The single crystal structures of two 2-acylaminopyrimidines, where alkyl groups in acyl moiety are iso-propyl (1) and dichloromethyl (2), were solved by X-ray diffraction method. The strength of intermolecular hydrogen bonding interactions depends on the C–H bond polarization increased by exchanging two methyl groups by chlorine atoms in the adjacent substituent. The computational methods provide an additional insight into the intermolecular interactions and are utilized in explaining the differences in the observed crystal structures. The experimental and computational data together explain the differences in the formed aggregates and revealed that these simple substitutions cause crucial changes in the intermolecular interactions. ; Graphical Abstract : Introduction of nitrogen atom instead of CH moiety completely changes the aggregation.