Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy of H+ and Ag+ mediated Cytosine-Guanine base pair: Structure and reactivity

A. F. CRUZ ORTIZ; M. BERDAKIN; G.A. PINO

Mendoza

Congreso; 9th INTERNATIONAL MEETING ON PHOTODYNAMICS AND RELATED ASPECTS; 2016

The study of the interaction of DNA bases with metal cations and/or proton has aroused the interest of the scientific community, in order to understand the intrinsic properties that result from the formation and stabilization of noncanonical base pairs. The formation of these noncanonical base pairs can lead to important changes affecting thestructure of DNA and also can present potential applications in materials science [1].In this work we present the results of experimental and theoretical studies of the structure of the pairs which occur between cytosine (C) and guanine (G) mediated by a proton (C-H + -G) and the Ag + cation (C-Ag + -G). The ionic complexes (C-H + -G) and (C-Ag + -G) were generated in a electrospray ionization (ESI) source of a high resolution tandem mass spectrometer, FT-ICR. The ions were isolated and the vibrational spectrum was obtained by Infrared Multiphoton Dissociation (IRMPD) spectroscopy with the Free Electron Laser at the University of Paris Sud (CLIO) in Orsay ? France and an OPO source couple to a CO 2 laser.The optimized geometry of the various isomers, their relative energies, their vibrational fequencies and the anharmonic corrections were performed at the DFT level 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 atom implemented in the packagesoftware Gaussian 09 [3].The calculations showed that in both pairs the most stable isomer is a Hoogsteen type. In addition, the IR spectra calculated for these isomers satisfactory fit the experimental spectra. In the case of the pair C-Ag + -G, the cation Ag + is found equidistant from both bases, forming a structure fairly rigid and the calculated vibrational frequencies fit very well the experimental values, when the scaling factors suggested in bibliography for each functional are applied. In the case of the pair C-H + -G, the local minimum indicates that H + is preferablybonded to the cytosine (C). However, this H + is mobile and at room temperature is delocalized between the two bases, because the energy barrier for this process is found below the energy of the system. This generates a big change in the vibrational frequencies of those modes that are coupled to the movement of this H + . It was found that thesefrequencies are better fitted when no scaling factors are applied to the calculated ones with both functionals. On the contrary, the frequencies of those modes that are not coupled to the movement of the H + are fitted by scaled calculated frequencies.[1]. N. C. Seeman, Nature 2003, 421, 427.[2]. Andrea, D.; Haussermann, U.; Dolg, M.; Stoll, M.; Preuss, H.Energy-Adjustedab Initio Pseudopotentials for the Second and Third Row Transition Elements.Theor. Chim. Acta. 1990, 77, 123−141.[3]. Gaussian, Inc.: Wallingford, CT, 2009.