The crystal structure of launayite from Taylor Pit, Madoc, Ontario, Canada: crystal chemistry, modulated superstructures, and parent modular structure compared with rouxelite

Abstract. The crystal structure of rouxelite from the Monte Arsiccio mine, Italy, has been investigated using single-crystal X-ray diffraction (SCXRD) to clarify its crystallography and crystal chemistry. The structure is described in space group C-1, with lattice parameters a= 43.1883(12), b= 8.1037(2), c= 38.1470(10) Å, α= 96.001(2), β= 116.615(2), γ= 95.372(2)°, and V = 11721.7(6) Å3. The structure can be considered as being a twofold superstructure (doubled b cell parameter) of the C2/m rouxelite structure previously reported from Buca della Vena mine. The asymmetric unit in the structure of rouxelite contains 53 cation sites and 66 anion sites. The metal sites are composed of 22 Pb positions, 28 Sb positions, one Hg position, and two Cu positions. Among the Pb sites, four are mixed with Tl, Sb, Ag, and As and two are split. Among the Sb sites, three Sb sites are mixed with Pb and As and three are split. The Hg position includes Ag, and two sulfur sites (S65 and S66) are partially occupied. Final refinement, performed as a twin with volume ratios of 0.5489 : 0.4510(14), resulted in an R1 value of 0.0855 for 55765 unique reflections. The crystal under investigation was an intergrowth with a second domain whose cell parameters correspond to those of launayite. The resulting structural formulae obtained from the SCXRD study for the unit cell is either Cu8Ag2.08Hg3.068Tl2Pb83.568As1.448Sb111.836S261.52 (for Z = 1, ch = 2.16) or Cu8Ag2.09Hg3.064Tl2Pb83.556As1.452Sb111.84S261.32O1.52 (for Z = 1, ch = −0.47) (O content could not be reliably determined), making the definition of an ideal formula difficult. Additionally, a substantial volume of new chemical data for rouxelite has been included, covering both the Monte Arsiccio mine and the neighbouring Buca della Vena occurrences, thereby enhancing the previously published data. The crystal chemistry, substitution mechanisms, and modular description of rouxelite as well as the modular relationship to other minerals are also addressed.

A detailed crystal-chemical study of the complex layered silicate molybdophyllite was conducted using single-crystal X-ray diffraction (XRD) methods, supplemented by powder XRD, infrared (IR) and Raman spectroscopic studies, chemical analyses by energy-dispersive spectrometry (EDS) on a scanning electron microscope (SEM), and electron probe microanalysis (EPMA). The results, based on several samples from both Långban and Harstigen, Filipstad, Sweden, show that the crystal structure of molybdophyllite has an order-disorder (OD) character. The latter is especially evident in specimens from Långban which display a complex diffraction pattern characterized by the simultaneous presence of sharp spots, diffuse reflections and continuous streaks. The sharp reflections define the unit cell of the family structure (a = 3.124, c = 41.832 Å, space group R32). Two main polytypes (maximum degree of order structures) are indicated by the OD approach: a trigonal one and a monoclinic one; the latter polytype is the most common in the samples that were studied and has space group C2, with a = 16.232(6), b = 9.373(2), c = 14.060(3) Å, b = 97.36(4)º and V = 2121.5(10) Å3.The crystal structure determination [R1= 0.096], together with the EPMA, IR and Raman data, reveal that molybdophyllite is built up by a regular alternation of complex layers with a composition {Mg9[Si10O28(OH)8][OPb4]2}6+and simple layers with a composition [(CO3)3·H2O]6–, leading to the ideal crystal-chemical formula Pb8Mg9[Si10O28(OH)8|O2|(CO3)3]·H2O (Z = 2).This contribution is mainly devoted to the results obtained for molybdophyllite sensu stricto, but new data for britvinite [i.e. 'molybdophyllite-18 Å'] are also presented and its modular relationship with molybdophyllite is discussed.

The crystal chemistry of three Li-bearing mica-2 M 2 crystals from pegmatites has been studied by chemical analyses and single crystal X-ray diffraction; their belonging to the trilithionite-polylithionite join is highlighted by the following compositional ranges in atoms per formula unit [based on O 12-(x+y) (OH) x F y ]: 3.198 ≤ Si ≤ 3.538, 0.462 ≤ [IV] Al ≤ 0.811, 1.195 ≤ [VI] Al ≤ 1.390, 0.031 ≤ (Fe+Mn) ≤ 0.072, 1.522 ≤ Li ≤ 1.757, 0.872 ≤ K ≤ 0.906, 0.030 ≤ Na ≤ 0.073, 0.000 ≤ (Cs+Rb) ≤ 0.099, 1.541 ≤ F ≤ 1.722. The correlation between F and Li content is confirmed, as observed in Li-rich micas. Crystal structure refinements were carried out in space group C 2/ c ( R values vary between 0.030 and 0.031). The crystal chemistry is mostly influenced by tetrahedral chemical composition. Increasing [IV] Al content, α and ψ M1 parameters increase; Si content involves a lowering of the interlayer separation and tetrahedral thickness. Li content affects octahedral thickness. The stability of 2 M 2 polytype seems to be induced by a relative increase of Δz tetrahedral parameter, which reduces the repulsion between basal tetrahedral oxygen atoms. Unlike Li-bearing muscovite, trioctahedral Li-bearing mica crystals show an octahedral occupancy not related to octahedral charge.

The crystal chemistry of trioctahedral micas-1 M from Mt. Vulture phonolitic-trachitic ignimbrites has been investigated by single crystal X-ray diffraction, microprobe analysis and plasma emission spectroscopy. Chemical analyses have shown that Mt. Vulture trioctahedral micas belong to the phlogopite-annite join, with minor component of kinoshitalite-ferrokinoshitalite solid solution. In addition, samples with remarkably different Mg/Fe ratio can coexist in the same volcano-stratigraphic level, Fe-rich samples having also higher Ti content. The crystal structure of all of the analysed samples is affected, to varying degrees, by structural disorder, due to ± b /3 slips of octahedral sheet along the [0 1 0], [3 1 0] and [3 −1 0] directions. The latter has been reported in the literature for a handful of cases. In the present work, for the first time, the disorder has been successfully interpreted and managed in the structure refinement. It is demonstrated that it leads to desymmetrization of the TOT layer and therefore of the whole structure, with reduction of symmetry from C 2/ m to C 2. For the sample mostly affected by disorder (17 %) the R -factor drops from 9.97% ( C 2/ m ) to 2.74 % ( C 2). The chemical and geometrical features show that Mt. Vulture micas are homo-octahedral, even if some structural details suggest a preferential partitioning of Ti at M2 sites. However the mechanism of Ti incorporation in the structure seems to be different in Mg-rich and Fe-rich samples. For the former the Ti-vacancy substitution mechanism seems to hold: \(2^{VI}Mg^{2}{+} {\longleftrightarrow} ^{VI}Ti^{4{+}} {+} ^{VI}[]\) For the latter, the occurrence of Li, as detected by emission spectroscopy plasma measurements, structural evidence and charge balance considerations suggest the following novel substitution mechanism, \(^{VI}Ti^{4{+}} {+} ^{VI}Li^{{+}} {+} O^{2{-}} {\longleftrightarrow} 2 ^{VI}M^{2{+}} {+} OH^{{-}}\) , to be active in the structure.

Ag-exchanged analcime: crystal structure and crystal chemistry

A lot of great work has been done since the high pressure research carried out on synchrotron radiation facility almost 40 years ago. The history of high pressure single-crystal diffraction research on synchrotron radiation facility has also been more than 20 years. Recently, with the development of synchrotron X-ray optical techniques and high pressure technology, especially the invention and improvement of large opening diamond anvil cell (DAC), high pressure single-crystal X-ray diffraction (HPSXRD) method has become more and more popular in high pressure studies. The HPSXRD can be used to perform structure determination and refinement to obtain the information about lattice parameter, space group, atomic coordinate and site occupation. Compared with powder X-ray diffraction, the HPSXRD can not only obtain the three-dimensional diffraction information of samples, but also have much better signal-to-noise ratio. Furthermore, the HPSXRD data can be used to study the electron density distribution to obtain more information about chemical bonds and electron distribution. In this work, we introduce the HPSXRD method in synchrotron radiation facilities, including the knowledge of single-crystal X-ray diffraction experimental system, DAC for HPSXRD, sample loading, and HPSXRD data processing.

Microprobe analysis, single crystal X-ray diffraction, X-ray photoelectron spectroscopy, atomic force microscopy, and X-ray absorption spectroscopy were applied on Fe-rich osumilite from the volcanic massif of Mt. Arci, Sardinia, Italy. Osumilite belongs to the space group P6/mcc with unit cell parameters a = 10.1550(6), c = 14.306(1) A and chemical formula (K0.729)C (Na0.029)B (Si10.498 Al1.502)T1 (Al2.706 Fe 0.294 2+ )T2 (Mg0.735 Mn0.091 Fe 1.184 2+ )AO30. Structure refinement converged at R = 0.0201. Unit cell parameter a is related to octahedral edge length as well as to Fe2+ content, unlike the c parameter which does not seem to be affected by chemical composition. The determination of the amount of each element on the mineral surface, obtained through X-ray photoelectron spectroscopy high-resolution spectra in the region of the Si2p, Al2p, Mg1s and Fe2p core levels, suggests that Fe presents Fe2+ oxidation state and octahedral coordination. Two peaks at 103.1 and 100.6 eV can be related to Si4+ and Si1+ components, respectively, both in tetrahedral coordination. The binding energy of Al2p, at 74.5 eV, indicates that Al is mostly present in the distorted T2 site, whereas the Mg peak at 1,305.2 eV suggests that this cation is located at the octahedral site. X-ray absorption at the Fe L2,3-edges confirms that iron is present in the mineral structure, prevalently in the divalent state and at the A octahedral site.

A family of inorganic-organic hybrid vanadium selenites with zero-, one-, two-, and three-dimensional structures, (1,10-phen)(2)V(2)SeO(7), (2,2'-bipy)VSeO(4), (4,4'-bipy)V(2)Se(2)O(8), and (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O (where phen = phenanthroline and bipy = bipyridine), were hydrothermally synthesized and characterized by single-crystal X-ray diffraction. Different bidentate organodiamine ligands and reactant concentrations were used in the four reaction systems, which are responsible for the variety of structural dimensions of the compounds. (1,10-phen)(2)V(2)SeO(7) crystallizes in a monoclinic system with space group P2(1)/n and cell parameters a = 8.6509(3) A,( )b = 7.8379(2) A, c = 34.0998(13) A, beta = 91.503(2) degrees, and Z = 4. (2,2'-bipy)VSeO(4) crystallizes in a monoclinic system with space group C2/c and cell parameters a = 17.0895(12) A, b = 14.7707(10) A, c = 11.7657(8) A, beta = 131.354(3) degrees, and Z = 8. (4,4'-bipy)V(2)Se(2)O(8) crystallizes in a triclinic system with space group Ponemacr; and cell parameters a = 7.1810(10) A, b = 10.8937(13) A, c = 11.1811(15) A, alpha = 115.455(3) degrees, beta = 107.582(3) degrees, gamma = 91.957(4) degrees, and Z = 2. (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O crystallizes in a monoclinic system with space group Pc and cell parameters a = 7.9889(9) A, b = 7.8448 A, c = 23.048(3) A, beta = 99.389(4) degrees, and Z = 2. (1,10-phen)(2)V(2)SeO(7) has an isolated structure, (2,2'-bipy)VSeO(4) has a chain structure, (4,4'-bipy)V(2)Se(2)O(8) has a layered structure, and (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O has a framework structure. The chains are constructed from VO(4)N(2) octahedra and SeO(3) pyramids, laced by organic ligands (2,2'-bipy). The layers consist of vanadium selenite chains [(VO)(2)(SeO(3))(2)]( infinity ), linked by 4,4'-bipy molecules. The framework is composed of vanadium selenite sheets [V(4)Se(3)O(16)]( infinity ), pillared by 4,4'-bipy molecules. All of the compounds are thermally stable to 300 degrees C, and the magnetic susceptibilities confirm the existence of tetravalent V atoms in the antiferromagnetic (4,4'-bipy)V(2)Se(2)O(8) complex and mixed tetravalent and pentavalent V atoms in the paramagnetic complex (4,4'-bipy)(2)V(4)Se(3)O(15).H(2)O.

The crystalline structures of three organic salts of triiodoaminobenzoic acid (1–3) and triiodoaminobenzoic acid monohydrate (4) are described, the structural features are established by the X-ray diffraction method. Compound 1: C20H19I6N3O6, М 1158.78; monoclinic syngony, space group Сс; cell parameters: a = 32.0782(10), b = 9.5284(3), c = 9.3745(3) Å;  = 90, β = 90,0(1),  = 90 deg.; V = 2865.35(16) Å3, Z = 4, ρcalc. = 2.684 g/cm3. Compound 2: C16H15I6N3O4, М 1074.71; monoclinic syngony, space group P21/c; cell parameters: a = 8.990(5), b = 28.541(11), c = 9.945(5) Å;  =  = 90, β = 91.23(2) deg.; V = 2551(2) Å3, Z = 4, ρcalc. = 2.798 g/cm3. Compound 3: C17H17I3N2O4, М 694.03; monoclinic syngony, space group I2/a; cell parameters: a = 36.02(2), b = 7.254(5), c = 16.468(9) Å;  =  = 90, β = 105.29(2) deg.; V = 4150(4) Å3, Z = 8, ρcalc. = 2.222 g/cm3. Compound 4: C7H6I3NO3, М 532.83; rhombic syngony, space group Iba2; cell parameters: a = 30.2146(4), b = 13.9830(2), c = 5.80740(10) Å;  = β =  = 90 deg.; V = 2453.57(6) Å3, Z = 8, ρcalc. = 2,885 g/cm3. The crystalline structure of two salts and triiodoaminobenzoic acid monohydrate is distinguished both by domination of hydrogen bonds and multiple halogen bonds. However, the 7-methylquinoline salt is devoid of halogen bonds due to peculiarities of the stack packaging of flat molecules. For two compounds (3 and 4), the features of their thermolysis by thermal analysis (in argon atmosphere) are determined: at the first stage (52 and 73 °C, respectively), the loss of crystallization water occurs; at 700 ° C under the thermolysis conditions of both compounds the decomposition product is glass carbon.

Thiosemicarbazones (TSCs) are very versatile tridentate ligands having the ability to bind transition metal ions by bonding through sulfur and hydrazinic terminal nitrogen atoms. TSC also inhibits the enzyme ribonucliotide diphosphate reductase (RDR) which is involved in the synthesis of DNA precursors in the mammalian cells. One of the important heterocyclic thiosemicarbazones, the title compound (MBCPT) has been synthesized based on the Mannich reaction and it was characterized by X-ray diffraction methods. The crystallographic data of MBCPT are: C19H20Cl2N4S; M.W = 407.35, Monoclinic, space group, P21/n, with cell parameters a = 12.053(8) A, b = 11.431(10) A, c = 14.695(7) A, β = 95.82(4)o; V = 2014(2) A3, Z = 4, Dcal = 1.343 Mg/m3, λ (Cu K α ) = 1.54184 A. The ring piperine adopts chair conformation. The phenyl rings are oriented equatorially at 2 and 6th positions of the piperidine ring. Molecular packing can be viewed as a dimer held together by two N–H⋯S intermolecular hydrogen bonds. Molecules are tightly bound in the unit cell by C–H⋯N, N–H⋯S and N–H⋯N types inter and intra molecular hydrogen bonds. One of the piperidin-4-one thiosemisemicarbazones, MBCPT, has been synthesized and its structural chemistry has been proved by X-ray crystallographic study.

Thiosemicarbazones (TSCs) are very versatile tridentate ligands having the ability to bind transition metal ions by bonding through sulfur and hydrazinic terminal nitrogen atoms. TSC also inhibits ribonucleotide diphosphate reductase (RDR), the enzyme involved in the synthesis of DNA precursors in the mammalian cells. One of the important phenyl thiosemicarbazones, the title compound (p-CBT) has been synthesized and it was characterized by X-ray diffraction methods. The crystallographic data of p-CBT are: C8H8ClN3S; M.W. = 213.68, Triclinic, space group, Pī, with cell parameters a = 7.934(2) A, b = 11.242(3) A, c = 11.615(2) A, α = 74.775(3), β = 75.389(2), γ = 83.448(2); V = 966.0(4) A3, Z = 4, Dcal = 1.469 Mg/m3, λ (Cu K α ) = 1.54184 A. Molecular packing can be viewed as a dimer held together by two N–H…S type intermolecular hydrogen bonds. In addition, C–H…Cl and N–H…N types of inter and intra molecular hydrogen bonds also help the molecules in crystal packing. One of the phenyl thiosemisemicarbazones, p-CBT, has been synthesized and its structural chemistry has been proved by X-ray crystallographic study.

The crystal structures of tobelite and NH 4 + -rich muscovite from the sedimentary rocks of the Armorican sandstones (Brittany, France) have been solved for the first time by single-crystal X-ray diffraction. The structural study was integrated by electron probe microanalyses, and X-ray photoelectron and micro-Fourier transform infrared spectroscopy. The crystals belong to the 2 M 2 polytype with the following unit-cell parameters: a = 9.024(1), b = 5.2055(6), c = 20.825(3) A, and β = 99.995(8)° for tobelite and a = 9.027(1), b = 5.1999(5), c = 20.616(3) A, and β = 100.113(8)° for NH 4 + -rich muscovite. Structure refinements in the space group C 2/ c converged at R 1 = 8.01%, wR 2 = 8.84% and R 1 = 5.59%, wR 2 = 5.63% for tobelite and NH 4 + -rich muscovite, respectively. X-ray photoelectron spectroscopy revealed nitrogen environments associated either with inorganic (B.E. 401.31 eV) or organic (B.E. 398.67 eV) compounds. Infrared spectra showed, in the OH − -stretching region (3700–3575 cm −1 ), two prominent bands, centered at ~3629 and ~3646 cm −1 , and two shoulders at ~3664 and ~3615 cm −1 that were assigned to Al 3+ Al 3+ □-OH − arrangements having OH − groups affected by different local configurations. In addition, a series of overlapping bands from about 3500 to 2700 cm −1 characteristic of the NH 4 + -stretching vibrations, a main band at ~1430 and a shoulder at ~1460 cm −1 that were associated to the NH 4 + -bending vibration (ν 4 ) were also present. The ammonium concentration was semi-quantitatively estimated in both crystals from the absorbance of the OH − -stretching and NH 4 + -bending vibrations in the infrared spectra. An additional estimate was obtained for the NH 4 + -rich muscovite by considering the normalized peak area between K2 p 3 / 2 and N1 s in the X-ray photoelectron spectrum. The obtained values are in agreement with those derived from the interlayer spacing in the simulated X-ray powder diffraction spectra. The results of this integrated approach converged to (K 0.18 Na 0.01 NH 4 + 0.62 ) ∑=0.81 (Al 1.98 Fe 2+ 0.02 ) ∑=2.00 (Si 3.19 Al 0.81 ) ∑=4.00 O 10.00 OH 2.00 for tobelite and to (K 0.46 Na 0.03 Ba 0.01 NH 4 + 0.36 ) ∑=0.86 (Al 1.98 Mg 0.01 Fe 2+ 0.01 V 3+ 0.01 ) ∑=2.01 (Si 3.13 Al 0.87 ) ∑=4.00 O 10.00 F 0.08 OH 1.92 for NH 4 + -rich muscovite.

Autotransporters are virulence-related proteins of Gram-negative bacteria that are secreted via an outer-membrane-based C-terminal extension, the translocator domain. This domain supposedly is sufficient for the transport of the N-terminal passenger domain across the outer membrane. We present here the crystal structure of the in vitro-folded translocator domain of the autotransporter NalP from Neisseria meningitidis, which reveals a 12-stranded beta-barrel with a hydrophilic pore of 10 x 12.5 A that is filled by an N-terminal alpha-helix. The domain has pore activity in vivo and in vitro. Our data are consistent with the model of passenger-domain transport through the hydrophilic channel within the beta-barrel, and inconsistent with a model for transport through a central channel formed by an oligomer of translocator domains. However, the dimensions of the pore imply translocation of the secreted domain in an unfolded form. An alternative model, possibly covering the transport of folded domains, is that passenger-domain transport involves the Omp85 complex, the machinery required for membrane insertion of outer-membrane proteins, on which autotransporters are dependent.

Dipyridylamine has been coupled with phenyl groups to yield new organic ligands. During the course of one reaction a lithium salt of dipyridylamine was isolated as the product. These new compounds were characterized by single crystal X-ray diffraction, which reveals that π–π stacking interactions as well as hydrogen bonding permeate the isolated compounds in the solid state. BrPhDPA, compound 1, crystallizes in the monoclinic P21 space group with cell parameters a = 5.8291(1), b = 8.8504(2), c = 13.2341(3) A and β = 91.928(1)°. 3-ThPh(DPA)2, compound 4, crystallizes in the orthorhombic C2/c space group with cell parameters a = 14.8033(7), b = 11.4124(4), c = 16.11780(7) A and β = 115.911(3)°. Finally the lithium salt, [Li(HDPA)(H2O)2](H2DPA)(Cl)2(H2O), compound 5, crystallizes in the monoclinic Cmcm space group with cell parameters a = 14.043(3), b = 12.370(3) and c = 13.389(3) A. Aromatic derivatives of dipyridylamine have been isolated and crystallographically characterized, showing π–π stacking and C–H···π interactions and an interesting Li+ coordination compound.

The crystal structure and crystal chemistry of two natural pollucite samples, from Buckfield, Oxford County, Maine (sample M3), and from Kanzit Mawaie, Laghman, Nooristan, Afghanistan (sample N5), have been investigated by means of wavelength-dispersive X-ray microanalysis, thermogravimetric analysis, single-crystal X-ray and neutron diffraction, and single-crystal Fourier-transform infrared spectroscopy. The X-ray and neutron diffraction patterns of the two pollucite crystals show a metrically cubic unit cell [with a M3 = 13.6914(6) A and a N5 = 13.6808(6) A by neutron diffraction data; the deviation from isometry is l i ), where l i is the unrestrained unit-cell length] and the reflection conditions are consistent with the space group Ia 3 d . Anisotropic neutron structural refinements gave final agreement indices: R 1 = 0.0543 for 32 refined parameters and 372 unique reflections with F o > 4σ( F o ) for M3 and R 1 = 0.0693 for 31 refined parameters and 331 unique reflections with F o > 4σ( F o ) for N5. The structure refinements show a disordered Si/Al-distribution in the tetrahedral framework. The analysis of the difference-Fourier maps of the nuclear density confirms the presence of extra-framework water molecules with oxygen sharing the Cs site (at 1/8, 1/8, 1/8, Wyckoff-16 b position). However, the minima, ascribable to the proton sites, are very weak in density. Two possible proton positions, leading to a reasonable H 2 O configuration, are given, and the possible hydrogen bonding is described. Sodium is located at 1/4, 1/8, 0 (Wyckoff-24 c position). The main IR absorption bands in the regions typical of H 2 O are assigned, and the presence of hydroxyls in the studied samples is ruled out. Neutron diffraction and FTIR data agree with the presence of very weak hydrogen bonds in the structure. The detailed description of the crystal structure and crystal chemistry of pollucite (e.g., Si/Al-distribution, configuration of the extra-framework content, possible hydrogen bonding scheme) reported in this study is the key to understand the high thermo-elastic stability of pollucite, the immobility of Cs at non-ambient conditions, and the extremely low leaching rate of Cs, which make this open-framework silicate a promising material with potential use for fixation and deposition of Cs radioisotopes.