Does stacking restrain the photodynamics of individual nucleobases?
Nonadiabatic photodynamical simulations of 4-aminopyrimidine (4-APy) used as a model for adenine were performed by embedding it between two stacking methyl-guanine (mGua) molecules to determine the effect of spatial restrictions on the ultrafast photodeactivation mechanism of this nucleobase. A hybrid multiconfigurational ab initio/molecular mechanical approach in combination with surface hopping was used. During the dynamics the formation of a significant fraction of intrastrand hydrogen bonding from 4-APy to mGua above and below is observed. These findings show that this type of hydrogen bond may play an important role for the photodynamics within one DNA strand and that it should be of interest even in irregular segments of double stranded nucleic acids structures. The relaxation mechanism of internal conversion to the ground state is dominated by ring puckering, and an overall elongation of the lifetime of the embedded system by approximately 20% as compared to the isolated 4-APy is computed.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic. dana.nachtigallova@uochb.cas.cz
Dana
D
Nachtigallová
Tomás
T
Zelený
Matthias
M
Ruckenbauer
Thomas
T
Müller
Mario
M
Barbatti
Pavel
P
Hobza
Hans
H
Lischka
D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008027:Light; D008958:Models, Molecular; D009690:Nucleic Acid Conformation / Q000528:radiation effects*; D011743:Pyrimidines / Q000737:chemistry
D011743:Pyrimidines; C034821:4-aminopyrimidine; D004247:DNA