Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models

• DOI: 10.1021/acs.jctc.6b00518
• Publication Date: 2016-08-16T16:52:55Z
• Authors: L. Martínez-Ferná...; A. J. Pepino; J. Segarra-Martí; A. Banyasz; M. Garavelli; R. Improta
• Keywords: STRUCTURAL DYNAMICS; 0307 Theoretical And Computational Chemistry; Cytidine; Physics, Atomic, Molecular & Chemical; Molecular Dynamics Simulation; Atomic; Molecular & Chemical; GAS-PHASE; 01 natural sciences; AQUEOUS-SOLUTION; TRANSIENT ABSORPTION; Computational spectroscopy; Physical and Theoretical Chemistry; Physical; Physical and Theoretical Chemistry; computational spectroscopy; PI-ASTERISK; AB-INITIO; Science & Technology; Chemical Physics; solvent effect; Chemistry, Physical; Physics; NUCLEIC-ACID BASES; Water; DNA; 540; Computer Science Applications; EXCITED-STATE DYNAMICS; 0104 chemical sciences; CYTOSINE DERIVATIVES; Chemistry; [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry; Spectrophotometry; Physical Sciences; Quantum Theory; RESONANCE RAMAN-SPECTROSCOPY; European Research Council

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.