Design of two series of 1:1 cocrystals involving 4-amino-5-chloro-2,6-dimethylpyrimidine and carboxylic acids (2018)
Type of ContentJournal Article
PublisherInternational Union of Crystallography (IUCr)
AuthorsRajam A, Muthiah PT, Butcher RJ, Jasinski JP, Wikaira Jshow all
© 2018 International Union of Crystallography. Two series of a total of ten cocrystals involving 4-amino-5-chloro-2,6-dimethyl-pyrimidine with various carboxylic acids have been prepared and characterized by single-crystal X-ray diffraction. The pyrimidine unit used for the cocrystals offers two ring N atoms (positions N1 and N3) as proton-accepting sites. Depending upon the site of protonation, two types of cations are possible [Rajam et al. (2017). Acta Cryst. C73, 862–868]. In a parallel arrangement, two series of cocrystals are possible depending upon the hydrogen bonding of the carboxyl group with position N1 or N3. In one series of cocrystals, i.e. 4-amino-5-chloro-2,6-dimethylpyrimidine–3-bromothiophene-2-carboxylic acid (1/1), 1, 4-amino-5-chloro-2,6-dimethylpyrimidine–5-chlorothiophene-2-carboxylic acid (1/1), 2, 4-amino-5-chloro-2,6-dimethylpyrimidine–2,4-dichlorobenzoic acid (1/1), 3, and 4-amino-5-chloro-2,6-dimethylpyrimidine–2-aminobenzoic acid (1/1), 4, the carboxyl hydroxy group (–OH) is hydrogen bonded to position N1 (O—H…N1) of the corresponding pyrimidine unit (single point supramolecular synthon). The inversion-related stacked pyrimidines are doubly bridged by the carboxyl groups via N—H…O and O—H…N hydrogen bonds to form a large cage-like tetrameric unit with an R24(20) graph-set ring motif. These tetrameric units are further connected via base pairing through a pair of N—H…N hydrogen bonds, generating R22(8) motifs (supramolecular homosyn-thon). In the other series of cocrystals, i.e. 4-amino-5-chloro-2,6-dimethyl-pyrimidine–5-methylthiophene-2-carboxylic acid (1/1), 5, 4-amino-5-chloro-2,6-dimethylpyrimidine–benzoic acid (1/1), 6, 4-amino-5-chloro-2,6-dimethylpyrimi-dine–2-methylbenzoic acid (1/1), 7, 4-amino-5-chloro-2,6-dimethylpyrimidine– 3-methylbenzoic acid (1/1), 8, 4-amino-5-chloro-2,6-dimethylpyrimidine– 4-methylbenzoic acid (1/1), 9, and 4-amino-5-chloro-2,6-dimethylpyrimidine– 4-aminobenzoic acid (1/1), 10, the carboxyl group interacts with position N3 and the adjacent 4-amino group of the corresponding pyrimidine ring via O—H…N and N—H…O hydrogen bonds to generate the robust R22(8) supramolecular heterosynthon. These heterosynthons are further connected by N—H…N hydrogen-bond interactions in a linear fashion to form a chain-like arrangement. In cocrystal 1, a Br…Br halogen bond is present, in cocrystals 2 and 3, Cl…Cl halogen bonds are present, and in cocrystals 5, 6 and 7, Cl…O halogen bonds are present. In all of the ten cocrystals, π–π stacking interactions are observed.
CitationRajam A, Muthiah PT, Butcher RJ, Jasinski JP, Wikaira J (2018). Design of two series of 1:1 cocrystals involving 4-amino-5-chloro-2,6-dimethylpyrimidine and carboxylic acids. Acta Crystallographica Section C: Structural Chemistry. 74(9). 1007-1019.
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Keywordscarboxylic acid; cocrystal; crystal structure; heterosynthon; hydrogen bonding; protonation; pyrimidine; supramolecular structure
ANZSRC Fields of Research03 - Chemical Sciences::0303 - Macromolecular and Materials Chemistry::030302 - Nanochemistry and Supramolecular Chemistry
03 - Chemical Sciences::0306 - Physical Chemistry (incl. Structural)::030606 - Structural Chemistry and Spectroscopy
34 - Chemical sciences::3405 - Organic chemistry::340505 - Physical organic chemistry