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  • 1. Augustsson, A.
    et al.
    Kashtanov, Stepan
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Chang, C.L.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Rubensson, J.-E.
    Nordgren, J.
    Conformations and core-excitation dynamics liquid water.Manuscript (preprint) (Other academic)
  • 2. Guo, J. H.
    et al.
    Augustsson, A.
    Kashtanov, Stepan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Spångberg, D.
    Nordgren, J.
    Hermansson, Kersti
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Augustsson, A.
    The interaction of cations and liquid water studied by resonant soft-X-ray absorption and emission spectroscopy2005In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 144, p. 287-290Article in journal (Refereed)
    Abstract [en]

    We report the soft-X-ray absorption and emission studies of NaCl, MgCl2, and AlCl3 in water solutions. The influences of cations on the water molecular structure can be seen as the absorption threshold edge shifted to high energy in the X-ray absorption spectra; the mixing of molecular orbital in 3a(1) symmetry is reinforced as the intensity of 3a(1) is further reduced; and the 1b(1)-emission peak shows the broadening and shift differently for Na+, Mg2+, and Al3+ water solutions, which indicates that the charge difference of the cations may not be the only playing role being responsible to the interactions between the cations and water molecules.

  • 3. Guo, J. -H
    et al.
    Kashtanov, Stepan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Soderstom, J.
    Glans, P. -A
    West, M.
    Learmonth, T.
    Chiou, J. -W
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nordgren, J.
    Smith, K.
    Pong, W. -F
    Cheng, H.
    Griffiss, J. M.
    Electronic structure study of the bases in DNA duplexes by in situ photon-in/photon-out soft X-ray spectroscopy2010In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 181, no 2-3, p. 197-201Article in journal (Refereed)
    Abstract [en]

    Understanding protein functionality is of fundamental importance in biochemistry. Soft X-ray transitions, where the core-level vacancies are filled by the valence-orbital electrons, give direct information about the chemical bonding. Soft X-ray absorption and emission study of poly(dG) -poly(dC) in aqueous solutions can elucidate the relation between the structure and functionality of proteins. We report the N K-edge soft X-ray absorption (XAS) and resonant soft X-ray emission spectroscopy (XES) to characterize the electronic structure near the Fermi level of DNA duplexes to specify the charge migration mechanism. Since N atoms are included in only bases in DNA duplexes, the XES spectra excited from N Is to unoccupied states purely extract the electronic orbital features of the bases in DNA. The fact that N atoms in different bonding environments form well-defined structure has been determined. The experimental findings provide the evidence for the charge-hopping and/or charge-transfer effects in understanding of electric conduction in DNA duplexes when electrons pass through the pi* states of DNA bases.

  • 4. Guo, J. H.
    et al.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Augustsson, A.
    Kashtanov, Stepan
    KTH, Superseded Departments, Chemistry.
    Rubensson, J. E.
    Shuh, D.
    Zhuang, V.
    Ross, P.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Nordgren, J.
    The molecular structure of alcohol-water mixtures determined by soft-X-ray absorption and emission spectroscopy2004In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 137-40, p. 425-428Article in journal (Refereed)
    Abstract [en]

    We have examined the influence of the intermolecular interaction on the local electronic structure by using X-ray absorption and emission spectra of liquid methanol, water, and their mixtures (in molar ratios of 9:1 and 7:3). We find a strong involvement of hydrogen bonding in the mixing of water and methanol molecules. The local electronic structure of water and methanol clusters, where water cluster is bridging within a 6-member open-ring structured methanol cluster, is separately determined. The experimental findings suggest an incomplete mixing of water-alcohol systems and a strong self- association between methanol chain and water cluster through hydrogen bonding. The enhancement of joint water-methanol open-ring structure owes the explanation to the loss of entropy of the aqueous solutions.

  • 5.
    Guo, J.-H.
    et al.
    Advanced Light Source, Lawrence Berkeley National Laboratory.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Augustsson, A.
    Uppsala Universitet.
    Kashtanov, Stepan
    KTH, Superseded Departments, Biotechnology.
    Rubensson, J. E.
    Uppsala Universitet.
    Shuh, D. K.
    Lawrence Berkeley National Laboratory.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Nordgren, J.
    Uppsala Universitet.
    Molecular structure of alcohol-water mixtures2003In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 91, no 15Article in journal (Refereed)
    Abstract [en]

    We use x-ray emission spectroscopy to elucidate the molecular structure of liquid methanol, water, and methanol-water solutions. We find that molecules in the pure liquid methanol predominantly persist as hydrogen-bonded chains and rings with six and/or eight molecules of equal abundance. For water-methanol solutions we find evidence of incomplete mixing at the microscopic level. Our results provide a new explanation for a smaller entropy increase in the solution due to water molecules bridging methanol chains to form rings.

  • 6.
    Hellgren, Niklas
    et al.
    Linköpings Universitet.
    Guo, Jinghua
    Lawrence Berkeley National Laboratory.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Såthe, Conny
    Uppsala Universitet.
    Agui, Akane
    Uppsla Universitet.
    Kashtanov, Stepan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Nordgren, Joseph
    Uppsla Universitet.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Sundgren, Jan- Eric
    Linköpings Universitet.
    Electronic structure of carbon nitride thin films studied by X-ray spectroscopy techniques2005In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 471, no 02-jan, p. 19-34Article in journal (Refereed)
    Abstract [en]

    Magnetron-sputtered carbon nitride thin films with different structures and compositions were analyzed by X-ray and ultraviolet photoelectron spectroscopy (XPS and UPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), as well as X-ray emission spectroscopy (XES). In all techniques, the carbon spectra are broad and featureless with little variation depending on growth conditions. The nitrogen spectra, on the other hand, show more distinct features, providing a powerful tool for structural characterization. By comparing the experimental spectra with calculations on different model systems, we are able to identify three major bonding structures of the nitrogen-N1: nitrile (C equivalent to N) bonds; N2: Pyridine-like N, i.e., N bonded to two C atoms; and N3: graphite-like N, i.e., N bonded to three C atoms as if substituted in a graphitic network, however, possibly positioned in a pentagon and/or with sp(3) carbon neighbors. The presence of N2 and N3 are best detected by XPS, while N1 is better detected by NEXAFS. The calculated XES spectra also give good indications how valence band spectra should be interpreted. Films grown at the higher temperatures ( greater than or equal to 350 degreesC) show a pronounced angular dependence of the incoming photon beam in NEXATS measurements, which suggests a textured microstructure with standing graphitic basal planes, while amorphous films grown at low temperatures show isotropic properties.

  • 7.
    Kashtanov, Stepan
    KTH, School of Biotechnology (BIO).
    Theoretical modeling of X-ray spectroscopy of liquids2005Doctoral thesis, comprehensive summary (Other scientific)
  • 8.
    Kashtanov, Stepan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Augustson, Andreas
    Uppsala Universitet.
    Rubensson, Jan-Erik
    Uppsala Universitet.
    Nordgren, Joseph
    Uppsala Universitet.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Guo, Jing. Hua
    Lawrence Berkeley National Laboratory.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chemical and electronic structures of liquid methanol from x-ray emission spectroscopy and density functional theory.2005In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 71, no 10Article in journal (Refereed)
    Abstract [en]

    We have applied x-ray emission spectroscopy and density functional theory (DFT) to study the chemical and electronic structures of liquid methanol. The x-ray emission spectra at carbon and oxygen K edges of methanol in different hydrogen-bonded clusters are simulated. It is shown that hydrogen bonding strongly influences the spectral profile of O K emission, but not the C K emission. The methanol chain and ring conformations show a distinct difference in their electronic structures. The molecular orbitals of chains are strongly localized, whereas for the ring structures they show strong delocalization characteristics and behaviorlike covalent pi orbitals in a conjugated system. A comparison of experimental spectra and DFT calculations suggests that liquid methanol comprises combinations of rings and chains of methanol molecules linked with hydrogen bonds and is dominated by structures with the size of six and eight molecules.

  • 9.
    Kashtanov, Stepan
    et al.
    KTH, Superseded Departments, Biotechnology.
    Augustsson, A.
    Uppsala Universitet.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Guo, J. H.
    Lawrence Berkeley National Laboratory.
    Såthe, C.
    Uppsala Universitet.
    Rubensson, J. E.
    Uppsala Universietet.
    Siegbahn, H.
    Uppsala Universitet.
    Nordgren, J.
    Uppsala Universietet.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Local structures of liquid water studied by x-ray emission spectroscopy2004In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 69, no 2Article in journal (Refereed)
    Abstract [en]

    The O Kalpha x-ray emission spectra of water clusters with different sizes and conformations embedded in a continuum medium are simulated. The calculations have successfully explained the experimental spectra of water in both gas and liquid phases. It is shown that the x-ray emission spectra are very sensitive to the local hydrogen bonding structures. Strong electron sharing between different water molecules is observed and its possible connection to the covalency of hydrogen bonding is discussed. The experimentally observed strong excitation energy dependence of the spectra has been interpreted in terms of the polarization and angular dependence for the gas phase, and in terms of variations of local hydrogen bonding structures for the liquid phase.

  • 10.
    Kashtanov, Stepan
    et al.
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Guo, J.-H.
    Augustsson, A.
    Rubensson, J.-E.
    Nordgren, J.
    Uppsala Universitet.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Electronic structure of water clusters in tetrahedral, ring, and chain conformations.Manuscript (preprint) (Other academic)
  • 11.
    Kashtanov, Stepan
    et al.
    KTH, Superseded Departments, Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Stäfstrom, Sven
    Linköpings Universitet.
    Csillag, Stefan
    Stockholms Universitet.
    Characterization of aza-fullerene C58N2 isomers by X-ray spectroscopy2003In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 371, no 02-jan, p. 98-104Article in journal (Refereed)
    Abstract [en]

    X-ray photoelectron and near-edge X-ray absorption fine-structure spectra (NEXAFS) of four isomers of C58N2 are predicted by means of density-functional theory calculations. A strong isomer dependence for both types of spectra are found. The spectroscopic findings are discussed in conjunction with results from electronic and geometric structure optimizations.

  • 12.
    Kashtanov, Stepan
    et al.
    KTH, Superseded Departments, Biotechnology.
    Schwegler, E.
    Lawrence Livermore National Laboratory .
    Galli, G.
    Lawrence Livermore National Laboratory.
    Guo, J.-H.
    Lawrence Berkley National Laboratory .
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Molecular dynamics simulations and X-ray emission studies of Mg2+ cation in liquid water.Manuscript (preprint) (Other academic)
  • 13. Söderström, J.
    et al.
    Gråsjö, J.
    Kashtanov, Stepan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Bergström, C.
    Agåker, M.
    Schmitt, T.
    Augustsson, A.
    Duda, L.
    Guo, J. H.
    Nordgren, J.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Artursson, P.
    Rubensson, J. E.
    X-ray yield and selectively excited X-ray emission spectra of atenolol and nadolol2005In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 144, p. 283-285Article in journal (Refereed)
    Abstract [en]

    A pre-study in a project aimed at increasing the understanding of drug solubility by applying X-ray spectroscopy to substances in solid phases, in aqueous solution, and in gas-phase is presented. Influence of the molecular surrounding on the local electronic structure is reflected in X-ray yield fine structure, and in site-selectively excited X-ray emission spectra. Results for atenolol and nadolol in solid form are discussed.

1 - 13 of 13
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