Molecular interactions of plumbagin inclusion complexes with β-cyclodextrin (BCD), dimethyl-β-cyclodextrin (MBCD), and hydroxypropyl-β-cyclodextrin (HPBCD) were investigated by semi-empirical, Parameterization Method 6 and 7 (PM6, and PM7) in the aqueous phase using polarizable continuum calculations. The results revealed two different binding modes of the plumbagin molecule inside the BCD cavity with a negative value of the complexation energy. In conformation-I, the hydroxyl phenolic group of plumbagin was placed in the BCD cavity near the narrow-side of the host molecule. In the other model, conformation-II, the methyl quinone group of plumbagin was placed in the cavity of BCD near the narrow-side of the host molecule. The higher the negative value of the complexation energy, the more favorable is the pathway of inclusion-complex formation.

We calculated the docking energies between plumbagin and cyclodextrins, using density functional theory (DFT) with several functionals and some semi-empirical methods. Our DFT results revealed that GD3 dispersion force correction significantly improves the reliability of prediction. Also sufficient amount of long-range exchange is important to make it reliable further, agreeing with the previous work on argon dimer. In the semi-empirical methods, PM6 and PM7 qualitatively reproduce the stabilization by docking , yet under-and over-estimating the docking energies by ∼10 kcal/mol, respectively.

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Ferrocene (F e(C5H5)2) is an organometallic compound which its structure consists of two cyclopentadienyl (Cp) rings bound on opposite sides of a central metal atom. This compound is usually added into rocket's solid propellant as a burning rate catalyst. However, this composition always migrates from the propellant system by both diffusion and surface migration mechanism that causes the unpredictability of the burning rate which in turn renders unpredictable rocket performance Therefore, the study of the method to investigate the role of Ferrocene in biological systems is highly significant. This paper proposes the use of molecular simulation to study the properties of Ferrocene molecular systems to get a deeper understanding of the physics of electronic correlation in real materials. The result from the studies shows that Gaussian and Monte Carlo is the suitable method to simulate the role of Ferrocene in biological systems.