Crystal structure of 4-amino-5-chloro-2,6-dimethylpyrimidinium thiophene-2,5-dicarboxylate

In the title salt, the cations and anions are linked through O—H⋯O,N—H⋯O, N—H⋯N and π–π stacking interactions, forming double layers parallel to (101). Weak C—H⋯O and C—H⋯S hydrogen bonds connect the double layers into a three-dimensional network.


Chemical context
In crystal engineering, non-covalent interactions, such as hydrogen bonding, play a key role in molecular recognition processes (Desiraju, 1989). Pyrimidine derivatives have gained considerable importance because of their remarkable biological properties, for example as anti-fungal, antiviral, anticancer and anti-allergenic agents (Ding et al., 2004). Thiophenecarboxylic acid and its derivatives have attracted attention because of their wide range of pharmacological properties and numerous applications, such as the preparation of DNA hybridization indicators, single-molecule magnets, photoluminescence materials and the treatment of osteoporosis as inhibitors of bone resorption in the tissue culture (Bharti et al., 2003;Taş et al., 2014;Boulsourani et al., 2011). The present study investigates the hydrogen-bonding patterns in 4-amino-5-chloro-2,6-dimethylpyrimidinium thiophene-2,5dicarboxylate (I).

Supramolecular features
The carboxylate group of the thiophene-2,5-dicarboxylate anion interacts with the protonated N1 atom of the pyrimidinium moiety with a single point heterosynthon via N-HÁ Á ÁO hydrogen bonds (Table 1). In addition, the components are connected through O-HÁ Á ÁO and N-HÁ Á ÁO hydrogen bonds (Table 1) Fig. 3) are interconnected by a selfcomplementary base pair between the pyrimidinium moiety through N-HÁ Á ÁN hydrogen bond interactions with an R 2 2 (8) ring graph set motif andstacking interactions between the pyrimidinium ring and the thiophene ring with an observed interplanar distance of 3.4188 (10) Å , a centroid-to-centroid (Cg1-Cg2) distance of 3.5414 (13) Å (where Cg1 is the centroid of the ring N1B/C2B-C6B and Cg2 is the centroid of the ring S1A/C2A-C5A) and slip angle (the angle between the centroid vector and the normal to the plane) of 18.0 ; these are typical aromatic stacking values (Hunter, 1994). Through these interactions, parallel inversion-related sheets are connected into double layers parallel to (101). In addition, weak C-HÁ Á ÁO, C-HÁ Á ÁS and C-HÁ Á Á intermolecular interactions connect the double layers into a three-dimensional network (Fig. 3).
Cg is the centroid of the S1A/C2A-C5A ring.

Figure 2
Packing diagram for (I), viewed along the a axis, showing a single sheet formed by O-HÁ Á ÁO and N-HÁ Á ÁO hydrogen bonds. Symmetry codes are given in Table 1. Dashed lines represent hydrogen bonds.

Figure 1
The asymmetric unit of the title compound, showing 30% probability displacement ellipsoids. The dashed line indicates a hydrogen bond.
half an hour over a water bath. The mixture was cooled slowly and kept at room temperature. After a few days colourless plate-like crystals were obtained.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. The N-H and O-H H atoms were located in difference Fourier maps and refined isotropically. All other H atoms were placed in calculated positions and refined using a riding-model approximation with C-H = 0.95 Å (CH) or 0.98 Å (CH 3 ). Isotropic displacement parameters for these atoms were set to 1.2 (CH) or 1.5 (CH 3 ) times U eq of the parent atom. Idealized Me H atoms were refined as rotating groups. There are larger than expected residual density peaks close to the Cl and S atoms but these are not chemically sensible and are assumed to be related to the quality of the crystal.

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.