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  • 1051.
    Siegbahn, Per E.M.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R.A.
    Stockholm University, Faculty of Science, Department of Physics.
    On the Proton Pumping Mechanism in Cytochrome c Oxidase2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, p. 12772-12780Article in journal (Refereed)
    Abstract [en]

    Two different issues, important for the pumping mechanism of cyctochrome c oxidase, have been addressed in the present study. One of them concerns the nature of two key proton transfer transition states. A simple electrostatic model is used to suggest that the transition state (TS) for transfer to the pump-site should be positively charged, while the one for transfer to the binuclear center should be charge-neutral. The character of the former TS will guarantee that the protons will be pumped to the outside and not return to the inside, while the neutral character of the latter one will allow transfer with a sufficiently low barrier. In the simple electrostatic analysis, leading to this qualitative picture of the pumping process, the results from the kinetic experiments are strictly followed, but it is at least as important to follow the fundamental requirements for pumping. In this perspective, the uncertainties in the quantitative analysis should be rather unimportant for the emerging qualitative picture of the pumping mechanism. The second problem addressed concerns the purpose of the K-channel. It is argued that the reason for the presence of the K-channel could be that protons cannot pass through the binuclear center at some stage of pumping. Barriers and water binding energies were computed using hybrid density functional theory (DFT) to investigate this question.

  • 1052. Siegbahn, Per
    et al.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Bjorn O. Roos: 1937-2010 Mentor, Colleague, Innovator2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 13, p. 3256-3259Article in journal (Refereed)
  • 1053. Simon, M.
    et al.
    Journel, L.
    Guillemin, R.
    Stolte, W. C.
    Minkov, Ivaylo
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Carniato, S.
    Taieb, R.
    Hudson, A. C.
    Lindle, D. W.
    Elastic peak of K shell excited HCl molecule: Comparison HCl-DCl - Experiment and theory2007In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 155, no 1-3, p. 91-94Article in journal (Refereed)
    Abstract [en]

    Fermosecond dynamics has been recently observed by resonant X-ray Raman scattering (RXRS) after excitation along the dissociative Cl 1s -> 6 sigma* resonance of gas phase HCl. In this paper, we show a method to take into account and correct for self-absorption of the elastic peak, in order to allow for quantitative comparison with theory. We have performed measurements on the DCl molecule exhibiting ultrafast nuclear motion. A comparison between HCl and DCl is presented.

  • 1054. Simon, M.
    et al.
    Journel, L.
    Guillemin, R.
    Stolte, W.C.
    Minkov, Ivaylo
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Carniato, S.
    Taïeb, R.
    Hudson, A.C.
    Lindle, D.W.
    Femtosecond nuclear motion of HCl probed by resonant x-ray Raman scattering in the Cl 1s region2006In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 73, no 2, p. 020706(R)-Article in journal (Refereed)
    Abstract [en]

    Femtosecond dynamics are observed by resonant x-ray Raman scattering (RXS) after excitation along the dissociative Cl 1s -> 6 sigma(*) resonance of gas-phase HCl. The short core-hole lifetime results in a complete breakdown of the common nondispersive behavior of soft-x-ray transitions between parallel potentials. We evidence a general phenomenon of RXS in the hard-x-ray region: a complete quenching of vibrational broadening. This opens up a unique opportunity for superhigh resolution x-ray spectroscopy beyond vibrational and lifetime limitations.

  • 1055.
    Singer, S. J.
    et al.
    Ohio State Univ, Dept Chem, Columbus, OH 43210 USA.
    Knight, C. J.
    Ohio State Univ, Dept Chem, Columbus, OH 43210 USA.
    Kuo, J. L.
    Univ Penn, Ctr Mol Modeling, Dept Chem, Philadelphia, PA 19104 USA.
    Hirsch, T. K.
    Univ Stockholm, Arrhenius Lab, S-10691 Stockholm, Sweden.
    Ojamäe, L.
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry .
    Klein, M. L.
    Univ Penn, Ctr Mol Modeling, Dept Chem, Philadelphia, PA 19104 USA.
    Hydrogen bond topology and proton ordering phase transitions in ice2005Conference paper (Other academic)
  • 1056. Sjöqvist, J.
    et al.
    González-Cano, R. C.
    López Navarrete, J. T.
    Casado, J.
    Ruiz Delgado, M. C.
    Linares, M.
    Norman, Patrick
    Linköping University, Sweden.
    A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 45, p. 24841-24852Article in journal (Refereed)
    Abstract [en]

    Infrared (IR) absorption and vibrational Raman spectra of a family of branched oligothiophenes have been determined experimentally as well as theoretically. The molecular spectra have been compared to those of the linear analogues, with identification made of spectral features due to structural properties that are valued in organic solar cell applications. The theoretical spectra have been obtained through a newly developed method in which individual conformer spectra, calculated at the time-dependent DFT level in this work, are weighted by statistics extracted from classical molecular dynamics trajectories. The agreement with experiment for the resulting averaged spectra is at least as good as, and often better than, what is observed for Boltzmann-weighted spectra. As the weights are available before the costly step of spectrum calculation, the method has the additional advantage of enabling efficient approximations. For simulating the molecular dynamics of the studied α,β-linked thiophenes and 2-methylthiophenes, high quality parameters have been derived for the CHARMM force field. Furthermore, the temperature dependence of the IR and Raman spectra has been investigated, both experimentally and theoretically.

  • 1057. Sjöqvist, J.
    et al.
    Linares, M.
    Lindgren, M.
    Norman, Patrick
    Linköping University, Sweden.
    Molecular dynamics effects on luminescence properties of oligothiophene derivatives: A molecular mechanics-response theory study based on the CHARMM force field and density functional theory2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 39, p. 17532-17542Article in journal (Refereed)
    Abstract [en]

    CHARMM force field parameter values for a class of oligothiophene derivatives have been derived with reference to density functional theory/B3LYP potential energy surfaces. The force field parametrization of these luminescent conjugated polyelectrolytes includes the electronic ground state as well as the strongly light absorbing first excited state. In conjunction with quantum chemical response theory calculations of transition state properties, a molecular dynamical model of the Stokes shift is obtained. The theoretical model is benchmarked against experimental data recorded at room temperature which refer to sodium salts of p-HTAA and p-FTAA with distilled water as a solvent. For p-HTAA the theoretically predicted Stokes shift of 112 nm is in good agreement with the experimental result of 124 nm, given the approximations about exciton localization that were introduced to obtain a force field for the excited state. This journal is © the Owner Societies.

  • 1058. Sjöqvist, J.
    et al.
    Linares, M.
    Mikkelsen, K. V.
    Norman, Patrick
    Linköping University, Sweden.
    QM/MM-MD simulations of conjugated polyelectrolytes: A study of luminescent conjugated oligothiophenes for use as biophysical probes2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 19, p. 3419-3428Article in journal (Refereed)
    Abstract [en]

    A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field description of the solvent in its electronic ground state as well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (iii) spectral response calculations by means of the quantum mechanics/molecular mechanics QM/MM approach. A detailed analysis of the combined polarization effects of the ionic moiety and the polar water solvent is presented. At an increased computational cost of 30% compared to a calculation excluding the solvent, the error in the transition wavelength of the dominant absorption band is kept as small as 1 nm as compared to the high-quality benchmark result, based largely on a QM description of the solvent. At a reduced computational cost the error of the same quantity is kept as small as 6 nm, with the cost reduction being the result of an effective description of the effects of the solvent by means of replacing the carboxylate ions with neutral hydrogens. In absorption spectroscopy, the obtained best theoretical results are in excellent agreement with the experimental benchmark measurement, regarding excitation energies as well as band intensities and profiles. In fluorescence spectroscopy, the experimental spectrum shows a vibrational progression that is not addressed by theory, but the theoretical band position is in excellent agreement with experiment, with a highly accurate description of the Stokes shift as a result.

  • 1059. Sjöqvist, J.
    et al.
    Linares, M.
    Norman, Patrick
    Linköping University, Sweden.
    Platinum(II) and phosphorus MM3 force field parametrization for chromophore absorption spectra at room temperature2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 14, p. 4981-4987Article in journal (Refereed)
    Abstract [en]

    Platinum(II) and phosphine MM3 force field parameters are derived from fits to the ground state potential energy surface at the level of Kohn-Sham density functional theory with employment of the B3LYP exchange-correlation functional. The parametrization includes bond stretch, angle bend, and torsional parameters for a planar platinum(II) center with phosphine and ethynyl ligands. The force field is used to study the dynamics of a fifth-generation dendrimer-coated platinum(II)organic compound in tetrahydrofurane solution at room temperature, and, based on a selection of conformations from the molecular dynamics simulation, the averaged linear absorption spectrum is determined with use of the CAM-B3LYP functional. The main absorption peak in the theoretical absorption spectrum is found at a transition wavelength of 325 nm with a full-width at half-maximum of 26 nm due to conformational broadening.

  • 1060. Sjöqvist, J.
    et al.
    Maria, J.
    Simon, R. A.
    Linares, M.
    Norman, Patrick
    Linköping University, Sweden.
    Nilsson, K. P. R.
    Lindgren, M.
    Toward a molecular understanding of the detection of amyloid proteins with flexible conjugated oligothiophenes2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 42, p. 9820-9827Article in journal (Refereed)
    Abstract [en]

    Molecular and electronic structures and optical absorption properties of oligothiophenes used for spectral assignment of amyloid deposits have been investigated for a family of probes known as luminescent conjugated oligothiophenes (LCOs). Theoretical absorption spectra have been determined using conformational averaging, combining classical molecular dynamics (MD) simulations with quantum mechanical/molecular mechanics (QM/MM) time-dependent density functional theory (TD-DFT) spectrum calculations. Theoretical absorption spectra are in excellent agreement with experiments, showing average errors below 5 nm for absorption maxima. To couple observed properties to molecular structures, a measure of planarity is defined, revealing a strong correlation between the transition wavelength of the first and dominating electronically excited state and dihedral rotations. It is shown that from this correlation, predictions can be made of the absorption properties of probes based only on information from MD trajectories. We show experimentally that red shifts observed in the excitation maxima of LCOs when bound to amyloid protein aggregates are also evident in absorption spectra. We predict that these red shifts are due to conformational restriction of the LCO in a protein binding pocket, causing a planarization of the conjugated backbone. On the basis of our studies of planarity, it is shown that such shifts are both possible and realistic.

  • 1061.
    Sjöqvist, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Light interactions in flexible conjugated dyes2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis methodological developments have been made for the description of flexible conjugated dyes in room temperature spectrum calculations.

    The methods in question target increased accuracy and efficiency by combining classical molecular dynamics (MD) simulations with time-dependent response theory spectrum calculations. For absorption and fluorescence spectroscopies a form of conformational averaging is used, where the final spectrum is obtained as an average of spectra calculated for geometries extracted from ground and excited state MD simulations. For infrared and Raman spectroscopies averaged spectra are calculated based on individual spectra, obtained for zero-temperature optimized molecular structures, weighted by conformational statistics from MD trajectories. Statistics for structural properties are also used in both cases to gain additional information about the systems, allowing more efficient utilization of computational resources. As it is essential that the molecular mechanics description of the system is highly accurate for methods of this nature to be effective, high quality force field parameters have been derived, describing the molecules of interest in either the MM3 or CHARMM force fields.

    These methods have been employed in the study of three systems. The first is a platinum(II) actylide chromophore used in optical power limiting materials, for which a ultraviolet/visible absorption spectrum has been calculated. The second is a family of molecular probes called luminescent conjugated oligothiophenes, used to detect and characterize amyloid proteins, for which both absorption and fluorescence spectra have been calculated. Finally, infrared and Raman spectra have been calculated for a group of branched oligothiophenes used in organic solar cells.

    In addition, solvation effects have been studied for conjugated poly\-eletrolytes in water, resulting in the development of two solvation models suitable for this class of molecules. The first uses a quantum meachanics/molecular mechanics (QM/MM) description, in which the solute mole\-cule is described using accurate quantum mechanical methods while the surrounding water molecules are described using point charges and polarizable point dipoles. The second discards the water entirely and removes the ionic groups of the solute. The QM/MM model provides highly accurate results while the cut-down model gives results of slightly lower quality but at a much reduced computational cost.

    Finally, a study of protein-dye interactions has been performed, with the goal of explaining changes in the luminescence properties of the LCO chromophores when in the presence of amyloid proteins. Results were less than conclusive.

  • 1062.
    Sjöqvist, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    González-Cano, Rafael C.
    University of Málaga, Spain.
    López Navarette, Juan T.
    University of Málaga, Spain.
    Casado, Juan
    University of Málaga, Spain.
    Ruiz Delgado, M. Carmen
    University of Málaga, Spain.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 45, p. 24841-24852Article in journal (Refereed)
    Abstract [en]

    Infrared (IR) absorption and vibrational Raman spectra of a family of branched oligothiophenes have been determined experimentally as well as theoretically. The molecular spectra have been compared to those of the linear analogues, with identification made of spectral features due to structural properties that are valued in organic solar cell applications. The theoretical spectra have been obtained through a newly developed method in which individual conformer spectra, calculated at the time-dependent DFT level in this work, are weighted by statistics extracted from classical molecular dynamics trajectories. The agreement with experiment for the resulting averaged spectra is at least as good as, and often better than, what is observed for Boltzmann-weighted spectra. As the weights are available before the costly step of spectrum calculation, the method has the additional advantage of enabling efficient approximations. For simulating the molecular dynamics of the studied α,β-linked thiophenes and 2-methylthiophenes, high quality parameters have been derived for the CHARMM force field. Furthermore, the temperature dependence of the IR and Raman spectra have been investigated, both experimentally and theoretically.

  • 1063.
    Sjöqvist, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Maria, Jerôme
    Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.
    Simon, Rozalyn
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Nilsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Lindgren, Mikael
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.
    Toward a molecular understanding of the detection of amyloid proteins with flexible conjugated oligothiophenes2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 42, p. 9820-9827Article in journal (Refereed)
    Abstract [en]

    Molecular and electronic structures and optical absorption properties of oligothiophenes used for spectral assignment of amyloid deposits have been investigated for a family of probes known as luminescent conjugated oligothiophenes (LCOs). Theoretical absorption spectra have been determined using conformational averaging, combining classical molecular dynamics (MD) simulations with quantum mechanical/molecular mechanics (QM/MM) time-dependent density functional theory (TD-DFT) spectrum calculations. Theoretical absorption spectra are in excellent agreement with experiments, showing average errors below 5 nm for absorption maxima. To couple observed properties to molecular structures, a measure of planarity is defined, revealing a strong correlation between the transition wavelength of the first and dominating electronically excited state and dihedral rotations. It is shown that from this correlation, predictions can be made of the absorption properties of probes based only on information from MD trajectories. We show experimentally that red shifts observed in the excitation maxima of LCOs when bound to amyloid protein aggregates are also evident in absorption spectra. We predict that these red shifts are due to conformational restriction of the LCO in a protein binding pocket, causing a planarization of the conjugated backbone. On the basis of our studies of planarity, it is shown that such shifts are both possible and realistic.

  • 1064.
    Sköld, Christian
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Kleimark, Jonatan
    Department of Chemistry, University of Gothenburg.
    Trejos, Alejandro
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Odell, Luke R.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Nilsson Lill, Sten O.
    Department of Chemistry, University of Gothenburg.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg.
    Larhed, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Transmetallation Versus β-Hydride Elimination: The Role of 1,4 Benzoquinone in Chelation-Controlled Arylation Reactions with Arylboronic Acids2012In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 18, no 15, p. 4714-4722Article in journal (Refereed)
    Abstract [en]

    The formation of an atypical, saturated, diarylated, Heck/Suzuki, domino product produced under oxidative Heck reaction conditions, employing arylboronic acids and a chelating vinyl ether, has been investigated by DFT calculations. The calculations highlight the crucial role of 1,4-benzoquinone (BQ) in the reaction. In addition to its role as an oxidant of palladium, which is necessary to complete the catalytic cycle, this electron-deficient alkene opens up a low-energy reaction pathway from the post-insertion sigma-alkyl complex. The association of BQ lowers the free-energy barrier for transmetallation of the s-alkyl complex to create a pathway that is energetically lower than the oxidative Heck reaction pathway. Furthermore, the calculations showed that the reaction is made viable by BQ-mediated reductive elimination and leads to the saturated diarylated product.

  • 1065. Solheim, H.
    et al.
    Ruud, K.
    Coriani, S.
    Norman, Patrick
    Linköping University, Sweden.
    Complex polarization propagator calculations of magnetic circular dichroism spectra2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 9, article id 094103Article in journal (Refereed)
    Abstract [en]

    It is demonstrated that the employment of the nonlinear complex polarization propagator enables the calculation of the complete magnetic circular dichroism spectra of closed-shell molecules, including at the same time both the so-called Faraday A and B terms. In this approach, the differential absorption of right and left circularly polarized light in the presence of a static magnetic field is determined from the real part of the magnetic field-perturbed electric dipole polarizability. The introduction of the finite lifetimes of the electronically excited states into the theory results in response functions that are well behaved in the entire spectral region, i.e., the divergencies that are found in conventional response theory approaches at the transition energies of the system are not present. The applicability of the approach is demonstrated by calculations of the ultraviolet magnetic circular dichroism spectra of para-benzoquinone, tetrachloro-para-benzoquinone, and cyclopropane. The present results are obtained with the complex polarization propagator approach in conjunction with Kohn-Sham density functional theory and the standard adiabatic density functionals B3LYP, CAM-B3LYP, and BHLYP.

  • 1066. Solheim, H.
    et al.
    Ruud, K.
    Coriani, S.
    Norman, Patrick
    Linköping University, Sweden.
    The A and B terms of magnetic circular dichroism revisited2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 40, p. 9615-9618Article in journal (Refereed)
    Abstract [en]

    The temperature-independent part of the magnetic circular dichroism spectrum is conventionally divided into the Faraday A and B terms, where the A term is nonzero only for systems with degenerate states. We propose that this separation is abandoned in favor of a unified temperature-independent term. This proposal is based on complex polarization propagator calculations on three structurally similar porphyrins. These calculations also suggest that the Soret band of Zn-porphyrin is determined by an isolated degenerate 2Eu state.

  • 1067.
    Sonet Ventosa, Adrià
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. University of Barcelona.
    Decoherence-assisted transport in pigment protein complexes2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Two chlorophylls of the FMO complex, the light-harvesting complex of the green sulfur bacteria, are modeled as two coupled qubits, each surrounded by one spin-bath simulating the environment. The dynamics of the system at a non-zero temperature provide exact analytical expressions for the transition probability and the coherence. It is shown that the decoherence-inducing interaction with the environment enhances the electronic energy transfer. Also the correlations in terms of entanglement and nonlocality are quantitatively studied, sensitively differing when introducing a decay term to resemble both chlorophylls being in their ground states. It is proved that nonlocality is a stronger form of correlation than entanglement.

  • 1068. Song, X.
    et al.
    Wang, G.
    Ma, Yong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Shandong Normal University, China.
    Jiang, S.
    Yue, W.
    Xu, S.
    Wang, C.
    Density functional theory study of NEXAFS spectra of 4-methylbenzenethiol molecule2016In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 645, p. 164-168Article in journal (Refereed)
    Abstract [en]

    We have employed density functional theory (DFT) to calculate the carbon K-edge NEXAFS spectroscopy of 4-methylbenzenethiol (4-MBT) on gold surface. Polarization-dependent NEXAFS spectra of 4-MBT at different orientation angles are systematically analyzed. The π∗ resonance at 285 eV, which is the result of the transitions from 1s orbitals of carbon atoms in benzene ring to the lowest unoccupied molecular orbital (LUMO), is selected to study the orientation of 4-MBT molecule on the gold surface. In comparison with the experimental results, it is found that the benzene ring of 4-MBT is tilted by 33° with respect to the gold surface.

  • 1069.
    Song, Xiuneng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical Characterization of Functional Molecular Materials2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Nowadays, material, energy and information technologies are three pillar industries. The materials that have close relation with our life have also been the foundation for the development of energy and information technologies. As the new member of the material family, functional molecular materials have become increasingly important for many applications, for which the design and characterization by the theoretical modeling have played the vital role. In this thesis, three different categories of functional molecular materials, the endohedral fullerenes, the fullerene derivatives and the self-assembled monolayers (SAMs), have been studied by means of first principles methods.

    The non-metal endohedral fullerene N@C60 is a special endohedral fullerene that is believed to be relevant to the construction of future quantum computer. The energy landscape inside the N@C60 has been carefully explored by density functional theory (DFT) calculations. The most energy favorable potential energysurfaces (PESs) for the N atom to move within the cavity have been identified. The effect of the charging on the PESs has also been examined. It is found that the inclusion of dispersion force is essential in determining the equilibriumstructure of N@C60. Furthermore, the performance of several commonly useddensity functionals with or without dispersion correction has been verified for ten different endohedral fullerenes A@C60 with the atom A being either reactive nonmetal or nobel gases elements. It shows that the inclusion of the dispersion forcedoes provide better description for the binding energy (BE), however, none ofthem could correctly describe the energy landscape inside all the ten endohedral fullerenes exclusively. It thus calls for the further improvement of current density functionals for weak interacting systems.

    Soft X-ray spectroscopy is a powerful tool for studying the chemical and electronic structures of functional molecular materials. Theoretical calculations have been proven to be extremely useful for providing correct assignments for spectraof large systems. In this thesis, we have performed first principles simulations forthe near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectra (XPS) of fullerene derivatives and aminothiolates SAMs. Our calculatedspectra can accurately reproduce experimental results available for all the systemsunder investigations, and identify the species or structures that are responsible for those unexpected spectral features observed in experiments. We have suggested a modified building block (MBB) approach that allows to calculate NEXAFS spectraof a large number of fullerene derivatives with very small computational cost, and resolved the long standing puzzle around the experimental XPS and NEXAFS spectra of SAMs with aminothiolates.

  • 1070.
    Song, Xiuneng
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hua, Weijie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ma, Yong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Chuankui
    Shandong Normal University.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical study of core excitation spectroscopy of fullerene-based solarcell acceptorsArticle in journal (Other academic)
  • 1071.
    Song, Xiuneng
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ma, Yong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Chuankui
    Shandong Normal University, Shandong, Peoples R China.
    Dietrich, Paul M.
    BAM Fed Inst Mat Res & Testing, Berlin, Germany .
    Unger, Wolfgang E. S.
    BAM Fed Inst Mat Res & Testing, Berlin, Germany .
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Effects of Protonation, Hydrogen Bonding, and Photodamaging on X-ray Spectroscopy of the Amine Terminal Group in Aminothiolate Monolayers2012In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 116, no 23, p. 12649-12654Article in journal (Refereed)
    Abstract [en]

    The amine head group, NH2, in aminothiolate monolayers can often generate unexpectedly rich structures in its N K-edge X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra that are difficult to assign. We have carried out density functional theory (DFT) calculations to study the XPS and NEXAFS of amine head group in four different aminothiolate monolayers, namely aliphatic 11-aminoundecane-1-thiol (AUDT), aromatic 4-aminobenzenethiol (ABT) and araliphatic 4-aminophenylbutane-1-thiol (APBT) and 3-(4”-amino-1,1’:4’,1”-terphenyl-4-yl)propane-1-thiol (ATPT), with the focus on structure changes caused by protonation, hydrogen bonding and X-ray damaging. Spectra of all possible saturated and unsaturated species, as well as X-ray damage products, such as imine, nitrile, azo species and cumulative double bonds, have been thoroughly examined. It is found that extra spectral structures observed in the experimental XPS spectra are not resulted from protonation, but from the formation of a primary ammonium. The X-ray excitation can induce cross linking between two neighboring molecules to form different complexes that contribute to the π features in NEXAFS spectra.

  • 1072.
    Song, Xiuneng
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Yong, Ma
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Chuankui
    Shandong Normal University.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Energy landscape inside the cage of neutral and charged N@C602011In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 517, no 4-6, p. 199-203Article in journal (Refereed)
    Abstract [en]

    Potential energy surfaces along different escaping paths of the nitrogen atom inside the neutral and charged endohedral fullerene N@C60 have been constructed at the density functional theory level. It is found that the dispersion force plays an important role in determining the equilibrium geometry of the neutral system. The most energetic favorable escaping path is towards the center of C = C/C–C bond connecting two neighboring rings for all three systems. The rate determining potential energy surface shows a very small dependence on the charging state. The presented theoretical results should be useful for the practical applications of N@C60 in quantum computing and information.

  • 1073. Sorensen, S. L.
    et al.
    Kitajima, M.
    Tanaka, T.
    Hoshino, M.
    Tanaka, H.
    Tamenori, Y.
    Sankari, R.
    Piancastelli, M. N.
    Ueda, K.
    Velkov, Yasen
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Minkov, Ivaylo
    KTH, School of Biotechnology (BIO).
    Carravetta, V.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO).
    Electronic Doppler effect in resonant Auger decay of CO molecules upon excitation near a shake-up Pi resonance2007In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 76, no 062704Article in journal (Refereed)
    Abstract [en]

    Wepresent an experimental observation of the electronic Doppler effect inresonant Auger spectra upon core excitation slightly above the carbonK edge of the CO molecule. Thus the electronic Dopplereffect has been identified in above-threshold excitation, and in atransition of symmetry. Ab initio calculations of the potentialenergy curves of the relevant states of CO and thewave packet technique have been employed to provide a theoreticalbackground to the experimental studies. The weak feature around 299.4  eVin the photoabsorption spectrum, whose decay has been investigated bythe present experiment, is assigned to double (core-valence) excitations toC 1s shake-up states |1s1−1*2 with a strong dissociative character,and the Doppler splitting of the atomic peak has beenreproduced by the simulation.

  • 1074.
    Sousa, Leonardo
    et al.
    University of Brasilia, Brazil.
    Volpi, Riccardo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Antonio da Silva Filho, Demetrio
    University of Brasilia, Brazil.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Mobility field and mobility temperature dependence in PC61BM: A kinetic Monte-Carlo study2017In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 689, p. 74-81Article in journal (Refereed)
    Abstract [en]

    A study of electron mobility in a PCBM system is performed by means of analytical considerations and Kinetic Monte Carlo simulations. Orbital energies are calculated at the ZINDO level of theory and successively corrected considering contributions from permanent charges and polarization interactions. The relative importance of these environmental effects is analyzed in details, furthermore the predicted mobilities are compared with experimental results and similar simulations performed in C60. (C) 2017 Elsevier B.V. All rights reserved.

  • 1075. Souza De Almeida, J.
    et al.
    Da Silva, A. J.
    Norman, P.
    Persson, C.
    Ahuja, R.
    Ferreira Da Silva, A.
    Optical properties of donor-triad cluster in GaAs and GaN2002In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 81, no 17, p. 3158-3160Article in journal (Refereed)
    Abstract [en]

    The effect of the transition energy of three-donor clusters on far infrared absorption in n-type semiconductor materials has been investigated by a multiconfigurational self-consistent-field model calculation and applied to GaAs and GaN systems. We show that it is crucial to consider the many-particle correlation effects within three-donor clusters. With electron correlation taken into account, the present results support the interpretation of a very recent unidentified peak energy observed in absorption measurement of GaN as due to electronic transitions in these clusters. We also corroborate the suggestion that the X line in GaAs arises from such transitions.

  • 1076.
    Stefanov, Bozhidar
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Photocatalysis for Indoor Air Cleaning: In situ FTIR and DFT Study of Acetaldehyde Photo-Oxidation on TiO2 and Sulfate-Modified TiO22013Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Acetaldehyde is among the group of VOC’s causing the so-called "sick building" syndrome. WHO has estimated that this problem, related to the indoor air-quality, affects one third of all buildings worldwide. TiO2 is an attractive material for the photocatalytic removal of VOC’s in the indoor environment. Deactivation of the photocatalyst is, however, commonly deteriorating its performance over usage time, and ways to mitigate this problem must be invented. Thus modification of TiO2 surface properties is an area of considerable interest. It is possible to enhance the surface acidity of TiO2 through sulfation which effectively lowers the affinity of acidic intermediates. In addition, surface modification of photocatalysts may be used to control adsorption and wetting properties, as well as providing scavengers for photo-excited electrons and holes to suppress unwanted recombination and increase the quantum yield.

    In this work the interaction of gaseous acetaldehyde with TiO2 and SO4-modified anatase TiO2 is investigated. Films were prepared by doctor-blading of commercial TiO2 nanoparticle suspensions and characterized by means of XRD and TEM. The adsorption and photo-oxidation of acetaldehyde were studied with in situ FTIR spectroscopy and DFT calculations.

    On TiO2 nanoparticles, which exhibit predominantly (101) facets, in situ FTIR shows that acetaldehyde adsorption is accompanied by the appearance of a hitherto non-assigned absorption band at 1643 cm−1, shown to be due to acetaldehyde dimers. The results are supported by DFT calculations performed at the M06/6-31++G** level. Vibrational frequencies calculated within a partially relaxed cluster model for molecular acetaldehyde and its dimer, and for the corresponding adsorbed species on the anatase (101) surface, were in good agreement with the experimental results. Inclusion of dimer formation is shown to give an improved description of the reaction kinetics on TiO2.

    Based on mode-resolved in situ FTIR, kinetic models were constructed, which describe the observed photo-oxidation surface products on both TiO2 and SO4-modified TiO2. The surface concentration of main surface products and corresponding reaction rates were determined. It was observed that formate is the major reaction product, whose further oxidation limits the complete oxidation to gaseous species. Formate thus acts as an inhibitor, blocking adsorption sites, and is responsible for photocatalyst deactivation. The oxidation reaction is characterized by two reaction pathways, one fast and one slow, associated with two types of surface reaction sites. On the SO4-modified TiO2 fewer intermediates are accumulated, and it resists deactivation much better compared with the pure TiO2 photocatalyst, which is attributed to the acidic character of the modified surface. The results presented here are of interest for applications to photocatalytic air purification, and surfaces with controlled wettability.

  • 1077.
    Stefanov, Bozhidar
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Photocatalytic TiO2 thin films for air cleaning: Effect of facet orientation, chemical functionalization, and reaction conditions2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Poor indoor air quality is a source of adverse health effects. TiO2 coatings deposited on well-illuminated surfaces, such as window panes, can be used to fully mineralize indoor air pollutants by photocatalysis. In such applications it is important to ensure stable photocatalytic activity for a wide range of operating conditions, such as relative humidity and temperature, and to avoid deactivation of the catalyst.

    In this thesis photocatalytic removal of the indoor-pollutant acetaldehyde (CH3CHO) on nanostructured TiO2 films is investigated, and in particular it is proposed how such films can be modified and operated for maximum performance. Catalyst deactivation can be reduced by purposefully changing the surface acidity of TiO2 by covalently attaching SO4 to the surface. Moreover, the overall photocatalytic activity on anatase TiO2 films can be improved by increasing the fraction of exposed reactive {001} surfaces, which otherwise are dominated by {101} surfaces.

    In the first part of the thesis mode-resolved in-situ FTIR is used to elucidate the reaction kinetics of CH3CHO adsorption and photo-oxidation on the TiO2 and SO4 – modified TiO2 surfaces. Surface concentrations of main products and corresponding reaction rates were determined. Formate is the major reaction product, whose further oxidation limits the complete oxidation to gaseous species, and is responsible for photocatalyst deactivation by site inhibition. The oxidation reaction is characterized by two reaction pathways, which are associated with two types of surface reaction sites. On the sulfate modified TiO2 catalyst fewer intermediates are accumulated, and this catalyst resists deactivation much better than pure TiO2. A hitherto unknown intermediate – surface-bound acetaldehyde dimer with an adsorption band at 1643 cm−1 was discovered, using interplay between FTIR spectroscopy and DFT calculations.

    The second part of the thesis treats the effect of increasing the relative abundance of exposed {001} facets on the photocatalytic activity of anatase TiO2 films prepared by DC magnetron sputtering. A positive effect was observed both for liquid-phase photo-oxidation of methylene blue, and for gas-phase photocatalytic removal of CH3CHO. In both cases it was found that the exposed {001} surfaces were an order of magnitude more reactive, compared to the {101} ones. Furthermore, it was found that the reactive films were more resilient towards deactivation, and exhibited almost unchanged activity under varying reaction conditions. Finally, a synergetic effect of SO4 – modification and high fraction of exposed {001} surfaces was found, yielding photocatalysts with sustained high activity.

    The results presented here for facet controlled and chemically modified TiO2 films are of interest for applications in the built environment for indoor air purification and as self-cleaning surfaces.

  • 1078.
    Stefanov, Bozhidar I
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Topalian, Zareh
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Granqvist, Claes-Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Österlund, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Acetaldehyde adsorption and condensation on anatase TiO2: Influence of acetaldehyde dimerization2014In: Journal of Molecular Catalysis A: Chemical, ISSN 1381-1169, E-ISSN 1873-314X, Vol. 381, p. 77-88Article in journal (Refereed)
    Abstract [en]

    Conversion of acetaldehyde to crotonaldehyde on anatase TiO2 films was studied by in situ Fourier transform infrared spectroscopy (FTIR) and by density functional theory (DFT) calculations. In situ FTIR showed that acetaldehyde adsorption is accompanied by the appearance of a hitherto non-assigned absorption band at 1643 cm−1, which is shown to be due to acetaldehyde dimers. The results were supported by DFT calculations. Vibrational frequencies calculated within a partially relaxed cluster model for molecular acetaldehyde and its dimer, and for the corresponding adsorbed species on the anatase (101) surface, were in good agreement with experimental results. A kinetic model was constructed based on the combined FTIR and DFT results, and was shown to explain the essential features of the acetaldehyde condensation reaction.

  • 1079.
    Stegeby, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    MATTER-ANTIMATTER INTERACTIONS: The hydrogen-antihydrogen system and antiproton-matter interactions2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Ever since antiparticles were discovered their nature has been something of a mystery. They were postulated to be identical to regular particles except for having opposite charge, but this would imply that an equal amount of antiparticles and particles should have been created at the beginning of time. However, everywhere we look the Universe seems to be constituted of regular particles, giving rise to the question whether there is something else that differentiates antiparticles from regular particles, or if there is something amiss in the Standard Model of particle physics.

    This thesis focuses on a central system of study in this field, the hydrogen-antihydrogen system and the theory surrounding it, as well as an expansion into systems with an antiproton interacting with small molecules, bridging the fields of quantum physics and quantum chemistry.

    Methods expanding on the Born-Oppenheimer approximation for the interaction between the two atoms are presented. The resulting 2-body interaction potential is then used for creating a part of the basis in a non-adiabatic 4-body method in order to look for resonance states whose existence could impact cross-sections of hydrogen-antihydrogen scattering. The eigenfunctions obtained from the non-adiabatic method are used by extracting the 2-body hadronic density function and comparing it to the adiabatic wave function, for measuring the adiabaticity of the hydrogen-antihydrogen system.

    The antiproton-matter interaction is first investigated by a quantum dynamical approach of an antiproton scattering on molecular hydrogen, common products in high-energy collision experiments, continued by a study of the potential energy surfaces of an antiproton interacting with a range of functional groups present in the human body.

  • 1080.
    Stegeby, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Overview Of Antiproton Affinities For Functional Groups Relevant In Particle-Beam Cancer TherapyIn: Cancer Reports, ISSN 2573-8348Article in journal (Other academic)
    Abstract [en]

    The potential energy surfaces for an antiproton in the vicinity of common functional groups inthe human body has been calculated at the CASSCF/CASPT2 level. A comparison of the impacton the antiproton affinity from atomic number, type of interatomic bond, bond polarization due toelectronegativity and charge is presented. The presented overview study is targeted at understandingthe effects involved in antiproton particle-beam cancer therapy, primarily in the ultra-low energycollision regime, but also as a starting point for quantum dynamical treatments.

  • 1081.
    Stegeby, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Kowalewski, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Piszczatowski, Konrad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Wave packet simulations of antiproton scattering on molecular hydrogen2015In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 48, no 19, p. 195204:1-7, article id 195204Article in journal (Refereed)
  • 1082.
    Stegeby, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Piszczatowski, Konrad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Froelich, Piotr
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Variational calculations for the hydrogen-antihydrogen system with a mass-scaled Born-Oppenheimer potential2012In: CENTRAL EUROPEAN JOURNAL OF PHYSICS, ISSN 1895-1082, Vol. 10, no 5, p. 1038-1053Article in journal (Refereed)
    Abstract [en]

    The problem of proton-antiproton motion in the H- system is investigated by means of the variational method. We introduce a modified nuclear interaction through mass-scaling of the Born-Oppenheimer potential. This improved treatment of the interaction includes the nondivergent part of the otherwise divergent adiabatic correction and shows the correct threshold behaviour. Using this potential we calculate the vibrational energy levels with angular momentum 0 and 1 and the corresponding nuclear wave functions, as well as the S-wave scattering length. We obtain a full set of all bound states together with a large number of discretized continuum states that might be utilized in variational four-body calculations. The results of our calculations gives an indication of resonance states in the hydrogen-antihydrogen system.

  • 1083.
    Stegeby, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Piszczatowski, Konrad
    Yamashita, Takuma
    Two-Body Hadronic Densities From The Four-Body Wave Functions For The Hydrogen-Antihydrogen SystemManuscript (preprint) (Other academic)
    Abstract [en]

    The quantum-mechanical four-body problem for the hydrogen-antihydrogen system has beensolved by means of the variational implementation of the coupled-arrangement channel method.The wave functions have been formed using the Gaussian expansion method (GEM) in Jacobi co-ordinates; they explicitly include components corresponding to the rearrangement from hydrogen and antihydrogen (H + H') into Protonium and Positronium (Pn + Ps). We analyse the solutionsbelonging to the discretized spectrum of the 4-body eigenvalue problem at energies correspondingto the low energy H { Hcollisions. Two-body nuclear correlation functions are calculated from thefour-body wave functions, as to investigate the proton-antiproton motion in the region of rearrangement from H+H' to Pn+Ps. We monitor the adiabatic versus nonadiabatic behavior of the system asa function of internuclear separation and nd that outside the rearrangement region the adiabaticdescription is quite adequate. The nonadiabatic behavior signicantly in uences the nuclear motionin the rearrangement region and reduces the rate of proton-antiproton annihilation in low-energy hydrogen-antihydrogen collisions.

  • 1084.
    Steiner, Emilie
    et al.
    Karolinska Institute, Sweden.
    Schlagnitweit, Judith
    Karolinska Institute, Sweden.
    Lundström, Patrik
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Petzold, Katja
    Karolinska Institute, Sweden.
    Capturing Excited States in the Fast-Intermediate Exchange Limit in Biological Systems Using (HNMR)-H-1 Spectroscopy2016In: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, ISSN 1433-7851, Vol. 55, no 51, p. 15869-15872Article in journal (Refereed)
    Abstract [en]

    Changes in molecular structure are essential for the function of biomolecules. Characterization of these structural fluctuations can illuminate alternative states and help in correlating structure to function. NMR relaxation dispersion (RD) is currently the only method for detecting these alternative, high-energy states. In this study, we present a versatile H-1 R-1 RD experiment that not only extends the exchange timescales at least three times beyond the rate limits of C-13/N-15 R-1 and ten times for CPMG experiments, but also makes use of easily accessible probes, thus allowing a general description of biologically important excited states. This technique can be used to extract chemical shifts for the structural characterization of excited states and to elucidate complex excited states.

  • 1085. Stenlid, Joakim H.
    et al.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Nucleophilic Aromatic Substitution Reactions Described by the Local Electron Attachment Energy2017In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, no 6, p. 3072-3083Article in journal (Refereed)
    Abstract [en]

    A local multiorbital electrophilicity descriptor, the local electron attachment energy [E(r)], is used to study the nucleophilic aromatic substitution reactions of SNAr and VNS (vicarious nucleophilic substitution). E(r) considers all virtual orbitals below the free electron limit and is determined on the molecular isodensity contour of 0.004 atomic units. Good (R-2 = 0.83) to excellent (R-2 = 0.98) correlations are found between descriptor values and experimental reactivity data for six series of electron deficient arenes. These include homo- and heteroarenes, rings of five to six atoms, and a variety of fluorine, bromine, and hydride leaving groups. The solvent, temperature, and nucleophile are in addition varied across the series. The surface E(r) [E-s(r)] is shown to provide reactivity predictions better than those of transition-state calculations for a concerted SNAr reaction with a bromine substantially stronger than those of LUMO energies, and is overall more reliable than the molecular electrostatic potential. With the use of E-s(r), one can identify the various electrophilic sites within a molecule and correctly predict isomeric distributions. Since the calculations of E-s(r) are computationally inexpensive, the descriptor offers fast but accurate reactivity predictions for the important nucleophilic aromatic substitution class of reactions. Applications in, e.g., drug discovery, synthesis, and toxicology studies are envisaged.

  • 1086.
    Stenrup, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Photo-induced molecular processes and charge recombination reactions driven by non-adiabatic couplings2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on a number of theoretical studies of molecular processes in which non-adiabatic effects play a crucial role. The main part is devoted to the photophysics and photochemistry of five-membered aromatic heterocyclic compounds, with particular focus on furan and thiophene. These species absorb light in the UV region of the spectrum, but exhibits neither fluorescence nor phosphorescence. A plausible explanation for this is the presence of very fast radiationless deactivation mechanisms that depopulate the excited states before emission can occur. In the present thesis, several possible such mechanisms are considered based on the results of static electronic structure calculations as well as mixed quantum-classical dynamics simulations. A common feature of the investigated pathways is the presence of easily accessible conical intersections (surface crossings) through which non-adiabatic population transfer to the electronic ground state may take place. Also considered in the present work are the bond-breaking/bond-forming processes that are expected to follow once the ground state has been reached.

    Another prominent example of non-adiabatic processes is charge recombination reactions involving either two oppositely charged ions or a cation and an electron. Here, the reactants and products belong to different electronic states of the system as a whole and therefore a non-adiabatic transition is necessary for the recombination to occur. Two such processes are considered in the present thesis; mutual neutralization of oppositely charged hydrogen ions and dissociative recombination of the formyl and iso-formyl cations. The cross sections (rate coefficients) and underlying mechanisms of these reactions are investigated at a fully quantum mechanical level.

  • 1087.
    Stenrup, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Radiationless deactivation and intermediate formation in photo-excited thiopheneManuscript (preprint) (Other academic)
  • 1088.
    Stenrup, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Theoretical study of the radiationless deactivation mechanisms of photo-excited thiophene2012In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 397, p. 18-25Article in journal (Refereed)
    Abstract [en]

    The radiationless deactivation mechanisms of photo-excited thiophene have been studied using the multi-reference second-order perturbation theory and linear response coupled cluster methods. The electronic spectrum has been established and various minimum energy structures and conical intersections involving the ground and lowest singlet excited states have been characterized. Simplified reaction paths connecting the optimized geometries have been calculated as well. Based on these investigations, several deactivation mechanisms have been identified leading from the lowest bright 1ππ states back to the electronic ground state. The excited state depletion in each case is possible due to the existence of low-lying conical intersections formed by either cleavage of one of the CS bonds or out-of-plane deformations of the aromatic ring. The deactivation mechanisms suggested in this work should provide some very efficient decay channels after excitation into the first UV absorption band of thiophene, and are good candidates to explain why this compound is non-fluorescent.

  • 1089.
    Stenrup, Michael
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Larson, Åsa
    Stockholm University, Faculty of Science, Department of Physics.
    A computational study of radiationless deactivation mechanisms of furan2011In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 379, no 1-3, p. 6-12Article in journal (Refereed)
    Abstract [en]

    Possible mechanisms for the radiationless deactivation of photo-excited furan have been investigated using high-level electronic structure methods. Two different conical intersections between the S0 and S1 electronic states have been characterized, both involving various degrees of CO bond cleavage. One of these corresponds to a planar ring-opened structure and the other to an asymmetric ring-puckered structure. Calculations have been performed in order to establish the vertical electronic spectrum and to investigate the behaviour of the potential energy surfaces as the intersections are approached. The present results indicate that both crossings can be accessed through exothermic and barrierless processes after vertical excitation into the optically bright S2(ππ∗) state. These features make them good candidates to account for efficient radiationless deactivation in furan. The deactivation pathways considered in the present work are close analogues of those previously described for other five-membered heterocycles.

  • 1090. Stich, Troy A.
    et al.
    Krzystek, J.
    Mercado, Brandon Q.
    McAlpin, J. Gregory
    Ohlin, C. Andre
    Olmstead, Marilyn M.
    Casey, William H.
    Britt, R. David
    Structural insights into [Co4O4(C5H5N)(4)(CH3CO2)(4)](+), a rare Co(IV)-containing cuboidal complex2013In: Polyhedron, ISSN 0277-5387, E-ISSN 1873-3719, Vol. 64, no SI, p. 304-307Article in journal (Refereed)
    Abstract [en]

    We report high-frequency (up to 219 GHz) and correspondingly high-field electron paramagnetic resonance spectra and X-ray crystal structure of [Co4O4(pyridine)(4)(acetate)(4)](+) ([Co4O4(py)(4)(OAc)(4)](+)) that serves as a structural and spectroscopic model of cobalt-oxide films that are capable of oxidizing water. These results are, in large part, consistent with those from our earlier, lower-frequency study and serve to benchmark future high-field studies on paramagnetic states of the catalyst film. (C) 2013 Published by Elsevier Ltd.

  • 1091.
    Ståhle, Jonas
    KTH, School of Chemical Science and Engineering (CHE).
    Computational chemical investigation of factors affecting the reactivity of the hetero Diels-Alder reaction2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Recent research has shown that small hydrogen bonding catalysts can catalyze the hetero Diels-Alder reaction. In this thesis such hydrogen bonding catalysts in conjunction with varying functional groups and their effect on the hetero Diels-Alder reaction have been investigated. The influence of the different solvents has been investigated as well. The activation barriers for the different region- and stereo isomeric pathways have been compared in order to determine the stereo specificity of the reactions. These calculations have been done using the B3LYP functional for the geometry optimizations and then M06-2X for single point calculations. For the solvated cases the cPCM model and the M06-2X functional were used. It was shown that for the catalyzed systems bulkier groups in the endo position tend to have a lower activation barrier, allowing for control over the stereoselectivity. Electron withdrawing groups have an activating effect and are also synergistic with the hydrogen bonding catalysts. The solvent with the lowest dielectric constant gave the lowest activation barrier.

  • 1092. Støchkel, K.
    et al.
    Hansen, C. N.
    Houmøller, J.
    Nielsen, L. M.
    Anggara, K.
    Linares, M.
    Norman, Patrick
    Linköping University, Sweden.
    Nogueira, F.
    Maltsev, O. V.
    Hintermann, L.
    Nielsen, S. B.
    Naumov, P.
    Milne, B. F.
    On the influence of water on the electronic structure of firefly oxyluciferin anions from absorption spectroscopy of bare and monohydrated ions in vacuo2013In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, no 17, p. 6485-6493Article in journal (Refereed)
    Abstract [en]

    A complete understanding of the physics underlying the varied colors of firefly bioluminescence remains elusive because it is difficult to disentangle different enzyme-lumophore interactions. Experiments on isolated ions are useful to establish a proper reference when there are no microenvironmental perturbations. Here, we use action spectroscopy to compare the absorption by the firefly oxyluciferin lumophore isolated in vacuo and complexed with a single water molecule. While the process relevant to bioluminescence within the luciferase cavity is light emission, the absorption data presented here provide a unique insight into how the electronic states of oxyluciferin are altered by microenvironmental perturbations. For the bare ion we observe broad absorption with a maximum at 548 ± 10 nm, and addition of a water molecule is found to blue-shift the absorption by approximately 50 nm (0.23 eV). Test calculations at various levels of theory uniformly predict a blue-shift in absorption caused by a single water molecule, but are only qualitatively in agreement with experiment highlighting limitations in what can be expected from methods commonly used in studies on oxyluciferin. Combined molecular dynamics simulations and time-dependent density functional theory calculations closely reproduce the broad experimental peaks and also indicate that the preferred binding site for the water molecule is the phenolate oxygen of the anion. Predicting the effects of microenvironmental interactions on the electronic structure of the oxyluciferin anion with high accuracy is a nontrivial task for theory, and our experimental results therefore serve as important benchmarks for future calculations.

  • 1093. Sulzer, D.
    et al.
    Norman, Patrick
    Linköping University, Sweden.
    Saue, T.
    Atomic C 6 dispersion coefficients: A four-component relativistic Kohn-Sham study2012In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 110, no 19-20, p. 2535-2541Article in journal (Refereed)
    Abstract [en]

    We present C 6 homo- and heteroatomic dispersion coefficients for all closed-shell atoms of the periodic table based on dipole-dipole polarizabilities at imaginary frequencies calculated using our recent extension of the complex polarization propagator approach to the four-component relativistic Kohn-Sham approach. Lack of proper reference data bars definite conclusions as to which density functional shows the overall best performance, and we therefore call for state-of-the-art wave function-based correlated calculations of dispersion coefficients. Scalar relativistic effects are significant already for elements as light as zinc, whereas spin-orbit effects must be taken into account only for very heavy elements.

  • 1094.
    Sun, Bing
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Mindemark, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Morozov, Evgeny V.
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, Teknikringen 36, SE-10044 Stockholm, Sweden.
    Costa, Luciano T.
    Univ Fed Fluminense, Inst Quim, Dept Quim Fis, Outeiro Sao Joao Batista S-N, BR-24020150 Niteroi, RJ, Brazil.
    Bergman, Martin
    Chalmers, Dept Phys, SE-41296 Gothenburg, Sweden.
    Johansson, Patrik
    Chalmers, Dept Phys, SE-41296 Gothenburg, Sweden.
    Fang, Yuan
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, Teknikringen 36, SE-10044 Stockholm, Sweden.
    Furó, István
    KTH Royal Inst Technol, Dept Chem, Div Appl Phys Chem, Teknikringen 36, SE-10044 Stockholm, Sweden.
    Brandell, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Ion transport in polycarbonate based solid polymer electrolytes: experimental and computational investigations2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 14, p. 9504-9513Article in journal (Refereed)
    Abstract [en]

    Among the alternative host materials for solid polymer electrolytes (SPEs), polycarbonates have recently shown promising functionality in all-solid-state lithium batteries from ambient to elevated temperatures. While the computational and experimental investigations of ion conduction in conventional polyethers have been extensive, the ion transport in polycarbonates has been much less studied. The present work investigates the ionic transport behavior in SPEs based on poly(trimethylene carbonate) (PTMC) and its co-polymer with epsilon-caprolactone (CL) via both experimental and computational approaches. FTIR spectra indicated a preferential local coordination between Li+ and ester carbonyl oxygen atoms in the P(TMC20CL80) co-polymer SPE. Diffusion NMR revealed that the co-polymer SPE also displays higher ion mobilities than PTMC. For both systems, locally oriented polymer domains, a few hundred nanometers in size and with limited connections between them, were inferred from the NMR spin relaxation and diffusion data. Potentiostatic polarization experiments revealed notably higher cationic transference numbers in the polycarbonate based SPEs as compared to conventional polyether based SPEs. In addition, MD simulations provided atomic-scale insight into the structure-dynamics properties, including confirmation of a preferential Li+-carbonyl oxygen atom coordination, with a preference in coordination to the ester based monomers. A coupling of the Li-ion dynamics to the polymer chain dynamics was indicated by both simulations and experiments.

  • 1095.
    Sun, Jianwu
    et al.
    Groupe d’Etudes des Semiconducteurs, Université Montpellier 2 and CNRS, cc 074‐GES, 34095 Montpellier Cedex 5, France.
    Ivanov, Ivan Gueorguiev
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Juillaguet, S.
    Groupe d’Etudes des Semiconducteurs, Université Montpellier 2 and CNRS, cc 074‐GES, 34095 Montpellier Cedex 5, France.
    Camassel, J.
    Groupe d’Etudes des Semiconducteurs, Université Montpellier 2 and CNRS, cc 074‐GES, 34095 Montpellier Cedex 5, France.
    Splitting of type-I (N-B, P-Al) and type-II (N-Al, N-Ga) donor-acceptor pair spectra in 3C-SiC2011In: Physical Review B, ISSN 2469-9950, Vol. 83, no 19-15Article in journal (Refereed)
    Abstract [en]

    Discrete series of lines have been observed for many years in donor-acceptor pair (DAP) spectra in 3C-SiC. In this work, the splitting of both type-I (N-B, P-Al) and type-II (N-Al, N-Ga) DAP spectra in 3C-SiC has been systematically investigated by considering the multipole terms. For type-I spectra, in which either N or B substitutes on C sites or P and Al replace Si, the splitting energy of the substructure for a given shell is almost the same for both pairs. For type-II spectra, in which N is on the C site while Al and Ga acceptors replace Si, we find that, when compared with literature data, the splitting energy for a given shell is almost independent of the identity of the acceptor. For both type-I and type-II spectra, this splitting energy can be successfully explained by the octupole term V 3   alone with k 3    =   −2 × 10 5    Å 4   meV. Comparing the experimental donor and acceptor binding energies with the values calculated by the effective-mass model, this suggests that the shallow donor (N,P) ions can be treated as point charges while the charge distribution of the acceptor ions (Al,Ga,B) is distorted in accord with the T d   point group symmetry, resulting in a considerable value for k 3   . This gives a reasonable explanation for the observed splitting energies for both type-I and type-II DAP spectra.

  • 1096.
    Svensson, Mats
    Stockholm University, Faculty of Science.
    Modelling organometallic reactions: a quantum chemical study of some oxidative addition reactions1994Doctoral thesis, comprehensive summary (Other academic)
  • 1097. Sylvester-Hvid, K. O.
    et al.
    Mikkelsen, K. V.
    Jonsson, D.
    Norman, P.
    Ågren, H.
    Cubic optical response of molecules in a nonequilibrium and equilibrium solvation model1999In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, no 42, p. 8375-8383Article in journal (Refereed)
    Abstract [en]

    The cubic response equations governing nonequilibrium and equilibrium solvation in the continuum approach are derived and implemented. We consider solvent effects on the frequency dependent second hyperpolarizability. We illustrate the effects of optical and static dielectric constants through sample calculations on H2O and H2CO.

  • 1098. Sylvester-Hvid, K. O.
    et al.
    Mikkelsen, K. V.
    Jonsson, D.
    Norman, P.
    Ågren, H.
    Nonlinear optical response of molecules in a nonequilibrium solvation model1998In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 109, no 13, p. 5576-5584Article in journal (Refereed)
    Abstract [en]

    The response equations governing nonequilibrium solvation in the continuum approach are derived and implemented for second order in response theory. Applications to a simple benchmark system consisting of a solvated water molecule are presented. We consider the role of nonequilibrium solvent configurations on the first hyperpolarizability. Effects of solvation parameters, such as optical and static dielectric constants, and frequency dispersion are discussed.

  • 1099.
    Szabo, Peter
    et al.
    Department of General and Inorganic Chemistry, Institute of Chemistry, University of Pannonia.
    Lendvay, György
    Department of General and Inorganic Chemistry, Institute of Chemistry, University of Pannonia.
    Dynamics of Complex-Forming Bimolecular Reactions: A Comparative Theoretical Study of the Reactions of H Atoms with O2(3Σg–) and O2(1Δg)2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 50, p. 12485-12497Article in journal (Refereed)
    Abstract [en]

    The atomic-level mechanism of the reaction of H atoms with triplet and singlet molecular oxygen, H(2S) + O2(3Σg–) → O(3P) + OH(2Πg) (R1) and H(2S) + O2(1Δg) → O(3P) + OH(2Πg) (R2) is analyzed in terms of the topology of the potential energy surfaces (PES) of the two reactions. Both PES exhibit a deep potential well corresponding to the ground and first excited electronic state of HO2. The ground-state reaction is endothermic with no barrier on either side of the well; the excited-state reaction is exothermic with a barrier in the entrance valley of the PES. The differences of the PES are manifested in properties such as the excitation functions, which show reaction R1 to be much slower and the effect of rotational excitation on reactivity, which speeds up reaction R1 and has little effect on R2. Numerous common dynamics features arise from the presence of the deep potential well on the PES. Such are the significant role of isomerization (for example, 90% of reactive collisions in R2 involve at least one H atom transfer from one of the O atoms to the other in reaction R2), which is shown to give rise to a significant rotational excitation of the product OH radicals. Common is the significant sideways scattering of the products that originates from collisions in propeller-type arrangements induced by the presence of two bands of acceptance around the O2 molecule. The HO2 complex in both reactions proves to behave nonstatistically, with signatures of the dynamics in lifetime distributions, angular distributions, opacity functions, and product quantum-state distributions.

  • 1100. Såthe, Conny
    et al.
    Guimaraes, Freddy
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rubensson, Jan-Erik
    Nordgren, J.
    Agui, A.
    Guo, J.
    Ekström, U.
    Norman, P.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Resonant LII, III x-ray raman scattering from HCIManuscript (Other academic)
19202122232425 1051 - 1100 of 1257
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