Crystal structure, hydrogen bonding and Hirshfeld surface analysis of 2-amino-4-methoxy-6-methylpyrimidinium 4-chlorobenzoate

Abstract

In the crystal structure of the title compound, C6H10N3O+·C7H4ClO2−, the pyrimidine N atom of the cation is hydrogen-bonded to the 4-chloro­benzoate anion through a pair of N—H⋯Ocarbox­yl hydrogen bonds, forming an (8) ring motif which is linked through centrosymmetric (8) ring motifs, forming a pseudo­tetra­meric DDAA array.

Insights on structure and interactions of 2-amino-4-methoxy-6-methylpyrimidinium salts with 4-aminosalicylate and 5-chlorosalicylate: a combined experimental and theoretical charge–density analysis

“…In the cation, one of the pyrimidine N atoms (N1) is protonated and this is confirmed from the increase of the bond angle at N1 [C2-N1-C1 = 121.7 ( 2) ]. This angle is comparable with that at the unprotonated N2 atom [C4-N2-C1 = 116.17 ( 19) ] and the unprotonation further confirmed from the corresponding reported bond angle of neutral 2-amino-4-methoxy-6methylpyrimidine (Glidewell et al, 2003;Jeevaraj et al, 2018), which is significantly higher [116.0 (18) ]. An intramolecular O4-H4Á Á ÁO3 hydrogen bond in the 5-chlorosalicyclic acid anion generates an S(6) ring motif (Bernstein et al, 1995;Thanigaimani et al, 2013).…”

“…The cation is protonated at atom N1, which lies between the C atoms with attached amine and methyl groups. This protonation is confirmed from the difference of the bond angles at the protonated N1 atom [C1-N1-C2 = 121.18 ( 14) ] and the unprotonated N2 atom [C4-N2-C1 = 115.93 ( 14) ], and is further confirmed on comparison with the corresponding reported bond angle of neutral 2-amino-4-methoxy-6-methylpyrimidine (Glidewell et al, 2003;Jeevaraj et al, 2018), which is significantly smaller [116.0 (18) ]. In I, the 4AMSA anion exhibits an intramolecular O4-H4Á Á ÁO3 hydrogen bond (Fig.…”

“…2). The hydroxy group of 5-chlorosalicylic acid is deprotonated and the proton transferred to the N atom of 2-aminopyrimidine (Ebenezer & Muthiah, 2012;Kantouch et al, 2013;Jeevaraj et al, 2018;Darious & Muthiah, 2018). In the cation, one of the pyrimidine N atoms (N1) is protonated and this is confirmed from the increase of the bond angle at N1 [C2-N1-C1 = 121.7 ( 2) ].…”

“…The protonated N1 atom and the N atom of the 2-amino group (N3) are hydrogen bonded to the carboxylate O atoms (O2 and O3) via a pair of intermolecular N1-H13Á Á ÁO2 v and N3-H3BÁ Á ÁO3 v hydrogen bonds (Table 2), forming an R 2 2 (8) ring motif (Bernstein et al, 1995;Jeevaraj et al, 2018). The main motif is assembled via a complementary hydrogen-bond interaction between the carboxylic acid and aminopyrimidine moieties to form a dimeric unit (Fig.…”

“…Pyrimidine and aminopyrimidine derivatives are biologically important compounds and they occur in nature as components of nucleic acids, such as cytosine, uracil and thymine (Glidewell et al, 2003). Pyrimidine derivatives have also been developed as antiviral agents, such as AZT, which is the most widely used anti-HIV drug, and in biology they have many applications in the areas of pesticides and pharmaceutical agents (Jeevaraj et al, 2018). Furthermore, the pyrimidine group offers two protonation sites (the two ring N atom) and the site of protonation depends on the nature of the substituent (Rajam et al, 2018;Odiase et al, 2015).…”