Investigation of proton affinities and gas phase vibrational spectra of protonated nucleosides, deoxynucleosides, and their analogs

• Proton affinities (PAs) are measured for selected nucleosides.
• IRMPD spectra of selected previously published protonated monomers are reproduced. An alternative interpretation of protonated 2′-deoxycytidine is proposed based on partial deuteration.
• PBDs of gemcitabine and decitabine match DFT-predicted scaled harmonic IR spectra.

DNA nucleobases make use of hydrogen bonding, whether in associating to form the Watson–Crick double-helix or in producing alternative structures such as the G-quadruplex or the i-motif. Nucleoside proton-bound dimers provide an avenue for investigating characteristics that they possess within the i-motif and related non-Watson–Crick conformations. In addition, several nucleosides are approved antiviral and anticancer agents. The nucleosides under investigation (2′-deoxycytidine, gemcitabine, and decitabine) are capable of forming proton-bound dimers (PBDs) with their conjugate acids. Protonated monomers of 2′-deoxycytidine, gemcitabine, and decitabine and proton-bound dimers of gemcitabine and decitabine have been produced in the gas phase using electrospray ionization (ESI). This paper reports proton affinities of the neutral nucleosides as well as their infrared multiple photon dissociation (IRMPD) spectra from 2800 to 3800 cm−1 collected using an Optical Parametric Oscillator (OPO) laser. In the case of the conjugate acid of 2′-deoxycytidine, a partial deuteration experiment suppresses overtones and combination bands, leading to the inference that a single tautomer predominates in the protonated monomer. IRMPD spectra of proton-bound dimers of gemcitabine and decitabine suggest furanose sugar ring puckering to be in the South orientation, as they are in the protonated monomers.

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