Omadacycline dihydrate, C29H40N4O7·2H2O, from X-ray powder diffraction data
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ABSTRACT:
SUBMITTER: Kaduk J
PROVIDER: S-EPMC10915668 | biostudies-literature | 2024 Feb
REPOSITORIES: biostudies-literature
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Project description:The crystal structure of trirubidium citrate, 3Rb+·C6H5O73-, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The two independent Rb+ cations are seven- and eight-coordinate, with bond-valence sums of 0.99 and 0.92 valence units. The coordination polyhedra share edges and corners to form a three-dimensional framework. The only hydrogen bond is an intra-molecular one between the hy-droxy group and the central carboxyl-ate, with graph set S(5). The hydro-phobic methyl-ene groups lie in pockets in the framework.
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Project description:The title mol-ecule, C19H18N4O2 {systematic name: (RS)-6-[2-(4-meth-oxy-phen-yl)-1H-benzimidazol-5-yl]-5-methyl-4,5-di-hydro-pyridazin-3(2H)-one}, adopts an extended conformation. The dihedral angles between the central benzimidazole ring sytem and the pendant meth-oxy-phenyl and pyridazinone residues are 1.41 (18) and 9.7 (3)°, respectively. In the crystal, N-H⋯N hydrogen bonds link the imadazole groups into [001] chains, and pairs of N-H⋯O hydrogen bonds link the pyridazinone groups into dimers. Together, these generate a two-dimensional supra-molecular structure parallel to (010). The layers are linked by C-H⋯π inter-actions.
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Project description:In the title compound, [CdL 2(H2O)4]·2H2O [L = (1-ammonio-1-phosphono-eth-yl)phospho-nate, C2H8NO6P2 (-)], the Cd(II) ion is situated on an inversion centre being coordinated by four aqua mol-ecules in the equatorial plane and two phosphonate O atoms from two deprotonated L ligands in the axial positions in a distorted octa-hedral geometry. The asymmetric unit contains one-half of the complex mol-ecule and one lattice water mol-ecule. The ligand L exists in a zwitterionic form, with a positive charge on the NH3 group and a negative charge on the O atom of the non-coordinating phospho-nate group, and with an intra-molecular O-H⋯O inter-action forming an S(6) ring motif and two intra-molecular N-H⋯O inter-actions each generating an S(5) ring motif. In the crystal, N-H⋯O and O-H⋯O hydrogen bonds link the complex mol-ecules into a three-dimensional network in which the voids of 38 Å(3) are filled with ordered lattice water mol-ecules, which are also involved in O-H⋯O hydrogen bonding.
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Project description:Time-of-flight neutron powder diffraction data have been measured from ∼90 mol% deuterated isotopologues of Na2MoO4·2H2O and Na2WO4·2H2O at 295 K to a resolution of sin (θ)/λ = 0.77 Å(-1). The use of neutrons has allowed refinement of structural parameters with a precision that varies by a factor of two from the heaviest to the lightest atoms; this contrasts with the X-ray based refinements where precision may be > 20× poorer for O atoms in the presence of atoms such as Mo and W. The accuracy and precision of inter-atomic distances and angles are in excellent agreement with recent X-ray single-crystal structure refinements whilst also completing our view of the hydrogen-bond geometry to the same degree of statistical certainty. The two structures are isotypic, space-group Pbca, with all atoms occupying general positions, being comprised of edge- and corner-sharing NaO5 and NaO6 polyhedra that form layers parallel with (010) inter-leaved with planes of XO4 (X = Mo, W) tetra-hedra that are linked by chains of water mol-ecules along [100] and [001]. The complete structure is identical with the previously described molybdate [Capitelli et al. (2006 ▸). Asian J. Chem. 18, 2856-2860] but shows that the purported three-centred inter-action involving one of the water mol-ecules in the tungstate [Farrugia (2007 ▸). Acta Cryst. E63, i142] is in fact an ordinary two-centred 'linear' hydrogen bond.
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