On the Ag⁺–cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory

Abstract

The gas-phase structures of cytosine-Ag(+) [CAg](+) and cytosine-Ag(+)-H2O [CAg-H2O](+) complexes have been studied by mass-selected infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1800 cm(-1) spectral region using the Free Electron Laser facility in Orsay (CLIO). The IRMPD experimental spectra have been compared with the calculated IR absorption spectra of the different low-lying isomers (computed at the DFT level using the B3LYP functional and the 6-311G++(d,p) basis set for C, H, N and O atoms and the Stuttgart effective core potential for Ag). For the [CAg](+) complex, only one isomer with cytosine in the keto-amino (KA) tautomeric form and Ag(+) interacting simultaneously with the C(2)[double bond, length as m-dash]O(7) group and N(3) of cytosine was observed. However, the mono-hydration of the complex in the gas phase leads to the stabilization of a two quasi-isoenergetic structure of the [CAg-H2O](+) complex, in which Ag(+) interacts with the O atom of the water molecule and with the N(3) or C(2)[double bond, length as m-dash]O(7) group of cytosine. The relative populations of the two isomers determined from the IRMPD kinetics plot are in good agreement with the calculated values. Comparison of these results with those of protonated cytosine [CH](+) and its mono-hydrated complex [CH-H2O](+) shows some interesting differences between H(+) and Ag(+). In particular, while a single water molecule catalyzes the isomerization reaction in the case of [CH-H2O](+), it is found that in the case of [CAg-H2O](+) the addition of water leads to the stabilization of two isomers separated by small energy barrier (0.05 eV).

Communication: UV photoionization of cytosine catalyzed by Ag+

“…43 The most unexpected result here is the fact that the dissociation of CytAg + yields Cyt + and Ag as the main products, which is completely different from the results observed in the ground state fragmentation of the CytAg + complex, achieved by IR-MPD leading to the loss of the HNCO neutral fragments as the main fragmentation channel. 44 This result strongly suggests that the excited state is a Charge Transfer (CT) state that involves the promotion of an electron from Cyt to Ag + and subsequent fragmentation.…”

“…The population of other tautomers was suggested to be negligible. 44 The calculated vertical transition energies at the TD-DFT/B3LYP and ADC(2) levels and adiabatic transition energies in Cs symmetry at the RI-ADC(2) levels of theory are shown in Table I. Among the ten A ′ and A ′′ excited states optimized, only three low lying A ′ states have enough oscillator strength to be potentially excited and detected (see Table I).…”

“…The ground state structure of the complex has been determined previously by combining IR-MPD spectroscopy and DFT/B3LYP calculations. 44 It was shown that the complex is planar (Cs symmetry group) with the cytosine molecule in the keto-amino tautomeric form, in which Ag + interacts simultaneously with N(3) and C(2)= =O (see Table I for atom labels), and the calculated binding energy (E b (S 0 )) at this theory level is 2.86 eV. In this ground state structure, the positive charge is mainly localized on the Ag + cation.…”

Improved Infrared Spectra Prediction by DFT from a New Experimental Database

“…The bandwidth of the IR laser is of the order of 0.5 % of the central wavelength . The wavelength stepping used for acquisition is between 3 and 5 cm −1 .…”

On the nature of ion‐stabilized cytosine pairs in DNA i‐motifs: The importance of charge transfer processes

“…[20][21][22][23][24][25] Although a few computational studies already investigated ion-mediated nucleobase pairing effects via electronic structure calculations, the underlying stabilization or destabilization mechanisms are not yet fully understood. [18,[26][27][28][29][30] Specifically the influence of water and π − π interactions between stacked nucleobases, which were often ignored in previous works, are known to change the stability of DNA conformations significantly. [31][32][33][34][35] With regard to a more careful analysis of these contributions, [31][32][33][34][35] the question arises which factors determine the stability of ion-mediated cytosine pairs?…”