Discontinuous modulation functions called crenel and saw-tooth have been developed for description and refinement of strongly modulated crystal structures with abrupt changes of modulation parameters. Although used for refinement of many modulated structures and mentioned in books on aperiodic crystals, technical details of such refinements have never been published and remained hidden in the source code of the refinement program Jana2006. In this article we explain how to recognize discontinuous modulations in a Fourier map and how to refine structures where crenel or saw-tooth functions are combined with additional secondary modulation. Three sets of functions suitable for such combination are presented: the traditional ortho-harmonics, and newly developed sets of Legendre polynomials and x-harmonics. Tiny differences between refinements based on particular function sets are demonstrated using simulated as well as existing modulated structures.
The room temperature structure with P21/c symmetry of the zinc(II) complex of pyridine-2,6-dicarboxylic acid was published by Okabe and Oya (N. Okabe, N. Oya, Copper(II) and zinc(II) complexes of pyridine-2,6-dicarboxylic acid. Acta Crystallogr. C. 2000, 56, 305). Here we report crystal structure of the low temperature phase β-[Zn(pydcH)2]·3H2O, pydc=C7H3NO4, resulting from the phase transition around 200K. The diffraction pattern of the low temperature phase revealed satellite reflections, which could be indexed with q-vector 0.4051(10)b* corresponding to (3+1)D incommensurately modulated structure. The modulated structure was solved in the superspace group X21/c(0b0)s0, where X stands for a non-standard centring vector (½, 0, 0, ½), and compared with the room temperature phase. It is shown that hydrogen bonds are the main driving force of modulation.
The title structure, (3R*, 1′S*, 3′R*)-3-(1′-tert-butylamino-1′H,3′H-benzo[c]furan-3′-yl)-2-tert-butyl-2,3-dihydro-1H-benzo[c]pyrrol-1-one has been determined at 290 and 150 K by single-crystal X-ray diffraction. The structure comprises two symmetry independent molecules with very similar conformations which differ mostly by orientations of the tert-butyl groups, situated at the periphery of these molecules. The molecules are composed of two parts, the cores of which are isoindolinone and isobenzofuran rings being bound by C–C bonds. The planarities of the pyrrolone and furan rings are compared with the known structures retrieved from the Cambridge Crystal Structure Database. It transpires in the title molecules, the planarity of the carbonyl-substituted pyrrole rings is exceptionally distorted in contrast to the furan rings. This fact is just the opposite of the tendency inferred from the Cambridge Crystal Structure Database. The reason may be the influence of the voluminous tert-butyl group which is attached to the nitrogen of the pyrrole group, as well as short centroid–centroid distances between the carbonyl-substituted pyrrole and furan rings. Cohesion forces between the molecules and their parts are provided by weak interactions only: The packing suggests C–H···O, π–π-electron ring interactions, N–H···π-electron ring as well as C–H···π-electron ring interactions. The structure determination of the title compound, the product of the reaction of o-phthalaldehyde with tert-butylamine, has provided indication about the mechanism of a chemical reaction which resulted in the formation of the title molecule.
A new cyclotriphosphazene, 2,2,4,4,6,6-hexakis (o-tolylamono)-1,3,5,2λ5,4λ5,6λ5-triazatriphosphinine (MPAP), was prepared using microwave irradiation and identified by elemental analysis, FT-IR, Raman, 31P NMR spectroscopy, and single-crystal X-ray diffraction. In the crystal, in addition to hydrogen bonds, the network is further stabilized by inter- and intramolecular π–π stacking interactions between aromatic rings.