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R2(2)(8) motifs in Aminopyrimidine sulfonate/carboxylate interactions: crystal structures of pyrimethaminium benzenesulfonate monohydrate (2:2:1) and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate (4:2:2).

Balasubramani K, Muthiah PT, Lynch DE - Chem Cent J (2007)

Bottom Line: In compound 2, two types of bimolecular cyclic hydrogen bonded R2(2)(8) motifs (one involving the carboxylate group and the other involving sulfonate group) coexist.In both the compounds base pairing also occurs.Thus homo and hetero synthons are present.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Chemistry, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India. bala1679@yahoo.com

ABSTRACT

Background: Pyrimethamine [2,4-diamino-5-(p-chlorophenyl)-6-ethylpyrimidine] is an antifolate drug used in anti-malarial chemotherapy. Pyrimidine and aminopyrimidine derivatives are biologically important compounds owing to their natural occurrence as components of nucleic acids.

Results: In the crystal structures of two organic salts, namely pyrimethaminium benzenesulfonate monohydrate 1 and 2-amino-4, 6-dimethylpyrimidinium 3-carboxy-4-hydroxy benzenesulfonate dihydrate 2, pyrimethamine (PMN) and 2-amino-4,6-dimethylpyrimidine (AMPY) are protonated at one of the nitrogens in the pyrimidine rings. In both the PMN and AMPY sulfonate complexes, the protonated pyrimidine rings are hydrogen bonded to the sulfonate groups, forming a hydrogen-bonded bimolecular ring motif with graph-set notation R2(2)(8). The sulfonate group mimics the carboxylate anion's mode of association, which is more commonly seen when binding with 2-aminopyrimidines. In compound 1, the PMN moieties are centrosymmetrically paired through a complementary DADA array of hydrogen bonds. In compound 2, two types of bimolecular cyclic hydrogen bonded R2(2)(8) motifs (one involving the carboxylate group and the other involving sulfonate group) coexist. Furthermore, this compound is stabilized by intra and intermolecular O-H...O hydrogen bonds.

Conclusion: The crystal structures of pyrimethaminium benzenesulfonate monohydrate and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate have been investigated in detail. In compound 1, the R2(2)(8) motif involving the sulfonate group is present. The role the sulfonic acid group plays in mimicking the carboxylate anions is thus evident. In compound 2, two types of bimolecular cyclic hydrogen bonded R2(2)(8) motifs (one involving the carboxylate group and the other involving sulfonate group) coexist. In both the compounds base pairing also occurs. Thus homo and hetero synthons are present.

No MeSH data available.


π-π stacking interactions in compound 2.
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Figure 9: π-π stacking interactions in compound 2.

Mentions: In compound 2, two types of bimolecular cyclic hydrogen-bonded R22(8) motifs (motif I and motif II) are formed. Motif I involves protonated aminopyrimidinium cations (N1A and N1B), and the 2-amino group and sulfosalicylate anions (carboxylate group) (O5A and O6B). Motif II is formed by protonated aminopyrimidinium cations (N1C and N1D), and the 2-amino group and sulfosalicylate anions (sulfonate group) (O2B and O2A). There is also base pairing via a pair of N-H...N hydrogen bonds (motif IV) involving two aminopyrimidinium molecules (cations C and D). These arrays are connected via a pair of C-H...O hydrogen bonds involving centrosymmetrically paired sulfosalicylates (B molecule) to form a supramolecular network (Figure 5). The commonly observed intramolecular hydrogen bond between the phenol -OH and carboxyl group in salicylic acid is also present in the sulfosalicylate anion (motif VI) [32]. The two sulfosalicylate (carboxylate group) oxygen atoms interact with 2-amino-4,6-dimethylpyrimidinium cations through C-H...O hydrogen bonds. The base pairing and C-H...O hydrogen bonds are arranged alternatively to form a chain (Figure 6). The two sulfosalicylate anions (O5B and O6A) are bridged by the water molecule (O1 W) via O-H...O hydrogen bonds (Figure 7). In compound 1, PMNBSA, π-π stacking interactions between benzenesulfonate molecules are observed with a perpendicular separation of 3.356Å, a centroid-to-centroid distance of 3.608(2) Å and a slip angle of 21.54° (Figure 8). In compound 2, AMPYSSA, the 2-amino-4,6-dimethylpyrimidinium cations (C), stack with sulfosalicylate anions A and B, with a perpendicular separation of 3.319Å and 3.359Å, a centroid-to-centroid distance of 3.529(11)Å and 3.554(11)Å and a slip angle of 17.49° and 19.30° respectively. A similar type of stacking is also observed between the 2-amino-4,6-dimethylpyrimidinium cation (D) and the sulfosalicylate anions (A and B), with a perpendicular separation of 3.238Å and 3.360Å, a centroid-to-centroid distance of 3.730(11)Å and 3.483(11)Å and a slip angle of 24.13° and 19.30° respectively (Figure 9). These are typical aromatic stacking values [34].


R2(2)(8) motifs in Aminopyrimidine sulfonate/carboxylate interactions: crystal structures of pyrimethaminium benzenesulfonate monohydrate (2:2:1) and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate (4:2:2).

Balasubramani K, Muthiah PT, Lynch DE - Chem Cent J (2007)

π-π stacking interactions in compound 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2238812&req=5

Figure 9: π-π stacking interactions in compound 2.
Mentions: In compound 2, two types of bimolecular cyclic hydrogen-bonded R22(8) motifs (motif I and motif II) are formed. Motif I involves protonated aminopyrimidinium cations (N1A and N1B), and the 2-amino group and sulfosalicylate anions (carboxylate group) (O5A and O6B). Motif II is formed by protonated aminopyrimidinium cations (N1C and N1D), and the 2-amino group and sulfosalicylate anions (sulfonate group) (O2B and O2A). There is also base pairing via a pair of N-H...N hydrogen bonds (motif IV) involving two aminopyrimidinium molecules (cations C and D). These arrays are connected via a pair of C-H...O hydrogen bonds involving centrosymmetrically paired sulfosalicylates (B molecule) to form a supramolecular network (Figure 5). The commonly observed intramolecular hydrogen bond between the phenol -OH and carboxyl group in salicylic acid is also present in the sulfosalicylate anion (motif VI) [32]. The two sulfosalicylate (carboxylate group) oxygen atoms interact with 2-amino-4,6-dimethylpyrimidinium cations through C-H...O hydrogen bonds. The base pairing and C-H...O hydrogen bonds are arranged alternatively to form a chain (Figure 6). The two sulfosalicylate anions (O5B and O6A) are bridged by the water molecule (O1 W) via O-H...O hydrogen bonds (Figure 7). In compound 1, PMNBSA, π-π stacking interactions between benzenesulfonate molecules are observed with a perpendicular separation of 3.356Å, a centroid-to-centroid distance of 3.608(2) Å and a slip angle of 21.54° (Figure 8). In compound 2, AMPYSSA, the 2-amino-4,6-dimethylpyrimidinium cations (C), stack with sulfosalicylate anions A and B, with a perpendicular separation of 3.319Å and 3.359Å, a centroid-to-centroid distance of 3.529(11)Å and 3.554(11)Å and a slip angle of 17.49° and 19.30° respectively. A similar type of stacking is also observed between the 2-amino-4,6-dimethylpyrimidinium cation (D) and the sulfosalicylate anions (A and B), with a perpendicular separation of 3.238Å and 3.360Å, a centroid-to-centroid distance of 3.730(11)Å and 3.483(11)Å and a slip angle of 24.13° and 19.30° respectively (Figure 9). These are typical aromatic stacking values [34].

Bottom Line: In compound 2, two types of bimolecular cyclic hydrogen bonded R2(2)(8) motifs (one involving the carboxylate group and the other involving sulfonate group) coexist.In both the compounds base pairing also occurs.Thus homo and hetero synthons are present.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Chemistry, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India. bala1679@yahoo.com

ABSTRACT

Background: Pyrimethamine [2,4-diamino-5-(p-chlorophenyl)-6-ethylpyrimidine] is an antifolate drug used in anti-malarial chemotherapy. Pyrimidine and aminopyrimidine derivatives are biologically important compounds owing to their natural occurrence as components of nucleic acids.

Results: In the crystal structures of two organic salts, namely pyrimethaminium benzenesulfonate monohydrate 1 and 2-amino-4, 6-dimethylpyrimidinium 3-carboxy-4-hydroxy benzenesulfonate dihydrate 2, pyrimethamine (PMN) and 2-amino-4,6-dimethylpyrimidine (AMPY) are protonated at one of the nitrogens in the pyrimidine rings. In both the PMN and AMPY sulfonate complexes, the protonated pyrimidine rings are hydrogen bonded to the sulfonate groups, forming a hydrogen-bonded bimolecular ring motif with graph-set notation R2(2)(8). The sulfonate group mimics the carboxylate anion's mode of association, which is more commonly seen when binding with 2-aminopyrimidines. In compound 1, the PMN moieties are centrosymmetrically paired through a complementary DADA array of hydrogen bonds. In compound 2, two types of bimolecular cyclic hydrogen bonded R2(2)(8) motifs (one involving the carboxylate group and the other involving sulfonate group) coexist. Furthermore, this compound is stabilized by intra and intermolecular O-H...O hydrogen bonds.

Conclusion: The crystal structures of pyrimethaminium benzenesulfonate monohydrate and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate have been investigated in detail. In compound 1, the R2(2)(8) motif involving the sulfonate group is present. The role the sulfonic acid group plays in mimicking the carboxylate anions is thus evident. In compound 2, two types of bimolecular cyclic hydrogen bonded R2(2)(8) motifs (one involving the carboxylate group and the other involving sulfonate group) coexist. In both the compounds base pairing also occurs. Thus homo and hetero synthons are present.

No MeSH data available.