Open AccessInfluence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations
Author(s) -
Fabrizio Santoro,
Vincenzo Barone,
Roberto Improta
Publication year - 2007
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.0703298104
Subject(s) - excited state , delocalized electron , stacking , polarizable continuum model , chemistry , excimer , molecular physics , density functional theory , ground state , chromophore , atomic physics , time dependent density functional theory , nucleobase , excitation , chemical physics , computational chemistry , solvation , fluorescence , molecule , photochemistry , physics , dna , biochemistry , organic chemistry , quantum mechanics
A thorough study of the excited-state properties of the stacked dimers and trimers of 9-methyladenine in B-DNA conformation has been performed in aqueous solution by using time-dependent density functional calculations and the solvent polarizable continuum model, and results were compared with experimental results on polyadenine oligomers. The effect of base stacking on the absorption and emission spectra is fully reproduced by our calculations. Although light absorption leads to a state (SB ) delocalized over several nucleobases, excited-state geometry optimization indicates that SB subsequently evolves into a state in which the excitation is localized on a single base. Analysis of the excited-state potential energy surfaces shows that SB can easily decay into the lowest energy excited state, SCT , which is a dark excimer produced by intermonomer charge transfer between two stacked bases. The subpicosecond features of the time-resolved experiments are interpreted in terms of ultrafast decay from SB . After localization, two easy, radiationless decay channels are indeed open for SB : (i ) ground-state recovery, according to the same mechanisms proposed for isolated adenine and/or (ii ) decay to SCT . Our calculations suggest that the slowest part of the excited-state dynamics detected experimentally involves the SCT state.