Weak interactions in the crystal structures of two indole derivatives

The weak intermolecular interactions in two indole derivatives are described.


Figure 3
Partial packing diagram for (I), showing the formation of [010] chains linked byand C-ClÁ Á Á interactions (yellow lines). The long C OÁ Á Á contact is indicated by a cyan line. All hydrogen atoms except H1 are omitted for clarity. Symmetry codes (ii) x, y + 1, z; (iii) x, y -1, z.

Figure 1
The molecular structure of (I) showing 50% displacement ellipsoids. Also shown with double-dashed lines are the pair of intermolecular N-HÁ Á ÁO hydrogen bonds to a nearby molecule related by inversion symmetry, which generate an R 2 2 (10) loop. Symmetry code: (i) 1 À x, 2 À y, 1 À z.
Despite the fact that (I) and the Wu et al. (2013) polymorph of the same phase crystallize in the same space group, their packing motifs are completely different. In the Wu phase, inversion dimers linked by pairs of N-HÁ Á ÁO hydrogen bonds also occur but there is no aromaticstacking (the shortest centroid-centroid separation is greater than 4.75 Å ) and no C-ClÁ Á Á contacts. The only significant interaction indicated by a PLATON (Spek, 2009) analysis of the structure is a weak C-HÁ Á Á 5 bond (HÁ Á Á = 2.72 Å ). Considered by itself, this interaction links the molecules into [010] chains; taken together, the N-HÁ Á ÁO and C-HÁ Á Á interactions generate (110) sheets.

Database survey
A search of the Cambridge Structural Database (CSD; Groom et al., 2016) revealed 24 indole derivatives with an ester group at the 2-position of the ring system. In terms of halogen substitution, there were 58 5-chloro and just two 3-iodo derivatives. As noted above, VIHMUW (Wu et al., 2013) is a polymorph of (I): crystals of this phase in the form of colourless prisms were obtained by recrystallization from ethanol solution at room temperature, compared to colourless needles obtained from methanol solution at room temperature in the present study.
There has recently been debate on the significance -or otherwise -of weak intermolecular interactions in establishing the packing in molecular crystals (Dunitz, 2015;Thakur et al., 2015). The latter authors mentioned the role of weak interactions in establishing the structures of polymorphs and it is  Table 2 Hydrogen-bond geometry (Å , ) for (II). (2) 168 (3) Symmetry code: (i) Àx; Ày þ 2; Àz þ 1.

Figure 4
Partial packing diagram for (II), showing part of an (001) sheet. N-HÁ Á ÁO hydrogen bonds are indicated by crimson lines,and IÁ Á Á interactions by yellow lines and IÁ Á ÁCl halogen bonds by green lines. All hydrogen atoms except H1 are omitted for clarity. Symmetry codes (i) striking to us how different the packing motifs of (I) and VIHMUW are.

Refinement
Crystal data, data collection and structure refinement details are summarized in   0.93-0.98 Å ) and refined as riding atoms. The constraint U iso (H) = 1.2U eq (carrier) or 1.5U eq (methyl carrier) was applied in all cases. The -CH 3 groups were allowed to rotate, but not to tip, to best fit the electron density.

(I) Ethyl 5-chloro-1H-indole-2-carboxylate
Crystal data Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 )
x y z U iso */U eq C1 0.52594 (9) 0.5040 ( Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.