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  • 1.
    Gopakumar, Geethanjali
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Svensson, Pamela
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Schwob, Lucas
    Deutsch Elektronen Synchrotron DESY, DE-22607 Hamburg, Germany..
    Unger, Isaak
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Saak, Clara-Magdalena
    Univ Vienna, Dept Phys Chem, A-1090 Vienna, Austria..
    Timm, Martin
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany.;Tech Univ Berlin, Inst Opt & Atomare Phys, DE-10623 Berlin, Germany..
    Buelow, Christine
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany.;Albert Ludwigs Univ Freiburg, Phys Inst, DE-79104 Freiburg, Germany..
    Kubin, Markus
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany..
    Zamudio-Bayer, Vicente
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany..
    Lau, J. Tobias
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany.;Albert Ludwigs Univ Freiburg, Phys Inst, DE-79104 Freiburg, Germany..
    von Issendorff, Bernd
    Albert Ludwigs Univ Freiburg, Phys Inst, DE-79104 Freiburg, Germany..
    Abid, Abdul Rahman
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Univ Oulu, Fac Sci, Nano & Mol Syst Res Unit, Oulu 90570, Finland..
    Lindblad, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Danielsson, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Koerfer, Ebba
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, DE-22607 Hamburg, Germany..
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Lindblad, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, DE-12489 Berlin, Germany.;Lund Univ, Dept Phys, SE-22100 Lund, Sweden.;Uppsala Univ, Dept Chem, Angstrom Lab, SE-75121 Uppsala, Sweden..
    X-ray Induced Fragmentation of Protonated Cystine2022In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 126, no 9, p. 1496-1503Article in journal (Refereed)
    Abstract [en]

    We demonstrate site-specific X-ray induced fragmentation across the sulfur L-edge of protonated cystine, the dimer of the amino acid cysteine. Ion yield NEXAFS were performed in the gas phase using electrospray ionization (ESI) in combination with an ion trap. The interpretation of the sulfur Ledge NEXAFS spectrum is supported by Restricted Open-Shell Configuration Interaction (ROCIS) calculations. The fragmentation pathway of triply charged cystine ions was modeled by Molecular Dynamics (MD) simulations. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons. The disulfide bridge breaks for resonant excitation at lower photon energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments initially formed subsequently break into smaller fragments.

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  • 2.
    Gopakumar, Geethanjali
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Svensson, Pamela H.W.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Schwob, L
    Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany.
    Unger, Isaak
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Saak, Clara-Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timm, M
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany; nstitut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, DE-10623 Berlin, Germany.
    Bülow, C
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany; Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany.
    Kubin, M
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.
    Zamudio-Bayer, V
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.
    Lau, J-T
    Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany; Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany.
    von Issendorff, B
    Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany.
    Abid, Abdul Rahman
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, P. O. Box 3000, Finland.
    Lindblad, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Danielsson, E
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Koerfer, E
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Lindblad, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry. Department of Physics, Lund University, Box 118, SE-22100 Lund, Sweden; Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.
    X-ray Induced Fragmentation of Protonated CystineManuscript (preprint) (Other academic)
    Abstract [en]

    Protein structure determination using high-intensity X-ray sources induces damage in the protein. Disulfide bridges, formed between two cysteine amino acid residues stabilize the protein structure. Owing to the higher absorption cross-section of sulfur for X-ray photons, and a large number of electrons released from sulfur atoms, these disulfide bridges are hot spots for a higher level of noise in structural studies. But it is yet to be understood how exactly the damage occurs through the interaction of the disulfide bridges with photons. Here we study the fragmentation of protonated cystine in the gas phase, which is the dimer of cysteine, by irradiation with X-rays across the sulfur L-edge using an electrospray ionization source (ESI) in combination with an ion trap. This is complemented with the calculation of the sulfur NEXAFS spectrum on the level of Restricted Open-Shell Configuration Interaction (ROCIS) and Density Functional Theory (DFT) calculations for molecular orbital visualization as well as Molecular Dynamics (MD) simulations for the fragmentation of triply charged cystine ions. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons by combining the experiments and simulations. The disulfide bridge breaks for resonant excitation at lower energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments formed subsequently break into smaller fragments. 

  • 3.
    Pihlava, Lassi
    et al.
    Univ Turku, Dept Phys & Astron, FI-20014 Turku, Finland..
    Svensson, Pamela
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Kukk, Edwin
    Univ Turku, Dept Phys & Astron, FI-20014 Turku, Finland..
    Kooser, Kuno
    Univ Tartu, Inst Phys, W Ostwald 1, EST-50411 Tartu, Estonia..
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Tonisoo, Arvo
    Univ Tartu, Inst Phys, W Ostwald 1, EST-50411 Tartu, Estonia..
    Käämbre, Tanel
    Univ Tartu, Inst Phys, W Ostwald 1, EST-50411 Tartu, Estonia..
    André, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Akiyama, Tomoko
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Hessenthaler, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Giehr, Flavia
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Ctr Free Electron Laser Sci, DESY, D-22607 Hamburg, Germany..
    Berholts, Marta
    Univ Tartu, Inst Phys, W Ostwald 1, EST-50411 Tartu, Estonia..
    Shell-dependent photofragmentation dynamics of a heavy-atom-containing bifunctional nitroimidazole radiosensitizer2024In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, no 11, p. 8879-8890Article in journal (Refereed)
    Abstract [en]

    Radiation therapy uses ionizing radiation to break chemical bonds in cancer cells, thereby causing DNA damage and leading to cell death. The therapeutic effectiveness can be further increased by making the tumor cells more sensitive to radiation. Here, we investigate the role of the initial halogen atom core hole on the photofragmentation dynamics of 2-bromo-5-iodo-4-nitroimidazole, a potential bifunctional radiosensitizer. Bromine and iodine atoms were included in the molecule to increase the photoionization cross-section of the radiosensitizer at higher photon energies. The fragmentation dynamics of the molecule was studied experimentally in the gas phase using photoelectron-photoion-photoion coincidence spectroscopy and computationally using Born-Oppenheimer molecular dynamics. We observed significant changes between shallow core (I 4d, Br 3d) and deep core (I 3d) ionization in fragment formation and their kinetic energies. Despite the fact, that the ions ejected after deep core ionization have higher kinetic energies, we show that in a cellular environment, the ion spread is not much larger, keeping the damage well-localized. A study on photodissociation dynamics of 2-bromo-5-iodo-nitroimidazole - a model radiosensitizer - using coincidence spectroscopy and computational methods.

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    fulltext
  • 4.
    Svensson, Pamela
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Schwob, Lucas
    Deutsch Elektronen Synchrotron DESY, Notke str 85, D-22607 Hamburg, Germany..
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Unger, Isaak
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Lindblad, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Vieli, Anna-Lydia
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Zamudio-Bayer, Vicente
    Helmholtz Zent Berlin Materialien & Energie, Abt Hochempfindl Rontgenspektroskopie, D-12489 Berlin, Germany..
    Timm, Martin
    Helmholtz Zent Berlin Materialien & Energie, Abt Hochempfindl Rontgenspektroskopie, D-12489 Berlin, Germany..
    Hirsch, Konstantin
    Helmholtz Zent Berlin Materialien & Energie, Abt Hochempfindl Rontgenspektroskopie, D-12489 Berlin, Germany..
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Berholts, Marta
    Univ Tartu, Inst Phys, W Ostwald 1, EE-50411 Tartu, Estonia..
    Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics2024In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, no 2, p. 770-779Article in journal (Refereed)
    Abstract [en]

    The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. These molecules possess dual functionality: improved photoabsorption capabilities and the ability to generate species that are relevant to cancer sensitization upon photofragmentation. Four samples were investigated by scanning the generated fragments in the energy regions around C 1s, N 1s, O 1s, and I 3d-edges with a particular focus on NO2+ production. The experimental summed ion yield spectra are explained using the theoretical near-edge X-ray absorption fine structure spectrum based on density functional theory. Born-Oppenheimer-based molecular dynamics simulations were performed to investigate the fragmentation processes.

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    fulltext
  • 5.
    Zhang, Teng
    et al.
    Beijing Inst Technol, Sch Integrated Circuits & Elect, MIIT Key Lab Low Dimens Quantum Struct & Devices, Beijing 100081, Peoples R China..
    Svensson, Pamela
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Brumboiu, Iulia Emilia
    Pohang Univ Sci & Technol POSTECH, Dept Chem, Pohang 37673, South Korea..
    Lanzilotto, Valeria
    Sapienza Univ Roma, Dept Chem, I-00185 Rome, Italy..
    Grazioli, Cesare
    IOM CNR, Lab TASC, Sincrotrone Trieste, I-34149 Trieste, Italy..
    Guarnaccio, Ambra
    ISM CNR, Ist Struttura Mat, I-85050 Tito, Pz, Italy..
    Johansson, Fredrik O.L.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Condensed Matter Physics of Energy Materials. KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, S-10044 Stockholm, Sweden.;Sorbonne Univ, Inst Nanosci Paris, UMR CNRS 7588, F-75005 Paris, France..
    Beranova, Klara
    Elettra Sincrotrone Trieste SCpA, I-34149 Trieste, Italy.;Czech Acad Sci, FZU Inst Phys, Prague 18221, Czech Republic..
    Coreno, Marcello
    ISM CNR, Ist Struttura Mat, I-85050 Tito, Pz, Italy..
    de Simone, Monica
    IOM CNR, Lab TASC, Sincrotrone Trieste, I-34149 Trieste, Italy..
    Floreano, Luca
    IOM CNR, Lab TASC, Sincrotrone Trieste, I-34149 Trieste, Italy..
    Cossaro, Albano
    IOM CNR, Lab TASC, Sincrotrone Trieste, I-34149 Trieste, Italy.;Univ Trieste, Dept Chem & Pharmaceut Sci, I-34127 Trieste, Italy..
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Puglia, Carla
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Condensed Matter Physics of Energy Materials.
    Clarifying the Adsorption of Triphenylamine on Au(111): Filling the HOMO-LUMO Gap2022In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 126, no 3, p. 1635-1643Article in journal (Refereed)
    Abstract [en]

    In this article, we analyze the electronic structure modifications of triphenylamine (TPA), a well-known electron donor molecule widely used in photovoltaics and optoelectronics, upon deposition on Au(111) at a monolayer coverage. A detailed study was carried out by synchrotron radiation-based photoelectron spectroscopy, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, scanning tunneling microscopy (STM), and ab initio calculations. We detect a new feature in the pre-edge energy region of the N K-edge NEXAFS spectrum that extends over 3 eV, which we assign to transitions involving new electronic states. According to our calculations, upon adsorption, a number of new unoccupied electronic states fill the energy region between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the free TPA molecule and give rise to the new feature the pre-edge region of the NEXAFS spectrum. This finding highlights the occurrence of a considerable modification of the electronic structure of TPA. The appearance of new states in the HOMO-LUMO gap of TPA when adsorbed on Au(111) has crucial implications for the design of molecular nanoelectronic devices based on similar donor systems.

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    FULLTEXT01
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