Showing papers in "Acta Crystallographica Section B-structural Science in 2011"

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Abstract: Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.

Structural analysis and multipole modelling of quercetin monohydrate--a quantitative and comparative study.

Abstract: The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.

Neutron powder diffraction refinement of PbZr1 − xTixO3

Abstract: Rietveld refinement of different structural models using neutron diffraction data for a series of powders of lead zirconate titanate, PbZr1 − xTixO3 (PZT), is described. It is found that at all the compositions and temperatures studied the best results include contributions from more than one phase in order to fit the data. Consequently a new phase diagram is proposed.

Structural building principles of complex face-centered cubic intermetallics

Abstract: Fundamental structural building principles are discussed for all 56 known intermetallic phases with approximately 400 or more atoms per unit cell and space-group symmetry F\bar{4}3m, Fd\bar{3}m, Fd\bar{3}, Fm\bar{3}m or Fm\bar{3}c. Despite fundamental differences in chemical composition, bonding and electronic band structure, their complex crystal structures show striking similarities indicating common building principles. We demonstrate that the structure-determining elements are flat and puckered atomic {110} layers stacked with periodicities 2p. The atoms on this set of layers, which intersect each other, form pentagon face-sharing endohedral fullerene-like clusters arranged in a face-centered cubic packing (f.c.c.). Due to their topological layer structure, all these crystal structures can be described as (p × p × p) = p3-fold superstructures of a common basic structure of the double-diamond type. The parameter p, with p = 3, 4, 7 or 11, is determined by the number of layers per repeat unit and the type of cluster packing, which in turn are controlled by chemical composition.

Structure analysis of titanate nanorods by automated electron diffraction tomography.

Abstract: A hitherto unknown phase of sodium titanate, NaTi3O6(OH)·2H2O, was identified as the intermediate species in the synthesis of TiO2 nanorods. This new phase, prepared as nanorods, was investigated by electron diffraction, X-ray powder diffraction, thermogravimetric analysis and high-resolution transmission electron microscopy. The structure was determined ab initio using electron diffraction data collected by the recently developed automated diffraction tomography technique. NaTi3O6(OH)·2H2O crystallizes in the monoclinic space group C2/m. Corrugated layers of corner- and edge-sharing distorted TiO6 octahedra are intercalated with Na+ and water of crystallization. The nanorods are typically affected by pervasive defects, such as mutual layer shifts, that produce diffraction streaks along c*. In addition, edge dislocations were observed in HRTEM images.

R-free factor and experimental charge-density analysis of 1-(2'-aminophenyl)-2-methyl-4-nitroimidazole: a crystal structure with Z' = 2.

Abstract: The experimental charge-density distribution was determined for 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole crystals. An anharmonic model was applied to the N atoms of both amino groups and to one nitro group in order to account for high residual peaks after harmonic multipole refinement and to obtain a better charge-density model. Free R-factor calculations [Brunger (1992). Nature, 355, 472–475] with restrained models implemented in MoPro were used to determine the degree of similarity of the two symmetry-independent molecules in the unit cell. The results are compared with 1-phenyl-4-nitroimidazole in order to analyze the influence of the amine and methyl functional groups. The asymmetric unit contains two symmetry-independent molecules giving rise to a dimer connected via strong N—H⋯N hydrogen bonds; these dimers are the building blocks of the crystal. In the crystal structure there are also weaker interactions and many short directional contacts (C—H⋯O, C—H⋯N and C—H⋯π), for which the Koch–Popelier topological criteria were applied. This analysis revealed that the C—H⋯π interactions lie at the border between weak hydrogen bonds and van der Waals interactions. Special attention was also paid to stabilizing H⋯H interactions. It turned out that the electron density, Laplacian and density energies at the critical points show an exponential dependence on the contact distance, similar to the relation found for other interactions.

Solid-state transformations in the β-form of chlorpropamide on cooling to 100 K.

Abstract: A single-crystal X-ray diffraction study of the effect of cooling down to 100 K on the β-form of chlorpropamide, 4-chloro-N-(propylaminocarbonyl)benzenesulfonamide, has revealed reversible phase transitions at ∼ 257 K and between 150 and 125 K: β (Pbcn, Z′ = 1)  βII (P2/c, Z′ = 2)  βIII (P2/n, a′ = 2a, Z′ = 4); the sequence corresponds to cooling. Despite changes in the space group and number of symmetry-independent molecules, the volume per molecule changes continuously in the temperature range 100–300 K. The phase transition at ∼ 257 K is accompanied by non-merohedral twinning, which is preserved on further cooling and through the second phase transition, but the original single crystal does not crack. DSC (differential scanning calorimetry) and X-ray powder diffraction investigations confirm the phase transitions. Twinning disappears on heating as the reverse transformations take place. The second phase transition is related to a change in conformation of the alkyl tail from trans to gauche in 1/4 of the molecules, regularly distributed in the space. Possible reasons for the increase in Z′ upon cooling are discussed in comparison to other reported examples of processes (crystallization, phase transitions) in which organic crystals with Z′ > 1 have been formed. Implications for pharmaceutical applications are discussed.

High-pressure experimental study on Rb2S: antifluorite to Ni2In-type phase transitions.

Abstract: The high-pressure behaviour of dirubidium sulfide, Rb2S, with antifluorite-type structure under room conditions (space group Fm\bar 3 m) has been studied up to 8 GPa at room temperature using angle-dispersive X-ray powder diffraction in a diamond–anvil cell (DAC). X-ray measurements have allowed us to completely characterize two phase transitions upon compression: (i) to an anticotunnite-type structure (Pnma) at some pressure between 1 bar and 0.7 GPa, and (ii) to a Ni2In-type structure (P63/mmc) at 2.6 GPa. A gradual transition from the Pnma to the P63/mmc structures seems to occur between 2.6 and 4.5 GPa. These results are in excellent agreement with previous theoretical predictions. Strong luminescence is observed above 2.6 GPa (band maximum at 703 nm) when the transition to the Ni2In-type phase starts to occur, the band maximum showing a non-linear blue shift with pressure. The observed sequence of phase transitions in Rb2S is discussed in relation to the high-pressure structural behaviour of isomorphic sulfides and the structures are compared with the cationic arrays of their corresponding oxides (e.g. rubidium sulfate, in which the sulfide has been oxidized).

The whole range of hydrogen bonds in one crystal structure: neutron diffraction and charge-density studies of N,N-dimethylbiguanidinium bis(hydrogensquarate).

Abstract: N,N-Dimethylbiguanidinium bis(hydrogensquarate) features an impressive range of hydrogen bonds within the same crystal structure: neighbouring anions aggregate to a dianionic pair through two strong O—H⋯O interactions; one of these can be classified among the shortest hydrogen bonds ever studied. Cations and anions in this organic salt further interact via conventional N—H⋯O and nonclassical C—H⋯O contacts to an extended structure. As all these interactions occur in the same sample, the title compound is particularly suitable to monitor even subtle trends in hydrogen bonds. Neutron and high-resolution X-ray diffraction experiments have enabled us to determine the electron density precisely and to address its properties with an emphasis on the nature of the X—H⋯O interactions. Sensitive criteria such as the Laplacian of the electron density and energy densities in the bond-critical points reveal the incipient covalent character of the shortest O—H⋯O bond. These findings are in agreement with the precise geometry from neutron diffraction: the shortest hydrogen bond is also significantly more symmetric than the longer interactions.

Determination of the local structure of a cage with an oxygen ion in Ca12Al14O33.

Abstract: The crystal structure of mayenite (12CaO·7Al2O3) has been investigated by single-crystal synchrotron diffraction with high resolution and accuracy, using a four-circle diffractometer equipped with an avalanche photodiode detector (APD) detector installed at PF14A in Tsukuba, Japan. Analysis revealed random displacements of ions by the electrostatic force of the O2− ion (O3) clathrated in two out of 12 cages. O3 ions are located at general positions close to the \bar 4 site at the centre of each cage. The difference-density map revealed two large peaks corresponding to displaced Ca ions. The positive ions close to O3 are displaced and one-to-one correspondence was found between one of the four equivalent O3 ions and the displaced ions. When an O3 ion is present in the cage the Al ion at the 16c position moves 0.946 (3) A toward the O3 ion. One of the Al—O bonds is broken and a new Al—O3 bond is created. The result is an AlO4 tetrahedron that is quite deformed. The three O1 ions and the O2 ion of the destroyed AlO4 tetrahedron are forcibly displaced. O1 and O2 have two and one displaced ions, respectively. The local structure of the cage occupied by one of the four O3 ions was determined by calculating the electrostatic potential and electric field in the deformed cage, although the position of one of the displaced O1 ions was not clearly identified.

Charge‐density analysis of 1‐nitroindoline: refinement quality using free R factors and restraints

Abstract: Nitramines and related N-nitro compounds have attracted significant attention owing to their use in rocket fuel and as explosives. The charge density of 1-nitroindoline was determined experimentally and from theoretical calculations. Electron-density refinements were performed using the multipolar atom formalism. In order to design the ideal restraint strategy for the charge-density parameters, R-free analyses were performed involving a series of comprehensive refinements. Different weights were applied to the charge-density restraints, namely the similarity between chemically equivalent atoms and local symmetry. Additionally, isotropic thermal motion and an anisotropic model calculated by rigid-body analysis were tested on H atoms. The restraint weights which resulted in the lowest values of the averaged R-free factors and the anisotropic H-atom model were considered to yield the best charge density and were used in the final refinement. The derived experimental charge density along with intra- and intermolecular interactions was analysed and compared with theoretical calculations, notably with respect to the symmetry of multipole parameters. A comparison of different refinements suggests that the appropriate weighting scheme applied to charge-density restraints can reduce the observed artefacts. The topological bond orders of the molecule were calculated.

Water channel structure of bassanite at high air humidity: crystal structure of CaSO4·0.625H2O.

Abstract: Structure analysis using single-crystal diffraction was carried out as a contribution to the dispute about the nature of the water channel structure of bassanite (CaSO4·05H2O) A recent result of Weiss & Brau (2009) for the crystal structure of bassanite (monoclinic, space group C2) at ambient conditions of air humidity was confirmed In the presence of high relative air humidity the crystal structure of bassanite transformed due to the incorporation of additional water of hydration The crystal structure of CaSO4·0625H2O was solved by single-crystal diffraction at 298 K and 75% relative air humidity The experimental results provided an insight into both crystal structures A model explaining the phase transition from CaSO4·0625H2O to CaSO4·05H2O was derived The monoclinic cell setting of CaSO4·05H2O and the trigonal cell setting of CaSO4·0625H2O were confirmed by powder diffraction

Experimental and theoretical electron-density study of three isoindole derivatives: topological and Hirshfeld surface analysis of weak intermolecular interactions.

Abstract: A combined experimental and theoretical study of three isoindole derivatives was made on the basis of a topological analysis of their electron-density distributions. Experimental electron densities were determined from high-resolution X-ray diffraction data sets measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using DFT methods at the B3LYP\6-311++G(3df,3pd) level of approximation. Both experimental and theoretical models are in good agreement with each other. Since the analysed structures possess a variety of hydrogen-bonding interactions, weak intermolecular contacts of C—H⋯C(π), C,N(π)⋯C,N(π) and H⋯H types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment.

Failures of fractional crystallization: ordered co-crystals of isomers and near isomers.

Abstract: A list of 270 structures of ordered co-crystals of isomers, near isomers and molecules that are almost the same has been compiled. Searches for structures containing isomers could be automated by the use of IUPAC International Chemical Identifier (InChI™) strings but searches for co-crystals of very similar molecules were more labor intensive. Compounds in which the heteromolecular A...B interactions are clearly better than the average of the homomolecular A...A and B...B interactions were excluded. The two largest structural classes found include co-crystals of configurational diastereomers and of quasienantiomers (or quasiracemates). These two groups overlap. There are 114 co-crystals of diastereomers and the same number of quasiracemates, with 71 structures being counted in both groups; together the groups account for 157 structures or 58% of the total. The large number of quasiracemates is strong evidence for inversion symmetry being very favorable for crystal packing. Co-crystallization of two diastereomers is especially likely if a 1,1 switch of a methyl group and an H atom, or of an inversion of a [2.2.1] or [2.2.2] cage, in one of the diastereomers would make the two molecules enantiomers.

Octahedral tilts, symmetry-adapted displacive modes and polyhedral volume ratios in perovskite structures

Abstract: The structures of tilted perovskites in each of the 15 tilt systems have been decomposed into the amplitudes of symmetry-adapted modes in order to provide a clear and unambiguous definition of the tilt angles. A full expression in terms of the mode amplitudes for the ratio of the volumes of the two polyhedra within the perovskite structure for each of the 15 tilt systems is derived, along with more general expressions in terms of either mode amplitudes or tilt angles that can be used to estimate this ratio when the distortions of the octahedra are small.

Determining the structure of a benzene7.2-silicalite-1 zeolite using a single-crystal X-ray method

Abstract: A simple method for preparing orthorhombic single crystals of benzene-silicalite-1 was developed. A silicalite-1 crystal was pressed with a weight of 2 g along the +c and −c crystallographic axes while the temperature was increased to 473 K. The temperature was then slowly reduced to 313 K, and these heating and cooling steps were repeated three times. After the orthorhombic single crystals adsorbed benzene, the crystal structure of the resulting benzene-silicalite-1 was determined. There were two kinds of benzene molecules in the asymmetric unit. One was located at the intersection of the straight channels and the sinusoidal channels with the benzene ring parallel to the ac plane. The other benzene was located in the middle of the straight channel.

Unifying cluster-based structure models of decagonal Al-Co-Ni, Al-Co-Cu and Al-Fe-Ni.

Abstract: The geometrical building principles of Al-based decagonal quasicrystals and their approximants are discussed from a cluster-based approach. Our investigations cover 11 modifications with two- or four-layer periodicity in the systems Al–Co–Ni, Al–Co–Cu and Al–Fe–Ni. We identified a cluster that leads to a unifying view of all these phases. This unit cluster has ∼ 20 A diameter, four-layer periodicity along its tenfold axis and rod symmetry group p \overline{10}2m. The models obtained are in agreement with all the electron-density maps and electron-microscopy images available.

Diffuse scattering resulting from macromolecular frustration

Abstract: Distinctive diffuse scattering in the form of diffuse rings around Bragg positions has been observed in the diffraction patterns of a crystal of the N-terminal fragment of the Gag protein from Feline Foamy Virus. It is shown that these are caused by geometric frustration as molecules try to pack on the triangular b-c mesh of the space group P6(1)22. In order to explain the strong diffuse scattering it is necessary for the crystal to contain occupational disorder such that each unit cell contains one or other of two different molecular arrangements, A and B. The frustration arises because the nearest-neighbour packing prefers neighbouring cells to be AB or BA, which cannot be achieved on all three sides of a triangle simultaneously. To explain the observation that reciprocal sections hk5n, where n = integer, contain only Bragg peaks it is necessary that A and B are identical molecular arrangements differing only by a translation of 0.2c. The implications of the disorder for solving the structure of the protein by conventional techniques as well as the possibility of using the diffuse scattering for this purpose are discussed.

The not so simple cubic structure of PbZr1 − xTixO3 (PZT): complex local structural effects in perovskites

Abstract: High-resolution neutron diffraction on the important piezoelectric lead zirconate titanate (PZT) has found that oxygen disorder exists well into the cubic phase. This unexpected result shows that within this phase there persists a remnant of the tilted oxygen octahedra present within the room-temperature ferroelectric phase. The result is that the cubic phase, far from having a simple crystal structure, exhibits a more complex local structure than had hitherto been thought.

Deducing chemical structure from crystallographically determined atomic coordinates.

Abstract: An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures.

Structural phase transitions in tetra(isopropylammonium) decachlorotricadmate(II), [(CH3)2CHNH3]4Cd3Cl10, crystal with a two-dimensional cadmium(II) halide network.

Abstract: Single crystals of tetra(isopropylammonium) decachlorotricadmate(II) as a rare example of a two-dimensional cadmium(II) halide network of [Cd(3)Cl(10)](n)(4-) have been synthesized and characterized by means of calorimetry and X-ray diffraction. The crystals exhibit polymorphism in a relatively narrow temperature range (three phase transitions at 353, 294 and 259 K). Our main focus was to establish the mechanism of these successive transformations. The crystal structure was solved and refined in the space group Cmce at 375 K (Phase I), Pbca at 320 K (Phase II) and P2(1)2(1)2(1) (Phase III) at 275 K in the same unit-cell metric. The structure is composed of face-sharing polyanionic [Cd(3)Cl(10)](4-) units which are interconnected at the bridging Cl atom into four-membered rings forming a unique two-dimensional network of [Cd(3)Cl(10)](n)(4-). The interstitial voids within the network are large enough to accommodate isopropylammonium cations and permit thermally activated rotations. While in Phase I isopropylammonium tetrahedra rotate almost freely about the C-N bond, the low-temperature phases are the playground of competition between the thermally activated disorder of isopropylammonium cations and stabilizing N-H···Cl hydrogen-bond interactions. The transition from Phase I to II is dominated by a displacive mechanism that leads to significant rearrangement of the polyanionic units. Cation order-disorder phenomena become prominent at lower temperatures.

Charge-density analysis in polymorphs of urea-barbituric acid co-crystals.

Abstract: High-resolution single-crystal X-ray diffraction measurements at 100 K were performed for the two polymorphs of urea–barbituric acid co-crystals: (I) P21/c and (II) Cc. Experimental and theoretical charge density and its properties were analysed for (I) and (II) in order to confirm the previous observation that in the polymorphs studied the barbituric acid molecules adopt different mesomeric forms, leading to different hydrogen-bond systems. Koch and Popelier criteria were applied to distinguish between hydrogen bonds and van der Waals interactions in the structures presented.

Determination of the crystal structure of nifedipine form C by synchrotron powder diffraction

Abstract: The crystal structure of the metastable form C polymorph of nifedipine [C17H18N2O6, 3,5-dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate] was determined by means of direct-space techniques applied to high-resolution synchrotron powder diffraction data. The polymorph crystallizes in the space group P\bar 1 and exhibits a molecular packing significantly different from that of the stable modification, with molecules aligned in an orthogonal configuration inside the unit cell. The molecular conformation, on the other hand, remains substantially unmodified between the two polymorphs. Additionally, in situ thermal characterization of nifedipine crystallization behaviour was performed, confirming the nucleation of another metastable polymorph (form B) prior to the complete crystallization of the stable modification. A complete structural characterization of form B was not possible owing to its very limited stability interval.

Dynamic orientational disorder in crystals of fluoroelpasolites, structural refinement of (NH4)3AlF6, (NH4)3TiOF5 and Rb2KTiOF5.

Abstract: Room-temperature crystal structures of triammonium hexafluoroaluminate, (NH(4))(3)AlF(6) (I), and triammonium oxopentafluorotitanate, (NH(4))(3)TiOF(5) (II), were refined, and the crystal structures of dirubidium potassium oxopentaflourotitanate, Rb(2)KTiOF(5), at 297 K (III) and 218 K (IV) were determined using single-crystal X-ray diffraction techniques In ammonium fluoroelpasolites [(I) and (II)], the ligand (O, F) atoms are located in the mixed 24e + 96j position of the Fm3m unit cell The 24e position is occupied by the ligand atoms predominantly in (III) and fully in (IV) 'Ordered' N1 and Rb atoms are tetrahedrally displaced from the 8c position into the 32f site, and the H atoms of the disordered ammonium group N2 are statistically distributed in the 96k and 32f positions The Ti atoms in (II) and (IV) are shifted from the 4a position to 24e thus allowing identification of the O and F atoms in the octahedron on a local scale The disorder in the crystals is of a dynamic nature Unique Raman spectra of Rb(2)KTiOF(5) under the laser beam of 1064 nm indicate fast octahedral reorientations resulting in physical equalizations of the Ti-O and Ti-F distances as well as in the appearance of totally synchronous Ti-O and Ti-F stretching vibrations at 750 cm(-1) This phenomenon is assumed to also take place under X-rays

Seven hexamethylenetetramine (HMTA) complexes with mono- and dicarboxylic acids: analysis of packing modes of HMTA complexes in the literature

Abstract: The crystal structures of seven hexamethylenetetramine (HMTA) complexes, or co-crystals, with carboxylic acid donor molecules are reported to explain the link between the molecular structure of HMTA and the crystal structure of the co-crystals, i.e. the dimension and shape of their hydrogen-bonded assembly. A comprehensive and detailed literature survey of HMTA complexes (38), be they neutral co-crystals or salts, with molecules containing carboxylic acid and phenol functional groups reveals that in general two N acceptors are used for strong O—H⋯N interactions. Owing to the relative arrangement of two of the four N atoms, the most common type of assembly features one-dimensional zigzag chains. Weak interactions of the C—H⋯N type are formed by N atoms not involved in strong interactions. These chains also form the basis of two-dimensional assemblies. These one- and two-dimensional assemblies feature either two or three functional groups. If only one functional group is on the donor molecule, then wing or V-shaped zero-dimensional assemblies are formed, which can be considered to be the building blocks for one- and two-dimensional assemblies. In general, the HMTA molecules form two-dimensional layers which are stabilized by weak hydrogen bonds. Co-crystals with cyclohexylcarboxylic acid (I), 4-fluorobenzoic acid (II), 4-methylbenzoic acid (III) and cinnamic acid (IV) all feature the V-shaped zero-dimensional assemblies. Co-crystals with cis-1,4-cyclohexyldicarboxylic acid (VI) and trans-1,4-cyclohexylcarboxylic acid (VII) feature the zigzag chains and can be structurally derived from co-crystal (I). Co-crystal (V), with 4-nitrobenzoic acid, has solvent water included and features hydrogen bonding to all four N atoms of the HMTA molecule.

Crystal packing and melting temperatures of small oxalate esters: the role of C-H···O hydrogen bonding.

Abstract: The simple dialkyl oxalates are generally liquids at room temperature except for dimethyl and di-tert-butyl oxalate which melt at 327 and 343 K. The crystal structures of diethyl, di-iso-propyl, di-n-butyl, di-tert-butyl and methyl ethyl oxalates were determined. The liquid esters were crystallized using the cryocrystallization technique. A comparison of the intermolecular interactions and packing features in these crystal structures was carried out. The crystal structure of dimethyl oxalate was redetermined at various temperatures. The other compounds were also studied at several temperatures in order to assess the attractive nature of the hydrogen bonds therein. A number of moderate to well defined C—H⋯O interactions account for the higher melting points of the two solid esters. Additionally, a diminished entropic contribution ΔSm in di-tert-butyl oxalate possibly increases the melting point of this compound further.

Temperature-dependent analysis of thermal motion, disorder and structures of tris(ethylenediamine)zinc(II) sulfate and tris(ethylenediamine)copper(II) sulfate.

Abstract: The crystal structures of the title compounds have been determined in the temperature range 140-290 K for the zinc complex, and 190-270 K for the copper complex. The two structures are isostructural in the trigonal space group P31c with the sulfate anion severely disordered on a site with 32 (D(3)) symmetry. This sulfate disorder leads to a disordered three-dimensional hydrogen-bond network, with the N-H atoms acting as donors and the sulfate O atoms as acceptors. The displacement parameters of the N and C atoms in both compounds contain disorder contributions in the out-of-ligand plane direction owing to ring puckering and/or disorder in hydrogen bonding. In the Zn compound the vibrational amplitudes in the bond directions are closely similar. Their differences show no significant deviations from rigid-bond behaviour. In the Cu compound, a (presumably) dynamic Jahn-Teller effect is identified from a temperature-independent contribution to the displacement ellipsoids of the N atom along the N-Cu bond. These conclusions derive from analyses of the atomic displacement parameters with the Hirshfeld test, with rigid-body models at different temperatures, and with a normal coordinate analysis. This analysis considers the atomic displacement parameters (ADPs) from all different temperatures simultaneously and provides a detailed description of both the thermal motion and the disorder in the cation. The Jahn-Teller radii of the Cu compound derived on the basis of the ADP analysis and from the bond distances in the statically distorted low-temperature phase [Lutz (2010). Acta Cryst. C66, m330-m335] are found to be the same.

Modulated structure of nepheline

Abstract: The incommensurately modulated structure of a natural nepheline of composition K054Na324Ca003Al384Si416O16 has been determined in superspace The compound crystallizes in the trigonal centered superspace group X3(00γ)0 with γ = 02048 (10), X = (0, 0, 0, 0), (1/3, 2/3, 0, 2/3), (2/3, 1/3, 0, 1/3), a = 172889 (8) and c = 83622 (10) A The structure is characterized by a framework of corner-connected (Al,Si)O4 tetrahedra The additional cations are incorporated in two different types of channels of the framework All atoms in the structure are displacively modulated with amplitudes below 01 A The modulation can be well described taking into account harmonics of first order only Atomic positions in the smaller channels of the framework are fully occupied by Na+ Cationic positions in the larger channel are occupationally modulated, yet the variation of electron density as a function of the internal coordinate t is very small and indicates that the incorporation of different types of cations (K+, Na+, Ca2+) and vacancies is realised in a highly disordered way Average T—O distances indicate a nearly complete Al/Si ordering in the tetrahedral framework A large part of the O atoms are approximated by split-atom positions, which are additionally affected by occupational modulation resulting in a high degree of disorder in the modulated structure Occupational probabilities for the split-atom positions are complementary Occupational modulations of the cations in the larger channels and the O atoms of the tetrahedral framework are coupled and correlations between occupational and displacive modulations exist

Charge-density distribution in hydrogen methylphosphonates of calcium and lithium.

Abstract: Two new crystal structures, calcium bis(hydrogen methylphos­phonate), Ca(CH3PO3H)2, and lithium hydrogen methylphos­phonate, Li(CH3PO3H), have been obtained, and the experimental and theoretical charge densities, as well as their topological properties, are reported. Both compounds display layered structures. Each hydrogen methylphosphonate anion coordinates three metal cations in the calcium compound and four in the lithium one. Weak polarization of oxygen lone pairs is observed, with lithium showing somewhat stronger polarization strength than calcium. The reported topological properties from the density functional theory (DFT) and X-ray approach are consistent with each other. In both structures the P—O bonds have a significant share of ionic character. The hyperconjugation effects within the phosphonate group are quenched upon coordination of the metal cations.

Bis(μ2-2-(dimethylamino)ethoxo-N,O,O)-di(phenolato-O)ditin(II): a high-resolution single-crystal X-ray diffraction and quantum chemical study

Abstract: Experimental and calculated electron density functions ρ(r) of the title compound in the crystal were obtained. These were compared with ρ(r) for an isolated dimer. Application of the `Atoms in Molecules' theory allowed the visualization of the electron lone pair (Lp) of tin(II) and the calculation of some bond energies and all atomic charges. The stereochemical activity of the Lp was demonstrated and its volume was estimated to be approximately 10 A3. The energies of N→Sn and Sn—O bonds were found to be 13–18 and 25–52 kJ mol−1. According to the experimental, AM05-PW and PBE0/6-311G(d,p) calculation data, µ2-2-(dimethylamino)ethoxoate accepts 0.68, 0.45 and 0.40 e from the Sn atom. Using the example of µ2-2-(dimethylamino)ethoxoates and complexes of bis(n-butyl)tin(IV) it was demonstrated that the more screened the Sn atom, the better the catalytic activity of its complex in polyurethane synthesis.