ELF isosurface maps for the Al2SiO5 polymorphs

This study examines the electron localization function (ELF) isosurfaces of the Al₂SiO₅ polymorphs kyanite, sillimanite, and andalusite to see how differences in coordination and geometry of the cations and anions affect the ELF isosurfaces. Examination of the ELF isosurfaces indicates that their shapes are dependent on the coordination and geometry of the oxygen atoms and are not sensitive to coordination of the surrounding cations. Of the 18 crystallographically distinct oxygen atoms in the Al₂SiO₅ polymorphs, 13 are bonded to two aluminum atoms and one silicon atom (Al₂–O–Si) and are associated with two different ELF isosurface shapes. The shape of the ELF isosurface is dependent on the distance at which the oxygen atom lies from a plane defined by the three surrounding cations: at a distance greater than 0.2 Å the ELF can be defined as horseshoe-shaped and at a distance less then 0.2 Å it can be described as concave hemispherical. This feature is also seen in the ELF isosurfaces for the oxygens bonded to three aluminum atoms (Al₃–O) where the isosurfaces can be defined as trigonally toroidal and uniaxially trigonally toroidal. The changes in the ELF isosurfaces for the three coordinated oxygens are also indicative of changes in hybridization. The ELF isosurface for the two-fold coordinated oxygen (Al–O–Si) has a large mushroom-shaped isosurface along the Al–O bond and a concave hemispherical isosurface along the Si–O. The four-fold coordinated oxygen (Al₄–O) contains two concave hemispherical isosurfaces along the shorter Al–O bonds and a banana-shaped isosurface, which encompasses the longer Al–O bonds. In addition, this study shows the homeomorphic relationship between the ELF isosurfaces and electron density difference maps with respect to number and arrangement of domains.     

Ab initio calculated geometries and charge distributions for H4SiO4 and H6Si2O7 compared with experimental values for silicates and siloxanes

Ab initio STO-3G molecular orbital theory has been used to calculate energy-optimized Si-O bond lengths and angles for molecular orthosilicic and pyrosilicic acids. The resulting bond length for orthosilicic acid and the nonbridging bonds for pyrosilicic acid compare well with Si-OH bonds observed for a number of hydrated silicate minerals. Minimum energy Si-O bond lengths to the bridging oxygen of the pyrosilicic molecule show a close correspondence with bridging bond length data observed for the silica polymorphs and for gas phase and molecular crystal siloxanes when plotted against the SiOSi angle. In addition, the calculations show that the mean Si-O bond length of a silicate tetrahedron increases slightly as the SiOSi angle narrows. The close correspondence between the Si-O bond length and angle variations calculated for pyrosilicic acid and those observed for the silica polymorphs and siloxanes substantiates the suggestion that local bonding forces in solids are not very different from those in molecules and clusters consisting of the same atoms with the same coordination numbers. An extended basis calculation for H₄SiO₄ implies that there are about 0.6 electrons in the 3d-orbitals on Si. An analysis of bond overlap populations obtained from STO-3G* calculations for H₆Si₂O₇ indicates that Si-O bond length and SiOSi angle correlations may be ascribed to changes in the hybridization state of the bridging oxygen and (d – p) π-bonding involving all five of the 3d AO's of Si and the lone-pair AO's of the oxygen. Theoretical density difference maps calculated for H₆Si₂O₇ show a build-up of charge density between Si and O, with the peak-height charge densities of the nonbridging bonds exceeding those of the bridging bonds by about 0.05 e Å^?3. In addition, atomic charges (+1.3 and ?0.65) calculated for Si and O in a SiO₂ moiety of the low quartz structure conform reasonably well with the electroneutrality postulate and with experimental charges obtained from monopole and radial refinements of diffraction data recorded for low quartz and coesite.     

Characterization of the amorphous state in metamict silicates and niobates by EXAFS and XANES analyses

X-ray absorption spectroscopy using synchrotron radiation has been applied to the investigation of the coordination geometries around Y, Zr and Nb atoms in metamict zircon, gadolinite, fergusonite, euxenite and samarskite. EXAFS and XANES spectra of their crystalline counterparts and synthetic compounds including ZrO₂, Y₂O₃, YNbTiO₆, YNbO₄, LiNbO₃, and NiNb₂O₆ were also measured for comparison. Metamict zircon shows a significant decrease in its Zr-O bond distances accompanying an increase in distortion of the Zr-O coordination polyhedra as compared with crystalline zircon. On the contrary, the average Nb-O bond distances and the symmetry of the coordination polyhedra around the Nb atoms in metamict euxenite and samarskite resemble those in the crystalline euxenite. Compared with crystalline fergusonite, a decrease in the distortion of the Nb-O octahedra is observed in metamict fergusonite. The structures of the second nearest neighbors (the metal-metal interactions) are largely disrupted in the metamict specimens except for metamict zircon and samarskite with high trivalent iron concentration. Nb in metamict samarskite is in octahedral coordination by oxygen and is similar to that in euxenite.     

Crystal chemistry of cobalt and nickel in lithiophorite and asbolane from New Caledonia

The crystal chemistry of Ni- and Co-bearing manganese oxides (lithiophorite and asbolane) has been investigated by X-ray Absorption Spectroscopy (XAS). The Mn oxides come from the lateritic weathering profiles of the ultrabasites of New Caledonia. The distinct behaviours of Ni and Co concern both oxidation states and local structures.The electronic structure and short range order around Co atoms do not depend on the nature of the Cocontaining phase. Co atoms are trivalent and 6-fold coordinated. Co-(O, OH) and Co-(Co, Mn) interatomic distances derived from EXAFS are equal to those found around Mn atoms which rules out the possibility of an adsorption of Co atoms directly above and below vacancies of MnO₂ layers. The high structural order around Co contrasts with the structural disorder observed around Mn. Cobalt atoms do not occupy specific Mn sites and are not randomly distributed within the octahedral Mn layers.Unlike Co, Ni exhibits distinct surroundings in both phases. In asbolane, Ni atoms build partial Ni(OH)₂ layers. Ni-OH distances are lower as compared with the free Ni hydroxide because of the formation of hydrogen bonds between Ni(OH)₂ and MnO₂ layers. In lithiophorite Ni atoms are located in the hydrargillite layer (Al(OH)₃). Both chemical composition and structural considerations militate for a Ni for Li substitution in lithiophorite. Finally, evidence is given for the existence of a mixed-layering between lithiophorite and asbolane and the chemical variations generally observed in these Mn oxides are interpreted as a variable proportion of (Mn, Co)(O, OH₂, Ni(OH)₂ and (Al, Li, Ni)(OH)₃ layers.     

The crystal structure of bøgvadite (Na2SrBa2Al4F20)

The crystal structure of bøgvadite, Na₂SrBa₂Al₄F₂₀, has been solved and refined to a R₁ factor of 4.4 % from single-crystal data (MoKα X-ray diffraction, CCD area detector) on a sample from the cryolite deposit at Ivittuut, SW Greenland. Bøgvadite is monoclinic, P2₁/n space group, with unit cell parameters a?=?7.134(1), b?=?19.996(3) and c?=?5.3440(8) Å, β?=?90.02(1)^o. A close proximity of the crystal structure to an orthorhombic symmetry and the presence of the two twin components in a nearly 1:1 ratio suggest that the investigated bøgvadite crystal has originally formed as a high-temperature orthorhombic polymorph which on cooling transformed to the stable low temperature monoclinic structure. The bøgvadite crystal structure has groupings of cation-fluoride coordination polyhedra similar to those found in the crystal structures of the genetically closely associated minerals jarlite and jørgensenite. However, its structure type is different from the latter two. The fluoridoaluminate framework of bøgvadite consists of infinite zig-zag chains of cis-connected AlF₆ coordination octahedra. The ¹ _∞[AlF₅] chains are interconnected by infinite chains of Na-F coordination polyhedra which extend in the same direction. Na is coordinated by nine F atoms if its full surrounding is taken in consideration, but makes significant chemical bonds only to closest five. The chains of AlF₆ and NaF₉ coordination polyhedra form double layers. In the centre of layers, relatively large voids in the form of pentagonal antiprisms are occupied by Sr atoms which make chemical bonds with the closest six F atoms. Between the SrF₁₀ coordinations in the centre of layers run empty channels. The double layers are interconnected by Ba atoms which are coordinated by eight F atoms and fill the spaces between the layers. Bøgvadite belongs to the group of fluoridoaluminates with infinite chains of cis-connected AlF₆ coordination octahedra, alike those found in the crystal structures of Ba-fluoridoaluminates.     

Rare earth and high field strength element partitioning between iron-rich clinopyroxenes and felsic liquids

Rare earth elements are commonly assumed to substitute only for Ca in clinopyroxene because of the similarity of ionic radii for REE³⁺ and Ca²⁺ in eightfold coordination. The assumption is valid for Mg-rich clinopyroxenes for which observed mineral/melt partition coefficients are readily predicted by the lattice strain model for substitution onto a single site (e.g., Wood and Blundy 1997). We show that natural Fe-rich pyroxenes in both silica-undersaturated and silica-oversaturated magmatic systems deviate from this behavior. Salites (Mg# 48–59) in phonolites from Tenerife, ferrohedenbergites (Mg# 14.2–16.2) from the rhyolitic Bandelier Tuff, and ferroaugites (Mg# 9.6–32) from the rhyolitic Rattlesnake Tuff have higher heavy REE contents than predicted by single-site substitution. The ionic radius of Fe²⁺ in sixfold coordination is substantially greater than that of Mg²⁺; hence, we propose that, in Fe-rich clinopyroxenes, heavy REE are significantly partitioned between eightfold Ca sites and sixfold Fe and Mg sites such that Yb and Lu exist dominantly in sixfold coordination. We also outline a REE-based method of identifying pyroxene/melt pairs in systems with multiple liquid and crystal populations, based upon the assumption that LREE and MREE reside exclusively in eightfold coordination in pyroxene. Contrary to expectations, interpolation of mineral/melt partition coefficient data for heavy REE does not predict the behavior of Y. We speculate that mass fractionation effects play a role in mineral/melt lithophile trace element partitioning that is detectable among pairs of isovalent elements with near-identical radii, such as Y and Ho, Zr and Hf, and Nb and Ta.     

Uranium co-precipitation with iron oxide minerals

In oxidizing environments, the toxic and radioactive element uranium (U) is most soluble and mobile in the hexavalent oxidation state. Sorption of U(VI) on Fe-oxides minerals (such as hematite [α-Fe₂O₃] and goethite [α-FeOOH]) and occlusion of U(VI) by Fe-oxide coatings are processes that can retard U transport in environments. In aged U-contaminated geologic materials, the transport and the biological availability of U toward reduction may be limited by coprecipitation with Fe-oxide minerals. These processes also affect the biological availability of U(VI) species toward reduction and precipitation as the less soluble U(IV) species by metal-reducing bacteria.To examine the dynamics of interactions between U(VI) and Fe oxides during crystallization, Fe-oxide phases (containing 0.5 to 5.4 mol% U/(U + Fe)) were synthesized by means of solutions of U(VI) and Fe(III). Wet chemical (digestions and chemical extractions) and spectroscopic techniques were used to characterize the synthesized Fe oxide coprecipitates after rinsing in deionized water. Leaching the high mol% U solids with concentrated carbonate solution (for sorbed and solid-phase U(VI) species) typically removed most of the U, leaving, on average, about 0.6 mol% U. Oxalate leaching of solids with low mol% U contents (about 1 mol% U or less) indicated that almost all of the Fe in these solids was crystalline and that most of the U was associated with these crystalline Fe oxides. X-ray diffraction and Fourier-transform infrared (FT-IR) spectroscopic studies indicate that hematite formation is preferred over that of goethite when the amount of U in the Fe-oxides exceeds 1 mol% U (∼4 wt% U). FT-IR and room temperature continuous wave luminescence spectroscopic studies with unleached U/Fe solids indicate a relationship between the mol% U in the Fe oxide and the intensity or existence of the spectra features that can be assigned to UO₂²⁺ species (such as the IR asymmetric υ₃ stretch for O = U = O for uranyl). These spectral features were undetectable in carbonate- or oxalate-leached solids, suggesting solid phase and sorbed U(VI)O₂²⁺ species are extracted by the leach solutions. Uranium L₃-edge x-ray absorption spectroscopic (XAFS) analyses of the unleached U-Fe oxide solids with less than 1 mol% U reveal that U(VI) exists with four O atoms at radial distances of 2.19 and 2.36 Å and second shell Fe at a radial distance at 3.19 Å.Because of the large ionic radius of UO₂²⁺ (∼1.8 Å) relative to that of Fe³⁺ (0.65 Å), the UO₂²⁺ ion is unlikely to be incorporated in the place of Fe in Fe(III)-oxide structures. Solid-phase U(VI) can exist as the uranyl [U(VI)O₂²⁺] species with two axial U-O double bonds and four or more equatorial U-O bonds or as the uranate species (such as γ-UO₃) without axial U-O bonds. Our findings indicate U⁶⁺ (with ionic radii of 0.72 to 0.8 Å, depending on the coordination environment) is incorporated in the Fe oxides as uranate (without axial O atoms) until a point of saturation is reached. Beyond this excess in U concentration, precipitating U(VI) forms discrete crystalline uranyl phases that resemble the uranyl oxide hydrate schoepite [UO₂(OH)₂·2H₂O]. Molecular modeling studies reveal that U⁶⁺ species could bond with O atoms from distorted Fe octahedra in the hematite structure with an environment that is consistent with the results of the XAFS. The results provide compelling evidence of U incorporation within the hematite structure.     

A study of speciation of Sb in bisulfide solutions by X-ray absorption spectroscopy.

Direct evidence of the structure of thioantimonide species in alkaline aqueous solutions is provided by X-ray absorption spectroscopy. Twenty solutions containing thioantimonide species were prepared by dissolving stibnite (Sb₂S₃) in deoxygenated aqueous NaHS solutions; the solution pH range was 8–14, the [Sb_tot] 1–100 mM and the [HS⁻] 0.009–2.5 M. The structural environment of the dissolved Sb was determined by EXAFS analysis of the Sb K-edge over the temperature range 80–473 K.Many of the solutions contain a species with Sb bonded to four S atoms at 2.34 Å, consistent with the presence of a [Sb(V)S₄³⁻] species, demonstrating that oxidation of Sb(III) to Sb(V) has occurred on dissolution. There is evidence that the complementary reduced phase is H₂. In three solutions, the Sb has three nearest neighbor S atoms and two of these solutions have an additional S shell of two atoms at 2.9Å, with one showing evidence of an Sb shell at 4.15 Å. This provides evidence of the presence of multimeric Sb(V) thioantimonide species. Analysis of several solutions reveals the presence of a species with three Sb–S interactions of 2.41–2.42 Å, supporting the presence of a Sb(III) species such as Sb₂S₂(SH)₂. Six solutions have S coordination numbers from 2.7–4 Å and Sb–S distances of 2.37–2.39 Å, and are likely to contain mixtures of at least two species in concentrations such that each make a significant contribution to the EXAFS. There was no clear relationship between either [Sb_tot] or [HS⁻] and the type of species present, but Sb(III) species were only present in the solutions with high pH. The effect of temperature was most significant in one solution, where at 423 K partial hydrolysis occurred and the presence of a species such as Sb₂S₂(OH)₂, with an Sb–O distance of 1.91 Å, is indicated.The study provides new information on the coordination environment of thioantimonide species, complementary to previous studies and provides a basis for a better understanding of Sb speciation in aqueous solutions found in hydrothermal systems, anoxic basins and man-made, high pH environments. In particular it demonstrates the need for Sb(V) to be considered in theoretical and experimental studies of such systems. However, more definitive interpretation of some of the data is inhibited by the presence of mixtures of species and the lack of information on the outer coordination shells that would confirm the presence of multimeric species.     

Characterization of Cu-complexes in smectite with different layer charge location: chemical, thermal and EXAFS studies

The retention of Cu and Cu-amino acid complexes by montmorillonite and beidellite, before and after repeated acidified aqueous solution treatments, was studied using X-ray diffraction, chemical and thermal analyses, mass spectrometry and synchrotron-based X-ray absorption spectroscopy (XAS).The results indicate that the extraction of metal complexes from smectites depends on the nature of the layer charge and on the kind of organic species. Cu-cysteine complexes are strongly retained in the interlayer position, whereas Cu-glycine complexes are mostly adsorbed in cationic form which can be easily removed from the silicate layer. The layer periodicity for Cu-smectites treated with glycine shows little or no layer expansion, whereas significant swelling of the layer periodicity is observed in smectites treated with cysteine.Thermal decomposition of both smectites with sorbed Cu-amino acid species shows the evolution of H₂O, NO, CH₃CH₃, and CO₂. In Cu-cysteine treated smectites, the release of H₂S, NO₂, SO₂, and N₂O₃ also occurs.X-ray absorption spectroscopy (XAS) was used to assess the relationships between the structure of the Cu complexes and their desorption from smectites. In Cu-exchanged smectites, the first coordination shell agrees with the hypothesis that the Cu coordinates to oxygen atoms to form monomer and/or dimer complexes. The first coordination shell of Cu in smectites treated with glycine shows four atoms at distances of ∼2 Å. Two of these bonds are with nitrogen and two with oxygen atoms. For copper-cysteine complexes XAS data are compatible with the existence of Cu-N clusters, thus suggesting that Cu links to the amino acid by the aminic group.     

The crystal structure of ilinskite, NaCu5O2(SeO3)2Cl3, and review of mixed-ligand CuOmCln coordination geometries in minerals and inorganic compounds

The crystal structure of ilinskite, NaCu₅O₂(SeO₃)₂Cl₃, a rare copper selenite chloride from volcanic fumaroles of the Great fissure Tolbachik eruption (Kamchatka peninsula, Russia), has been solved by direct methods and refined to R ₁?=?0.044 on the basis of 2720 unique observed reflections. The mineral is orthorhombic, Pnma, a?=?17.769(7), b?=?6.448(3), c?=?10.522(4) Å, V?=?1205.6(8) ų, Z?=?4. The The CuO_mCl_n coordination polyhedra share edges to form tetramers that have 'additional' O1 and O2 atoms as centers. The O1Cu₄ and O2Cu₄ tetrahedra share common Cu atoms to form [O₂Cu₅]⁶⁺ sheets. The SeO₃ groups and Cl atoms are adjacent to the [O₂Cu₅]⁶⁺ sheets to form complex layers parallel to (100). The Na⁺ cations are located in between the layers. A review of mixed-ligand CuO_mCl_n coordination polyhedra in minerals and inorganic compounds is given. There are in total 26 stereochemically different mixed-ligand Cu-O-Cl coordinations.     

Iron (III)-silica interactions in aqueous solution: insights from X-ray absorption fine structure spectroscopy

The influence of aqueous silica on the hydrolysis of iron(III) nitrate and chloride salts in dilute aqueous solutions (m_Fe ∼ 0.01 mol/kg) was studied at ambient temperature using X-ray absorption fine structure (XAFS) spectroscopy at the Fe K-edge. Results show that in Si-free iron nitrate and chloride solutions at acid pH (pH < 2.5), Fe is hexa-coordinated with 6 oxygens of H₂O- and/or OH-groups in the first coordination sphere of the metal, at an Fe-O distance of 2.00 ± 0.01 Å. With increasing pH (2.7 < pH < 13), these groups are rapidly replaced by bridging hydroxyls (-OH-) or oxygens (-O-), and polymerized Fe hydroxide complexes form via Fe-(O/OH)-Fe bonds. In these polymers, the first atomic shell of iron represents a distorted octahedron with six O/OH groups and Fe-O distances ranging from 1.92 to 2.07 Å. The Fe octahedra are linked together by their edges (Fe-Fe distance 2.92-3.12 Å) and corners (Fe-Fe distance ∼3.47 ± 0.03 Å). The Fe-Fe coordination numbers (N_edge = 1-2; N_corner = 0.5-0.7) are consistent with the dominant presence of iron dimers, trimers and tetramers at pH 2.5 to 2.9, and of higher-polymerized species at pH > 3.At pH > 2.5 in the presence of aqueous silica, important changes in Fe(III) hydrolysis are detected. In 0.05-m Si solutions (pH ∼ 2.7-3.0), the corner linkages between Fe octahedra in the polymeric complexes disappear, and the Fe-Fe distances corresponding to the edge linkages slightly increase (Fe-Fe_edge ∼ 3.12-3.14 Å). The presence of 1 to 2 silicons at 3.18 ± 0.03 Å is detected in the second atomic shell around iron. At basic pH (∼12.7), similar structural changes are observed for the iron second shell. The Fe-Si and Fe-Fe distances and coordination numbers derived in this study are consistent with (1) Fe-Si complex stoichiometries Fe₂Si_1-2 and Fe₃Si_2-3 at pH < 3; (2) structures composed of Fe-Fe dimers and trimers sharing one or two edges of FeO₆-octahedra; and (3) silicon tetrahedra linked to two neighboring Fe octahedra via corners. At higher Si concentration (0.16 m, polymerized silica solution) and pH ∼ 3, the signal of the Fe second shell vanishes indicating the destruction of the Fe-Fe bonds and the formation of different Fe-Si linkages. Moreover, ∼20 mol.% of Fe is found to be tetrahedrally coordinated with oxygens in the first coordination shell (R_Fe-O = 1.84 Å). This new finding implies that Fe may partially substitute for Si in the tetrahedral network of the silica polymers in Si-rich solutions.The results of this study demonstrate that aqueous silica can significantly inhibit iron polymerization and solid-phase formation, and thus increase the stability and mobility of Fe(III) in natural waters. The silica “poisoning” of the free corner sites of iron-hydroxide colloids should reduce the adsorption and incorporation of trace elements by these colloids in Si-rich natural waters.     

Impact of amide–amide hydrogen bonding on the stability of two nicotinamide complexes of silver(I)

The nicotinamide (pyridine-3-carboxamide, nia) complexes of silver(I), [Ag(nia)₂(NO₃)]·H₂O (1), [Ag(nia)₂(NO₃)] (2), and {K[Ag(nia)₂](NO₃)₂} _n (3), were prepared and characterised by IR spectroscopy and TG/DTA thermal methods. The solid state structures of 2 and 3 were determined by single-crystal X-ray diffraction analysis. In both complexes two nicotinamide ligands are coordinated to silver(I) through the nitrogen atom of the pyridine ring in a near-linear fashion. In 2, additional coordination by two oxygen atoms of one nitrate group leads to the distorted tetrahedral coordination environment of silver(I). In 3, nitrate ions bridge potassium cations giving rise to a 2D coordination network which is further stabilised by cross-bridging of each two potassium atoms in [1 0 0] direction by complex cations, [Ag(nia)₂]⁺. Despite different aggregation of 2 and 3 in the solid state, both complexes demonstrate quite similar thermal stability. The amide self-complementary hydrogen bonds appear to be the main driving force for establishing the crystal structures of both 2 and 3.     

Low-temperature crystal structures of stibnite implying orbital overlap of Sb 5s2 inert pair electrons

The crystal structure of stibnite [Sb₂S₃, Pnma, a=11.314(2), b=3.837(2), c=11.234(3) Å, V= 487.7(3) ų at 293 K] was refined in situ at 230, 173, and 128 K. It is a major characteristic of the structure that the Sb–S secondary bonds enclosing Sb 5s² inert lone-pair electrons at 293 K are significantly shorter than the corresponding sum of the Sb and S van der Waals radii. Concerning the temperature dependence, although both the polyhedral volume and the cation eccentricity of the two SbS₇ polyhedra exhibit continuous contractions with decreasing temperature, the sphericity values remain constant, indicating isotropic shrinkage. Consequently, the geometries of Sb 5s² inert lone-pair electrons and ligand atoms remain unchanged at low temperatures. This is because the crystal structure of stibnite at low temperature induces contraction with attractive interactions, which is called the orbital overlap between Sb 5s² inert lone-pair electrons and ligand orbitals to maintain the coordination environment. In this case, Sb 5s² lone-pair electrons are not inert, but active. Such orbital overlaps of inert lone-electron pairs can provide a reasonable explanation for shorter secondary bonds and lower band gap energy of the binary compounds containing heavy elements such as Sb, Te, Pb, and Bi, which are key factors in tracing the origins of color, luster, and semiconductivity of their minerals or compounds.     

Effect of the Si/Al ordering on structural parameters and the energetic stabilization of vermiculites – a theoretical study

The effect of the Si/Al distribution in the tetrahedral sheets of the vermiculite mineral has been investigated employing density functional theory. The structures of six models for vermiculite with the structural formula (Mg₄)(Mg₁₂)(Si₈Al₈)O₄₀(OH)₈·24(H₂O) per unit cell were fully optimized. The models differ by the T···Mg²⁺···T coordination of the interlayer Mg²⁺ cations by two central cations from the adjacent tetrahedral sheets of the 2:1 vermiculite layers (T,T=Si,Al). We observed the formation of very strong hydrogen bonds between water molecules solvating the interlayer Mg²⁺ cations and the surface basal oxygen atoms of the 2:1 layers. The directionality of hydrogen bonds is the major factor determining the layer stacking in the vermiculite structure. Results showed that the most stable model is that where only silicon atoms in the tetrahedral sheets coordinate all interlayer Mg²⁺ cations.     

Molecular modeling of water structure in nano-pores between brucite (001) surfaces

Molecular dynamics (MD) computer simulations of liquid water held in one-dimensional nano-confinement by two parallel, electrostatically neutral but hydrophilic surfaces of brucite, Mg(OH)₂, provide greatly increased, atomistically detailed understanding of surface-related effects on the spatial variation in the structural ordering, hydrogen bond (H-bond) organization, and local density of H₂O molecules at this important model hydroxide surface. NVT-ensemble MD simulations (i.e., at constant number of atoms, volume and temperature) were performed for a series of model systems consisting of 3 to 30 Å-thick water layers (containing 35 to 360 H₂O molecules) confined between two 19 Å-thick brucite substrate layers. The results show that the hydrophilic substrate significantly influences the near-surface water structure, with both H-bond donation to the surface oxygen atoms and H-bond acceptance from the surface hydrogen atoms in the first surface layer of H₂O molecules playing key roles. Profiles of oxygen and hydrogen atomic density and H₂O dipole orientation show significant deviation from the corresponding structural properties of bulk water to distances as large as 15 Å (∼5 molecular water layers) from the surface, with the local structural environment varying significantly with the distance from the surface. The water molecules in the first layer at about 2.45 Å from the surface have a two-dimensional hexagonal arrangement parallel to brucite layers, reflecting the brucite surface structure, have total nearest neighbor coordinations of 5 or 6, and are significantly limited in their position and orientation. The greatest degree of the tetrahedral (ice-like) ordering occurs at about 4 Å from the surface. The translational and orientational ordering of H₂O molecules in layers further from the surface become progressively more similar to those of bulk liquid water. A quantitative statistical analysis of the MD-generated instantaneous molecular configurations in terms of local density, molecular orientation, nearest neighbor coordination, and the structural details of the H-bonding network shows that the local structure of interfacial water at the brucite surface results from a combination of “hard wall” (geometric and confinement) effects, highly directional H-bonding, and thermal motion. This structure does not resemble that of bulk water at ambient conditions or at elevated or reduced temperature, but shares some similarities with that of water under higher pressure.     

Experimental multipole-refined and theoretical charge density study of LiGaSi<Subscript>2</Subscript>O<Subscript>6</Subscript> clinopyroxene at ambient conditions

The synthetic LiGaSi₂O₆ clinopyroxene is monoclinic C2/c at room-T. Its experimental electron density, ρ(r), has been derived starting from accurate room-T single-crystal diffraction data. Topological analysis confirms an intermediate ionic-covalent character for Si–O bonding, as found by previous electron-density studies on other silicates such as diopside, coesite and stishovite. The non-bridging Si–O bonds have more covalent character than the bridging ones. The Ga–O bonds have different bonding characters, the Ga–O2 bond being more covalent than the two Ga–O1 bonds. Li–O bonds are classified as pure closed-shell ionic interactions. Similar to spodumene (LiAlSi₂O₆), Li has sixfold coordination, but the bond critical points associated to the two longest bonds are characterized by very low electron density values. Similar to what previously found in spodumene and diopside, O···O interactions were detected from the topological analysis of ρ(r), and indicate a cooperative interaction among the lone pairs of neighbouring oxygen atoms. In particular, this kind of interaction has been obtained for the O1···O1 edge shared between two Ga octahedra. Integration over the atomic basins gives net charges of −1.39(10), 2.82(10), 1.91(10) and 0.82(8) e for O (averaged), Si, Ga and Li atoms, respectively. Periodic Hartree–Fock and DFT calculations confirm the results obtained by multipole refinement of the experimental data. Moreover, the theoretical topological properties of the electron density distribution on the Si₂O₆ group are very similar to those calculated for spodumene. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structure and specification of iron complexes in aqueous solutions determined by X-ray absorption spectroscopy

X-ray absorption spectroscopy, including extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) techniques, have been used to determine the structure and speciation of complexes for Fe²⁺ and Fe³⁺ chloride solutions at a variety of pH's, ionic strengths, and chloride/iron ratios.Low intensity K-edge transition features and analysis of modified pair correlation functions, derived from Fourier transformation of EXAFS spectra, show a regular octahedral coordination of Fe(II) by water molecules with a first-shell Fe²⁺-O bond distance, closely matching octahedral Fe²⁺-O bonds obtained from solid oxide model compounds. Solution Fe²⁺-O bond distances decrease with chloride/iron ratio, pH, and total FeCl₂ concentration. A slight intensification of the $\text{1s → 3d}$ transition with increasing FeCl₂ concentration suggests that chloride may begin to mix with water as a nearest-neighbor octahedral ligand. Fe³⁺ solutions show a pronounced increase in the $\text{1s → 3d}$ transition intensities between 1.0 M FeCl₃/7.8 M Cl^? to 1.0 M FeCl₃/ 15 M Cl^?, indicating a coordination change from octahedral to tetrahedral complexes. EXAFS analyses of these solutions show an increase in first-shell Fe³⁺-ligand distances despite this apparent reduction in coordination number. This can be best explained by a change from regular octahedral complexes of ferric iron (either Fe(H₂O)₆³⁺ or trans-Fe(H₂O)₄Cl₂ or both; Fe³⁺-O bond distances of 2.10 Å) to tetra-chloro complexes [Fe³⁺-Cl bond distances of 2.25 Å].     

Fully automated microcomputer calculation of vibrational spectra

A fully automated method for computing frequencies and atomic displacements of normal modes, giving synthetic infrared and Raman spectra, has been developed for use on small computers. No expertise in group theory or the mathematics of normal-mode calculation are required to use the computer program. The method takes full account of symmetry and is applicable to any crystal or molecule. Force constants can be specified in terms of any two-atom “bonds” or three-atom angles. The essential steps in the computer program are: (1) Locate all atoms in the unit cell or molecule and compute displacement vectors for each internal coordinate; (2) Convert the basis of the force constants from bonds and angles to cartesian displacements; (3) Construct the full-matrix irreducible representations of the point or factor group in question, using appropriate symmetry matrices and polynomial basis functions; (4) Derive the symmetry coordinates in terms of cartesian displacements using the projection/transfer-operator technique; (5) construct secular equations for each species with Wilson's f–g method; (6) solve for frequencies and atomic motions; and (7) use simple models of infrared and Raman intensities to calculate spectra.     

Structural state and differusion of impurities in natural quartz of different genesis

Impurity inhomogeneities and other structural defects have been studied by means of transmission electron microscopy (TEM), X-ray microanalysis and electron paramagnetic resonance (EPR) in untreated and heat-treated quartz samples of three genetic types: hydrothermal, pegmatitic and magmatic. The impurities present are Al, Na and H₂O, which occupy tetrahedral (Al³⁺) or interstitial (Na⁺, H₂O) positions in the quartz lattice. Impurities form imperfections of various degrees of segregation: from point defects to micropores with a gas-liquid content. Their size, form, density and distribution in the lattice depend on the formation conditions of the quartz, the presence of dislocations and plane defects serving as sinks for the impurity atoms, and the heat treatment regime. Experimental data indicate that gas-liquid inclusions of dimensions up to some microns are the result of impurity segregation during postcrystallizational cooling. Crystalline quartz amorphizes upon electron irradiation. A model of structural water explaining experimentally observed features of this phenomenon is proposed whereby the water molecule, represented as a dipole, enters microregions of the silica lattice with a high impurity content and there forms a bond between ‘defective’ [SiO₃]^2? and [AlO₄]^5? tetrahedra. On irradiation, the Si---O donor-acceptor bonds trap nonelastically scattered electrons and are ruptured as a result. The water released by this lattice discontinuity forms microbubbles that diffuse along sinks into the larger micropores thus further increasing their volume.     

Coordination of Fe,Ga and Ge in high pressure glasses by Mössbauer,Raman and X-ray absorption spectroscopy,and geological implications

Mössbauer spectra of glasses of NaFeSi₃O₈ and 3NaAlSi₂O₆ · NaFeSiO₄ starting compositions consist of a dominant Fe³⁺ and subordinate Fe²⁺ quadrupole-split doublet, in agreement with previous work. Fe³⁺ is assigned to tetrahedral coordination. Pressure-induced coordination changes are not observed in the pressure range 1 bar to 30 kbar. A gradual increase in isomer shift of the Fe³⁺ doublet with increase in pressure is attributed to steric effects. Raman spectra of GeO₂, NaGaSi₃O₈ and NaGaSiO₄ glasses are dominated by network structure vibrations. There is no detectable change in the nearest-neighbor coordination of Ge⁴⁺ in GeO₂ from 1 bar to 14 kbar, of Ga³⁺ in NaGaSi₃O₈ from 1 bar to 28 kbar and of Ga³⁺ in NaGaSiO₄ from 1 bar to 25 kbar. However, some structural reorganization outside of the first coordination sphere occurs in the high pressure glasses.XANES and EXAFS spectra on powdered samples of 1 bar and 25 kbar NaGaSiO₄ glasses and crystalline NaGaSiO₄ were obtained from K edge absorption spectra at the Stanford Synchrotron Radiation Laboratory using a double crystal monochromator equipped with Si(220) crystals. The XANES spectra indicate that Ga³⁺ has a similar extended coordination geometry in both glasses. The EXAFS spectra reveal that Ga³⁺ is four-coordinated with oxygen in all three samples with a Ga³⁺-O distance of about 1.83 Å. The radial distribution functions of the two glasses are virtually identical. However, both XANES and EXAFS spectra indicate significant structural differences between crystalline NaGaSiO₄ (nepheline-type structure) and vitreous NaGaSiO₄ beyond the first coordination shell of Ga³⁺. Thus, X-ray absorption spectroscopy independently confirms the Raman results on the unchanged coordination of Ga³⁺ in NaGaSiO₄ glasses with pressures up to 25 kbar.Glass compositions were selected in anticipation that larger and/or lower charged cations would exhibit pressure-induced coordination changes at lower pressures than Al³⁺ and Si⁴⁺. The present null result suggests that the stabilizing features of open network structures in the liquid state (large entropy and minimized cation-cation repulsion) more than compensate for large molar volume in the pressure range accessible to experimentation. It appears that network structures in natural magmas should remain stable throughout the upper mantle. Consequently, the densities of magmas at high pressures which are calculated from compressibility data and the appropriate equation of state will be only slightly underestimated, due to the effect of minor structural changes beyond the first coordination sphere.