Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Synchrotron radiation studies of gas phase molecules: from hydrogen to DNA sugars
KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
2008 (English)Doctoral 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].

Place, publisher, year, edition, pages
Stockholm: KTH , 2008. , x, 56 p.
Series
Trita-FYS, ISSN 0280-316X ; 2008:1
Keyword [en]
KTH thesis, synchrotron radiation, gas phase, bio molecules
National Category
Atom and Molecular Physics and Optics
Identifiers
URN: urn:nbn:se:kth:diva-4640ISBN: 978-91-7178-852-8 (print)OAI: oai:DiVA.org:kth-4640DiVA: diva2:13205
Public defence
2008-03-13, FA31, Albanova, Roslagstullabacken 21, Stockholm, 10:15
Opponent
Supervisors
Note
QC 20100916Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-09-16Bibliographically approved
List of papers
1. The npσ,π to EF emission systems in D2 studied by selective excitation
Open this publication in new window or tab >>The npσ,π to EF emission systems in D2 studied by selective excitation
Show others...
2005 (English)In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 38, no 6, 659-664 p.Article in journal (Refereed) Published
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).

Keyword
Absorption spectroscopy, Dispersion (waves), Dissociation, Electric excitation, Electron energy levels, Synchrotron radiation, Dispersed emissions, Emission bands, Grating spectrometers, Molecular hydrogen
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-7997 (URN)10.1088/0953-4075/38/6/004 (DOI)000228455000008 ()2-s2.0-16244367150 (Scopus ID)
Note
QC 20100916Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-09-16Bibliographically approved
2. Fluorescence emission from photo-fragments after resonant S 2p excitations in H2S
Open this publication in new window or tab >>Fluorescence emission from photo-fragments after resonant S 2p excitations in H2S
Show others...
2007 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 9, no 3, 389-395 p.Article in journal (Refereed) Published
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.

Keyword
X-RAY EXCITATION, DECAY CHANNELS, PHOTOELECTRON-SPECTROSCOPY, AUGER DECAY, MOLECULES, PHOTOIONIZATION, STATES, ATOMS
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-7998 (URN)10.1039/b610199b (DOI)000243204200008 ()2-s2.0-33845962796 (Scopus ID)
Note
QC 20100916Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-09-16Bibliographically approved
3. Lyman and Balmer emission following core excitations in methane and ammonia molecules
Open this publication in new window or tab >>Lyman and Balmer emission following core excitations in methane and ammonia molecules
Show others...
2007 (English)In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 40, no 8, 1489-1500 p.Article in journal (Refereed) Published
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.

Keyword
Ammonia, Dissociation, Fluorescence, Methane, Photons, Rydberg states, Balmer series emission lines, Core excitations, Photon energies, Quantum defect analysis, Rydberg excitations
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-7999 (URN)10.1088/0953-4075/40/8/003 (DOI)000246010300004 ()2-s2.0-34247098021 (Scopus ID)
Note
QC 20100916Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-11-17Bibliographically approved
4. The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase
Open this publication in new window or tab >>The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase
Show others...
2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 4, 044316-1-044316-12 p.Article in journal (Refereed) Published
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.

Keyword
Density functional theory; Ionization potential; Molecular orbitals; Resonance; Rydberg states; X ray absorption near edge structure spectroscopy; Gas phases; Pyrimidine; Rydberg orbitals
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-8340 (URN)10.1063/1.2822985 (DOI)000252821200039 ()2-s2.0-38849108213 (Scopus ID)
Note
QC 20100726Available from: 2008-05-06 Created: 2008-05-06 Last updated: 2010-09-16Bibliographically approved
5. VUV photoionisation of free azabenzenes: pyridine, pyrazine, pyrimidine, pyridazine and s-triazine
Open this publication in new window or tab >>VUV photoionisation of free azabenzenes: pyridine, pyrazine, pyrimidine, pyridazine and s-triazine
Show others...
2008 (English)In: International Journal of Mass Spectrometry, ISSN 1387-3806, Vol. 275, no 1-3, 55-63 p.Article in journal (Refereed) Published
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.

Keyword
gas phase, aromatic rings, photolysis, synchrotron radiation
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-8001 (URN)10.1016/j.ijms.2008.05.019 (DOI)000258518200006 ()2-s2.0-47549097714 (Scopus ID)
Note
QC 20100916. Uppdaterad från submitted till published (20100916).Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-09-16Bibliographically approved
6. Photofragmentation of 2-deoxy-D-ribose molecules in the gas phase
Open this publication in new window or tab >>Photofragmentation of 2-deoxy-D-ribose molecules in the gas phase
Show others...
2008 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 9, no 7, 1020-1029 p.Article in journal (Refereed) Published
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.

Keyword
cleavage reactions, DNA damage, gas-phase reactions, mass spectrometry, photolysis
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-8002 (URN)10.1002/cphc.200700635 (DOI)000255845500010 ()2-s2.0-43649083041 (Scopus ID)
Note
QC 20100916Available from: 2008-02-20 Created: 2008-02-20 Last updated: 2010-09-16Bibliographically approved

Open Access in DiVA

fulltext(3480 kB)940 downloads
File information
File name FULLTEXT01.pdfFile size 3480 kBChecksum MD5
c71f1cf032d4bb3d1ca1fda8c8102443d755ace3a901ee532fb7822cef98b2aab5e56797
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Vall-llosera, Gemma
By organisation
Atomic and Molecular Physics
Atom and Molecular Physics and Optics

Search outside of DiVA

GoogleGoogle Scholar
Total: 940 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 680 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf