Crystal structure and Hirshfeld surface analysis of 2,4,6-triaminopyrimidine-1,3-diium dinitrate

In the crystal, hydrogen-bonding interactions between the 2,4,6-triaminopyrimidine cation and the nitrate anions lead to a one-dimensional supramolecular network with weak anionic interactions forming a three-dimensional network. Energy framework analysis showed that of the components of the framework energies, electrostatic repulsion (E rep) is dominant.


Chemical context
Nitrogen heterocycles and pyrimidines are examples of the most important biologically active compounds and find wide use in modern medicine (Pałasz & Cież, 2015;Takeshita et al., 2006;Henderson et al., 2003). Pyrimidine derivatives are used as intermediates for the production of various complex organic molecules for the treatment of cancer and AIDS (Fawcett et al., 1996). Several pyrimidine derivatives belong to the class of central nervous system depressants (Soayed et al., 2015). Pyrimidine and its derivatives have great importance as they constitute a significant class of natural and non-natural products, many of which possess remarkable biological activities and clinical applications such as antibacterial, antimalarial and anticancer agents (Sharma et al., 2014). Many pyrimidine derivatives are reported to possess potential central nervous system (CNS) depressant properties and also act as calcium channel blockers (Kumar et al., 2002). Pyrimido[4,pyrimidine-2,5-dione and 2,4-diamino-5-(substituted)pyrimidines have been reported to have potent antimicrobial activity (Sharma et al., 2004) and 2,4,6-triaminopyrimidine (TAP) acts as a fast-killing and long-acting antimalarial agent (Hameed, et al., 2015). It is also known to inhibit sodium transport in the skin of frogs (Bowman et al., 1978). It can be synthesized by a regioselective cycloaddition process in high yield by reaction between two moles of cyanamide and one mole of ynamide in the presence of triflic acid as catalyst (Dubovtsev, et al., 2021). Many pyrimidine derivatives display interesting optical and sensing properties (Achelle et al., 2012, Seenan et al., 2020. Methylpyrimidinium push-pull derivatives have been shown to be promising materials for optical data processing. Organometallic methylpyrimidinium chromophores incorporating a ruthenium fragment within the -conjugated spacer are among the best metal-diyne NLO chromophores (Fecková , et al., 2020). Herein, we report the structure of 2,4,6-triamino-1,3,5-triazine-1,3-diium dinitrate, Fig. 1, which was synthesized via reaction of 2,4,6-triaminopyrimidine with nitric acid.

Structural commentary
In the asymmetric unit, the mean planes of the nitrate anions are inclined to one another by 5.97 (8) . The plane of the anion containing N6 is inclined to the mean plane of the cation by 3.25 (6) while that of the other anion is inclined by 2.84 (6) . Thus the whole asymmetric unit lies close to a common plane (Fig.1). The ring C-N bond lengths in the cation [C1-N2 = 1.3531 (16) Å and C2-N3 = 1.3267 (16) Å ] are only slightly altered from those in the corresponding conjugate base (Schwalbe et al., 1982). The C-C bond lengths in the pyrimidine ring [C2-C3 = 1.3834 (18) and C3-C4 = 1.3888 (17) Å ] are consistent with literature values (Ali et al., 2021). The exocyclic C2-N3 and C4-N4 bond lengths [1.3267 (16) and 1.3240 (17) Å , respectively] are equivalent within experimental error but the C1-N1 bond length is markedly shorter at 1.3010 (17) Å . As it lies between the two protonated ring nitrogen atoms, this suggests that the neighboring positive charge induces a contribution from a chargeseparated quinoid form to the overall electronic structure, as has been proposed for the analogous chloride salt (Portalone & Colapietro, 2007)

Figure 2
A portion of one cation/anion layer projected onto (101) with N-HÁ Á ÁO hydrogen bonds depicted by dashed lines.

Figure 1
ORTEP diagram of the title compound with atom labeling and 50% probability ellipsoids.

Hirshfeld Surface Analysis
The Hirshfeld surface analysis (Spackman & Jayatilaka et al. 2009) was performed and the two-dimensional fingerprint plots (McKinnon et al., 2007) were generated with Crystal Explorer17 (Turner et al., 2017) to quantify the intermolecular contacts present within the crystal structure. The Hirshfeld surface is mapped over d norm in the range À0.6823 to 0.9826 in arbitrary units with colors ranging from red (shorter distance than the sum of van der Waals radii) through white to blue (longer distance than the sum of the van der Waals radii). Top and bottom views of the surface together with curvedness, and shape-index plots are given in Fig. 4a-d. The red spots symbolize N-HÁ Á ÁO contacts and C-HÁ Á ÁO interactions. The fingerprint plots (Fig. 5) give an insight into the overall packing characteristics of the contents of the unit cell, being plots of d e versus d i , where d i is the distance to the nearest atom center interior to the surface, and d e to the nearest atom exterior to the surface. These plots show that the main contributions to the overall surface involve OÁ Á ÁH/ HÁ Á ÁO contacts at 53.2% (Fig. 5b), followed by NÁ Á ÁH/HÁ Á ÁN contacts at 12.5% (Fig. 5c) and CÁ Á ÁH/HÁ Á ÁC contacts at 9.6% (Fig. 5d).

Synthesis and crystallization
To synthesize the title compound, 20 mg of 2,4,6-triaminopyrimidine were dissolved in ethanol (10 mL) and the solution stirred for 3 h. A mixture of ethanol (5 mL) and nitric acid (0.5 mL) was taken in a separate round-bottom flask and stirred for 3 h at 333 K. Afterwards, the 2,4,6-triamino-    Packing view of the title compound showing the anionic-interaction that forms the supramolecular structure.
pyrimidine solution was added dropwise to the above mixture. The reaction was continued for 4 h at the same temperature. After completion of the reaction, a pale-yellow solution was obtained, which was filtered and kept for slow evaporation at room temperature. After 15 days, pale-yellow crystals were obtained that were suitable for data collection (Fig. 6).

Interaction energy calculations
The interaction energies for the title compound (Fig. 7). were computed using the HF/3-21G quantum level of theory, which is available in CrystalExplorer 17.5. Electrostatic (E ele ), polarization (E pol ), dispersion (E disp ), and exchange-repulsion (E rep ) are the four energy variables that make up the total intermolecular interaction energy (E tot ). Cylinder-shaped energy frameworks represent the relative strengths of interaction energies in individual directions and give the topologies of pair-wise intermolecular interaction energies within the crystal (Mackenzie et al., 2017). The energies between molecular pairs are represented as cylinders connecting the centroids of pairs of molecules, with the cylinder radius equal to the amount of interaction energy between the molecules (Wu et al., 2020). The dark-blue-colored molecule at symmetry position (x, Ày + 1 2 , z + 1 2 ) located 6.25 Å from the centroid of the selected molecule has the highest total interaction energy of À40.1 kJ mol À1 , as shown in Fig.7. The net interaction energies for the title compound are E ele = À58.9 kJ mol À1 , E pol = À92.0 kJ mol À1 , E dis = À148.8 kJ mol À1 , E rep = 176.9 kJ mol À1 , with a total interaction energy E tot of À110.4 kJ mol À1 (Fig. 8). Clearly, E rep is the major interaction energy in the title compound. Energy frameworks for a 2Â2Â2 supercell viewed down the crystallographic b axis for the threefold interpenetrated crystal structure. The red-colored frame shows the Coulombic energy, green shows dispersion, and blue shows total energy.

Figure 6
Synthesis of title compound.

Figure 7
Interaction energies for the title compound were calculated with the HF/3-21 G model.  Voronina et al., 2012) anions. Most of the discussions of these structures are concerned more with their supramolecular structures than the detailed geometry of the cation but, as noted in Section 3, some details similar to those in the present work are seen in the structure of the chloride salt.

2,4,6-Triaminopyrimidine-1,3-diium dinitrate
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.