Collect. Czech. Chem. Commun. 2011, 76, 631-643
Published online 2011-05-02 08:34:52

Photodynamics of the adenine model 4-aminopyrimidine embedded within double strand of DNA

Tomáš Zelenýa, Pavel Hobzab, Dana Nachtigallováb,*, Matthias Ruckenbauerc and Hans Lischkac,*

a Department of Physical Chemistry, Faculty of Sciences, Palacký University, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
b Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
c Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria


On-the-fly surface hopping nonadiabatic photodynamical simulations using hybrid quantum mechanical/molecular mechanical approach of 4-aminopyrimidine were performed to model the relaxation mechanism of adenine within DNA double strand. The surrounding bases do not affect the overall ring-puckering relaxation mechanisms significantly, however, interesting hydrogen-bond dynamics is observed. First, formation of intra-strand hydrogen bonds is found. It is shown that this effect speeds up the decay process. In addition, the Watson–Crick structure is altered by breaking one of the inter-strand hydrogen bonds also leading to a decrease of the life time.

Keywords: Ab initio calculations; Excited states; Nucleic acids; Photodynamics; QM/MM method.

References: 79 live references.