Crystal structure of ethyl 2-methyl-5,10-dioxo-4-phenyl-5,10-dihydro-4H-11-thia-1,4a-diazabenzo[b]fluorene-3-carboxylate

The dihydropyrimidine ring adopts a twist-boat conformation while the quinone ring is slightly non-planar. In the crystal, molecules are linked by weak C—H⋯O and C—H⋯S hydrogen bonds and C—H⋯π interactions. In addition, a short intermolecular S⋯N contact occurs.


Chemical context
The three-component Biginelli reaction allows the assembly of a wide variety of dihydropyrimidine (DHPM) compounds that can be modified easily depending on the starting materials used during the reaction (Nagarajaiah et al., 2016). DHPMs exhibit antibacterial (Wani et al., 2017) and antifungal properties (Akhaja & Raval, 2012) and their thioanalogues such as monastrol are being used as inhibitors of mitotic kinesin Eg5 in the treatment of breast and ovarian tumors (Bobylev et al., 2017;Duan et al., 2015). In this work we investigated reactivity of thioDHPMs 1 in their reaction with the di-halogen-substituted nucleophile 2. It was expected that the reaction would proceed with substitution of one or both chlorine atoms and the formation of a thiazole ring in the product 3 (Fig. 1).

Structural commentary
Compound 3 crystallizes in the non-centrosymmetric chiral space group P2 1 2 1 2 1 . This indicates the existence of only one enantiomer in the crystal with an S-configuration of the C12 chiral center according to the Flack parameter (Parsons et al., ISSN 2056-9890 2013). The quinone ring is slightly non-planar (Fig. 2). Its conformation can be described as a flattened asymmetric screw-boat with the C7 and C10 atoms deviating by 0.053 (3) and 0.082 (3) Å from the mean plane through the remaining ring atoms. This non-planarity may be caused by the formation of the weak intramolecular C12-H12Á Á ÁO2 hydrogen bond. Taking into account high conformational flexibility of the quinone ring (Shishkin, 1997;Kovalevsky et al., 1998), it could be suggested that the out-of plane deformation of the ring represents the easiest way for relaxation of its structure because of steric clashes.

Figure 3
The view of the SÁ Á ÁN intermolecular interaction.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were located in difference-Fourier maps and treated as riding (C-H = 0.93-0.97 Å ) with U iso (H) = nU eq (C) (n = 1.5 for CH 3 and n = 1.2 for all other H atoms).

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.