Crystal Engineering of Organic Salts:  Hydrogen-Bonded Supramolecular Motifs in Trimethoprim Sorbate Dihydrate and Trimethoprim o-Nitrobenzoate

Abstract

In the crystal structures of two organic salts, namely, trimethoprim sorbate dihydrate (1) and trimethoprim o-nitrobenzoate (2), the pyrimidine moieties of trimethoprim are protonated at one of the ring nitrogens. In both the compounds, the carboxylate oxygens are hydrogen-bonded to the protonated pyrimidine rings to form the hydrogen-bonded cyclic bimolecular motif. These motifs further self-organize in two different ways to give different types of hydrogen-bonded networks in the two crystal structures. In compound 1, the two inversion related motifs pair through a pair of N-H‚‚‚N hydrogen bonds involving an unprotonated ring nitrogen and 4-amino group. In addition to this pairing, one of the water oxygens bridges the 2-and 4-amino groups on both sides of pairing to form a complementary DADA (D refers to the hydrogen-bond donor and A refers to the hydrogen-bond acceptor) array of quadruple hydrogen bonds. In compound 2, there is no base-pairing, and the cyclic hydrogen-bonded bimolecular motifs self-assemble into a hydrogen-bonded supramolecular ladder through N-H‚‚‚O and C-H‚‚‚O hydrogen bonds. The o-nitrobenzoate ions form a supramolecular chain, the ions being linked by aromatic C-H‚‚‚O (of the nitro group) hydrogen bonds.

Hydrogen-bonding patterns in trimethoprim picolinate and 2-amino-4,6-dimethylpyrimidinium picolinate hemihydrate

“…In (I), the dihedral angle between the pyrimidine and benzene rings is 76.06 (7) . This value is close to that found in TMP± carboxylate salts (Raj, Stanley et al, 2003). The C4ÐC5Ð C7ÐC8 and C5ÐC7ÐC8ÐC9 torsion angles are À68.79 (18) and 168.05 14, respectively.…”

2,6-Diamino-5-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-ylmethyl)-4-oxopyrimidin-1-ium 3,5-dinitrobenzoate

“…The carboxylate group (atoms O2 and O3) of the 3,5-dinitrobenzoate anion interact with the protonated atom N1 and the 2-amino group of the pyrimidine moiety through a pair of N-H•••O hydrogen bonds, leading to the common ring motif with graph-set notation R 2 2 (8) (Lynch & Jones, 2004). This motif is reminiscent of the cyclic hydrogen-bonded motif occurring in the crystal structures of many aminopyrimidine carboxylates (Allen et al, 1998;Raj et al, 2003). Adjacent pyrimidinium cations are linked together by way of N-H•••O bonds from the N3 and N2 amino donors to the O1′ keto acceptor, resulting in chains containing R 1 2 (6) rings (Etter, 1990;Bernstein et al, 1995).…”

“…For related literature, see: Allen et al (1998); Baker & Santi (1965); Bernstein et al (1995); Desiraju (1989); Etter (1990); Francis (2003); Hunt et al (1980); Lynch & Jones (2004); Prince et al (1991); Raj et al (2003); Stanley et al (2005); Subashini, Samuel et al (2007); ; Skoweranda et al (1990). Table 1 Hydrogen-bond geometry (Å , ).…”

Bis[2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidin-1-ium]DL-malate

“…This motif is a well known supramolecular synthon in aminopyrimidine-carboxylate salts (Stanley et al, 2005). It self-organizes in different ways to give different types of hydrogen-bonding patterns (Raj, Stanley et al, 2003) Part of the crystal structure of (I), showing the formation of an R 2 2 (8) hydrogen-bonded motif. For the sake of clarity, only H atoms involved in hydrogen bonding are shown.…”