Armel Le Bail

Crystallography Open Database - an open-access collection of crystal structures

The Crystallography Open Database (COD) is an ongoing initiative by crystallographers to gather all published inorganic, metal–organic and small organic molecule structures in one database, providing a straightforward search and retrieval interface. The COD adopts an open-access model for its >80 000 structure files.

Whole powder pattern decomposition methods and applications: A retrospection

A modern definition for whole powder pattern decomposition WPPD methods would be that they simultaneously have to refine the unit-cell parameters and extract the best estimations of the Bragg peak intensities from a complete diffractogram. This is done very fast nowadays, irrespective of the number of Bragg peaks present in a powder diffraction pattern, but we did not attain this comfortable situation without some past efforts. The WPPD methods’ introduction occurred slowly and progressively thanks to the increase in computer power, the improvements in graphical user interfaces, the diffractometer data digitalization, the availability of synchrotron and neutron radiation, and last but not least, the proposition of new algorithms. Innovations were not instantly accepted this being true for all the whole powder pattern fitting methods including the Rietveld and the decomposition methods or could not be applied immediately to every radiation source or diffractometer the hardware before adaptations made by an essential category of crystallographers being conceivers and developers of the software. Ancestors of the WPPD methods extracted peak intensities without the cell restraint, so that each peak position was a parameter to be refined as well as the peak intensity, the peak shape and its width. This is still useful if the aim is the search for the peak positions for indexing, though derivative methods can make that peak-position-hunting job faster. Taking advantage of the indexing see a recent review paper by Bergmann et al. 2004, new WPPD methods, applying cell restraint to the peak position, opened the door to a long list of new possibilities and applications including first indexing confirmation which are detailed in this paper. However, only some selected application references will be provided because the number of papers involved is quite high and increasing more than 2000 texts specify the use of WPPD methods. Contributions from Rennes by Louer’s group from 1987 to 1993 will be especially enlightened, not forgetting the other players during that same time, restraining generally to the structure determinations by powder diffractometry SDPD applications published in the early stages of this retrospection because the subsequent activity increased too considerably, by more than 850 SDPDs in the last ten years. If only a partial review of applications can be given, the evolution of the methods will be discussed as completely as possible.

Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration

Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

Inorganic structure prediction with GRINSP

A new computer program is described, GRINSP (geometrically restrained inorganic structure prediction), which allows the exploration of the possibilities of occurrence of 3-, 4-, 5- and 6-connected three-dimensional networks. Hypothetical (as well as known structure) models for binary compounds are produced with exclusive connection of polyhedra by corners, such as [MX3] triangles in M2X3 formulation, [MX4] tetrahedra in MX2 (zeolites or dense SiO2 polymorphs), [MX5] polyhedra in M2X5, and finally [MX6] octahedra in MX3 polymorphs. Moreover, hypothetical ternary compounds are built up by combinations of either two different polyhedra or two different radii for two different cations adopting the same coordination. The cost function is based on the agreement of the model interatomic distances with ideal distances provided by the user. The Monte Carlo algorithm first finds structure candidates selected after the verification of the expected geometry, and then optimizes the cell parameters and the atomic coordinates. A satellite software (GRINS) uses the predicted models and produces the characteristics of isostructural compounds which would be obtained by cationic substitutions. A huge list of CIF files of hypothetical boron oxide polymorphs (including nanotubes), zeolites, aluminium and 3d-element fluorides, fluoroaluminates, borosilicates, titanosilicates, gallophosphates etc., is freely available at the PCOD (Predicted Crystallography Open Database).

Structure determination of β- and γ-BaAlF5 by X-ray and neutron powder diffraction: A model for the α → β γ transitions

{beta}-BaAlF{sub 5} is monoclinic (space group P2{sub 1}/n): a = 5.1517(1) {angstrom}, b = 19.5666(4) {angstrom}, c = 7.5567(2) {angstrom}, {beta} = 92.426(1){degree}, Z = 8. {gamma}-BaAlF{sub 5} is monoclinic (space group P2{sub 1}): a = 5.2584(1) {angstrom}, b = 9.7298(2) {angstrom}, c = 7.3701(2) {angstrom}, {beta} = 90.875(1){degree}, Z = 4. Both structures are determined ab initio from X-ray powder data; final results are given from neutron powder data refinements (R{sub I} = 0.038, R{sub P} = 0.072, and R{sub WP} = 0.087 and R{sub I} = 0.048, R{sub P} = 0.083, and R{sub WP} = 0.101 for the {beta} and {gamma} phases, respectively). Like {alpha}-BaAlF{sub 5}, the {beta} and {gamma} phases are built up from isolated infinite (AlF{sub 5}){sup 2n{minus}}{sub n} chains with AlF{sub 6} octahedra sharing corners in a cis-position. Close structural relationships are shown to exist between the Ba-Al cationic subnetwork of: {alpha}-BaAlF{sub 5} and the CrB-type structure; {beta}-BaAlF{sub 5} and the SrAg-type; {gamma}-BaAlF{sub 5} and the FeB-type.

SYNTHETIC PATHWAYS TO VANADYL PHOSPHATES

Abstract A general scheme concerning the synthesis and reactivity of oxovanadium phosphates is presented. In particular, the isolation of new materials of composition NH 4 (VO 2 )(HPO 4 ), [M(en) 2 ] x VOPO 4 ·(2−2 x )H 2 O (M=Cu or Ni; 0.03⩽ x ⩽0.20; en=ethylendiamine) and Na x VOPO 4 is described. The structures of α-NH 4 (VO 2 ) (HPO 4 ), β-A(VO 2 ) (HPO 4 ) (A=NH + 4 , k + , Rb + , Cs + ) and VOHPO 4 ·2H 2 O are reported. New spectroscopic (IR, EPR, NMR) results are furnished. The magnetic properties of vanadium (IV)-containing derivatives are discussed on the basis of the structural results.

Frontiers between crystal structure prediction and determination by powder diffractometry

The fuzzy frontiers between structure determination by powder diffractometry and crystal structure prediction are discussed. The application of a search-match program combined with a database of more than 60 000 predicted powder diffraction patterns is demonstrated. Immediate structure solution (before indexing) is shown to be possible by this method if the discrepancies between the predicted crystal structure cell parameters and the actual ones are

La10W2O21: an anion-deficient fluorite-related superstructure with oxide ion conduction.

The crystal structure of La10W2O21, which has to be reformulated (La5.667W0.333)LaWO14□2, is best described, on average, by a 2 × 2 × 2 anion-deficient fluorite-related superstructure cubic cell, with space group F4 3m, Z = 4, and a = 11.17932(6) Å, similar to Y7ReO14--δ. The 32 cations are distributed with lanthanum on the 4a-site, tungsten on the 4b-site, and a partial occupancy of the 24g-site by La (94%) and W. The 56 oxygen atoms occupy four 16e-sites, three of them fully and with an occupancy of 1/2 for the fourth one. Others M10W2O21 (M = Er, Y) adopt a 3 × 2 × 2 fluorite superstructure with W in octahedral sites, whereas W is mainly in tetrahedral sites in La10W2O21. Several powerful techniques such as crystal image furnace synthesis, (139)La nuclear magnetic resonance (NMR) and convergent beam electron diffraction (CBED) were used to achieve our results. Transmission electron microscopy (microdiffraction, CBED, and Tanaka patterns) brought us the real symmetry, showing that indeed classical cubic twinning along the 3-fold axis does take place. The surprising La/W mixed site is nicely confirmed by (139)La NMR. This compound exhibits interesting fast oxide ion conducting properties, comparable with LAMOX (Lacorre et al. Nature 2000, 404, 856-858) at low temperature. As opposed to many ionic conductors, no temperature structural transition is observed. Its conductivity is about 6.4 × 10(-4) S·cm(-1) at 700 °C.

A crystal structure for the souzalite/gormanite series from synchrotron powder diffraction data

In absence of suitable single crystal due to polysynthetic twinning, the crystal structure of a specimen in the souzalite/gormanite series (Fe, Mg) 3 (Al, Fe) 4 (PO 4 ) 4 (OH) 6 -2H O is determined ab initio from synchrotron powder diffraction data. The crystals belong to space group P 1, the cell is different from previously reported with a = 7.2223(1), b = 11.7801(1), c = 5.1169(1) A; α = 90.158(1), β = 109.938(1), γ = 81.330(1)°; V = 404.02(1) A 3 ; Z = 1. The structure consists of infinite chains of alternating [FeO 6 ], [MgO 6 ] and [AlO 6 ] octahedra sharing faces and/or edges. These chains are connected by corners with clusters of three corner-sharing [AlO 6 ] octahedra, forming octahedral layers which are interconnected by [PO 4 ] groups. A comparison with other minerals of similar composition and structure is made (dufrenite, burangaite).

Decafluorocyclohex-1-ene at 4.2 K - crystal structure and theoretical analysis of weak interactions.

The crystal structure of 1,2,3,3,4,4,5,5,6,6-decafluorocyclohex-1-ene (decafluorocyclohex-1-ene, C6F10) was solved in direct space from neutron powder diffraction data previously collected at 4.2 K [Pawley, G. S. (1981). J. Appl. Cryst. 14, 357-361] and refined by energy minimization in the solid state. To optimize the positions of the 64 atoms in the monoclinic computational cell the PBESOL and hybrid PBE0 functionals were used. The crystal structure of the title compound, which is liquid at room temperature, is built of antiparallel pairs of molecules assembled into molecular columns stacked along the a axis. Dominating the crystal-building forces are weak intermolecular dispersion interactions. Bonding conditions in the structure were analysed by theoretical molecular calculations of representative next-neighbor molecular dimers carried out using dispersion-corrected density functional theory (DFT) functionals and the SCS-MP2 wavefunction method. The largest interaction energy is of the order of ∼ 21 kJ mol(-1), above the interaction energy of a benzene dimer (11.3 kJ mol(-1)) and close to that of a water dimer (20.9 kJ mol(-1)). The interaction energy for the second most stable dimer can be compared with either that of a benzene dimer or of a C-H...π hydrogen bond. The remaining five weakly interacting dimers (∼ 4.2-8.4 kJ mol(-1)) can be characterized as having stronger interactions than those of methane dimers (-2.2 kJ mol(-1)), but weaker than those of benzene molecule pairs or weak C-H...C interactions for instance.