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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: 2017-09-20


Approaches to crystal structure landscape exploration


Three approaches to the exploration of the crystal structure landscape are outlined. These are crystal structure prediction, non-ambient crystallography and charge density analysis.

Quantitative analysis of solid-state diversity in trifluoromethylated phenylhydrazones


The cooperative roles of various structural motifs associated with the presence of different intermolecular interactions in the formation of molecular crystals are investigated in a series of trifluoromethylated phenylhydrazones. Out of the six compounds analysed, two exhibit three-dimensional structural similarities with geometrically equivalent building blocks, while a third exists as two polymorphic forms crystallized from ethanol solutions at low temperature (277 K) and room temperature (298 K), respectively. The compounds were characterized via single-crystal and powder X-ray diffraction techniques and differential scanning calorimetry. In the absence of any strong hydrogen bonding, the supramolecular constructs are primarily stabilized via molecular pairs with a high dispersion-energy contribution, due to the presence of molecular stacking along the molecular backbone along with C—H...π interactions in the solid state, in preference to an electrostatic contribution. The interaction energies for the most stabilizing molecular building blocks are in the range −29 to −43 kJ mol−1. In addition, weak N—H...F, C—H...F and N—H...C interactions and F...F, F...C, F...N and C...N contacts act as secondary motifs, providing additional stability to the crystal packing. The overall molecular arrangements are carefully analysed in terms of their nature and energetics, and the roles of different molecular pairs towards the crystal structure are delineated. A topological study using the quantum theory of atoms in molecules was used to characterize all the atomic interactions in the solid state. It established the presence of (3, −1) bond critical points and the closed-shell nature of all the interactions.

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides


Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp2—H...F—Csp2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp2—F...F—Csp2 contacts.

Structural changes of relaxor ferroelectric Sr0.52Ba0.48Nb2O6 (SBN52) on quenching and reheating


Quenching of Sr0.52Ba0.48Nb2O6 (SBN52) from temperatures above 700°C causes small modifications in the strontium distribution over the large cation sites (Me1 and Me2), changed off-centre shifts of the Nb atoms and slightly increased modulation amplitudes. The higher disorder of cation incorporation can explain the enhanced ferroelectric properties. The quenched structural disorder can be healed by reheating followed by slow cooling. A change of the modulation dimension on quenching such as for CaxBa1−xNb2O6 (CBN) mixed crystals was not observed.

Evolution of the α-BaMg(CO3)2 low-temperature superstructure and the tricritical nature of its α–β phase transition


The crystal structure of the synthetic double carbonate norsethite [BaMg(CO3)2] has been reinvestigated using X-ray diffraction data within the temperature range 100–500 K using a high-sensitivity PILATUS pixel detector. The previously assumed positional shift of the crystallographically unique oxygen atom is confirmed. The shift is associated with a coupled rotation of symmetry-equivalent carbonate groups. It was possible to follow the shift using high-accuracy experiments under varying temperature conditions between 100 K and the critical transition temperature occurring at Tc = 363 ± 3 K. The transition of the α-form (space group R{\bar 3}c; below Tc), which represents a superstructure of the β-form (space group R{\bar 3}m, with c′ = c/2; above Tc) was studied in detail. The tricritical order character of this displacive phase transition was verified by tracking the intensities of the recorded superstructure reflections (l = 2n + 1) from single-crystal diffraction and using high-precision lattice parameters obtained from powder diffraction in transmission geometry. Thermodynamic properties suggest both rotation of the CO3 group and a coordination change of the BaO12 coordination polyhedra as the order parameters driving the temperature-dependent α–β phase transition. Nevertheless, a detailed structural analysis reveals the coordination change of the barium atoms to be the main driving force for the observed transformation.

Incommensurately modulated structure of morpholinium tetrafluoroborate and configurational versus chemical entropies at the incommensurate and lock-in phase transitions


Morpholinium tetrafluoroborate, [C4H10NO]+[BF4]−, belongs to a class of ferroelectric compounds ABX4. However, [C4H10NO]+[BF4]− does not develop ferroelectric properties because the incommensurate phase below Tc,I = 153 K is centrosymmetric with superspace group Pnam(σ100)00s and σ1 = 0.42193 (12) at T = 130 K; the threefold superstructure below Tc,II = 117–118 K possesses the acentric but non-ferroelectric space group P212121. At ambient conditions, [C4H10NO]+[BF4]− comprises orientationally disordered [BF4]− anions accommodated in cavities between four morpholinium cations. A structure model for the incommensurately modulated phase, which involves modulated orientational ordering of [BF4]− together with modulated distortions and displacements of the morpholinium ions is reported. A mechanism is proposed for the phase transitions, whereby at low temperatures morpholinium cations are shaped around the tetrafluoroborate anion in order to optimize the interactions with one orientation of this anion and, thus, forcing [BF4]− into this orientation. This mechanism is essentially different from a pure order–disorder phase transition. It is supported by consideration of the transition entropy. The difference in configurational entropy between the disordered and incommensurate phases has been computed from the structure models. It is shown to be much smaller than the experimental transition entropy reported by Owczarek et al. [Chem. Phys. (2011), 381, 11–20]. These features show that the order–disorder contribution is only a minor contribution to the transition entropy and that other factors, such as conformational changes, play a larger role in the phase transitions.

Phase transition sequences in tetramethylammonium tetrachlorometallates by X-ray diffraction and spectroscopic measurements


The phase transition sequences of two members of the tetramethylammonium tetrachlorometallate(III) family of hybrid organic–inorganic salts have been determined and structurally characterized as a function of temperature for the first time. Unusually, a reduction in point-group symmetry with increasing temperature until reaching a cubic prototype phase is observed. Two additional intermediate phases are observed for Fe3+. First-principles calculations and the presence of short Cl...Cl contacts for Ga3+ suggest the [GaCl4]− anion to be conformationally hindered due to stronger lone-pair–σ-hole interactions. The conformationally more flexible Fe3+ structures show sublattice melting with the onset of rotational disorder in the [NMe4]+ cations occurring 40 K below the corresponding onset of rotational disorder in the [FeCl4]− sublattice.

A commensurately modulated structure of parabutlerite, FeIIISO4(OH)·2H2O


Parabutlerite, orthorhombic FeIIISO4(OH)·2H2O, has been reinvestigated using single-crystal X-ray diffraction. The structure of parabutlerite is commensurately modulated, with a = 20.0789 (8), b = 7.4024 (7), c = 7.2294 (15) Å and q = 0.4b*. The superstructure has been determined, using a superspace approach, as having the superspace group Pnma(0β0)s0s and t0 = 1/20, and refined to R = 0.0295 for 2392 main reflections with I > 3σ(I). The structure consists of infinite chains of Fe octahedra that are linked via vertices (OH groups); these chains are encased from both sides by SO4 tetrahedra. The displacive modulation of atoms in parabutlerite is connected with a tilt of the chains around the b axis towards the adjacent chains due to the accommodation of an energetically more favorable hydrogen-bond geometry.

Effect of cationic substitution on the double-well hydrogen-bond potential in [K1−x(NH4)x]3H(SO4)2 proton conductors: a single-crystal neutron diffraction study


The structure of the mixed crystal [K1−x(NH4)x]3H(SO4)2 as obtained from single-crystal neutron diffraction is compared with the previously reported room-temperature neutron structure of crystalline K3H(SO4)2. The two structures are very similar, as indicated by the high value of their isostructurality index (94.8%). It was found that the replacement of even a small amount (3%) of K+ with NH4+ has a significant influence on the short strong hydrogen bond connecting the two SO42− ions. Earlier optical measurements had revealed that the kinetics of the superionic transition in the solid solution [K1−x(NH4)x]3H(SO4)2 are much faster than in K3H(SO4)2; this reported difference in the kinetics of the superionic phase transition in this class of crystal is explained on the basis of the difference in strength of the hydrogen-bond interactions in the two structures.

Crystal structure of cobalt hydroxide carbonate Co2CO3(OH)2: density functional theory and X-ray diffraction investigation


The cobalt carbonate hydroxide Co2CO3(OH)2 is a technologically important solid which is used as a precursor for the synthesis of cobalt oxides in a wide range of applications. It also has relevance as a potential immobilizer of the toxic element cobalt in the natural environment, but its detailed crystal structure is so far unknown. The structure of Co2CO3(OH)2 has now been investigated using density functional theory (DFT) simulations and powder X-ray diffraction (PXRD) measurements on samples synthesized via deposition from aqueous solution. Two possible monoclinic phases are considered, with closely related but symmetrically different crystal structures, based on those of the minerals malachite [Cu2CO3(OH)2] and rosasite [Cu1.5Zn0.5CO3(OH)2], as well as an orthorhombic phase that can be seen as a common parent structure for the two monoclinic phases, and a triclinic phase with the structure of the mineral kolwezite [Cu1.34Co0.66CO3(OH)2]. The DFT simulations predict that the rosasite-like and malachite-like phases are two different local minima of the potential energy landscape for Co2CO3(OH)2 and are practically degenerate in energy, while the orthorhombic and triclinic structures are unstable and experience barrierless transformations to the malachite phase upon relaxation. The best fit to the PXRD data is obtained using a rosasite model [monoclinic with space group P1121/n and cell parameters a = 3.1408 (4) Å, b = 12.2914 (17) Å, c = 9.3311 (16) Å and γ = 82.299 (16)°]. However, some features of the PXRD pattern are still not well accounted for by this refinement and the residual parameters are relatively poor. The relationship between the rosasite and malachite phases of Co2CO3(OH)2 is discussed and it is shown that they can be seen as polytypes. Based on the similar calculated stabilities of these two polytypes, it is speculated that some level of stacking disorder could account for the poor fit of the PXRD data. The possibility that Co2CO3(OH)2 could crystallize, under different growth conditions, as either rosasite or malachite, or even as a stacking-disordered phase intermediate between the two, requires further investigation.

A note on the distortion theorem


The distortion theorem is a conditional statement that establishes the certain relations between the variation of the mean bond length and the variation of the valence of a central ion of a coordination polyhedron. It was found that in some principal cases the conditional part of the distortion theorem is not necessary. A combinatorial evaluation of the distortion theorem and a theoretical analysis of the bond length–bond valence correlation were performed. An extension of the distortion theorem is proposed.

Temperature-induced order–disorder structural phase transitions of two-dimensional isostructural hexamethylenetetramine co-crystals


Hexamethylenetetramine-benzoic acid (1/2) (HBA) and hexamethylenetetramine-4-methylbenzoic acid (1/2) (HMBA) co-crystals undergo order–disorder structural phase transition from a low-temperature monoclinic crystal structure to a high-temperature orthorhombic crystal structure at the transition temperatures of 257.5 (5) K (Pn ↔ Fmm2) and 265.5 (5) K (P21/n ↔ Cmcm), respectively, using variable-temperature single-crystal X-ray diffraction analysis. The observed phase transitions were confirmed to be reversible first-order transitions as indicated by the sharp endothermic and exothermic peaks in the differential scanning calorimetry measurement. The three-molecule aggregate of HBA and HMBA consists of a hexamethylenetetramine molecule and two benzoic acid or two 4-methylbenzoic acid molecules, respectively. The acid molecules are ordered at the low-temperature phase and are equally disordered over two positions, which are related by a mirror symmetry, at the high-temperature phase. The two-dimensional supramolecular constructs common to both co-crystals are formed by three-molecule aggregates via weak intermolecular C—H...O and C—H...π interactions into molecular trilayers parallel to the ac plane with small XPac dissimilarity indices and parameters. The PIXEL interaction energies of all corresponding molecular contacts were calculated and the results are comparable between HBA and HMBA co-crystals, resulting in similar lattice energies and transition temperatures despite their two-dimensional isostructural relationship. The observed phase transitions of these two energetically similar co-crystals are triggered by similar mechanisms, i.e. the molecular rotator ordering and structural order–disorder transformation, which induced non-merohedral twinning with similar twin matrices in the low-temperature crystal form of both co-crystals.

Comparison of the crystal structures and thermochemistry of a novel soluble guanylate cyclase stimulator riociguat and its solvates


Riociguat (Rio) is the first oral soluble guanylate cyclase stimulator to be approved for pulmonary arterial hypertension. In this study, form (II) of riociguat and three solvates with acetonitrile [form (III)], N,N-dimethylformamide [form (IV)] and ethyl acetate [form (V)] were crystallized. They were identified and characterized by differential scanning calorimetry, thermogravimetric analysis, X-ray powder diffraction, and their crystal structures were determined by single-crystal X-ray diffraction. No crystal structure has previously been reported for the known form (II) of riociguat. Crystal structure determination of Rio and its new solvates revealed that the dimeric R22(14) motif is common in both structures. The crystal packing of solvates adopts channel-like patterns, whereas form (II) of riociguat adopts sheet-like patterns. Strong π–π interactions exist in the above four forms. The conformation of the riociguat in one molecule of 0.5-DMF solvate was found to be significantly different from the conformations found in the other solvates. Desolvation of the three solvates was studied by thermogravimetric analysis and X-ray diffraction, and was shown to transform them into form (I) of riociguat.

Crystal structure of the OH-dominant gadolinite-(Y) analogue (Y,Ca)2(Fe,□)Be2Si2O8(OH,O)2 from Heftetjern pegmatite, Norway


A hydroxyl-dominant analogue of gadolinite-(Y) (OH-Gad) has been discovered in the Heftetjern granitic pegmatite, southern Norway, in association with late-stage rare-earth-element containing minerals. The empirical formula, based on ten O atoms per formula unit, is (Y1.285Ca0.55Ce0.07La0.04Nd0.01)Σ1.955(Fe2+0.57□0.43)Be2.02Si1.995O8.48(OH)1.52. The mineral is monoclinic, space group P21/c, a = 4.7514 (10), b = 7.5719 (16), c = 9.9414 (2) Å, β = 90.015 (4)°, V = 357.663 (3) Å3 and Z = 2. The density calculated using the empirical formula is 3.903 g cm−3. The crystal structure was refined to R = 0.0217 for 776 reflections with I > 2σ(I). OH-Gad is isostructural with gadolinite-(Y) and it is characterized by the predominance of OH− over O2− at the anionic Ø-site. The refined crystal-chemical formula is: A(Y1.25Ca0.55Ce0.2)X(Fe2+0.57□0.43)ZBe2TSi2O8Ø[(OH)0.86O0.59(OH)*0.55] (Z = 2). The possible orientation and local environment of the hydroxyl group were suggested based on bond-valence sum calculations and geometrical analysis of the crystal structure. The infrared spectrum confirms disordering of H atoms. OH-Gad seems to be a potentially new mineral, the first simultaneously hydroxyl- and iron-dominant member of the gadolinite subgroup. It is an OH-analogue of gadolinite-(Y) and an Fe2+-analogue of hingganite-(Y).

Crystal chemistry and the role of ionic radius in rare earth tetrasilicates: Ba2RE2Si4O12F2 (RE = Er3+–Lu3+) and Ba2RE2Si4O13 (RE = La3+–Ho3+)


Structural variations across a series of barium rare earth (RE) tetrasilicates are studied. Two different formulas are observed, namely those of a new cyclo-silicate fluoride, BaRE2Si4O12F2 (RE = Er3+–Lu3+) and new compounds in the Ba2RE2Si4O13 (RE = La3+–Ho3+) family, covering the whole range of ionic radii for the rare earth ions. The Ba2RE2Si4O13 series is further subdivided into two polymorphs, also showing a dependence on rare earth ionic radius (space group P{\overline 1} for La3+–Nd3+, and space group C2/c for Sm3+–Ho3+). Two of the structure types identified are based on dinuclear rare earth units that differ in their crystal chemistries, particularly with respect to the role of fluorine as a structural director. The broad study of rare earth ions provides greater insight into understanding structural variations within silicate frameworks and the nature of f-block incorporation in oxyanion frameworks. The single crystals are grown from high-temperature (ca 953 K) hydrothermal fluids, demonstrating the versatility of the technique to access new phases containing recalcitrant rare earth oxides, enabling the study of structural trends.

Markedly different molecular formation in DPP-based small-molecule solar cells probed by grazing-incidence wide-angle X-ray scattering


This study comprehensively explores the nanostructural properties of two diketopyrrolo[3,4-c]pyrrole-1,4-dione (DPP)-based small molecules with different alkyl side groups and their blends with the fullerene derivative PC71BM, using grazing-incidence wide-angle X-ray scattering synchrotron techniques. Preferentially relative face-on orientation within the larger and more ordered stacking phase of SM1 with its shorter side group (ethylhexyl) was observed in the majority of both pristine and blend thin films, whereas SM2 crystals showed strictly perpendicular orientation. These contrasting crystalline characteristics led to significant differences in the results, from which crystalline structure–performance property correlations are proposed. Thus, the results not only demonstrate important scientific insights into the relationship between molecular structure and crystalline formation but also provide molecular design directions that will facilitate further improvement to the morphology and performance of DPP-based small-molecule solar cells.

Low-temperature behaviour of K2Sc[Si2O6]F: determination of the lock-in phase and its relationships with fresnoite- and melilite-type compounds


K2Sc[Si2O6]F exhibits, at room temperature, a (3 + 2)-dimensional incommensurately modulated structure [a = 8.9878 (1), c = 8.2694 (2) Å, V = 668.01 (2) Å3; superspace group P42/mnm(α,α,0)000s(−α,α,0)0000] with modulation wavevectors q1 = 0.2982 (4)(a* + b*) and q2 = 0.2982 (4)(−a* + b*). Its low-temperature behaviour has been studied by single-crystal X-ray diffraction. Down to 45 K, the irrational component α of the modulation wavevectors is quite constant varying from 0.2982 (4) (RT), through 0.2955 (8) (120 K), 0.297 (1) (90 K), 0.298 (1) (75 K), to 0.299 (1) (45 K). At 25 K it approaches the commensurate value of one-third [i.e. 0.332 (3)]: thus indicating that the incommensurate–commensurate phase transition takes place between 45 K and 25 K. The commensurate lock-in phase of K2Sc[Si2O6]F has been solved and refined with a 3 × 3 × 1 supercell compared with the tetragonal incommensurately modulated structure stable at room temperature. This corresponds to a 3 × 1 × 3 supercell in the pseudo-orthorhombic monoclinic setting of the low-temperature structure, space group P2/m, with lattice parameters a = 26.786 (3), b = 8.245 (2) c = 26.824 (3) Å, β = 90.00 (1)°. The structure is a mixed tetrahedral–octahedral framework composed of chains of [ScO4F2] octahedra that are interconnected by [Si4O12] rings with K atoms in fourfold to ninefold coordination. Distorted [ScO4F2] octahedra are connected to distorted Si tetrahedra to form octagonal arrangements closely resembling those observed in the incommensurate structure of fresnoite- and melilite-type compounds.