Synthesis, crystal structure and Hirshfeld surface analysis of the 1-(3,6-dihydropyrimidin-2-yl)urea salt structurally related to dihydropyrimidinon-2-ylurea-type RNA-binding ligands

Abstract

The postmulticomponent synthesis and crystal structure of 1-(3,6-dihydropyrimidin-2-yl)urea salt, 5-(ethoxycarbonyl)-4-methyl-6-phenyl-2-ureido-3,6-dihydropyrimidin-1-ium chloride monohydrate, C15H21O4N4+·ClH2O; structurally related to dihydropyrimidinon-2-ylurea-type RNA-binding ligands is reported. The structure of this new type of hydrated organic salt was investigated by FT-IR, NMR and HRMS methods, and its structure was unambiguous confirmed using X-ray single crystal diffraction techniques. X-ray diffraction analysis show that this material crystallizes in the monoclinic space group P21/c (N°14), Z = 4 with the 3,6-dihydropyrimidin-1-ium ring in a pucked-boat conformation attached to the ester group in an s−trans relationship. The molecular structure and crystal packing are stabilized by intermolecular N − H···O, O − H···O, and N − H···Cl hydrogen bonds formed an infinite three-dimensional (3D) network. Furthermore, the Hirshfeld surface analysis confirms that the most important contributions for the crystal packing are the C − H···H (52.5%), C − H···C (17.8%), C − H···O (15.4%) and N − H···Cl (5.80%) surface contacts.