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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: 2017-06-01

 



Is there a future for topological analysis in experimental charge-density research?

2017-06-01

Topological analysis using Bader and co-worker's Atoms in Molecules theory has seen many applications in theoretical chemistry and experimental charge-density research. A brief overview of successful early developments, establishing topological analysis as a research tool for characterizing intramolecular chemical bonding, is provided. A lack of vision in many `descriptive but not predictive' subsequent studies is discussed. Limitations of topology for providing accurate energetic estimates of intermolecular interaction energies are put into perspective. It is recommended that topological analyses of well understood bonding situations are phased out and are only reported for unusual bonding. Descriptive studies of intermolecular interactions should have a clear research focus.



The future of topological analysis in experimental charge-density research

2017-06-01

In a recent paper, Dittrich (2017) critically discussed the benefits of analysing experimental electron density within the framework of the quantum theory of atoms in molecules, often called simply the topological analysis of the charge density. The point he raised is important because it challenges the scientific production of a very active community. The question whether this kind of investigation is still sensible is intriguing and it fosters a multifaceted answer. Granted that none can predict the future of any field of science, but an alternative point of view emerges after answering three questions: Why should we investigate the electron charge (and spin) density? Is the interpretative scheme proposed by the quantum theory of atoms in molecules useful? Is an experimental charge density necessary?



Temperature-induced reversible structural phase transition and X-ray diffuse scattering in 2-amino-3-nitropyridinium hydrogen sulfate

2017-05-12

The novel polar material 2-amino-3-nitropyridinium hydrogen sulfate, C5H6N3O2(HSO4) (abbreviated as 2A3NP-HS), was obtained and structurally characterized by means of single-crystal X-ray diffraction. At room temperature, 2A3NP-HS crystallizes as a non-centrosymmetric disordered phase (I) in the orthorhombic Pna21 space group. On cooling below 298 K, 2A3NP-HS undergoes a reversible phase transition to phase (II) with the monoclinic non-centrosymmetric P21 space group. This transition might be classified as an `order–disorder' type. The structural details in both phases are analysed. Additionally, for phase (I), in the 304–365 K temperature range, diffuse scattering was found to be present in the form of elongated streaks parallel to the a* direction. This can be unravelled when implementing a short-range order affecting anionic cationic ribbons occurring in the structure, with correlations acting both in the a-direction and in the bc-plane. The results of Monte Carlo simulations, adapting a two-dimensional Ising-type model, reveal the formation of domains, which are b-elongated and thin along a. Locally, the stacking of the ribbons in the domains reflects the ordered arrangement observed in the low-temperature monoclinic phase (II).



Growth, crystal structure, Hirshfeld surface, optical, piezoelectric, dielectric and mechanical properties of bis(l-asparaginium hydrogensquarate) single crystal

2017-05-12

Molecular organic single crystals of bis(l-asparaginium hydrogensquarate) monohydrate [BASQ; (C8H10N2O7)2·H2O] have been grown by solution technique. Crystallographic information was investigated by single-crystal X-ray diffraction (SCXRD) analysis. Hirshfeld surface and fingerprint plot studies were performed to understand the intermolecular interactions of the BASQ crystal in graphical representation. Functional group identification was studied with FT–IR (Fourier transform–IR) spectroscopy. The positions of proton and carbon atoms in the BASQ compound were analyzed using NMR spectroscopy. High transparency and a wide band gap of 3.49 eV were observed in the linear optical study by UV–vis–NIR spectroscopy. Intense and broad photoluminescence emissions at room temperature were observed in blue and blue–green regions. The frontier molecular orbitals of the BASQ molecule were obtained by the DFT/B3LYP method employing 6-311G** as the basis set. The dielectric study was carried out with temperature at various frequency ranges. The piezoelectric charge coefficient (d33) value of BASQ crystal was found to be 2 pC/N, which leads to its application in energy harvesting, mechanical sensors and actuators applications. In the non-linear optical study, the BASQ crystal showed promising SHG conversion efficiency. Mechanical properties of the BASQ crystal were studied experimentally by Vicker's microhardness technique, which revealed that the grown crystal belonged to the softer category. BASQ crystal void estimation reveals the mechanical strength and porosity of the material.



Identification of a deleterious phase in photocatalyst based on Cd1 − xZnxS/Zn(OH)2 by simulated XRD patterns

2017-05-12

The X-ray diffraction (XRD) pattern of a deleterious phase in the photocatalyst based on Cd1 − xZnxS/Zn(OH)2 contains two relatively intense asymmetric peaks with d-spacings of 2.72 and 1.56 Å. Very small diffraction peaks with interplanar distances of (d) ≃ 8.01, 5.40, 4.09, 3.15, 2.49 and 1.35 Å are characteristic of this phase but not always observed. To identify this phase, the XRD patterns for sheet-like hydroxide β-Zn(OH)2 and sheet-like hydrozincite Zn5(CO3)2(OH)6 as well as for turbostratic hydrozincite were simulated. It is shown that the XRD pattern calculated on the basis of the last model gives the best correspondence with experimental data. Distances between layers in the turbostratically disordered hydrozincite fluctuate around d ≃ 8.01 Å. This average layer-to-layer distance is significantly higher than the interlayer distance 6.77 Å in the ordered Zn5(CO3)2(OH)6 probably due to a deficiency of CO32− anions, excess OH− and the presence of water molecules in the interlayers. It is shown by variable-temperature XRD and thermogravimetric analysis (TGA) that the nanocrystalline turbostratic nonstoichiometric hydrozincite-like phase is quite thermostable. It decomposes into ZnO in air above 473 K.



Could incommensurability in sulfosalts be more common than thought? The case of meneghinite, CuPb13Sb7S24

2017-05-12

The structure of meneghinite (CuPb13Sb7S24), from the Bottino mine in the Apuan Alps (Italy), has been solved and refined as an incommensurate structure in four-dimensional superspace. The structure is orthorhombic, superspace group Pnma(0β0)00s, cell parameters a = 24.0549 (3), b = 4.1291 (6), c = 11.3361 (16) Å, modulation vector q = 0.5433 (4)b*. The structure was refined from 6604 reflections to a final R = 0.0479. The model includes modulation of both atomic positions and displacement parameters, as well as occupational waves. The driving forces stabilizing the modulated structure of meneghinite are linked to the occupation modulation of Cu and some of the Pb atoms. As a consequence of the Cu/[] and Pb/Sb modulations, three- to sevenfold coordinations of the M cations (Pb/Sb) occur in different parts of the structure. The almost bimodal distribution of the occupation of Cu/[] and Pb/Sb at M5 conforms with the coupled substitution Sb3+ + [] → Pb2+ + Cu+, thus corroborating the hypothesis deduced previously for the incorporation of copper in the meneghinite structure. The very small departure (∼0.54 versus 0.50) from the commensurate value of the modulation raises the question of whether other sulfosalts considered superstructures have been properly described, and, in this light, if incommensurate modulation in sulfosalts could be much more common than thought.



Ordered vacancy distribution in 2/1 mullite: a superspace model

2017-05-12

A mullite single crystal with composition Al4.84Si1.16O9.58 (2) exhibiting sharp satellite reflections was investigated by means of X-ray diffraction. For the refinement of a superspace model in the superspace group Pbam(α0½)0ss different scale factors for main and satellite reflections were used in order to describe an ordered mullite structure embedded in a disordered polymorph. The ordered fraction of the mullite sample exhibits a completely ordered vacancy distribution and can be described as a block structure of vacancy blocks (VBs) that alternate with vacancy-free blocks (VFBs) along a and c. The incommensurate nature of mullite originates from a modulation of the block size, which depends on the composition. The displacive modulation is analyzed with respect to the vacancy distribution and a possible Al/Si ordering scheme is derived, although the measurement itself is not sensitive to the Al/Si distribution. An idealized, commensurate approximation for 2/1 mullite is also presented. Comparison of the ordered superspace model with different preceding models reconciles many key investigations of the last decades with partly contradicting conclusions, where mullite was usually treated as either ordered or disordered instead of considering simultaneously different states of order.



The impact of anion ordering on octahedra distortion and phase transitions in SrTaO2N and BaTaO2N

2017-06-01

In this work we synthesized BaTaO2N and SrTaO2N using a two-step high-temperature solid-state reaction method and analysed the structural distortions, relative to the ideal cubic perovskite structure, according to group theory. From a complete distortion analysis/refinement using high-resolution neutron diffraction data in the temperature range 8 to 613 K, we identified tetragonal structures for BaTaO2N [P4/mmm (No. 123)] and SrTaO2N [I4/mcm (No. 140)]. In contrast to an anion-disordered cubic perovskite (Pm \overline{3}m No. 221) with Ta at the cell center, both systems show a site preference for oxygen anions in the two opposite corners (along the c axis) of the Ta–O/N octahedra rather than the four square corners in the ab plane (Γ3+ occupancy distortion), which induces a tetragonal elongation of the unit cell with the c axis being longer than the a axis. A further Ta–O/N octahedra displacement [R5−(a,0,0), rotation about the c axis] distortion was observed in SrTaO2N. This distortion mode is accompanied by an increased unit-cell distortion that decreases as the temperature increases. Ultimately a second-order phase transition caused by the loss of the R5−(a,0,0) mode was observed at 400–450 K.



Synthesis, crystallization, X-ray structural characterization and solid-state assembly of a cyclic hexapeptoid with propargyl and methoxyethyl side chains

2017-06-01

The synthesis and the structural characterization of a cyclic hexapeptoid with four methoxyethyl and two propargyl side chains have disclosed the presence of a hydrate crystal form [form (I)] and an anhydrous crystal form [form (II)]. The relative amounts of form (I) and form (II) in the as-purified product were determined by Rietveld refinement and depend on the purification procedures. In crystal form (I), peptoid molecules assemble in a columnar arrangement by means of side-chain-to-backbone C=CH...OC hydrogen bonds. In the anhydrous crystal form (II), cyclopeptoid molecules form ribbons by means of backbone-to-backbone CH2...OC hydrogen bonds, thus mimicking β-sheet secondary structures in proteins. In both crystal forms side chains act as joints among the columns or the ribbons and contribute to the stability of the whole solid-state assembly. Water molecules in the hydrate crystal form (I) bridge columns of cyclic peptoid molecules, providing a more efficient packing.



An ordering phase transition, short hydrogen bonds and high Z′ in the structure of Ni(Hpydc)2·3H2O

2017-06-01

The structure of Ni(Hpydc)2·3H2O (H2pydc = pyridine-2,6-dicarboxylic acid, also known as dipicolinic acid) has been reinvestigated at variable temperatures. At room temperature, it matches the known structure in the space group P21/c, but at 180 K it undergoes a phase transformation to a twinned structure in Cc. By 120 K, the structure is ordered and twinned with Z′ = 4, and shows interesting short hydrogen-bonding interactions that include the formation of hydroxonium species.



Structural and Raman spectroscopic characterization of pyroxene-type compounds in the CaCu1−xZnxGe2O6 solid-solution series

2017-06-01

Pyroxene-type germanate compounds with the composition CaCuGe2O6–CaZnGe2O6 have been synthesized via a solid-state ceramic sintering route. Phase-pure polycrystalline and small single-crystal material was obtained all over the series, representing a complete solid-solution series. Differential thermal analysis, single-crystal X-ray diffraction and Raman spectroscopy were used to characterize phase stability, phase changes and structural alterations induced by the substitution of Cu2+ with Zn2+. Whereas pure CaCuGe2O6 exhibits P21/c symmetry with a strong distortion of the M1 octahedra and two different Ge sites, one of them with an unusual fivefold coordination, the replacement of Cu2+ by Zn2+ induces a chemically driven phase change to the C2/c symmetry. The phase change takes place around Zn2+ contents of 0.12 formula units and is associated with large changes in the unit-cell parameters. Here, the increase of c by as much as 3.2% is remarkable and it is mainly controlled by an expansion of the tetrahedral chains. Further differences between the P21/c and C2/c structures are a more regular chain of edge-sharing M1 octahedra as a consequence of more and more reduced Jahn–Teller distortion and a less kinked, symmetry-equivalent tetrahedral chain. The coordination of the Ca site increases from sevenfold to eightfold with large changes in the Ca—O bond lengths during the phase change. Raman spectroscopy was mainly used to monitor the P21/c to C2/c phase change as a function of composition, but also as a function of temperature and to follow changes in specific Raman modes throughout the solid-solution series.



Formation and distortion of iodidoantimonates(III): the first isolated [SbI6]3− octahedron

2017-06-01

The ability to intentionally construct, through different types of interactions, inorganic–organic hybrid materials with desired properties is the main goal of inorganic crystal engineering. The primary deformation, related to intrinsic interactions within inorganic substructure, and the secondary deformation, mainly caused by the hydrogen bond interactions, are both responsible for polyhedral distortions of halogenidoantimonates(III) with organic cations. The evolution of structural parameters, in particular the Sb—I secondary- and O/N/C—H...I hydrogen bonds, as a function of temperature assists in understanding the contribution of those two distortion factors to the irregularity of [SbI6]3− polyhedra. In tris(piperazine-1,4-diium) bis[hexaiodidoantimonate(III)] pentahydrate, (C4H12N2)3[SbI6]2·5H2O (TPBHP), where the isolated [SbI6]3– units were found, distortion is governed only by O/N/C—H...I hydrogen bonds, whereas in piperazine-1,4-diium bis[tetraiodidoantimonate(III)] tetrahydrate, (C4H12N2)[SbI4]2·4H2O (PBTT), both primary and O—H...I secondary factors cause the deformation of one-dimensional [{SbI4}n]n− chains. The larger in spatial dimensions piperazine-1,4-diium cations, in contrast to the smaller water of crystallization molecules, do not significantly contribute to the octahedral distortion, especially in PBTT. The formation of isolated [SbI6]3− ions in TPBHP is the result of specific second coordination sphere hydrogen bond interactions that stabilize the hybrid structure and simultaneously effectively separate and prevent [SbI6]3− units from mutual interactions. The temperature-induced changes, further supported by the analysis of data retrieved from the Cambridge Structural Database, illustrate the significance of both primary and secondary distortion factors on the deformation of octahedra. Also, a comparison of packing features in the studied hybrids with those in the non-metal containing piperazine-1,4-diium diiodide diiodine (C4H12N2)I2·I2 (PDD) confirms the importance and hierarchy of different types of interactions.



Die Symmetrie von Spiralketten

2017-06-01

In crystals, polymeric chain molecules often adopt helical structures. Neglecting small distortions possibly caused by an anisotropic environment within the crystal, the symmetry of the single helix can be described by a rod group, which has translational symmetry in one dimension. The rod groups have Hermann–Mauguin symbols similar to space groups, beginning with a script style \scr p followed by a screw-axis symbol; the order of the screw axis can adopt any value. In a crystal, the rod-site symmetry, the so-called penetration rod group, must be a common crystallographic rod subgroup of the molecular rod group and the space group. Instructions are given for the derivation of the rod subgroups in question for a molecular helical rod group of any order. In polymer chemistry, a helix is designated by a (chemical) symbol like 7/2, which means 7 repeating units in 2 coil turns of covalent bonds per translational period. The corresponding Hermann–Mauguin screw-axis symbol is easily derived with a simple formula from this chemical symbol; for a 7/2 helix it is 73 or 74, depending on chirality. However, it is not possible to deduce the chemical symbol from the Hermann–Mauguin symbol, because it depends on where the covalent bonds are assumed to exist. Covalent bonds are irrelevant for symmetry considerations; a symmetry symbol does not depend on them. A chemically right-handed helix can have a left-handed screw axis. The derivation of the Hermann–Mauguin symbol of a multiple helix is not that easy, as it depends on the mutual position of the interlocked helices; conversion formulae for simpler cases are presented. Instead of covalent bonds, other kinds of linking can serve to define the chemical helix, for example, edge- or face-sharing coordination polyhedra.



Searching for stereoisomerism in crystallographic databases: algorithm, analysis and chiral curiosities

2017-06-01

The automated identification of chiral centres in molecular residues is a non-trivial task. Current tools that allow the user to analyze crystallographic data entries do not identify chiral centres in some of the more complex ring structures, or lack the possibility to determine and compare the chirality of multiple structures. This article presents an approach to identify asymmetric C atoms, which is based on the atomic walk count algorithm presented by Rücker & Rücker [(1993), J. Chem. Inf. Comput. Sci. 33, 683–695]. The algorithm, which we implemented in a computer program named ChiChi, is able to compare isomeric residues based on the chiral centres that were identified. This allows for discrimination between enantiomers, diastereomers and constitutional isomers that are present in crystallographic databases. ChiChi was used to process 254 354 organic entries from the Cambridge Structural Database (CSD). A thorough analysis of stereoisomerism in the CSD is presented accompanied by a collection of chiral curiosities that illustrate the strength and versatility of this approach.



Sr1/2Ce5/14□1/7WO4: a new modulated ternary scheelite compound

2017-06-01

For the first time, a ternary tetragonal scheelite structure tungstate with strontium and cerium cations, (Sr,Ce)WO4, was synthesized. As much as 35% Ce could be inserted into the structure, leaving 1\over 7 of the (Sr,Ce) cation sites vacant. Partial ordering of Sr and Ce, with atomic displacements, were shown by high-resolution electron microscopy. Two-dimensional incommensurate modulations occur in this material, in small domains 20 nm in size. The band gap of this compound is significantly lower than the band gap of SrWO4 and this was related to the distortions of WO4 and (Sr,Ce)O8 polyhedra. The band gap value of 3.2 eV makes Sr1/2Ce5/14□1/7WO4 a promising candidate for violet luminescence.



The hydrogen bond between N—H or O—H and organic fluorine: favourable yes, competitive no

2017-06-01

A study was made of X—H...F—C interactions (X = N or O) in small-molecule crystal structures. It was primarily based on 6728 structures containing X—H and C—F and no atom heavier than chlorine. Of the 28 451 C—F moieties in these structures, 1051 interact with X—H groups. However, over three-quarters of these interactions are either the weaker components of bifurcated hydrogen bonds (so likely to be incidental contacts) or occur in structures where there is a clear insufficiency of good hydrogen-bond acceptors such as oxygen, nitrogen or halide. In structures where good acceptors are entirely absent, there is about a 2 in 3 chance that a given X—H group will donate to fluorine. Viable alternatives are X—H...π hydrogen bonds (especially to electron-rich aromatics) and dihydrogen bonds. The average H...F distances of X—H...F—C interactions are significantly shorter for CR3F (R = C or H) and Csp2—F acceptors than for CRF3. The X—H...F angle distribution is consistent with a weak energetic preference for linearity, but that of H...F—C suggests a flat energy profile in the range 100–180°. X—H...F—C interactions are more likely when the acceptor is Csp2—F or CR3F, and when the donor is C—NH2. They also occur significantly more often in structures containing tertiary alcohols or solvent molecules, or with Z′ > 1, i.e. when there may be unusual packing problems. It is extremely rare to find X—H...F—C interactions in structures where there are several unused good acceptors. When it does happen, there is often a clear reason, e.g. awkwardly shaped molecules whose packing isolates a donor group from the good acceptors.



Synthesis and crystal structure of pyrroloquinoline quinol (PQQH2) and pyrroloquinoline quinone (PQQ)

2017-06-01

Pyrroloquinoline quinone (PQQ) is a water-soluble quinone compound first identified as a cofactor of alcohol- and glucose-dehydrogenases (ADH and GDH) in bacteria. For example, in the process of ADH reaction, alcohol is oxidized to the corresponding aldehyde, and inversely PQQ is reduced to pyrroloquinoline quinol (PQQH2). PQQ and PQQH2 molecules play an important role as a cofactor in ADH and GDH reactions. However, crystal structure analysis has not been performed for PQQ and PQQH2. In the present study, the synthesis of PQQH2 powder crystals was performed under air, by utilizing vitamin C as a reducing agent. By reacting a trihydrate of disodium salt of PQQ (PQQNa2·3H2O) with excess vitamin C in H2O at 293 and 343 K, yellowish brown and black powder crystals of PQQH2 having different properties were obtained in high yield, respectively. The former was PQQH2 trihydrate (PQQH2·3H2O) and the latter was PQQH2 anhydrate (PQQH2). Furthermore, sodium-free red PQQ powder crystal (a monohydrate of PQQ, PQQ·H2O) was prepared by the reaction of PQQNa2·3H2O with HCl in H2O. Single crystals of PQQH2 and PQQ were prepared from Me2SO/CH3CN mixed solvent, and we have succeeded in the crystal structure analyses of PQQH2 and PQQ for the first time.



Crystallographic and optical study of LiNb1 − xTaxO3

2017-06-01

Powders of lithium niobate-tantalate across the full compositional range have been made and crystals grown using a lithium vanadate flux growth technique. The Li-content of a lithium tantalate crystal has been determined using the zero-birefringence temperature and Curie measurements, confirming the Li content is between that of congruent and stoichiometric crystals. X-ray diffraction measurements show the Nb/Ta displacement and octahedral tilt both decrease as the Ta content is increased. This also results in a decrease in the lattice parameters from lithium niobate to lithium tantalate. Birefringence measurements on the crystals as a function of temperature have been used to determine the point that the crystals become zero-birefringent, and by comparison with the structural studies have confirmed that it is not related to a phase transition and the structures remain polar through the zero-birefringence points.



Chiral and achiral crystals, charge-assisted hydrogen-bond patterns and self-organization of selected solid diaminium thiosulfates

2017-06-01

A series of diaminium thiosulfates, derivatives of diamines: NH2CH2CH(CH3)NH2 (1) and NH2(CH2)nNH2, n = 3–6 [(2)–(5)] and thiosulfuric acid were prepared and their structures determined by single-crystal X-ray diffraction analysis. Compounds (1), (2) and (4) turned out to be hydrates. The crystal structure of 1,2-propylenediaminium thiosulfate is chiral and exhibits spontaneous resolution. Crystals for both enantiomers [(1a) and (1b)] were obtained with high enantiometric excess and examined. An extended network of strong, charge-assisted hydrogen bonding of the +N—H...O− type (also O—H...O and O—H...S for hydrates) is most likely the main factor defining crystal packing and the variable conformation of the cations. The formation of chiral hydrogen-bond motifs – distorted cubans – seems to induce the formation of chiral solid-state structure from achiral components in the case of (4). Diaminium thiosulfates with an odd number of C atoms in the alkyl chain [compounds (1), (2) and (4)] form three-dimensional supramolecular networks, while in the case of diaminium salts with an even number of C atoms [(3) and (5)], two-dimensional layers of hydrogen-bond domains are observed. The aminium thiosulfates were also characterized by elemental analysis, NMR and Fourier transform (FT)–IR spectroscopy. The conformations of α,ω-alkyldiaminium cations in the solid state are discussed and rationalized by DFT calculations.