IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Studies of Sodium Cationized Thymidine and 5-Methyluridine: Kinetic Trapping During the ESI Desolvation Process Preserves the Solution Structure of [Thd+Na]⁺

Abstract

Thymidine (dThd) is a fundamental building block of DNA nucleic acids, whereas 5-methyluridine (Thd) is a common modified nucleoside found in tRNA. In order to determine the conformations of the sodium cationized thymine nucleosides [dThd+Na] and [Thd+Na] produced by electrospray ionization, their infrared multiple photon dissociation (IRMPD) action spectra are measured. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations and frequency analyses are performed at the B3LYP/6-311+G(d,p) level of theory, whereas energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory. As protonation preferentially stabilizes minor tautomers of dThd and Thd, tautomerization facilitated by Na binding is also considered. Comparisons of the measured IRMPD and computed IR spectra find that [dThd+Na] prefers tridentate (O2,O4',O5') coordination to the canonical 2,4-diketo form of dThd with thymine in a syn orientation. In contrast, [Thd+Na] prefers bidentate (O2,O2') coordination to the canonical 2,4-diketo tautomer of Thd with thymine in an anti orientation. Although 2,4-dihydroxy tautomers and O2 protonated thymine nucleosides coexist in the gas phase, no evidence for minor tautomers is observed for the sodium cationized species. Consistent with experimental observations, the computational results confirm that the sodium cationized thymine nucleosides exhibit a strong preference for the canonical form of the thymine nucleobase. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized dThd and Thd follow the order [dThd+H] < [Thd+H] < [dThd+Na] < [Thd+Na]. Graphical Abstract ᅟ.

Vibrational signatures of curcumin’s chelation in copper(II) complexes: An appraisal by IRMPD spectroscopy

“…83,84 Indeed, several cases where the relative amount of isomers extracted from solution by ESI does not adhere to the corresponding gas phase stabilities have been already discussed. 36,80,[85][86][87][88] The thermally averaged spectra weighted according to the relative ∆G values of each species presented in Fig. S18 support a joint presence of HK_1 and HE_1.…”

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

“…ER-CID experiments of the HPLC fractions containing the AlaPt-Ado and OrnPt-Ado adducts were performed on a quadrupole ion trap mass spectrometer (QIT MS, amaZon ETD, Bruker Daltonics, Billerica, MA, USA). The method has been described in detail in previous work [42, 50, 51]. Briefly, HPLC fractions were vacuum dried and then redissolved in an MeOH:ddH 2 O (50:50 v/v) mixture.…”

“…(1) [57]in which and are the ion intensities of the fragment and precursor ions, respectively; x represents fragments in which the glycosidic bond remains intact. Data analyses were performed using SigmaPlot 10.0 (Systat Software, Inc., San Jose, CA, USA) and custom software developed in the Rodgers laboratory and reported previously [42, 48–51]. The GBC survival yield was plotted as a function of the rf excitation amplitude.…”

“…Stability of the glycosidic bond may also be influenced differentially by platination at varying sites on the nucleobase. In this study, we investigated the impact of AlaPt and OrnPt adducts on relative glycosidic bond strengths by employing energy-resolved collision-induced dissociation (ER-CID) tandem mass spectrometry and survival yield analysis [42, 48–51]. In a previous theoretical study, evaluation of the effects of cisPt modification indicated that platination at N7 does not destabilize the dGuo glycosidic bond [52].…”

On the Interaction between Deprotonated Cytosine [C(−H)]− and Ba2+: Infrared Multiphoton Spectroscopy and Dynamics

“…Since experimentally, only the [C (À H) KAN1OÀ Ba] + and [C (À H) KAN3OÀ Ba] + isomers are observed, it allows suggesting that the isomers population observed in the gas phase most likely resembles the isomers population in the solution, indicating that these structures are maintained upon vaporization of the solution in the soft ESI source, as previously observed in other works for [CGH] + [12] and [ThdÀ Na] + . [50] The solvent reduces the overall energy difference between the most and the less stable isomers substantially changing their relative stability. The most stabilized isomers by the solvent are those with the highest dipole moment ( [32] reported for the [C (À H) Pb] + complex to be present in the [C (À H) KAN1OÀ Ba] + and C ðÀ HÞ KI N1 anti N3N8 À Ba � � + isomeric forms.…”