This study provides the set of theoretical anharmonic fundamental transitions for cytosine in its anhydrous and hydrated forms from a vibrational analysis issuing from a time-dependent approach. This evaluation is compared to the time-independent VPT2 approach and to the experimental data available in the literature for the two forms. To investigate the vibrational property of a solute in a polar protic solvent, that is, the aqueous form of cytosine in this particular case, a practicable computational strategy to properly take into account the solvent effect is proposed. This is done by considering a combination of polarizable continuum model and of discrete solvent molecules model. The number of solvent molecules was chosen in such a way that the solute-solvent complex presents only one dominant stable conformer at 298 K. The quality of this combined solvent model is illustrated by comparing the structural and anharmonic vibrational properties achieved with those obtained from a purely implicit and purely explicit solvent model. Structural optimizations, harmonic frequencies, and anharmonic frequencies issuing from the VPT2 evaluation [33] were performed with the Gaussian09 program [34]. Electronic structure calculations were performed at the DFT level using CARBONNIERE ET AL.

This theoretical study provides the physically reasonable structures of the microhydrated thymine clusters, from the mono- to the penta-hydrated species, by the exploration of their B3LYP and B3LYP-D potential energy surfaces using a global search algorithm of minima (GSAM). The anharmonic vibrational computations of the isolated and aqueous thymine are also reported. They were performed from B3LYP and B3LYP-D potential electronic surfaces followed by a second order perturbative treatment of the anharmonicity. On that point, the computational strategy to properly take into account the effect of the polar protic solvent consists in considering a micro-hydrated thymine cluster [T,nH2O] surrounded by a polarizable continuum model (PCM). The number of solvent molecules was chosen in such a way that the micro-hydrated cluster presents only one dominant stable conformer at 298 K. All the VPT2 fundamental transitions obtained from the B3LYP and B3LYP-D quartic force fields are reported for the isolated form ([T,0H2O]) and for the aqueous form ([T,nH2O + PCM]). The theoretical results are compared to the available experimental data, which are for some of them reassigned, in order to assess the reliability of the B3LYP and B3LYP-D methods for the anharmonic treatment of such organic species in a polar protic solvent.

This study presents structural properties of microhydrated nucleic acid bases (NABs) - uracil (U), thymine (T), guanine (G), adenine (A), and cytosine (C) - investigated by theoretical computations at the B3LYP level of theory. To obtain the different representations of these microhydrated species, we applied the GSAM procedure: the most stable conformers labeled X,nH2O (X = U, T, G, A and n = 1...5) for which the Boltzmann population is higher than 2% at 298K are calculated at the B3LYP and B3LYP-D levels of theory. At the B3LYP level, our calculated geometries are compared with those obtained in the literature. New physically relevant isomers are found with the GSAM algorithm, especially for the tetra- and pentahydrated species. The use of DFT-D functional does not strongly modify the relative energies of the isomers for the monohydrated species. When the number of water molecules increases, the results become extremely sensitive to the consideration of dispersion contributions.