Adenine Adsorption on GeO<sub>2</sub> Nanoclusters: DFT, MD and Solvent Effects Analyses
Jamelah S. Al-Otaibi, Y. Sheena Mary, Ravi Trivedi, Brahmananda Chakraborty, M.S. Roxy
Abstract
This study presents the adsorption of adenine (AD) nucleobase over GeO 2 nanocluster using density functional theory (DFT) analysis. The effect of AD adsorption with GeO 2 nanocluster was thoroughly investigated by calculating adsorption energies, other parameters and vibrational spectra. The adsorption of AD over the nanocluster was examined at different sites (-N 4 , -N 5 , -N 1 and -N[Formula: see text] present on the biomolecule with different configurations. The adsorption energies varied from −18.22 kcal/mol to −80.02/−59.73 kcal/mol to 142.51 kcal/mol in vacuum/water. The changes in energy at different sites suggest that the interaction of the AD nucleobase through the N 5 site is good for forming thermodynamically stable and energetically favorable states. The relevant phenomenon of a decrease in band gap energy due to the adsorption of the biomolecule validates the significant chemical reactions between the biomolecule and the GeO 2 nanoclusters. Partial density of state analysis supports charge transfer from nucleo-based AD to Ge 5 O[Formula: see text] cluster. Molecular dynamics (MD) simulation studies of ligands in water and the ligands displayed enhanced stability and well-balanced behavior in water, although a slightly higher range of fluctuations was observed in root mean square deviation (RMSD) plots, which may be caused due to the distinct nature of each ligand in the solution.