title: A TDDFT study of the excited states of DNA bases and their assemblies.
abstract: We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional. Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and pi-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.
authors.affiliation: Departamento de Física de Materiales, Facultad de Quimicas, Universidad del País Vasco and Donostia International Physics Center (DIPC), 20080 San Sebastian, Spain.
authors.forename: Daniele
authors.initials: D
authors.lastname: Varsano
authors.forename: Rosa
authors.initials: R
authors.lastname: Di Felice
authors.forename: Miguel A L
authors.initials: MA
authors.lastname: Marques
authors.forename: Angel
authors.initials: A
authors.lastname: Rubio
mesh_terms: D020029:Base Pairing; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry
chemical_list: D011687:Purines; D011743:Pyrimidines; D004247:DNA