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 Title: GAS-PHASE CONFORMATIONS AND ENERGETICS OF PROTONATED 2_-DEOXYADENOSINE-5_-MONOPHOSPHATE AND ADENOSINE-5_-MONOPHOSPHATE: IRMPD ACTION SPECTROSCOPY AND THEORETICAL STUDIES Author(s): Wu, Ranran Contributor(s): Rodgers, M T; Oomens, J.; Berden, Giel; Hamlow, Lucas; He, Chenchen; Nei, Y-W Subject(s): Comparing theory and experiment Abstract: Nature uses protonation to alter the structures and reactivities of molecules to facilitate various biological functions and chemical transformations. For example, in nucleobase repair and salvage processes, protonation facilitates nucleobase removal by lowering the activation barrier for glycosidic bond cleavage. Systematic studies of the structures of protonated 2'-deoxyribonucleotides and ribonucleotides may provide insight into the roles protonation plays in altering the nucleobase orientation relative to the glycosidic bond and sugar puckering. In this study, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments in conjunction with electronic structure calculations are performed to probe the effects of protonation on the structures and stabilities of $2^prime$-deoxyadenosine-$5^prime$-monophosphate (pdAdo) and adenosine-$5^prime$-monophosphate (pAdo). Photodissociation as a function of IR wavelength is measured to generate the IRMPD action spectra. Geometry optimizations and frequency analyses performed at the B3LYP/6-311+G(d,p) level of theory are used to characterize the stable low-energy structures and to generate their linear IR spectra. Single point energy calculations performed at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels of theory provide relative stabilities of the optimized conformations. The structures accessed in the experiments are determined by comparing the calculated linear IR spectra for the stable low-energy conformers computed to the measured IRMPD action spectra. The effects of the $2^prime$-hydroxyl moiety are elucidated by comparing the structures and IRMPD spectra of [pAdo+H]$^{+}$ to those of its DNA analogue. Comparisons are also made to the deprotonated forms of these nucleotides and the protonated forms of the analogous nucleosides to elucidate the effects of protonation and the phosphate group on the structures. Issue Date: 26-Jun-15 Publisher: International Symposium on Molecular Spectroscopy Citation Info: ACS Genre: CONFERENCE PAPER/PRESENTATION Type: Text Language: English URI: http://hdl.handle.net/2142/79231 Date Available in IDEALS: 2016-01-05
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