On the conformation, molecular interactions and electron density of a natural flavonoid derivative.

Abstract

The molecular structure of limonianin (1), a natural compound isolated from the root of Citrus limonia, was determined by X-ray diffraction. The structure of 1 crystallizes in the monoclinic space group P21/c with one molecule per asymmetric unit. The compound has four six-membered rings: two benzenoid and one g-pyrone ring in a planar conformation, and one chromene ring presenting a half-boat conformation. Also, the molecule shows a pseudo-six-membered ring by resonance assisted hydrogen bond (RAHB). The molecular self-assembly of limonianin is stabilized by intra and intermolecular hydrogen bonding, which were assessed by Hirshfeld surfaces and two-dimensional fingerprint plots. Moreover, a detailed study of the molecular electron density and its corresponding topology and charge distribution based on the quantum theory of atom in molecules (QTAIM) was also one of the main aims of this work. Different methodologies were used to model the electron density distribution in limonianin molecule. The RAHB effect relating the crystal structure with its electron density analysis is discussed in detail. Therefore, this report contributes to the better understanding of the structural behavior of a flavonoid derivative, suggesting suitable methodologies to explore the electron density distribution, even in the absence of high-resolution experimental data.