Structure of protonated thymidine characterized by infrared multiple photon dissociation and quantum calculations

Abstract

Tautomerization can be characterized by IRMPD spectroscopy. Interestingly, the dominant enolic tautomeric form(s) presently observed cannot be directly generated from the most stable neutral tautomer of the thymine residue.

Protonation of methyluracils in the gas phase: The particular case of 3-methyluracil

“…The computed spectrum for the global minimum 1MeU2_ha cannot account, however, for the small signal observed experimentally at 1785 cm -1 . This signal (position, intensity) has already been observed for protonated uracil and thymine, [11,12] as well as for protonated uridine [21] and thymidine, [23] and results from a resonant absorption through an active C=O stretch. This IR mode is characteristic of the presence of an oxo protonated form, as attested by the agreement observed with the computed C=O stretch of oxo forms such as 1MeU1_hd (Figure 3c) and 1MeU1_hc (Figure 3d).…”

“…The second one is the development of structure-sensitive activation techniques, which enables one to obtain direct structural information on gaseous ions. Among those, Infrared Multiple Photon Dissociation spectroscopy (IRMPD) of mass-selected ions, is now established as a very powerful approach to probe the structure of gaseous ions of moderate size, [7][8][9][10], and different groups have used IRMPD spectroscopy to study the structure and tautomerization of protonated DNA and RNA building blocks generated by electrospray [11][12][13][14][15][16][17][18][19][20][21][22][23][24]. In our continuing effort to study the structure and unimolecular reactivity of gaseous nucleobases, either protonated [11][12][13]25,26] or complexed to metals [27][28][29][30][31][32], the present paper reports the IRMPD study in the fingerprint region between 1000 and 2000 cm -1 of three protonated methyluracils, namely 1-Me, 3-Me and 6-Me-uracil (Scheme 1), generated by electrospray ionization and trapped in a quadrupole ion trap.…”

2,4-Dihydroxy and O2 Protonated Tautomers of dThd and Thd Coexist in the Gas Phase: Methylation Alters Protonation Preferences versus dUrd and Urd

“…Therefore, comparisons between this work and the previous IRMPD study of [ [22] provide insight into the effects of methylation on the preferred tautomeric conformations of these nucleosides. Most recently, and virtually simultaneous with this work, Salpin et al [23] have characterized the gas-phase conformations of [dThd + H] + by IRMPD spectroscopy in the IR fingerprint region using CLIO free electron laser. Comparison of the present results to those just reported by Salpin et al show that the general conclusions remain valid.…”

Deep Ultraviolet Single‐Photon Ionization Mass Spectrometry

“…Simply by measuring the ions abundance relating to their mass-to-charge ratios, mass spectrometry is known as the most powerful tool for identifying the quantity and type of chemicals present in a sample. According to the ionization strategies, mass spectrometry can be classified into hard ionization techniques (typically by direct electron impact, i.e., EI method) [1] and soft ionization techniques which usually include photoionization (PI) [2][3][4][5][6][7][8], chemical ionization (CI) [9,10], matrix-assisted laser desorption/ionization (MALDI) [11], and electrospray ionization (ESI) [12]. Comparing with the EI technique which readily brings rigorous fragmentation for organic compounds, soft ionization techniques find their own advantages of maximal ionization efficiency without using high-energy electron impact.…”