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  • 1.
    Agosta, Lorenzo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Dzugutov, Mikhail
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Supercooled liquid-like dynamics in water near a fully hydrated titania surface: Decoupling of rotational and translational diffusion2021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 9, article id 094708Article in journal (Refereed)
    Abstract [en]

    We report an ab initio molecular dynamics (MD) simulation investigating the effect of a fully hydrated surface of TiO2 on the water dynamics. It is found that the universal relation between the rotational and translational diffusion characteristics of bulk water is broken in the water layers near the surface with the rotational diffusion demonstrating progressive retardation relative to the translational diffusion when approaching the surface. This kind of rotation-translation decoupling has so far only been observed in the supercooled liquids approaching glass transition, and its observation in water at a normal liquid temperature is of conceptual interest. This finding is also of interest for the application-significant studies of the water interaction with fully hydrated nanoparticles. We note that this is the first observation of rotation-translation decoupling in an ab initio MD simulation of water.

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  • 2.
    Agosta, Lorenzo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Metere, Alfredo
    Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Phys Div, Livermore, CA 94550 USA.
    Oleynikov, Peter
    Shanghai Tech Univ, Sch Phys Sci & Technol, Shanghai, Peoples R China.
    Dzugutov, Mikhail
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Self-assembly of a triply periodic continuous mesophase with Fddd symmetry in simple one-component liquids2020In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 19, article id 191101Article in journal (Refereed)
    Abstract [en]

    Triply periodic continuous morphologies (networks) arising as a result of the microphase separation in block copolymer melts have so far never been observed self-assembled in systems of particles with spherically symmetric interaction. We report a molecular dynamics simulation where two simple one-component liquids form upon cooling an equilibrium network with the Fddd space group symmetry. This complexity reduction in the liquid network formation in terms of the particle geometry and the number of components evidences the generic nature of this class of phase transition, suggesting opportunities for producing these structures in a variety of new systems.

  • 3. Ahmadi, Sareh
    et al.
    Agnarsson, Bjorn
    Bidermane, Ieva
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Wojek, Bastian M.
    Noel, Quentin
    Sun, Chenghua
    Gothelid, Mats
    Site-dependent charge transfer at the Pt(111)-ZnPc interface and the effect of iodine2014In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 17, p. 174702-Article in journal (Refereed)
    Abstract [en]

    The electronic structure of ZnPc, from sub-monolayers to thick films, on bare and iodated Pt(111) is studied by means of X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, and scanning tunneling microscopy. Our results suggest that at low coverage ZnPc lies almost parallel to the Pt(111) substrate, in a non-planar configuration induced by Zn-Pt attraction, leading to an inhomogeneous charge distribution within the molecule and an inhomogeneous charge transfer to the molecule. ZnPc does not form a complete monolayer on the Pt surface, due to a surface-mediated intermolecular repulsion. At higher coverage ZnPc adopts a tilted geometry, due to a reduced molecule-substrate interaction. Our photoemission results illustrate that ZnPc is practically decoupled from Pt, already from the second layer. Pre-deposition of iodine on Pt hinders the Zn-Pt attraction, leading to a non-distorted first layer ZnPc in contact with Pt(111)-I(root 3x root 3) or Pt(111)-I(root 7x root 7), and a more homogeneous charge distribution and charge transfer at the interface. On increased ZnPc thickness iodine is dissolved in the organic film where it acts as an electron acceptor dopant. (C) 2014 AIP Publishing LLC.

  • 4. Ahmadi, Sareh
    et al.
    Shariati, M. Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Yu, Shun
    Göthelid, Mats
    Molecular layers of ZnPc and FePc on Au(111) surface: Charge transfer and chemical interaction2012In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, no 8, p. 084705-Article in journal (Refereed)
    Abstract [en]

    We have studied zinc phthalocyanine (ZnPc) and iron phthalocyanine (FePc) thick films and monolayers on Au(111) using photoelectron spectroscopy and x-ray absorption spectroscopy. Both molecules are adsorbed flat on the surface at monolayer. ZnPc keeps this orientation in all investigated coverages, whereas FePc molecules stand up in the thick film. The stronger inter-molecular interaction of FePc molecules leads to change of orientation, as well as higher conductivity in FePc layer in comparison with ZnPc, which is reflected in thickness-dependent differences in core-level shifts. Work function changes indicate that both molecules donate charge to Au; through the pi-system. However, the Fe3d derived lowest unoccupied molecular orbital receives charge from the substrate when forming an interface state at the Fermi level. Thus, the central atom plays an important role in mediating the charge, but the charge transfer as a whole is a balance between the two different charge transfer channels; pi-system and the central atom.

  • 5. Ajitha, D
    et al.
    Wierzbowska, M
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Malmqvist, P A
    Spin-orbit ab initio study of alkyl halide dissociation via electronic curve crossing2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 121, no 12, p. 5761-5766Article in journal (Refereed)
    Abstract [en]

    An ab initio study of the role of electronic curve crossing in the photodissociation dynamics of the alkyl halides is presented. Recent experimental studies show that curve crossing plays a deterministic role in deciding the channel of dissociation. Coupled repulsive potential energy curves of the low-lying n-sigma* states are studied including spin-orbit and relativistic effects. Basis set including effect of core correlation is used. Ab initio vertical excitation spectra of CH3I and CF3I are in agreement with the experimental observation. The curve crossing region is around 2.371 Angstrom for CH3I and CF3I. The potential curves of the repulsive excited states have larger slope for CF3I, suggesting a higher velocity and decreased intersystem crossing probability on fluorination. We also report the potential curves and the region of curve crossing for CH3Br and CH3Cl.

  • 6. Al-Abdalla, A
    et al.
    Barandiaran, Z
    Seijo, L
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Ab initio model potential embedded-cluster study of the ground and lowest excited states of Cr3+ defects in the elpasolites Cs2NaYCl6 and Cs2NaYBr61998In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 108, p. 2005-2014Article in journal (Refereed)
    Abstract [en]

    In this paper we present the results of an ab initio model potential (AIMP) embedded-cluster study of the ground and lowest excited states of Cr3+ defects in the elpasolites Cs2NaYCl6 and Cs2NaYBr6; complete active space SCF (CASSCF) and averaged coupled-pair functional (ACPF) calculations are performed on CrCl63- and CrBr63- clusters embedded in ab initio model potential representations of the surrounding lattices Cs2NaYCl6 and Cs2NaYBr6. The experimental structural data are revisited and some new results are found which differ significantly from those available in the literature. The calculated local structure parameters and electronic transition energies which can be compared to experiments are found to be very good; new structural and spectroscopic results are produced which have been neither measured nor calculated, which are complementary to the available ones, and whose quality is expected to be high as well. In particular, the question of the competition of the excited-state absorptions with the potential vibronic laser emission has been adressed: A considerable overlap between the broad E-2(g) –> (2)A(1g) excited-state absorption and (4)A(2g) <– T-4(2g) emission bands is predicted in both materials, which must result in a reduction in the emission efficiency. Finally, it is shown that the quantum mechanical embedding effects due to the fact that the external Cs+, Na+, Y3+, Cl-, and Br- ions are not point charges, are non-negligible; lacking of these effects must be one of the reasons which make previous Density Functional Theory calculations show significantly larger discrepancies with the available experiments.

  • 7.
    Alfredsson, Ylvi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Brena, Barbara
    Nilson, Katharina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Åhlund, John
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Kjeldgaard, Lisbeth
    Nyberg, Mats
    Luo, Yi
    Mårtensson, Nils
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Sandell, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Puglia, Carla
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Siegbahn, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Electronic structure of a vapor-deposited metal-free phthalocyanine thin film2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 21, p. 214723-Article in journal (Refereed)
    Abstract [en]

    The electronic structure of a vapor-sublimated thin film of metal-free phthalocyanine(H2Pc) is studied experimentally and theoretically. An atom-specific picture of the occupied and unoccupied electronic states is obtained using x-ray-absorption spectroscopy (XAS), core- and valence-level x-ray photoelectron spectroscopy (XPS), and density-functional theory (DFT) calculations. The DFT calculations allow for an identification of the contributions from individual nitrogen atoms to the experimental N1sXAS and valence XPS spectra. This comprehensive study of metal-free phthalocyanine is relevant for the application of such molecules in molecular electronics and provides a solid foundation for identifying modifications in the electronic structure induced by various substituent groups.

  • 8.
    Allum, Felix
    et al.
    Univ Oxford, Chem Res Lab, Dept Chem, Oxford OX1 3TA, England.
    Burt, Michael
    Univ Oxford, Chem Res Lab, Dept Chem, Oxford OX1 3TA, England.
    Amini, Kasra
    Univ Oxford, Chem Res Lab, Dept Chem, Oxford OX1 3TA, England.
    Boll, Rebecca
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Kockert, Hansjochen
    Univ Oxford, Chem Res Lab, Dept Chem, Oxford OX1 3TA, England.
    Olshin, Pavel K.
    St Petersburg State Univ, 7-9 Univ Skaya Nab, St Petersburg 199034, Russia.
    Bari, Sadia
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Bomme, Cedric
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Brausse, Felix
    Max Born Inst, Max Born Str 2A, D-12489 Berlin, Germany.
    de Miranda, Barbara Cunha
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Duesterer, Stefan
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Erk, Benjamin
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Geleoc, Marie
    Univ Paris Saclay, LIDYL, CEA, CNRS,CEA Saclay, F-91191 Gif Sur Yvette, France.
    Geneaux, Romain
    Univ Paris Saclay, LIDYL, CEA, CNRS,CEA Saclay, F-91191 Gif Sur Yvette, France.
    Gentleman, Alexander S.
    Univ Oxford, Phys & Theoret Chem Lab, Dept Chem, Oxford OX1 3QZ, England.
    Goldsztejn, Gildas
    Max Born Inst, Max Born Str 2A, D-12489 Berlin, Germany.
    Guillemin, Renaud
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Holland, David M. P.
    Daresbury Lab, Warrington WA4 4AD, Cheshire, England.
    Ismail, Iyas
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Johnsson, Per
    Lund Univ, Dept Phys, S-22100 Lund, Sweden.
    Journel, Loic
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Kuepper, Jochen
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany;Univ Hamburg, Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany;Univ Hamburg, Dept Chem, Martin Luther King Pl 6, D-20146 Hamburg, Germany.
    Lahl, Jan
    Lund Univ, Dept Phys, S-22100 Lund, Sweden.
    Lee, Jason W. L.
    Univ Oxford, Chem Res Lab, Dept Chem, Oxford OX1 3TA, England.
    Maclot, Sylvain
    Lund Univ, Dept Phys, S-22100 Lund, Sweden.
    Mackenzie, Stuart R.
    Univ Oxford, Phys & Theoret Chem Lab, Dept Chem, Oxford OX1 3QZ, England.
    Manschwetus, Bastian
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Mereshchenko, Andrey S.
    St Petersburg State Univ, 7-9 Univ Skaya Nab, St Petersburg 199034, Russia.
    Mason, Robert
    Univ Oxford, Chem Res Lab, Dept Chem, Oxford OX1 3TA, England.
    Palaudoux, Jerome
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Piancastelli, Maria Novella
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Penent, Francis
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Rompotis, Dimitrios
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany;European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Rouzee, Arnaud
    Max Born Inst, Max Born Str 2A, D-12489 Berlin, Germany.
    Ruchon, Thierry
    Univ Paris Saclay, LIDYL, CEA, CNRS,CEA Saclay, F-91191 Gif Sur Yvette, France.
    Rudenko, Artem
    Kansas State Univ, Dept Phys, JR Macdonald Lab, Manhattan, KS 66506 USA.
    Savelyev, Evgeny
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Simon, Marc
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Schirmel, Nora
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Stapelfeldt, Henrik
    Aarhus Univ, Dept Chem, Langelandsgade 140, DK-8000 Aarhus C, Denmark.
    Techert, Simone
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany;Max Planck Inst Biophys Chem, D-37077 Gottingen, Germany;Univ Gottingen, Inst Xray Phys, D-37077 Gottingen, Germany.
    Travnikova, Oksana
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Trippel, Sebastian
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany;Univ Hamburg, Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany.
    Underwood, Jonathan G.
    UCL, Dept Phys & Astron, London WC1E 6BT, England.
    Vallance, Claire
    Univ Oxford, Chem Res Lab, Dept Chem, Oxford OX1 3TA, England.
    Wiese, Joss
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany;Univ Hamburg, Dept Chem, Martin Luther King Pl 6, D-20146 Hamburg, Germany.
    Ziaee, Farzaneh
    Kansas State Univ, Dept Phys, JR Macdonald Lab, Manhattan, KS 66506 USA.
    Brouard, Mark
    Univ Oxford, Chem Res Lab, Dept Chem, Oxford OX1 3TA, England.
    Marchenko, Tatiana
    Sorbonne Univ, LCPMR, CNRS, F-75005 Paris, France.
    Rolles, Daniel
    Kansas State Univ, Dept Phys, JR Macdonald Lab, Manhattan, KS 66506 USA.
    Coulomb explosion imaging of CH3I and CH2CII photodissociation dynamics2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 149, no 20, article id 204313Article in journal (Refereed)
    Abstract [en]

    The photodissociation dynamics of CH3I and CH2CII at 272 nm were investigated by time-resolved Coulomb explosion imaging, with an intense non-resonant 815nmprobe pulse. Fragment ion momenta over a widem/z range were recorded simultaneously by coupling a velocity map imaging spectrometer with a pixel imaging mass spectrometry camera. For both molecules, delay-dependent pump-probe features were assigned to ultraviolet-induced carbon-iodine bond cleavage followed by Coulomb explosion. Multi-mass imaging also allowed the sequential cleavage of both carbon-halogen bonds in CH2ClI to be investigated. Furthermore, delay-dependent relative fragment momenta of a pair of ions were directly determined using recoil-frame covariance analysis. These results are complementary to conventional velocity map imaging experiments and demonstrate the application of time-resolved Coulomb explosion imaging to photoinduced real-time molecular motion.

  • 9.
    Amft, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Johansson, Börje
    Skorodumova, Natalia V.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Influence of the cluster dimensionality on the binding behavior of CO and O(2) on Au(13)2012In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 136, no 2, p. 024312-Article in journal (Refereed)
    Abstract [en]

    We present an ab initio density functional theory study of the binding behavior of CO and O(2) molecules to two-and three-dimensional isomers of Au(13) in order to investigate the potential catalytic activity of this cluster towards low-temperature CO oxidation. First, we scanned the potential energy surface of Au(13) and studied the effect of spin-orbit coupling on the relative stabilities of the 21 isomers we identified. While spin-orbit coupling increases the stability of the three-dimensional more than the two-dimensional isomers, the ground state structure at 0 K remains planar. Second, we systematically studied the binding of CO and O(2) molecules onto the planar and three-dimensional structures lowest in energy. We find that the isomer dimensionality has little effect on the binding of CO to Au(13). O(2), on the other hand, binds significantly to the three-dimensional isomer only. The simultaneous binding of multiple CO molecules decreases the binding energy per molecule. Still, the CO binding remains stronger than the O(2) binding. We did not find a synergetic effect due to the co-adsorption of both molecular species. On the three-dimensional isomer, we find O(2) dissociation to be exothermic with an dissociation barrier of 1.44 eV.

  • 10.
    Amira, Sami
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    OD vibrations and hydration structure in an Al3+(aq) solution from a Car-Parrinello Molecular Dynamics Simulation2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 124, no 10, p. 104501-Article in journal (Refereed)
    Abstract [en]

    The optimized geometry, energetics, and vibrational properties of Al(D2O) clusters, with n=1,2,4, and 6, have been studied using plane waves, different local basis sets, different methodologies [density-functional theory, MP2, CCSD(T)], and different functionals (BLYP, PBE). Moreover, Car-Parrinello molecular-dynamics (MD) simulations using the BLYP functional, plane waves, and the Vanderbilt ultrasoft pseudopotentials have been performed for an aqueous Al3+ solution with 1 ion and 32 D2O molecules in a periodic box at room temperature, studied for 10 ps. The cluster calculations were performed to pinpoint possible shortcomings of the electronic structure description used in the Car-Parinello MD (CPMD) simulation. For the clusters, the hydration structure and interaction energies calculated with the `BLYP/plane-wave' approach agree well with high-level ab initio methods but the exchange-correlation functional introduces errors in the OD stretching frequencies (both in the absolute values and in the ion-induced shifts). For the aqueous solution, the CPMD simulation yields structural properties in good agreement with experimental data. The CPMD-simulated OD stretching vibrational band for the first-shell water molecules around Al3+ is strongly downshifted by the influence of the ion and is compared with experimental data from the literature. To make such a comparison meaningful, the influences of a number of systematic effects have been addressed, such as the exchange-correlation functional, the fictitious electron mass, anharmonicity effects, and the small box size in the simulation. Each of these factors (except the last one) is found to affect the OD frequency by 100 cm–1 or more. The final "corrected" frequencies agree with experiment within ~30 cm–1 for bulk water but are too little downshifted for the first-shell Al3+(aq) water molecules (by ~200 cm–1).

  • 11.
    Andersson, Egil
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Soft X-Ray Physics.
    Niskanen, Johannes
    Hedin, Lage
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Soft X-Ray Physics.
    Eland, John H. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Soft X-Ray Physics.
    Linusson, Per
    Karlsson, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Soft X-Ray Physics.
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Soft X-Ray Physics.
    Carravetta, V.
    Ågren, Hans
    Feifel, Raimund
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Soft X-Ray Physics.
    Core-valence double photoionization of the CS2 molecule2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 9, p. 094305-Article in journal (Refereed)
    Abstract [en]

    Double photoionization spectra of the CS2 molecule have been recorded using the TOF-PEPECO technique in combination with synchrotron radiation at the photon energies h nu=220, 230, 240, 243, and 362.7 eV. The spectra were recorded in the S 2p and C 1s inner-shell ionization regions and reflect dicationic states formed out of one inner-shell vacancy and one vacancy in the valence region. MCSCF calculations were performed to model the energies of the dicationic states. The spectra associated with a S 2p vacancy are well structured and have been interpreted in some detail by comparison to conventional S 2p and valence photoelectron spectra. The lowest inner-shell-valence dicationic state is observed at the vertical double ionization energy 188.45 eV and is associated with a (2p(3/2))(-1)(2 pi(g))(-1) double vacancy. The spectrum connected to the C 1s vacancy shows a distinct line at 310.8 eV, accompanied by additional broad features at higher double ionization energies. This line is associated with a (C 1s)(-1)(2 pi(g))(-1) double vacancy.

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  • 12.
    Andersson, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Zhang, Chaofan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Rosso, Aldana
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Bradeanu, Ioana
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Legendre, Sebastien
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Canton, S. E.
    Tchaplyguine, M.
    Ohrwall, G.
    Sorensen, S. L.
    Svensson, Svante
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Mårtensson, Nils
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Plasmon single- and multi-quantum excitation in free metal clusters as seen by photoelectron spectroscopy2011In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, no 9, p. 094511-Article in journal (Refereed)
    Abstract [en]

    Plasmons are investigated in free nanoscale Na, Mg, and K metal clusters using synchrotron radiation-based x-ray photoelectron spectroscopy. The core levels for which the response from bulk and surface atoms can be resolved are probed over an extended binding energy range to include the plasmon loss features. In all species the features due to fundamental plasmons are identified, and in Na and K also those due to either the first order plasmon overtones or sequential plasmon excitation are observed. These features are discussed in view of earlier results for planar macroscopic samples and free clusters of the same materials.

  • 13.
    Andersson, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Zhang, Chaofan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Tchaplyguine, Maxim
    Svensson, Svante
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Mårtensson, Nils
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    The electronic structure of free aluminum clusters: Metallicity and plasmons2012In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 136, no 20, p. 204504-Article in journal (Refereed)
    Abstract [en]

    The electronic structure of free aluminum clusters with similar to 3-4 nm radius has been investigated using synchrotron radiation-based photoelectron and Auger electron spectroscopy. A beam of free clusters has been produced using a gas-aggregation source. The 2p core level and the valence band have been probed. Photoelectron energy-loss features corresponding to both bulk and surface plasmon excitation following photoionization of the 2p level have been observed, and the excitation energies have been derived. In contrast to some expectations, the loss features have been detected at energies very close to those of the macroscopic solid. The results are discussed from the point of view of metallic properties in nanoparticles with a finite number of constituent atoms.

  • 14.
    Angelova Hamberg, Gergana
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Rate constants and branching ratios for the dissociative recombination of C3D7+ and C4D9+2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690Article in journal (Refereed)
  • 15.
    Aquilante, Francesco
    et al.
    Ecole Polytech Fed Lausanne EPFL, Theory & Simulat Mat THEOS, CH-1015 Lausanne, Switzerland.;Ecole Polytech Fed Lausanne EPFL, Natl Ctr Computat Design & Discovery Novel Mat MA, CH-1015 Lausanne, Switzerland..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Baiardi, Alberto
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Battaglia, Stefano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Borin, Veniamin A.
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium..
    Conti, Irene
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    De Vico, Luca
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Delcey, Mickael G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Ferre, Nicolas
    Aix Marseille Univ, CNRS, Inst Chim Radicalaire, Marseille, France..
    Freitag, Leon
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Garavelli, Marco
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Gong, Xuejun
    Natl Univ Singapore, Dept Chem, 3 Sci Dr 3, Singapore 117543, Singapore..
    Knecht, Stefan
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Larsson, Ernst D.
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Malmqvist, Per Ake
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Nenov, Artur
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Norell, Jesper
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Olivucci, Massimo
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA..
    Pedersen, Thomas B.
    Univ Oslo, Dept Chem, Hylleraas Ctr Quantum Mol Sci, POB 1033 Blindern, N-0315 Oslo, Norway..
    Pedraza-Gonzalez, Laura
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Phung, Quan M.
    Nagoya Univ, Inst Transformat Biomol WPI ITbM, Chikusa Ku, Nagoya, Aichi 4648602, Japan..
    Pierloot, Kristine
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium..
    Reiher, Markus
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Schapiro, Igor
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Segarra-Marti, Javier
    Imperial Coll London, Dept Chem, Mol Sci Res Hub, White City Campus,80 Wood Lane, London W12 0BZ, England..
    Segatta, Francesco
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Seijo, Luis
    Univ Autonoma Madrid, Dept Quim, Inst Univ Ciencia Mat Nicolas Cabrera, Madrid 28049, Spain.;Univ Autonoma Madrid, Condensed Matter Phys Ctr IFIMAC, Madrid 28049, Spain..
    Sen, Saumik
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Sergentu, Dumitru-Claudiu
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Stein, Christopher J.
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Ungur, Liviu
    Natl Univ Singapore, Dept Chem, 3 Sci Dr 3, Singapore 117543, Singapore..
    Vacher, Morgane
    Univ Nantes, Lab CEISAM UMR CNRS 6230, F-44300 Nantes, France..
    Valentini, Alessio
    Univ Liege, Res Unit MolSys, Theoret Phys Chem, Allee 6 Aout 11, B-4000 Liege, Belgium..
    Veryazov, Valera
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Modern quantum chemistry with [Open]Molcas2020In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 21Article in journal (Refereed)
    Abstract [en]

    MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

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  • 16. Aquilante, Francesco
    et al.
    Barone, V
    Roos, B O
    A theoretical investigation of valence and Rydberg electronic states of acrolein.2003In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 119, no 23, p. 12323-12334Article in journal (Refereed)
    Abstract [en]

    The main features of the ultraviolet spectrum of acrolein have been studied by a multireference perturbative treatment and by a time dependent density functional approach. The valence and Rydberg transition energies have been calculated and the assignment of the experimental bands has been clarified. The different relaxation trends of the three lowest singlet and triplet excited states have been analyzed by unconstrained geometry optimizations. This has allowed, in particular, the characterization of a twisted (3)(pipi*) state, which is crucial for the interesting photophysics and photochemistry of the acrolein molecule and, more generally, of the alpha,beta-enones. Solvatochromic shifts in aqueous solution have been investigated using a combined discrete/continuum approach based on the so called polarizable continuum model. The experimental trends are well reproduced by this approach and a closer degeneracy in the triplet manifold has been detected in solution with respect to gas phase.

  • 17. Aquilante, Francesco
    et al.
    Gagliardi, Laura
    Pedersen, Thomas Bondo
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Atomic Cholesky decompositions: A route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, p. 154107-Article in journal (Refereed)
    Abstract [en]

    Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante , J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

  • 18. Aquilante, Francesco
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Pedersen, Thomas Bondo
    Analytic derivatives for the Cholesky representation of the two-electron integrals2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 3, p. 034106-Article in journal (Refereed)
    Abstract [en]

    We propose a formalism for calculating analytic derivatives of the electronic energy with respect to nuclear coordinates using Cholesky decomposition of the two-electron integrals. The formalism is derived by exploiting the equivalence of Cholesky decomposition and density fitting when a suitable auxiliary basis set is used for expanding atomic orbital product densities in the latter. An implementation of gradients at the nonhybrid density functional theory level is presented, and sample calculations demonstrate that the errors in equilibrium geometries due to the Cholesky representation of the integrals can be controlled by adjusting the decomposition threshold.

  • 19. Aquilante, Francesco
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Pedersen, Thomas Bondo
    Unbiased auxiliary basis sets for accurate two-electron integral approximations2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, no 11, p. 114107-Article in journal (Refereed)
    Abstract [en]

    We propose Cholesky decomposition (CD) of the atomic two-electron integral matrix as a robust and general technique for generating auxiliary basis sets for the density fitting approximation. The atomic CD (aCD) auxiliary basis set is calculated on the fly and is not biased toward a particular quantum chemical method. Moreover, the accuracy of the aCD basis set can be controlled with a single parameter.

  • 20. Aquilante, Francesco
    et al.
    Pedersen, Thomas Bondo
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Low-cost evaluation of the exchange Fock matrix from Cholesky and density fitting representations of the electron repulsion integrals2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 126, no 19, p. 194106-Article in journal (Refereed)
    Abstract [en]

    The authors propose a new algorithm, “local K” (LK), for fast evaluation of the exchange Fock matrix in case the Cholesky decomposition of the electron repulsion integrals is used. The novelty lies in the fact that rigorous upper bounds to the contribution from each occupied orbital to the exchange Fock matrix are employed. By formulating these inequalities in terms of localized orbitals, the scaling of computing the exchange Fock matrix is reduced from quartic to quadratic with only negligible prescreening overhead and strict error control. Compared to the unscreened Cholesky algorithm, the computational saving is substantial for systems of medium and large sizes. By virtue of its general formulation, the LK algorithm can be used also within the class of methods that employ auxiliary basis set expansions for representing the electron repulsion integrals.

  • 21. Aquilante, Francesco
    et al.
    Pedersen, Thomas Bondo
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Roos, Björn Olof
    De Merás, Alfredo Sánchez
    Koch, Henrik
    Accurate ab initio density fitting for multiconfigurational self-consistent field methods2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 2, p. 024113-Article in journal (Refereed)
    Abstract [en]

    Using Cholesky decomposition and density fitting to approximate the electron repulsion integrals, an implementation of the complete active space self-consistent field (CASSCF) method suitable for large-scale applications is presented. Sample calculations on benzene, diaquo-tetra-mu-acetato-dicopper(II), and diuraniumendofullerene demonstrate that the Cholesky and density fitting approximations allow larger basis sets and larger systems to be treated at the CASSCF level of theory with controllable accuracy. While strict error control is an inherent property of the Cholesky approximation, errors arising from the density fitting approach are managed by using a recently proposed class of auxiliary basis sets constructed from Cholesky decomposition of the atomic electron repulsion integrals.

  • 22. Aquilante, Francesco
    et al.
    Pedersen, Thomas Bondo
    Sanchez de Meras, Alfredo
    Koch, Henrik
    Fast noniterative orbital localization for large molecules.2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 125, no 17Article in journal (Refereed)
    Abstract [en]

    We use Cholesky decomposition of the density matrix in atomic orbital basis to define a new set of occupied molecular orbital coefficients. Analysis of the resulting orbitals (”Cholesky molecular orbitals”) demonstrates their localized character inherited from the sparsity of the density matrix. Comparison with the results of traditional iterative localization schemes shows minor differences with respect to a number of suitable measures of locality, particularly the scaling with system size of orbital pair domains used in local correlation methods. The Cholesky procedure for generating orthonormal localized orbitals is noniterative and may be made linear scaling. Although our present implementation scales cubically, the algorithm is significantly faster than any of the conventional localization schemes. In addition, since this approach does not require starting orbitals, it will be useful in local correlation treatments on top of diagonalization-free Hartree-Fock optimization algorithms.

  • 23.
    Aquilante, Francesco
    et al.
    Department of Physical Chemistry, Sciences II, University of Geneva.
    Todorova, Tanya Kumanova
    Gagliardi, Laura
    Pedersen, Thomas Bondo
    Roos, Bjorn
    Systematic truncation of the virtual space in multiconfigurational perturbation theory2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, p. 034113-Article in journal (Refereed)
    Abstract [en]

    A method is suggested which allows truncation of the virtual space in Cholesky decomposition-based multiconfigurational perturbation theory (CD-CASPT2) calculations with systematic improvability of the results. The method is based on a modified version of the frozen natural orbital (FNO) approach used in coupled cluster theory. The idea is to exploit the near-linear dependence among the eigenvectors of the virtual-virtual block of the second-order Moller-Plesset density matrix. It is shown that FNO-CASPT2 recovers more than 95% of the full CD-CASPT2 correlation energy while requiring only a fraction of the total virtual space, especially when large atomic orbital basis sets are in use. Tests on various properties commonly investigated with CASPT2 demonstrate the reliability of the approach and the associated reduction in computational cost and storage demand of the calculations.

  • 24.
    Arismendi-Arrieta, Daniel J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Sen, Anik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Eriksson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    H2O2(s) and H2O22H2O(s) crystals compared with ices: DFT functional assessment and D3 analysis2023In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 159, no 19, article id 194701Article in journal (Refereed)
    Abstract [en]

    The H2O and H2O2 molecules resemble each other in a multitude of ways as has been noted in the literature. Here, we present density functional theory (DFT) calculations for the H2O2(s) and H2O2<middle dot>2H(2)O(s) crystals and make selected comparisons with ice polymorphs. The performance of a number of dispersion-corrected density functionals-both self-consistent and a posteriori ones-are assessed, and we give special attention to the D3 correction and its effects. The D3 correction to the lattice energies is large: for H2O2(s) the D3 correction constitutes about 25% of the lattice energy using PBE, much more for RPBE, much less for SCAN, and it primarily arises from non-H-bonded interactions out to about 5 & Aring;.The large D3 corrections to the lattice energies are likely a consequence of several effects: correction for missing dispersion interaction, the ability of D3 to capture and correct various other kinds of limitations built into the underlying DFT functionals, and finally some degree of cell-contraction-induced polarization enhancement. We find that the overall best-performing functionals of the twelve examined are optPBEvdW and RPBE-D3. Comparisons with DFT assessments for ices in the literature show that where the same methods have been used, the assessments largely agree.

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  • 25.
    Arismendi-Arrieta, Daniel J.
    et al.
    Department of Chemistry-Ångström, Uppsala University , P.O. Box 530, S-75121 Uppsala, Sweden.
    Sen, Anik
    Department of Chemistry-Ångström, Uppsala University , P.O. Box 530, S-75121 Uppsala, Sweden.
    Eriksson, Anders
    Department of Chemistry-Ångström, Uppsala University , P.O. Box 530, S-75121 Uppsala, Sweden.
    Broqvist, Peter
    Department of Chemistry-Ångström, Uppsala University , P.O. Box 530, S-75121 Uppsala, Sweden.
    Kullgren, Jolla
    Department of Chemistry-Ångström, Uppsala University , P.O. Box 530, S-75121 Uppsala, Sweden.
    Hermansson, Kersti
    Department of Chemistry-Ångström, Uppsala University , P.O. Box 530, S-75121 Uppsala, Sweden.
    H2O2(s) and H2O2·2H2O(s) crystals compared with ices: DFT functional assessment and D3 analysis2023In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 159, no 19Article in journal (Refereed)
  • 26.
    Assis Silva, Flavia Cristina
    et al.
    Univ Fed Fluminense, Dept Fis Quim, MolMod CS, Niteroi, RJ, Brazil..
    Lourenco, Tuanan da Costa
    Univ Fed Fluminense, Dept Fis Quim, MolMod CS, Niteroi, RJ, Brazil..
    Van der Spoel, David
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Aparicio, Santiago
    Univ Burgos, Dept Chem, Burgos, Spain..
    dos Reis, Rodrigo Azevedo
    Univ Estado Rio de Janeiro, Dept Operacoes & Projetos Ind, Rio De Janeiro, Brazil..
    Costa, Luciano T.
    Univ Fed Fluminense, Dept Fis Quim, MolMod CS, Niteroi, RJ, Brazil..
    The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view2021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 155, no 4, article id 044704Article in journal (Refereed)
    Abstract [en]

    The world desperately needs new technologies and solutions for gas capture and separation. To make this possible, molecular modeling is applied here to investigate the structural, thermodynamic, and dynamical properties of a model for the poly(urethane urea) (PUU) oligomer model to selectively capture CO2 in the presence of CH4. In this work, we applied a well-known approach to derive atomic partial charges for atoms in a polymer chain based on self-consistent sampling using quantum chemistry and stochastic dynamics. The interactions of the gases with the PUU model were studied in a pure gas based system as well as in a gas mixture. A detailed structure characterization revealed high interaction of CO2 molecules with the hard segments of the PUU. Therefore, the structural and energy properties explain the reasons for the greater CO2 sorption than CH4. We find that the CO2 sorption is higher than the CH4 with a selectivity of 7.5 at 298 K for the gas mixture. We characterized the Gibbs dividing surface for each system, and the CO2 is confined for a long time at the gas-oligomer model interface. The simulated oligomer model showed performance above the 2008 Robeson's upper bound and may be a potential material for CO2/CH4 separation. Further computational and experimental studies are needed to evaluate the material.

  • 27. Barnes, Leslie A
    et al.
    Lie, Bowen
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Structure and energetics of Cr(CO)6 and Cr(CO)51993In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 98, no 5, p. 3978-3989Article in journal (Refereed)
    Abstract [en]

    The geometric structure of Cr(CO)6 is optimized at the modified coupled-pair functional (MCPF), single and double excitation coupled-cluster (CCSD), and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), and the force constants for the totally symmetric representation are determined. The geometry of Cr(CO)5 is partially optimized at the MCPF, CCSD, and CCSD(T) levels of theory. Comparison with experimental data shows that the CCSD(T) method gives the best results for the structures and force constants, and that remaining errors are probably due to deficiencies in the one-particle basis sets used for CO. The total binding energies of Cr(CO)6 and Cr(CO)5 are also determined at the MCPF, CCSD, and CCSD(T) levels of theory. The CCSD(T) method gives a much larger total binding energy than either the MCPF or CCSD methods. An analysis of the basis set superposition error (BSSE) at the MCPF level of treatment points out limitations in the one-particle basis used here and in a previous study. Calculations using larger basis sets reduce the BSSE, but the total binding energy of Cr(CO)6 is Still Significantly smaller than the experimental value, although the first CO bond dissociation energy of Cr(CO)6 is well described. An investigation of 3s3p correlation reveals only a small effect. In the largest basis set, the total CO binding energy of Cr(CO)6 is estimated to be 140 kcal/mol at the CCSD(T) level of theory, or about 86% of the experimental value. The remaining discrepancy between the experimental and theoretical value is probably due to limitations in the one-particle basis, rather than limitations in the correlation treatment. In particular, an additional d function and an f function on each C and 0 are needed to obtain quantitative results. This is underscored by the fact that even using a very large primitive set (1042 primitive functions contracted to 300 basis functions), the superposition error for the total binding energy of Cr(CO)6 is 22 kcal/mol at the MCPF level of treatment.

  • 28. Barnes, Leslie A
    et al.
    Liu, Bowen
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Bond length, dipole moment, and harmonic frequency of CO1993In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 98, no 5, p. 3972-3977Article in journal (Refereed)
    Abstract [en]

    A detailed comparison of some properties of CO is given, at the modified coupled-pair functional, single and double excitation coupled-cluster (CCSD), and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), using a variety of basis sets. With very large one-particle basis sets, the CCSD(T) method gives excellent results for the bond distance, dipole moment, and harmonic frequency of CO. In a [6s 5p 4d 3f 2g 1h] + (1s 1p 1d) basis set, the bond distance is about 0.005a0 too large, the dipole moment about 0.005 a.u. too small, and the frequency about 6 cm-1 too small, when compared with experimental results.

  • 29.
    Battaglia, Stefano
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    On the role of symmetry in XDW-CASPT22021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 3, article id 034102Article in journal (Refereed)
    Abstract [en]

    Herewith, we propose two new exponents for the recently introduced XDW-CASPT2 method [S. Battaglia and R. Lindh, J. Chem. Theory Comput. 16, 1555-1567 (2020)], which fix one of the largest issues hindering this approach. By using the first-order effective Hamiltonian coupling elements, the weighting scheme implicitly takes into account the symmetry of the states, thereby averaging Fock operators only if the zeroth-order wave functions interact with each other. The use of Hamiltonian couplings also provides a physically sounder approach to quantitate the relative weights; however, it introduces new difficulties when these rapidly die off to zero. The improved XDW-CASPT2 method is critically tested on several systems of photochemical relevance, and it is shown that it succeeds in its original intent of maintaining MS-CASPT2 accuracy for the evaluation of transition energies and at the same time providing smooth potential energy surfaces around near-degenerate points akin to XMS-CASPT2.

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  • 30.
    Bergersen, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Abu-samha, M.
    Lindblad, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Marinho, Ricardo
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Öhrwall, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Tchaplyguine, M.
    Børve, K. J.
    Svensson, Svante
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Two size regimes of methanol clusters produced by adiabatic expansion2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 125, no 18, p. 184303-Article in journal (Refereed)
    Abstract [en]

    Free neutral methanol clusters produced by adiabatic expansion have been studied by photoelectron spectroscopy and line shape modeling. The results show that clusters belonging to two distinct size regimes can be produced by changing the expansion conditions. While the larger size regime can be well described by line shapes calculated for clusters consisting of hundreds of molecules, the smaller size regime corresponds to methanol oligomers, predominantly of cyclic structure. There is little contribution from dimers to the spectra.

  • 31.
    Bidermane, Ieva
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Lüder, Johann
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Boudet, S.
    Zhang, T.
    Ahmadi, S.
    Grazioli, C.
    Bouvet, M.
    Rusz, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Puglia, Carla
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Witkowski, N.
    Experimental and theoretical study of electronic structure of lutetium bi-phthalocyanine2013In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, no 23, p. 234701-Article in journal (Refereed)
    Abstract [en]

    Using Near Edge X-Ray Absorption Fine Structure (NEXAFS) Spectroscopy, the thickness dependent formation of Lutetium Phthalocyanine (LuPc2) films on a stepped passivated Si(100)2x1 reconstructed surface was studied. Density functional theory (DFT) calculations were employed to gain detailed insights into the electronic structure. Photoelectron spectroscopy measurements have not revealed any noticeable interaction of LuPc2 with the H-passivated Si surface. The presented study can be considered to give a comprehensive description of the LuPc2 molecular electronic structure. The DFT calculations reveal the interaction of the two molecular rings with each other and with the metallic center forming new kinds of orbitals in between the phthalocyanine rings, which allows to better understand the experimentally obtained NEXAFS results. 

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  • 32. Bowen, K. P.
    et al.
    Stolte, W. C.
    Lago, A. F.
    Daacutevalos, J. Z.
    Piancastelli, M. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Lindle, D. W.
    Partial-ion-yield studies of SOCl 2 following x-ray absorption around the S and Cl K edges2012In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, no 20, p. 204313-Article in journal (Refereed)
    Abstract [en]

    We present a series of photoabsorption and partial-ion-yield experiments on thionyl chloride, SOCl2, at both the sulfur and chlorine K edges. The photoabsorption results exhibit better resolution than previously published data, leading to alternate spectral assignments for some of the features, particularly in the Rydberg-series region. Based on measured fragmentation patterns, we suggest the LUMO, of a' character, is delocalized over the entire molecular skeleton. Unusual behavior of the S2+ fragment hints at a relatively localized bond rupture (the S-O bond below the S K edge and the S-Cl bonds below the Cl K edge) following excitation to some of the higher lying intermediate states. 

  • 33.
    Brena, Barbara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Puglia, Carla
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    de Simone, Monica
    Coreno, Marcello
    Tarafder, Kartick
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Feyer, Vitaly
    Banerjee, Rudra
    Gothelid, Emmanuelle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Oppeneer, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Valence-band electronic structure of iron phthalocyanine: An experimental and theoretical photoelectron spectroscopy study2011In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, no 7, p. 074312-Article in journal (Refereed)
    Abstract [en]

    The electronic structure of iron phthalocyanine (FePc) in the valence region was examined within a joint theoretical-experimental collaboration. Particular emphasis was placed on the determination of the energy position of the Fe 3d levels in proximity of the highest occupied molecular orbital (HOMO). Photoelectron spectroscopy (PES) measurements were performed on FePc in gas phase at several photon energies in the interval between 21 and 150 eV. Significant variations of the relative intensities were observed, indicating a different elemental and atomic orbital composition of the highest lying spectral features. The electronic structure of a single FePc molecule was first computed by quantum chemical calculations by means of density functional theory (DFT). The hybrid Becke 3-parameter, Lee, Yang and Parr (B3LYP) functional and the semilocal 1996 functional of Perdew, Burke and Ernzerhof (PBE) of the generalized gradient approximation (GGA-) type, exchange-correlation functionals were used. The DFT/B3LYP calculations find that the HOMO is a doubly occupied pi-type orbital formed by the carbon 2p electrons, and the HOMO-1 is a mixing of carbon 2p and iron 3d electrons. In contrast, the DFT/PBE calculations find an iron 3d contribution in the HOMO. The experimental photoelectron spectra of the valence band taken at different energies were simulated by means of the Gelius model, taking into account the atomic subshell photoionization cross sections. Moreover, calculations of the electronic structure of FePc using the GGA+U method were performed, where the strong correlations of the Fe 3d electronic states were incorporated through the Hubbard model. Through a comparison with our quantum chemical calculations we find that the best agreement with the experimental results is obtained for a U-eff value of 5 eV.

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  • 34.
    Brooks, Charles L., III
    et al.
    Univ Michigan, Dept Chem, Ann Arbor, MI 48109 USA..
    Case, David A.
    Rutgers State Univ, Dept Chem & Chem Biol, New Brunswick, NJ 08854 USA..
    Plimpton, Steve
    Sandia Natl Labs, Computat Multiscale Dept, POB 5800, Albuquerque, NM 87185 USA..
    Roux, Benoit
    Univ Chicago, Dept Chem, 5735 S Ellis Ave, Chicago, IL 60637 USA..
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala Univ, Dept Cell & Mol Biol, Uppsala, Sweden..
    Tajkhorshid, Emad
    Univ Illinois, NIH Ctr Macromolecular Modeling & Bioinformat, Theoret & Computat Biophys Grp, Beckman Inst Adv Sci & Technol,Dept Biochem, Urbana, IL 61801 USA.;Univ Illinois, Ctr Biophys & Quantitat Biol, Urbana, IL 61801 USA..
    Classical molecular dynamics2021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 10, article id 100401Article in journal (Other academic)
  • 35.
    Brumboiu, Iulia Emilia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ericsson, Leif
    Hansson, Rickard
    Moons, Ellen
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    The influence of oxygen adsorption on the NEXAFS and core-level XPS spectra of the C-60 derivative PCBM2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 142, no 5, article id 054306Article in journal (Refereed)
    Abstract [en]

    Fullerenes have been a main focus of scientific research since their discovery due to the interesting possible applications in various fields like organic photovoltaics (OPVs). In particular, the derivative [6,6]-phenyl-C-60-butyric acid methyl ester (PCBM) is currently one of the most popular choices due to its higher solubility in organic solvents compared to unsubstituted C-60. One of the central issues in the field of OPVs is device stability, since modules undergo deterioration (losses in efficiency, open circuit voltage, and short circuit current) during operation. In the case of fullerenes, several possibilities have been proposed, including dimerization, oxidation, and impurity related deterioration. We have studied by means of density functional theory the possibility of oxygen adsorption on the C-60 molecular moiety of PCBM. The aim is to provide guidelines for near edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS) measurements which can probe the presence of atomic or molecular oxygen on the fullerene cage. By analysing several configurations of PCBM with one or more adsorbed oxygen atoms, we show that a joint core level XPS and O1s NEXAFS investigation could be effectively used not only to confirm oxygen adsorption but also to pinpoint the bonding configuration and the nature of the adsorbate.

  • 36.
    Brumboiu, Iulia Emilia
    et al.
    KTH Royal Inst Technol, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden;Korea Adv Inst Sci & Technol, Dept Chem, Daejeon 34141, South Korea.
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Norman, Patrick
    KTH Royal Inst Technol, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden.
    Atomic photoionization cross sections beyond the electric dipole approximation2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 4, article id 044306Article in journal (Refereed)
    Abstract [en]

    A methodology is developed to compute photoionization cross sections beyond the electric dipole approximation from response theory, using Gaussian type orbitals and plane waves for the initial and final states, respectively. The methodology is applied to compute photoionization cross sections of atoms and ions from the first four rows of the periodic table. Analyzing the error due to the plane wave description of the photoelectron, we find kinetic energy and concomitant photon energy thresholds above which the plane wave approximation becomes applicable. The correction introduced by going beyond the electric dipole approximation increases with photon energy and depends on the spatial extension of the initial state. In general, the corrections are below 10% for most elements, at a photon energy reaching up to 12 keV.

  • 37.
    Brumboiu, Iulia Emilia
    et al.
    Royal Inst Technol, Sch Biotechnol, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Prokopiou, Georgia
    Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel..
    Kronik, Leeor
    Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel..
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Valence electronic structure of cobalt phthalocyanine from an optimally tuned range-separated hybrid functional2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 147, no 4, article id 044301Article in journal (Refereed)
    Abstract [en]

    We analyse the valence electronic structure of cobalt phthalocyanine (CoPc) by means of optimally tuning a range-separated hybrid functional. The tuning is performed by modifying both the amount of short-range exact exchange (alpha) included in the hybrid functional and the range-separation parameter (gamma), with two strategies employed for finding the optimal gamma for each alpha. The influence of these two parameters on the structural, electronic, and magnetic properties of CoPc is thoroughly investigated. The electronic structure is found to be very sensitive to the amount and range in which the exact exchange is included. The electronic structure obtained using the optimal parameters is compared to gas-phase photo-electron data and GWcalculations, with the unoccupied states additionally compared with inverse photo-electron spectroscopy measurements. The calculated spectrum with tuned gamma, determined for the optimal value of alpha = 0.1, yields a very good agreement with both experimental results and with GW calculations that well-reproduce the experimental data.

  • 38.
    Butorin, Sergei
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Condensed Matter Physics of Energy Materials.
    Advanced x-ray spectroscopy of actinide trichlorides2021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 155, no 16, article id 164103Article in journal (Refereed)
    Abstract [en]

    The application of core-to-core (3d-to-4f) resonant inelastic x-ray scattering (RIXS) and high-energy-resolution fluorescence-detected x-ray absorption (HERFD-XAS) at actinide M-4,M-5 edges, as techniques with the enhanced sensitivity to changes in the chemical state, was analyzed for trivalent actinide compounds. As an example, a series of actinide chlorides AnCl(3) (An = U, Np, Pu, Am, Cm, Bk, and Cf) was used. The crystal-field multiplet formalism was applied to calculate the 3d-4f RIXS maps, and the HERFD-XAS spectra were extracted as cuts of these RIXS maps along the incident energy axis at the constant emitted energy, corresponding to the maximum of the RIXS intensity. A relation between HERFD and conventional XAS methods was also examined. Despite some differences between profiles of the An M-5 HERFD and conventional XAS spectra of trivalent actinides, the results of calculations indicate that the HERFD method can be used at the An M-5 edge for monitoring even small variations in the An chemical state. As a whole, better agreement between the HERFD and XAS spectra was found for the An M-4 edges as compared to the An M-5 edges. By using the point charge electrostatic model, the dependence of the An M-4,M-5 HERFD-XAS spectra on the An coordination number was studied, which indicates the significant sensitivity of the distribution of the An 5f states to the ligand structural arrangement around the An sites.

  • 39.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Temperature and structural changes of water clusters in vacuum due to evaporation2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 125, no 15, p. 154508-Article in journal (Refereed)
    Abstract [en]

    This paper presents a study on evaporation of pure water clusters. Molecular dynamics simulations between 20 ns and 3 mu s of clusters ranging from 125 to 4096 molecules in vacuum were performed. Three different models (SPC, TIP4P, and TIP5P) were used to simulate water, starting at temperatures of 250, 275, and 300 K. We monitored the temperature, the number of hydrogen bonds, the tetrahedral order, the evaporation, the radial distribution functions, and the diffusion coefficients. The three models behave very similarly as far as temperature and evaporation are concerned. Clusters starting at a higher temperature show a higher initial evaporation rate and therefore reach the point where evaporation stop (around 240 K) sooner. The radius of the clusters is decreased by 0.16-0.22 nm after 0.5 mu s (larger clusters tend to decrease their radius slightly more), which corresponds to around one evaporated molecule per nm(2). The cluster temperature seems to converge towards 215 K independent of cluster size, when starting at 275 K. We observe only small structural changes, but the clusters modeled by TIP5P show a larger percentage of molecules with low diffusion coefficient as t ->infinity, than those using the two other water models. TIP4P seems to be more structured and more hydrogen bonds are formed than in the other models as the temperature falls. The cooling rates are in good agreement with experimental results, and evaporation rates agree well with a phenomenological expression based on experimental observations.

  • 40.
    Candanedo, J.
    et al.
    Arizona State Univ, Dept Phys, Tempe, AZ 85282 USA..
    Caleman, C
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, Hamburg, Germany..
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Beckstein, O.
    Arizona State Univ, Dept Phys, Tempe, AZ 85282 USA.;Arizona State Univ, Ctr Biol Phys, Tempe, AZ 85282 USA..
    Spence, J. C. H.
    Arizona State Univ, Dept Phys, Tempe, AZ 85282 USA..
    Dynamics of rare gas solids irradiated by electron beams2020In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 14, article id 144303Article in journal (Refereed)
    Abstract [en]

    The remarkable success of x-ray free-electron lasers and their ability to image biological macromolecules while outrunning secondary radiation damage due to photoelectrons, by using femtosecond pulses, raise the question of whether this can be done using pulsed high-energy electron beams. In this paper, we use excited state molecular dynamics simulations, with tabulated potentials, for rare gas solids to investigate the effect of radiation damage due to inelastic scattering (by plasmons, excitons, and heat) on the pair distribution function. We use electron energy loss spectra to characterize the electronic excitations responsible for radiation damage.

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  • 41. Carniato, S.
    et al.
    Journel, L.
    Guillemin, R.
    Piancastelli, Maria Novella
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Surface and Interface Science.
    Stolte, W. C.
    Lindle, D. W.
    Simon, M.
    A new method to derive electronegativity from resonant inelastic x-ray scattering2012In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, no 14, p. 144303-Article in journal (Refereed)
    Abstract [en]

    Electronegativity is a well-known property of atoms and substituent groups. Because there is no direct way to measure it, establishing a useful scale for electronegativity often entails correlating it to another chemical parameter; a wide variety of methods have been proposed over the past 80 years to do just that. This work reports a new approach that connects electronegativity to a spectroscopic parameter derived from resonant inelastic x-ray scattering. The new method is demonstrated using a series of chlorine-containing compounds, focusing on the Cl 2p(-1)LUMO(1) electronic states reached after Cl 1s -> LUMO core excitation and subsequent KL radiative decay. Based on an electron-density analysis of the LUMOs, the relative weights of the Cl 2p(z) atomic orbital contributing to the Cl 2p(3/2) molecular spin-orbit components are shown to yield a linear electronegativity scale consistent with previous approaches.

  • 42.
    Carvalho, Rodrigo P.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Marchiori, Cleber F. N.
    Karlstad Univ, Dept Engn & Phys, S-65188 Karlstad, Sweden..
    Brandell, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Araujo, C. Moyses
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Department of Engineering and Physics, Karlstad University.
    Understanding the lithiation limits of high-capacity organic battery anodes by atomic charge derivative analysis2022In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 157, no 18, article id 181101Article in journal (Refereed)
    Abstract [en]

    The superlithiation of organic anodes is a promising approach for developing the next generation of sustainable Li-ion batteries with high capacity. However, the lack of fundamental understanding hinders its faster development. Here, a systematic study of the lithiation processes in a set of dicarboxylate-based materials is carried out within the density functional theory formalism. It is demonstrated that a combined analysis of the Li insertion reaction thermodynamics and the conjugated-moiety charge derivative is able of establishing the experimentally observed maximum storage limits allowing also the assessment of the structure-function relationships.

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  • 43.
    Castleton, Christopher
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Tuning LDA+U for electron localization and structure at oxygen vacancies in ceria2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, no 24, p. 244704-244704-11Article in journal (Refereed)
    Abstract [en]

    We examine the real space structure and the electronic structure (particularly Ce4f electron localization) of oxygen vacancies in CeO2 (ceria) as a function of U in density functional theory studies with the rotationally invariant forms of the LDA+U and GGA+U functionals. The four nearest neighbor Ce ions always relax outwards, with those not carrying localized Ce4f charge moving furthest. Several quantification schemes show that the charge starts to become localized at U~3 eV and that the degree of localization reaches a maximum at ~6 eV for LDA+U or at ~5.5 eV for GGA+U. For higher U it decreases rapidly as charge is transferred onto second neighbor O ions and beyond. The localization is never into atomic corelike states; at maximum localization about 80-90% of the Ce4f charge is located on the two nearest neighboring Ce ions. However, if we look at the total atomic charge we find that the two ions only make a net gain of (0.2-0.4)e each, so localization is actually very incomplete, with localization of Ce4f electrons coming at the expense of moving other electrons off the Ce ions. We have also revisited some properties of defect-free ceria and find that with LDA+U the crystal structure is actually best described with U=3-4 eV, while the experimental band structure is obtained with U=7-8 eV. (For GGA+U the lattice parameters worsen for U>0 eV, but the band structure is similar to LDA+U.) The best overall choice is U~6 eV with LDA+U and ~5.5 eV for GGA+U, since the localization is most important, but a consistent choice for both CeO2 and Ce2O3, with and without vacancies, is hard to find.

  • 44.
    Ceolin, Denis
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics V.
    Piancastelli, Maria Novella
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics V.
    Guillemin, R.
    Stolte, W. C.
    Yu, S. -W
    Hemmers, O.
    Lindle, D. W.
    Fragmentation of methyl chloride studied by partial positive and negative ion-yield spectroscopy2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 126, no 8, p. 084309-Article in journal (Refereed)
    Abstract [en]

    The authors present partial-ion-yield experiments on the methyl chloride molecule excited in the vicinity of the C12p and C1s inner shells. A large number of fragments, cations produced by dissociation or recombination processes, as well as anionic species, have been detected. Although the spectra exhibit different intensity distributions depending on the core-excited atom, general observations include strong site-selective fragmentation along the C-Cl bond axis and a strong intensity dependence of transitions involving Rydberg series on fragment size.

  • 45.
    Chattopadhyay, Samir
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Indian Assoc Cultivat Sci, Sch Chem Sci, 2A & 2B Raja SC Mullick Rd, Kolkata 700032, India..
    Samanta, Soumya
    Indian Assoc Cultivat Sci, Sch Chem Sci, 2A & 2B Raja SC Mullick Rd, Kolkata 700032, India..
    Sarkar, Ankita
    Indian Assoc Cultivat Sci, Sch Chem Sci, 2A & 2B Raja SC Mullick Rd, Kolkata 700032, India..
    Bhattacharya, Aishik
    Indian Assoc Cultivat Sci, Sch Chem Sci, 2A & 2B Raja SC Mullick Rd, Kolkata 700032, India..
    Patra, Suman
    Indian Assoc Cultivat Sci, Sch Chem Sci, 2A & 2B Raja SC Mullick Rd, Kolkata 700032, India..
    Dey, Abhishek
    Indian Assoc Cultivat Sci, Sch Chem Sci, 2A & 2B Raja SC Mullick Rd, Kolkata 700032, India..
    Silver nanostructure-modified graphite electrode for in-operando SERRS investigation of iron porphyrins during high-potential electrocatalysis2023In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 158, no 4, article id 044201Article in journal (Refereed)
    Abstract [en]

    In-operando spectroscopic observation of the intermediates formed during various electrocatalytic oxidation and reduction reactions is crucial to propose the mechanism of the corresponding reaction. Surface-enhanced resonance Raman spectroscopy coupled to rotating disk electrochemistry (SERRS-RDE), developed about a decade ago, proved to be an excellent spectroscopic tool to investigate the mechanism of heterogeneous oxygen reduction reaction (ORR) catalyzed by synthetic iron porphyrin complexes under steady-state conditions in water. The information about the formation of the intermediates accumulated during the course of the reaction at the electrode interface helped to develop better ORR catalysts with second sphere residues in the porphyrin rings. To date, the application of this SERRS-RDE setup is limited to ORR only because the thiol self-assembled monolayer (SAM)-modified Ag electrode, used as the working electrode in these experiments, suffers from stability issues at more cathodic and anodic potential, where H2O oxidation, CO2 reduction, and H+ reduction reactions occur. The current investigation shows the development of a second-generation SERRS-RDE setup consisting of an Ag nanostructure (AgNS)-modified graphite electrode as the working electrode. These electrodes show higher stability (compared to the conventional thiol SAM-modified Ag electrode) upon exposure to very high cathodic and anodic potential with a good signal-to-noise ratio in the Raman spectra. The behavior of this modified electrode toward ORR is found to be the same as the SAM-modified Ag electrode, and the same ORR intermediates are observed during electrochemical ORR. At higher cathodic potential, the signatures of Fe(0) porphyrin, an important intermediate in H+ and CO2 reduction reactions, was observed at the electrode-water interface.

  • 46.
    Chenchiliyan, Manoop
    et al.
    Univ Gothenburg, Dept Chem & Mol Biol, Box 462, S-40530 Gothenburg, Sweden..
    Kuebel, Joachim
    Univ Gothenburg, Dept Chem & Mol Biol, Box 462, S-40530 Gothenburg, Sweden..
    Ooi, Saik Ann
    Univ Gothenburg, Dept Chem & Mol Biol, Box 462, S-40530 Gothenburg, Sweden..
    Salvadori, Giacomo
    Univ Pisa, Dept Chem & Ind Chem, Via G Moruzzi 13, I-56126 Pisa, Italy..
    Mennucci, Benedetta
    Univ Pisa, Dept Chem & Ind Chem, Via G Moruzzi 13, I-56126 Pisa, Italy..
    Westenhoff, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry. Univ Gothenburg, Dept Chem & Mol Biol, Box 462, S-40530 Gothenburg, Sweden..
    Maj, Michal
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy2023In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 158, no 8, article id 085103Article in journal (Refereed)
    Abstract [en]

    Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm(-1) band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.

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  • 47. Choe, Yong-Kee
    et al.
    Nakajima, Takahito
    Hirao, Kimihiko
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Theoretical study of the electronic ground state of iron(II) porphine. II1999In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 111, no 9, p. 3837-3845Article in journal (Refereed)
    Abstract [en]

    Ten low-lying electronic states of Fe(II) porphine, (5)A(1g), E-5(g), B-5(2g), (3)A(2g), B-3(2g), E-3(g)(A), E-3(g)(B), (1)A(1g), B-1(2g), and E-1(g) states, are studied with multiconfigurational second-order perturbation (CASPT2) calculations with complete active space self-consistent field (CASSCF) reference functions with larger active space and basis sets. The enlargement of active space and basis sets has no influence on the conclusion of a previous multireference Moller-Plesset perturbation (MRMP) study. The present CASPT2 calculation concludes that the (5)A(1g) state is the ground state. A relativistic correction has been performed by the relativistic scheme of eliminating small components (RESC). For energetics, no significant contribution from the relativistic correction was found. The relative energies and orbital energies are not changed appreciably by the introduction of a relativistic correction. The present result does not agree with all the spectroscopic observations, but is consistent with a magnetic moment study.

  • 48. Chwee, Tsz S
    et al.
    Szilva, Andrew B
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Carter, Emily A
    Linear scaling multireference singles and doubles configuration interaction2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 22, p. 224106-Article in journal (Refereed)
    Abstract [en]

    A linear scaling multireference singles and doubles configuration interaction (MRSDCI) method has been developed. By using localized bases to span the occupied and virtual subspace, local truncation schemes can be applied in tandem with integral screening to reduce the various bottlenecks in a MRSDCI calculation. Among these, the evaluation of electron repulsion integrals and their subsequent transformation, together with the diagonalization of the large CI Hamiltonian matrix, correspond to the most computationally intensive steps in a MRSDCI calculation. We show that linear scaling is possible within each step. The scaling of the method with system size is explored with a system of linear alkane chains and we proceed to demonstrate this method can produce smooth potential energy surfaces via calculating the dissociation of trans-6-dodecene (C12H24) along the central C=C bond.

  • 49. Costa, Luciano T.
    et al.
    Sun, Bing
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Jeschull, Fabian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Brandell, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Polymer-ionic liquid ternary systems for Li-battery electrolytes: Molecular dynamics studies of LiTFSI in a EMIm-TFSI and PEO blend2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, no 2, article id 024904Article in journal (Refereed)
    Abstract [en]

    This paper presents atomistic molecular dynamics simulation studies of lithium bis(trifluoromethane) sulfonylimide (LiTFSI) in a blend of 1-ethyl-3-methylimidazolium (EMIm)-TFSI and poly(ethylene oxide) (PEO), which is a promising electrolyte material for Li- and Li-ion batteries. Simulations of 100 ns were performed for temperatures between 303 K and 423 K, for a Li:ether oxygen ratio of 1:16, and for PEO chains with 26 EO repeating units. Li+ coordination and transportation were studied in the ternary electrolyte system, i.e., PEO16LiTFSI center dot 1.0 EMImTFSI, by applying three different force field models and are here compared to relevant simulation and experimental data. The force fields generated significantly different results, where a scaled charge model displayed the most reasonable comparisons with previous work and overall consistency. It is generally seen that the Li cations are primarily coordinated to polymer chains and less coupled to TFSI anion. The addition of EMImTFSI in the electrolyte system enhances Li diffusion, associated to the enhanced TFSI dynamics observed when increasing the overall TFSI anion concentration in the polymer matrix. (C) 2015 AIP Publishing LLC.

  • 50.
    Coulier, Adrien
    et al.
    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.
    Hellander, Stefan
    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.
    Hellander, Andreas
    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.
    A multiscale compartment-based model of stochastic gene regulatory networks using hitting-time analysis2021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 18, article id 184105Article in journal (Refereed)
    Abstract [en]

    Spatial stochastic models of single cell kinetics are capable of capturing both fluctuations in molecular numbers and the spatial dependencies of the key steps of intracellular regulatory networks. The spatial stochastic model can be simulated both on a detailed microscopic level using particle tracking and on a mesoscopic level using the reaction–diffusion master equation. However, despite substantial progress on simulation efficiency for spatial models in the last years, the computational cost quickly becomes prohibitively expensive for tasks that require repeated simulation of thousands or millions of realizations of the model. This limits the use of spatial models in applications such as multicellular simulations, likelihood-free parameter inference, and robustness analysis. Further approximation of the spatial dynamics is needed to accelerate such computational engineering tasks. We here propose a multiscale model where a compartment-based model approximates a detailed spatial stochastic model. The compartment model is constructed via a first-exit time analysis on the spatial model, thus capturing critical spatial aspects of the fine-grained simulations, at a cost close to the simple well-mixed model. We apply the multiscale model to a canonical model of negative-feedback gene regulation, assess its accuracy over a range of parameters, and demonstrate that the approximation can yield substantial speedups for likelihood-free parameter inference.

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