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1.  Calcioferrite with composition (Ca3.94Sr0.06)Mg1.01(Fe2.93Al1.07)(PO4)6(OH)4·12H2O 
Calcioferrite, ideally Ca4MgFe3+ 4(PO4)6(OH)4·12H2O (tetra­calcium magnesium tetrairon(III) hexakis-phosphate tetra­hydroxide dodeca­hydrate), is a member of the calcioferrite group of hydrated calcium phosphate minerals with the general formula Ca4 AB 4(PO4)6(OH)4·12H2O, where A = Mg, Fe2+, Mn2+ and B = Al, Fe3+. Calcioferrite and the other three known members of the group, montgomeryite (A = Mg, B = Al), kingsmountite (A = Fe2+, B = Al), and zodacite (A = Mn2+, B = Fe3+), usually occur as very small crystals, making their structure refinements by conventional single-crystal X-ray diffraction challenging. This study presents the first structure determination of calcioferrite with composition (Ca3.94Sr0.06)Mg1.01(Fe2.93Al1.07)(PO4)6(OH)4·12H2O based on single-crystal X-ray diffraction data collected from a natural sample from the Moculta quarry in Angaston, Australia. Calcioferrite is isostructural with montgomeryite, the only member of the group with a reported structure. The calcioferrite structure is characterized by (Fe/Al)O6 octa­hedra (site symmetries 2 and -1) sharing corners (OH) to form chains running parallel to [101]. These chains are linked together by PO4 tetra­hedra (site symmetries 2 and 1), forming [(Fe/Al)3(PO4)3(OH)2] layers stacking along [010], which are connected by (Ca/Sr)2+ cations (site symmetry 2) and Mg2+ cations (site symmetry 2; half-occupation). Hydrogen-bonding inter­actions involving the water mol­ecules (one of which is equally disordered over two positions) and OH function are also present between these layers. The relatively weaker bonds between the layers account for the cleavage of the mineral parallel to (010).
PMCID: PMC3998495  PMID: 24764934
2.  Redetermination of katayamalite, KLi3Ca7Ti2(SiO3)12(OH)2  
The crystal structure of katayamalite, ideally KLi3Ca7Ti2(SiO3)12(OH)2 (potassium trilithium hepta­calcium dititanium dodeca­silicate di­hydroxide), was previously reported in triclinic symmetry (C-1), with isotropic displacement parameters for all atoms and without the H-atom position [Kato & Murakami (1985 ▶). Mineral. J. 12, 206–217]. The present study redetermines the katayamalite structure with monoclinic symmetry (space group C2/c) based on single-crystal X-ray diffraction data from a sample from the type locality, Iwagi Island, Ehime Prefecture, Japan, with anisotropic displacement parameters for all non-H atoms, and with the H atoms located by difference Fourier analysis. The structure of katayamalite contains a set of six-membered silicate rings inter­connected by sheets of Ca atoms on one side and by an ordered mixture of Li, Ti and K atoms on the other side, forming layers which are stacked normal to (001). From the eight different metal sites, three are located on special positions, viz. one K and one Li atom on twofold rotation axes and one Ca atom on an inversion center. The Raman spectrum of kataymalite shows a band at 3678 cm−1, similar to that observed for hydroxyl-amphiboles, indicating no or very weak hydrogen bonding.
PMCID: PMC3772399  PMID: 24046542
3.  Penikisite, BaMg2Al2(PO4)3(OH)3, isostructural with bjarebyite 
The bjarebyite group of minerals, characterized by the general formula BaX 2 Y 2(PO4)3(OH)3, with X = Mg, Fe2+ or Mn2+, and Y = Al or Fe3+, includes five members: bjarebyite BaMn2+ 2Al2(PO4)3(OH)3, johntomaite BaFe2+ 2Fe3+ 2(PO4)3(OH)3, kulanite BaFe2+ 2Al2(PO4)3(OH)3, penikisite BaMg2Al2(PO4)3(OH)3, and perloffite BaMn2+ 2Fe3+ 2(PO4)3(OH)3. Thus far, the crystal structures of all minerals in the group, but penikisite, have been determined. The present study reports the first structure determination of penikisite (barium dimagnesium dialuminium triphosphate trihydroxide) using single-crystal X-ray diffraction data of a crystal from the type locality, Mayo Mining District, Yukon Territory, Canada. Penikisite is isotypic with other members of the bjarebyite group with space group P21/m, rather than triclinic (P1 or P-1), as previously suggested. Its structure consists of edge-shared [AlO3(OH)3] octa­hedral dimers linking via corners to form chains along [010]. These chains are decorated with PO4 tetra­hedra (one of which has site symmetry m) and connected along [100] via edge-shared [MgO5(OH)] octa­hedral dimers and eleven-coordinated Ba2+ ions (site symmetry m), forming a complex three-dimensional network. O—H⋯O hydrogen bonding provides additional linkage between chains. Microprobe analysis of the crystal used for data collection indicated that Mn substitutes for Mg at the 1.5% (apfu) level.
PMCID: PMC3569169  PMID: 23424395
4.  Redetermination of clinobaryl­ite, BaBe2Si2O7  
Clinobaryl­ite, ideally BaBe2Si2O7 (chemical name barium diberyllium disilicate), is a sorosilicate mineral and dimorphic with baryl­ite. It belongs to a group of compounds characterized by the general formula BaM 2+ 2Si2O7, with M 2+ = Be, Mg, Fe, Mn, Zn, Co, or Cu, among which the Be-, Fe-, and Cu-members have been found in nature. The crystal structure of clinobaryl­ite has been re-examined in this study based on single-crystal X-ray diffraction data collected from a natural sample from the type locality (Khibiny Massif, Kola Peninsula, Russia). The structure of clinobaryl­ite can be considered as a framework of BeO4 and SiO4 tetra­hedra, with one of the O atoms coordinated to two Be and one Si, one coordinated to two Si, and two O atoms coordinated to one Si and one Be atom. The BeO4 tetra­hedra share corners, forming chains parallel to the c axis, which are inter­linked by the Si2O7 units oriented parallel to the a axis. The Ba2+ cations (site symmetry m..) are in the framework channels and are coordinated by eleven O atoms in form of an irregular polyhedron. The Si—Obr (bridging O atom, at site symmetry m..) bond length, the Si—Onbr (non-bridging O atoms) bond lengths, and the Si—O—Si angle within the Si2O7 unit are in marked contrast to the corresponding values determined in the previous study [Krivovichev et al. (2004 ▶). N. Jb. Miner. Mh. pp. 373–384].
PMCID: PMC3470124  PMID: 23125568
5.  Redetermination of junitoite, CaZn2Si2O7·H2O 
The crystal structure of the mineral junitoite, ideally CaZn2Si2O7·H2O (calcium dizinc disilicate monohydrate), was first determined by Hamilton & Finney [Mineral. Mag. (1985), 49, 91–95] based on the space group Ama2, yielding a reliability factor R of 0.10, with isotropic displacement parameters for all non-H atoms. The present study reports a structure redetermination of junitoite using single-crystal X-ray diffraction data from a natural sample, demonstrating that the space group of this mineral is actually Aea2, which can be attained simply by shifting the origin. Topologically, the structure models in the space groups Aea2 and Ama2 are analogous, consisting of chains of corner-sharing ZnO4 tetra­hedra parallel to the b axis, cross-linked by Si2O7 tetra­hedral dimers (the site symmetry of the bridging O atom is ..2) along a and c, forming a three-dimensional framework. The Ca2+ cations (site symmetry ..2) are situated in cavities of the framework and are bonded to five O atoms and one H2O mol­ecule (site symmetry ..2) in a distorted octa­hedral coordination environment. However, some bond lengths, especially for the SiO4 tetra­hedron, are noticeably different between the two structure models. Hydrogen bonding in junitoite is found between the water mol­ecule and a framework O atom.
PMCID: PMC3470120  PMID: 23125564
6.  Nioboaeschynite-(Ce), Ce(NbTi)O6  
Nioboaeschynite-(Ce), ideally Ce(NbTi)O6 [cerium(III) niobium(V) titanium(IV) hexa­oxide; refined formula of the natural sample is Ca0.25Ce0.79(Nb1.14Ti0.86)O6], belongs to the aeschynite mineral group which is characterized by the general formula AB 2(O,OH)6, where eight-coordinated A is a rare earth element, Ca, Th or Fe, and six-coordinated B is Ti, Nb, Ta or W. The general structural feature of nioboaeschynite-(Ce) resembles that of the other members of the aeschynite group. It is characterized by edge-sharing dimers of [(Nb,Ti)O6] octa­hedra which share corners to form a three-dimensional framework, with the A sites located in channels parallel to the b axis. The average A—O and B—O bond lengths in nioboaeschynite-(Ce) are 2.471 and 1.993 Å, respectively. Moreover, another eight-coordinated site, designated as the C site, is also located in the channels and is partially occupied by A-type cations. Additionally, the refinement revealed a splitting of the A site, with Ca displaced slightly from Ce (0.266 Å apart), presumably resulting from the crystal-chemical differences between the Ce3+ and Ca2+ cations.
PMCID: PMC3414094  PMID: 22904701
7.  High-pressure synthetic (Na0.97Mg0.03)(Mg0.43Fe0.17 3+Si0.40)Si2O6, with six-coordinated silicon, isostructural with P2/n omphacite 
The title compound, (sodium magnesium) [magnesium iron(III) silicon] disilicate, (Na0.97Mg0.03)(Mg0.43Fe0.17 3+Si0.40)Si2O6, is isotypic with ordered P2/n omphacite. Its structure is characterized by single chains of corner-sharing SiO4 tetra­hedra, extending along the c axis, which are crosslinked by bands of edge-sharing octa­hedra (site symmetry 2), statistically occupied by (Mg2+ + Fe3+ + Si4+). Between the bands built up of the octahedra are two non-equivalent highly distorted six-coordinated sites (site symmetry 2), statistically occupied by (Na + Mg). In contrast to omphacites, the great differences in size and charge between Mg2+ and Si4+ result in complete, rather than partial, ordering of Mg and Si into two distinct octa­hedral sites, whereas Fe3+ is disordered between the two sites. The octa­hedron filled by (Mg + Fe) is larger and markedly more distorted than that occupied by (Si + Fe). The average (Mg + Fe)—O and (VISi + Fe)—O bond lengths are 2.075 and 1.850 Å, respectively.
PMCID: PMC3274841  PMID: 22346794
8.  Redetermination of kovdorskite, Mg2PO4(OH)·3H2O 
The crystal structure of kovdorskite, ideally Mg2PO4(OH)·3H2O (dimagnesium phosphate hydroxide trihydrate), was reported previously with isotropic displacement paramaters only and without H-atom positions [Ovchinnikov et al. (1980 ▶). Dokl. Akad. Nauk SSSR. 255, 351–354]. In this study, the kovdorskite structure is redetermined based on single-crystal X-ray diffraction data from a sample from the type locality, the Kovdor massif, Kola Peninsula, Russia, with anisotropic displacement parameters for all non-H atoms, with all H-atom located and with higher precision. Moreover, inconsistencies of the previously published structural data with respect to reported and calculated X-ray powder patterns are also discussed. The structure of kovdorskite contains a set of four edge-sharing MgO6 octa­hedra inter­connected by PO4 tetra­hedra and O—H⋯O hydrogen bonds, forming columns and channels parallel to [001]. The hydrogen-bonding system in kovdorskite is formed through the water mol­ecules, with the OH− ions contributing little, if any, to the system, as indicated by the long H⋯A distances (>2.50 Å) to the nearest O atoms. The hydrogen-bond lengths determined from the structure refinement agree well with Raman spectroscopic data.
PMCID: PMC3274836  PMID: 22346789
9.  Lotharmeyerite, Ca(Zn,Mn)2(AsO4)2(H2O,OH)2  
Lotharmeyerite, calcium bis­(zinc/manganese) bis­(arsenate) bis­(hydroxide/hydrate), Ca(Zn,Mn3+)2(AsO4)2(H2O,OH)2, is a member of the natrochalcite group of minerals, which are characterized by the general formula AM 2(XO4)2(H2O,OH)2, where A may be occupied by Pb2+, Ca2+, Na+, and Bi3+, M by Fe3+, Mn3+, Cu2+, Zn2+, Co2+, Ni2+, Al3+, and Mg2+, and X by PV, AsV, VV, and SVI. The minerals in the group display either monoclinic or triclinic symmetry, depending on the ordering of chemical components in the M site. Based on single-crystal X-ray diffraction data of a sample from the type locality, Mapimi, Durango, Mexico, this study presents the first structure determination of lotharmeyerite. Lotharmeyerite is isostructural with natrochalcite and tsumcorite. The structure is composed of rutile-type chains of edge-shared MO6 octa­hedra (site symmetry ) extending along [010], which are inter­connected by XO4 tetra­hedra (site symmetry 2) and hydrogen bonds to form [M 2(XO4)2(OH,H2O)2] sheets parallel to (001). These sheets are linked by the larger A cations (site symmetry 2/m), as well as by hydrogen bonds. Bond-valence sums for the M cation, calculated with the parameters for Mn3+ and Mn2+ are 2.72 and 2.94 v.u., respectively, consistent with the occupation of the M site by Mn3+. Two distinct hydrogen bonds are present, one with O⋯O = 2.610 (4) Å and the other O⋯O = 2.595 (3) Å. One of the H-atom positions is disordered over two sites with 50% occupancy, in agreement with observations for other natrochalcite-type minerals, such as natrochalcite and tsumcorite.
PMCID: PMC3254273  PMID: 22259316
10.  Pyrosmalite-(Fe), Fe8Si6O15(OH,Cl)10  
Pyrosmalite-(Fe), ideally FeII 8Si6O15(OH,Cl)10 [refined composition in this study: Fe8Si6O15(OH0.814Cl0.186)10·0.45H2O, octa­iron(II) hexa­silicate deca­(chloride/hydroxide) 0.45-hydrate], is a phyllosilicate mineral and a member of the pyrosmalite series (Fe,Mn)8Si6O15(OH,Cl)10, which includes pyrosmalite-(Mn), as well as friedelite and mcgillite, two polytypes of pyrosmalite-(Mn). This study presents the first structure determination of pyrosmalite-(Fe) based on single-crystal X-ray diffraction data from a natural sample from Burguillos del Cerro, Badajos, Spain. Pyrosmalite-(Fe) is isotypic with pyrosmalite-(Mn) and its structure is characterized by a stacking of brucite-type layers of FeO6-octa­hedra alternating with sheets of SiO4 tetra­hedra along [001]. These sheets consist of 12-, six- and four-membered rings of tetra­hedra in a 1:2:3 ratio. In contrast to previous studies on pyrosmalite-(Mn), which all assumed that Cl and one of the four OH-groups occupy the same site, our data on pyrosmalite-(Fe) revealed a split-site structure model with Cl and OH occupying distinct sites. Furthermore, our study appears to suggest the presence of disordered structural water in pyrosmalite-(Fe), consistent with infrared spectroscopic data measured from the same sample. Weak hydrogen bonding between the ordered OH-groups that are part of the brucite-type layers and the terminal silicate O atoms is present.
PMCID: PMC3254272  PMID: 22259315
11.  Lithio­marsturite, LiCa2Mn2Si5O14(OH) 
Lithio­marsturite, ideally LiCa2Mn2Si5O14(OH), is a member of the pectolite–pyroxene series of pyroxenoids (hydro­pyroxenoids) and belongs to the rhodonite group. A previous structure determination of this mineral based on triclinic symmetry in space group P by Peacor et al. [Am. Mineral. (1990), 75, 409–414] converged with R = 0.18 without reporting any information on atomic coordinates and displacement param­eters. The current study redetermines its structure from a natural specimen from the type locality (Foote mine, North Carolina) based on single-crystal X-ray diffraction data. The crystal structure of lithio­marsturite is characterized by ribbons of edge-sharing CaO6 and two types of MnO6 octa­hedra as well as chains of corner-sharing SiO4 tetra­hedra, both extending along [110]. The octa­hedral ribbons are inter­connected by the rather irregular CaO8 and LiO6 polyhedra through sharing corners and edges, forming layers parallel to (1), which are linked together by the silicate chains. Whereas the coordination environments of the Mn and Li cations can be compared to those of the corresponding cations in nambulite, the bonding situations of the Ca cations are more similar to those in babingtonite. In contrast to the hydrogen-bonding scheme in babingtonite, which has one O atom as the hydrogen-bond donor and a second O atom as the hydrogen-bond acceptor, our study shows that the situation is reversed in lithio­marsturite for the same two O atoms, as a consequence of the differences in the bonding environments around O atoms in the two minerals.
PMCID: PMC3238580  PMID: 22199471
12.  Redetermination of despujolsite, Ca3Mn4+(SO4)2(OH)6·3H2O 
The crystal structure of despujolsite [tricalcium manganese bis­(sulfate) hexahydroxide tri­hydrate], the Ca/Mn member of the fleischerite group, ideally Ca3Mn4+(SO4)2(OH)6·3H2O, was previously determined based on X-ray diffraction intensity data from photographs, without H-atom positions located [Gaudefroy et al. (1968 ▶). Bull. Soc. Fr. Minéral. Crystallogr. 91, 43–50]. The current study redetermines the structure of despujolsite from a natural specimen, with all H atoms located and with higher precision. The structure of despujolsite is characterized by layers of CaO8 polyhedra (m.. symmetry) inter­connected by Mn(OH)6 octa­hedra (32. symmetry) and SO4 tetra­hedra (3.. symmetry) along [001]. The average Ca—O, Mn—O and S—O bond lengths are 2.489, 1.915, and 1.472 Å, respectively. There are two distinct hydrogen bonds that stabilize the structural set-up. This work represents the first description of hydrogen bonds in the fleischerite group of minerals.
PMCID: PMC3200628  PMID: 22064218
13.  Kôzulite, an Mn-rich alkali amphibole 
The crystal structure of kôzulite, an Mn-rich alkali amphibole with the ideal formula NaNa2[Mn4 2+(Fe3+,Al)]Si8O22(OH)2, tris­odium tetra­manganese iron/aluminium octa­silicate dihydroxide, was refined from a natural specimen with composition (K0.20Na0.80)(Na1.60Ca0.18Mn2+ 0.22)(Mn2+ 2.14Mn3+ 0.25Mg2.20Fe3+ 0.27Al0.14)(Si7.92Al0.06Ti0.02)O22[(OH)1.86F0.14]. The site occupancies determined from the refinements are M1 = 0.453 (1) Mn + 0.547 (1) Mg, M2 = 0.766 (1) Mn + 0.234 (1) Mg, and M3 = 0.257 (1) Mn + 0.743 (1) Mg, where Mn and Mg represent (Mn+Fe) and (Mg+Al), respectively. The average M—O bond lengths are 2.064 (1), 2.139 (1), and 2.060 (1) Å for the M1, M2, and M3 sites, respectively, indicating the preference of large Mn2+ for the M2 site. Four partially occupied amphibole A sites were revealed from the refinement, with A(m) = 0.101 (4) K, A(m)′ = 0.187 (14) Na, A(2) = 0.073 (6) Na, and A(1) = 0.056 (18) Na, in accord with the result derived from microprobe analysis (0.20 K + 0.80 Na), considering experimental uncertainties.
PMCID: PMC3011386  PMID: 21589206
14.  Safflorite, (Co,Ni,Fe)As2, isomorphous with marcasite 
Safflorite, a naturally occurring cobalt-nickel-iron diarsenide (Co,Ni,Fe)As2, possesses the marcasite-type structure, with cations (M = Co + Ni + Fe) at site symmetry 2/m and As anions at m. The MAs6 octa­hedra share two edges, forming chains parallel to c. The chemical formula for safflorite should be expressed as (Co,Ni,Fe)As2, rather than the end-member format CoAs2, as its structure stabilization requires the simultaneous inter­action of the electronic states of Co, Ni, and Fe with As2 2− dianions.
PMCID: PMC2960506  PMID: 21201568
15.  Redetermination of olivenite from an untwinned single-crystal 
The crystal structure of olivenite, ideally Cu2(AsO4)(OH) [dicopper(II) arsenate(V) hydroxide], was redetermined from an untwinned and phosphate-containing natural sample, composition Cu2(As0.92P0.08O4), from Majuba Hill (Nevada, USA). Olivenite is structurally analogous with the important rock-forming mineral andalusite, Al2OSiO4. Its structure consists of chains of edge-sharing, distorted [CuO4(OH)2] octa­hedra extending parallel to [001]. These chains are cross-linked by isolated AsO4 tetra­hedra through corner-sharing, forming channels in which dimers of edge-sharing [CuO4(OH)] trigonal bipyramids are located. The structure is stabilized by medium to weak O—H⋯O hydrogen bonds. In contrast to the previous refinements from powder and single crystal X-ray data, all non-H atoms were refined with anisotropic displacement parameters and the H atom was located.
PMCID: PMC2960593  PMID: 21201567
16.  Redetermination of conichalcite, CaCu(AsO4)(OH) 
The crystal structure of conichalcite [calcium copper(II) arsenate(V) hydroxide], with ideal formula CaCu(AsO4)(OH), was redetermined from a natural twinned specimen found in the Maria Catalina mine (Chile). In contrast to the previous refinement from photographic data [Qurashi & Barnes (1963 ▶). Can. Mineral. 7, 561–577], all atoms were refined with anisotropic displacement parameters and with the H atom located. Conichalcite belongs to the adelite mineral group. The Jahn–Teller-distorted [CuO6] octa­hedra share edges, forming chains running parallel to [010]. These chains are cross-linked by eight-coordinate Ca atoms and by sharing vertices with isolated AsO4 tetra­hedra. Of five calcium arsenate minerals in the adelite group, the [MO6] (M = Cu, Zn, Co, Ni and Mg) octa­hedron in conichalcite is the most distorted, and the donor–acceptor O—H⋯O distance is the shortest.
PMCID: PMC2960568  PMID: 21201563

Results 1-16 (16)