Crystal chemistry of layered structures formed by linear rigid silyl-capped molecules

Silyl capped aryl bis-ene–yne compounds and their derivatives possess a rich crystal chemistry: merotypism, polymorphism, polytypism, twinning and incommensurate modulation.

with JANA2006 (Petříček et al., 2014). Non-H atoms were refined with anisotropic ADPs. H atoms were placed at computed positions and refined as riding on the parent C-atoms. Details of data collections and structure refinements are compiled in Tables 1-4. Deviations from the standard procedure and specific remarks will be given in the following sections.       (2), oxESEM (3b) and ASYM (6).
For TSEM (2), oxESEM (3b) and ASYM (6), automatic unit cell determination failed at determining reasonable lattice parameters. Therefore the locations of the diffraction spots in reciprocal space were analyzed manually using RLATT (Bruker, 2008). In all three cases the spots could be assigned to two domains, related by rotation of 180 • about [001] (TSEM (2)) and [100] (oxESEM (3b), ASYM (6)). Intensity data of the twin domains were integrated concurrently and written to "HKLF5" files with overlap information.

TSEM (2).
TSEM (2)  Due to the small size, the crystal was only weakly diffracting, leading to mediocre residuals and large peaks in the difference Fourier density.
Polytype I grew on the walls and featured satisfactory diffraction quality. Polytype II was isolated from the bottom of the wessel among oil and featured weak diffraction intensities and diffuse scattering. Accordingly, the residuals were comparatively large.

oxBSEM (1b).
When mounting samples of oxBSEM (1b) on the diffractometer cooled in a stream of N 2 to our routine measurement temperature of 100 K, the crystals burst suggesting a phase transition. Therefore we slowly (2 K/min) cooled a crystal from room temperature to 150 K, while monitoring the lattice parameters. Since no phase transition was observed down to 150 K, a data set was collected at this temperature. On further cooling, a phase transition was apparent by fragmentation of the crystal accompanied by a dramatic worsening of reflection quality. Despite mediocre data quality we were able to solve and refine the structure, though with high residuals and large peaks in the differene Fourier density.
To highlight the structural relationship between polymorphs I and II of oxBSEM (1b), the latter was refined using a non-reduced setting. The reduced setting is related to the chosen one by

ESEM (3).
Since automatic indexing of the reflections failed, the locations of the diffraction spots in reciprocal space were analyzed manually using RLATT (Bruker, 2008). The strongest spots could be indexed using a C-centered monoclinic lattice. The remaining diffraction spots were interpreted as satellites located at ±σ 2 b * and ±2σ 2 b * from main reflections, with irrational σ 2 close to 5 8 .
Data reduction turned out to be difficult, since first and second order satellites were close and reflections featured distinct enlargement in a * direction. The best overall result was obtained using EVAL14 (Duisenberg et al., 2003), by tuning anisotropic mosaicity. Nevertheless, intensities of the strongest reflections were systematically overestimated, leading to slightly worse partial reliability factors of main reflections compared to first order satellites.
Systematic absences of the main reflections indicated a superspace group derived from Ic or I2/c. Since satellites 0k0m with |m| = 1 were absent, a structure solution in superspace group I2/c(0σ 2 0)s0 was attempted. The correctness of the choice was confirmed by the symmetry of the four-dimensional electron density obtained by charge-flipping as implemented in SUPERFLIP (Palatinus & Chapuis, 2007). The positions of all non-H atoms and first order displacive modulation functions were directly located in SUPERFLIP output. To achieve decent reliability factors, notably concerning satellites, the positions of the non-H atoms were refined with second order harmonics. The ADPs of the heavy atoms S and Si were modulated with second order harmonics, for C and O atoms with first order harmonics. H atoms were placed at computed positions and refined as riding on the parent C-atoms. The methyl groups were fixed into anti -positions to obtain converging refinements.
The C9 atom of the TMS group features large ADPs in parts of internal space hinting towards disorder. Introducing discontinuous modulation functions for C9 (Legendre polynomials) led to distinctly more reasonable ADPs. Unfortunately attachment of H atoms to this C9 atom resulted in non-converging refinements and thus the continuous harmonics were used in the final refinements.