3,5,7-Trimethoxyphenanthrene-1,4-dione: a new biologically relevant natural phenanthrenequinone derivative from Dioscorea prazeri and studies on its single X-ray crystallographic behavior, molecular docking and other physico-chemical properties

Abstract

A naturally occurring new phenanthrenequinone derivative has been isolated from the yams of Dioscorea prazeri Prain and Burkil (Dioscoreaceae) and identified as 3,5,7-trimethoxyphenanthrene-1,4-dione (1) on the basis of its detailed spectral and single crystal X-ray analyses. The compound crystallizes in the triclinic space group P with the following unit-cell parameters: a = 7.7045(3), b = 8.5088(4), c = 16.3254(7) A, α = 98.908(2)°, β = 96.316(2)°, γ = 103.939(2)° and Z = 2. The crystal structure was solved by direct methods using single-crystal X-ray diffraction data collected at room temperature and refined by full-matrix least-squares procedures to a final R-value of 0.0559 for 2832 observed reflections. Exhaustive theoretical studies on the molecular structure, vibrational spectra, HOMO, LUMO, MESP surfaces, reactivity descriptor and molecular docking of this plant-derived hitherto unknown natural molecule have also been performed. The equilibrium geometry of the title compound has been obtained and analyzed using the DFT-B3LYP/6-31+G(d,p) method. A comparison between the calculated vibrational spectral data with the experimental observations for the phenanthrenequinone molecule has been performed. The reactivity of this molecule is explained using various local as well as global molecular descriptors and reactivity surfaces have also been analyzed. The molecular docking study of the title molecule for predicting its possible anticancer property has also been investigated.