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Crystal structures of three halide salts of l-asparagine: an isostructural series.

ABSTRACT: The structures of three monohydrated halide salt forms of l-asparagine are presented, viz. l-asparaginium chloride monohydrate, C₄H₉N₂O₃ ⁺·Cl^-·H₂O, (I), l-asparaginium bromide monohydrate, C₄H₉N₂O₃ ⁺·Br^-·H₂O, (II), and l-asparaginium iodide monohydrate, C₄H₉N₂O₃ ⁺·I^-·H₂O, (III). These form an isomorphous and isostructural series. The C-C-C-C backbone of the amino acid adopts a gauche conformation in each case [torsion angles for (I), (II) and (III) = -55.4 (2), -55.6 (5) and -58.3 (7)°, respectively]. Each cation features an intra-molecular N-H⋯O hydrogen bond, which closes an S(6) ring. The extended structures feature chains of cations that propagate parallel to the b-axis direction. These are formed by carb-oxy-lic acid/amide complimentary O-H⋯O + N-H⋯O hydrogen bonds, which generate R ₂ ²(8) loops. These chains are linked by further hydrogen bonds mediated by the halide ions and water mol-ecules to give a layered structure with cation and anion layers parallel to the ab plane. Compound (III) was refined as an inversion twin.

SUBMITTER: de Moraes LS

PROVIDER: S-EPMC6218909 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Crystal structures of three halide salts of l-asparagine: an isostructural series.

de Moraes Lygia S LS Kennedy Alan R AR Logan Charlie R CR

Acta crystallographica. Section E, Crystallographic communications 20181019 Pt 11

The structures of three monohydrated halide salt forms of l-asparagine are presented, viz. l-asparaginium chloride monohydrate, C4H9N2O3 +·Cl-·H2O, (I), l-asparaginium bromide monohydrate, C4H9N2O3 +·Br-·H2O, (II), and l-asparaginium iodide monohydrate, C4H9N2O3 +·I-·H<sub ...[more]

PMID: 30443393

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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.

Project description:The structures and Hirshfeld surface analysis of three salts of 1-(4-nitro-phenyl)-piperazine are discussed. In 4-(4-nitro-phen-yl)piperazin-1-ium salicylate (C10H14N3O2 +·C7H5O3 -), there are strong hydrogen bonds between cation and anion and the 4-nitro-phenyl substituent occupies an equatorial position in the piperazinium ring. The cation and anion are linked together by supra-molecular inter-actions [graph-set notation of hydrogen bonding (6) propagating in the a-axis direction]. Additionally, there is π-π stacking involving the salicylate anion and the piperazinium cation in adjacent asymmetric units as well as a C-H⋯π inter-action between a hydrogen atom on the piperazine ring and the phenyl ring within the salicyclate anion. In bis-[4-(4-nitro-phen-yl)piperazin-1-ium] bis-(4-fluoro-benzoate) trihydrate (2C10H14N3O2 +·2C7H4FO2 -·3H2O), there are two cations, two anions, and three water mol-ecules of solvation in the asymmetric unit, all linked by hydrogen bonds [graph-set notation of hydrogen bonding R 2 2(20) between adjacent cations and R 3 3(9) between a cation and its adjacent anion]. In the anion, the 4-nitro-phenyl ring occupies an axial substitution position in the piperazinium ring, which is relatively rare. Within the asymmetric unit, the phenyl groups in the cations show an offset π-π inter-action. Additionally, there is a C-H⋯π inter-action between a hydrogen atom on the phenyl ring within a cation and the phenyl ring within an anion. In 4-(4-nitro-phen-yl)piperazin-1-ium 3,5-di-nitro-benzoate (C10H14N3O2 +·C7H4N2O6 -), there is a strong N-H⋯O hydrogen bond linking the cation and anion and the 4-nitro-phenyl ring occupies an axial substitution position in the piperazinium ring, as seen in the previous structure. In the crystal, the cation and the anion form a complex three-dimensional hydrogen-bonded array involving R 2 2(8), R 4 4(12) and R 4 4(20) rings propogating in the a-axis direction. The nitro-phenyl group is disordered with occupancies of 0.806 (10) and 0.194 (10).

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Crystal structures of three halide salts of l-asparagine: an isostructural series.

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Crystal structures of three halide salts of l-asparagine: an isostructural series.

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