title: N3 Protonation Induces Base Rotation of 2'-Deoxyadenosine-5'-monophosphate and Adenosine-5'-monophosphate.
abstract: 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.
authors.affiliation: Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.
authors.forename: R R
authors.initials: RR
authors.lastname: Wu
authors.affiliation: Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.
authors.forename: C C
authors.initials: CC
authors.lastname: He
authors.affiliation: Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.
authors.forename: L A
authors.initials: LA
authors.lastname: Hamlow
authors.affiliation: Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.
authors.forename: Y-W
authors.initials: YW
authors.lastname: Nei
authors.affiliation: FELIX Laboratory, Institute for Molecules and Materials, Radboud University , Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
authors.forename: G
authors.initials: G
authors.lastname: Berden
authors.affiliation: FELIX Laboratory, Institute for Molecules and Materials, Radboud University , Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.|van't Hoff Institute for Molecular Sciences, University of Amsterdam , 1090 GD Amsterdam, The Netherlands.
authors.forename: J
authors.initials: J
authors.lastname: Oomens
authors.affiliation: Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.
authors.forename: M T
authors.initials: MT
authors.lastname: Rodgers
mesh_terms: D000249:Adenosine Monophosphate / Q000737:chemistry*; D003838:Deoxyadenine Nucleotides / Q000737:chemistry*; D006860:Hydrogen Bonding; D009584:Nitrogen / Q000737:chemistry; D011522:Protons; D013055:Spectrophotometry, Infrared
chemical_list: D003838:Deoxyadenine Nucleotides; D011522:Protons; D000249:Adenosine Monophosphate; C012873:2'-deoxy-5'-adenosine monophosphate; D009584:Nitrogen