Journal
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
Volume 28, Issue 8, Pages 1638-1646Publisher
SPRINGER
DOI: 10.1007/s13361-017-1653-8
Keywords
Cytosine mononucleotides; Electronic structure theory; Infrared multiple photon dissociation action spectroscopy; Phosphate moiety; Protonation
Funding
- National Science Foundation [OISE-0730072, OISE-1357887, CHE-1409420]
- Wayne State University
- WSU Cte University
- Nederlandse Organisatie voor Wetenschappeklijk Onderzoek (NWO)
- Division Of Chemistry
- Direct For Mathematical & Physical Scien [1409420] Funding Source: National Science Foundation
- Office Of The Director
- Office Of Internatl Science &Engineering [1357887] Funding Source: National Science Foundation
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The gas-phase conformations of the protonated forms of the DNA and RNA cytosine mononucleotides, [pdCyd+H](+) and [pCyd+H](+), are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy over the IR fingerprint and hydrogen-stretching regions complemented by electronic structure calculations. The low-energy conformations of [pdCyd+H](+) and [pCyd+H](+) and their relative stabilities are computed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers allow the conformers present in the experiments to be determined. Similar to that found in previous IRMPD action spectroscopy studies of the protonated forms of the cytosine nucleosides, [dCyd+H](+) and [Cyd+H](+), both N3 and O2 protonated cytosine mononucleotides exhibiting an anti orientation of cytosine are found to coexist in the experimental population. The 2'-hydroxyl substituent does not significantly influence the most stable conformations of [pCyd+H](+) versus those of [pdCyd+H](+), as the IRMPD spectral profiles of [pdCyd+H](+) and [pCyd+H](+) are similar. However, the presence of the 2'-hydroxyl substituent does influence the relative intensities of the measured IRMPD bands. Comparisons to IRMPD spectroscopy studies of the deprotonated forms of the cytosine mononucleotides, [pdCyd-H](-) and [pCyd-H](-), provide insight into the effects of protonation versus deprotonation on the conformational features of the nucleobase and sugar moieties. Likewise, comparisons to results of IRMPD spectroscopy studies of the protonated cytosine nucleosides provide insight into the influence of the phosphate moiety on structure. Comparison with previous ion mobility results shows the superiority of IRMPD spectroscopy for distinguishing various protonation sites.
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