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Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra

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Abstract

Accurate ab initio modeling of spectroscopic signals in nonlinear electronic spectra, such as bidimensional (2D) spectra, requires the computation of the electronic transitions induced by the incoming pump/probe pulses, resulting in a challenging calculation of many electronic excited states. A protocol is thus required to evaluate the variations of spectral properties, like transition energies and dipole moments, with the computational level, and to estimate the sensitivity of the spectra to these variations. Such a protocol is presented here within the framework of complete and restricted active space self-consistent field (CASSCF/RASSCF) theory and its second-order perturbation theory extensions (CASPT2/RASPT2). The electronic excited-state manifolds of pyrimidine nucleobases (thymine, uracil, and cytosine) are carefully characterized in vacuo employing high-level RAS(0,0|10,8|2,12)//SS-RASPT2 calculations. The results provide a reference data set that can be used for optimizing computational efforts and costs, as required for studying computationally more demanding multichromophoric systems (e.g., di- and oligonucleotides). The spectroscopic signatures of the 2D electronic spectrum of a perfectly stacked uracil–cytosine dimer model are characterized, and experimental setups are proposed that can resolve non-covalent interchromophoric interactions in canonical pyrimidine nucleobase-stacked dimers.

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Acknowledgments

M.G. acknowledges support by the European Research Council Advanced Grant STRATUS (ERC-2011-AdG No. 291198). I. R. gratefully acknowledges the support of the École Normale Supérieure de Lyon (Fonds Recherche 900/S81/BS81-FR14). M.G. and I.R. acknowledge support of the Agence National de la Recherche (FEMTO-2DNA, ANR-15-CE29-0010). S. M. gratefully acknowledges the support of the National Science Foundation (grant CHE-1361516) and of the Chemical Sciences, Geosciences, and Biosciences division, Office of Basic Energy Sciences, Office of Science, US Department of Energy. A.G. and J.S.-M. acknowledge support of Project No. CTQ2014-58624-P of the Spanish MINECO (Ministerio de Economía y Competitividad) and Project. No. GV2015-057 of the Generalitat Valenciana.

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    1. Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via Selmi 2, 40126, Bologna, Italy

      Angelo Giussani, Javier Segarra-Martí, Artur Nenov, Alessandra Tolomelli & Marco Garavelli

    2. Univ Lyon, Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France

      Ivan Rivalta & Marco Garavelli

    3. Department of Chemistry, University of California, Irvine, CA, 92697-2025, USA

      Shaul Mukamel

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    Published as part of the special collection of articles “Health and Energy from the Sun”.

    Angelo Giussani and Javier Segarra-Martí have contributed equally to this work.

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    Giussani, A., Segarra-Martí, J., Nenov, A. et al. Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra. Theor Chem Acc 135, 121 (2016). https://doi.org/10.1007/s00214-016-1867-z

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