Atsushi Kyono

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.

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.

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.

High-pressure phase transitions of Fe3–xTixO4 solid solution up to 60 GPa correlated with electronic spin transition

Abstract The structural phase transition of the titanomagnetite (Fe3-xTixO4) solid solution under pressures up to 60 GPa has been clarified by single-crystal and powder diffraction studies using synchrotron radiation and a diamond-anvil cell. Present Rietveld structure refinements of the solid solution prove that the prefered cation distribution is based on the crystal field preference rather than the magnetic spin ordering in the solid solution. The Ti-rich phases in 0.734 ≤ x ≤1.0 undergo a phase transformation from the cubic spinel of F̅d̅3̅m to the tetragonal spinel structure of I41/amd with c/a < 1.0. The transition is driven by a Jahn-Teller effect of IVFe2+ (3d6) on the tetrahedral site. The c/a < 1 ratio is induced by lifting of the degeneracy of the e orbitals by raising the dx2-y2 orbital below the energy of the dz2 orbital. The distortion characterized by c/a < 1 is more pronounced with increasing Ti content in the Fe3-xTixO4 solid solutions and with increasing pressure. An X-ray emission experiment of Fe2TiO4 at high pressures confirms the spin transition of FeKβ from high spin to intermediate spin (IS) state. The high spin (HS)-to-low spin (LS) transition starts at 14 GPa and the IS state gradually increases with compression. The VIFe2+ in the octahedral site is more prone for the HS-to-LS transition, compared with Fe2+ in the fourfold- or eightfold-coordinated site. The transition to the orthorhombic post-spinel structure with space group Cmcm has been confirmed in the whole compositional range of Fe3-xTixO4. The transition pressure decreases from 25 GPa (x = 0.0) to 15 GPa (x = 1.0) with increasing Ti content. There are two cation sites in the orthorhombic phase: M1 and M2 sites of eightfold and sixfold coordination, respectively. Fe2+ and Ti4+ are disordered on the M2 site. This structural change is accelerated at higher pressures due to the spin transition of Fe2+ in the octahedral site. This is because the ionic radius of VIFe2+ becomes 20% shortened by the spin transition. At 53 GPa, the structure transforms to another high-pressure polymorph with Pmma symmetry with the ordered structure of Ti and Fe atoms in the octahedral site. This structure change results from the order-disorder transition.

The crystal structure of TlAlSiO4: The role of inert pairs in exclusion of Tl from silicate minerals

Abstract Thallium aluminosilicate, TlAlSiO4, synthesized hydrothermally is monoclinic with space group P21/n [a = 5.4095(3), b = 9.4232(7), c = 8.2629(6) Å, γ = 90.01(2)°, V = 421.20(6) Å3, Z = 4]. The crystal structure was refined to an R index of 3.8% based on 1852 observed unique reflections. The compound is a unique framework silicate with a topology similar to that of the tridymite structure. The TlO8 polyhedron resembles a truncated rectangular pyramid, and shares its edges with three adjacent AlO4 tetrahedra, three SiO4 tetrahedra, and six TlO8 polyhedra. Local understaturation at the Tl position suggested by bond-valence analysis implies that lone-pair electrons are present. The geometrical data indicate that the inert pair causes distortion of the Tl-polyhedron. Polyhedral distortion analysis using the software IVTON places the lone-pair parallel to [010], pointing to the largest base of Tl polyhedron. The rule in the valence shell electron pair repulsion model that a nonbonding pair occupies more space on the “surface” of the central atom than a bonding pair supports the orientation of inert-pair electrons in thallium provided by IVTON. The remarkable structure distortion caused by the inert-pair effect explains the rarity of Tl as a major element in silicate minerals because these cannot accommodate extremely distorted polyhedra. In contrast, about forty species of Tl-sulfide minerals exist because these structures are more flexible. Furthermore this effect probably explains why atoms such as Ge2+, Pb2+, Sn2+, Sb3+, and Bi3+, crystallize not as silicate phases but mainly as sulfide ones in nature.

The crystal structure of synthetic TIAISi3O8Influence of the inert-pair effect of thallium on the feldspar structure

The crystal structure of synthetic Tl feldspar, TIAISi3O8, was determined based on single-crystal X-ray diffraction data; monoclinic, a = 8.882(3), b = 13.048(2), c = 7.202(2) A, β = 116.88(1)°, V = 744.5(4)A3, Z = 4, space group C 2/ m (R = 7.33% for 462 observed reflections). The underlying framework is similar to Rb feldspar, RbAlSi3O8, and can be regarded as isotypic with sanidine. The structure accommodates Tl+ cations occupying the M site coordinated by nine O atoms. The more expanded Tl polyhedra as compared to the Rb polyhedra, in spite of the small ion radius of Tl+ relative to Rb+, result from the behavior of the stereoactive lone-pair electrons of Tl+ called “ inert-pair effect ”. The difference in centroid-central atom distance in the TlO9 polyhedron suggests that the lone-pair electrons are orienting parallel to the [001] direction in the feldspar structure. Therefore, Tl found as a trace element in analyses of natural K-feldspar can be considered as an actual constituent of this mineral. The syntheses of the present Tl-feldspar, TlAlSi3O8, together with Tl-leucite, TlAlSi2O6, and the chemical analogue of kalsilite, TlAlSiO4, shed new light on the crystal chemistry of potassium aluminosilicate minerals.

Synthesis of thallium-leucite (TlAlSi 2 O 6 ) pseudomorph after analcime

Abstract Thallium leucite, TlAlSi2O6, has been synthesized at 450°C for 7 days, under ambient conditions, by the transformation of dehydrated analcime NaAlSi2O6 in the presence of excess TlCl. This substitution of Tl for Na leads to confirmation of a thallium-leucite pseudomorph after analcime. Their optical properties, X-ray powder diffraction patterns, electron microprobe analysis, infrared spectra, and X-ray photoelectron spectroscopy have characterized the synthetic Tl-leucites. The IR spectra show that the mid-IR modes T-O stretching and T-O-T bending vibrations for TlAlSi2O6 are more resemblant of those for analcime than for leucite, KAlSi2O6. This resemblance implies that Tl cation enters the W-site rather than the S-site in the analcime structure: Na (S) + H2O (W) ⇌ ⃞ + K (leucite) ⇌ ⃞+ Tl (Tl- leucite), where ⃞ represents an S-site vacancy. The mechanism of this substitution is supported by the crystal chemical constraints: inasmuch as the S-site is smaller than the W-site, Tl+ cations being larger than Na+ plainly prefer the latter site to the former. One inference from the binding energy for Tl+ by XPS is that Tl+ occupies the extra-framework site in synthetic leucite pseudomorph, rather than the smaller tetrahedral site. The difference in Al/Si disordering between analcime and leucite and the nonstoichiometry due to the solid solution of the ⃞Si3O6 component into the leucite structure may provide a fundamental insight into understanding why TlAlSi2O6 deviates from the trend defined by K-, Rb- and CsAlSi2O6 leucite series on the a-c parameter diagram, inasmuch as these three cations in the leucite structure occupy the W-sites. Finally, synthesis of TlAlSi2O6 leucite has an implication for the existence of other polymorphs due to different degrees of Al/Si disordering, except for high- and low-temperature leucites already known: natural leucites crystallized directly through igneous processes are different from those formed by substitution of K for Na in analcimes.