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Crystal structures of 2-amino-pyridine citric acid salts: C5H7N2+·C6H7O7- and 3C5H7N2+·C6H5O73.

ABSTRACT: 2-Amino-pyridine and citric acid mixed in 1:1 and 3:1 ratios in ethanol yielded crystals of two 2-amino-pyridinium citrate salts, viz. C5H7N2+·C6H7O7- (I) (systematic name: 2-amino-pyridin-1-ium 3-carb-oxy-2-carb-oxy-methyl-2-hy-droxy-propano-ate), and 3C5H7N2+·C6H5O73- (II) [systematic name: tris-(2-amino-pyridin-1-ium) 2-hy-droxy-propane-1,2,3-tri-carboxyl-ate]. The supra-molecular synthons present are analysed and their effect upon the crystal packing is presented in the context of crystal engineering. Salt I is formed by the protonation of the pyridine N atom and deprotonation of the central carb-oxy-lic group of citric acid, while in II all three carb-oxy-lic groups of the acid are deprotonated and the charges are compensated for by three 2-amino-pyridinium cations. In both structures, a complex supra-molecular three-dimensional architecture is formed. In I, the supra-molecular aggregation results from Namino-H?Oacid, Oacid?H-Oacid, Oalcohol-H?Oacid, Namino-H?Oalcohol, Npy-H?Oalcohol and Car-H?Oacid inter-actions. The mol-ecular conformation of the citrate ion (CA3-) in II is stabilized by an intra-molecular Oalcohol-H?Oacid hydrogen bond that encloses an S(6) ring motif. The complex three-dimensional structure of II features Namino-H?Oacid, Npy-H?Oacid and several Car-H?Oacid hydrogen bonds. In the crystal of I, the common charge-assisted 2-amino-pyridinium-carboxyl-ate heterosynthon exhibited in many 2-amino-pyridinium carboxyl-ates is not observed, instead chains of N-H?O hydrogen bonds and hetero O-H?O dimers are formed. In the crystal of II, the 2-amino-pyridinium-carboxyl-ate heterosynthon is sustained, while hetero O-H?O dimers are not observed. The crystal structures of both salts display a variety of hydrogen bonds as almost all of the hydrogen-bond donors and acceptors present are involved in hydrogen bonding.

SUBMITTER: Prakash SM

PROVIDER: S-EPMC6073010 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Crystal structures of 2-amino-pyridine citric acid salts: C5H7N2+·C6H7O7- and 3C5H7N2+·C6H5O73.

Prakash Shet M SM Naveen S S Lokanath N K NK Suchetan P A PA Warad Ismail I

Acta crystallographica. Section E, Crystallographic communications 20180717 Pt 8

2-Amino-pyridine and citric acid mixed in 1:1 and 3:1 ratios in ethanol yielded crystals of two 2-amino-pyridinium citrate salts, viz. C5H7N2+·C6H7O7- (I) (systematic name: 2-amino-pyridin-1-ium 3-carb-oxy-2-carb-oxy-methyl-2-hy-droxy-propano-ate), and 3C5H7N2+·C6H5O73- (II) [systematic name: tris-(2-a ...[more]

PMID: 30116573

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Project description:The crystal structures of two ammonium salts of 2-amino-4-nitro-benzoic acid are described, namely di-methyl-aza-nium 2-amino-4-nitro-benzoate, C2H8N+·C7H5N2O4-, (I), and di-butyl-aza-nium 2-amino-4-nitro-benzoate, C8H20N+·C7H5N2O4-, (II). The asymmetric unit of (I) comprises a single cation and a single anion. In the anion, small twists are noted for the carboxyl-ate and nitro groups from the ring to which they are connected, as indicated by the dihedral angles of 11.45 (13) and 3.71 (15)°, respectively; the dihedral angle between the substituents is 7.9 (2)°. The asymmetric unit of (II) comprises two independent pairs of cations and anions. In the cations, different conformations are noted in the side chains in that three chains have an all-trans [(+)-anti-periplanar] conformation, while one has a distinctive kink resulting in a (+)-synclinal conformation. The anions, again, exhibit twists with the dihedral angles between the carboxyl-ate and nitro groups and the ring being 12.73 (6) and 4.30 (10)°, respectively, for the first anion and 8.1 (4) and 12.6 (3)°, respectively, for the second. The difference between anions in (I) and (II) is that in the anions of (II), the terminal groups are conrotatory, forming dihedral angles of 17.02 (8) and 19.0 (5)°, respectively. In each independent anion of (I) and (II), an intra-molecular amino-N-H⋯O(carboxyl-ate) hydrogen bond is formed. In the crystal of (I), anions are linked into a jagged supra-molecular chain by charge-assisted amine-N-H⋯O(carboxyl-ate) hydrogen bonds and these are connected into layers via charge-assisted ammonium-N-H⋯O(carboxyl-ate) hydrogen bonds. The resulting layers stack along the a axis, being connected by nitro-N-O⋯π(arene) and methyl-C-H⋯O(nitro) inter-actions. In the crystal of (II), the anions are connected into four-ion aggregates by charge-assisted amino-N-H⋯O(carboxyl-ate) hydrogen bonding. The formation of ammonium-N-H⋯O(carboxyl-ate) hydrogen bonds, involving all ammonium-N-H and carboxyl-ate O atoms leads to a three-dimensional architecture; additional C-H⋯O(nitro) inter-actions contribute to the packing. The Hirshfeld surface analysis confirms the importance of the hydrogen bonding in both crystal structures. Indeed, O⋯H/H⋯O inter-actions contribute nearly 50% to the entire Hirshfeld surface in (I).

Project description:Bedaquiline [systematic name: 1-(6-bromo-2-methoxyquinolin-3-yl)-4-(dimethylamino)-2-(naphthalen-1-yl)-1-phenylbutan-2-ol, C32H31BrN2O2] is one of two important new drugs for the treatment of drug-resistant tuberculosis (TB). It is marketed in the US as its fumarate salt {systematic name: [4-(6-bromo-2-methoxyquinolin-3-yl)-3-hydroxy-3-(naphthalen-1-yl)-4-phenylbutyl]dimethylazanium 3-carboxyprop-2-enoate, C32H32BrN2O2+·C4H3O4-}, and about a dozen other salts of bedaquiline have been described in patent literature, but none have so far been structurally described. In a first communication, we present the crystal structure of bedaquilinium fumarate and of two new benzoate salts, as well as that of a degradation product of the reaction of bedaquilinium fumarate with sodium ethoxide, 3-benzyl-6-bromo-2-methoxyquinoline, C17H14BrNO. The fumarate and benzoate salts both feature cations monoprotonated at the dimethylamino group. The much less basic quinoline N atom remains unprotonated. Both salts feature a 1:1 cation-to-anion ratio, with the fumarate being present as monoanionic hydrofumarate. The conformations of the cations are compared to that of free base bedaquiline and with each other. The flexible backbone of the bedaquiline structure leads to a landscape of conformations with little commonalities between the bedaquiline entities in the various structures. The conformations are distinctively different for the two independent molecules of the free base, the two independent molecules of the hydrofumarate salt, and the one unique cation of the benzoate salt. Packing of the salts is dominated by hydrogen bonding. Hydrogen-bonding motifs, as well as the larger hydrogen-bonded entities within the salts, are quite similar for the salts, despite the vastly differing conformations of the cations, and both the hydrofumarate and the benzoate structure feature chains of hydrogen-bonded anions that are surrounded by and hydrogen bonded to the larger bedaquilinium cations, leading to infinite broad ribbons of anions, cations, and (for the benzoate salt) water molecules. The benzoate salt was isolated in two forms: as a 1.17-hydrate (C32H32BrN2O2+·C7H5O2-·1.166H2O), obtained from acetone or propanol solution, with one fully occupied water molecule tightly integrated into the hydrogen-bonding network of anions and cations, and one partially occupied water molecule [refined occupancy 16.6 (7)%], only loosely hydrogen bonded to the quinoline N atom. The second form is an acetonitrile solvate (C32H32BrN2O2+·C7H5O2-·0.742CH3CN·H2O), in which the partially occupied water molecule is replaced by a 74.2 (7)%-occupied acetonitrile molecule. The partial occupancy induces disorder for the benzoate phenyl ring. The acetonitrile solvate is unstable in atmosphere and converts into a form not distinguishable by powder XRD from the 1.17-hydrate.

Dataset Information

Crystal structures of 2-amino-pyridine citric acid salts: C5H7N2+·C6H7O7- and 3C5H7N2+·C6H5O73.

Publications

Crystal structures of 2-amino-pyridine citric acid salts: C<sub>5</sub>H<sub>7</sub>N<sub>2</sub><sup>+</sup>·C<sub>6</sub>H<sub>7</sub>O<sub>7</sub><sup>-</sup> and 3C<sub>5</sub>H<sub>7</sub>N<sub>2</sub><sup>+</sup>·C<sub>6</sub>H<sub>5</sub>O<sub>7</sub><sup>3</sup>.

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