Gemma Vall-llosera

Tautomerism in cytosine and uracil: an experimental and theoretical core level spectroscopic study

The O, N, and C 1s core level photoemission spectra of the nucleobases cytosine and uracil have been measured in the vapor phase, and the results have been interpreted via theoretical calculations. Our calculations accurately predict the relative binding energies of the core level features observed in the experimental photoemission results and provide a full assignment. In agreement with previous work, a single tautomer of uracil is populated at 405 K, giving rise to relatively simple spectra. At 450 K, three tautomers of cytosine, one of which may consist of two rotamers, are identified, and their populations are determined. This resolves inconsistencies between recent laser studies of this molecule in which the rare imino-oxo tautomer was not observed and older microwave spectra in which it was reported.

An Experimental and Theoretical Core-Level Study of Tautomerism in Guanine

The core level photoemission and near edge X-ray photoabsorption spectra of guanine in the gas phase have been measured and the results interpreted with the aid of high level ab initio calculations. Tautomers are clearly identified spectroscopically, and their relative free energies and Boltzmann populations at the temperature of the experiment (600 K) have been calculated and compared with the experimental results and with previous calculations. We obtain good agreement between experiment and the Boltzmann weighted theoretical photoemission spectra, which allows a quantitative determination of the ratio of oxo to hydroxy tautomer populations. For the photoabsorption spectra, good agreement is found for the C 1s and O 1s spectra but only fair agreement for the N 1s edge.

The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase

Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with pi(*) symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are assigned to sigma or pi [corrected] orbitals with mixed valence/Rydberg [corrected] character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to sigma(*) orbitals. Calculating the experimental and theoretical Delta(pi) term values at both edges, we observe that they are almost the same within +/-1 eV as expected for isoelectronic bonded pairs. The term values of the pi(*) and sigma(*) resonances are discussed in terms of the total Z number of the atoms participating in the bond.

Photofragmentation of 2-deoxy-D-ribose molecules in the gas phase

We have measured the synchrotron-induced photofragmentation of isolated 2-deoxy-D-ribose molecules (C(5)H(10)O(4)) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV. At all photon energies above the molecules ionization threshold we observe the formation of a large variety of molecular cation fragments, including CH(3) (+), OH(+), H(3)O(+), C(2)H(3) (+), C(2)H(4) (+), CH(x)O(+) (x=1,2,3), C(2)H(x)O(+) (x=1-5), C(3)H(x)O(+) (x=3-5), C(2)H(4)O(2) (+), C(3)H(x)O(2) (+) (x=1,2,4-6), C(4)H(5)O(2) (+), C(4)H(x)O(3) (+) (x=6,7), C(5)H(7)O(3) (+), and C(5)H(8)O(3) (+). The formation of these fragments shows a strong propensity of the DNA sugar to dissociate upon absorption of vacuum ultraviolet photons. The yields of particular fragments at various excitation photon energies in the range between 10 and 28 eV are also measured and their appearance thresholds determined. At all photon energies, the most intense relative yield is recorded for the m/q=57 fragment (C(3)H(5)O(+)), whereas a general intensity decrease is observed for all other fragments- relative to the m/q=57 fragment-with decreasing excitation energy. Thus, bond cleavage depends on the photon energy deposited in the molecule. All fragments up to m/q=75 are observed at all photon energies above their respective threshold values. Most notably, several fragmentation products, for example, CH(3) (+), H(3)O(+), C(2)H(4) (+), CH(3)O(+), and C(2)H(5)O(+), involve significant bond rearrangements and nuclear motion during the dissociation time. Multibond fragmentation of the sugar moiety in the sugar-phosphate backbone of DNA results in complex strand lesions and, most likely, in subsequent reactions of the neutral or charged fragments with the surrounding DNA molecules.

Fluorescence emission following core excitations in the water molecule

Photon-induced fluorescence spectroscopy has been used to study the fragmentation of the water molecule at the O 1s is edge. Fluorescence emission has been observed from the neutral fragments H, ...

Lyman and Balmer emission following core excitations in methane and ammonia molecules

The intensities of hydrogen Lyman-α and Balmer series emission lines as a result of photoexcitation of free CH4 and NH3 molecules at the C 1s and N 1s edges have been measured. For methane, the total fluorescence yield in the visible region (300–650 nm) was also recorded. Excitation functions of the Balmer lines show relative intensity enhancement of Balmer-β emission in comparison with Balmer-α at higher core-to-Rydberg excitations. The Lyman-α emission intensity, in general, follows the relations observed in the corresponding total ion yield measurements. Additionally, the Balmer-γ and -δ yields were measured for ammonia molecules and they show intensity maxima at photon energies shifted closer to the N 1s threshold than Balmer-α and -β. A quantum defect analysis is performed to find out which core excitations are responsible for this enhanced intensity. Dissociation pathways leading to the emission in H atoms are discussed.

Publisher’s Note: “The C1s and N1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase” [J. Chem. Phys.128, 044316 (2008)]

The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase (vol 128, artn 044316, 2008)

Line shape narrowing in the ultraviolet yield at the N 1s →π* resonance of the N2 molecule

The intensity of fluorescence emission in the wavelength region of 250-320 nm has been measured across the N 1s -> pi* resonance of the N-2 molecule. It displays a narrower line shape than the t ...

Fluorescence emission at core-to-Rydberg excitations in the N2 molecule

Fluorescence emission at the N 1s edge of the N2 molecule has been studied with synchrotron radiation excitation. The partial fluorescence yields in the ultraviolet (250–320 nm) and visible (300–650 nm) wavelengths were collected by scanning the photon energy across the core-to-Rydberg excitations and the N 1s ionization potential (IP). When compared to the total ion yield, both fluorescence yields are most enhanced at the excitations to high Rydberg orbitals. A discrete structure appears just below the N 1s IP only in the UV yield and is assigned to core-valence doubly excited states. Dispersed fluorescence spectra in selected wavelength windows were measured at several photon energies in order to find out which fragments are responsible for the enhancement of fluorescence emission just below the N 1s IP. The excitation functions determined and considerations on de-excitation pathways indicate that the main responsible is the N+ ion.

Erratum: “The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase” [J. Chem. Phys.128, 044316 (2008)]

The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase (vol 128, 044316, 2008)