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

Tomáš Zelený, Pavel Hobza, Dana Nachtigallová, Matthias Ruckenbauer, Hans Lischka

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)631-643
Number of pages13
JournalCollection of Czechoslovak Chemical Communications
Volume76
Issue number6
DOIs
StatePublished - 2011

Keywords

  • Ab initio calculations
  • Excited states
  • Nucleic acids
  • Photodynamics
  • QM/MM method

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