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Acta Crystallographica Section B

Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials publishes scientific articles related to the structural science of compounds and materials in the widest sense. Knowledge of the arrangements of atoms, including their

Published: 2017-02-01


Crystallographic features of ammonium fluoroelpasolites: dynamic orientational disorder in crystals of (NH4)3HfF7 and (NH4)3Ti(O2)F5


A classical elpasolite-type structure is considered with respect to dynamically disordered ammonium fluoro-(oxofluoro-)metallates. Single-crystal X-ray diffraction data from high quality (NH4)3HfF7 and (NH4)3Ti(O2)F5 samples enabled the refinement of the ligand and cationic positions in the cubic Fm \bar 3 m (Z = 4) structure. Electron-density atomic profiles show that the ligand atoms are distributed in a mixed (split) position instead of 24e. One of the ammonium groups is disordered near 8c so that its central atom (N1) forms a tetrahedron with vertexes in 32f. However, a center of another group (N2) remains in the 4b site, whereas its H atoms (H2) occupy the 96k positions instead of 24e and, together with the H3 atom in the 32f position, they form eight spatial orientations of the ammonium group. It is a common feature of all ammonium fluoroelpasolites with orientational disorder of structural units of a dynamic nature.

Charge density analysis of metformin chloride, a biguanide anti-hyperglycemic agent


The experimental charge density analysis of the anti-hyperglycemic agent metformin chloride with high-resolution X-ray diffraction data at low temperature (100 K) has been performed and these experimental results were compared with that derived from the corresponding periodic theoretical calculations at the B3LYP/6-31G** level of theory. The experimental and theoretical multipolar charge-density analyses of metformin chloride have been accomplished in order to understand its structural and electronic properties. The C and N atoms of the molecular backbone adopt a near trigonal geometry due to the occurrence of extensive delocalization/resonance of C—N bonds, as confirmed by topological analysis and also found by Natural Resonance Theory calculations performed in the isolated metformin cation. The molecule contains six C—N bonds and the topological bond order analysis shows that four bonds have bond orders close to 4/3 and two bonds can be considered as single. The analysis of numerical parameters of the valence shell charge concentration reports that the N3 atom, which forms two bonds with C atoms, possesses one non-bonding valence-shell charge concentration (VSCC) in the direction of the electron lone pair. Among the intermolecular interactions of the chloride atom with the H—C and H—N atoms, eight have been found to be shorter than the sum of van der Waals radii. The analysis of contacts on the Hirshfeld surface reveals that the H—N...Cl hydrogen bonds are enriched (over-represented) and act as the driving force in the crystal packing formation. The metformin cations form favorable electrostatic interactions with the chloride anions which have globally a stronger energy than the unfavorable cation/cation interactions.

A priori checking of the light-response and data quality before extended data collection in pump–probe photocrystallography experiments


In picosecond and slower pump–probe diffraction experiments, collection of response–ratio correlation sets prior to full data collection provides an invaluable confirmation of the existence of a light-induced signal prior to full data collection. If a response to light exposure is observed, the quality of the data being collected can be assessed. A number of such correlation plots both for synchrotron and in-house pump–probe data collection are presented.

Deformations of the α-Fe2O3 rhombohedral lattice across the Néel temperature


High-resolution synchrotron radiation powder diffraction patterns of α-Fe2O3 measured between room temperature and 1100 K, i.e. above the Néel temperature TN = 950 K, have been analyzed. The integral breadths of the Bragg peaks show a hkl-dependent anisotropy, both below and above TN. This anisotropy can be quantitatively described by using a statistical peak-broadening model [Stephens (1999). J. Appl. Cryst. 32, 281]. Model calculations show that the rhombohedral α-Fe2O3 lattice is deformed and the deformation leads to a monoclinic lattice with the unique monoclinic axis along the hexagonal [110] direction both below and above TN. The monoclinic symmetry of bulk α-Fe2O3 is compatible with α-Fe2O3 nanowire growth along the [110] direction reported in Fu et al. [Chem. Phys. Lett. (2001), 350, 491].

Isothermal equation of state and high-pressure phase transitions of synthetic meridianiite (MgSO4·11D2O) determined by neutron powder diffraction and quasielastic neutron spectroscopy


We have collected neutron powder diffraction data from MgSO4·11D2O (the deuterated analogue of meridianiite), a highly hydrated sulfate salt that is thought to be a candidate rock-forming mineral in some icy satellites of the outer solar system. Our measurements, made using the PEARL/HiPr and OSIRIS instruments at the ISIS neutron spallation source, covered the range 0.1 < P < 800 MPa and 150 < T < 280 K. The refined unit-cell volumes as a function of P and T are parameterized in the form of a Murnaghan integrated linear equation of state having a zero-pressure volume V0 = 706.23 (8) Å3, zero-pressure bulk modulus K0 = 19.9 (4) GPa and its first pressure derivative, K′ = 9 (1). The structure's compressibility is highly anisotropic, as expected, with the three principal directions of the unit-strain tensor having compressibilities of 9.6 × 10−3, 3.4 × 10−2 and 3.4 × 10−3 GPa−1, the most compressible direction being perpendicular to the long axis of a discrete hexadecameric water cluster, (D2O)16. At high pressure we observed two different phase transitions. First, warming of MgSO4·11D2O at 545 MPa resulted in a change in the diffraction pattern at 275 K consistent with partial (peritectic) melting; quasielastic neutron spectra collected simultaneously evince the onset of the reorientational motion of D2O molecules with characteristic time-scales of 20–30 ps, longer than those found in bulk liquid water at the same temperature and commensurate with the lifetime of solvent-separated ion pairs in aqueous MgSO4. Second, at ∼ 0.9 GPa, 240 K, MgSO4·11D2O decomposed into high-pressure water ice phase VI and MgSO4·9D2O, a recently discovered phase that has hitherto only been formed at ambient pressure by quenching small droplets of MgSO4(aq) in liquid nitrogen. The fate of the high-pressure enneahydrate on further compression and warming is not clear from the neutron diffraction data, but its occurrence indicates that it may also be a rock-forming mineral in the deep mantles of large icy satellites.

Structure, thermal expansion and incompressibility of MgSO4·9H2O, its relationship to meridianiite (MgSO4·11H2O) and possible natural occurrences


Since being discovered initially in mixed-cation systems, a method of forming end-member MgSO4·9H2O has been found. We have obtained powder diffraction data from protonated analogues (using X-rays) and deuterated analogues (using neutrons) of this compound over a range of temperatures and pressures. From these data we have determined the crystal structure, including all hydrogen positions, the thermal expansion over the range 9–260 K at ambient pressure, the incompressibility over the range 0–1.1 GPa at 240 K and studied the transitions to other stable and metastable phases. MgSO4·9D2O is monoclinic, space group P21/c, Z = 4, with unit-cell parameters at 9 K, a = 6.72764 (6), b = 11.91154 (9), c = 14.6424 (1) Å, β = 95.2046 (7)° and V = 1168.55 (1) Å3. The structure consists of two symmetry-inequivalent Mg(D2O)6 octahedra on sites of \bar 1 symmetry. These are directly joined by a water–water hydrogen bond to form chains of octahedra parallel with the b axis at a = 0. Three interstitial water molecules bridge the Mg(D2O)6 octahedra to the SO42− tetrahedral oxyanion. These tetrahedra sit at a ≃ 0.5 and are linked by two of the three interstitial water molecules in a pentagonal motif to form ribbons parallel with b. The temperature dependences of the lattice parameters from 9 to 260 K have been fitted with a modified Einstein oscillator model, which was used to obtain the coefficients of the thermal expansion tensor. The volume thermal expansion coefficient, αV, is substantially larger than that of either MgSO4·7D2O (epsomite) or MgSO4·11D2O (meridianiite), being ∼ 110 × 10−6 K−1 at 240 K. Fitting to a Murnaghan integrated linear equation of state gave a zero-pressure bulk modulus for MgSO4·9D2O at 240 K, K0 = 19.5 (3) GPa, with the first pressure derivative of the bulk modulus, K′ = 3.8 (4). The bulk modulus is virtually identical to meridianiite and only ∼ 14% smaller than that of epsomite. Above ∼ 1 GPa at 240 K the bulk modulus begins to decrease with pressure; this elastic softening may indicate a phase transition at a pressure above ∼ 2 GPa. Synthesis of MgSO4·9H2O from cation-pure aqueous solutions requires quench-freezing of small droplets, a situation that may be relevant to spraying of MgSO4-rich cryomagmas into the surface environments of icy satellites in the outer solar system. However, serendipitously, we obtained a mixture of MgSO4·9H2O, mirabilite (Na2SO4·10H2O) and ice by simply leaving a bottle of mid-winter brine from Spotted Lake (Mg/Na ratio = 3), British Columbia, in a domestic freezer for a few hours. This suggests that MgSO4·9H2O can occur naturally – albeit on a transient basis – in certain terrestrial and extraterrestrial environments.

An unusual case of OD-allotwinning: 9,9′-(2,5-dibromo-1,4-phenylene)bis[9H-carbazole]


9,9′-(2,5-Dibromo-1,4-phenylene)bis[9H-carbazole] (1) crystallizes as a category I order–disorder (OD) structure composed of non-polar layers of one kind with B2/m(1)1 layer symmetry. The crystals are made up of the two polytypes with a maximum degree of order (MDO). The monoclinic MDO1 polytype (B21/d) possesses an orthorhombic B-centered lattice and appears in two orientations, which are related by reflection at (100). The orthorhombic MDO2 polytype (F2dd) has a doubled b-axis and appears in two orientations, which are related by inversion. The crystal structures of both polytypes were determined in a concurrent refinement. The MDO1:MDO2 ratio is 69:31.

Crystal structure prediction by ionic network analysis: the example of (p–T–X)-structure relationships in olivines


The method of Ionic Network Analysis (INA) is defined by reference to the known crystal structures of olivine minerals. It is based on a reversible transformation between two alternative representations of ionic crystal structures: (a) the crystallographic and (b) the interactional. Whereas the former encompasses unit-cell parameters and atomic coordinates, the latter consists of selected interaction vectors between ions. Since the lengths and orientations of these vary only slightly between crystal structures obtained under systematically varying (p, T, X) conditions, they may be used to predict the crystal structures at intermediate (p, T, X) values by interpolation. Two interactional networks are constructed, one for the anions and the other for cations. As both networks lead to independent calculated values of the unit-cell parameters, it is possible to exploit the known, continuous (p, T, X) variations of cell parameters as normative constraints for the prediction of atomic coordinates within a predictive structural refinement procedure. Continuously varying structurally based parameters such as the volumes of cation coordination polyhedra may likewise be used. The choice of olivines for developing the method has been guided by the availability of pressure, temperature and compositional structural data for them. However, the ideas are expounded sufficiently generally for the method to be applied to other minerals.

Neutron and X-ray investigations of the Jahn–Teller switch in partially deuterated ammonium copper Tutton salt, (NH4)2[Cu(H2O)6](SO4)2


The structural phase transition accompanied by a Jahn–Teller switch has been studied over a range of H/D ratios in (NH4)2[Cu(H2O)6](SO4)2 (ACTS). In particular, single-crystal neutron diffraction investigations of crystals with deuteration in the range 50 to 82% are shown to be consistent with previous electron paramagnetic resonance (EPR) experiments exhibiting a phase boundary at 50% deuteration under ambient pressure. Polycrystalline samples show that the two phases can co-exist. In addition, single-crystal neutron and polycrystalline X-ray diffraction pressure experiments show a shift to lower pressure at 60% deuteration versus previous measurements at 100% deuteration.

A revised interpretation of the structure of (NH4)2Ge7O15 in the light of the Extended Zintl–Klemm Concept


The structure of (NH4)2Ge7O15 recently described as being a microporous material containing rings, in which GeO6 octahedra coexist with GeO4 tetrahedra, is re-examined in the light of the Extended Zintl–Klemm Concept as applied to cations in oxides. The Ge[6] atoms together with the NH4+ groups act as true cations, transferring their 6 valence electrons to the acceptor Ge2O5 moiety, so converting it into the [Ge6O15]6−[triple-bond]3(Ψ-As2O5) ion (where Ψ refers to a pseudo-lattice) and yielding threefold connectivity. The tetrahedral Ge network shows similarities with the Sb2O3 analogue. At the same time, the Ge[6] atoms are connected to other Ge[4] atoms forming blocks that are part of a rutile-type GeO2 structure. Such an analysis shows that both substructures (the Zintl polyanion and the rutile fragments) must be satisfied simultaneously as has already been illustrated in previous articles which considered stuffed-bixbyites [Vegas et al. (2009). Acta Cryst. B65, 11–21] as well as the compound FeLiPO4 [Vegas (2011). Struct. Bond. 138, 67–91]. This new insight conforms well to previous (differential thermal analysis) DTA–TGA (thermogravimetric analysis) experiments [Cascales et al. (1998). Angew. Chem. Int. Ed. 37, 129–131], which show endothermic loss of NH3 and H2O to give rise to the metastable structure Ge7O14, which further collapses to the rutile-type GeO2 structure. We analyze the stability change in terms of ionic strength, I, and so provide a means of rationalizing the driving force behind this concept capable of explaining the atomic arrangements found in these types of crystal structures. Although the concept was formulated in 2003, later than the publication of the germanate structure, it was not used or else ignored by colleagues who solved this crystal structure.

Formation of co-racemic uranyl chromate constructed from chiral layers of different topology


Four new inorganic uranyl chromates were obtained by evaporation and hydrothermal methods: [(CH3)2NH2]2[(UO2)2(CrO4)3(H2O)](H2O) (1), K(Rb0.6K0.4)[(UO2)2(CrO4)3(H2O)](H2O)3 (2) [(CH3)3CNH3]2[(UO2)2(CrO4)3H2O] (3), [(CH3)2NH2]4[(UO2)2(CrO4)3H2O]2(H2O) (4). Their structures are based on two-dimensional chiral or achiral units with the composition [(UO2)2(CrO4)3(H2O)]2− and two types of topologies (A or/and B). The structural architecture of (4) is unique amongst all known uranyl-based structures, and unusual among hybrid organic/inorganic structures in general as it contains layers of identical composition, but of different topology. The unique structural configurations and non-centrosymmetry in (1) and (4) is governed by selective formation of hydrogen bonding rather than by the formation of hydrophobic and hydrophilic zones in the organic interlayer. It is shown that chiral architectures in uranyl systems may form from achiral building units as observed in (3) and (4). This is somewhat analogous to certain organic compounds, where achiral molecules are also able to form chiral layers. Within the concept of such an interpretation the structure of (3) can then be described as a racemate consisting of two A and A′ chiral layers. In a similar approach the structure of (4) can be interpreted as being formed by four chiral layers. Layer pairs AA′ and BB′ can then be considered as racemic pairs and the whole structure is a co-racemate built by a combination of two racemates. Two-stage formation can be suggested for (4).

Synchrotron X-ray diffuse scattering from a stable polymorphic material: terephthalic acid, C8H6O4


Terephthalic acid (TPA, C8H6O4) is an industrially important chemical, one that shows polymorphism and disorder. Three polymorphs are known, two triclinic [(I) and (II)] and one monoclinic (III). Of the two triclinic polymorphs, (II) has been shown to be more stable in ambient conditions. This paper presents models of the local order of polymorphs (I) and (II), and compares the single-crystal diffuse scattering (SCDS) computed from the models with that observed from real crystals. TPA shows relatively weak and less-structured diffuse scattering than some other polymorphic materials, but it does appear that the SCDS is less well modelled by a purely harmonic model in polymorph (I) than in polymorph (II), according to the idea that the diffuse scattering is sensitive to anharmonicity that presages a structural phase transition. The work here verifies that displacive correlations are strong along the molecular chains and weak laterally, and that it is not necessary to allow the —COOH groups to librate to successfully model the diffuse scattering – keeping in mind that the data are from X-ray diffraction and not directly sensitive to H atoms.

Structures and thermal stability of the α-LiNH4SO4 polytypes doped with Er3+ and Yb3+


In order to clarify the polymorphism in the lithium sulfate family, LiREx(NH4)1 − xSO4 (0.5 ≤ x ≤ 4.0 mol%, nominal value; RE = Er3+, Yb3+ and Dy3+) crystals were grown from aqueous solution by slow evaporation between 298 and 313 K. The doping of the samples allowed us to obtain two polymorphic forms, α and β, of LiNH4SO4 (LAS). By means of X-ray diffraction (XRD) in single crystals, we determined the crystal structures of two new α-polytypes, which we have named α1- and α2-LAS. They present the same space group P21/c and the following relation among their lattice parameters: a2 = −c1, b2 = −b1, c2 = −2a1 − c1. In order to evaluate the stability of the new α-polytypes, we performed thermal analysis, X-ray diffraction and dielectric spectroscopy on single crystals and polycrystalline samples over the cyclic temperature range: 190 → 575  → 190 K. The results obtained by all the techniques used in this study demonstrate that α-polytypes are stable across a wide range of temperatures and they show an irreversible phase transition to the paraelectric β-phase above 500 K. In addition, a comparative study of α- and β-polytypes shows that both polymorphic structures have a common axis, with a possible intergrowth that facilitates their coexistence and promotes the reconstructive α → β transition. This intergrowth was related to small anomalies detected between 240 and 260 K, in crystals with an α-habit.