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Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

Abstract

A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows us to analyse ground state dynamics and to sample and measure different conformations attained by flexible molecular systems in solution. An explicit mixed quantum mechanics/molecular mechanics (QM/MM) approach is employed for the evaluation of the necessary electronic excited state energies and transition dipole moments. The method is applied towards the study of the highly flexible water-solvated adenine-adenine monophosphate (ApA), a system featuring two interacting adenine moieties that display variours intermolecular arrangements, known to deeply affect their photochemical outcome. Molecular dynamics simulations and cluster analysis have been used to select molecular conformations, reducing the complexity of the flexible ApA conformational space. By using our Sum-over-states (SOS) approach to obtain 2DES spectra for each of these selected conformations, we can discern spectral changes and relate them to specific nuclear arrangements: close lying π-stacked bases display a splitting of their respective 1La signal traces; T-stacked ones show the appearance of charge transfer states in the low-energy Vis probing window while displaying no 1La splitting, being particularly favoured when promoting amino to 5-ring interactions; unstacked and distant adenine moieites feature signals similar to those of adenine monomer, as expected for non-interacting nucleobases. 2DES maps thus reveal spectral fingerprints associated with specific molecular conformations, a promising option to enable their quantitative spectroscopic detection beyond standard 1D pump-probe techniques. This is expected to aid the understanding of how nucleobase aggregation controls and modulates the photostability and photo-damage of extended DNA/RNA systems.

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Publication details

The article was accepted on 17 Oct 2017 and first published on 24 Oct 2017


Article type: Paper
DOI: 10.1039/C7FD00201G
Citation: Faraday Discuss., 2017, Accepted Manuscript
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    Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

    J. Segarra-Martí, V. K. Jaiswal, A. J. Pepino, A. Giussani, A. Nenov, S. Mukamel, M. Garavelli and I. Rivalta, Faraday Discuss., 2017, Accepted Manuscript , DOI: 10.1039/C7FD00201G

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