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The optical properties of adenine cation in different oligonucleotides: a PCM/TD-DFT study

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Abstract

The absorption spectra of several systems containing an adenine (A) cation are computed in water by TD-DFT calculations, using three different functionals and including solvent effects by a mixed discrete–continuum approach. Our calculations well reproduce the experimental absorption spectrum of deoxyadenosine nucleoside cation (dA+), which provides an intense peak at 350 nm and a weaker one at 600 nm, allowing its assignment. M052X and CAM-B3LYP predict that the hole is essentially localized on a single A base also in the cationic forms of dApdA dinucleotide, both in single and in double strand, and of (dApdT) duplex, exhibiting absorption spectra similar to that of dA+. For all these compounds, B3LYP predicts instead the delocalization of the hole over two A bases. On this ground, it is possible to propose which would be the spectral signature of partial hole delocalization. Vertical and adiabatic ionization potentials for the compounds under investigation are also computed, providing values in good agreement with the available experimental results.

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Acknowledgements

The authors thank CNRS-CNR PICS project (No. 6827-2015)/Bilateral CNR/CNRS for financial support. R.I. thanks the Université Paris-Saclay (Chaire d’Alembert No. 2016-10751). L.M-F thanks the ‘OSPEG’ LABEX PALM project.

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Authors and Affiliations

  1. LIDYL, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France

    Lara Martinez-Fernandez & Roberto Improta

  2. Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134, Naples, Italy

    Lara Martinez-Fernandez, Luciana Esposito & Roberto Improta

  3. Área de Didáctica de las Ciencias Experimentales, University of Extremadura, Avda. de la Universidad, 10071, Cáceres, Spain

    Aurora Muñoz-Losa

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  1. Lara Martinez-Fernandez
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Published as part of the special collection of articles “Festschrift in honour of A. Rizzo”.

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Martinez-Fernandez, L., Muñoz-Losa, A., Esposito, L. et al. The optical properties of adenine cation in different oligonucleotides: a PCM/TD-DFT study. Theor Chem Acc 137, 39 (2018). https://doi.org/10.1007/s00214-018-2223-2

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