Crystal structure determination of 1-pentanol from low-temperature powder diffraction data by Patterson search methods

In the course of our research on normal alkanols, the crystal structure of 1-pentanol has been solved by applying Patterson-search methods to laboratory powder X-ray diffraction data recorded on a curved position-sensitive detector (CPS120) at 183 K. The crystal structure was refined with the rigid-body Rietveld least-squares method. The cell is monoclinic, space group P21∕c, Z=4, and the cell parameters are a=15.592(9) Å, b=4.349(1) Å, c=9.157(1) Å, β=104.7(7)°, V=600.6(3) Å3. There is one molecule in the asymmetric unit with the O–H bond in gauche conformation with respect to the alkyl skeleton. Packing is defined by the hydrogen bonds linking the 1-pentanol molecules along zigzag chains parallel to b.

Powder diffraction crystal structure analysis using derivative difference minimization: example of the potassium salt of 1-(tetrazol-5-yl)-2-nitroguanidine

The crystal structure of the potassium salt of 1-(tetrazol-5-yl)-2-nitroguanidine [K(C2H3N8O2)] was solved and refined from X-ray powder diffraction data by applying the derivative difference minimization (DDM) method. The compound is of interest as an energetic substance. The structure model was found from a Patterson search. The reflection intensities for the Patterson synthesis were derived from the powder profile by applying a newly developed DDM-based profile decomposition procedure. The use of the DDM method allowed successful location and unconstrained refinement of all the atomic positions, including those of three independent H atoms. The advantages of DDM in terms of the precision and reproducibility of the structural parameters are discussed in comparison to Rietveld refinement results. The failure to refine the H-atom positions by the Rietveld method was attributed to systematic errors associated with the background modelling, which are avoided by DDM.

Structure solution with PATSEE

Patterson search is a powerful tool for solving difficult crystal structures since it actively uses chemical information. Our program PATSEE, which attempts to combine the merits of Patterson and direct methods in order to locate a fragment with known geometry in the unit cell, has solved a large number of crystal structures during the last decade and proved to be reliable and widely applicable. We have tested PATSEE successfully on 20 structures of different size and complexity contained in a test data bank using fragments either taken from related crystal structures or calculated by force-field methods. Even structures with several torsional degrees of freedom (like those of oligopeptides) could be solved convincingly. As a result, general experiences – such as requirements for the minimum size and the accuracy of a search fragment, the reliability of the various figures of merit, the chances to locate single atoms and to tackle larger structures – were gained, which should help in finding an optimum strategy for the solution of problem structures with PATSEE.

Crystallization, preliminary X-ray diffraction analysis and Patterson search of oxyhaemoglobin I from the wolf (Chrysocyon brachiurus)

Oxyhaemoglobin I isolated from the Brazilian wolf Chrysocyon brachiurus has been crystallized and X-ray diffraction data has been collected to 2.06 Å resolution using a synchrotron-radiation source. Crystals were determined to belong to the space group P212121 and preliminary structural analysis revealed the presence of one tetramer in the asymmetric unit. The structure was determined using standard molecular-replacement techniques and is currently being refined using maximum-likelihood protocols. This is the first haemoglobin isolated from a member of the Canidae family to be crystallized and it will provide further insights in the comparative biochemistry of vertebrate haemoglobins.

Phase Transitions in Tris(3,5-dimethylpyrazol-1-yl)methane. The Structure of the High-Temperature Phase from X-ray Powder Diffraction

The crystal structure of the sublimated form (m.p. = 424 K) of tris(3,5-dimethylpyrazol-l-yl)methane has been solved by a Patterson search method from laboratory X-ray powder diffraction data. Crystal data: trigonal symmetry with the unit-cell parameters a = 16.152 (1) and c = 5.353 (1) Å, space group P3, C16H22N6, Z = 3, 293 K. After indexing the powder pattern by two methods, the unit-cell parameters found were refined by a least-squares technique. A whole pattern-fitting program was used to extract the integrated intensities. The structure was solved taking a related compound as a search model and the final Rietveld refinement converged to R wp = 0.077 and R p = 0.059. This study is one of the first examples of Patterson search structure determination from an hemihedral space group using powder data. The complexity of the structural determination is increased by the presence of three molecules in the asymmetric unit.

Chiral Molecular Alloys: Patterson-Search Structure Determination of L-Carvone and DL-Carvone from X-ray Powder Diffraction Data at 218 K

The crystal structures of pure L-carvone [(R)-(−)-2-methyl-5-(1-methylethenyl)-2-cyclohexen-1-one, C10H14O] and the equimolar mixture DL-carvone (RS) have been determined by Patterson-search methods at low resolution from laboratory X-ray powder diffraction data (218 K). Crystal data: (L) a = 6.8576 (3), b = 6.8831 (5), c = 19.988 (2) Å, P212121 space group, Z = 4; (DL) a = 6.9744 (3), b = 6.8094 (6), c = 20.038 (7) Å, Pcmn space group, Z = 4. The L-carvone structure has been refined by the Rietveld method as a rigid body, allowing the rotation of the isopropenyl group (R\rho, = 0.030 and R wp = 0.043). Although the structure of DL-carvone could be unambiguously established, the Rietveld refinement was not possible due to the existence of preferred orientation in the sample and the difficulty in modelling the disorder. The molecular packing is essentialy the same for both compounds and can be explained as a stacking of two different molecular layers in the [001] direction. In each layer the molecules are placed with their long axis perpendicular to the layer plane, in a head-to-tail manner. The great similarity between the molecular shapes of L and D enantiomers favours the positional disorder in DL-carvone. This result confirms the mixed crystal formation for the chiral carvone system as proposed in recent thermodynamic studies. The DL-carvone crystal must be considered as a pseudo-racemate, since both enantiomers are randomly distributed over all the lattice sites.