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  • 1. Feyer, Vitaliy
    et al.
    Plekan, Oksana
    Richter, Robert
    Coreno, Marcello
    Vall-Llosera, Gemma
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Prince, Kevin C.
    Trofimov, Alexander B.
    Zaytseva, Irina L.
    Moskovskaya, Tatyana E.
    Gromov, Evgeniy V.
    Schirmer, Jochen
    Tautomerism in Cytosine and Uracil: An Experimental and Theoretical Core Level Spectroscopic Study2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 19, p. 5736-5742Article in journal (Refereed)
    Abstract [en]

    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.

  • 2.
    Jakubowska, Katarzyna
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Vall-llosera, Gemma
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Kivimäki, Antti
    CNR-INFM, Laboratorio Nazionale TASC.
    Coreno, Marcello
    CNR-INFM, Laboratorio Nazionale TASC.
    Melero García, Emilio
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Stankiewicz, Marek
    Instytut Fizyki Im. Mariana Smoluchowskiego, Uniwersytet Jagielloński.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Lyman and Balmer emission following core excitations in methane and ammonia molecules2007In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 40, no 8, p. 1489-1500Article in journal (Refereed)
    Abstract [en]

    The intensities of hydrogen Lyman-alpha 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-beta emission in comparison with Balmer-alpha at higher core- to- Rydberg excitations. The Lyman-alpha emission intensity, in general, follows the relations observed in the corresponding total ion yield measurements. Additionally, the Balmer-gamma and -delta yields were measured for ammonia molecules and they show intensity maxima at photon energies shifted closer to the N 1s threshold than Balmer-alpha and -beta. 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.

  • 3. Kivimaki, A.
    et al.
    Vall Llosera, Gemma
    Coreno, M.
    Huels, M. A.
    Stankiewicz, M.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Fluorescence emission at core-to-Rydberg excitations in the N-2 molecule2009In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 42, no 18Article in journal (Refereed)
    Abstract [en]

    Fluorescence emission at the N 1s edge of the N-2 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.

  • 4. Kivimaki, A.
    et al.
    Vall-Llosera, Gemma
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Coreno, M.
    Huels, M. A.
    Stankiewicz, M.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Line shape narrowing in the ultraviolet yield at the N 1s -> pi* resonance of the N-2 molecule2009In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 42, no 7Article in journal (Refereed)
    Abstract [en]

    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 total ion yield recorded simultaneously. We explain the finding by the particularities of the resonant Auger transitions from the N 1s(-1) pi* state to the D-2 Pi(g) state in N-2(+) and by the subsequent D-2 Pi(g) -> A(2)Pi(u) emission.

  • 5. Kivimäki, Antti
    et al.
    Coreno, M.
    Richter, R.
    Alvarez Ruiz, Jesus
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Melero Garcia, Emilio
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    De Simone, M.
    Feyer, V.
    Vall Llosera, Gemma
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Prince, K. C
    Fluorescence emission following core excitations in the water molecule2006In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 39, no 5, p. 1101-1112Article in journal (Refereed)
    Abstract [en]

    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, O and OH as well as from the ionic fragments O+ and OH+. The extracted fluorescence yields of the H Lyman-alpha emission and O 2p(3)(S-4)3p(P-3) -> 2p(3)(S-4)3s(S-3) transitions show the same structures as the total ion yield spectrum but with different relative intensities. The most intense fluorescence emission is restricted to the region of the core excitations, while above the O 1s ionization limit the signal is much weaker (in the case of H) or below the detection limit (O, OH and OH+). The fluorescence emission is concluded to follow from the following general cascade: the core-excited states decay by resonant Auger transitions, the final states reached undergo dissociation into ionic and neutral fragments, and fluorescence occurs from excited fragments. In the case of the OH (A(2)Sigma(+) -> X-2 Pi) emission, the decay of core-excited states through soft x-ray emission may also be responsible for the observed fluorescence.

  • 6. Plekan, Oksana
    et al.
    Feyer, Vitaliy
    Richter, Robert
    Coreno, Marcello
    Vall-llosera, Gemma
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Prince, Kevin C.
    Trofimov, Alexander B.
    Zaytseva, Irina L.
    Moskovskaya, Tatyana E.
    Gromov, Evgeniy V.
    Schirmer, Jochen
    An Experimental and Theoretical Core-Level Study of Tautomerism in Guanine2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 33, p. 9376-9385Article in journal (Refereed)
    Abstract [en]

    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 I 1s spectra but only fair agreement for the N 1s edge.

  • 7.
    Vall Llosera, Gemma
    et al.
    KTH, School of Engineering Sciences (SCI), Physics.
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kivimaeki, A.
    Coreno, M.
    Ruiz, J. Alvarez
    de Simone, M.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics.
    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)2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 16Article in journal (Refereed)
  • 8.
    Vall-Llosera, Gemma
    KTH, School of Engineering Sciences (SCI), Physics.
    Flourescence properties of trendy molecules studied with synchrotron radiation2006Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    This thesis summarises the experimental results on molecular spectroscopy of gas phase molecules using synchrotron radiation in the UV- VUV and soft-X rays regions. The results of applying Photon Induced Fluorescence Spectroscopy (PIFS) to D2, H2S, H2O and pyrimidine are presented and discussed. Both inner and outer shell excitations of free molecules lead to different relaxation processes. However, a common result is that when the molecule breaks and the resulting neutral fragments are left in an excited state, they might fluoresce in the UV- Vis range. PIFS technique has two main advantages, it permits to detect neutral fragments and to identify the fluorescing species. From this fact, we can infer dissociation channels and trace back the electronic processes that led to the fluorescence. For these molecules we have analysed and interpreted both dispersed and undispersed fluorescence. What motivates our work is the lack of fluorescence studies and in a more general sense, to contribute to the knowledge of important molecules for life such as water and pyrimidine.

  • 9.
    Vall-llosera, Gemma
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Synchrotron radiation studies of gas phase molecules: from hydrogen to DNA sugars2008Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    This thesis summarises experimental results on the molecular spectroscopy of gas phase molecules excited by synchrotron radiation in the VUV and soft X-ray regions. We have used three different detection techniques, photon induced fluorescence spectroscopy, photoionisation mass spectroscopy and near edge X-ray absorption fine structure spectroscopy to study molecular deuterium, hydrogen sulphide, ammonia, methanol, pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, and 2-deoxy-D-ribose, the last one also known as the DNA sugar. Out of this variety of techniques and molecules we have shown that: (1) high resolution dispersed fluorescence allows us to identify vibrational and rotational bands in molecular deuterium, as well as to estimate the predissociation probability of the same molecule [paper I]; (2) the main species fluorescing after core excitation of methane, ammonia [paper III], hydrogen sulphide [paper II], pyridine, pyrimidine and s-triazine is H Balmer α, followed by fluorescence from ionised species, molecular bands and Balmer β, γ , δ; (3) the Rydberg enhancement seen in fluorescence measurements of water [Melero et al. PRL 96 (2006) 063003], corroborated later in H2S [paper II], NH3 [paper III] and CH4 [paper III] and postulated as general behaviour for molecules formed by low-Z atoms, is also seen in larger organic cyclic molecules, e.g. azabenzenes; (4) when dissociative ionisation of pyridine, pyridazine, pyrimidine, pyrazine, s-triazine and 2-deoxy-D-ribose occurs, concerted bond rearrangement and nuclear motion takes place as opposed to stepwise dissociation [papers V and VI].

  • 10.
    Vall-llosera, Gemma
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Coreno, Marcello
    CNR-IMIP, Montelibretti.
    Erman, Peter
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Huels, Michael A.
    Ion Reaction Laboratory, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Sherbrooke, Que. .
    Jakubowska, Katarzyna
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Kivimäki, Antti
    CNR-INFM, TASC Laboratory.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Stankiewicz, Marek
    Instytut Fizyki im. Mariana Smoluchowskiego, Uniwersytet Jagielloński.
    VUV photoionisation of free azabenzenes: pyridine, pyrazine, pyrimidine, pyridazine and s-triazine2008In: International Journal of Mass Spectrometry, ISSN 1387-3806, E-ISSN 1873-2798, Vol. 275, no 1-3, p. 55-63Article in journal (Refereed)
    Abstract [en]

    Photoionisation Mass spectrometry was used to obtain the fragmentation pathways of pyridine, pyridazine, pyrimidine, pyrazine and s-triazine molecules upon absorption of 23.0, 15.7 and 13.8eV synchrotron photons. The ionic fragments observed vary from molecule to molecule, however C2H2+, HCN+ and HCNH+ are common to all five molecules at the three photon energies. Furthermore, the presence of C2H2N2+,C3H3N+ and C4H4+ in the spectra of some of the molecules suggests dissociation pathways via loss of HCN moieties. The respective parent cations, m/q = 79, 80 and 81 have a greater yield at low photon energies when compared to the most intense fragment peak in each spectra. We recorded two of the fragment cation yields, as well as the parent photoion yield Curves of pyridine, pyridazine, and pyrimidine in the 8-30 eV range. The formation of abundant cation fragments show a strong propensity of the molecules for dissociation after the absorption of VUV photons higher than 14eV. The differences in relative fragment yields from molecule to molecule, and when changing the excitation energy, Suggest significant bond rearrangements and nuclear motion during the dissociation time. Thus, bond cleavage is dependent on the photon energy deposited in the molecule and on intramolecular reactivity. With the aid of photoion yield Curves and energy estimations we have assigned major peaks in the spectra and discussed their fragmentation pathways.

  • 11.
    Vall-llosera, Gemma
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kivimäki, A.
    CNR-INFM, Laboratorio Nazionale TASC, Trieste.
    Coreno, M.
    CNR-IMIP, Montelibretti, Rome.
    Álvarez Ruiz, Jesús
    CSIC, Inst Quim Fis Rocasolano, Dept Quim Laser, Madrid.
    de Simone, M.
    CNR-INFM, Laboratorio Nazionale TASC, Trieste.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 4, p. 044316-1-044316-12Article in journal (Refereed)
    Abstract [en]

    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 transitions to valence/Rydberg orbitals with mixed pi*/sigma* 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.

  • 12.
    Vall-llosera, Gemma
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Huels, Michael A.
    Ion Reaction Laboratory, Department of Nuclear Medicine and Radiobiology, University of Sherbrooke.
    Coreno, Marcello
    CNR-IMIP, Montelibretti.
    Kivimäki, Antti
    CNR-INFM, Laboratorio Nazionale TASC.
    Jakubowska, Katarzyna
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Stankiewicz, Marek
    Instytut Fizyki Im. Mariana Smoluchowskiego, Uniwersytet Jagielloński.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Photofragmentation of 2-deoxy-D-ribose molecules in the gas phase2008In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 9, no 7, p. 1020-1029Article in journal (Refereed)
    Abstract [en]

    We have measured the synchrotron-induced photofragmentation of isolated 2-deoxy-D-ribose molecules (C5H10O4) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV At all photon energies above the molecule's ionization threshold, we observe the formation of a large variety of molecular cation fragments, including CH3+, OH+, H3O+, C2H3+, C2H4+, CHxO+ (x=1,2,3), C2HxO+ (x=1-5), C3HxO+ (x=3-5), C2H4O2+, C3HxO2+ (x=1,2,4-6), C4H5O2+, C4HxO3+ (x=6,7), C5H7O3+, and C5H8O3+. 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 (C3H5O+), 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, CH3+, H3O+, C2H4+, CH3O+, and C2H5O+, 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.

  • 13.
    Vall-llosera, Gemma
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Melero García, Emilio
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Kivimäki, Antti
    CNR-INFM, Laboratorio Nazionale TASC.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Coreno, Marcello
    CNR-IMIP, Montelibretti.
    de Simone, Monica
    CNR-INFM, Laboratorio Nazionale TASC.
    Richter, Robert
    Sincrotrone Trieste, Basovizza.
    Prince, Kevin C.
    Sincrotrone Trieste, Basovizza.
    Fluorescence emission from photo-fragments after resonant S 2p excitations in H2S2007In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 9, no 3, p. 389-395Article in journal (Refereed)
    Abstract [en]

    Visible-UV fluorescence emission of gas-phase hydrogen sulfide, H2S, has been studied at the S 2p edge with synchrotron radiation excitation. Dispersed fluorescence measurements in the wavelength range 300 - 900 nm were taken at several photon energies corresponding to the excitations of the S 2p electrons to the unoccupied molecular and Rydberg orbitals. The spectra reveal fluorescence from the H, S, S+, HS and HS+ photo-fragments. H is found to be the strongest emitter at Rydberg excitations, while the emission from S+ is dominant at the molecular resonances and above the S 2p ionization thresholds. The intensities of hydrogen Lyman-alpha (122 nm), Balmer-alpha (656 nm), Balmer-beta (486 nm) transitions as well as the visible-UV total fluorescence yield (300 - 900 nm) and the total ion yield were measured by scanning the photon energy in small steps across the S 2p edge. The different Balmer lines show some sensitivity to the specific core excitations, which is, however, not so strong as that recently observed in the water molecule.

  • 14.
    Vall-llosera, Gemma
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Álvarez Ruiz, Jesús
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Erman, Peter
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Melero García, Emilio
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Menmuir, Sheena
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Stankiewicz, Marek
    Instytut Fizyki, Jageillonian University.
    The npσ,π to EF emission systems in D2 studied by selective excitation2005In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 38, no 6, p. 659-664Article in journal (Refereed)
    Abstract [en]

    The np sigma 1 Sigma(u)(+) and np pi (1)Pi(u) states in D-2 have been selectively excited using monoenergetic synchrotron light in the range of 13.97-15.84 eV and the subsequent dispersed emission to the EF (1)Sigma(g)(+) state was observed using a grating spectrometer. In total, 18 emission bands from the levels n = 3-6 were studied and rotationally analysed. The intensities of the P and R branches relative to the Q branch were found to vary strongly in the np pi (1)Pi(u)(+)-EF(1)Sigma(g)(+) bands indicating the existence of predissociations of np pi (1)Pi(u)(+) levels above the dissociation limit D(1s) + D(2l).

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