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

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Book cover Radiation Induced Molecular Phenomena in Nucleic Acids

Part of the book series: Challenges and Advances In Computational Chemistry and Physics ((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)

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Author information

Authors and Affiliations

  1. Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Spain

    Luis Blancafort

  2. Department of Chemistry, Imperial College London, London SW7 2AZ, UK

    Michael J. Bearpark & Michael A. Robb

Authors
  1. Luis Blancafort
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  2. Michael J. Bearpark
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  3. Michael A. Robb
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Editor information

Editors and Affiliations

  1. Department of Chemistry, Jackson State University, 1325 J. R. Lynch Street, Jackson, MS 39217, USA

    Manoj K. Shukla  & Jerzy Leszczynski  & 

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Blancafort, L., Bearpark, M.J., Robb, M.A. (2008). Computational Modeling of Cytosine Photophysics and Photochemistry: From the Gas Phase to DNA. In: Shukla, M.K., Leszczynski, J. (eds) Radiation Induced Molecular Phenomena in Nucleic Acids. Challenges and Advances In Computational Chemistry and Physics, vol 5. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8184-2_17

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