Infrared multiple photon dissociation action spectroscopy of sodiated uracil and thiouracils: Effects of thioketo-substitution on gas-phase conformation
“…These data also show that other higher energy structures are not present in the experiments, based on the comparison of their calculated spectra with the experimental spectrum [26]. Thus, it would be expected that in our experiments, the conformer 4 alone or both 4 + 4a are the precursors for [4SU]Na + (H 2 O) n = 1,2 .…”
Section: Resultssupporting
confidence: 69%
“…The first-excited conformer, 4a , is 3.9 kJ/mol higher in free energy and the hydrogen atom is oriented toward the N3 atom. The results obtained [26] indicate that these structures are spectroscopically indistinguishable because their calculated IR spectra are virtually the same.Scheme 5The ground-state ( 4 ) and the first-excited state ( 4a ) conformers of sodiated 4-thiouracil…”
Section: Resultsmentioning
confidence: 99%
“…These observations may be understood as the result of conformational differences in the protonated forms of the nucleobases as the precursors for the hydrated systems. As mentioned in the Introduction section, the experimental IRMPD and computational studies by Rodgers et al [25, 26] have provided very useful information about the structures of protonated and sodium-cationized uracil and thiouracils formed by ESI. Their results show that for [2SU]H + and [6Me2SU]H + , as in the case of [U]H + , the ground-state enolic form, 1 , is the dominant conformer.Figure 2van’t Hoff plots of equilibrium constants for the gas-phase reactions [SU]H + ·(H 2 O) n -1 + H 2 O <=> [SU]H + ·(H 2 O) n
…”
Section: Resultsmentioning
confidence: 99%
“…The experimentally derived MIA values are also similar within 7 kJ/mol.Figure 6Plot of the binding free energy, – ΔG
o , at 298 K for the first (●) and second (○) water molecule versus corresponding sodium ion affinity of uracil and thiouracils. For U, 2-SU, and 6Me2SU, the calculated sodium ion affinity values are taken from Reference [18]; for 4SU from Reference [26]; see Table 2
…”
Hydration reactions of protonated and sodiated thiouracils (2-thiouracil, 6-methyl-2-thiouracil, and 4-thiouracil) generated by electrospray ionization have been studied in a gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔHon, ΔSon, and ΔGon, for the hydrated systems were obtained by equilibrium measurements. The water binding energies of protonated thiouracils, [2SU]H+ and [6Me2SU]H+, were found to be of the order of 51 kJ/mol for the first, and 46 kJ/mol for the second water molecule. For [4SU]H+, these values are 3–4 kJ/mol lower. For sodiated complexes, these energies are similar for all studied systems, and varied between 62 and 68 kJ/mol for the first and between 48 and 51 kJ/mol for the second water molecule. The structural aspects of the precursors for hydrated complexes are discussed in conjunction with available literature data.Graphical Abstractᅟ
“…These data also show that other higher energy structures are not present in the experiments, based on the comparison of their calculated spectra with the experimental spectrum [26]. Thus, it would be expected that in our experiments, the conformer 4 alone or both 4 + 4a are the precursors for [4SU]Na + (H 2 O) n = 1,2 .…”
Section: Resultssupporting
confidence: 69%
“…The first-excited conformer, 4a , is 3.9 kJ/mol higher in free energy and the hydrogen atom is oriented toward the N3 atom. The results obtained [26] indicate that these structures are spectroscopically indistinguishable because their calculated IR spectra are virtually the same.Scheme 5The ground-state ( 4 ) and the first-excited state ( 4a ) conformers of sodiated 4-thiouracil…”
Section: Resultsmentioning
confidence: 99%
“…These observations may be understood as the result of conformational differences in the protonated forms of the nucleobases as the precursors for the hydrated systems. As mentioned in the Introduction section, the experimental IRMPD and computational studies by Rodgers et al [25, 26] have provided very useful information about the structures of protonated and sodium-cationized uracil and thiouracils formed by ESI. Their results show that for [2SU]H + and [6Me2SU]H + , as in the case of [U]H + , the ground-state enolic form, 1 , is the dominant conformer.Figure 2van’t Hoff plots of equilibrium constants for the gas-phase reactions [SU]H + ·(H 2 O) n -1 + H 2 O <=> [SU]H + ·(H 2 O) n
…”
Section: Resultsmentioning
confidence: 99%
“…The experimentally derived MIA values are also similar within 7 kJ/mol.Figure 6Plot of the binding free energy, – ΔG
o , at 298 K for the first (●) and second (○) water molecule versus corresponding sodium ion affinity of uracil and thiouracils. For U, 2-SU, and 6Me2SU, the calculated sodium ion affinity values are taken from Reference [18]; for 4SU from Reference [26]; see Table 2
…”
Hydration reactions of protonated and sodiated thiouracils (2-thiouracil, 6-methyl-2-thiouracil, and 4-thiouracil) generated by electrospray ionization have been studied in a gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔHon, ΔSon, and ΔGon, for the hydrated systems were obtained by equilibrium measurements. The water binding energies of protonated thiouracils, [2SU]H+ and [6Me2SU]H+, were found to be of the order of 51 kJ/mol for the first, and 46 kJ/mol for the second water molecule. For [4SU]H+, these values are 3–4 kJ/mol lower. For sodiated complexes, these energies are similar for all studied systems, and varied between 62 and 68 kJ/mol for the first and between 48 and 51 kJ/mol for the second water molecule. The structural aspects of the precursors for hydrated complexes are discussed in conjunction with available literature data.Graphical Abstractᅟ
“…An additional very weak IRMPD signal observed at about 1800 cm -1 suggests the presence of the second lowest energy oxo tautomer. Oomens et al studied protonated cytosine dimers, concluding that the proton moves from one basic atom to another when the dimer ion dissociates (50) (54,55). On the other hand, Crampton et al found that protonation preferentially stabilizes minor tautomers of halouracils (56).…”
Section: Ionic Nucleobases and Nucleotidesmentioning
Abstract.IR spectroscopy of nucleobases in the gas phase reflects simultaneous advances in both experimental and computational technique. Important properties, such as excited state dynamics, depend in subtle ways on structure variations, which can be followed by their infrared signatures. Isomer specific spectroscopy is a particularly powerful tool for studying the effects of nucleobase tautomeric form and base pair hydrogen bonding patterns.
The chemistry of singlet O2 toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels-Alder cycloaddition of singlet O2 to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at -100 °C. Herein, gas-phase ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O2 at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O2 induced guanine oxidation, which is missing from conventional condensed-phase studies.
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