N3 Protonation Induces Base Rotation of 2′-Deoxyadenosine-5′-monophosphate and Adenosine-5′-monophosphate

• Published in: The journal of physical chemistry. B Vol. 120; no. 20; pp. 4616 - 4624
• Main Authors: Wu, R. R, He, C. C, Hamlow, L. A, Nei, Y.-w, Berden, G, Oomens, J, Rodgers, M. T
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 26.05.2016
• Subjects: Adenines; Adenosine Monophosphate - chemistry; Deoxyadenine Nucleotides - chemistry; Hydrogen Bonding; Infrared spectroscopy; Mathematical analysis; Nitrogen - chemistry; Nucleosides; Phosphates; Photons; Protonation; Protons; Spectra; Spectrophotometry, Infrared
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.6b04052

Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments combined with theoretical calculations are performed to investigate the stable gas-phase conformations of the protonated adenine mononucleotides, [pdAdo+H]+ and [pAdo+H]+. Conformations that are present in the experiments are elucidated via comparative analyses of the experimental IRMPD spectra and the B3LYP/6-311+G­(d,p) IR spectra predicted for the conformers optimized at this level of theory. N3 protonation is preferred as it induces base rotation, which allows a strong hydrogen bond to be formed between the excess proton of adenine and the phosphate moiety. In contrast, both N1 and N7 protonation are predicted to be >35 kJ/mol less favorable than N3 protonation. Only N3 protonated conformers are present in the experiments in measurable abundance. Both the low-energy conformers computed and the experimental IRMPD spectra of [pdAdo+H]+ and [pAdo+H]+ indicate that the 2′-hydroxyl moiety does not significantly impact the structure of the most stable conformer or the IRMPD spectral profile of [pAdo+H]+ vs that of [pdAdo+H]+. However, the 2′-hydroxyl leads to a 3-fold enhancement in the IRMPD yield of [pAdo+H]+ in the fingerprint region. Comparison of present results to those reported in a previous IRMPD study of the analogous protonated adenine nucleosides allows the effects of the phosphate moiety on the gas-phase conformations to be elucidated.