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PubMed2001

Structure of C15-, C17- and C19-mono-acid beta-triacylglycerols.

The crystal structures of beta-1,2,3-tris(pentadecanoyl)glycerol (beta-C15C15C15), beta-1,2,3-tris(heptadecanoyl)glycerol (beta-C17C17C17) and beta-1,2,3-tris(nonadecanoyl)glycerol (beta-C19C19C19) have been determined from high-resolution X-ray powder diffraction data. Grid search and Rietveld refinement have been used to determine and refine the structures, respectively. As in beta-1,2,3-tris(tridecanoyl)glycerol (beta-C13C13C13) and the even-numbered mono-acid triacylglycerols, all three odd-numbered monoacid triacylglycerols crystallize in space group P1 with Z = 2 in an asymmetric tuning-fork conformation and have a lateral acyl chain packing resulting in a layered structure.

Journal Article↗
PubMed2002

CRYSTMET: a database of the structures and powder patterns of metals and intermetallics.

CRYSTMET is a database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) and associated bibliographic, chemical and physical information. Also included are simulated powder diffraction patterns for all of the entries. The database currently contains almost 70,000 entries and covers the literature exhaustively from 1922 to the present. The database is available on CD-ROM with search/analysis software for use on personal computers. This software can be used with any database in the appropriate format; currently CRYSTMET and the ICSD databases are available. This paper describes the database content, the procedures used in its construction, the software made available to the user and a number of potential uses for the data.

Journal Article↗
PubMed2002

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

Journal Article↗
PubMed2002

Simulated annealing structure solution of a new phase of dicalcium silicate Ca(2)SiO(4) and the mechanism of structural changes from alpha-dicalcium silicate hydrate to alpha(L)'-dicalcium silicate via the new phase.

A new phase of dicalcium silicate (Ca(2)SiO(4)) was formed by heating alpha-dicalcium silicate hydrate [alpha-Ca(2)(SiO(4)H)OH = alpha-C(2)SH] at temperatures of approximately 663-763 K, and it was transformed into alpha(L)'-Ca(2)SiO(4) (= alpha(L)'-C(2)S) above approximately 1193 K. The crystal structure of the new phase (hereafter called x-C(2)S) has been determined by simulated annealing and refined by the Rietveld method using synchrotron radiation powder diffraction data. The structure consists of isolated SiO(4) tetrahedra and a three-dimensional CaO(n) polyhedral network, forming a new structural type of dicalcium silicate. A structural change from alpha-C(2)SH to x-C(2)S is compelled by large displacements of SiO(4) tetrahedra, accompanied by dehydration, in the direction perpendicular to the two-dimensional Ca(O,OH)(n) polyhedral network in alpha-C(2)SH. With increasing temperature, sizes of CaO(n) polyhedra in x-C(2)S become too large to confine Ca atoms at the sixfold to eightfold coordination sites. Then the structure of x-C(2)S is transformed into alpha(L)'-C(2)S, having eightfold to tenfold coordination sites for the Ca atoms.

Journal Article↗
PubMed2002

Crystal structure prediction of small organic molecules: a second blind test.

The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were invited to test their prediction programs within a range of named common space groups. Several different computer programs were used, using the methodology wherein a molecular model is used to construct theoretical crystal structures in given space groups, and prediction is usually based on the minimum calculated lattice energy. A maximum of three predictions were allowed per molecule. The results showed two correct predictions for the first molecule, four for the second molecule and none for the third molecule (which had torsional flexibility). The correct structure was often present in the sorted low-energy lists from the participants but at a ranking position greater than three. The use of non-indexed powder diffraction data was investigated in a secondary test, after completion of the ab initio submissions. Although no one method can be said to be completely reliable, this workshop gives an objective measure of the success and failure of current methodologies.

Journal Article↗
PubMed2002

The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base.

The previously unknown crystal structure of the biogenic compound tryptamine, in the form of a free base (C(10)H(12)N(2)), has been solved from X-ray powder diffraction data using simulated annealing followed by restrained Rietveld refinement [space group P2(1)2(1)2(1), a = 12.28593 (6), b = 8.53351 (4), c = 8.49385 (4) A, Z = 4, final reduced-chi(2) = 5.255]. A restrained Rietveld refinement was carried out in which the global weight factor, f, of the stereochemical restraints was gradually lowered. The effect of the relaxation of restraints on the crystal structure and on chi(2) was studied and a criterion for the final choice of f is reported. The crystal structure reported here shows efficient packing involving weak intermolecular hydrogen bonding and a herringbone-type packing pattern.

Journal Article↗
PubMed2003

The incommensurate structure of K3InPO42.

The incommensurately modulated structure of K(3)In(PO(4))(2) has been solved and refined. The origin of the modulation relates to the ordering of K cations within the hexagonal close packing of the PO(4) anions. The driving forces for the modulation of the other cations are In-P and K-P interactions. The modulation of O atoms of rigid PO(4) units follows the cations in order to stabilize the InO(6) octahedron. It is shown that the previously published three-dimensional structure refined from powder diffraction data obtained at room temperature is an average structure. Therefore the incommensurately modulated phase of K(3)In(PO(4))(2) is the only one that has been unequivocally identified at room temperature. The origin of the modulation is discussed in comparison with the structures of Na(3)InP(2), alpha- and beta-Na(3)In(PO(4))(2), Na(3)Fe(PO(4))(2) and Rb(3)In(PO(4))(2).

Journal Article↗
PubMed2003

influence of the molecular structures on the high-pressure and low-temperature phase transitions of plastic crystals.

The crystal structures of tert-butyl-tris(trimethylsilyl)silane, Si[C(CH(3))(3)](1)[Si(CH(3))(3)](3) (Bu1), and di-tert-butyl-bis(trimethylsilyl)silane, Si[C(CH(3))(3)](2)[Si(CH(3))(3)](2) (Bu2), at room temperature and at 105 K have been determined by X-ray powder diffraction; the high-pressure behavior for pressures between 0 and 5 GPa is reported. The room-temperature structures have cubic Fm3m symmetry (Z = 4) with a = 13.2645 (2) A, V = 2333.87 (4) A(3) for Bu1 and a = 12.9673 (1) A, V = 2180.46 (3) A(3) for Bu2. The molecules are arranged in a cubic close packing (c.c.p.) and exhibit at least 48-fold orientational disorder. Upon cooling both compounds undergo a first-order phase transition at temperatures T(c) = 230 (5) K (Bu1) and T(c) = 250 (5) K (Bu2) into monoclinic structures with space group P2(1)/n. The structures at 105 K have a = 17.317 (1), b = 15.598 (1), c = 16.385 (1) A, gamma = 109.477 (4) degrees, V = 4172.7 (8) A(3) and Z = 8 for Bu1and a = 17.0089 (9), b = 15.3159 (8), c = 15.9325 (8) A, gamma = 110.343 (3) degrees, V = 3891.7 (5) A(3) and Z = 8 for Bu2. The severe disorder of the room-temperature phase is significantly decreased and only a two- or threefold rotational disorder of the molecules remains at 105 K. First-order phase transitions have been observed at pressures of 0.13-0.28 GPa for Bu1 and 0.20-0.24 GPa for Bu2. The high-pressure structures are isostructural to the low-temperature structures. The pressure dependencies of the unit-cell Volumes were fitted with Vinet equations of state and the bulk moduli were obtained. At still higher pressures further anomalies in the pressure dependencies of the lattice parameters were observed. These anomalies are explained as additional disorder-order phase transitions.

Journal Article↗
PubMed2003

Intermolecular -CH(3)...O(2)N-- contacts in two polymorphic modifications of (1E)-N'-[(E)-2-cyano-1-(dimethylamino)-2-nitrovinyl]-N,N-dimethylethanimidamide.

The title compound was synthesized and isolated in two crystal modifications. The structure of the orthorhombic modification was determined by the X-ray powder diffraction method and the structure of the monoclinic modification was determined using the X-ray single-crystal diffraction technique. The molecules in both polymorphs are E,E isomers. Intermolecular H(3)C....NO(2) contacts and their role in the formation of the polymorphic modifications are analyzed.

Journal Article↗
PubMed2003

Mechanism of the morphotropic transformation between the rutile and corundum structural types.

The rutile/corundum structural transformation which is based on crystallographic shear is discussed in terms of a one-dimensional disorder model. The transformation process is described by a simple model based on the structural relationship between the rutile-type and corundum-type phases. The model is able to handle randomly spaced crystallographic shear planes, the so-called Wadsley defects, as well as clustered CS planes. Calculations hsow that simply modifying the probability parameters of the model can lead to phase segregation. X-ray powder diffraction patterns are calculated for the proposed transformation mechanism as a function of the stoichiometry x in MO(2-x) in order to show the influence of such defects on the intensities and linewidths of the Bragg reflections.

Journal Article↗
PubMed2003

Structure-property correlation over five phases and four transitions in Pb5Al3F19.

The calorimetric and dielectric properties of Pb(5)Al(3)F(19) in the five phases stable under ambient pressure are correlated with structure for fuller characterization of each phase. The first-order transition between ferroelectric phase V and antiferroelectric phase IV at T(V,IV) = 260 (5) K exhibits a thermal hysteresis of 135 (5) K on heating, with a maximum atomic displacement Delta(xyz)(max) = 1.21 (6) A; the transition from phase IV to ferroelastic phase III at 315 (5) K is also first order but with a thermal hysteresis of 10 (5) K and Delta(xyz)(max) = 0.92 (7) A; that from phase III to paraelastic phase II at 360 (5) K is second order without hysteresis and has Delta(xyz)(max) = 0.69 (4) A; and the transition from phase II to paraelectric phase I at 670 (5) K is second or higher order, with Delta(xyz)(max) = 0.7 (4) A. The measured entropy change DeltaS at T(V,IV) agrees well with DeltaS as derived from the increased configurational energy by Stirling's approximation. For all other phase transitions, 0.5 > or = DeltaS > 0 J mol(-1) K(-1) is consistent with an entropy change caused primarily by the changes in the vibrational energy. The structure of phase III is determined both by group theoretical/normal mode analysis and by consideration of the structures of phases II, IV and V reported previously; refinement is by simultaneous Rietveld analysis of the X-ray and neutron diffraction powder profiles. The structure of prototypic phase I is predicted on the basis of the atomic arrangement in phases II, III, IV and V. The introduction of 3d electrons into the Pb(5)Al(3)F(19) lattice disturbs the structural equilibrium, the addition of 0.04% Cr(3+) causing significant changes in atomic positions and increasing T(IV,III) by approximately 15 K. Substitution of Al(3+) by 20% or more Cr(3+) eliminates the potential minima that otherwise stabilize phases IV, III and II.

Journal Article↗
PubMed2003

Protonation site and hydrogen bonding in anhydrous and hydrated crystalline forms of doxazosin mesylate from powder data.

The three-dimensional solid-state structures of two modifications of doxazosin mesylate (C23H26N5O5)+.(CH3SO3)-, 4-amino-2-[4-[(2,3-dihydro-1,4-benzodioxin-2-yl)carbonyl]piperazin-1-yl]-6,7-dimethoxyquinazoline methanesulfonate, a commonly used antihypertensive agent, have been determined by synchrotron X-ray powder diffraction. An anhydrous form (A) and a dihydrate form (dG) crystallize in monoclinic space groups. In both forms the doxazosin molecule is protonated at the N1 atom of the quinazoline bicycle. The N1 atom, and the amino H atoms and O atoms of the mesylate moieties are involved in three-dimensional hydrogen-bonding networks, while solvent water molecules and carboxamide O atoms are also incorporated in a hydrogen-bonding network in dG.

Crystallization↗
PubMed2004

Structures and phase transitions of trigonal ZrMo2O8 and HfMo2O8.

This paper describes the structures, thermal-expansion properties and phase transitions of the trigonal forms of ZrMo(2)O(8) and HfMo(2)O(8). Both phases adopt a P(-)3m structure at room temperature and show positive thermal expansion. Both phases also undergo a displacive phase transition at high temperature (ZrMo(2)O(8) at 487 K and HfMo(2)O(8) at 463 K) to a higher-symmetry structure that has lower thermal expansion. The structure of the high-temperature alpha'-AMo(2)O(8) form (A = Zr and Hf) has been refined from powder diffraction data in space group P(-)3m1.

Journal Article↗
PubMed2004

Structure of a high-pressure phase of vanadium pentoxide, beta-V2O5.

A high-pressure phase of vanadium pentoxide, denoted beta-V2O5, has been prepared at P = 6.0 GPa and T = 1073 K. The crystal structure of beta-V2O5 has been studied by X-ray and neutron powder diffraction, and high-resolution transmission electron microscopy. The V atoms are six-coordinated within distorted VO6 octahedra. The structure is built up of quadruple units of edge-sharing VO6 octahedra linked by sharing edges along [010] and mutually connected by sharing corners along [001]. This arrangement forms layers of V4O10 composition in planes parallel to (100). The layers are mutually held together by weak forces. beta-V2O5 is metastable and transforms to alpha-V2O5 at 643-653 K under ambient pressure. Structural relationships between beta- and alpha-V2O5, and between beta-V2O5 and B-Ta2O5-type structures are discussed. The high-pressure beta-V2O5 layer structure can be considered as the parent of a new series of vanadium oxide bronzes with cations intercalated between the layers.

Journal Article↗
PubMed2004

Geikielite-ecandrewsite solid solutions: synthesis and crystal structures of the Mg(1-x)Zn(x)TiO(3) (0 < or = x < or = 0.8) series.

The crystal structures of members of the geikielite-ecandrewsite solid solution series, Mg(1 - x)Zn(x)TiO(3) (0 < or = x <or = 0.8 a.p.f.u. Zn; a.p.f.u. = atoms per formula unit), synthesized by ceramic methods in air at ambient pressure, have been characterized by Rietveld analysis of X-ray powder diffraction patterns. These synthetic titanates adopt an ordered R3; structure similar to that of ilmenite. The maximum solubility of Zn in MgTiO(3) is considered to be approximately 0.8 a.p.f.u. Zn, as compounds with greater Zn content could not be synthesized at ambient conditions. Data are given for the cell dimensions and atomic coordinates, together with bond lengths, volumes and distortion indices for all the coordination polyhedra. Within the solid-solution series unit-cell parameters and unit-cell volumes increase with Zn content. All compounds consist of distorted (Mg,Zn)O(6) and TiO(6) polyhedra and, in common with geikielite and ilmenite (sensu lato), TiO(6) polyhedra are distorted to a greater extent than (Mg,Zn)O(6). The displacements of (Mg,Zn) and Ti from the centers of their coordination polyhedra vary insignificantly with increasing Zn content. The interlayer distance across the vacant octahedral site in the TiO(6) layer decreases slightly with the entry of the larger Zn(2+) cation into the (vi)A site. The empirically obtained upper limit of the Goldschmidt tolerance factor (t) for A(2+)BO(3) compounds adopting an ordered R3; structure is 0.755. The absence of natural solid solutions between geikielite and ecandrewsite seems to be due to the contrasting geochemistry of Mg and Zn rather than for crystallochemical reasons.

Journal Article↗
PubMed2004

The compression mechanism of CrF3.

The structure of CrF3 has been studied in the pressure range from ambient to 9.12 GPa by time-of-flight neutron powder diffraction. Rietveld refinements of the crystal structure were performed in the space group R3 c for all the recorded data sets. It was found that volume reduction is achieved through rotation of the CrF6 octahedra and that the Cr-F-Cr bond angle decreases from 144.80 (7) to 133.9 (4) degrees within the investigated pressure range. Furthermore, a small octahedral strain was found to develop during compression. The octahedral strain reflects an elongation of the CrF6 octahedra along the c-axis direction. The zero-pressure bulk modulus Bo and its pressure derivative Bo' were determined to be Bo = 29.2 (4) GPa and Bo' = 10.1 (3).

Journal Article↗
PubMed2005

Anti-KSbF6 structure of CaTbF6 and CdTbF6: a confirmation of the singular crystal chemistry of Tb4+ in fluorides.

The crystal structures of two new tetravalent terbium fluorides, CaTbF6 and CdTbF6, have been determined from X-ray and neutron powder diffraction data. The title compounds exhibit an anti-KSbF6 structure, the three-dimensional framework of which is built of [TbF6]2- chains of edge-sharing dodecahedra further linked, by sharing corners, to isolated [MF6]4- octahedra (M=Ca, Cd). The mechanism of the anionic sublattice rearrangement when going from KSbF6 to CaTbF6 is described and related to a simple cubic fluoride-ion packing. Comparison with the crystal structures of beta-BaTbF6 and other representatives of the M(II)M('IV)F6 family allows the singular crystal-chemical properties of some fluoroterbates to be emphasized.

Cadmium↗
PubMed2005

Determination of the low-temperature structure of hexamethylbenzene.

The low-temperature structure of hexamethylbenzene has been determined from neutron powder diffraction data and found to differ from the room-temperature phase predominantly by a translation of molecular planes to a form a cubic close-packed type structure. By performing measurements as a function of temperature, the role of thermally induced agitation of the molecular units in the first-order phase transition is clearly demonstrated.

Journal Article↗