Showing papers in "Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry in 2018"

Crystal structures of alkali metal (Group 1) citrate salts

Abstract: 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, A). 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.

Bond-length distributions for ions bonded to oxygen: metalloids and post-transition metals

Abstract: Bond-length distributions have been examined for 33 configurations of the metalloid ions and 56 configurations of the post-transition metal ions bonded to oxygen, for 5279 coordination polyhedra and 21 761 bond distances for the metalloid ions, and 1821 coordination polyhedra and 10 723 bond distances for the post-transition metal ions For the metalloid and post-transition elements with lone-pair electrons, the more common oxidation state between n versus n+2 is n for Sn, Te, Tl, Pb and Bi and n+2 for As and Sb There is no correlation between bond-valence sum and coordination number for cations with stereoactive lone-pair electrons when including secondary bonds, and both intermediate states of lone-pair stereoactivity and inert lone pairs may occur for any coordination number > [4] Variations in mean bond length are ∼006–009 A for strongly bonded oxyanions of metalloid and post-transition metal ions, and ∼01–03 A for ions showing lone-pair stereoactivity Bond-length distortion is confirmed to be a leading cause of variation in mean bond lengths for ions with stereoactive lone-pair electrons For strongly bonded cations (ie oxyanions), the causes of mean bond-length variation are unclear; the most plausible cause of mean bond-length variation for these ions is the effect of structure type, ie stress resulting from the inability of a structure to adopt its characteristic a priori bond lengths

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

Abstract: 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' [Rottger 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.

Bond-length distributions for ions bonded to oxygen: results for the lanthanides and actinides and discussion of the f-block contraction

Abstract: Bond-length distributions have been examined for 84 configurations of the lanthanide ions and 22 configurations of the actinide ions bonded to oxygen, for 1317 coordination polyhedra and 10 700 bond distances for the lanthanide ions, and 671 coordination polyhedra and 4754 bond distances for the actinide ions. A linear correlation between mean bond length and coordination number is observed for the trivalent lanthanides ions bonded to O2−. The lanthanide contraction for the trivalent lanthanide ions bonded to O2− is shown to vary as a function of coordination number, and to diminish in scale with an increasing coordination number. The decrease in mean bond length from La3+ to Lu3+ is 0.25 A for coordination number (CN) 6 (9.8%), 0.22 A for CN 7 (8.7%), 0.21 A for CN 8 (8.0%), 0.21 A for CN 9 (8.2%) and 0.18 A for CN 10 (6.9%). The crystal chemistry of Np5+ and Np6+ is shown to be very similar to that of U6+ when bonded to O2−, but differs for Np7+.

Copper minerals from volcanic exhalations – a unique family of natural compounds: crystal-chemical review

Abstract: The crystal-chemical characterization of oxysalts (sulfates, arsenates, vanadates, selenites, silicates, molybdates and borates), chlorides and oxides with species-defining Cu2+ formed in volcanic fumaroles (96 minerals representing 80 structure types; 81 species are endemic to fumarolic formation) is given. Copper minerals are known only from oxidizing-type fumaroles. The most diverse copper mineralization occurs at the Tolbachik volcano (Kamchatka, Russia). Copper minerals from fumarolic systems are subdivided into two genetic groups: Group I are minerals formed in the hot zones of fumaroles (>473 K, mainly 673–973 K) and Group II are minerals formed in the moderately hot zones of fumaroles (<473 K, mainly at 343–423 K). Group I includes 81 mineral species. Their most defining chemical feature is that all of them are hydrogen-free, and many of them contain the additional anion O2−. In comparison with minerals from other geological environments, in minerals of Group I the Cu2+ cation exhibits the strongest affinity for four- and fivefold coordinations and the strongest distortion of Cu2+-centred octahedra. Group II consists of 15 chlorides and sulfates including 13 H-bearing species. In these minerals the Cu2+ cation shows affinity for octahedral coordination, with OH− and/or H2O0 as ligands. In terms of crystal chemistry these minerals are closer to supergene minerals rather than to high-temperature fumarolic species. Temperature is the major factor governing the crystal chemistry of Cu2+ oxysalts and chlorides in low-pressure systems. The defining feature of fumarolic copper mineralization over this whole temperature range is the important role of alkali cations. The available data on complexes of Cu2+-centred polyhedra in the structures of natural oxysalts and halides are summarized and reviewed. Isomorphism in copper minerals from volcanic exhalations is discussed. The structures of high-temperature Cu oxysalts with additional O2− anions (i.e. O atoms non-bonded to S6+, Mo6+, As5+, V5+, Se4+ or B3+) are also interpreted using an approach based on oxocentred tetrahedra.

ZnO/ZnS (hetero)structures: ab initio investigations of polytypic behavior of mixed ZnO and ZnS compounds

Abstract: The range of feasible ZnO/ZnS polytypes has been explored, predicting alternative structural arrangements compared with previously suggested or observed structural forms of ZnO/ZnS compounds, including bulk crystal structures, various nanostructures, heterostructures and heterojunctions. All calculations were performed ab initio using density functional theory–local density approximation and hybrid Heyd–Scuseria–Ernzerhof functionals. Specifically, pure ZnO and ZnS compounds and mixed ZnO1–xSx compounds (x = 0.20, 0.25, 0.33, 0.50, 0.60, 0.66 and 0.75) are investigated and a multitude of possible stable polytypes for ZnO/ZnS compounds creating new possibilities for synthesis of new materials with improved physical and chemical properties are identified.

Bond-length distributions for ions bonded to oxygen: results for the non-metals and discussion of lone-pair stereoactivity and the polymerization of PO4

Abstract: Bond-length distributions are examined for three configurations of the H+ ion, 16 configurations of the group 14–16 non-metal ions and seven configurations of the group 17 ions bonded to oxygen, for 223 coordination polyhedra and 452 bond distances for the H+ ion, 5957 coordination polyhedra and 22 784 bond distances for the group 14–16 non-metal ions, and 248 coordination polyhedra and 1394 bond distances for the group 17 non-metal ions. H⋯O and O—H + H⋯O distances correlate with O⋯O distance (R2 = 0.94 and 0.96): H⋯O = 1.273 × O⋯O – 1.717 A; O—H + H⋯O = 1.068 × O⋯O – 0.170 A. These equations may be used to locate the hydrogen atom more accurately in a structure refined by X-ray diffraction. For non-metal elements that occur with lone-pair electrons, the most observed state between the n versus n+2 oxidation state is that of highest oxidation state for period 3 cations, and lowest oxidation state for period 4 and 5 cations when bonded to O2−. Observed O—X—O bond angles indicate that the period 3 non-metal ions P3+, S4+, Cl3+ and Cl5+ are lone-pair seteroactive when bonded to O2−, even though they do not form secondary bonds. There is no strong correlation between the degree of lone-pair stereoactivity and coordination number when including secondary bonds. There is no correlation between lone-pair stereoactivity and bond-valence sum at the central cation. In synthetic compounds, PO4 polymerizes via one or two bridging oxygen atoms, but not by three. Partitioning our PO4 dataset shows that multi-modality in the distribution of bond lengths is caused by the different bond-valence constraints that arise for Obr = 0, 1 and 2. For strongly bonded cations, i.e. oxyanions, the most probable cause of mean bond length variation is the effect of structure type, i.e. stress induced by the inability of a structure to follow its a priori bond lengths. For ions with stereoactive lone-pair electrons, the most probable cause of variation is bond-length distortion.

X‐ray, dielectric, piezoelectric and optical analyses of a new nonlinear optical 8‐hydroxyquinolinium hydrogen squarate crystal

Abstract: The 1:1 complex of 8-hy­droxy­quinoline with squaric acid has been characterized using single-crystal X-ray diffraction, UV–vis spectroscopy, density functional theory (DFT) calculations, and photoluminescence, dielectric, piezoelectric and second-harmonic generation (SHG) studies. The title compound (8-hy­droxy­quinolinium hydrogen squarate; HQS) contains one protonated 8-hy­droxy­quinoline cation (C9H8NO+) and one hydrogen squarate mono-anion (C4HO4−). All the intermolecular hydrogen-bonding interactions present in the HQS crystal structure are analyzed by three-dimensional molecular Hirshfeld surface analysis and their relative contributions are determined from two-dimensional fingerprint plots. The structure of C9H8NO+·C4HO4− molecular complex has been optimized at the DFT/B3LYP/6-31G(d,p) level. The UV–vis spectroscopic data calculated by time-dependent density functional theory are compared with the experimental data. The LUMO+1, LUMO, HOMO and HOMO−1 energy values, their shapes and energy gaps are calculated using the B3LYP/6-31G(d,p) level of theory. The HQS material exhibits high SHG output (2.6 times of that of potassium dihydrogen phosphate), high photoluminescence emission centred at 474 nm and a piezoelectric charge coefficient of 3 pC N−1. Henceforth, HQS can serve as an alternative potential candidate for multifunctional nonlinear optically active and piezoelectric crystals.

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

Abstract: 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.

High-density HNIW/TNT cocrystal synthesized using a green chemical method.

Abstract: The main challenge for achieving better energetic materials is to increase their density. In this paper, cocrystals of HNIW (2,4,6,8,10,12-hexa­nitro-2,4,6,8,10,12-hexa­aza­isowurtzitane, often referred to as CL-20) with TNT (2,4,6-tri­nitro­toluene) were synthesized using ethanol in a green chemical method. The cocrystal was formulated as C13H11N15O18 and possesses a higher density (1.934 g cm−3) than published previously (1.846 g cm−3). This high-density cocrystal possesses a new structure, which can be substantiated by the different types of hydrogen bonds. The predominant driving forces that connect HNIW with TNT in the new cocrystal were studied at ambient conditions using single-crystal X-ray diffraction, powder X-ray diffraction, Fourier transform–infrared spectroscopy and Raman spectroscopy. The results reveal that the structure of the new HNIW/TNT cocrystals consists of three one-dimensional hydrogen-bonded chains exploiting the familiar HNIW–TNT multi-component supramolecular structure, in which two hydrogen-bonded chains are between —NO2 (HNIW) and —CH (TNT), and one hydrogen-bonded chain is between —CH (HNIW) and —NO2 (TNT). The changes to the electron binding energy and type of element in the new cocrystal were traced using X-ray photoelectron spectroscopy. Meanwhile, the physicochemical characteristics alter after cocrystallization due to the hydrogen bonding. It was found that the new HNIW/TNT cocrystal is more thermodynamically stable than HNIW. Thermodynamic aspects of new cocrystal decomposition are investigated in order to explain this observation. The detonation velocity of new HNIW/TNT cocrystals is 8631 m s−1, close to that of HNIW, whereas the mechanical sensitivity is lower than HNIW.

Structure of russellite (Bi2WO6): origin of ferroelectricity and the effect of the stereoactive lone electron pair on the structure.

Abstract: The structure of the low-temperature polar (orthorhombic) phase of russellite (Bi2WO6) was examined on artificial specimens with precise single-crystal X-ray diffraction experiments. The final atomic arrangement thus obtained was identical to that reported by Knight [Miner. Mag. (1992), 56, 399–409] with powder neutron diffraction. The residual density attributable to a stereochemically-active lone pair of electrons of bis­muth was prominent at approximately the centre of a larger cap of BiO8 square antiprisms, that is on the line from the Bi sites to an adjacent WO42− slab along the b-axis direction. Quite uneven Bi—O distances and the formation of a vacant coordination hemisphere (within 3 A) should, therefore, be ascribed to the strong demand of bis­muth to form shorter Bi—O bonds to use up its electrostatic charge within its coordination environment. The shift of bis­muth along −c propagates via the correlated shift of the W site and these cooperative shifts cause ferroelectricity in the compound. This propagation was easily effected by the intrusion of molecules such as acetone into the structure.

Theory of order-disorder phase transitions of B-cations in AB'1/2B''1/2O3 perovskites.

Abstract: Perovskite-like oxides AB′1/2B′′1/2O3 with two different cations in the B-sublattice may experience cation order–disorder phase transitions. In many cases the degree of cation ordering can be varied by suitable synthesis conditions or subsequent sample treatment, which has a fundamental impact on the physical properties of such compounds. Therefore, understanding the mechanism of cation order–disorder phase transition and estimation of the phase transition temperature is of paramount importance for tuning of properties of such double perovskites. In this work, based on the earlier proposed cation–anion elastic bonds model, a theory of order–disorder phase transitions of B-cations in AB′1/2B′′1/2O3 perovskites is presented, which allows reliable estimation of the phase transition temperatures and of the reduced lattice constants of such double perovskites.

Azulene revisited: solid-state structure, invariom modeling and lattice-energy minimization of a classical example of disorder.

Abstract: The molecular and solid-state structure of azulene both raise fundamental questions. Therefore, the disordered crystal structure of azulene was re-refined with invariom non-spherical atomic scattering factors from new single-crystal X-ray diffraction data with a resolution of d = 0.45 A. An unconstrained refinement results in a molecular geometry with Cs symmetry. Refinements constrained to fulfill C2v symmetry, as observed in the gas phase and in high-level ab initio calculations, lead to similar figures of merit and residual densities as unconstrained ones. Such models are consistent with the structures from microwave spectroscopy and electron diffraction, albeit they are not the same. It is shown that for the disorder present in azulene, the invariom model describes valence electron density as successfully as it does for non-disordered structures, although the disorder still leads to high correlations mainly between positional parameters. Lattice-energy minimizations on a variety of ordered model structures using dispersion-corrected DFT calculations reveal that the local deviations from the average structure are small. Despite the molecular dipole moment there is no significant molecular ordering in any spatial direction. A superposition of all ordered model structures leads to a calculated average structure, which explains not only the experimental determined atomic coordinates, but also the apparently unusual experimental anisotropic displacement parameters.

A crystallographic excursion in the extraordinary world of minerals: the case of Cu‐ and Ag‐rich sulfosalts

Abstract: Copper and silver are common constituents in natural sulfosalts and can be present as minor or major components. Owing to the different kinds of coordination they can assume, these elements give rise to a number of sulfosalts that are usually quite complex to describe from a structural point of view because of the presence of twinning, disorder, polytypism and sometimes incommensurate modulation. Moreover, it is common to find them in different, partially occupied split sites, favoring the presence of strong ionic conductivity that can be related to a number of interesting technological properties. In this regard, a series of Cu- and Ag-rich sulfosalts showing an excess of these cations with respect to As, Sb and Bi is particularly interesting. Their crystal structures as well as their potential interest for materials science and solid-state physics are outlined. Copper- and mixed (Cu, Ag)-sulfosalts belonging to the wittichenite, tetrahedrite, galkhaite, routhierite and nowackiite series are discussed, together with some related compounds. Whereas in the wittichenite series Cu has either a trigonal planar or tetrahedral coordination, in members of the other series this element forms three-dimensional tetrahedral frameworks giving rise to cavities hosting other cations and anions. More difficult is the description of Ag-rich sulfosalts owing to the highly variable coordination environments shown by this element. Structural features of selected Ag sulfosalts together with members of the argyrodite series are discussed, highlighting the particular properties derived from the behavior of Ag.

Understanding geology through crystal engineering: coordination complexes, coordination polymers and metal–organic frameworks as minerals

Abstract: Recent structural studies of organic minerals, coupled with the intense search for new carbon-containing mineral species, have revealed naturally occurring structures analogous to those of advanced materials, such as coordination polymers and even open metal–organic frameworks exhibiting nanometre-sized channels. While classifying such `non-conventional' minerals represents a challenge to usual mineral definitions, which focus largely on inorganic structures, this overview highlights the striking similarity of organic minerals to artificial organic and metal–organic materials, and shows how they can be classified using the principles of coordination chemistry and crystal engineering.

The atacamite family of minerals : a testbed for quantum spin liquids

Abstract: Polymorphism of Cu2(OH)3Cl coupled with partial substitution of Jahn–Teller active Cu2+ by other divalent metal cations gives rise to the complex mineralogy of the atacamite family of secondary basic copper chlorides. Herbertsmithite, Cu3Zn(OH)6Cl2, in which Zn substitutes for one quarter of the Cu atoms, provides a lattice of corner-sharing triangles of paramagnetic Cu2+ (spin ½) cations, rendering the mineral a perfect realization of a kagome antiferromagnet. Geometric frustration of conventional antiferromagnetism is expected to give rise to exotic ground states, with dynamic magnetic structures that might turn out to be physical realizations of quantum spin liquids. In this paper, a synopsis of the key topological, compositional and behavioural features of minerals in the atacamite family is given, with emphasis on the kagome character of the resulting lattice of Cu2+ cations.

Hydrophobic dipeptides: the final piece in the puzzle.

Abstract: The crystal structure of l-valyl-l-leucine aceto­nitrile solvate presented here adds to 24 previously reported structures of dipeptides constructed from the five nonpolar amino acids l-alanine, l-valine, l-isoleucine, l-leucine and l-phenyl­alanine. It thus constitutes the final piece in the 5 × 5 puzzle of hydro­phobic dipeptide structures. This opportunity is taken to review the crystal packing arrangements and hydrogen-bonding preferences of a rather unique group of substances, with updated information on the various hydrogen-bonding patterns and the associated peptide conformations.

Determination of the miscibility gap in the solid solutions series of methylammonium lead iodide/chloride.

Abstract: Perovskites are widely known for their enormous possibility of elemental substitution, which leads to a large variety of physical properties. Hybrid perovskites such as CH3NH3PbI3 (MAPbI3) and CH3NH3PbCl3 (MAPbCl3) are perovskites with an A[XII]B[VI]X[II]3-structure, where A is an organic molecule, B is a lead(II) cation and X is a halide anion of iodine or chlorine. Whereas MAPbCl3 crystallizes in the cubic space group Pm{\overline 3}m, MAPbI3 is in the tetragonal space group I4/mcm. The substitution of I by Cl leads to an increased tolerance against humidity but is challenging or even impossible due to their large difference in ionic radii. Here, the influence of an increasing Cl content in the reaction solution on the miscibility of the solid solution members is examined systematically. Powders were synthesized by two different routes depending on the I:Cl ratio. High-resolution synchrotron X-ray data are used to establish values for the limits of the miscibility gap which are 3.1 (1.1) mol% MAPbCl3 in MAPI and 1.0 (1) mol% MAPbI3 in MAPCl. The establishment of relations between average pseudo-cubic lattice parameters for both phases allows a determination of the degree of substitution from the observed lattice parameters.

Inflexible stoichiometry in bulk pyrite FeS2 as viewed by in situ and high‐resolution X‐ray diffraction

Abstract: Non-stoichiometry is considered to be one of the main problems limiting iron pyrite, FeS2, as a photovoltaic absorber material. Although some historical diffraction experiments have implied a large solubility range of FeS2−δ with δ up to 0.25, the current consensus based on calculated formation energies of intrinsic defects has lent support to line-compound behavior. Here it is shown that pyrite stoichiometry is relatively inflexible in both reductive conditions and in autogenous sulfur partial pressure, which produces samples with precise stoichiometry of FeS2 even at different Fe/S ratios. By properly standardizing in situ gas-flow X-ray diffraction measurements, no significant changes in the lattice parameter of FeS2 can be resolved, which portrays iron pyrite as prone to forming sulfur-deficient compounds, but not intrinsic defects in the manner of NiS2−δ.

(Al,Mg)3La: a new phase in the Mg–Al–La system

Abstract: During an investigation of the Mg-rich end of the Mg–Al–La system, a new ternary phase with the composition of (Al,Mg)3La was identified. The crystal structure of this phase was determined by conventional X-ray powder diffraction and transmission electron microscopy analysis and refined using high-resolution X-ray powder diffraction. The (Al,Mg)3La phase is found to have an orthorhombic structure with a space group of C2221 and lattice parameters of a = 4.3365 (1) A, b = 18.8674 (4) A and c = 4.4242 (1) A, which is distinctly different from the binary Al3La phase (P63/mmc). The resolved structure of the (Al,Mg)3La phase is further verified by high-angle annular dark-field scanning transmission electron microscopy.

Crystal packing control of a trifluoromethyl‐substituted furan/phenylene co‐oligomer

Abstract: Furan/phenylene co-oligomer single crystals are considered as future materials for organic optoelectronics. Here, the effects of trifluoromethyl substituents on the crystallization, structure and optical properties of furan/phenylene co-oligomer 1,4-bis{5-[4-(trifluoromethyl)phenyl]furan-2-yl}benzene are studied systematically. The solution growth methods and physical vapor transport result in the formation of three polymorphs depending on the growth method and the solvent. Single-crystal X-ray analysis reveals the crystal structures to correspond to H-, J- or mixed aggregates. All obtained crystals exhibit high photoluminescence efficiency and have optical properties which strongly depend on the crystal packing. Variable-temperature X-ray powder diffraction analysis shows the thermal transition of two forms (H- and J-aggregates) into a third one (mixed aggregate). Terminal trifluoro­methyl groups induce weak intermolecular interactions which control the crystal packing and optical properties of co-oligomer single crystals.

Fundamental aspects of symmetry and order parameter coupling for martensitic transition sequences in Heusler alloys

Abstract: Martensitic phase transitions in which there is a group–subgroup relationship between the parent and product structures are driven by combinations of soft-mode and electronic instabilities. These have been analysed from the perspective of symmetry, by considering possible order parameters operating with respect to a parent structure which has space group Im{\bar 3} m. Heusler structures with different stoichiometries are derived by operation of order parameters belonging to irreducible representations {\rm H}^{+}_{1}and P1 to describe the atomic ordering configurations. Electronic instabilities are ascribed to an order parameter belonging to the Brillouin zone centre, \Gamma^{+}_{3}, which couples with shear strains to give tetragonal and orthorhombic distortions. An additional zone centre order parameter, with \Gamma^{+}_{5} symmetry, is typically a secondary order parameter but in some cases may drive a transition. Soft-mode instabilities produce commensurate and incommensurate structures for which the order parameters have symmetry properties relating to points along the Σ line of the Brillouin zone for the cubic I lattice. The electronic and soft-mode order parameters have multiple components and are coupled in a linear–quadratic manner as \lambda q_{\Gamma}q_{\Sigma}^{2}. As well as providing comprehensive tables setting out the most important group–subgroup relationships and the order parameters which are responsible for them, examples of NiTi, RuNb, Ti50Ni50−xFex, Ni2+xMn1−xGa and Ti50Pd50−xCrx are used to illustrate practical relevance of the overall approach. Variations of the elastic constants of these materials can be used to determine which of the multiple order parameters is primarily responsible for the phase transitions that they undergo.

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

Abstract: 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 Mossbauer spectroscopies.

Charge density and electrostatic potential of hepatitis C anti‐viral agent andrographolide: an experimental and theoretical study

Abstract: Andrographolide (AGH) is a hepatitis C anti-viral agent which targets the host cell by covalently binding with the NF-κBreceptor. The experimental electron density distribution study of AGH has been carried out from high-resolution X-ray diffraction data collected at 110.2 (3) K. The unit-cell packing of AGH was stabilized by strong O—H⋯O and weak C—H⋯O types of intermolecular interactions. The dissociation energy of the strong hydrogen bond O2—H22⋯O1 is very high, 32 kJ mol−1. The percentage occupancy of H⋯H interactions is found to be maximum (68.5%) when it comparing with the other types of interactions occurring in the AGH crystalline phase. The atomic valance index (Vtopo) of the C16 atom is low compared with other carbon atoms; this shows that C16 could be the possible reactive location of the AGH molecule. All atoms in the OH groups have very low Vtopo values; this indicates their role in strong hydrogen bonding interactions. The electrostatic potential (ESP) surface of AGH shows the polarization of the C16=C17 bond and ESP contour map shows several maxima at the vicinity of the C16 atom; these results strongly demonstrate that the C16 atom is the reactive location of the AGH molecule. The molecular covalent docking analysis of AGH with the NF-κB receptor has been performed and confirmed this result. The highly electronegative region around γ-butyrolactone can be helpful for initial alignment of the AGH molecule in NF-κB receptor active site. The atomic volumes of the hydrogen atoms which participate in the H⋯H interaction are found to be low.

Vanadium clusters formation in geometrically frustrated spinel oxide AlV2O4.

Abstract: The spinel oxide AlV2O4 is a unique material, in which the formation of clusters is accompanied by atomic, charge and orbital ordering and a rhombohedral lattice distortion. In this work a theory of the structural phase transition in AlV2O4 is proposed. This theory is based on the study of the order-parameter symmetry, thermodynamics, electron density distribution, crystal chemistry and mechanisms of formation of the atomic and orbital structures of the rhombohedral phase. It is established that the critical order parameter is transformed according to irreducible representation k9(τ4) (in Kovalev notation) of the Fd \bar{3}m space group. Knowledge of the order-parameter symmetry allows us to show that the derived AlV2O4 rhombohedral structure is a result of displacements of all atom types and the ordering of Al atoms (1:1 order type in tetrahedral spinel sites), V atoms (1:1:6 order type in octahedral sites) and O atoms (1:1:3:3 order type), and the ordering of dxy, dxz and dyz orbitals. Application of the density functional theory showed that V atoms in the Kagome sublattice formed separate trimers. Also, no sign of metallic bonding between separate vanadium trimers in the heptamer structure was found. The density functional theory study and the crystal chemical analysis of V-O bond lengths allowed us to assume the existence of dimers and trimers as main clusters in the structure of the AlV2O4 rhombohedral modification. The trimer model of the low-symmetry AlV2O4 structure is proposed. Within the Landau theory of phase transitions, typical diagrams of possible phase states are built. It is shown that phase states can be changed as a first-order phase transition close to the second order in the vicinity of tricritical points of the phase diagrams.

Positive and negative monoclinic deformation of corundum-type trigonal crystal structures of M2O3 metal oxides

Abstract: The crystal structures of several transition metal oxides, Ti2O3, V2O3, Cr2O3, Al2O3 and α-Fe2O3, are studied using synchrotron radiation X-ray powder diffraction. The observed angular dependence of the integral breadths is described by two models: (i) the distorted corundum-type structure model described by the space group C2/c and (ii) the Stephens model of anisotropic Bragg peak broadening. These two models are shown to be equivalent. Ti2O3, V2O3 and Cr2O3 show a `positive' distortion which is related to the possible metal–metal bond suggested by Goodenough in the literature (the deformation leads to shorter metal–metal distances) whereas Al2O3 and α-Fe2O3 show a `negative' distortion which leads to relatively longer metal–metal distances.

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

Abstract: 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.

Copper–lead selenite bromides: a new large family of compounds partly having Cu2+ substructures derivable from kagome nets

Abstract: Extensive experiments in the Pb–Cu–Se–O–Br system at 400°C yielded single crystals of nine new compounds (Cu2+Pb6(SeO3)4Br6, Cu2+Pb2(SeO3)2Br2, Cu2+3Pb2.4(SeO3)5Br0.8, Cu2+2Pb(SeO3)2Br2, Cu2+4Pb(SeO3)4Br2, [Cu2+9Pb2O4](Cu+Br2)(SeO3)4Br5, [Cu2+7PbO3](Cu+Br)0.35(SeO3)3Br4, [Cu2+8Pb2O4](Cu+Br)1.5(SeO3)4Br4, [Cu2+6Pb3O4](Cu+Pb1.27Br3.54)(SeO3)4Br2), all but one exhibiting new complex layered or open-framework architectures, organized via the host–guest principle. Five of these structures contain only bivalent copper: three with well ordered 2D structures and completely filled atomic positions, two structures have 3D frameworks. The four remaining compounds contain both, Cu2+ and Cu+, and comprise layers formed by edge- and vertex-sharing of oxocentered OCu2+4–nPbn tetrahedra decorated with SeO32− and Br− anions. The interlayer spaces are filled by partially disordered Cu+–Br and Pb–Br associations. One remarkable feature of the latter group of compounds is the presence of tetrahedral (Cu2+)4 complexes with arrangements derivable from a kagome network.

Electronic structure of two isostructural `paddle-wheel' complexes: a comparative study

Abstract: The experimental electron density distribution in two isostructural and isomorphous complexes, tetra­kis(μ2-acetato)di­aquadicopper(II) [H2OCu(ac)2Cu(ac)2H2O] (I) and tetra­kis(μ2-acetato)diaquadichromium(II), [H2OCr(ac)2Cr(ac)2H2O] (II), has been obtained from high-resolution X-ray diffraction data in order to shed light on the bonding properties in the compounds studied. It has been shown that from accurate X-ray data it is possible to discuss the bonding capability of the metal atom (Cu/Cr) and the ligands in these complexes. A comparison of results obtained from averaged and non-averaged X-ray data demonstrates that using the non-averaged data and introducing an anisotropic correction for secondary extinction errors provides a more detailed distribution of the electron density in the area of the metal atoms. In both complexes studied, the bonding of the acetate oxygen atom to the central metal atom is significantly affected by the formation of hydrogen bonds. The electron density and its Laplacian at the bond critical point of metal–oxygen coordination bonds for those oxygen atoms not involved in the intermolecular hydrogen bonds are approximately 10% larger compared with the case when oxygen atoms take part in hydrogen bonds with the neighboring water molecules. It is shown that metal–oxygen bonds in a quasi-equatorial plane are typical coordination bonds and differ significantly from the apical metal–oxygen bond. Metal–metal inter­action with a small positive value of the electron density Laplacian at this bond critical point is mainly of electrostatic character. The metal–metal inter­action is definitely not a bond according to the classical definition. Based on a search of the Cambridge Structural Database, it can be argued that there are four typical coordination bonds in the [CuO6] chromophore, similar to the four Cu—O coordination bonds in the basal plane of the CuO5 pyramid in one of the complexes under study.

A Priori Bond-Valence and Bond-Length Calculations in Rock-Forming Minerals

Abstract: Within the framework of the bond-valence model, one may write equations describing the valence-sum rule and the loop rule in terms of the constituent bond valences. These are collectively called the network equations, and can be solved for a specific bond topology to calculate its a priori bond valences. A priori bond valences are the ideal values of bond strengths intrinsic to a given bond topology that depend strictly on the formal valences of the ion at each site in the structure, and the bond-topological characteristics of the structure (i.e. the ion connectivity). The a priori bond valences are calculated for selected rock-forming minerals, beginning with a simple example (magnesiochromite, = 1.379 bits per atom) and progressing through a series of gradually more complex minerals (grossular, diopside, forsterite, fluoro-phlogopite, phlogopite, fluoro-tremolite, tremolite, albite) to finish with epidote (= 4.187 bits per atom). The effects of weak bonds (hydrogen bonds, long Na+—O2− bonds) on the calculation of a priori bond valences and bond lengths are examined. For the selected set of minerals, a priori and observed bond valences and bond lengths scatter closely about the 1:1 line with an average deviation of 0.04 v.u. and 0.048 A and maximum deviations of 0.16 v.u. and 0.620 A. The scatter of the corresponding a priori and observed bond lengths is strongly a function of the Lewis acidity of the constituent cation. For cations of high Lewis acidity, the range of differences between the a priori and observed bond lengths is small, whereas for cations of low Lewis acidity, the range of differences between the a priori and observed bond lengths is large. These calculations allow assessment of the strain in a crystal structure and provide a way to examine the effect of bond topology on variation in observed bond lengths for the same ion-pair in different bond topologies.