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

J Chem Theory Comput. 2016 Sep 13;12(9):4430-9. doi: 10.1021/acs.jctc.6b00518. Epub 2016 Aug 30.

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.

MeSH terms

  • Cytidine / analogs & derivatives*
  • Cytidine / chemistry
  • Molecular Dynamics Simulation
  • Quantum Theory
  • Spectrophotometry
  • Water / chemistry*

Substances

  • Water
  • Cytidine
  • 5-methylcytidine