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Computational Modeling of Cytosine Photophysics and Photochemistry: From the Gas Phase to DNA

  • Luis Blancafort
  • Michael J. Bearpark
  • Michael A. Robb
Part of the Challenges and Advances In Computational Chemistry and Physics book series (COCH, volume 5)

Abstract

In this chapter we review computations that help to explain the photostability and lifetimes of the DNA nucleobases, using cytosine and the cytosine-guanine Watson-Crick base-pair as examples. For cytosine (and other pyrimidine nucleobases), photostability is the result of an ethylenic type conical intersection associated with torsion around a C = C double bond, and the barrier height is solvent dependent. By contrast, in the cytosine-guanine Watson-Crick base-pair, radiationless decay occurs via an intermolecular charge transfer state. This is triggered by proton transfer, along a coordinate that displaces the locally excited states that were studied in the isolated cytosine to higher energy. The protein environment causes a part of the conical intersection seam to become accessible which cannot be reached in the gas phase. Because there is a dense manifold of excited states present, all of these computations are sensitive to dynamic electron correlation and the details of the reaction coordinates involved. For cytosine-guanine, trajectory calculations proved to be necessary to determine the extent of the conical intersection that is actually accessible. Subsequent improvements in the level of theory used for the static calculation of single molecules will be possible, but these will need to be balanced against a more realistic treatment of vibrational kinetic energy and any environmental effects (solvent/protein)

Keywords

Cytosine Guanine Watson-Crick Base-Pair DNA Oligomers Conical Intersection Radiationless Decay Internal Conversion 

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Luis Blancafort
    • 1
  • Michael J. Bearpark
    • 2
  • Michael A. Robb
    • 2
  1. 1.Institut de Química Computacional and Departament de QuímicaUniversitat de Girona17071 GironaSpain
  2. 2.Department of ChemistryImperial College LondonLondon SW7 2AZUK

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