Interaction of Cu+ with cytosine and formation of i-motif-like C-M+-C complexes: alkali versus coinage metals

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Diverse mixtures of 2,4-dihydroxy tautomers and O4 protonated conformers of uridine and 2 '-deoxyuridine coexist in the gas phaset

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Infrared Multiple Photon Dissociation Action Spectroscopy and Theoretical Studies of Triethyl Phosphate Complexes: Effects of Protonation and Sodium Cationization on Structure

The gas-phase structures of protonated and sodium cationized complexes of triethyl phosphate, [TEP + H](+) and [TEP + Na](+), are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated by a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer with an electrospray ionization source, and theoretical electronic structure calculations. Measured IRMPD action spectra are compared to linear IR spectra calculated at the B3LYP/6-31 G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison, theoretical studies of neutral TEP are also performed. Sodium cationization and protonation produce changes in the central phosphate geometry, including an increase in the alkoxy a OPO bond angle and shortening of the alkoxy P-O bond. Changes associated with protonation are more pronounced than those produced by sodium cationization

Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated RNA Mononucleotides: Gas-Phase Conformations and Energetics

The IRMPD action spectra of the deprotonated forms of the four common RNA mononucleotides, adenosine-5'-monophosphate (A5'p), guanosine-5'-monophosphate (G5'p), cytidine-5'-monophosphate (C5'p), and uridine-5'-monophosphate (U5'p), are measured to probe their gas-phase structures. The IRMPD action spectra of all four deprotonated RNA mononucleotides exhibit distinct IR signatures in the frequency region investigated, 570-1900 cm(-1), that allows these deprotonated mononucleotides to be easily differentiated from one other. Comparison of the measured IRMPD action spectra to the linear IR spectra calculated at the B3LYP/6-31+G(d,p) level of theory finds that the most stable conformations of the deprotonated forms of AS'p, C5'p, and U5'p are accessed in the experiments, and these conformers adopt the C3' endo conformation of the ribose moiety and the anti conformation of the nucleobase. In the case of deprotonated G5'p, the most stable conformer is also accessed in the experiments. However, the ground-state conformer differs from the other three deprotonated RNA mononucleotides in that it adopts the syn rather than anti conformation for the nucleobase. Present results are compared to results previously obtained for the deprotonated forms of the four common DNA mononucleotides to examine the fundamental conformational differences between these species, and thus elucidate the effects of the 2'-hydroxyl group on their structure, stability, and fragmentation behavior

Infrared Multiple Photon Dissociation Action Spectroscopy of Deprotonated DNA Mononucleotides: Gas-Phase Conformations and Energetics

The gas phase structures of the deprotonated 2'-deoxymononucleotides including 2'-deoxyadenosine-5'-monophosphate (dA5'p), 2'-deoxycytidine-5'-monophosphate (dC5'p), 2'-deoxyguanosine-5'-monophosphate (dG5'p), and thymidine-5'-monophosphate (T5'p) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. The measured IRMPD action spectra of all four deprotonated DNA mononucleotides exhibit unique spectral features in the region extending from similar to 600 to 1800 cm(-1) such that they can be readily differentiated from one another. The measured IRMPD action spectra are compared to the linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformations of these species accessed in the experiments. On the basis of these comparisons and the computed energetic information, the most stable conformations of the deprotonated forms of dA5'p, dC5'p, and T5'p are conformers where the ribose moiety adopts a C3' Endo conformation and the nucleobase is in an anti conformation. By contrast, the most stable conformations of the deprotonated form of dG5'p are conformers where the ribose adapts a C3' endo conformation and the nucleobase is in a syn conformation. In addition to the ground-state conformers, several stable low-energy excited conformers that differ slightly in the orientation of the phosphate ester moiety were also accessed in the experiments

Gas-Phase Conformations and Energetics of Protonated 2′-Deoxyadenosine and Adenosine: IRMPD Action Spectroscopy and Theoretical Studies

The gas-phase conformations of protonated 2'-deoxyadenosine, [dAdo +H](+), and its RNA analogue protonated adenosine, [Ado+H](+), generated upon electrospray ionization are examined uSing infrared multiple photon dissociation (IRMPD) action spectroscopy techniques- and supported by complementary theoretical electronic structure calculations. IRMPD action spectra are measured over the IR fingerprint region- using the FELIX free-electron laser and the hydrogen-Stretching region using an optical parametric oscillator/amplifier laser system. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy -conformations of [dAdo+H](+) and [Ado+H](+) computed at the B3LYP/6-311+G(d,p) level of theory to determine the preferred site of protonation and to identify the structures populated in the experiments. N-3 is found to be the most favorable site of protonation for bOth [dAdo+H] and [Ado+H](+), whereas conformers protonated at the N1 and N7 positions are much less stable by >25 k, J/mol. The 2'-hydroxyl substittent of Ado does not lead to a significant change in the Structure of the ground-state Conformer of [Ado+H](+) as compared to that of [dAdo+H](+), Wept that it provides additional stabilization via the formation of an O2'H center dot center dot center dot-O3' hydrogen bond. Therefore, [dAdo+H](+) and [Ado+H](+) exhibit highly parallel IRMPD spectral features in both the fingerprint, and hydrogen-stretching regions. However, the additional 2'-hydroxyl substituent markedly affects the IRMPD yield of the measured IR bands. The spectral signatures in the hydrogen-stretching region provide complementary information to that of the fingerprint region and enable facile differentiation of the conformers that arise from different protonation sites. In spite of the relative gas-phase stabilities of the N3 and N1 protonated conformers, present results suggest, that both are accessed in the experiments and contribute to the measured IRMPD spectrum, indicating that the relative stabilities in solution also influence the populations generated by electrospray ionization

Infrared multiple photon dissociation action spectroscopy of protonated uracil and thiouracils: Effects of thioketo-substitution on gas-phase conformation

The gas-phase structures of protonated complexes of uracil and five thiouracils including 2-thiouracil (2SU), 5-methyl-2-thiouracil (5Me2SU), 6-methyl-2-thiouracil (6Me2SU), 4-thiouracil (4SU), and 2,4-dithiouracil (24dSU) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. IRMPD action spectra of all six protonated complexes exhibit both similar and distinct spectral features over the range of similar to 1000-1900 cm(-1), such that the complexes are easily differentiated by their IRMPD action spectra. Absence of the carbonyl stretch at similar to 1825 cm(-1) in the IRMPD spectra for the H+(U), H+(2SU), H+(5Me2SU), and H+(6Me2SU) complexes suggests that the binding of a proton preferentially stabilizes alternative tautomers of the nucleobases in these complexes such that no free carbonyl stretch is observed. In contrast, the intense band at similar to 1825 cm(-1) in the IRMPD action spectrum of H+ (4SU) indicates that a free carbonyl group is still present in this complex. Measured IRMPD action spectra are compared to linear IR spectra calculated at the B3LYP/6-31G(d) level of theory to identify the structures accessed in the experimental studies. On the basis of these comparisons and energetics derived from the calculations, protonation results in preferential stabilization of a minor tautomer of the nucleobase in the H+(U), H+(2SU), H+(5Me2SU),H+(6Me2SU), and H+(24dSU) complexes, where both keto (thioketo) groups are converted to hydroxy (sulfhydryl) groups by proton binding and proton transfer from the neighboring N3H group. In contrast, the proton preferentially binds at the 4-thioketo position to the canonical keto-thioketo tautomer in the H+(4SU) complex. Additional band(s) are present in the IRMPD action spectra of the H+(U) and H(4SU) complexes that suggest that a small population of excited low-energy conformers are also accessed in those systems