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  • 1.
    Ahrén, Maria
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Selegård, Linnéa
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Söderlind, Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Nanostructured Materials. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Kauczor, Joanna
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Käll, Per-Olov
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry. Linköping University, The Institute of Technology.
    Uvdal, Kajsa
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    A simple polyol-free synthesis route to Gd2O3 nanoparticles for MRI applications: an experimental and theoretical study2012In: Journal of nanoparticle research, ISSN 1388-0764, E-ISSN 1572-896X, Vol. 14, no 8Article in journal (Refereed)
    Abstract [en]

    Chelated gadolinium ions, e. g., GdDTPA, are today used clinically as contrast agents for magnetic resonance imaging (MRI). An attractive alternative contrast agent is composed of gadolinium oxide nanoparticles as they have shown to provide enhanced contrast and, in principle, more straightforward molecular capping possibilities. In this study, we report a new, simple, and polyol-free way of synthesizing 4-5-nm-sized Gd2O3 nanoparticles at room temperature, with high stability and water solubility. The nanoparticles induce high-proton relaxivity compared to Gd-DTPA showing r(1) and r(2) values almost as high as those for free Gd3+ ions in water. The Gd2O3 nanoparticles are capped with acetate and carbonate groups, as shown with infrared spectroscopy, near-edge X-ray absorption spectroscopy, X-ray photoelectron spectroscopy and combined thermogravimetric and mass spectroscopy analysis. Interpretation of infrared spectroscopy data is corroborated by extensive quantum chemical calculations. This nanomaterial is easily prepared and has promising properties to function as a core in a future contrast agent for MRI.

  • 2.
    Ahrén, Maria
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    Söderlind, Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Nanostructured Materials. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Nordblad, Per
    Division of Solid State Physics, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Uvdal, Kajsa
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
    One-step synthesis of sub 5 nm sized manganese oxide based nanoparticles2013Manuscript (preprint) (Other academic)
    Abstract [en]

    Sub 5 nm sized manganese oxide nanoparticles; MnOx (1 ≤ x ≤ 2), were synthesized via a short time room temperature synthesis route. The nanoparticles are crystalline, spherically shaped and in the size range of 2-4 nm as shown by transmission electron microscopy studies. Selected area electron diffraction patterns were collected and their appearance indicated that the nanoparticle cores are composed of MnO. Also, co-existence of the (II) and (III) oxidation states at the nanoparticle surface was verified by results achieved from infrared spectroscopy and X-ray photoelectron spectroscopy. These measurements also supported presence of a minor amount of acetate groups as well as a negligible fraction of carbonate groups at the nanoparticle surfaces. The interpretation of the IR spectra was confirmed by quantum chemical calculations using the high spin manganese nanoparticle Mn12O12(OAc)16(H2O)4, as a model system for the MnOx nanoparticle surface. Bulk MnO and Mn2O3 are known to be antiferromagnetic. The magnetic properties are however somewhat dependent of the crystallite size and changes when scaling down to the nanoregion. The MnOx (1 ≤ x ≤ 2) nanoparticles investigated in this work show a superparamagnetic behavior with a blocking temperature of approximately 12 K proven by means of SQUID measurements. The relaxivities of the nanoparticles and the Mn(OAc)2 precursors were studied with a bench top NMR analyzer verifying nanoparticle r1 and r2 of 0.5 and 6 mMs-1 respectively. The r1 relaxivity is lower than what is earlier reported for Gd based contrast agent, but improvements are expected by further surface modification, due to increased rotational time and higher water dispersability.

  • 3.
    Aidas, Kestutis
    et al.
    Vilnius University, Lithuania .
    Angeli, Celestino
    University of Ferrara, Italy .
    Bak, Keld L.
    University of Aarhus, Denmark .
    Bakken, Vebjorn
    University of Oslo, Norway .
    Bast, Radovan
    KTH Royal Institute Technology, Sweden .
    Boman, Linus
    EMGS ASA, Norway .
    Christiansen, Ove
    University of Aarhus, Denmark .
    Cimiraglia, Renzo
    University of Ferrara, Italy .
    Coriani, Sonia
    University of Trieste, Italy .
    Dahle, Pal
    Norwegian Comp Centre, Norway .
    Dalskov, Erik K.
    Systematic, Denmark .
    Ekstrom, Ulf
    University of Oslo, Norway .
    Enevoldsen, Thomas
    University of So Denmark, Denmark .
    Eriksen, Janus J.
    University of Aarhus, Denmark .
    Ettenhuber, Patrick
    University of Aarhus, Denmark .
    Fernandez, Berta
    University of Santiago de Compostela, Spain University of Santiago de Compostela, Spain .
    Ferrighi, Lara
    UiT Arctic University of Norway, Norway .
    Fliegl, Heike
    University of Oslo, Norway .
    Frediani, Luca
    UiT Arctic University of Norway, Norway .
    Hald, Kasper
    Danske Bank, Denmark .
    Halkier, Asger
    CSC Scandihealth, Denmark .
    Hattig, Christof
    Ruhr University of Bochum, Germany .
    Heiberg, Hanne
    Norwegian Meteorol Institute, Norway .
    Helgaker, Trygve
    University of Oslo, Norway .
    Christian Hennum, Alf
    Norwegian Def Research Estab, Norway .
    Hettema, Hinne
    University of Auckland, New Zealand .
    Hjertenaes, Eirik
    Norwegian University of Science and Technology, Norway .
    Host, Stinne
    University of Aarhus, Denmark .
    Hoyvik, Ida-Marie
    University of Aarhus, Denmark .
    Francesca Iozzi, Maria
    University of Oslo, Norway .
    Jansik, Branislav
    Technical University of Ostrava, Czech Republic .
    Jorgen Aa. Jensen, Hans
    University of So Denmark, Denmark .
    Jonsson, Dan
    UiT Arctic University of Norway, Norway .
    Jorgensen, Poul
    University of Aarhus, Denmark .
    Kauczor, Joanna
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Kirpekar, Sheela
    KVUC, Denmark .
    Kjrgaard, Thomas
    University of Aarhus, Denmark .
    Klopper, Wim
    Karlsruhe Institute Technology, Germany .
    Knecht, Stefan
    Swiss Federal Institute Technology, Switzerland .
    Kobayashi, Rika
    Australian National University, Australia .
    Koch, Henrik
    Norwegian University of Science and Technology, Norway .
    Kongsted, Jacob
    University of So Denmark, Denmark .
    Krapp, Andreas
    Jotun AS, Norway .
    Kristensen, Kasper
    University of Aarhus, Denmark .
    Ligabue, Andrea
    University of Modena and Reggio Emilia, Italy .
    B. Lutnaes, Ola
    Cisco Syst, Norway .
    I. Melo, Juan
    University of Buenos Aires, Argentina University of Buenos Aires, Argentina .
    V. Mikkelsen, Kurt
    University of Copenhagen, Denmark .
    H. Myhre, Rolf
    Norwegian University of Science and Technology, Norway .
    Neiss, Christian
    University of Erlangen Nurnberg, Germany .
    B. Nielsen, Christian
    Sun Chemistry, Denmark .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Olsen, Jeppe
    University of Aarhus, Denmark University of So Denmark, Denmark .
    Magnus H. Olsen, Jogvan
    University of Aarhus, Denmark University of So Denmark, Denmark .
    Osted, Anders
    Koge Gymnasium, Denmark .
    J. Packer, Martin
    University of So Denmark, Denmark .
    Pawlowski, Filip
    Kazimierz Wielki University, Poland .
    B. Pedersen, Thomas
    University of Oslo, Norway .
    F. Provasi, Patricio
    Northeastern University, Argentina IMIT CONICET, Argentina .
    Reine, Simen
    University of Oslo, Norway .
    Rinkevicius, Zilvinas
    KTH Royal Institute Technology, Sweden KTH Royal Institute Technology, Sweden .
    A. Ruden, Torgeir
    Kjeller Software Commun, Norway .
    Ruud, Kenneth
    UiT Arctic University of Norway, Norway .
    V. Rybkin, Vladimir
    Karlsruhe Institute Technology, Germany .
    Salek, Pawel
    PSS9 Dev, Poland .
    C. M. Samson, Claire
    Karlsruhe Institute Technology, Germany .
    Sanchez de Meras, Alfredo
    University of Valencia, Spain .
    Saue, Trond
    University of Toulouse 3, France .
    P. A. Sauer, Stephan
    University of Copenhagen, Denmark .
    Schimmelpfennig, Bernd
    Karlsruhe Institute Technology, Germany .
    Sneskov, Kristian
    Danske Bank, Denmark .
    H. Steindal, Arnfinn
    UiT Arctic University of Norway, Norway .
    O. Sylvester-Hvid, Kristian
    Danish Technology Institute Nano and Microtechnol Prod, Denmark .
    R. Taylor, Peter
    University of Melbourne, Australia University of Melbourne, Australia .
    M. Teale, Andrew
    University of Nottingham, England .
    I. Tellgren, Erik
    University of Oslo, Norway .
    P. Tew, David
    University of Bristol, England .
    J. Thorvaldsen, Andreas
    University of Aarhus, Denmark .
    Thogersen, Lea
    CLC bio, Denmark .
    Vahtras, Olav
    KTH Royal Institute Technology, Sweden .
    A. Watson, Mark
    Princeton University, NJ 08544 USA .
    J. D. Wilson, David
    La Trobe University, Australia La Trobe University, Australia .
    Ziolkowski, Marcin
    Clemson University, SC USA .
    Agren, Hans
    KTH Royal Institute Technology, Sweden .
    The Dalton quantum chemistry program system2014In: WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, ISSN 1759-0876, Vol. 4, no 3, p. 269-284Article in journal (Refereed)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 4.
    Alagia, M.
    et al.
    ISMN-CNR, Sez. Roma1, P.le A. Moro 5, I-00185 Roma, Italy and TASC-CNR, Area Science Park, Basovizza, I-34012 Trieste, Italy.
    Lavollée, M.
    LIXAM-CNRS, F-91898 Orsay-Cedex, France.
    Richter, R.
    Sincrotrone Trieste, Area Science Park, I-34012 Basovizza, Trieste, Italy.
    Ekström, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Carravetta, V.
    Institute of Chemical Physical Processes (CNR), Via Moruzzi 1, I-56124 Pisa, Italy.
    Stranges, D.
    Dipartimento di Chimica and INSTM, Universitá La Sapienza, P.le A. Moro 5, I-00185 Roma, Italy and ISMN-CNR, Sez. Roma1, P.le A. Moro 5, I-00185 Roma, Italy.
    Brunetti, B.
    ISMN-CNR, Sez. Roma1, P.le A. Moro 5, I-00185 Roma, Italy.
    Stranges, S.
    Dipartimento di Chimica and INSTM, Universitá La Sapienza, P.le A. Moro 5, I-00185 Roma, Italy; ISMN-CNR, Sez. Roma1, P.le A. Moro 5, I-00185 Roma, Italy; and TASC-CNR, Area Science Park, Basovizza, I-34012 Trieste, Italy.
    Probing the potential energy surface by highresolution x-ray absorption spectroscopy: The umbrella motion of the coreexcited CH3 free radical2007In: Physical Review. A, ISSN 1050-2947, Vol. 76, no 2, p. 124305-Article in journal (Refereed)
    Abstract [en]

    A detailed study of the umbrellalike vibration in inner-shell spectroscopy is presented. The high-resolution x-ray absorption spectrum for the lowest lying core excitation of the CH3 free radical was recorded. High quality potential energy surfaces (PES) for the initial and final states of the transition were calculated as a function of the symmetrical stretching and the umbrella deformation coordinates. The strong anharmonicity along the umbrella coordinate in the double-well region of the PES of the core excited state has a strong effect on the bending vibrational progressions. The excellent agreement between the experiment and theory allows an accurate spectroscopic characterization of the vibrational structure of the electronic transition, and the estimation of the umbrella inversion time of 149  fs.

  • 5.
    Alagia, Michele
    et al.
    ISMN-CNR, Rom.
    Baldacchini, Chiara
    Università di Roma "La Sapienza" .
    Betti, Maria Grazia
    Università di Roma "La Sapienza" .
    Bussolotti, Fabio
    Università di Modena e Reggio Emilia.
    Carravetta, Vincenzo
    IPCF-CNR, Pisa.
    Ekström, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Mariani, Carlo
    Università di Roma "La Sapienza" .
    Stranges, Stefano
    Università di Roma "La Sapienza" .
    Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: Experiment and theory2005In: Journal of chemical physics Online, ISSN 1089-7690, Vol. 122, no 12, p. 124305-Article in journal (Refereed)
    Abstract [en]

    The C K-edge photoabsorption and 1s core-level photoemission of pentacene (C22H14) free molecules are experimentally measured, and calculated by self-consistent-field and static-exchange approximation ab initio methods. Six nonequivalent C atoms present in the molecule contribute to the C 1s photoemission spectrum. The complex near-edge structures of the carbon K-edge absorption spectrum present two main groups of discrete transitions between 283 and 288  eV photon energy, due to absorption to * virtual orbitals, and broader structures at higher energy, involving * virtual orbitals. The sharp absorption structures to the * empty orbitals lay well below the thresholds for the C 1s ionizations, caused by strong excitonic and localization effects. We can definitely explain the C K-edge absorption spectrum as due to both final (virtual) and initial (core) orbital effects, mainly involving excitations to the two lowest-unoccupied molecular orbitals of * symmetry, from the six chemically shifted C 1s core orbitals. ©2005 American Institute of Physics

  • 6.
    Al-Saidi, W A
    et al.
    University of Pittsburgh, USA .
    Asher, Sanford A
    University of Pittsburgh, USA .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Resonance Raman Spectra of TNT and RDX Using Vibronic Theory, Excited-State Gradient, and Complex Polarizability Approximations2012In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, no 30, p. 7862-7872Article in journal (Refereed)
    Abstract [en]

    Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined lowenergy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX.

  • 7.
    Baev, Alexander
    et al.
    Institute for lasers, Photonics and Biophotonics SUNY at Buffalo, USA.
    Henriksson, Johan
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Norman, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Ågren, Hans
    KTH, Stockholm.
    A quantum mechanical - Electrodynamical approach to nonlinear properties: Application to optical power limiting with platinum-organic compounds2007In: Journal of nonlinear optical physics and materials, ISSN 0218-8635, Vol. 16, no 2, p. 157-169Article in journal (Refereed)
    Abstract [en]

    Light propagation in a medium is sensitively dependent on the shape and intensity of the optical pulse as well as on the electronic and vibrational structure of the basic molecular units. We review in this paper the results of systematic studies of this problem for isotropic media. Our theoretical approach - the quantum mechanical-electrodynamical (QMED) approach - is based on a quantum mechanical account of the many-level electron-nuclear medium coupled to a numerical solution of the density matrix and Maxwell's equations. This allows us to accommodate a variety of nonlinear effects which accomplish the propagation of strong light pulses. Particular attention is paid to the understanding of the role of coherent and sequential excitations of electron-nuclear degrees of freedom. The QMED combination of quantum chemistry with classical pulse propagation enables us to estimate the optical transmission from cross sections of multi-photon absorption processes and from considerations of propagation effects, saturation and pulse effects. Results of the theory suggest that in the nonlinear regime, it is often necessary to simultaneously account for coherent one-step and incoherent step-wise multi-photon absorption, as well as for off-resonant excitations even when resonance conditions prevail. The dynamic theory of nonlinear propagation of a few interacting intense light pulses is highlighted here in a study of the optical power limiting with platinum-organic molecular compounds. © World Scientific Publishing Company.

  • 8.
    Baev, Alexander
    et al.
    Institute for Lasers, Photonics and Biophotonics, SUNY at Buffalo, Buffalo, New York .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Henriksson, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Ågren, Hans
    Theoretical Chemistry, Royal Institute of Technology, Stockholm.
    Theoretical Simulations of Clamping Levels in Optical Power Limiting2006In: Journal of Physical Chemistry B, ISSN 1520-5215, Vol. 110, no 42, p. 20912-20916Article in journal (Refereed)
    Abstract [en]

    Multiphysics modeling, combining quantum mechanical and classical wave mechanical theories, of clamping levels has been performed for a platinum(II) organic compound in a sol−gel glass matrix. A clamping level of 2.5 μJ is found for a pulse duration of 10 ns. The excited-state absorption in the triplet manifold is shown to be crucial for clamping to occur.

  • 9.
    Bast, Radovan
    et al.
    CNRS.
    Saue, Trond
    CNRS.
    Henriksson, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Norman , Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Role of noncollinear magnetization for the first-order electric-dipole hyperpolarizability at the four-component Kohn-Sham density functional theory level2009In: JOURNAL OF CHEMICAL PHYSICS, ISSN 0021-9606 , Vol. 130, no 2, p. 024109-Article in journal (Refereed)
    Abstract [en]

    The quadratic response function has been derived and implemented at the adiabatic four-component Kohn-Sham density functional theory level with inclusion of noncollinear spin magnetization and gradient corrections in the exchange-correlation functional-a work that is an extension of our previous report where magnetization dependencies in the exchange-correlation functional were ignored [J. Henriksson, T. Saue, and P. Norman, J. Chem. Phys. 128, 024105 (2008)]. The electric-field induced second-harmonic generation experiments on CF3Cl and CF3Br are addressed by a determination of (beta) over bar (-2 omega;omega,omega) for a wavelength of 694.3 nm, and the same property is also determined for CF3I. The relativistic effects on the static hyperpolarizability for the series of molecules amount to 1%, 5%, and 9%, respectively. At the experimental wavelength, the contributions to beta due to the magnetization dependence in the exchange-correlation functional are negligible for CF3Cl and CF3Br and small for CF3I. The noticeable effect of magnetization in the latter case is attributed to a near two-photon resonance with the excited state 1 E-3 (nonrelativistic notation). It is emphasized, however, that the effect of magnetization on beta for CF3I is negligible both in comparison to the total relativistic correction as well as to the effects of electron correlation. It is concluded that, in calculations of hyperpolarizabilities under nonresonant conditions, the magnetization dependence in the exchange-correlation functional may be ignored.

  • 10.
    Baughman, R.H.
    et al.
    Honeywell International, Honeywell Technology Center, Morristown, NJ 07962-1021, United States.
    Dantas, S.O.
    Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, 36036-330, Mina Gerais, Brazil.
    Stafström, Sven
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Zakhidov, A.A.
    Honeywell International, Honeywell Technology Center, Morristown, NJ 07962-1021, United States.
    Mitchell, T.B.
    Natl. Inst. of Std. and Technology, Boulder, CO 80303, United States.
    Dubin, D.H.E.
    Department of Physics, Univ. of California at San Diego, San Diego, CA 92093, United States.
    Negative Poisson's ratios for extreme states of matter2000In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 288, no 5473, p. 2018-2022Article in journal (Refereed)
    Abstract [en]

    Negative Poisson's ratios are predicted for body-centered-cubic phases that likely exist in white dwarf cores and neutron star outer crusts, as well as those found for vacuumlike ion crystals, plasma dust crystals, and colloidal crystals (including certain virus crystals). The existence of this counterintuitive property, which means that a material laterally expands when stretched, is experimentally demonstrated for very low density crystals of trapped ions. At very high densities, the large predicted negative and positive Poisson's ratios might be important for understanding the asteroseismology of neutron stars and white dwarfs and the effect of stellar stresses on nuclear reaction rates. Giant Poisson's ratios are both predicted and observed for highly strained coulombic photonic crystals, suggesting possible applications of large, tunable Poisson's ratios for photonic crystal devices.

  • 11.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hanke, Felix
    Accelrys, 334 Science Park, Cambridge, CB4 0WN, United Kingdom.
    Towards Design Rules for Covalent Nanostructures on Metal Surfaces2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 4, p. 928-934Article in journal (Refereed)
    Abstract [en]

    The covalent molecular assembly on metal surfaces is explored, outlining the different types of applicable reactions. Density functional calculations for on-surface reactions are shown to yield valuable insights into specific reaction mechanisms and trends across the periodic table. Finally, it is shown how design rules could be derived for nanostructures on metal surfaces.

  • 12.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hanke, Felix
    Surface Science Research Centre, University of Liverpool, UK.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Mechanisms of halogen-based covalent self-assembly on metal surfaces2013In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, no 15, p. 5768-5775Article in journal (Refereed)
    Abstract [en]

    We computationally study the reaction mechanisms of halogen-based covalent self-assembly, a major route for synthesizing molecular nanostructures and nanographenes on surfaces. Focusing on biphenyl as a small model system, we describe the dehalogenation, recombination, and diffusion processes. The kinetics of the different processes are also investigated, in particular how diffusion and coupling barriers affect recombination rates. Trends across the periodic table are derived from three commonly used close-packed (111) surfaces (Cu, Ag, and Au) and two halogens (Br and I). We show that the halogen atoms can poison the surface, thus hindering long-range ordering of the self-assembled structures. Finally, we present core-level shifts of the relevant carbon and halogen atoms, to provide reference data for reliably detecting self-assembly without the need for atomic-resolution scanning tunneling microscopy.

  • 13.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Adsorption of large hydrocarbons on coinage metals: a van der Waals density functional study2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 13, p. 2851-2858Article in journal (Refereed)
    Abstract [en]

    The adsorption of organic molecules onto the close-packed facets of coinage metals is studied, and how accurately adsorption heights can be described by using recent advances of the van der Waals density functional (vdWDF), with optPBE/vdWDF, optB86b/vdWDF, vdWDF2, and rev/vdWDF2 functionals is illustrated. The adsorption of two prototypical aromatic hydrocarbons is investigated, and the calculated adsorption heights are compared to experimental literature values from normal incident X-ray standing wave absorption and a state-of-the-art semi-empirical method. It is shown that both the optB86b/vdWDF and rev/vdWDF2 functionals describe adsorption heights with an accuracy of 0.1 Å, compared to experimental values, and are concluded as reliable methods of choice for related systems.

  • 14.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Hanke, Felix
    University of Liverpool.
    Zipping Up: Cooperativity Drives the Synthesis of Graphene Nanoribbons2011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 38, p. 14884-14887Article in journal (Refereed)
    Abstract [en]

    We investigate the cooperative effects controlling the synthesis of a graphene nanoribbon on the Au(111) surface starting from an anthracene polymer using density functional calculations including van der Waals interactions. We focus on the high-temperature cyclodehydrogenation step of the reaction and find that the reaction proceeds by simultaneously transferring two H-atoms from the anthracene units to the Au surface, leaving behind a C C bond in the process. This step is significantly more favorable than the three other potential reaction paths. Moreover, we find that successive dehydrogenations proceed from one end of the polyanthracene and propagate step-by-step through the polymer in a domino-like fashion.

  • 15.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Zhang, Yi-Qi
    Technische Universität München, Garching, Germany.
    Klappenberger, Florian
    Technische Universität München, Garching, Germany.
    Barth, Johannes V.
    Technische Universität München, Garching, Germany.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Unraveling the Mechanism of the Covalent Coupling Between Terminal Alkynes on a Noble Metal2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 6, p. 3181-3187Article in journal (Refereed)
    Abstract [en]

    The mechanism of the newly reported route for surface-assisted covalent coupling of terminal alkynes on Ag(111) is unraveled by density functional theory based transition state calculations. We illustrate that the reaction path is fundamentally different from the classical coupling schemes in wet chemistry. It is initiated by the covalent coupling between two molecules instead of single-molecule dehydrogenation. The silver substrate is found to play an important role stabilizing the intermediate species by chemical bonds, although it is hardly active electronically in the actual coupling step. The dimer intermediate is concluded to undergo two subsequent dehydrogenation processes expected to be rate-limiting according to the comparatively large barriers, which origin is discussed.

  • 16.
    Boström, Mathias
    et al.
    Royal Institute Technology, Sweden.
    Persson, Clas
    Royal Institute Technology, Sweden.
    Ninham, Barry W
    Australian National University, Australia.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Sernelius, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, The Institute of Technology.
    Resonance interaction induced by metal surfaces catalyzes atom-pair breakage2013In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 87, no 4Article in journal (Refereed)
    Abstract [en]

    We present the theory for retarded resonance interaction between two identical atoms at arbitrary positions near a metal surface. The dipole-dipole resonance interaction force that binds isotropically excited atom pairs together in free space may turn repulsive close to an ideal (totally reflecting) metal surface. On the other hand, close to an infinitely permeable surface it may turn more attractive. We illustrate numerically how the dipole-dipole resonance interaction between two oxygen atoms near a metal surface may provide a repulsive energy of the same order of magnitude as the ground-state binding energy of an oxygen molecule. As a complement we also present results from density-functional theory.

  • 17.
    Bouchet, Aude
    et al.
    University of Bordeaux 1.
    Brotin, Thierry
    Ecole Normale Super Lyon.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Cavagnat, Dominique
    University of Bordeaux 1.
    Buffeteau, Thierry
    University of Bordeaux 1.
    Influence of the Chemical Structure of Water-Soluble Cryptophanes on Their Overall Chiroptical and Binding Properties2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 19, p. 7816-7825Article in journal (Refereed)
    Abstract [en]

    The synthesis and the chiroptical properties of the two enantiomers of the hexacarboxylic acid cryptophane-A derivative, 1, are described in this article. The chiroptical and binding properties of 1 toward achiral and chiral guests have been investigated in water under basic conditions by polarimetry, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and (1)H NMR spectroscopy. These experiments reveal that the (1)H NMR spectra of 1 are very sensitive to the nature of the guest trapped in its cavity whereas ECD and VCD spectra remain unchanged. We also show that the two enantiomers of 1 are able to distinguish between the two enantiomers of a series of small chiral epoxides. The enantiodiscrimination increases with the size of the chiral guest whereas the corresponding binding constants decrease. In contrast to what was observed for other water-soluble cryptophanes, the molecular recognition process is found independent of the nature of the counterions surrounding host 1, shedding light on the importance of the chemical structure of cryptophanes on their binding and chiroptical properties.

  • 18.
    Brede, Jens
    et al.
    University of Hamburg.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Kuck, Stefan
    University of Hamburg.
    Schwoebel, Joerg
    University of Hamburg.
    Scarfato, Alessandro
    University of Hamburg.
    Chang, Shih-Hsin
    University of Hamburg.
    Hoffmann, Germar
    University of Hamburg.
    Wiesendanger, Roland
    University of Hamburg.
    Lensen, Roy
    Radboud University Nijmegen.
    Kouwer, Paul H J
    Radboud University Nijmegen.
    Hoogboom, Johan
    Radboud University Nijmegen.
    Rowan, Alan E
    Radboud University Nijmegen.
    Broering, Martin
    University of Marburg.
    Funk, Markus
    University of Marburg.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Zerbetto, Francesco
    University of Bologna.
    Lazzaroni, Roberto
    University of Mons.
    Dynamics of molecular self-ordering in tetraphenyl porphyrin monolayers on metallic substrates2009In: NANOTECHNOLOGY, ISSN 0957-4484, Vol. 20, no 27, p. 275602-Article in journal (Refereed)
    Abstract [en]

    A molecular model system of tetraphenyl porphyrins (TPP) adsorbed on metallic substrates is systematically investigated within a joint scanning tunnelling microscopy/molecular modelling approach. The molecular conformation of TPP molecules, their adsorption on a gold surface and the growth of highly ordered TPP islands are modelled with a combination of density functional theory and dynamic force field methods. The results indicate a subtle interplay between different contributions. The molecule-substrate interaction causes a bending of the porphyrin core which also determines the relative orientations of phenyl legs attached to the core. A major consequence of this is a characteristic (and energetically most favourable) arrangement of molecules within self-assembled molecular clusters; the phenyl legs of adjacent molecules are not aligned parallel to each other (often denoted as pi-pi stacking) but perpendicularly in a T-shaped arrangement. The results of the simulations are fully consistent with the scanning tunnelling microscopy observations, in terms of the symmetries of individual molecules, orientation and relative alignment of molecules in the self-assembled clusters.

  • 19.
    Brede, Jens
    et al.
    University of Hamburg.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Lensen, Roy
    Radboud University.
    Rowan, Alan E
    Radboud University.
    Funk, Markus
    University of Marburg.
    Broering, Martin
    University of Marburg.
    Hoffmann, Germar
    University of Marburg.
    Wiesendanger , Roland
    University of Marburg.
    Adsorption and conformation of porphyrins on metallic surfaces2009In: JOURNAL OF VACUUM SCIENCE and TECHNOLOGY B, ISSN 1071-1023 , Vol. 27, no 2, p. 799-804Article in journal (Refereed)
    Abstract [en]

    Tetraphenyl porphyrins (TPP) belong to a highly interesting class of molecules with a large variety of electronic, magnetic, and structural properties. So far, local investigations by scanning probe techniques were primarily focused on larger agglomerates of TPP molecules. Here, experimental results of the observation and manipulation of isolated molecules adsorbed on cold metal substrates by means of low temperature scanning tunneling microscopy are presented. Depending on the surface geometry, i.e., Cu(111) VS, Cu(100) three distinct deformations of the molecular structure are identified reflecting the interaction of the phenyl periphery with the substrate. In a second step, controlled manipulation in terms of deformation of the porphyrin core, ligand dissociation, and lateral displacement of the phenyl periphery are demonstrated.

  • 20.
    Brocorens, Patrick
    et al.
    University of Mons Mat Nova, Belgium .
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Guyard-Duhayon, Carine
    CNRS, France .
    Guillot, Regis
    University of Paris 11, France .
    Andrioletti, Bruno
    University of Lyon 1, France .
    Suhr, Dominique
    University of Paris 06, France .
    Isare, Benjamin
    University of Paris 06, France .
    Lazzaroni, Roberto
    University of Mons Mat Nova, Belgium .
    Bouteiller, Laurent
    University of Paris 06, France .
    Conformational Plasticity of Hydrogen Bonded Bis-urea Supramolecular Polymers2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 17, p. 5379-5386Article in journal (Refereed)
    Abstract [en]

    We report a detailed structural investigation of supramolecular polymers formed by hydrogen bonded self assembly of bis-urea monomers The careful exploration of the energy landscape by molecular mechanics/molecular dynamics (MM/MD) simulations has allowed us to identify three distinct self assembled structures of similar stabilities. These structures have been compared to X-ray crystal data. We observe that a slight change in the molecular structure can favor a particular structure over the others. Detailed analysis shows that hydrogen bonds stabilize all three structures to a similar extent Therefore, it is the interactions among the lateral substituents, and with the filament environment, that are the decisive factors in the competition between the possible self-assembled structures. This study constitutes a clear reminder that the conformation of a supramolecular polymer is a sensitive function of the molecular structure and may significantly differ from the solid-state conformation of a model compound.

  • 21.
    Broitman, E.
    et al.
    Carnegie Mellon Univ, Dept Chem Engn, Pittsburgh, PA 15213 USA.
    Furlan, Andrej
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Kostov Gueorguiev, Gueorgui
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Czigany, Zs.
    Res Inst Tech Phys and Mat Sci, H-1525 Budapest, Hungary.
    Tarditi, A M
    Univ Nacl Litoral, RA-3000 Santa Fe, Argentina.
    Gellman, A J
    Carnegie Mellon Univ, Dept Chem Engn, Pittsburgh, PA 15213 USA.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Hultman, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Water adsorption on phosphorous-carbide thin films2009In: Surface & Coatings Technology, ISSN 0257-8972, E-ISSN 1879-3347, Vol. 204, no 6-7, p. 1035-1039Article in journal (Refereed)
    Abstract [en]

    Amorphous phosphorous-carbide films have been considered as a new tribological coating material with unique electrical properties. However, such CPx films have not found practical use until now because they tend to oxidize/hydrolyze rapidly when in contact with air. Recently, we demonstrated that CPx thin films with a fullerene-like structure can be deposited by magnetron sputtering, whereby the structural incorporation of P atoms induces the formation of strongly bent and inter-linked graphene planes. Here, we compare the uptake of water in fullerene-like phosphorous-carbide (FL-CPx) thin films with that in amorphous phosphorous-carbide (a-CPx), and amorphous carbon (a-C) thin films. Films of each material were deposited on quartz crystal substrates by reactive DC magnetron sputtering to a thickness in the range 100-300 nm. The film microstructure was characterized by X-ray photoelectron spectroscopy, and high resolution transmission electron microscopy. A quartz crystal microbalance placed in a vacuum chamber was used to measure their water adsorption. Measurements indicate that FL-CPx films adsorbed less water than the a-CPx and a-C ones. To provide additional insight into the atomic structure of defects in the FL-CPx and a-CPx compounds, we performed first-principles calculations within the framework of density functional theory. Cohesive energy comparison reveals that the energy cost formation for dangling bonds in different configurations is considerably higher in FL-CPx than for the amorphous films. Thus, the modeling confirms the experimental results that dangling bonds are less likely in FL-CPx than in a-CPx and a-C films.

  • 22.
    Broitman, E
    et al.
    Carnegie Mellon University.
    Kostov Gueorguiev, Gueorgui
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Furlan, Andrej
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Son, Tien Nguyen
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Gellman, A J
    Carnegie Mellon University.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Hultman , Lars
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Water adsorption on fullerene-like carbon nitride overcoats2008In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 517, no 3, p. 1106-1110Article in journal (Refereed)
    Abstract [en]

    Humidity influences the tribological performance of the head-disk interface in magnetic data storage devices. In this work we compare the uptake of water of amorphous carbon nitride (a-CNx) films, widely used as protective overcoats in computer disk drive systems, with fullerene-like carbon nitride (FL-CNx) and amorphous carbon (a-C) films. Films with thickness in the range 10-300 run were deposited on quartz crystal substrates by reactive DC magnetron sputtering. A quartz crystal microbalance placed in a vacuum chamber was used to measure the water adsorption. Electron paramagnetic resonance (EPR) has been used to correlate water adsorption with film microstructure and surface defects (dangling bonds). Measurements indicate that the amount of adsorbed water is highest for the pure a-C films and that the FL-CNx films adsorbed less than a-CNx. EPR data correlate the lower water adsorption on FL-CNx films with a possible lack of dangling bonds on the film surface. To provide additional insight into the atomic structure of defects in the FL-CNx, a-CNx and a-C compounds, we performed first-principles calculations within the framework of Density Functional Theory. Emphasis was put on the energy cost for formation of vacancy defects and dangling bonds in relaxed systems. Cohesive energy comparison reveals that the energy cost formation for dangling bonds in different configurations is considerably higher in FL-CNx than for the amorphous films. These simulations thus confirm the experimental results showing that dangling bonds are much less likely in FL-CNx than in a-CNx and a-C films.

  • 23.
    Bucher, Denis
    et al.
    University of Sydney.
    M Sandala, Gregory
    University of Sydney.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Radom, Leo
    University of Sydney.
    Smith, David M
    Rudjer Boskovic Institute.
    The elusive 5'-deoxyadenosyl radical in coenzyme-B12-mediated reactions2012In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, no 3, p. 1591-1599Article in journal (Refereed)
    Abstract [en]

    Vitamin B12 and its biologically active counterparts possess the only examples of carbon-cobalt bonds in living systems. The role of such motifs as radical reservoirs has potential application in future catalytic and electronic nanodevices. To fully understand radical generation in coenzyme B12 (dAdoCbl)-dependent enzymes, however, major obstacles still need to be overcome. In this work, we have used Car-Parrinello molecular dynamics (CPMD) simulations, in a mixed quantum mechanics/molecular mechanics (QM/MM) framework, to investigate the initial stages of the methylmalonyl-CoA-mutase-catalyzed reaction. We demonstrate that the 5'-deoxyadenosyl radical (dAdo(center dot)) exists as a distinct entity in this reaction, consistent with the results of extensive experimental and some previous theoretical studies. We report free energy calculations and first-principles trajectories enzymes catalyze coenzyme activation and control highly reactive radical intermediates. that help understand how B12 enzymes catalyze coenzyme activation and control highly reactive radical intermediates.

  • 24.
    Böhlin, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Molecular electronics : a theoretical study of electronic structure in molecular crystals and surfaces2007Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

      

    This thesis deals with theoretical studies of the electronic structures of molecules in organic crystal and molecules adsorbed on metal surfaces. Both studies with first principle calculations and classical mechanics were performed. The materials include pentacene and bis(9-cyclohexylimino-l-oxyphenalenyl)boron and the

    Tetrakis( dimethylamino )ethylene (TDAE) molecule chemisorbed on a gold surface. Molecular crystals of pentacene are reported to have the highest field-effect mobility values for organic thin film field effect transistors, and are therefore suitable to be the active material in such devices. The increase in conductivity obtained experimentally by doping with alkali metals showed great promise, and we therefore performed calculations on pentacene crystals doped with potassium. Phase transitions occured upon doping, and the herringbone arrangement of the pristine pentacene molecules relaxes towards a 1r stacked structure. Charge transfer between the crystal and the potassium occurs, which shifts the Fermi level into the lowest unoccupied molecular orbitals bands and turns the crystal metallic. The study of bis(9-cyclohexylimino-l-oxyphenalenyl)boron, a biphenalenyl based neutral radical, was performed in order to investigate the electronic properties since experimental studies had shown simultaneous electrical, optical and magnetical bistability. The system is quasi one-dimensional, as shown from band structure calculations.. The injection of charge carriers from metals to organic semiconductors is one of the most central processes when it comes to the performance of organic devices. The interface between the metal and the semiconductor is one of the device parameters that will significantly influence the device performance. The addition of a molecular layer on the interface can, by the introduction of a dipole, reduce the energy barrier for charge injection. ·we found that a molecular layer of TDAE deposited on a gold surface results in a charge transfer from the molecule to the surface which reduced the charge injection barrier by as much as 2.4 eV.

    List of papers
    1. Structural and electronic transitions in potassium doped pentacene
    Open this publication in new window or tab >>Structural and electronic transitions in potassium doped pentacene
    2006 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 73, no 18Article in journal (Refereed) Published
    Abstract [en]

    We calculate the ground state geometrical structure of potassium-intercalated pentacene lattices using molecular mechanics and the density-functional theory. Both methods result in a structural phase transition in going from the pristine form to the intercalated state with one potassium ion per pentacene molecule. The phase transition is characterized by a sliding of adjacent pentacene molecules relative to each other. The electronic properties of this phase is studied with the density-functional theory. As a result of the geometrical changes, the - overlap in the direction perpendicular to the molecular planes of the layered pristine pentacene structure increases substantially and many of the electronic bands show strong dispersion in this direction. The Fermi energy of the doped phase appears in the middle of the conduction band where the density of states is maximum. The bandwidth of the conduction band is 0.7  eV.

    Keywords
    potassium, organic semiconductors, density functional theory, solid-state phase transformations, conduction bands, Fermi level, electronic density of states, ground states
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-14063 (URN)10.1103/PhysRevB.73.184114 (DOI)
    Available from: 2006-10-05 Created: 2006-10-05 Last updated: 2017-12-13
    2. Electronic structure calculations of the phenalenyl-based neutral radical conductor bis(9-cyclohexylimino-1-phenalenyl) boron
    Open this publication in new window or tab >>Electronic structure calculations of the phenalenyl-based neutral radical conductor bis(9-cyclohexylimino-1-phenalenyl) boron
    2006 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 74, no 15Article in journal (Refereed) Published
    Abstract [en]

    The solid state of free radicals of bis(9-cyclohexylimino-1-oxyphenalenyl) boron is one of few neutral molecular systems which exhibit high conductivity at room temperature. The system is crystalline but highly anistotropic. We have performed band structure calculations based on the density functional theory on this system. It is evident from these studies that the system is quasi-one-dimensional with strong intermolecular interactions along one crystal direction. The bandwidth is 0.424 eV along this direction as compared to 0.055 eV perpendicular to it. Despite the quasi-one-dimensional character of the system, no signature of a Peierls distortion towards a dimerized state is observed. We argue that this is due to the fact that the Fermi energy lies slightly below the middle of the conduction band. In this case the electronic driving force for the distortion to occur is weakened and overcome by the restoring force of the lattice. Also the optical properties of the system have been investigated and the origin of the low lying excitations in the system has been clarified.

    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-50104 (URN)10.1103/PhysRevB.74.155111 (DOI)
    Available from: 2009-10-11 Created: 2009-10-11 Last updated: 2017-12-12
    3. TDAE chemisorbed on gold
    Open this publication in new window or tab >>TDAE chemisorbed on gold
    2008 (English)In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 20, no 31Article in journal (Refereed) Published
    Abstract [en]

    DFT calculations on tetrakis(dimethylamino)ethylene (TDAE) interacting with a gold surface have been performed. A monolayer of TDAE deposited on a gold surface creates an interface dipole, which decreases the barrier for electron injection from a gold contact into an (organic) electroactive material. This was studied by simulating the complex in two different ways, using a slab model and using a gold cluster surface. These approaches are shown to be complementary: the cluster results apply to the situation of isolated molecules and the slab results describe the case of interacting TDAE molecules on the gold surface. We found that there is a transfer of around one electronic charge per TDAE to the gold in the limit of non-interacting TDAE molecules. This charge transfer results in the formation of an interface dipole and a corresponding lowering of the work function of the surface. The lowering of the work function increases with increasing coverage and is as large as 2.4 eV for a monolayer of TDAE on gold. Due to depolarization effects, the charge transfer in this state is reduced to 0.56 times the electronic charge.

    Place, publisher, year, edition, pages
    Bristol, United Kingdom: Institute of Physics Publishing (IOPP), 2008
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-13872 (URN)10.1088/0953-8984/20/31/315008 (DOI)000257759600025 ()
    Available from: 2006-06-28 Created: 2006-06-28 Last updated: 2017-12-13Bibliographically approved
  • 25.
    Böhlin, Johan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Hansson, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics.
    Stafström, Sven
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics.
    Electronic structure calculations of the phenalenyl-based neutral radical conductor bis(9-cyclohexylimino-1-phenalenyl) boron2006In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 74, no 15Article in journal (Refereed)
    Abstract [en]

    The solid state of free radicals of bis(9-cyclohexylimino-1-oxyphenalenyl) boron is one of few neutral molecular systems which exhibit high conductivity at room temperature. The system is crystalline but highly anistotropic. We have performed band structure calculations based on the density functional theory on this system. It is evident from these studies that the system is quasi-one-dimensional with strong intermolecular interactions along one crystal direction. The bandwidth is 0.424 eV along this direction as compared to 0.055 eV perpendicular to it. Despite the quasi-one-dimensional character of the system, no signature of a Peierls distortion towards a dimerized state is observed. We argue that this is due to the fact that the Fermi energy lies slightly below the middle of the conduction band. In this case the electronic driving force for the distortion to occur is weakened and overcome by the restoring force of the lattice. Also the optical properties of the system have been investigated and the origin of the low lying excitations in the system has been clarified.

  • 26.
    Böhlin, Johan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Linares, M
    Royal Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Effect of dynamic disorder on charge transport along a pentacene chain2011In: PHYSICAL REVIEW B, ISSN 1098-0121, Vol. 83, no 8, p. 085209-Article in journal (Refereed)
    Abstract [en]

    The lattice equation of motion and a numerical solution of the time-dependent Schrodinger equation provide us with amicroscopic picture of charge transport in highly ordered molecular crystals. We have chosen the pentacene single crystal as a model system, and we study charge transport as a function of phonon-mode time-dependent fluctuations in the intermolecular electron transfer integral. For comparison, we include similar fluctuations also in the intramolecular potentials. The variance in these energy quantities is closely related to the temperature of the system. The pentacene system is shown to be very sensitive to fluctuation in the intermolecular transfer integral, revealing a transition from adiabatic to nonadiabatic polaron transport for increasing temperatures. The extension of the polaron at temperatures above 200 K is limited by the electron localization length rather than the interplay between the electron transfer integral and the electron-phonon coupling strength.

  • 27.
    Cappelli, Chiara
    et al.
    Istituto per i Processi Chimico-Fisici del CNR, Area della Ricerca, Pisa, Italy.
    Ekström, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Rizzo, Antonio
    Istituto per i Processi Chimico-Fisici del CNR, Area della Ricerca, Pisa, Italy.
    Coriani, Sonia
    Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, Trieste, Italy.
    The molecular electric quadrupole moment and electric field gradient induced birefringence (Buckingham effect) of Cl22004In: Journal of Computational Methods in Sciences and Engineering, ISSN 1472-7978, Vol. 4, no 3, p. 365-380Article in journal (Refereed)
    Abstract [en]

    An ab initio investigation of the molecular properties rationalizing the electric-field-gradient induced birefringence (Buckingham effect) for Cl_2 is presented. The quadrupole moment is determined using hierarchies of basis sets and wavefunction models. The electric dipole polarizability, the dipole - dipole - quadrupole and dipole - dipole - magnetic dipole hyperpolarizabilities are determined exploiting a Coupled Cluster Singles and Doubles (CCSD) response approach. The properties are zero-point vibrationally averaged, and the contribution of excited ro-vibrational states accounted for. To this end, the interatomic ^1Σ_g^+ ground state potential has been computed at CCSD plus perturbative triples - CCSD(T) - level employing a large augmented correlation consistent basis set. The effect of relativity is estimated at the Dirac-Hartree-Fock level. Our best value for the quadrupole moment of Cl_2 is (2.327 ± 0.010) au and it is in excellent agreement with experiment which, after revision and dependent on the procedure employed for correcting the original estimate of (2.24 ± 0.04) au of Graham et al., [Mol. Phys., 93, 49, (1998)], ranges from (2.31 ± 0.04) au to (2.36 ± 0.04) au.

  • 28.
    Christodoulou, C.
    et al.
    Humboldt University, Germany .
    Giannakopoulos, A.
    University of Mons, Belgium .
    Nardi, M.V.
    Humboldt University, Germany .
    Ligorio, G.
    Humboldt University, Germany .
    Oehzelt, M.
    Humboldt University, Germany Helmholtz Zentrum Berlin Mat and Energie GmbH, Germany .
    Chen, L.
    University of Mons, Belgium .
    Pasquali, L.
    University of Modena and Reggio Emilia, Italy IOM CNR, Italy University of Johannesburg, South Africa .
    Timpel, M.
    Humboldt University, Germany .
    Giglia, A.
    IOM CNR, Italy .
    Nannarone, S.
    University of Modena and Reggio Emilia, Italy IOM CNR, Italy .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Parvez, K.
    Max Planck Institute Polymer Research, Germany .
    Muellen, K.
    Max Planck Institute Polymer Research, Germany .
    Beljonne, D.
    University of Mons, Belgium .
    Koch, N.
    Humboldt University, Germany Helmholtz Zentrum Berlin Mat and Energie GmbH, Germany .
    Tuning the Work Function of Graphene-on-Quartz with a High Weight Molecular Acceptor2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 9, p. 4784-4790Article in journal (Refereed)
    Abstract [en]

    Ultraviolet and X-ray photoelectron spectroscopies in combination with density functional theory (DFT) calculations were used to study the change in the work function (Phi) of graphene, supported by quartz, as induced by adsorption of hexaazatriphenylene-hexacarbonitrile (HATCN). Near edge X-ray absorption fine structure spectroscopy (NEXAFS) and DFT modeling show that a molecular-density-dependent reorientation of HATCN from a planar to a vertically inclined adsorption geometry occurs upon increasing surface coverage. This, in conjunction with the orientation-dependent magnitude of the interface dipole, allows one to explain the evolution of graphene (Phi) from 4.5 eV up to 5.7 eV, rendering the molecularly modified graphene-on-quartz a highly suitable hole injection electrode.

  • 29.
    Coriani, Sonia
    et al.
    University of Aarhus.
    Christiansen, Ove
    University of Aarhus.
    Fransson, Thomas
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Coupled-cluster response theory for near-edge x-ray-absorption fine structure of atoms and molecules2012In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 85, no 2, p. 022507-Article in journal (Refereed)
    Abstract [en]

    Based on an asymmetric Lanczos-chain subspace algorithm, damped coupled cluster linear response functions have been implemented for the hierarchy of coupled cluster (CC) models including CC with single excitations (CCS), CC2, CC with single and double excitations (CCSD), and CCSD with noniterative triple corrected excitation energies CCSDR(3). This work is a first step toward the extension of these theoretical electronic structure methods of well-established high accuracy in UV-vis absorption spectroscopies to applications concerned with x-ray radiation. From the imaginary part of the linear response function, the near K-edge x-ray absorption spectra of neon, water, and carbon monoxide are determined and compared with experiment. Results at the CCSD level show relative peak intensities in good agreement with experiment with discrepancies in transition energies due to incomplete treatment of electronic relaxation and correlation that amount to 1-2 eV. With inclusion of triple excitations, errors in energetics are less than 0.9 eV and thereby capturing 90%, 95%, and 98% of the relaxation-correlation energies for C, O, and Ne, respectively.

  • 30.
    Coriani, Sonia
    et al.
    University of Trieste.
    Fransson, Thomas
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Christiansen, Ove
    Aarhus University.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Asymmetric-Lanczos-Chain-Driven Implementation of Electronic Resonance Convergent Coupled-Cluster Linear Response Theory2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 5, p. 1616-1628Article in journal (Refereed)
    Abstract [en]

    We present an implementation of the damped coupled-cluster linear response function based on an asymmetric Lanczos chain algorithm for the hierarchy of coupled-cluster approximations CCS (coupled-cluster singles), CC2 (coupled. cluster singles and approximate doubles), and CCSD (coupled-cluster singles and doubles). Triple corrections to the excitation energies can be included via the CCSDR(3) (coupled-cluster singles and doubles with noniterative-triples-corrected excitation energies) approximation. The performance and some of the potentialities of the approach are investigated in calculations of the visible/ultraviolet absorption spectrum and the dispersion of the real polarizability in near-resonant regions of pyrimidine, the near-edge absorption fine structure (NEXAFS) of ammonia, and the direct determination of the C-6 dipole-dipole dispersion coefficient of the benzene dimer.

  • 31.
    Cronstrand, P
    et al.
    Royal Inst Technol, SE-10044 Stockholm, Sweden Ctr Chem, Dept Theoret Chem, SE-22100 Lund, Sweden Linkoping Univ, Dept Phys & Measurement Technol, SE-58183 Linkoping, Sweden.
    Christiansen, O
    Royal Inst Technol, SE-10044 Stockholm, Sweden Ctr Chem, Dept Theoret Chem, SE-22100 Lund, Sweden Linkoping Univ, Dept Phys & Measurement Technol, SE-58183 Linkoping, Sweden.
    Norman, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Agren, H
    Royal Inst Technol, SE-10044 Stockholm, Sweden Ctr Chem, Dept Theoret Chem, SE-22100 Lund, Sweden Linkoping Univ, Dept Phys & Measurement Technol, SE-58183 Linkoping, Sweden.
    Ab initio modeling of excited state absorption of polyenes2001In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 3, no 13, p. 2567-2575Article in journal (Refereed)
    Abstract [en]

    Vertical excitation energies and transition dipole moments between excited electronic states have been calculated for the trans-polyenes series C4H6-C12H14 in order to study the formation of excited state absorption spectra of these species. Quadratic response theory is applied in conjunction with the self-consistent field method and a hierarchical set of coupled-cluster methods. The convergence of the excited state absorption, with respect to wavefunction and treatment of electron correlation and also the length of the oligomer unit, is studied, revealing a considerable demand on the computational effort in order to predict the excited state spectra with precision. The organization of the excited states is found to change in character along the polyene series. The inflexion point for the vertical excitation energies between the one-photon allowed 1(1)B(u) and the two-photon 2(1)A(g) state is predicted to occur between hexatriene and octatetraene. Good agreement with experiment is obtained for butadiene and hexatriene for which the most accurate calculations have been carried out.

  • 32.
    Cronstrand, P
    et al.
    Royal Inst Technol, SE-10044 Stockholm, Sweden Univ Lund, Ctr Chem, Dept Theoret Chem, SE-22100 Lund, Sweden Linkoping Univ, Dept Phys & Measurement Technol, SE-58183 Linkoping, Sweden.
    Christiansen, O
    Royal Inst Technol, SE-10044 Stockholm, Sweden Univ Lund, Ctr Chem, Dept Theoret Chem, SE-22100 Lund, Sweden Linkoping Univ, Dept Phys & Measurement Technol, SE-58183 Linkoping, Sweden.
    Norman, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Agren, H
    Royal Inst Technol, SE-10044 Stockholm, Sweden Univ Lund, Ctr Chem, Dept Theoret Chem, SE-22100 Lund, Sweden Linkoping Univ, Dept Phys & Measurement Technol, SE-58183 Linkoping, Sweden.
    Theoretical calculations of excited state absorption2000In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 2, no 23, p. 5357-5363Article in journal (Refereed)
    Abstract [en]

    Excitation energies and transition dipole moments between excited electronic states have been calculated using various theoretical methods to investigate the ability to describe excited state absorption. Quadratic response theory is used in combination with self-consistent field, multi-configurational self-consistent field, and coupled-cluster electronic structure methods. The results of these different methods are compared. The set of molecules considered includes lithium hydride, carbon monoxide, formaldehyde, formamide, and sym-tetrazine. For some of the molecules results are also compared with the method of applying linear response theory to an excited state wavefunction separately optimized by means of the multi-configurational self-consistent field method.

  • 33.
    Cronstrand, P.
    et al.
    Theoretical Chemistry, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden.
    Luo, Y.
    Theoretical Chemistry, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden.
    Norman, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Agren, H.
    Ågren, H., Theoretical Chemistry, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden.
    Ab initio calculations of three-photon absorption2003In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 375, no 1-2, p. 233-239Article in journal (Refereed)
    Abstract [en]

    We present large scale ab initio calculations of three-photon absorption of a series of dithienothiophene based charge transfer molecules using response theory within the random phase approximation. The structure-to-property relations obtained for the three-photon absorption cross-sections are discussed and compared with those for one- and two-photon absorption. © 2003 Published by Elsevier Science B.V.

  • 34.
    Cronstrand, P.
    et al.
    Theoretical Chemistry, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden.
    Norman, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Luo, Y.
    Theoretical Chemistry, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden.
    Agren, H.
    Ågren, H., Theoretical Chemistry, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden.
    Few-states models for three-photon absorption2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 121, no 5, p. 2020-2029Article in journal (Refereed)
    Abstract [en]

    The validity of few-states models for several systems ranging from lithium hydride to a series of large p-conjugated systems was discussed. Various aspects of the models which include convergence, behavior, merits and shortcomings were studied. The role of various characteristics of the electronic structure such as symmetry and charge transfer was elaborated. Analysis suggests that few-states models can be useful for interpretation purposes when applied to three-photon absorption.

  • 35.
    Cukras, Janusz
    et al.
    University of Trieste, Italy.
    Coriani, Sonia
    University of Trieste, Italy.
    Decleva, Piero
    University of Trieste, Italy.
    Christiansen, Ove
    Aarhus University, Denmark.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra2013In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 139, no 9Article in journal (Refereed)
    Abstract [en]

    A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

  • 36.
    da Cunha, Wiliam Ferreira
    et al.
    University of Brasilia, Brazil.
    Ribeiro, Luiz Antonio
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    de Almeida Fonseca, Antonio Luciano
    University of Brasilia, Brazil.
    Gargano, Ricardo
    University of Brasilia, Brazil.
    Magela e Silva, Geraldo
    University of Brasilia, Brazil.
    Reactive Scattering between Excitons and Charge Carriers in Conjugated Polymers2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 41, p. 23451-23458Article in journal (Refereed)
    Abstract [en]

    The temperature influence on the scattering process between an exciton and a positively charged carrier (polaron or bipolaron) is theoretically investigated using a version of the SuSchriefferHeeger (SSH) model modified to include temperature, Coulomb interactions, and an external electric field. In general, it is observed that the products of the reactive scattering are spin independent when thermal effects are taken into account. For the interaction between a polaron and an exciton, the polaron can be annihilated, when subjected to temperatures higher than a critical value, or pass through the exciton maintaining both their consistencies, if a lower temperature regime is considered. Regarding the recombination between a bipolaron and an exciton, it is observed that the bipolaron can be annihilated whereas the exciton dissociates into two trions or into one polaron and one trion. In all cases, the recombination mechanisms depend on a suitable balance between temperature and electric field. These results may extend the knowledge about electroluminescence process in conjugated polymers, thus being of potential use to improve internal quantum efficiency in polymer light-emitting diodes.

  • 37.
    Demeyu, Lemi
    et al.
    Department of Physics Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
    Stafström, Sven
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics.
    Monte Carlo simulation of controlled charge carriers diffusion in highly ordered iodine doped pentacene film2007In: Physica Status Solidi (a) applications and materials science, ISSN 1862-6300, E-ISSN 1862-6319, Vol. 204, no 10, p. 3545-3555Article in journal (Refereed)
  • 38.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    A computational perspective on the photochemistry of photosensory proteins: phytochromes and Anabaena sensory rhodopsin2012In: Quantum Simulations of Materials and Biological Systems / [ed] Jun Zeng, Rui-Qin Zhang and Herbert R. Treutlein, Springer Netherlands, 2012, p. 169-194Chapter in book (Refereed)
    Abstract [en]

    The merits of quantum simulations in photobiology are illustrated by presenting recent computational studies investigating the basic photochemistry of phytochromes, a ubiquitous family of photosensory proteins, and Anabaena sensory rhodopsin, a recently discovered member of the rhodopsins. Focusing on the chromophore photoisomerization reactions that trigger these proteins’ responses to light and using density functional methods and multiconfigurational ab initio methods in combination with molecular mechanics, three surprising results can be singled out. First, it is found that the photochemical reactivity of the bilin chromophores of phytochromes is fundamentally different in solution and in the protein, with different photoisomerization channels being preferred. Second, it is found that the two retinal photoisomerizations that govern the interconversion of Anabaena sensory rhodopsin between its two major forms proceed in such a way that the chromophore completes a full 360° rotation during one photocycle. This means that this protein is a biological realization of a light-driven molecular rotor. Third, and finally, it is demonstrated that the stereochemical origin of this remarkable behavior is actually a key element for the function of a class of synthetic light-driven molecular rotors developed from overcrowded alkenes, thereby identifying Anabaena sensory rhodopsin as a possible source of inspiration for the future design and construction of such molecular machines.

  • 39.
    Ekström, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Birefringences and X-ray absorption from relativistic and nonrelativistic quantum chemical methods2005Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Application of quantum chemical methods for the prediction and interpretation of optical and X-ray experiments have been performed. X-ray absorption and X-ray photo-electron spectroscopy of pentacene in the gas phase has been studied using the static exchange approximation. A generalizat ion of the static exchange approximation, to the relativistic four-component realm is presented and applied to the H2S molecule. This generalization allows for a description of the effects the strong spin-orbit coupling in the core region of atoms. Two types of birefringences, Faraday effect and electric field gradient induced birefringence, a re calculated for small molecules in the gas phase, and the effects of relativity are considered for these nonlinear optical properties.

    List of papers
    1. The molecular electric quadrupole moment and electric field gradient induced birefringence (Buckingham effect) of Cl2
    Open this publication in new window or tab >>The molecular electric quadrupole moment and electric field gradient induced birefringence (Buckingham effect) of Cl2
    2004 (English)In: Journal of Computational Methods in Sciences and Engineering, ISSN 1472-7978, Vol. 4, no 3, p. 365-380Article in journal (Refereed) Published
    Abstract [en]

    An ab initio investigation of the molecular properties rationalizing the electric-field-gradient induced birefringence (Buckingham effect) for Cl_2 is presented. The quadrupole moment is determined using hierarchies of basis sets and wavefunction models. The electric dipole polarizability, the dipole - dipole - quadrupole and dipole - dipole - magnetic dipole hyperpolarizabilities are determined exploiting a Coupled Cluster Singles and Doubles (CCSD) response approach. The properties are zero-point vibrationally averaged, and the contribution of excited ro-vibrational states accounted for. To this end, the interatomic ^1Σ_g^+ ground state potential has been computed at CCSD plus perturbative triples - CCSD(T) - level employing a large augmented correlation consistent basis set. The effect of relativity is estimated at the Dirac-Hartree-Fock level. Our best value for the quadrupole moment of Cl_2 is (2.327 ± 0.010) au and it is in excellent agreement with experiment which, after revision and dependent on the procedure employed for correcting the original estimate of (2.24 ± 0.04) au of Graham et al., [Mol. Phys., 93, 49, (1998)], ranges from (2.31 ± 0.04) au to (2.36 ± 0.04) au.

    Keywords
    molecular quadrupole moment, birefringence, electric field gradient, electric dipole (hyper)polarizabilities, coupled cluster theory, relativistic effects, molecular vibrations
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12696 (URN)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2013-11-25
    2. Four-component Hartree–Fock calculations of magnetic-field induced circular birefringence—Faraday effect—in noble gases and dihalogens
    Open this publication in new window or tab >>Four-component Hartree–Fock calculations of magnetic-field induced circular birefringence—Faraday effect—in noble gases and dihalogens
    2005 (English)In: The Journal of Chemical Physics, ISSN 1050-2947, Vol. 122, p. 074321-Article in journal (Refereed) Published
    Abstract [en]

    Theeffects of relativity on the magnetic-field induced circular birefringence, orFaraday effect, in He, Ne, Ar, Xe, Rn, F2, Cl2,Br2, and I2 have been determined at the four-component Hartree–Focklevel of theory. A measure of the birefringence is givenby the Verdet constant, which is a third-order molecular propertyand thus relates to quadratic response functions. A fully analyticalnonlinear polarization propagator approach is employed. The results are gaugeinvariant as a consequence of the spatial symmetries in themolecular systems. The calculations include electronic as well as vibrationalcontributions to the property. Comparison with experiment is made forHe, Ne, Ar, Xe, and Cl2, and, apart from neon,the theoretical values of the Verdet constant are within 10%of the experimental ones. The inclusion of nonrelativistically spin-forbidden excitationsin the propagator parametrization has significant effects on the dispersionin general, but such effects are in the general caselargely explained by the use of a resonant-divergent propagator theory.In the present work we do, however, observe noticeable relativisticcorrections to the Verdet constant in the off-resonant regions forsystems with light elements (F2 and Cl2), and nonrelativistic resultsfor the Verdet constant of Br2 are in error by25% in the low-frequency region. ©2005 American Institute of Physics.

    Keywords
    HF calculations, birefringence, helium, neon, argon, xenon, radon, fluorine, chlorine, bromine, iodine, Faraday effect, polarisation, relativistic corrections, vibrational states, excited states, resonant states, magnetic fields
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12695 (URN)10.1063/1.1849167 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2013-11-25
    3. Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: Experiment and theory
    Open this publication in new window or tab >>Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: Experiment and theory
    Show others...
    2005 (English)In: Journal of chemical physics Online, ISSN 1089-7690, Vol. 122, no 12, p. 124305-Article in journal (Refereed) Published
    Abstract [en]

    The C K-edge photoabsorption and 1s core-level photoemission of pentacene (C22H14) free molecules are experimentally measured, and calculated by self-consistent-field and static-exchange approximation ab initio methods. Six nonequivalent C atoms present in the molecule contribute to the C 1s photoemission spectrum. The complex near-edge structures of the carbon K-edge absorption spectrum present two main groups of discrete transitions between 283 and 288  eV photon energy, due to absorption to * virtual orbitals, and broader structures at higher energy, involving * virtual orbitals. The sharp absorption structures to the * empty orbitals lay well below the thresholds for the C 1s ionizations, caused by strong excitonic and localization effects. We can definitely explain the C K-edge absorption spectrum as due to both final (virtual) and initial (core) orbital effects, mainly involving excitations to the two lowest-unoccupied molecular orbitals of * symmetry, from the six chemically shifted C 1s core orbitals. ©2005 American Institute of Physics

    Keywords
    organic compounds, photoexcitation, photoelectron spectra, SCF calculations, ab initio calculations, chemical shift, molecular electronic states, molecule-photon collisions
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12685 (URN)10.1063/1.1864852 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2013-11-25
    4. Relativistic four-component static-exchange approximation for core-excitation processes in molecules
    Open this publication in new window or tab >>Relativistic four-component static-exchange approximation for core-excitation processes in molecules
    2006 (English)In: Physical review A, ISSN 1050-2947, Vol. 73, no 2, p. 022501-Article in journal (Refereed) Published
    Abstract [en]

    A generalization of the static-exchange approximation for core-electron spectroscopies to the relativistic four-component realm is presented. The initial state is a Kramers restricted Hartree-Fock state and the final state is formed as the configuration-interaction single excited state, based on the average of configurations for (n–1) electrons in n near-degenerate core orbitals for the reference ionic state. It is demonstrated that the static-exchange Hamiltonian can be made real by considering a set of time-reversal symmetric electron excitation operators. The static-exchange Hamiltonian is constructed at a cost that parallels a single Fock matrix construction in a quaternion framework that fully exploits time-reversal and spatial symmetries for the D2h point group and subgroups. The K- and L-edge absorption spectra of H2S are used to illustrate the methodology. The calculations adopt the Dirac-Coulomb Hamiltonian, but the theory is open ended toward improvements in the electron-electron interaction operator. It is demonstrated that relativistic effects are substantial for the L-edge spectrum of sulfur, and substantial deviations from the statistical 2:1 spin-orbit splitting of the intensity distribution are found. The average ratio in the mixed region is 1.54 at the present level of theory.

    Keywords
    hydrogen compounds, relativistic corrections, configuration interactions, HF calculations, excited states, spin-orbit interactions
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12688 (URN)10.1103/PhysRevA.73.022501 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2013-11-25
    5. X-ray absorption spectra from the resonantconvergent first-order polarization propagator approach
    Open this publication in new window or tab >>X-ray absorption spectra from the resonantconvergent first-order polarization propagator approach
    2006 (English)In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 74, no 4, p. 042722-Article in journal (Refereed) Published
    Abstract [en]

    The one-photon absorption cross sections of molecular systems have been determined in the high-energy region from the imaginary part of the electric dipole polarizability tensor. In contrast to commonly adopted state-specific methodologies, the complex polarization propagator approach does not require explicit consideration of the excited states and it is open-ended towards multiphoton absorption. It is shown that the electronic relaxation in the core-hole state is well accounted for in the present approach with use of standard density-functional based electronic structure methods. Sample calculations are presented of the K-edge x-ray absorption spectra for H2O, CO, C4H4N, and C6H6.

    Keywords
    water, carbon compounds, organic compounds, X-ray absorption spectra, molecular moments, polarisability, electric moments, excited states, multiphoton spectra, density functional theory
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12691 (URN)10.1103/PhysRevA.74.042722 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2017-12-14
  • 40.
    Ekström, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Time-dependent molecular properties in the optical and x-ray regions2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Time-dependent molecular properties are important for the experimental characterization of molecular materials. We show how these properties can be calculated, for optical and x-ray frequencies, using novel quantum chemical methods. For xray absorption there are important relativistic effects appearing, due to the high velocity electrons near the atomic nuclei. These effects are treated rigorously within the four-component static exchange approximation. We also show how electron correlation can be taken into account in the calculation of x-ray absorption spectra, in time-dependent density functional theory based on the complex polarization propagator approach. The methods developed have been applied to systems of experimental interest|molecules in the gas phase and adsorbed on metal surfaces. The effects of molecular vibrations have been take into account both within and beyond the harmonic approximation.

    List of papers
    1. Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: Experiment and theory
    Open this publication in new window or tab >>Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: Experiment and theory
    Show others...
    2005 (English)In: Journal of chemical physics Online, ISSN 1089-7690, Vol. 122, no 12, p. 124305-Article in journal (Refereed) Published
    Abstract [en]

    The C K-edge photoabsorption and 1s core-level photoemission of pentacene (C22H14) free molecules are experimentally measured, and calculated by self-consistent-field and static-exchange approximation ab initio methods. Six nonequivalent C atoms present in the molecule contribute to the C 1s photoemission spectrum. The complex near-edge structures of the carbon K-edge absorption spectrum present two main groups of discrete transitions between 283 and 288  eV photon energy, due to absorption to * virtual orbitals, and broader structures at higher energy, involving * virtual orbitals. The sharp absorption structures to the * empty orbitals lay well below the thresholds for the C 1s ionizations, caused by strong excitonic and localization effects. We can definitely explain the C K-edge absorption spectrum as due to both final (virtual) and initial (core) orbital effects, mainly involving excitations to the two lowest-unoccupied molecular orbitals of * symmetry, from the six chemically shifted C 1s core orbitals. ©2005 American Institute of Physics

    Keywords
    organic compounds, photoexcitation, photoelectron spectra, SCF calculations, ab initio calculations, chemical shift, molecular electronic states, molecule-photon collisions
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12685 (URN)10.1063/1.1864852 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2013-11-25
    2. Probing the potential energy surface by highresolution x-ray absorption spectroscopy: The umbrella motion of the coreexcited CH3 free radical
    Open this publication in new window or tab >>Probing the potential energy surface by highresolution x-ray absorption spectroscopy: The umbrella motion of the coreexcited CH3 free radical
    Show others...
    2007 (English)In: Physical Review. A, ISSN 1050-2947, Vol. 76, no 2, p. 124305-Article in journal (Refereed) Published
    Abstract [en]

    A detailed study of the umbrellalike vibration in inner-shell spectroscopy is presented. The high-resolution x-ray absorption spectrum for the lowest lying core excitation of the CH3 free radical was recorded. High quality potential energy surfaces (PES) for the initial and final states of the transition were calculated as a function of the symmetrical stretching and the umbrella deformation coordinates. The strong anharmonicity along the umbrella coordinate in the double-well region of the PES of the core excited state has a strong effect on the bending vibrational progressions. The excellent agreement between the experiment and theory allows an accurate spectroscopic characterization of the vibrational structure of the electronic transition, and the estimation of the umbrella inversion time of 149  fs.

    Keywords
    free radicals, molecular configurations, optical rotation, organic compounds, potential energy surfaces, vibrational states, X-ray absorption spectra
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-12686 (URN)10.1103/PhysRevA.76.022509 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2009-04-23Bibliographically approved
    3. The umbrella motion of core-excited CH3 and CD3 methyl radicals
    Open this publication in new window or tab >>The umbrella motion of core-excited CH3 and CD3 methyl radicals
    Show others...
    2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 4, p. 044302-1-044302-11Article in journal (Refereed) Published
    Abstract [en]

    An accurate experimental and theoretical study of the lowest core excitationof CH3 and CD3 methyl radicals is presented. The complexvibrational structure of the lowest band of the x-ray absorptionspectrum (XAS) is due to the large variation of themolecular geometry, which is planar in the ground state andpyramidal in the core-excited state. The XAS spectra of thetwo radicals were recorded at high resolution and assigned bytheoretical simulations of the spectra, taking into account the couplingof symmetrical stretching and symmetrical bending (umbrellalike) deformations of theradicals. An excellent agreement between experimental and theoretical spectral profilesallowed us to accurately characterize the vibrational structure of theelectronic transition. The similarities, as well as the differences, ofthe peculiar vibrational progression observed for the two radicals areexplained by the strong anharmonicity along the umbrella coordinate andby the isotopic variation, leading to a different probing ofthe double-well potential energy surface of the core excited stateduring the nuclear motion.

    Place, publisher, year, edition, pages
    College Park, MD United States: American Institute of Physics (AIP), 2008
    Keywords
    excited states, free radicals, ground states, molecular configurations, organic compounds, potential energy surfaces, vibrational states, X-ray scattering
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12687 (URN)10.1063/1.2822246 (DOI)000252821200025 ()
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2017-12-14Bibliographically approved
    4. Relativistic four-component static-exchange approximation for core-excitation processes in molecules
    Open this publication in new window or tab >>Relativistic four-component static-exchange approximation for core-excitation processes in molecules
    2006 (English)In: Physical review A, ISSN 1050-2947, Vol. 73, no 2, p. 022501-Article in journal (Refereed) Published
    Abstract [en]

    A generalization of the static-exchange approximation for core-electron spectroscopies to the relativistic four-component realm is presented. The initial state is a Kramers restricted Hartree-Fock state and the final state is formed as the configuration-interaction single excited state, based on the average of configurations for (n–1) electrons in n near-degenerate core orbitals for the reference ionic state. It is demonstrated that the static-exchange Hamiltonian can be made real by considering a set of time-reversal symmetric electron excitation operators. The static-exchange Hamiltonian is constructed at a cost that parallels a single Fock matrix construction in a quaternion framework that fully exploits time-reversal and spatial symmetries for the D2h point group and subgroups. The K- and L-edge absorption spectra of H2S are used to illustrate the methodology. The calculations adopt the Dirac-Coulomb Hamiltonian, but the theory is open ended toward improvements in the electron-electron interaction operator. It is demonstrated that relativistic effects are substantial for the L-edge spectrum of sulfur, and substantial deviations from the statistical 2:1 spin-orbit splitting of the intensity distribution are found. The average ratio in the mixed region is 1.54 at the present level of theory.

    Keywords
    hydrogen compounds, relativistic corrections, configuration interactions, HF calculations, excited states, spin-orbit interactions
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12688 (URN)10.1103/PhysRevA.73.022501 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2013-11-25
    5. Resonant LII;III x-ray raman scattering from HCl
    Open this publication in new window or tab >>Resonant LII;III x-ray raman scattering from HCl
    Show others...
    2006 (English)In: Physical Review A, ISSN 1050-2947, Vol. 74, no 6, p. 062512-Article in journal (Refereed) Published
    Abstract [en]

    We have studied the spectral features of Cl LII,III resonant x-ray Raman scattering of HCl molecules in gas phase both experimentally and theoretically. The theory, formulated in the intermediate-coupling scheme, takes into account the spin-orbital and molecular-field splittings in the Cl 2p shells, as well as the Coulomb interaction of the core hole with unoccupied molecular orbitals. Experiment and theory display nondispersive dissociative peaks formed by decay transitions in both molecular and dissociative regions. The molecular and atomic peaks collapse in a single narrow resonance because the dissociative potentials of core-excited and final states are parallel to each other along the whole pathway of the nuclear wave packet.

    Keywords
    hydrogen compounds, X-ray spectra, Raman spectra, dissociation energies, spin-orbit interactions, excited states
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12689 (URN)10.1103/PhysRevA.74.062512 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2009-06-05
    6. Characterization of the chemisorption of methylsilane on a Au(1,1,1) surface from the silicon K- and L-edge spectra: a theoretical study using the four-component static exchange approximation
    Open this publication in new window or tab >>Characterization of the chemisorption of methylsilane on a Au(1,1,1) surface from the silicon K- and L-edge spectra: a theoretical study using the four-component static exchange approximation
    2005 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 111, p. 13846-13850Article in journal (Refereed) Published
    Abstract [en]

    X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectra (NEXAFS) of methylsilane, isolated and chemisorbed to a Au(1,1,1) surface, are determined in the fully relativistic four-component static exchange approximation¯both the K- and the L-edge of silicon are addressed in this investigation. In the fully chemisorbed structure, three H(Si) atoms have been cleaved off when Si binds in the hollow site of Au forming three Si−Au bonds of normal length. As due to the tri-coordinated chemisorption, the onsets of the K- and L-edge NEXAFS absorption bands occur some 2.0 and 2.5 eV lower in energy, respectively. The spin−orbit splittings in the silicon 2p-shell are not significantly changed due to adsorption. A partly chemisorbed methylsilane with only one H(Si) bond cleaved was also studied, and it is shown that the polarization dependence in the surface spectra contains details that can be used experimentally to identify the surface coordination of silicon. The red-shifts in the XPS silicon 1s (2p) spectra upon surface binding are 0.95 (0.65) and 1.15 (0.83) eV for the mono- and tricoordinated system, respectively.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12690 (URN)10.1021/jp0717084 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2017-12-14
    7. X-ray absorption spectra from the resonantconvergent first-order polarization propagator approach
    Open this publication in new window or tab >>X-ray absorption spectra from the resonantconvergent first-order polarization propagator approach
    2006 (English)In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 74, no 4, p. 042722-Article in journal (Refereed) Published
    Abstract [en]

    The one-photon absorption cross sections of molecular systems have been determined in the high-energy region from the imaginary part of the electric dipole polarizability tensor. In contrast to commonly adopted state-specific methodologies, the complex polarization propagator approach does not require explicit consideration of the excited states and it is open-ended towards multiphoton absorption. It is shown that the electronic relaxation in the core-hole state is well accounted for in the present approach with use of standard density-functional based electronic structure methods. Sample calculations are presented of the K-edge x-ray absorption spectra for H2O, CO, C4H4N, and C6H6.

    Keywords
    water, carbon compounds, organic compounds, X-ray absorption spectra, molecular moments, polarisability, electric moments, excited states, multiphoton spectra, density functional theory
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12691 (URN)10.1103/PhysRevA.74.042722 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2017-12-14
    8. Polarization propagator for x-ray spectra
    Open this publication in new window or tab >>Polarization propagator for x-ray spectra
    2006 (English)In: Physical Review Letters, ISSN 1050-2947, Vol. 97, no 14, p. 143001-Article in journal (Refereed) Published
    Abstract [en]

    A polarization propagator for x-ray spectra is outlined and implemented in density functional theory. It rests on a formulation of a resonant-convergent first-order polarization propagator approach which makes it possible to directly calculate the x-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted x-ray spectrum relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12692 (URN)10.1103/PhysRevLett.97.143001 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2009-05-11
    9. Self-interaction-corrected time-dependent density functional theory calculations of x-ray absorption spectra
    Open this publication in new window or tab >>Self-interaction-corrected time-dependent density functional theory calculations of x-ray absorption spectra
    Show others...
    2007 (English)In: Physical Review A, ISSN 1050-2947, Vol. 76, no 2, p. 022506-Article in journal (Refereed) Published
    Abstract [en]

    We outline an approach within time-dependent density functional theory that predicts x-ray spectra on an absolute scale. The approach rests on a recent formulation of the resonant-convergent first-order polarization propagator [P. Norman et al., J. Chem. Phys. 123, 194103 (2005)] and corrects for the self-interaction energy of the core orbital. This polarization propagator approach makes it possible to directly calculate the x-ray absorption cross section at a particular frequency without explicitly addressing the excited-state spectrum. The self-interaction correction for the employed density functional accounts for an energy shift of the spectrum, and fully correlated absolute-scale x-ray spectra are thereby obtained based solely on optimization of the electronic ground state. The procedure is benchmarked against experimental spectra of a set of small organic molecules at the carbon, nitrogen, and oxygen K edges.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12693 (URN)10.1103/PhysRevA.76.022506 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2009-05-15
    10. Near-edge X-ray absorption and natural circular dichroism spectra of L-alanine: a theoretical study based on the complex polarization propagator approach
    Open this publication in new window or tab >>Near-edge X-ray absorption and natural circular dichroism spectra of L-alanine: a theoretical study based on the complex polarization propagator approach
    2007 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, no 16, p. 165104-Article in journal (Refereed) Published
    Abstract [en]

    The complex polarization propagator method [J. Chem. Phys. 123, 194103 (2005)] has been employed in conjunction with density functional theory and gauge-including atomic orbitals in order to determine the near-edge x-ray absorption and natural circular dichroism spectra of L-alanine in its neutral and zwitterionic forms. Results are presented for the K-edges of carbon, nitrogen, and oxygen. In contrast to traditional methods, the proposed approach enables a direct determination ofspectra at an arbitrary frequency instead of focusing on the rotatory strengths for individual electronic transitions. The propagator includes a complete set ofand allows for full core-hole relaxation. The theoretical spectrum at the nitrogen K-edge of the zwitterion compares well with the experimental spectrum. the nonredundant electron-transfer operators

    Keywords
    X-ray absorption near edge structure, absorption spectra, dichroism, polarization spectroscopy, density functionals, atomic orbitals
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12724 (URN)10.1063/1.2800024 (DOI)
    Available from: 2007-11-16 Created: 2007-11-16 Last updated: 2017-12-14
    11. Four-component Hartree–Fock calculations of magnetic-field induced circular birefringence—Faraday effect—in noble gases and dihalogens
    Open this publication in new window or tab >>Four-component Hartree–Fock calculations of magnetic-field induced circular birefringence—Faraday effect—in noble gases and dihalogens
    2005 (English)In: The Journal of Chemical Physics, ISSN 1050-2947, Vol. 122, p. 074321-Article in journal (Refereed) Published
    Abstract [en]

    Theeffects of relativity on the magnetic-field induced circular birefringence, orFaraday effect, in He, Ne, Ar, Xe, Rn, F2, Cl2,Br2, and I2 have been determined at the four-component Hartree–Focklevel of theory. A measure of the birefringence is givenby the Verdet constant, which is a third-order molecular propertyand thus relates to quadratic response functions. A fully analyticalnonlinear polarization propagator approach is employed. The results are gaugeinvariant as a consequence of the spatial symmetries in themolecular systems. The calculations include electronic as well as vibrationalcontributions to the property. Comparison with experiment is made forHe, Ne, Ar, Xe, and Cl2, and, apart from neon,the theoretical values of the Verdet constant are within 10%of the experimental ones. The inclusion of nonrelativistically spin-forbidden excitationsin the propagator parametrization has significant effects on the dispersionin general, but such effects are in the general caselargely explained by the use of a resonant-divergent propagator theory.In the present work we do, however, observe noticeable relativisticcorrections to the Verdet constant in the off-resonant regions forsystems with light elements (F2 and Cl2), and nonrelativistic resultsfor the Verdet constant of Br2 are in error by25% in the low-frequency region. ©2005 American Institute of Physics.

    Keywords
    HF calculations, birefringence, helium, neon, argon, xenon, radon, fluorine, chlorine, bromine, iodine, Faraday effect, polarisation, relativistic corrections, vibrational states, excited states, resonant states, magnetic fields
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12695 (URN)10.1063/1.1849167 (DOI)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2013-11-25
    12. The molecular electric quadrupole moment and electric field gradient induced birefringence (Buckingham effect) of Cl2
    Open this publication in new window or tab >>The molecular electric quadrupole moment and electric field gradient induced birefringence (Buckingham effect) of Cl2
    2004 (English)In: Journal of Computational Methods in Sciences and Engineering, ISSN 1472-7978, Vol. 4, no 3, p. 365-380Article in journal (Refereed) Published
    Abstract [en]

    An ab initio investigation of the molecular properties rationalizing the electric-field-gradient induced birefringence (Buckingham effect) for Cl_2 is presented. The quadrupole moment is determined using hierarchies of basis sets and wavefunction models. The electric dipole polarizability, the dipole - dipole - quadrupole and dipole - dipole - magnetic dipole hyperpolarizabilities are determined exploiting a Coupled Cluster Singles and Doubles (CCSD) response approach. The properties are zero-point vibrationally averaged, and the contribution of excited ro-vibrational states accounted for. To this end, the interatomic ^1Σ_g^+ ground state potential has been computed at CCSD plus perturbative triples - CCSD(T) - level employing a large augmented correlation consistent basis set. The effect of relativity is estimated at the Dirac-Hartree-Fock level. Our best value for the quadrupole moment of Cl_2 is (2.327 ± 0.010) au and it is in excellent agreement with experiment which, after revision and dependent on the procedure employed for correcting the original estimate of (2.24 ± 0.04) au of Graham et al., [Mol. Phys., 93, 49, (1998)], ranges from (2.31 ± 0.04) au to (2.36 ± 0.04) au.

    Keywords
    molecular quadrupole moment, birefringence, electric field gradient, electric dipole (hyper)polarizabilities, coupled cluster theory, relativistic effects, molecular vibrations
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-12696 (URN)
    Available from: 2007-10-30 Created: 2007-10-30 Last updated: 2013-11-25
    13. On the evaluation of quadratic response functions at the four-component Hartree-Fock level: Nonlinear polarization and two-photon absorption in bromo- and iodobenzen
    Open this publication in new window or tab >>On the evaluation of quadratic response functions at the four-component Hartree-Fock level: Nonlinear polarization and two-photon absorption in bromo- and iodobenzen
    2006 (English)In: The Journal of Chemical Physics, ISSN 0021-9606, Vol. 124, no 21, p. 214311-Article in journal (Refereed) Published
    Abstract [en]

    The nonlinear polarization and two-photon absorption parameters have been determined for dibromo- and di-iodobenzene in their meta- and ortho-conformations and with relativistic effects accounted for to a varying degree. By exclusion of small component integrals in the calculations of the first-order hyperpolarizability, results within 1% of fully relativistic four-component Hartree-Fock values are obtained at a cost of 8.7 times the corresponding nonrelativistic calculations. It is shown that the nonlinear absorption in bromobenzene (and even more so in iodobenzene) is broad banded due to spin-orbit interactions among the excited states, and nonrelativistic and scalar relativistic calculations are not to be used in this case.

    Keywords
    organic compounds, HF calculations, two-photon processes, relativistic corrections, polarisability, spin-orbit interactions, excited states
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13999 (URN)10.1063/1.2204604 (DOI)
    Available from: 2006-10-05 Created: 2006-10-05 Last updated: 2009-05-18
  • 41.
    Ekström, Ulf
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Carravetta, V.
    Institute of Chemical Physical Processes, CNR, Pisa, Italy.
    Alagia, M.
    Istituto per lo Studio dei Materiali Nanostrutturati, CNR, Roma, Italy and TASC-CNR, Area Science Park, Trieste, Italy.
    Lavollée, M.
    CNRS, Université Paris-Sud, Orsay-Cedex, France.
    Richter, R.
    Sincrotrone Trieste, Trieste, Italy.
    Bolcato, C.
    Dipartimento di Scienze Farmaceutiche, Universitá di Trieste, Trieste, Italy.
    Stranges, S.
    Dipartimento di Chimica and INSTM, Universitá La Sapienza, Roma, Italy.
    The umbrella motion of core-excited CH3 and CD3 methyl radicals2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 4, p. 044302-1-044302-11Article in journal (Refereed)
    Abstract [en]

    An accurate experimental and theoretical study of the lowest core excitationof CH3 and CD3 methyl radicals is presented. The complexvibrational structure of the lowest band of the x-ray absorptionspectrum (XAS) is due to the large variation of themolecular geometry, which is planar in the ground state andpyramidal in the core-excited state. The XAS spectra of thetwo radicals were recorded at high resolution and assigned bytheoretical simulations of the spectra, taking into account the couplingof symmetrical stretching and symmetrical bending (umbrellalike) deformations of theradicals. An excellent agreement between experimental and theoretical spectral profilesallowed us to accurately characterize the vibrational structure of theelectronic transition. The similarities, as well as the differences, ofthe peculiar vibrational progression observed for the two radicals areexplained by the strong anharmonicity along the umbrella coordinate andby the isotopic variation, leading to a different probing ofthe double-well potential energy surface of the core excited stateduring the nuclear motion.

  • 42.
    Ekström, Ulf
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    X-ray absorption spectra from the resonantconvergent first-order polarization propagator approach2006In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 74, no 4, p. 042722-Article in journal (Refereed)
    Abstract [en]

    The one-photon absorption cross sections of molecular systems have been determined in the high-energy region from the imaginary part of the electric dipole polarizability tensor. In contrast to commonly adopted state-specific methodologies, the complex polarization propagator approach does not require explicit consideration of the excited states and it is open-ended towards multiphoton absorption. It is shown that the electronic relaxation in the core-hole state is well accounted for in the present approach with use of standard density-functional based electronic structure methods. Sample calculations are presented of the K-edge x-ray absorption spectra for H2O, CO, C4H4N, and C6H6.

  • 43.
    Ekström, Ulf
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Carravetta, Vincenzo
    Istituto per i Processi Chimico-Fisici, Area della Ricerca del C.N.R., Pisa, Italy.
    Relativistic four-component static-exchange approximation for core-excitation processes in molecules2006In: Physical review A, ISSN 1050-2947, Vol. 73, no 2, p. 022501-Article in journal (Refereed)
    Abstract [en]

    A generalization of the static-exchange approximation for core-electron spectroscopies to the relativistic four-component realm is presented. The initial state is a Kramers restricted Hartree-Fock state and the final state is formed as the configuration-interaction single excited state, based on the average of configurations for (n–1) electrons in n near-degenerate core orbitals for the reference ionic state. It is demonstrated that the static-exchange Hamiltonian can be made real by considering a set of time-reversal symmetric electron excitation operators. The static-exchange Hamiltonian is constructed at a cost that parallels a single Fock matrix construction in a quaternion framework that fully exploits time-reversal and spatial symmetries for the D2h point group and subgroups. The K- and L-edge absorption spectra of H2S are used to illustrate the methodology. The calculations adopt the Dirac-Coulomb Hamiltonian, but the theory is open ended toward improvements in the electron-electron interaction operator. It is demonstrated that relativistic effects are substantial for the L-edge spectrum of sulfur, and substantial deviations from the statistical 2:1 spin-orbit splitting of the intensity distribution are found. The average ratio in the mixed region is 1.54 at the present level of theory.

  • 44.
    Ekström, Ulf
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Carravetta, Vincenzo
    Istituto per i Processi Chimico-Fisici, Area della Ricerca del C.N.R., Pisa, Italy.
    Ågren, Hans
    Laboratory of Theoretical Chemistry, Royal Institute of Technology, Stockholm, Sweden.
    Polarization propagator for x-ray spectra2006In: Physical Review Letters, ISSN 1050-2947, Vol. 97, no 14, p. 143001-Article in journal (Refereed)
    Abstract [en]

    A polarization propagator for x-ray spectra is outlined and implemented in density functional theory. It rests on a formulation of a resonant-convergent first-order polarization propagator approach which makes it possible to directly calculate the x-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted x-ray spectrum relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects.

  • 45.
    Ekström, Ulf
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Ottosson, Henrik
    Department of Biochemistry and Organic Chemistry, Uppsala university, Sweden.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Characterization of the chemisorption of methylsilane on a Au(1,1,1) surface from the silicon K- and L-edge spectra: a theoretical study using the four-component static exchange approximation2005In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 111, p. 13846-13850Article in journal (Refereed)
    Abstract [en]

    X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectra (NEXAFS) of methylsilane, isolated and chemisorbed to a Au(1,1,1) surface, are determined in the fully relativistic four-component static exchange approximation¯both the K- and the L-edge of silicon are addressed in this investigation. In the fully chemisorbed structure, three H(Si) atoms have been cleaved off when Si binds in the hollow site of Au forming three Si−Au bonds of normal length. As due to the tri-coordinated chemisorption, the onsets of the K- and L-edge NEXAFS absorption bands occur some 2.0 and 2.5 eV lower in energy, respectively. The spin−orbit splittings in the silicon 2p-shell are not significantly changed due to adsorption. A partly chemisorbed methylsilane with only one H(Si) bond cleaved was also studied, and it is shown that the polarization dependence in the surface spectra contains details that can be used experimentally to identify the surface coordination of silicon. The red-shifts in the XPS silicon 1s (2p) spectra upon surface binding are 0.95 (0.65) and 1.15 (0.83) eV for the mono- and tricoordinated system, respectively.

  • 46.
    Ekström, Ulf
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Rizzo, Antonio
    Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Area della Ricerca, Pisa, Italy.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Four-component Hartree–Fock calculations of magnetic-field induced circular birefringence—Faraday effect—in noble gases and dihalogens2005In: The Journal of Chemical Physics, ISSN 1050-2947, Vol. 122, p. 074321-Article in journal (Refereed)
    Abstract [en]

    Theeffects of relativity on the magnetic-field induced circular birefringence, orFaraday effect, in He, Ne, Ar, Xe, Rn, F2, Cl2,Br2, and I2 have been determined at the four-component Hartree–Focklevel of theory. A measure of the birefringence is givenby the Verdet constant, which is a third-order molecular propertyand thus relates to quadratic response functions. A fully analyticalnonlinear polarization propagator approach is employed. The results are gaugeinvariant as a consequence of the spatial symmetries in themolecular systems. The calculations include electronic as well as vibrationalcontributions to the property. Comparison with experiment is made forHe, Ne, Ar, Xe, and Cl2, and, apart from neon,the theoretical values of the Verdet constant are within 10%of the experimental ones. The inclusion of nonrelativistically spin-forbidden excitationsin the propagator parametrization has significant effects on the dispersionin general, but such effects are in the general caselargely explained by the use of a resonant-divergent propagator theory.In the present work we do, however, observe noticeable relativisticcorrections to the Verdet constant in the off-resonant regions forsystems with light elements (F2 and Cl2), and nonrelativistic resultsfor the Verdet constant of Br2 are in error by25% in the low-frequency region. ©2005 American Institute of Physics.

  • 47.
    Elm, Jonas
    et al.
    University of Copenhagen, Denmark .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Bilde, Merete
    Aarhus University, Denmark .
    Mikkelsen, Kurt V.
    University of Copenhagen, Denmark .
    Computational study of the Rayleigh light scattering properties of atmospheric pre-nucleation clusters2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 22, p. 10883-10890Article in journal (Refereed)
    Abstract [en]

    The Rayleigh and hyper Rayleigh scattering properties of the binary (H2SO4)(H2O)(n) and ternary (H2SO4)(NH3)(H2O) n clusters are investigated using a quantum mechanical response theory approach. The molecular Rayleigh scattering intensities are expressed using the dipole polarizability alpha and hyperpolarizability beta tensors. Using density functional theory, we elucidate the effect of cluster morphology on the scattering properties using a combinatorial sampling approach. We find that the Rayleigh scattering intensity depends quadratically on the number of water molecules in the cluster and that a single ammonia molecule is able to induce a high anisotropy, which further increases the scattering intensity. The hyper Rayleigh scattering activities are found to be extremely low. This study presents the first attempt to map the scattering of atmospheric molecular clusters using a bottom-up approach.

  • 48.
    Engström, Maria
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Quantum chemical calculations of electron paramagnetic resonance of biological radicals2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The aim of this thesis was to use state-of-the-art quantum chemical calculations of electron paramagnetic resonance (EPR) with applications to radicals in biomolecular systems. Special emphasis has been devoted to investigations of structure-to-property relations of amino acid radicals and spin labels in proteins. The g-tensor calculations constitute the principal point employing novel response theory and density functional theory (DFT) algorithms. The A-tensor calculations supply additional means for a comprehensive comparison with experimental results. Calculations on substituted benzene radicals as a test set showed that restricted open-shell Hartree-Fock (ROHF) wave functions provide accurate results for the g-tensor. Some radicals, however, like the phenoxyl radical, call for a more sophisticated approach such as the multi-configuration self-consistent field (MCSCF) method. This method provide accurate results for the g-tensor in every case. The main contributions to the g-tensor could be traced qualitatively to the organization of the few lowest excited states of the radical. However, to obtain quantitative accurate results the contributions from all excited states must be accounted for, as attained by the response theory method.

    The EPR parameters are sensitive probes of molecular interactions in the close vicinity of the radical. In a combined theoretical and experimental study it was possible to specify the causes of the parameter shifts in detail. The calculations confirmed that 9xx decreases and Azz increases at hydrogen bonding of the label. MCSCF calculations on tyrosyl radicals resulted in a lower 9xx at hydrogen bonding as observed experimentally in ribonucleotide reductase (RNR). A sulfur substitution, modeling the tyrosyl radical in galactose oxidase (GO), did unexpectedly not significantly influence the g-tensor or the spin density distribution. Calculations on sulfur centered radicals with different structures and charges showed that the g-tensor pattern is significantly different among these radicals. Thus the calculations provided means to distinguish different radical structures from each other. By DFT it is possible to make EPR calculations on large molecular systems. This was shown by calculations on a nitroxide spin label and nearby amino acids in a protein complex. The combination of EPR spectroscopy and DFT calculations provide a prospect of obtaining detailed knowledge about protein radicals.

  • 49.
    Eriksson, Olivia
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Brinne, Björn
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Zhou, Y
    Stockholm University.
    Bjorkegren, J
    Karolinska University Hospital.
    Tegnér , Jesper
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit2009In: IET SYSTEMS BIOLOGY, ISSN 1751-8849 , Vol. 3, no 2, p. 113-23Article in journal (Refereed)
    Abstract [en]

    Complex regulatory dynamics is ubiquitous in molecular networks composed of genes and proteins. Recent progress in computational biology and its application to molecular data generate a growing number of complex networks. Yet, it has been difficult to understand the governing principles of these networks beyond graphical analysis or extensive numerical simulations. Here the authors exploit several simplifying biological circumstances which thereby enable to directly detect the underlying dynamical regularities driving periodic oscillations in a dynamical nonlinear computational model of a protein-protein network. System analysis is performed using the cell cycle, a mathematically well-described complex regulatory circuit driven by external signals. By introducing an explicit time delay and using a tearing-and-zooming approach the authors reduce the system to a piecewise linear system with two variables that capture the dynamics of this complex network. A key step in the analysis is the identification of functional subsystems by identifying the relations between state-variables within the model. These functional subsystems are referred to as dynamical modules operating as sensitive switches in the original complex model. By using reduced mathematical representations of the subsystems the authors derive explicit conditions on how the cell cycle dynamics depends on system parameters, and can, for the first time, analyse and prove global conditions for system stability. The approach which includes utilising biological simplifying conditions, identification of dynamical modules and mathematical reduction of the model complexity may be applicable to other well-characterised biological regulatory circuits.

  • 50.
    Fahleson, Tobias
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Kauczor, Joanna
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Coriani, Sonia
    University of Trieste, Italy .
    The magnetic circular dichroism spectrum of the C-60 fullerene2013In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, no 9-11, p. 1401-1404Article in journal (Refereed)
    Abstract [en]

    The magnetic circular dichroism spectrum of the C-60 fullerene has been determined with the use of Kohn-Sham density functional theory in conjunction with the CAM-B3LYP exchange-correlation functional. The experimental spectrum of Gasyna etal. [Chem. Phys. Lett. 183, 283 (1991)] covering the wavelength region above 200 nm is explained by the signal responses from the three lowest singlet states of T-1u symmetry.

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