Structural and electronic properties of DNA-intercalated aromatic chromophore complexes : a combined quantum mechanics and molecular dynamics study

Abstract

The quantum mechanical calculations and molecular dynamic simulations were used to investigatethe structural and electronic properties of DNA-Intercalated aromatic chromophore complexes. In the first step, electronic spectra of chromophores, acridine, aminoacridine derivatives, pyronine 6G and rhodamine 6G, were studied in gas phase and in aqueous solution using semiempirical, NDDO-G and AM1 and quantum mechanical methods, TDDFT. The calculated absorption energies of the acridine and aminoacridine derivatives agree well with the experiment and the high level of theory, while overestimates that of the rhodamine 6G the experimental value. Changes of the absorption spectra were observed when solvent effects were included. Then, molecular dynamics simulations on the dimers of the positively charged pyronine 6G and rhodamine 6G in aqueous solutions were carried out using newly generated force field parameters. It was found that monomers of pyronine 6G and rhodamine 6G easily undergo relative rotations. Moreover, stability of the dimer was observed to be obviously dominated by the electrostatic interaction between the solute and its aqueous environment. Finally, MD simulations were performed to study conformational features and dynamics of three complexes of rhodamine-6G derivative with DNA. Highly flexible of the chromophore orientations relative to guanine base of DNA was observed. Additionally, the stacking interaction with chromophore effects only slightly on the second and the third base pairs.