Eight anhydrous organic salt forms of 2-amino-4,6-dimethoxypyrimidine and organic acids: Preparation, structure, characterizations, synthons diversity, and hirshfeld surface analysis

Abstract

The intricate part of the non-covalent associates in numerous realms covering from chemistry, biology, catalysis, material science, to medicinal chemistry inspires a continuous motivation towards the discovery of new synthons that stabilize the supramolecular systems. In this work the co-crystallization between 2-amino-4,6-dimethoxypyrimidine (admpym) and eight organic acids resulted in the manufacturing of eight new crystalline salts, which were further fully characterized via the single crystal X-ray diffraction (SCXRD), spectroscopic (FT-IR) and elemental analysis methods. Their melting points were also measured. All the fabricated salts exhibited the identical stoichiometry regarding the number of the acidic unit and the admpym, namely with the 1:1 ratio at the monacids and 2 : 1 ratio in the diacids.Among the eight crystals, the H-shift from the acid to pyrimidine ring N atom has occurred, yet the NH2 group was not protonated ever. In all the crystals, the respective molecular fragments are permanently tethered to each other via the energetic H-bonds as the Npyrimidinium-Ophenolate/carboxylate type. The various weaker intermolecular linkages, embodying CH···O/CH3···O, CH···CH, CH3···N, CH···Br, CH3···CH, CH3···Cl, Cl···O, CH···π/CH3···π, C···π, O···π and π···π also contributed to the stabilization of the crystal structures in the respective conglomerates. The percentage contribution of the significant non-covalent contacts were calculated via the Hirshfeld surface analysis. The R22(8) graph was enclosed in all the systems when an acid pairs with an admpym. The job ensures that there engender both principle contact modes between the admpym and the acids, which appear in the relative higher frequency, linear heterotetramer (LHT), and cyclic heterotetramer (CHT). LHT is dominant as it appears in 5 cases, CHT in 2 ones, with the rest one structure building a rare heterodimer. The heterotrimer (HT) was never occurred here.