Mitsuyoshi Kimata

Re-investigation of the crystal structure of whewellite [Ca(C2O4)·H2O] and the dehydration mechanism of caoxite [Ca(C2O4)·3H2O]

Abstract The crystal structure of whewellite [Ca(C2O4)·H2O] and the dehydration mechanism of caoxite [Ca(C2O4)·3H2O] have been studied by means of differential thermal analysis, X-ray diffraction (powder and single-crystal) analysis and infrared analysis. The first and second analyses confirmed the direct transformation of caoxite into whewellite without an intermediate weddellite [Ca(C2O4)·2H2O] stage. Infrared spectra obtained from caoxite, weddellite and whewellite emphasize the similarity of the O−H-stretching band and O−C−O-stretching band in whewellite and caoxite and the unique bands of weddellite. The structure refinement at low temperature (123 K) reveals that all the hydrogen atoms of whewellite form hydrogen bonds and the two water molecules prop up the crystal structure by the hydrogen bonds that cause a strong anisotropy of the displacement parameter. Comparing the structural features of whewellite with those of weddellite and caoxite suggests that caoxite and whewellite have a sheet structure consisting of Ca2+ ions and oxalate ions although weddellite does not. It is additionally confirmed that the sheets of caoxite are corrugated by hydrogen bonds but whewellite has flat sheets. The corrugated sheets of caoxite would be flattened by dehydration so the direct transformation of caoxite into whewellite would not occur via weddellite. Essential for this transformation is the dehydration of interlayered water molecules in caoxite leading to the building of the crystal structure of whewellite on its intralayered water molecules. The difference in conformation of water molecules between those two crystal structures may explain the more common occurrence of whewellite than of caoxite in nature.

The structural properties of synthetic Sr-åkermanite, Sr2MgSi2O7

The crystal structure of Sr2MgSi207 with tetragonal, a = .7.9957(10),c = 5.1521(9) A, Z = 2, space group P421m has been refined to R = 4.3 % from three-dimensional single-crystal, X-ray diffraction data by full-matrix least-squares calculations. This compound is completely isomorphous with akermanite, Ca2MgSi207, and the Mg and Si atoms are distributed respectively in the T( 1) and T(2) sites of the melilite structure. The tetrahedral Mg-O bond length (1.942A) is clearly longer than that in Ca2MgSi207 (1.915 A), which exhibits the flexibility of T(1) site in melilite structures, In the system Ca2MgSi207 Sr2MgSi207 the tetragonal parameters of the solid solutions are linear functions of molar compositions, which implies that this solid solution is continuous. All of the rare silicates with tetrahedrally coordinated Mg cations contain alkali or alkali-earth cations in their structures and the ratios Mg: Si are below one.

Light-induced degradation dynamics in realgar: in situ structural investigation using single-crystal X-ray diffraction study and X-ray photoelectron spectroscopy

Abstract Light-induced degradation in realgar (arsenic sulfide) has been studied by means of four-circle single-crystal X-ray diffraction and X-ray photoelectron spectroscopy. Because of the alteration of realgar exposed to light, the a lattice parameter and c sinβ value increase linearly from 9.327 to 9.385 Å and fro|m 6.320 to 6.364 Å, respectively. In contrast, the b lattice parameter remains substantially constant. Anisotropic variations of the lattice parameters engender a continuous increase of the unit-cell volume from 799.5 to 810.4 Å3. Nevertheless, no correlation exists between the continuous increase of the unit-cell volume and the bond distance variations in As4S4 molecules because the As4S4 molecule in the unit cell expands very little during light exposure. The most pronounced change was in the distance between centroids UiAs4S4 cages. The spread of As4S4 intermolecular distances increases continuously from 5.642 to 5.665 Å, which directly affects the unit-cell volume expansion of realgar. In addition, the O1s peak increases rapidly after light exposure. The result substantiates the following reaction proposed by Biudi et al. (2003): 5As4S4 + 3O2 -> 4As4S5 + 2As2O5. That is, realgar is transformed into pararealgar if oxygen exists and produces the As4S5 molecule. The additional S atom contributes to anisotropic expansion for the a and c axes because the direction of the additional S atom points toward [41̅4] in the unit cell. Furthermore, an S atom in the As4S5 molecule is released from one of the equivalent As-S-As linkages in As4S5 which becomes the As4S4 molecular of pararealgar. After the As4S5 molecule is divided into an S atom (radical) and the As4S4 (pararealgar type) molecule, the free S atom is re-attached to another As4S4 (realgar type) molecule, and reproduces an As4S5 molecule. The reproduced As4S5 molecule is again divided into an S atom (radical) and an As4S4 (pararealgar type) molecule. This cycle whereby realgar is indirectly transformed into pararealgar via the As4S5 molecule is promoted by light and repeated during light exposure.

Crystal structures of chalcostibite (CuSbS2) and emplectite (CuBiS2): Structural relationship of stereochemical activity between chalcostibite and emplectite

Abstract The crystal structures of chalcostibite CuSbS2 (orthorhombic, space group Pnma, a = 6.018(1), b = 3.7958(6), and c = 14.495(7) Å, V = 331.1(1) Å3, Z = 4, R1 = 0.040, wR2 = 0.155 for 533 reflections) and emplectite CuBiS2 (orthorhombic, space group Pnma, a = 6.134(1), b = 3.9111(8), and c = 14.548(8) Å, V = 348.8(2) Å3, Z = 4, R1 = 0.037, wR2 = 0.112 for 492 reflections) were redetermined using a four-circle diffractometer and graphite-monochromatized MoKα radiation. These two crystal structures are composed of MS5 square pyramids (M = Sb and Bi) and nearly regular CuS4 tetrahedra. The five M-S bond distances in the SbS5 square pyramid in chalcostibite are always shorter than corresponding distances in the BiS5 square pyramid in emplectite because the Sb atom is smaller than the Bi atom. The a cell parameter increases appreciably from chalcostibite to emplectite not only because of increasing M-S bond distances in the MS5 square pyramid, but also because of increasing Cu-S2-Cu bond angles along a. The increase in the b cell parameter is caused mainly by increasing M-S bond distances along b. In contrast, the slight increase of the c cell parameter is largely brought about by decreasing Cu-S2-Cu bond angles ascribed to weakened stereochemical activity of Bi 6s2 lone-pair electrons. The anisotropic change of unit-cell parameters from chalcostibite to emplectite is strongly associated with the positions of the lone-pair electrons in the unit cell.

Structural variations induced by difference of the inert pair effect in the stibnite-bismuthinite solid solution series (Sb,Bi)2S3

Abstract Structural refinements of single crystal X-ray diffraction data for synthetic (Sb,Bi)2S3 solid solutions revealed structural variations in the stibnite (Sb2S3)-bismuthinite (Bi2S3) series. Coordination environments of the M cations are (3 + 4)-fold for the M1 site and (5 + 2)-fold for the M2 site. For the M1 and M2 polyhedra, the short M-S bond lengths increase constantly with increasing Bi concentration, whereas the long M-S bond lengths decrease continuously. The S-M-S interatomic angles interposing lone-pair electrons increase continuously from stibnite to bismuthinite. Stereochemical activity of the lone-pair electrons induces configurational changes of ligands around the M cations from elongated ellipsoidal coordinations to spheroidal ones. Substitution of Bi3+ for Sb3+ in the solid solution expands the basic building block, which causes linear increase of the b lattice parameter with slight positive deviation from Vegardʼs law. This feature is ascribed to order-disorder with concentration of Sb at the M1 site and Bi at the smaller M2 site. Furthermore, increased Bi content engenders both expansion of the basic building block and contraction of intervals between these blocks, contributing to smaller changes in the a and c lattice parameters than in the b lattice parameter. The M2 polyhedra expand relative to the M1 polyhedra with increasing Bi content because the large Bi cation is concentrated at the smaller M2 site. One striking characteristic of (Sb,Bi)2S3 crystal structures is that geometries of central M cation and ligand atoms can be adapted flexibly to transformation of stereochemical activity from 5s2 lone-pair electrons to Bi 6s2 lone-pair electrons by altering the centroid-central atom distance and by changing angles of the centroid-central atom to the a axis.

Anorthite megacrysts from island arc basalts

Abstract Anorthite megacrysts are common in basalts from the Japanese Island Arc, and signally rare in other global fields. These anorthites are 1 to 3 cm in size and often contain several corroded Mg-olivine inclusions. The megacrysts generally range from An94Ab4Ot2 to An89Ab6Ot5 (Ot: other minor end-members, including CaFeSi3O8, CaMgSi3O8, AlAl3SiO8, □Si4O8) and show no chemical zoning. They often show parting. Redclouded megacrysts contain microcrystals of native copper with a distribution reminiscent of the shape of a planetary nebula. Hydrocarbons are also present, both in the anorthite megacrysts and in the olivines included within them. Implications of lateral variations in the Fe/Mg ratio of the included olivines, in Sr-content and in Sr-isotope ratio of the anorthite megacrysts with respect to the Japanese island arc, relate to mixing of crustal components and subducted slab-sediments into the basaltic magmas.

Crystal-chemical and carbon-isotopic characteristics of karpatite (C24H12) from the Picacho Peak Area, San Benito County, California: Evidences for the hydrothermal formation

Abstract Karpatite from the Picacho Peak Area, San Benito County, California, has been characterized as an exceptionally pure crystal of coronene (C24H12) by infrared absorption analysis, Raman scattering analysis, and differential thermal analysis. Furthermore, the crystal structure of karpatite was determined using a single-crystal X-ray diffraction method for the first time. The mineral crystallizes in the monoclinic system, space group P21/a, with unit-cell dimensions of a = 16.094(9), b = 4.690(3), c = 10.049(8) Å, β = 110.79(2)°, V = 709.9(8) Å3, and Z = 2. The structure was solved and Finally refined to R1 = 3.44% and wR2 = 2.65%, respectively. The coronene molecules in the crystal structure of karpatite are all isolated and the intermolecular distances correspond to van der Waals interactions. The coronene molecules have the high degree of aromaticity and no overcrowded hydrogen atoms, both of which avoid a mixing of other polycyclic aromatic hydrocarbons (PAHs) in karpatite. The corrugated arrangement of coronene molecules constituting karpatite prevents intercalation reactions, accounting for the exceptional purity of this mineral. The isotopic composition of carbon was measured, using an elemental analyzer-isotopic ratio mass spectrometer (EA/IRMS). The present karpatite yielded a δ13C value of -22.39 ± 0.18‰ (vs. VPDB), which is similar to carbon isotopic compositions of sedimentary organic matter in the far-reaching tectonic regions. This organic matter might be converted to coronene molecules by hydrothermal Fluids leading to formation of karpatite. Textural relationships indicate that after the strong concentration of coronene molecules in hydrothermal Fluids, karpatite growth postdates both hydrothermal quartz precipitation, and subsequent cinnabar formation. Keywords: Crystal structure, karpatite, stable isotopes, coronene, IR spectroscopy, Raman spectroscopy, DTA, polycyclic aromatic hydrocarbons

The chemistry of allanite from the Daibosatsu Pass, Yamanashi, Japan

Abstract The crystal structure of allanite from granitic pegmatite, the Daibosatsu Pass, Yamanashi, Japan, has been refined under the constraint of chemical composition determined by electron microprobe analysis of rare earth elements. Back-scattered-electron images and X-ray element maps of the allanites show that each of their crystal grains has chemically homogeneous distribution of major elements. A typical formula for the chemistry is: (Ca0.920 ⃞0.080)∑1.000(La0.238Ce0.443Pr0.048Nd0.100Sm0.019Th0.042Mn0.008 ⃞0.102)∑1.000(Al0.607Fe3+0.317Ti0.076)∑1.000(Al1.000)(Fe2+0.543Fe3+0.365Mn0.055Mg0.037)∑1.000(SiO4)(Si2O7)O(OH). The crystal structure of allanite, monoclinic, a 8.905 (1), b 5.7606 (5), c 10.123 (1) Å, β 114.78°(1), space group P21/m, Z = 2, has been refined to an unweighted R factor of 3.46% for 1459 observed reflections. Although the H atom position was not determined on the Difference-Fourier map, inspection of the bond valence sums demonstrates that the H atom is uniquely located at the O10 atom and involved in a hydrogen bond to O4. A systematic examination as to crystal chemistry of allanites suggests that the isolated SiO4 tetrahedron has the largest distortion of three kinds of the tetrahedron containing Si2O7 groups in the allanite structure. This observation is common to the epidote group minerals, while the larger distortion of A2 sites caused by occupancy by REE in allanites contrasts with the smaller one of A sites in other epidote group minerals. In the allanite groups the bond angles between the O10−H bond and hydrogen bond H…O4 are found to range from 170 to 180°. Compilation of the chemical compositions of the title allanite and the others from granitic rocks, Japan, which reveals Th-incorporation as the coupled substitution of 3Th4+ + ⃞ (vacancy) ⇌ 4REE3+, provides an explanation for the observation that higher Th concentrations characterize allanites from the island arcs. The ternary Al2O3-Fe2O3-∑REE diagram illustrates that allanites are grouped, according to their origins, into three classes suggestive of tectonic backgrounds for the crystallization localities; (1) intracontinental, (2) island arc and (3) continental margin.

Refinement of the crystal structure of a synthetic non-stoichiometric Rb-feldspar

Abstract The crystal structure of hydrothermally synthesized Rb-feldspar (monoclinic, space group C2/m, a = 8.839(2)Å , b = 13.035(2) Å , c = 7.175(2) Å , β = 116.11(1)8, V = 742.3(3) Å3, Z = 4) has been refined to a final R of 0.0574 for 692 independent X-ray reflections. Microprobe analyses of the Rb-feldspar suggest deviation from stoichiometry, with excess Si and Al, resulting in a unit formula of Rb0.811⃞0.127Al1.059Si3.003O8. Infrared (IR) spectra indicate the structural occupancy of large H2O content, which implies that the ⃞Si4O8 substitution favours the structural incorporation of the H2O molecule at the M-site. The mean T−O distances are 1.632 AÊ for T1 and 1.645 Å for T2, revealing highly disordered (Al,Si) distribution with Al/Si = 0.245/0.755 (T1 site) and 0.255/0.745 (T2 site). There are two geochemical implications from this refinement: (1) identification of both rubicline triclinic with (Al,Si) ordered distribution and synthetic monoclinic RbAlSi3O8 with (Al,Si) disordered distribution implies that Rb cannot be one of factors disrupting the (Al,Si) ordered and disordered distributions in feldspars; and (2) natural and synthetic feldspars capable of accommodating the large cations tend to incorporate ⃞Si4O8, excess Al and H2O components in their crystal structures.

Crystal chemistry of zircon from granitic rocks, Japan: genetic implications of HREE, U and Th enrichment

Zircon from granitic rocks, Japan is classified into two major types; based on the minor element content determined by electron microprobe, a heavy rare earth element (HREE)-U-Thpoor (Type I) and a HREE-U-Th-rich (Type 2). Zircons characteristically occurring in common granites of type-1 are relatively poor in HREE including Y and Sc, up to 2.72 wt% HREE2O3; up to 0.44 wt% ThO2; up to 2.10 wt% UO2, while zircons characteristically occurring in granitic pegmatites of type-2 are much richer in HREE including Y and Sc, up to 18.99 wt% HREE2O3; up to 11.09 wt% UO2; and up to 6.58 wt% ThO2 However, analyses showing a significantly high amount of REE+Y almost certainly represent altered zircon and/or accidental analysis of inclusions (Hoskin & Schaltegger 2003). Only crystal structure of zircon free of inclusions and zoning (type-2; Takenouchi granitic pegmatite) was refined to R = 4.3 % and for the first time has been confirmed that zircons of type-2 exist as a single-crystal phase in nature. .