Journal Article

PreJuSER-11461

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Does Stacking Restrain the Photodynamics of Individual Nucleobases?

Nachtigallova, D. ; Zeleny, T. ; Ruckenbauer, M. ; Müller, T.FZJ* ; Barbatti, M. ; Hobza, P. ; Lischka, H.

2010
American Chemical Society Washington, DC

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Please use a persistent id in citations: doi:10.1021/ja1029705

Abstract: 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.

Keyword(s): DNA: chemistry (MeSH) ; Hydrogen Bonding (MeSH) ; Light (MeSH) ; Models, Molecular (MeSH) ; Nucleic Acid Conformation: radiation effects (MeSH) ; Pyrimidines: chemistry (MeSH) ; Pyrimidines ; 4-aminopyrimidine ; DNA ; J

Note: This work has been supported by grants from the Ministry of Education of the Czech Republic (Center for Biomolecules and Complex Molecular Systems, LC512) and by the Austrian Science Fund within the framework of the Special Research Program F16 (Advanced Light Sources) and Project P18411-N19. It was part of research project Z40550506. Support from the Praemium Academiae of the AS CR, awarded to P.H. in 2007, is acknowledged. T.Z. acknowledges a grant of the Grant Agency of the Czech Republic 203/09/H046 and grant of the Ministry of Education of the Czech Republic MSM6198959216.

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Contributing Institute(s):

1. Jülich Supercomputing Centre (JSC)

Research Program(s):

1. Scientific Computing (FUEK411) (FUEK411)
2. 411 - Computational Science and Mathematical Methods (POF2-411) (POF2-411)

Appears in the scientific report 2010

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