Subscribe: Acta Crystallographica Section B
Preview: Acta Crystallographica Section B

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: 2018-03-28


The crystal structure of [Fe2(PIMIC6)(AnthCO2)(CH3CN)]·[Fe2(PIMIC6)(AnthCO2)(CH3CN)0.9(CH2Cl2)0.1]·[Fe2(PIMIC6)(AnthCO2)(OH2)]·0.75CH3CN: a crystallographer's nightmare or a fascinating case of disorder?


Refinement of large crystal structures as well as that of disordered structures can be challenging. If both features come together, structure refinement has the potential of becoming a crystallographer's nightmare. Here, the refinement of the large and highly disordered structure of [Fe2(PIMIC6)(AnthCO2)(CH3CN)]·[Fe2(PIMIC6)(AnthCO2)(CH3CN)0.9(CH2Cl2)0.1]·[Fe2(PIMIC6)(AnthCO2)(OH2)]·0.75CH3CN [(1), PIMIC6 is a phenol–imine-based macrocycle, AnthCO2 is an anthracene acid anion] is described and discussed. A total of 5311 parameters had to be refined to generate a model that allows for 14 400 possible arrangements of (1) in the asymmetric unit, making this structure one of the most complex structures in the Cambridge Structural Database to date. All disorders are exceptionally well resolved and exhaustive parameterizing affords a refinement model that is unique with respect to the detail of disorder refinement.

Crystal growth, structure and characterization of Er6B4O15 as self-activated eye-safe laser material within the near-infrared waveband


A new rare-earth borate Er6B4O15 was synthesized by a solid-state reaction technique. The crystal was obtained by a flux method. Single-crystal X-ray diffraction analysis revealed that the crystal structure is composed of ErO6 polyhedra sharing edges and BO3 groups. The absorption, near-infrared fluorescence spectra and the fluorescence decay curve of Er: 4I13/2 energy level in the Er6B4O15 crystal were measured at room temperature. The absorption peak was located at 977 nm with absorption cross section of 1.16 × 10−21 cm2 and a full width at half-maximum (FWHM) of 16 nm, which is very suitable for commercial 980 nm laser diode pumping. A maximum emission peak at 1560 mm with a broad FWHM of 64 nm was observed in this crystal because of the Er3+ transition 4I13/2→4I15/2, while the emission cross section was calculated to be 8.53 × 10−20 cm2. These results imply that the Er6B4O15 crystal is a promising candidate material for the achievement of an eye-safe near-infrared wavelength laser.

A method for visualization of the variation of noncovalent interactions in crystal structures of conformational polymorphs


A method for clear visualization of the variation of noncovalent interactions in crystal structures of conformational polymorphs is developed and introduced. The first stage of the method establishes the characteristics of all, without exception, noncovalent interactions in all crystal structures under discussion. This is possible using a strict and objective method of construction of Voronoi–Dirichlet polyhedra within the framework of the stereoatomic model of crystal structures. The second stage of the method then involves plotting of diagrams, showing the relation between parameters characterizing interatomic interactions and chosen geometric parameters of molecules. Application of the title method to highly polymorphic systems of ROY and flufenamic acid allows several imperceptible features of real crystal structures to be revealed and determines the value of different types of interactions in their conformational polymorphs. The method is universal as it can be readily adapted to any system of crystal structures in which noncovalent interactions change as a function of any parameters. Employment of the title method along with quantum chemical calculations offers opportunities for the correlation of potential energy of crystalline materials with noncovalent interactions in their structures, which is a giant step forward towards a more complete understanding of the relationship between the structure and properties of compounds.

Aromaticity of benzene derivatives: an exploration of the Cambridge Structural Database


The harmonic oscillator model of aromaticity (HOMA) index, one of the most popular aromaticity indices for solid-state benzene rings in the Cambridge Structural Database (CSD), has been analyzed. The histograms of HOMA for benzene, for benzene derivatives with one formyl, nitro, amino or hydroxy group as well as the histograms for the derivatives with two formyl, nitro, amino or hydroxy groups in ortho, meta and para positions were investigated. The majority of the substituted benzene derivatives in the CSD are characterized by a high value of HOMA, indicating fully aromatic character; however, the distribution of the HOMA value from 1 to about 0 indicates decreasing aromaticity down to non-aromatic character. Among the benzene derivatives investigated, a significant decrease in aromaticity can be related to compounds with diamino and dinitro groups in the meta position.

Revisiting the I{\overline {\bf 1}} structures of high-temperature Ca-rich plagioclase feldspar – a single-crystal neutron and X-ray diffraction study


The I{\overline 1} structures of four natural Ca-rich plagioclase feldspars formed at high temperature were analysed using single-crystal neutron and X-ray diffraction. The neutron time-of-flight Laue diffractometer at the ORNL Spallation Neutron Source (Tennessee, USA) combined with a single-crystal X-ray diffraction instrument were able to reveal some new details about these already intensively studied structures. The split oxygen atoms refined from the neutron diffraction data show the underlying mechanism of Ca–Na ordering and the anisotropic P{\overline 1} ordering along the c-axis. The compositional ranges covered by the samples studied are quite rare for I{\overline 1} structures. The incommensurately modulated e2 structure of some plagioclase samples can easily be confused with an I{\overline 1} structure from the diffraction pattern, which puts some previously published I{\overline 1} structures into question. An incomplete phase diagram for Ca-rich plagioclase feldspar is proposed to explain the rarity of the I{\overline 1} structure in this compositional range, and a time–temperature–transformation diagram for the composition ∼An66 is provided accordingly.

Ionic network analysis of tectosilicates: the example of coesite at variable pressure


The method of ionic network analysis [Thomas (2017). Acta Cryst. B73, 74–86] is extended to tectosilicates through the example of coesite, the high-pressure polymorph of SiO2. The structural refinements of Černok et al. [Z. Kristallogr. (2014), 229, 761–773] are taken as the starting point for applying the method. Its purpose is to predict the unit-cell parameters and atomic coordinates at (p–T–X) values in-between those of diffraction experiments. The essential development step for tectosilicates is to define a pseudocubic parameterization of the O4 cages of the SiO4 tetrahedra. The six parameters aPC, bPC, cPC, αPC, βPC and γPC allow a full quantification of the tetrahedral structure, i.e. distortion and enclosed volume. Structural predictions for coesite require that two separate quasi-planar networks are defined, one for the silicon ions and the other for the O4 cage midpoints. A set of parametric curves is used to describe the evolution with pressure of these networks and the pseudocubic parameters. These are derived by fitting to the crystallographic data. Application of the method to monoclinic feldspars and to quartz and cristobalite is discussed. Further, a novel two-parameter quantification of the degree of tetrahedral distortion is described. At pressures in excess of ca 20.45 GPa it is not possible to find a self-consistent solution to the parametric curves for coesite, pointing to the likelihood of a phase transition.

Hydrocerussite-related minerals and materials: structural principles, chemical variations and infrared spectroscopy


White lead or basic lead carbonate, 2PbCO3·Pb(OH)2, the synthetic analogue of hydrocerussite Pb3(OH)2(CO3)2, has been known since antiquity as the most frequently used white paint. A number of different minerals and synthetic materials compositionally and structurally related to hydrocerussite have been described within the last two decades. Herein, a review is given of general structural principles, chemical variations and IR spectra of the rapidly growing family of hydrocerussite-related minerals and synthetic materials. Only structures containing a hydroxo- and/or oxo-component, i.e. which are compositionally directly related with hydrocerussite and `white lead', are reviewed in detail. An essential structural feature of all the considered phases is the presence of electroneutral [PbCO3]0 cerussite-type layers or sheets. Various interleaved sheets can be incorporated between the cerussite-type sheets. Different sheets are stacked into two-dimensional blocks separated by the stereochemically active 6s2 lone electron pairs on Pb2+ cations. Minerals and synthetic materials described herein, together with a number of still hypothetical members, constitute a family of modular structures. Hydrocerussite, abellaite and grootfonteinite can be considered to constitute a merotype family of structures. The remaining hydrocerussite-related structures discussed are built on similar principles, but are more complex. Structural architectures of somersetite and slag phase from Lavrion, Attica, Greece, are unique for oxysalt mineral structures in general. Thus, the whole family of hydrocerussite-related phases can be denoted as a plesiotype family of modular structures. The crystal structures of hydrocerussite from Merehead quarry, Somerset, England, and of its synthetic analogue, both determined from single crystals, are reported here for the first time. The results of the infrared (IR) spectroscopy show that this method is useful for distinguishing several different minerals related to hydrocerussite and their synthetic analogues.

Accurate and precise lattice parameters of H2O and D2O ice Ih between 1.6 and 270 K from high-resolution time-of-flight neutron powder diffraction data


Accurate and precise lattice parameters for D2O and H2O varieties of hexagonal ice (ice Ih, space group P63/mmc) have been obtained in the range 1.6 to 270 K. Precision of the lattice parameters (∼0.0002% in a and 0.0004% in c for D2O, 0.0008% in a and 0.0015% in c for H2O) is ensured by use of the time-of-flight method on one of the longest primary neutron flight-path instruments in the world, the High-Resolution Powder Diffractometer at the ISIS neutron source. These data provide a more precise description of the negative thermal expansion of the material at low temperatures than the previous synchrotron `gold standard' [Röttger et al. (1994). Acta Cryst. B50, 644–648], including the region below 10 K where the lattice parameters saturate. The volume expansivity of both isotopologues turns negative below 59–60 K, in excellent agreement with a recent dilatometry study. The axial expansivities are highly isotropic (differing by < 1% in D2O ice Ih). Furthermore, the c/a ratio of different D2O ice samples exhibit a statistically significant dispersion of ∼0.015% below 150 K that appears to depend on the thermal history of the sample, which disappears on warming above 150 K. Similarly, H2O ice exhibits a `kink' in the c/a ratio at ∼115 K. The most plausible explanation is a freezing-in of the molecular reorientation process on cooling and subsequent relaxation on warming.

Phase transitions in ferroelectric 4-aminopyridinium tetrachloroantimonate(III) – revisited


New X-ray diffraction studies on the crystal structure of ferroelectric [4-NH2C5H4NH][SbCl4] indicate that in the broad temperature range from 240 to 304 K covering the three intermediate phases, the crystal structure is modulated. Phase II is incommensurately modulated with modulation vector q = βb*, β varying from 0.60 to 0.66 and monoclinic C2/c(0β0)s0 superspace group. Ferroelectric phase III is commensurate with q = 2\over 3b* and Cc(0β0)0 symmetry. Polar phase IV is incommensurately modulated with β varying from 0.66 to 0.70 and Cc(0β0)0 superspace group. In all phases only first-order satellites are observed along the b* direction. Two types of periodic deformation are present in the structure of modulated phases. The 4-aminopyridinium cations are subjected to occupation modulation whereas [SbCl4]−n chains are displacively modulated. The paraelectric–ferroelectric phase transition is an example of the incommensurate–commensurate transition of the lock-in type. A new mechanism for this transformation is proposed.

Crystal structure, phase transition and structural deformations in iron borate (Y0.95Bi0.05)Fe3(BO3)4 in the temperature range 90–500 K


An accurate X-ray diffraction study of (Y0.95Bi0.05)Fe3(BO3)4 single crystals in the temperature range 90–500 K was performed on a laboratory diffractometer and used synchrotron radiation. It was established that the crystal undergoes a diffuse structural phase transition in the temperature range 350–380 K. The complexity of localization of such a transition over temperature was overcome by means of special analysis of systematic extinction reflections by symmetry. The transition temperature can be considered to be Tstr ≃ 370 K. The crystal has a trigonal structure in the space group P3121 at temperatures of 90–370 K, and it has a trigonal structure in the space group R32 at 375–500 K. There is one type of chain formed by the FeO6 octahedra along the c axis in the R32 phase. When going into the P3121 phase, two types of nonequivalent chains arise, in which Fe atoms are separated from the Y atoms by a different distance. Upon lowering the temperature from 500 to 90 K, a distortion of the Y(Bi)O6, FeO6, B(2,3)O3 coordination polyhedra is observed. The distances between atoms in helical Fe chains and Fe—O—Fe angles change non-uniformly. A sharp jump in the equivalent isotropic displacement parameters of O1 and O2 atoms within the Fe—Fe chains and fluctuations of the equivalent isotropic displacement parameters of B2 and B3 atoms were observed in the region of structural transition as well as noticeable elongation of O1, O2, B2, B3, Fe1, Fe2 atomic displacement ellipsoids. It was established that the helices of electron density formed by Fe, O1 and O2 atoms may be structural elements determining chirality, optical activity and multiferroicity of rare-earth iron borates. Compression and stretching of these helices account for the symmetry change and for the manifestation of a number of properties, whose geometry is controlled by an indirect exchange interaction between iron cations that compete with the thermal motion of atoms in the structure. Structural analysis detected these changes as variations of a number of structural characteristics in the c unit-cell direction, that is, the direction of the helices. Structural results for the local surrounding of the atoms in (Y0.95Bi0.05)Fe3(BO3)4 were confirmed by EXAFS and Mössbauer spectroscopies.

Crystal structures of alkali metal (Group 1) citrate salts


The crystal structures of 16 new alkali metal citrates were determined using powder and/or single crystal techniques. These structures and 12 previously determined citrate structures were optimized using density functional techniques. The central portion of a citrate ion is fairly rigid, while the conformations of the terminal carboxylate groups exhibit no preferences. The citrate–metal bonding is ionic. Trends in metal–citrate coordination are noted. The energy of an O—H...O hydrogen bond is proportional to the square root of the H...acceptor Mulliken overlap population, and a correlation between the hydrogen bond energy and the H...acceptor distance was developed: E (kJ mol−1) = 137.5 (5) − 45.7 (8) (H...A, Å). The hydrogen bond contribution to the crystal energy ranges from 62.815 to 627.6 kJ mol−1 citrate−1 and comprises ∼5 to 30% of the crystal energy. The general order of ionization of the three carboxylic acid groups of citric acid is: central, terminal, terminal, although there are a few exceptions. Comparisons of the refined and DFT-optimized structures indicate that crystal structures determined using powder diffraction data may not be as accurate as single-crystal structures.