The studyof the interaction of DNA bases with metal cations and/or proton has arousedthe interest of the scientific community, in order to understand the intrinsicproperties that result from the formation and stabilization of noncanonicalbase pairs. The formation of these noncanonical base pairs can lead toimportant changes affecting the structure of DNA and also can present potentialapplications in materials science [1].

In thiswork we present the results of experimental and theoretical studies of thestructure of the pairs which occur between cytosine (C) and guanine (G) mediatedby a proton (C-H⁺-G) and the Ag⁺cation (C-Ag⁺-G).

Theionic complexes(C-H⁺-G) and (C-Ag⁺-G) were generated in aelectrosprayionization (ESI) source of a high resolution tandem mass spectrometer, FT-ICR. Theions were isolated and the vibrational spectrum was obtained by Infrared MultiphotonDissociation (IRMPD) spectroscopy with the Free Electron Laser at theUniversity of Paris Sud (CLIO) in Orsay ? France and an OPO source couple to aCO₂ laser.

The optimized geometry of the various isomers, their relative energies, theirvibrational fequencies and the anharmonic corrections were performed at the DFTlevel with the B3LYP and M06-2X functionals, with the basis set 6-311G++ (d, p)for the C, H, N, and O and the effective core potential SDD [2] for Ag atomimplemented in the package software Gaussian 09 [3].

Thecalculations showed that in both pairs the most stable isomer is a Hoogsteentype. In addition, the IR spectra calculated for theseisomers satisfactory fit the experimental spectra.

Inthe case of the pair C-Ag⁺-G, the cation Ag⁺ is found equidistantfrom both bases, forming a structure fairly rigid and the calculated vibrationalfrequencies fit very well the experimental values, when the scaling factors suggestedin bibliography for each functional are applied.

Inthe case of the pair C-H⁺-G, the local minimum indicates that H⁺is preferably bonded to the cytosine (C). However, this H⁺ is mobileand at room temperature is delocalized between the two bases, because theenergy barrier for this process is found below the energy of the system. Thisgenerates a big change in the vibrational frequencies of those modes that arecoupled to the movement of this H⁺. It was found that thesefrequencies are better fitted when no scaling factors are applied to thecalculated ones with both functionals.On the contrary, the frequencies of thosemodes that are not coupled to the movement of the H⁺ are fitted byscaled calculated frequencies.