Towards understanding high-Z' organic molecular crystals through the superspace method.
Final Report Abstract
Molecular crystals, for example those of pharmaceutical ingredients, usually contain one symmetry-independent molecule in the unit cell (Z' = 1). This experimental fact can be understood from the argument that this molecule will attain its most favorable conformation and will lie in the most favorable environment (principle of minimum of energy). However, sometimes it is not possible to fully satisfy all interactions, and crystals may appear that have Z' > 1 symmetry independent copies of the molecule. A small fraction (less than 0.1%) of the molecular crystals are so-called high-Z' crystals, where Z' > 4. Goal of the project is the application to high-Z' crystals of the superspace method for structural analysis of modulated crystals, with the purpose of developing a better understanding of the high-Z' phenomena. For sodium saccharinate 1.875-hydrate, a superspace structure model has been successfully developed for the known Z' = 16 crystal structure. Temperature-dependent X-ray diffraction for 20-298 K led to the description of a temperature-dependent disorder, which becomes smaller upon cooling from 298 to 130 K. We have discovered a phase transition between 130 and 120 K, where below 120 K the disorder is almost perfect again. We have discovered a phase transition of the dipeptide glycyl-L-valine, from the known Z' = 7 crystal structure at and below room temperature towards a Z' = 1 structure at 323 K. The superspace description of these structures revealed that the basic structure at room temperature is equal to the Z' = 1 crystal structure at 323 K. Analysis of the sevenfold modulation of the Z' = 7 structure has shown that the source of high-Z' in this compound is an optimization of the intermolecular hydrogen bonding. Six out of seven molecules have more hydrogen bonds than the basic structure, while only one out of seven molecules is in a less favorable environment than the basic structure. In the third part of the project, a superspace model has been developed for the cocrystal of 4,4'-dinitrobiphenyl (44DNBP) and biphenyl (BP). It indicated that this molecular crystal is a commensurate composite crystal. The superspace structure model revealed the different symmetries and pseudosymmetries of the packing of the 44DNBP and BP molecules in the crystalline state. The superspace structure model employs modulation functions for the description of the structural variations of the molecular constituent over its Z' independent copies. It requires less parameters than the standard supercell approach and thus leads to a more accurate structure model. Accordingly, we could accurately describe the temperature dependence of the disorder in sodium saccharinate 1.875-hydrate and hydrogen bonding in the high-Z' and Z' = 1 structures of glycyl-L-valine.
Publications
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The superspace method for understanding incommensurate modulations and high-Z' phenomena in crystals. Invited lecture at the XXIV Conference on Applied Crystallography—CAC-2018, 2 – 6 September 2018, Arlamow, Poland
S. van Smaalen
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On the puzzling case of sodium saccharinate 1.875-hydrate: structure description in (3+1)-dimensional superspace. Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials, 76(1), 18-27.
Rekis, Toms; Schönleber, Andreas & van, Smaalen Sander
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Modulated molecular crystals: Incommensurate, high Z´ forms and their variation as function of temperature and stress. Poster P-35-08 in poster session P35 "Composite and Incommensurate Modulated Crystals" at the 25th Congress of the International Union of Crystallography, 14-21 August 2021, Prague, Czech Republic
S. Dey, C. Malla Reddy, A. Schoenleber & S. van Smaalen
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Single-crystal-to-single-crystal phase transitions of commensurately modulated sodium saccharinate 1.875-hydrate. IUCrJ, 8(1), 139-147.
Rekis, Toms; Schaller, Achim M.; Kotla, Surya Rohith; Schönleber, Andreas; Noohinejad, Leila; Tolkiehn, Martin; Paulmann, Carsten & van, Smaalen Sander
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Toward Understanding High-Z′ Organic Molecular Crystals through the Superspace Method: The Example of Glycyl-l-valine. Crystal Growth & Design, 21(4), 2324-2331.
Rekis, Toms; Schönleber, Andreas; Noohinejad, Leila; Tolkiehn, Martin; Paulmann, Carsten & van, Smaalen Sander
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Une étude cristallographique: superspace description of a commensurate composite cocrystal of 4,4′-dinitrobiphenyl and biphenyl. CrystEngComm, 24(3), 512-517.
Rekis, Toms; Ramakrishnan, Sitaram; Kotla, Surya Rohith; Bao, Jin-Ke; Eisele, Claudio; Schönleber, Andreas; Noohinejad, Leila; Paulmann, Carsten; Tolkiehn, Martin & van, Smaalen Sander
