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First principles modeling of soft X-ray spectroscopy of complex systems
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
2005 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

The electronic structures of complex systems have been studied by theoretical calculations of soft x-ray spectroscopies like x-ray photoelectron spectroscopy, near edge x-ray absorption fine structure, and x-ray emission spectroscopies. A new approach based on time dependent density functional theory has been developed for the calculation of shake-up satellites associated with photoelectron spectra. This method has been applied to the phthalocyanine molecule, describing in detail its electronic structure, and revealing the origin of controversial experimental features. It is illustrated in this thesis that the theoretical intepretation plays a fundamental role in the full understanding of experimental spectra of large and complex molecular systems. Soft x-ray spectroscopies and valence band photoelectron spectroscopies have proved to be powerful tools for isomer identification, in the study of newly synthesized fullerene molecules, the azafullerene C48N12 and the C50Cl10 molecule, as well as for the determination of the conformational changes in the polymeric chain of poly(ethylene oxide). The dynamics of the core excitation process, revealed by the vibrational fine structure of the absorption resonances, has been studied by means of density functional and transition state theory approaches.

Place, publisher, year, edition, pages
Stockholm: KTH , 2005. , vi, 76 p.
Keyword [en]
Molecular
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-403ISBN: 91-7178-128-5 (print)OAI: oai:DiVA.org:kth-403DiVA: diva2:10481
Public defence
2005-09-15, Sal FA32, AlbaNova, Roslagstullsbacken 21, Stockholm, 10:15
Opponent
Supervisors
Note
QC 20100929Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2010-09-29Bibliographically approved
List of papers
1. Equivalent core-hole time-dependent density functional theory calculations of carbon 1s shake-up states of phthalocyanine
Open this publication in new window or tab >>Equivalent core-hole time-dependent density functional theory calculations of carbon 1s shake-up states of phthalocyanine
Show others...
2004 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 70, no 19, 195214- p.Article in journal (Refereed) Published
Abstract [en]

The shake-up transition energies of the carbon 1s photoelectron spectrum of metal-free phthalocyanine (H2Pc) have been calculated by means of time-dependent density functional theory, for which an equivalent core approximation is adopted. Model calculations for the C 1s shake-up states of benzene are in excellent agreement with the latest experimental results. The complex C 1s shake-up structures associated with the aromatic and pyrrole carbons in the phthalocyanine are computed, as well as their ionization potentials. They allow us to determine the origin of the anomalous intensity ratio between the pyrrole and benzene carbons in a high resolution C 1s photoelectron spectrum measured for a H2Pc film, as due to a benzene-related shake-up contribution, hidden under the pyrrole main intensity feature.

Keyword
benzene, carbon, phthalocyanine, pyrrole, article, chemical structure, density functional theory, electron, film, ionization, mathematical analysis, theoretical model, X ray photoelectron spectroscopy
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-5931 (URN)10.1103/PhysRevB.70.195214 (DOI)000225477800076 ()2-s2.0-19944432507 (Scopus ID)
Note
QC 20100914 QC 20110915Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2011-09-15Bibliographically approved
2. Functional and basis set dependence of K-edge shake-up spectra of molecules
Open this publication in new window or tab >>Functional and basis set dependence of K-edge shake-up spectra of molecules
2005 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 18, 184316- p.Article in journal (Refereed) Published
Abstract [en]

A straightforward approach for computing the K -edge shake-up spectra of molecules based on equivalent core-hole linear response theory at both Hartree-Fock and density functional theory levels is proposed. Benchmark calculations have been performed to explore its sensitivity to different types of functionals and basis sets for the carbon 1s shake-up spectra of benzene and metal-free phthalocyanine (H2 Pc). A very good agreement with previous theoretical and experimental works for the benzene molecule has been obtained for all the functionals and basis sets tested. Electron correlation is found to be essential for a good description of the H2 Pc system, whose experimental C 1s shake-up spectrum is best reproduced by the hybrid density functional.

Keyword
Algebra, Approximation theory, Benzene, Binding energy, Computer simulation, Correlation methods, Electron energy levels, Emission spectroscopy, Green's function, Nitrogen compounds, Optimization, X ray photoelectron spectroscopy
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-5932 (URN)10.1063/1.1891686 (DOI)000229275600032 ()2-s2.0-18844411611 (Scopus ID)
Note
QC 20100915Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2010-09-15Bibliographically approved
3. Electronic structure of a vapor-deposited metal-free phthalocyanine thin film
Open this publication in new window or tab >>Electronic structure of a vapor-deposited metal-free phthalocyanine thin film
Show others...
2005 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 21Article in journal (Refereed) Published
Abstract [en]

The electronic structure of a vapor-sublimated thin film of metal-free phthalocyanine (H2Pc) is studied experimentally and theoretically. An atom-specific picture of the occupied and unoccupied electronic states is obtained using x-ray-absorption spectroscopy (XAS), core- and valence-level x-ray photoelectron spectroscopy (XPS), and density-functional theory (DFT) calculations. The DFT calculations allow for an identification of the contributions from individual nitrogen atoms to the experimental N1s XAS and valence XPS spectra. This comprehensive study of metal-free phthalocyanine is relevant for the application of such molecules in molecular electronics and provides a solid foundation for identifying modifications in the electronic structure induced by various substituent groups.

Keyword
ray photoelectron-spectroscopy, light-emitting devices, valence-band, absorption-spectra, naphthalocyanine, h-2-phthalocyanine, porphyrazine, distinction, porphyrins, resolution
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-14819 (URN)10.1063/1.1924539 (DOI)000229700600057 ()2-s2.0-21344450504 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2012-03-22Bibliographically approved
4. Time-dependent DFT calculations of core electron shake-up states of metal-(free)-phthalocyanines
Open this publication in new window or tab >>Time-dependent DFT calculations of core electron shake-up states of metal-(free)-phthalocyanines
2006 (English)In: Radiation Physics and Chemistry, ISSN 0969-806X, Vol. 75, no 11, 1578-1581 p.Article in journal (Refereed) Published
Abstract [en]

We have introduced a new approach for the calculation of the shake-up structures of molecular photoelectron spectra, based on the combination of time-dependent density functional theory (TD-DFT) and equivalent core hole (or Z + 1) approximation. The method, suitable for large molecules, has been applied to compute the complex shake-up states associated with the carbon Is X-ray photoelectron spectroscopy (XPS) of metal-free and nickel phthalocyanines (H2Pc and NiPc, respectively). A similar satellite profile emerges for both molecules.

Keyword
shake-up, phthalocyanine, time-dependent DFT
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-5934 (URN)10.1016/j.radphyschem.2005.07.017 (DOI)000242185600028 ()2-s2.0-33750146717 (Scopus ID)
Note
QC 20100929. Uppdaterad från in press till published (20100929). Conference: 20th International Conference on X-Ray and Inner-Shell Processes. Univ Melbourne, Melbourne, AUSTRALIA. JUL 04-08, 2005.Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2011-09-29Bibliographically approved
5. The electronic structure of iron phthalocyanine probed by photoelectron and x-ray absorption spectroscopies and density functional theory calculations
Open this publication in new window or tab >>The electronic structure of iron phthalocyanine probed by photoelectron and x-ray absorption spectroscopies and density functional theory calculations
Show others...
2006 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 125, no 3, 034709-1-034709-7 p.Article in journal (Refereed) Published
Abstract [en]

A joint experimental and theoretical work to explain the electronic and geometrical structure of an in situ prepared film of iron phthalocyanine (FePc) on silicon (100) is presented. FePc molecular films have been characterized by core and valence photoemission spectroscopy (PES) and x-ray absorption spectroscopy (XAS), and the results have been interpreted and simulated by density functional theory (DFT) calculations. C1s and N1s PE spectra have been analyzed by taking into account all chemically nonequivalent C and N atoms in the molecule. In the Fe2p(3/2) spectra it has been possible to resolve two components that can be related to the open shell structure of the molecule. By valence PES and N1s XAS data, the geometrical orientation of the FePc molecules in the film could be determined. Our results indicate that for the FePc on Si(100), the molecules within the film are mainly standing on the surface. The experimental N1s XAS spectra are very well reproduced by the theoretical calculations, which are both angle and atomic resolved, giving a detailed description of the electronic and geometric structure of the FePc film. Furthermore, the asymmetry and the intensity angle variation of the first N1s XAS threshold feature could be explained by the presented DFT calculations as due to the chemical nonequivalence of the N atoms and the symmetry character of the lowest unoccupied molecular orbital.

Keyword
Electronic structure, Molecular structure, Photoemission, Probability density function, Silicon, Thin films, X ray photoelectron spectroscopy, Chemical nonequivalence, Geometrical structure, Molecular films, Photoemission spectroscopy (PES)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-5935 (URN)10.1063/1.2212404 (DOI)000239174500039 ()2-s2.0-33746428439 (Scopus ID)
Note
QC 20100929. Uppdaterad från manuskript till artikel (20100929). Tidigare titel: The electronic structure of iron phthalocyanine probed by means of PES, XAS and DFT calculations Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2012-03-22Bibliographically approved
6. Conformation dependence of electronic structures of poly(ethylene oxide)
Open this publication in new window or tab >>Conformation dependence of electronic structures of poly(ethylene oxide)
Show others...
2005 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 16, 7907-7914 p.Article in journal (Refereed) Published
Abstract [en]

The electronic structure of pure poly(ethylene oxide) (PEO) for four different polymeric chain conformations has been studied by Hartree-Fock (HF) and density functional theory (DFT) through the analysis of their valence band photoelectron spectroscopy (VB-PES), X-ray emission spectroscopy (XES), and resonant inelastic X-ray scattering (RIXS). It is shown that the valence band of PEO presents specific conformation dependence, which can be used as a fingerprint of the polymeric structures. The calculated spectra have been compared with experimental results for PEO powder.

Keyword
ray photoelectron-spectroscopy, polymer electrolytes, polyethylene oxide, vibrational spectroscopy, emission-spectroscopy, molecular-dynamics, nanocomposites, transformation, polyethers, scattering
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-14692 (URN)10.1021/jp045685u (DOI)000228603700046 ()2-s2.0-18544371046 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2010-09-29Bibliographically approved
7. Electronic structures of azafullerene C48N12
Open this publication in new window or tab >>Electronic structures of azafullerene C48N12
2003 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 119, no 14, 7139-7144 p.Article in journal (Refereed) Published
Abstract [en]

Two recently proposed low-energy azafullerene C48N12 isomers have been theoretically characterized using x-ray spectroscopies. The x-ray photoelectron spectroscopy, the near-edge absorption fine structure, the x-ray emission spectroscopy, and the ultraviolet photoelectron spectroscopy for both isomers have been predicted at the gradient-corrected density functional theory level. These spectroscopies together give a comprehensive insight of the electronic structure on the core, valence, and unoccupied orbitals. They have also provided a convincing way for identifying the isomer structures.

Keyword
Absorption spectroscopy, Electron energy levels, Electronic structure, Emission spectroscopy, Isomers, Probability density function, Ultraviolet spectroscopy, X ray photoelectron spectroscopy, Isomer structures, Near edge absorption fine structure, Ultraviolet photoelectron spectroscopy
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-5937 (URN)10.1063/1.1605935 (DOI)000185575700020 ()
Note
QC 20100929Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2010-09-29Bibliographically approved
8. Characterization of the electronic structure of C50Cl10 by means of soft x-ray spectroscopies
Open this publication in new window or tab >>Characterization of the electronic structure of C50Cl10 by means of soft x-ray spectroscopies
2005 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 24, 244305-1-244305-4 p.Article in journal (Refereed) Published
Abstract [en]

The electronic structure of the last synthesized fullerene molecule, the C50Cl10, has been characterized by theoretical simulation of x-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, and near-edge x-ray-absorption fine structure. All the calculations were performed at the gradient-corrected and hybrid density-functional theory levels. The combination of these techniques provides detailed information about the valence band and the unoccupied molecular orbitals, as well as about the carbon core orbitals.

Keyword
Band structure, Characterization, Computer simulation, Electronic structure, Molecular orientation, Ultraviolet spectroscopy, X ray photoelectron spectroscopy, Gradient-corrected theory, Hybrid density-functional theory, Molecular orbitals, Valence bands
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-5938 (URN)10.1063/1.2137317 (DOI)000234340100010 ()2-s2.0-29744465112 (Scopus ID)
Note
QC 20100929. Uppdaterad från manuskript till artikel (20100929).Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2010-09-29Bibliographically approved
9. Molecular ordering in isonicotinic acid on rutile TiO2(110) investigated with valence band photoemission
Open this publication in new window or tab >>Molecular ordering in isonicotinic acid on rutile TiO2(110) investigated with valence band photoemission
Show others...
2004 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 121, no 20, 10203-10208 p.Article in journal (Refereed) Published
Abstract [en]

The adsorption of isonicotinic acid on rutile TiO2(110) has been investigated using synchrotron-based valence band photoemission. Structural ordering in multilayer films of the molecules is found to give rise to a strong angular dependence in the valence band intensities when measured using linearly polarized radiation. Molecular ordering in this case is proposed to be induced by intermolecular hydrogen bonding which is found to be highly dependent upon the deposition rate of the isonicotinic acid. Through comparison of the experimental data with density functional calculated valence band spectra of hydrogen-bonded isonicotinic acid molecules, we can account for the angular dependence in terms of the spatial distribution of the molecular orbitals.

Keyword
core-level shift, charge-transfer, surface, adsorption, systems, tio2
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-23873 (URN)10.1063/1.1802292 (DOI)000225042700047 ()2-s2.0-10844290434 (Scopus ID)
Note
QC 20100525 QC 20110916Available from: 2010-08-10 Created: 2010-08-10 Last updated: 2011-09-16Bibliographically approved
10. N-K near edge x-ray absorption fine structures of acetonitrile in gas phase
Open this publication in new window or tab >>N-K near edge x-ray absorption fine structures of acetonitrile in gas phase
Show others...
2005 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 21, 214301- p.Article in journal (Refereed) Published
Abstract [en]

 The dynamic processes of N(1s) core-hole excitation in gas-phase CH3CN molecule have been studied at both Hartree-Fock and hybrid density-functional theory levels. The vibrational structure is analyzed for fully optimized core-excited states. Frank-Condon factors are obtained using the linear coupling model for various potential surfaces. It is found that the vibrational profile of the N-K absorption can be largely described by a summation of two vibrational progressions: a structure-rich profile of nu((CN)) stretching mode and a large envelope of congestioned vibrational levels related to the strong (-C-CN) terminal bending bond. Excellent agreement between theoretical and experimental spectra is obtained.

Keyword
Electric excitation, Mathematical models, Nitrogen compounds, Optimization, Probability density function, X ray analysis
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-5940 (URN)10.1063/1.2104327 (DOI)000233824800015 ()2-s2.0-28944448406 (Scopus ID)
Note
QC 20100923. Uppdaterad från Submitted till Published (20100923).Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2010-09-23Bibliographically approved
11. Electronic and geometrical structures of the N1s-13(pi) excited states in the N2O molecule
Open this publication in new window or tab >>Electronic and geometrical structures of the N1s-13(pi) excited states in the N2O molecule
(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-5941 (URN)
Note
QC 20100929Available from: 2005-09-05 Created: 2005-09-05 Last updated: 2010-09-29Bibliographically approved

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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
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  • en-GB
  • en-US
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