Omadacycline dihydrate, C₂₉H₄₀N₄O₇·2H₂O, from X-ray powder diffraction data

Area of Science:

• Crystallography
• Chemical structure determination
• Materials science

Background:

• Understanding the precise three-dimensional arrangement of atoms in complex organic molecules is crucial for predicting their properties and potential applications.
• Tetra-cene derivatives are a class of compounds with diverse biological activities, necessitating detailed structural characterization.

Purpose of the Study:

• To elucidate the crystal structure of the title tetra-cene derivative, {(4S,4aS,5aR,12aR)-4,7-bis-(di-methyl-amino)-9-[(2,2-di-methyl-propyl-amino)-meth-yl]-1,10,11,12a-tetra-hydroxy-3,12-dioxo-4a,5,5a,6-tetra-hydro-4H-tetra-cene-2-carb-oxamide dihydrate, C29H40N4O7·2H2O}.
• To investigate the intermolecular interactions and packing in the solid state.

Main Methods:

• Synchrotron X-ray powder diffraction data collection and refinement.
• Analysis of crystallographic data to determine space group, unit cell parameters, and atomic positions.
• Identification and analysis of intra- and inter-molecular hydrogen bonding networks.

Main Results:

• The compound crystallizes in the R3 space group with specific unit cell dimensions (a = 24.34430(7) Å, c = 14.55212(4) Å, V = 7468.81(2) ų).
• A three-dimensional framework is formed through intra-molecular hydrogen bonds and two classical N-H⋯O inter-molecular hydrogen bonds, along with weaker C-H⋯O and C-H⋯N interactions.
• The framework contains voids occupied by disordered water molecules, and keto-enol tautomerism appears to be significant, leading to ambiguity in the exact molecular structure.

Conclusions:

• The crystal structure provides fundamental insights into the solid-state organization of this complex tetra-cene derivative.
• The presence of voids and disordered water suggests potential for host-guest chemistry or influence on material properties.
• The ambiguity due to keto-enol tautomerism highlights the dynamic nature of the molecule in the crystalline state and warrants further investigation.