Organa– a program package for structure determination from powder diffraction data by direct-space methods

Two mefenamic acid derivatives: structural study using powder X-ray diffraction, Hirshfeld surface and molecular electrostatic potential calculations

Two mefenamic acid (1) derivatives, prop-2-ynyl 2-(2,3-dimethylphynylamino)benzoate (2) and N′-(dihydro-2H-pyran-4(3H)-ylidene)-2-((2,3-dimethylphenyl)amino)benzohydrazide (3), have been synthesized and their crystal structures have been determined from laboratory powder X-ray diffraction data. The DFT optimized molecular geometry in 2 and 3 agrees closely to that obtained from the crystallographic study. The nature of intermolecular interactions in 2 and 3 has been analyzed through Hirshfeld surfaces and two-dimensional fingerprint plots, and compared with that in the mefenamic acid polymorphs. Intermolecular N–H···N, C–H···O/N and C–H···π(arene) interactions in 2 and 3 assemble molecules into two and three-dimensional supramolecular frameworks, respectively. Hydrogen-bond based interactions in 2 and 3 have been complimented by calculating molecular electrostatic potential surfaces. Hirshfeld surface analyses of 2, 3, three mefenamic acid polymorphs and a few related mefenamic acid derivatives retrieved from the Cambridge Structural Database (CSD) indicate that about 80% of the Hirshfeld surface areas in these compounds are due to H···H and C···H/H···C contacts.

The principles underlying the use of powder diffraction data in solving pharmaceutical crystal structures

Solving pharmaceutical crystal structures from powder diffraction data is discussed in terms of the methodologies that have been applied and the complexity of the structures that have been solved. The principles underlying these methodologies are summarized and representative examples of polymorph, solvate, salt and cocrystal structure solutions are provided, together with examples of some particularly challenging structure determinations.

Exploiting powder X-ray diffraction for direct structure determination in structural biology: the P2X4 receptor trafficking motif YEQGL

We report the crystal structure of the 5-residue peptide acetyl-YEQGL-amide, determined directly from powder X-ray diffraction data recorded on a conventional laboratory X-ray powder diffractometer. The YEQGL motif has a known biological role, as a trafficking motif in the C-terminus of mammalian P2X4 receptors. Comparison of the crystal structure of acetyl-YEQGL-amide determined here and that of a complex formed with the μ2 subunit of the clathrin adaptor protein complex AP2 reported previously, reveals differences in conformational properties, although there are nevertheless similarities concerning aspects of the hydrogen-bonding arrangement and the hydrophobic environment of the leucine sidechain. Our results demonstrate the potential for exploiting modern powder X-ray diffraction methodology to achieve complete structure determination of materials of biological interest that do not crystallize as single crystals of suitable size and quality for single-crystal X-ray diffraction.

Selective transformation pathways between crystalline forms of an organic material established from powder X-ray diffraction analysis

The methanol solvate crystalline phase (M) of benzene-1,2,4,5-tetracarboxylic acid transforms selectively to a hydrate phase (H) or a non-solvate phase (N) depending on the presence of atmospheric water vapour; knowledge of the crystal structures of M and N, determined here using single-crystal and powder X-ray diffraction, respectively, yields insights into mechanistic aspects of the solid-state transformations.

Counteracting stagnation in genetic algorithm calculations by implementation of a micro genetic algorithm strategy

A new strategy for implementing the concept of a "micro genetic algorithm" within a standard genetic algorithm (GA) procedure is proposed. The strategy operates by applying criteria to test for the occurrence of stagnation within the population of a standard GA calculation, and triggering the micro-GA procedure whenever stagnation is detected. The micro-GA is implemented in terms of the parallel evolution of a number of small sub-populations (comprising predominantly new randomly generated structures together with a few of the best structures from the stagnated population), and the sub-population of highest quality following the micro-GA procedure is used in the construction of the next population of the standard GA calculation. The micro-GA procedure is applied in the context of a GA for carrying out direct-space structure solution from powder X-ray diffraction data, and the results demonstrate that this strategy is an effective means of promoting structural diversity within a stagnated population, leading to significantly improved evolutionary progress. This strategy may prove to be more generally applicable as an approach for alleviating problems due to stagnation in GA calculations in other fields of application.

Structure determination from powder diffraction data

Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.

Complex zeolite structure solved by combining powder diffraction and electron microscopy

Many industrially important materials, ranging from ceramics to catalysts to pharmaceuticals, are polycrystalline and cannot be grown as single crystals. This means that non-conventional methods of structure analysis must be applied to obtain the structural information that is fundamental to the understanding of the properties of these materials. Electron microscopy might appear to be a natural approach, but only relatively simple structures have been solved by this route. Powder diffraction is another obvious option, but the overlap of reflections with similar diffraction angles causes an ambiguity in the relative intensities of those reflections. Various ways of overcoming or circumventing this problem have been developed, and several of these involve incorporating chemical information into the structure determination process. For complex zeolite structures, the FOCUS algorithm has proved to be effective. Because it operates in both real and reciprocal space, phase information obtained from high-resolution transmission electron microscopy images can be incorporated directly into this algorithm in a simple way. Here we show that by doing so, the complexity limit can be extended much further. The power of this approach has been demonstrated with the solution of the structure of the zeolite TNU-9 (|H9.3|[Al9.3Si182.7O384]; ref. 10) with 24 topologically distinct (Si,Al) atoms and 52 such O atoms. For comparison, ITQ-22 (ref. 11), the most complex zeolite known to date, has 16 topologically distinct (Si,Ge) atoms.