is small [a = 11.64463 (1), c = 11.65481 (2) Å, c/a = 1.0009]. Point analyses and back-scattered electron images, obtained by electron-probe microanalysis, indicate a homogeneous composition. The Z2 site is fully occupied, but the Z1 site contains vacancies. The occupied Z1 and Z2 sites with Si atoms are surrounded by four O atoms, as in anhydrous cubic garnets. Pairs of split sites are O1 with F11 and O2 with O22. When the Z1 site is vacant, a larger [(O2H2)F2] tetrahedron is formed by two OH and two F anions in the O22 and F11 sites, respectively. This [(O2H2)F2] tetrahedron is similar to the O4H4 tetrahedron in hydrogarnets. These results indicate ^{X}{{\rm Mn}^ {2+}_{3}}\,^{Y}{\rm Al}_{2}^{Z}[({\rm SiO}_{4})_{2}({\rm O}_{2}{\rm H}_{2})_{0.5}({\rm F}_{2})_{0.5}]_{\Sigma3} as a possible end member, which is yet unknown. The H atom that is bonded to the O22 site is not located because of the small number of OH groups. In contrast, tetragonal henritermierite, ideally ^{X}{\rm Ca}_{3}\,^{Y}{\rm Mn}^{3+}_{2}\,^{Z}[({\rm SiO}_{4})_{2}({\rm O}_{4}{\rm H}_{4})_1]_{\Sigma3}, has a vacant Z2 site that contains the O4H4 tetrahedron. The H atom is bonded to an O3 atom [O3—H3 = 0.73 (2) Å]. Because of O2—Mn3+—O2 Jahn–Teller elongation of the Mn3+O6 octahedron, a weak hydrogen bond is formed to the under-bonded O2 atom. This causes a large deviation from cubic symmetry (c/a = 0.9534).



Determination of hydrogen site and occupancy in hydrous Mg2SiO4 spinel by single-crystal neutron diffraction

2018-01-25

Ringwoodite [(Mg,Fe2+)2SiO4 spinel] has been considered as one of the most important host minerals of water in the Earth's deep mantle. Its extensive hydration was observed in high-pressure synthesis experiments and also by its natural occurrence. Water can dissolve into ringwoodite as structurally bound hydrogen cations by substituting other cations, although the hydrogen site and its occupancy remain unclear. In this study, neutron time-of-flight single-crystal Laue diffraction analysis was carried out for synthetic hydrous ringwoodite. Hydrogen cations were found only in the sites in MgO6 octahedra in the ringwoodite structure, which compensated the reduced occupancies of both magnesium and silicon cations. The refined cation occupancies suggest that the most plausible hydration mechanism is that three hydrogen cations simultaneously occupy an MgO6 octahedron, whereas four such hydrogenated octahedra surround a vacant SiO4 tetrahedron.