Crystal structure and Hirshfeld surface analysis of dimethyl 5-[2-(2,4,6-trioxo-1,3-diazinan-5-ylidene)hydrazin-1-yl]benzene-1,3-dicarboxylate 0.224-hydrate

In the crystal, molecules are linked by pairs of N—H⋯O hydrogen bonds into ribbons along the c-axis direction. The layered crystal packing is further consolidated by van der Waals and C—H⋯π interactions.


Chemical context
Arylhydrazones, besides their biological significance (Viswanathan et al., 2019), can also be used as precursors in the synthesis of coordination compounds (Gurbanov et al., 2017Ma et al., 2017a,b) and as building blocks in the construction of supramolecular structures owing to their hydrogen-bond donor and acceptor capabilities (Mahmoudi et al., 2016(Mahmoudi et al., , 2017a(Mahmoudi et al., ,b,c, 2018a. All the reported hydrazone ligands are stabilized in the hydrazone form by intramolecular resonance-assisted hydrogen bonding (RAHB) between the hydrazone N-NH-fragment and the carbonyl group, giving a six-membered ring (Gurbanov et al., 2020a;Kopylovich et al., 2011a,b;Mizar et al., 2012). The use of multifunctional ligands in coordination chemistry is a common way to increase the water solubility of metal complexes, which is important for catalytic applications in aqueous medium (Ma et al., 2020(Ma et al., , 2021Mahmudov et al., 2013;Sutradhar et al., 2015Sutradhar et al., , 2016. Moreover, non-covalent interactions such as hydrogen, halogen and chalcogen bonds as well as -interactions or their cooperation are able to contribute to synthesis and catalysis and improve the properties of materials (Gurbanov et al., 2020b;Karmakar et al., 2017;Khalilov et al., 2018a,b;Mac Leod et al., 2012;Shikhaliyev et al., 2019;Shixaliyev et al., 2014). For that, the main skeleton of the hydrazone ligand should be decorated by non-covalent bond donor centre(s). In a continuation of our work in this area, we have prepared a new hydrazone ligand, dimethyl 5-{2-[2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene] hydrazineyl}isophthalate, which provides the centres for coordination and intermolecular noncovalent interactions.

Structural commentary
The asymmetric unit of the title structure contains one title molecule and a water molecule, which partially occupies a small cavity with an occupancy factor of 0.224 (5). The title molecule ( Fig. 1) is nearly planar with the largest deviation from the least-squares plane being 0.352 (1) Å for the methylcarboxylate atom O6. The 1,3-diazinane ring makes a dihedral angle of 9.96 (5) with the benzene ring. The planar molecular conformation is stabilized by an intramolecular N-HÁ Á ÁO contact (Table 1), generating an S(6) ring motif (Bernstein et al., 1995).

Supramolecular features
In the crystal, the molecules are linked by pairs of N-HÁ Á ÁO hydrogen bonds into ribbons along the c-axis direction (Table 1). These ribbons are connected by van der Waals interactions, forming sheets parallel to the ac plane. There are also other van der Waals contacts and C-HÁ Á Á interactions between the sheets (Table 2) The molecular structure of the title compound, showing the atom labelling and displacement ellipsoids drawn at the 50% probability level.

Hirshfeld surface analysis
The Hirshfeld surface for the title molecule was performed and its associated two-dimensional fingerprint plots were prepared using Crystal Explorer 17 (Turner et al., 2017) to further investigate the intermolecular interactions in the title structure. The oxygen atom of the water molecule with partial occupancy was not taken into account. The Hirshfeld surface mapped over d norm with corresponding colours representing intermolecular interactions is shown in Fig. 5. The red spots on the surface correspond to the N-HÁ Á ÁO and C-HÁ Á ÁO interactions (Tables 1 and 2). The Hirshfeld surface mapped over electrostatic potential (Spackman et al., 2009) is shown in A view of the projection on the ab plane showing the contacts between layers.

Figure 5
A view of the Hirshfeld surface mapped over d norm , with interactions to neighbouring molecules shown as green dashed lines. Table 1 Hydrogen-bond geometry (Å , ).

Figure 6
The Hirshfeld surface of the title compound plotted over electrostatic potential energy in the range from À0.0500 to 0.0500 a.u. using the STO-3G basis set at the Hartree-Fock level of theory. Hydrogen-bond donors and acceptors are shown as blue and red regions around the atoms, corresponding to positive and negative potentials, respectively.  Table 3. These interactions play a crucial role in the overall cohesion of the crystal packing.  Bocian et al., 2020) and
In the structures of QUGVEW, QUGVIA, QUGVOG, QUGVUM and QUGWAT, the most important contribution to the stabilization of the crystal packing is provided byinteractions, especially between cations in the structures of salts, while the characteristics of the crystal architecture are influenced by directional interactions, especially relatively strong hydrogen bonds. In one of the structures (QUGWAT), an interesting example of a non-typical FÁ Á ÁO interaction was found whose length, 2.859 (2) Å , is one of the shortest ever reported.

Synthesis and crystallization
Diazotization: 2.09 g (10 mmol) of dimethyl 5-aminoisophthalate were dissolved in 50 mL of water, the solution was cooled on an ice bath to 273 K and 0.69 g (10 mmol) of NaNO 2 were added; 2.00 mL of HCl were then added in 0.5 mL portions over 1 h. The temperature of the mixture should not exceed 278 K.
Azocoupling: NaOH (0.40 g, 10 mmol) was added to a mixture of 10 mmol (1.28 g) of barbituric acid with 25.00 mL of water. The solution was cooled on an ice bath and a suspension of 3,5-bis(methoxycarbonyl)benzenediazonium chloride, prepared according to the procedure described above, was added in two equal portions under vigorous stirring for 1 h. The formed precipitate of the title compound was filtered off, recrystallized from methanol and dried in air.

Refinement details
Crystal data, data collection and structure refinement details are summarized in Table 4. The H atoms of the NH groups were located by difference Fourier synthesis and their coordinates were fixed. All C-bound H atoms were positioned geometrically and refined using a riding model, with C-H = 0.95 and 0.98 Å , and with U iso (H) = 1.2 or 1.5U eq (C). There is a small cavity in the crystal, which is only partially occupied by a water molecule, with an occupancy of 0.224 (5), and its hydrogen atoms could not be located. Computer programs: APEX2 and SAINT (Bruker, 2007), SHELXT (Sheldrick, 2015a), SHELXL (Sheldrick, 2015b), ORTEP-3 for Windows (Farrugia, 2012) and PLATON (Spek, 2020

Dimethyl 5-[2-(2,4,6-trioxo-1,3-diazinan-5-ylidene)hydrazin-1-yl]benzene-1,3-dicarboxylate 0.224-hydrate
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 Occ. (