A theoretical study of Ru(II) polypyridyl DNA intercalators structure and electronic absorption spectroscopy of [Ru(phen)2(dppz)]2+ and [Ru(tap)2(dppz)]2+ complexes intercalated in guanine-cytosine base pairs.

The structural and spectroscopic properties of [Ru(phen)(2)(dppz)](2+) and [Ru(tap)(2)(dppz)](2+) (phen=1,10-phenanthroline; tap=1,4,5,8-tetraazaphenanthrene; dppz=dipyridophenazine ) have been investigated by means of density functional theory (DFT), time-dependent DFT (TD-DFT) within the polarized continuum model (IEF-PCM) and quantum mechanics/molecular mechanics (QM/MM) calculations. The model of the Delta and Lambda enantiomers of Ru(II) intercalated in DNA in the minor and major grooves is limited to the metal complexes intercalated in two guanine-cytosine base pairs. The main experimental spectral features of these complexes reported in DNA or synthetic polynucleotides are better reproduced by the theoretical absorption spectra of the Delta enantiomers regardless of intercalation mode (major or minor groove). This is especially true for [Ru(phen)(2)(dppz)](2+). The visible absorption of [Ru(tap)(2)(dppz)](2+) is governed by the MLCT(tap) transitions regardless of the environment (water, acetonitrile or bases pair), the visible absorption of [Ru(phen)(2)(dppz)](2+) is characterized by transitions to metal-to-ligand-charge-transfer MLCT(dppz) in water and acetonitrile and to MLCT(phen) when intercalated in DNA. The response of the IL(dppz) state to the environment is very sensitive. In vacuum, water and acetonitrile these transitions are characterized by significant oscillator strengths and their positions depend significantly on the medium with blue shifts of about 80 nm when going from vacuum to solvent. When the complex is intercalated in the guanine-cytosine base pairs the (1)IL(dppz) transition contributes mainly to the band at 370 nm observed in the spectrum of [Ru(phen)(2)(dppz)](2+) and to the band at 362 nm observed in the spectrum of [Ru(tap)(2)(dppz)](2+). Copyright (c) 2010 Elsevier Inc. All rights reserved.