Site-occupancy Factors Research Articles

2-Amino-5-oxo-4-(thiophen-2-yl)-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile

The crystal structure of the title compound, C14H12N2O2S, reveals two symmetrically independent molecules within the asymmetric unit. Each molecule contains a chromenone core attached to a 2-thiophene ring, cyano, and amino groups. The 2-thiophene ring of one of the two molecules in the asymmetric unit was found to be disordered over two positions, with the major component having a site occupancy factor of 0.837 (2). The 2-thiophene ring is nearly orthogonal to the fused 4H-pyran ring, with dihedral angles between the two sets of planes being 89.5 (5) and 89.63 (8)°. Intermolecular hydrogen bonding, involving N—H...N and N—H...O interactions, creates two distinct motifs leading to the formation of a two-dimensional supramolecular network along the crystallographic ac plane.

Diisobutyl-ammonium tri-phenyl(2-thiolato-acetato-κ2 O,S)stannate(IV).

Crystals of the title salt, (C8H20N)[Sn(C6H5)3(C2H2O2S)], comprise diisobutyl-ammonium cations and mercapto-acetato-tri-phenyl-stannate(IV) anions. The bidentate binding mode of the mercapto-acetate ligand gives rise to a five-coordinated, ionic tri-phenyl-tin complex with a distorted cis-trigonal-bipyramidal geometry around the tin atom. In the crystal, charge-assisted ammonium-N-H⋯O(carboxyl-ate) hydrogen-bonding connects two cations and two anions into a four-ion aggregate. Two positions were resolved for one of the phenyl rings with the major component having a site occupancy factor of 0.60 (3).

Synthesis and in-depth structure determination of a novel metastable high-pressure CrTe3 phase

This study reports the synthesis and crystal structure determination of a novel CrTe3 phase using various experimental and theoretical methods. The average stoichiometry and local phase separation of this quenched high-pressure phase were characterized by ex situ synchrotron powder X-ray diffraction and total scattering. Several structural models were obtained using simulated annealing, but all suffered from an imperfect Rietveld refinement, especially at higher diffraction angles. Finally, a novel stoichiometrically correct crystal structure model was proposed on the basis of electron diffraction data and refined against powder diffraction data using the Rietveld method. Scanning electron microscopy–energy-dispersive X-ray spectrometry (EDX) measurements verified the targeted 1:3 (Cr:Te) average stoichiometry for the starting compound and for the quenched high-pressure phase within experimental errors. Scanning transmission electron microscopy (STEM)–EDX was used to examine minute variations of the Cr-to-Te ratio at the nanoscale. Precession electron diffraction (PED) experiments were applied for the nanoscale structure analysis of the quenched high-pressure phase. The proposed monoclinic model from PED experiments provided an improved fit to the X-ray patterns, especially after introducing atomic anisotropic displacement parameters and partial occupancy of Cr atoms. Atomic resolution STEM and simulations were conducted to identify variations in the Cr-atom site-occupancy factor. No significant variations were observed experimentally for several zone axes. The magnetic properties of the novel CrTe3 phase were investigated through temperature- and field-dependent magnetization measurements. In order to understand these properties, auxiliary theoretical investigations have been performed by first-principles electronic structure calculations and Monte Carlo simulations. The obtained results allow the observed magnetization behavior to be interpreted as the consequence of competition between the applied magnetic field and the Cr–Cr exchange interactions, leading to a decrease of the magnetization towards T = 0 K typical for antiferromagnetic systems, as well as a field-induced enhanced magnetization around the critical temperature due to the high magnetic susceptibility in this region.

Kenoargentotetrahedrite-(Zn), [Ag6]4+(Cu4Zn2)Sb4S12□, a new member of the tetrahedrite group from the Yindongpo Au deposit, China

Abstract. The new mineral kenoargentotetrahedrite-(Zn), [Ag6]4+(Cu4Zn2)Sb4S12□, was discovered at the Yindongpo Au deposit, Henan Province, China. It occurs as black metallic anhedral grains or equant crystals up to 40 µm in size. It is opaque in transmitted light and shows a greenish-grey colour in reflected light. Electron microprobe analysis for the studied material gave the empirical formula (on the basis of total cations being equal to 16 atoms per formula unit, apfu): M(2)(Ag3.75Cu2.25)Σ6M(1)[Cu3.90(Zn1.18Fe0.69Cd0.26)Σ2.13]Σ6.03X(3)(Sb3.69As0.27)Σ3.96S(1)S11.94 S(2)□. Kenoargentotetrahedrite-(Zn) is cubic, I4‾3m (no. 217), with a = 10.4624(4) Å, V= 1145.23(13) Å3, and Z= 2. The crystal structure has been refined to a final value of R1= 0.0247 on the basis of 274 independent reflections (Fo > 4σ (Fo)) by using single-crystal X-ray diffraction data. The seven strongest X-ray powder diffraction lines (d in Å (I) (hkl)) are the following: 3.010 (100) (222), 1.844 (30) (044), 2.606 (22) (004), 1.572 (15) (226), 2.046 (9) (134), 7.35 (6) (011), and 1.909 (5) (125). Kenoargentotetrahedrite-(Zn) is isostructural with other keno-member tetrahedrites with the [Ag6]4+ cluster. The structure refinement result confirms the coupling between the site occupancy factor of subvalent hexasilver clusters at the M(2) site and that of the vacancy at the S(2) site. This relationship further substantiates the charge balance substitution mechanism of S-deficiency tetrahedrites: 6M(2)Ag++S(2)S2-= M(2)[Ag6]4++S(2)□.

Synthesis and crystal structure of (NH4)[Ni3(HAsO4)(AsO4)(OH)2

The title compound, ammonium trinickel(II) hydrogen arsenate arsenate di-hydroxide, was synthesized under hydro-thermal conditions. Its crystal structure is isotypic with that of K[Cu3(HAsO4)(AsO4)(OH)2] and is characterized by pseudo-hexa-gonal (001) 2 ∞[Ni3As2O18/3(OH)6/3O1/1(OH)1/1]- layers formed from vertex- and edge-sharing [NiO4(OH)2] octa-hedra and [AsO3.5(OH)0.5] tetra-hedra as the building units. The hydrogen atom of the OH group shows occupational disorder and was refined with a site occupation factor of 1/2, indicating the equal presence of [HAsO4]2- and [AsO4]3- groups. Strong asymmetric hydrogen bonds between symmetry-related (O,OH) groups of the arsenate units [O⋯O = 2.588 (18) Å] as well as hydrogen bonds accepted by these (O,OH) groups from OH groups bonded to the NiII atoms [O⋯O = 2.848 (12) Å] link adjacent layers. Additional consolidation of the packing is achieved through N-H⋯O hydrogen bonds from the ammonium ion, which is sandwiched between adjacent layers [N⋯O = 2.930 (7) Å] although the H atoms could not be located in the present study. The presence of the pseudo-hexa-gonal 2 ∞[Ni3As2O18/3(OH)6/3O1/1(OH)1/1]- layers may be the reason for the systematic threefold twinning of (NH4)[Ni3(HAsO4)(AsO4)(OH)2] crystals. Significant overlaps of the reflections of the respective twin domains complicated the structure solution and refinement.

Crystal structure of AlFe0.95.

Three B2-type inter-metallic AlFe1 - δ phases (0.18 < δ < 0.05) in the Al-Fe binary system were synthesized by smelting and high temperature sinter-ing methods. The exact crystal structure for δ = 0.05 was refined by single-crystal X-ray diffraction. The amount of vacancy defects at the Fe atom sites was obtained by refining the corresponding site occupancy factor, converging to the chemical formula AlFe0.95, with a structure identical to that of ideal AlFe models inferred from powder X-ray or neutron diffraction patterns.

Site-occupancy factors in the Debye scattering equation. A theoretical discussion on significance and correctness.

The Debye scattering equation (DSE) [Debye (1915). Ann. Phys. 351, 809-823] is widely used for analyzing total scattering data of nanocrystalline materials in reciprocal space. In its modified form (MDSE) [Cervellino et al. (2010). J. Appl. Cryst. 43, 1543-1547], it includes contributions from uncorrelated thermal agitation terms and, for defective crystalline nanoparticles (NPs), average site-occupancy factors (s.o.f.'s). The s.o.f.'s were introduced heuristically and no theoretical demonstration was provided. This paper presents in detail such a demonstration, corrects a glitch present in the original MDSE, and discusses the s.o.f.'s physical significance. Three new MDSE expressions are given that refer to distinct defective NP ensembles characterized by: (i) vacant sites with uncorrelated constant site-occupancy probability; (ii) vacant sites with a fixed number of randomly distributed atoms; (iii) self-excluding (disordered) positional sites. For all these cases, beneficial aspects and shortcomings of introducing s.o.f.'s as free refinable parameters are demonstrated. The theoretical analysis is supported by numerical simulations performed by comparing the corrected MDSE profiles and the ones based on atomistic modeling of a large number of NPs, satisfying the structural conditions described in (i)-(iii).

Orthorhombic Crystal Structure of Grossular Garnet (Suva Česma, Western Serbia): Evidence from the Rietveld Refinement

The grossular garnet from rodingite-type rock from the Suva Česma area in western Serbia is characterized with its weak anisotropic nature. Because its anisotropy could indicate a non-cubic lower symmetry, SEM-EDS and Rietveld powder refinement methods were used. The SEM-EDS results have shown that the garnet has a (Ca3.00Mn0.01)3.01(Al1.82Fe0.15Ti0.02)1.99(Si2.97Al0.03)3.00O12 chemical composition (i.e., Grs91Adr08), which can be more specifically explained as ferric iron containing grossular. The next step further used Rietveld powder refinements of the various crystal structures in the Ia‾3d, R‾3c, R‾3, I41/a, Fddd, C2/c, and I‾1 space groups as well as a single mixture, which was followed by a comparative analysis of the R-values, site occupancy factors, and bond lengths and angles. The synthesis of these results showed both that the studied grossular garnet is not cubic and that it crystallized in the disordered Fddd space group with the final RB = 5.29% and RF = 1.75%. It was presumed that the grossular formed at temperatures between 150 and ~600 °C.

Crystal structure and Hirshfeld surface analysis of 1,6-di-amino-2-oxo-4-(thio-phen-2-yl)-1,2-di-hydro-pyridine-3,5-dicarbo-nitrile.

The asymmetric unit of the title compound, C11H7N5OS, contains two independent mol-ecules (1 and 2). The thio-phene ring in mol-ecule 2 is rotationally disordered (flip disorder) by ca 180° (around the single C-C bond, to which it is attached) over two sites with the site-occupation factors of 0.9 and 0.1. These two orientations of the thio-phene ring in mol-ecule 2 are not equivalent. In the crystal, mol-ecules are linked by inter-molecular N-H⋯O and N-H⋯N hydrogen bonds into ribbons parallel to (022) along the a axis. Within the (022) planes, these ribbons are connected by van der Waals inter-actions and between the (022) planes by N-H⋯O hydrogen bonds. In mol-ecule 1, Hirshfeld surface analysis showed that the most important contributions to the crystal packing are from N⋯H/H⋯N (27.1%), H⋯H (17.6%), C⋯H/H⋯C (13.6%) and O⋯H/H⋯O (9.3%) inter-actions, while in mol-ecule 2, H⋯H (25.4%) inter-actions are the most significant contributors to the crystal packing.

Morphology-structural change of C-A-S-H gel in blended cements

Pastes of white Portland cement (wPC) and wPC-30 % pulverized fuel ash (PFA), -60 % ground granulated blast furnace slag (GGBS), -30 % or 60 % inert filler (anatase-type TiO2) blends were prepared to investigate the dominant factors for morphological change of outer product (OP) C-A-S-H gel in blended cement systems. The OP C-A-S-H gel in SCMs-blended cements changes its morphology from fibrillar-like to mixed fine-fibrillar/foil-like when its Ca/(Si + Al) ratio < 1.30 and Al/Si ratio > 0.15. Meanwhile, the fine-fibrillar/foil-like C-A-S-H has the mean length of the aluminosilicate chain longer than 7– 8, of which, the [SiO4] bridging site occupancy factor (SOFBT) is higher than 0.6 and the [AlO4] SOFBT is higher than 0.3. The pore solutions show the characteristics of effective saturation index (ESI) of CH < −0.15 and ESI of jennite-based C-S-H gel < 0.10. The morphology of C-A-S-H gel in inert filler blends remains fibrillar throughout the hydration.

K[(CuII,MnII,MnIII)2(TeO3)3]∙2H2O, the first zemannite-type structure based on a Jahn-Teller-distorted framework

Synthetic single crystals of K[(CuII,MnII,MnIII)2(TeO3)3]·2H2O were obtained from an overconcentrated alkaline aqueous solution in the system K2O-MnO-CuO-TeO2 under hydrothermal conditions at T ≤ 220 °C. Subeuhedral single crystals have been investigated by means of single-crystal X-ray diffraction. The crystal structure of this new zemannite-type representative adopts a monoclinic twofold superstructure. The doubling of the unit-cell volume is accompanied by a hexagonal-to-monoclinic symmetry reduction, resulting in threefold twinning with individual crystal domains following the space group symmetry P21. Refinements of site-occupation factors and the evaluation of bond valences suggest a distribution of di- and trivalent cations at the octahedrally coordinated M sites with a ratio (CuII + MnII):MnIII approximating 1:1. Based on arguments about the cation sizes and the individual bond valence sums, a distribution of CuII1–xMnIIIx and MnIIx MnIII1–x at each two of the four M sites can be assumed with x between ~ 0.14 and ~ 0.50. The K+ cations and H2O molecules inside the channels are located off the central channel axis. In contrast to most other known zemannite-type phases, the extra-framework atoms show full occupancies and are not disordered. The distribution of the channel contents supports the anisotropic deformation of the surrounding framework, which follows the local symmetry reduction as required for the Jahn-Teller distortion of the octahedrally coordinated M sites within the framework. The arrangement of the deformed channels can be understood as the origin of the existing superstructure.

A comprehensive study on the thermodynamics of the Al13Fe4 solid solution in the Al-Fe-Mn ternary system

This paper presents investigations on the thermodynamic stability of the Al13Fe4 solid solution in the Al-Fe-Mn ternary system as well as its crystal chemistry characterisation. In order to carry out this study, the isobaric heat capacity of the solution was measured at high temperature using a high precision three-dimensional probe. The heat capacity of the Al13Fe4 binary compound measured in this study between 600 K and 1223 K is CP(T) = 23.97 + 8.18.10−2T − 7.63.105T2. This value is significantly different from other measurements reported in the literature. We show in this paper that our measurements are more accurate than those available in the literature thanks to the use of a more precise sensor (3D-Cp sensor versus planar DSC sensor). As a result, our measurements are more thermodynamically consistent with the enthalpy of formation values of the Al13Fe4 compound available in the literature, as well as with our own enthalpy of formation measurement performed independently of the heat capacity measurement presented in this paper. Measurements of the enthalpy of formation of the solid solution were also performed by in-situ synthesis in a DSC. These new measurements were complemented by DFT calculations of the enthalpy of formation at 0 K of the solid solution. Our calculations and measurements show that the substitution of Fe by Mn is responsible for a large increase in the solid solution enthalpy of formation. These new experimental and calculated data were used to develop a thermodynamic model of the solution. Finally, we utilized our model to calculate the Fe site occupation factors (sof) of the solid solution structure over its entire chemical composition range (simulating the complete substitution of all Fe atoms with Mn) as a function of temperature. The chemical ordering of the solid solution was thus quantified, revealing its ideal nature near its melting temperature. These results allowed the development of a new SL-model for the solution, both simpler and more reliable than those used in the literature.

Hydrogen-Induced Order–Disorder Effects in FePd3

Binary intermetallic compounds, such as FePd3, attract interests due to their physical, magnetic and catalytic properties. For a better understanding of their hydrogenation properties, both ordered FePd3 and disordered Fe0.25Pd0.75 are studied by several in situ methods, such as thermal analysis, X-ray powder diffraction and neutron powder diffraction, at moderate hydrogen pressures up to 8.0 MPa. FePd3 absorbs small amounts of hydrogen at room temperature and follows Sieverts’ law of hydrogen solubility in metals. [Pd6] octahedral voids are filled up to 4.7(9)% in a statistical manner at 8.00(2) MPa, yielding the hydride FePd3H0.047(9). This is accompanied by decreasing long-range order of Fe and Pd atoms (site occupancy factor of Fe at Wyckoff position 1a decreasing from 0.875(3) to 0.794(4)). This trend is also observed during heating, while the ordered magnetic moment decreases up to the Curie temperature of 495(8) K. The temperature dependences of the magnetic moments of iron atoms in FePd3 under isobaric conditions (p(D2) = 8.2(2) MPa) are consistent with a 3D Ising or Heisenberg model (critical parameter β = 0.28(5)). The atomic and magnetic order and hydrogen content of FePd3 show a complex interplay.

Ethyl 2-[4-(4-meth-oxy-benz-yl)-3-methyl-6-oxopyridazin-1-yl]acetate.

In the title mol-ecule, C17H20N2O4, the inner part of the ester substituent is nearly perpendicular to the di-hydro-pyridazine ring, forming a dihedral angle of 83.21 (7)°. In the crystal, inversion dimers are formed by pairwise C-H⋯O inter-actions with the dimers connected into chains extending along the b-axis direction by C-H⋯π(ring) inter-actions. The chains are connected by π-stacking inter-actions to give corrugated layers parallel to the ab plane. The terminal ethyl group is disordered over two two sets of sites with the major component having a site occupancy factor of 0.715 (10).

Ligand Modified and Light Switched On/Off Single-Chain Magnets of {Fe 2 Co} Coordination Polymers via Metal-to-Metal Charge Transfer

Ligand Modified and Light Switched On/Off Single-Chain Magnets of {Fe ₂ Co} Coordination Polymers via Metal-to-Metal Charge Transfer

Rietveld crystal structure refinement of a natural rhombohedral grossular-andradite garnet from Serbia

Four macroscopically visible B–E (rim) zones of the natural grossular-andradite garnet with Grs 58 –64 Adr 36 –42 Sps 2 composition were crystallographically studied. The applied procedure includes the Rietveld refinements of the crystal structures in a series of six space groups, which were followed by the comparative analysis of the R -values, site occupancy factors, and the bond lengths and angles. It was established that it crystallized in the rhombohedral R ‾ 3 c space group. Various polyhedral distortions and structural order-disorder variations between the studied zones were also observed, determined and discussed. Therefore, rhombohedral symmetry of the studied grandite could be treated as primary and residual strain as the second cause for its slight optical anisotropy.

The complex mechanism of Ti4+ incorporation into litidionite from the Somma–Vesuvius volcano, Italy

AbstractFor this study, the rare Cu-bearing silicate fumarolic assemblages from the Somma–Vesuvius volcano, Italy, characterised by the rare mineral litidionite, CuKNaSi4O10, were investigated. We report new data about Cu- and Ti-bearing phases found in these mineralisations, in which Ti-bearing litidionite occurs together with kamenevite, perovskite and rutile. Ti-bearing litidionite appears on the latest stages of partial crystallisation of Ti-bearing silica glass. Incorporation of Ti4+ into the litidionite crystal structure was investigated in detail. The Raman spectra of Ti-bearing litidionite contains an intense band at 597 cm−1 related to anti-symmetric bending vibrations of Si‒O bonds or overlapping stretching vibrations of Ti‒O bonds. The bands in the range 350‒500 cm−1 correspond to symmetric bending vibrations of O‒Si‒O bonds and overlapping stretching vibrations of Ti‒O bonds. The crystal structure of Ti-litidionite has been refined in the P$\bar{1}$ space group, a = 6.9699(7), b = 7.9953(10), c = 9.8227(10) Å, α = 105.186(9), β = 99.458(8) and γ = 114.489(10) to R1 = 0.064 for 1726 unique observed reflections. The refinement of the site-occupation factors confirmed the presence of Ti at a five-coordinated M site. The mean bond distance of 2.125 Å for the M site agrees with its refined occupancy (Ti0.32Cu0.30Ca0.29Fe0.09)1.00. The incorporation of Ti into the litidionite structure is accompanied by the complex heteropolyhedral substitution according to the scheme VTi4+ + VII–VIII□ + IVAl3+ ↔ VCu2+ + VII-VIII(Na,K)+ + IVSi4+. Two possible configurations for the phase with maximal TiO2 content (12.06 wt.% or 0.56 Ti apfu) CuTiK□Na2Si7AlO20 (Z = 1) or CuTiK2Na□Si7AlO20 (Z = 1) have been proposed.

Crystal structure of tris-(4,7-diphenyl-1,10-phenanthroline-κ2 N,N')cobalt(III) tris-(hexa-fluoro-phosphate) monohydrate.

The title compound, [Co(C72H48N6)](PF6)3·H2O, crystallizes with one tripositive complex mol-ecule, three hexa-fluoro-phosphate anions and one solvent mol-ecule of water in the asymmetric unit. The N6 coordination set around the central CoIII atom defines a distorted octa-hedral environment. Four fluorine atoms of one hexa-fluoro-phosphate anion are disordered over two sets of positions with site-occupancy factors of 0.697 (5) and 0.303 (5). In the crystal, inter-molecular π-π stacking inter-actions, C-H⋯π, C-H⋯F and O-H⋯F and inter-actions are present.

Crystal structure of a dicationic PdII dimer containing a 2-[(diisopropylphosphanyl)methyl]quinoline-8-thiolate pincer ligand.

A dicationic PdII dimer, bis{2-[(diisopropylphosphanyl)methyl]quinoline-8-thiolato}palladium(II) bis(hexafluoridoantimonate) dichloromethane monosolvate, [Pd2(C32H42N2P2S2)](SbF6)2·CH2Cl2, containing a 2-[(diisopropylphos-phanyl)methyl]quinoline-8-thiolate pincer ligand, was isolated and its crystal structure determined. The title compound crystallizes in the ortho-rhom-bic space group Pbca. A dimeric structure is formed by bridging coordination of the S atoms. The geometry of the butterfly-shaped Pd2S2 core is bent, with a hinge angle of 108.0 (1)° and a short Pd⋯Pd distance of 2.8425 (7) Å. These values are the lowest measured compared to ten dicationic dimers with a Pd2S2 core featuring sulfur atoms embedded in a chelating ligand. One of the two hexa-fluorido-anti-monate anions is disordered over two sets of positions with site-occupancy factors of 0.711 (5) and 0.289 (5). The crystal structure is stabilized by many C-H⋯F and C-H⋯π inter-actions, forming a supra-molecular network.

Investigating the Chemical Ordering in Quaternary Clathrate Ba8AlxGa16-xGe30.

Recently, there has been an increased interest in quaternary clathrate systems as promising thermoelectric materials. Because of their increased complexity, however, the chemical ordering in the host framework of quaternary clathrates has not yet been comprehensively analyzed. Here, we have synthesized a prototypical quaternary type-I clathrate Ba8AlxGa16–xGe30 by Czochralski and flux methods, and we employed a combination of X-ray and neutron diffraction along with atomic scale simulations to investigate chemical ordering in this material. We show that the site occupancy factors of trivalent elements at the 6c site differ, depending on the synthesis method, which can be attributed to the level of equilibration. The flux-grown samples are consistent with the simulated high-temperature disordered configuration, while the degree of ordering for the Czochralski sample lies between the ground state and the high-temperature state. Moreover, we demonstrate that the atomic displacement parameters of the Ba atoms in the larger tetrakaidecahedral cages are related to chemical ordering. Specifically, Ba atoms are either displaced toward the periphery or localized at the cage centers. Consequently, this study reveals key relationships between the chemical ordering in the quaternary clathrates Ba8AlxGa16–xGe30 and the structural properties, thereby offering new perspectives on designing these materials and optimizing their thermoelectric properties.