title: Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.
abstract: The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.
authors.affiliation: Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Martínez-Fernández
authors.affiliation: Dipartimento di Chimica "G. Ciamician", Università di Bologna , Bologna, Italy.
authors.forename: A J
authors.initials: AJ
authors.lastname: Pepino
authors.affiliation: Dipartimento di Chimica "G. Ciamician", Università di Bologna , Bologna, Italy.|École Normale Supérieure de Lyon, CNRS, UMR 5182, Université de Lyon , 46 Allée d'Italie, F-69364 Lyon Cedex 07, France.
authors.forename: J
authors.initials: J
authors.lastname: Segarra-Martí
authors.affiliation: LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France.
authors.forename: A
authors.initials: A
authors.lastname: Banyasz
authors.affiliation: Dipartimento di Chimica "G. Ciamician", Università di Bologna , Bologna, Italy.|École Normale Supérieure de Lyon, CNRS, UMR 5182, Université de Lyon , 46 Allée d'Italie, F-69364 Lyon Cedex 07, France.
authors.forename: M
authors.initials: M
authors.lastname: Garavelli
authors.affiliation: Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
authors.forename: R
authors.initials: R
authors.lastname: Improta
mesh_terms: D003562:Cytidine / Q000031:analogs & derivatives* / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D013053:Spectrophotometry; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D003562:Cytidine; C016568:5-methylcytidine