• A multi-model study of impacts of climate change on surface ozone in Europe 

      Langner, J.; Engardt, M.; Baklanov, A.; Christensen, J. H.; Gauss, Michael; Geels, Camila; Hedegaard, G.B.; Nuterman, R.; Simpson, D.; Soares, J; Sofiev, M; Wind, Peter; Zakey, A. (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      The impact of climate change on surface ozone over Europe was studied using four offline regional chemistry transport models (CTMs) and one online regional integrated climate-chemistry model (CCM), driven by the same global projection of future climate under the SRES A1B scenario. Anthropogenic emissions of ozone precursors from RCP4.5 for year 2000 were used for simulations of both present and ...
    • Lipopolysaccharide O-Antigen Prevents Phagocytosis of Vibrio anguillarum by Rainbow Trout (Oncorhynchus mykiss) Skin Epithelial Cells 

      Lindell, Kristoffer; Fahlgren, Anna; Hjerde, Erik; Willassen, Nils Peder; Fällman, Maria; Milton, Debra L (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      Colonization of host tissues is a first step taken by many pathogens during the initial stages of infection. Despite the impact of bacterial disease on wild and farmed fish, only a few direct studies have characterized bacterial factors required for colonization of fish tissues. In this study, using live-cell and confocal microscopy, rainbow trout skin epithelial cells, the main structural component ...
    • Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida 

      Hansen, Geir Åsmund; Ahmad, Rafi; Hjerde, erik; Fenton, Christopher Graham; Willassen, Nils Peder; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria. One member of this family, Aliivibrio ...
    • The Methylococcus capsulatus (Bath) secreted protein, MopE*, binds both reduced and oxidized copper. 

      Ve, Thomas; Mathisen, Karina; Helland, Ronny; Karlsen, Odd Andre; Fjellbirkeland, Anne; Røhr, Åsmund Kjendseth; Andersson, K. Kristoffer; Pedersen, Rolf B.; Lillehaug, Johan R.; Jensen, Harald B (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      Under copper limiting growth conditions the methanotrophic bacterium Methylococcus capsulatus (Bath) secrets essentially only one protein, MopE*, to the medium. MopE* is a copper-binding protein whose structure has been determined by X-ray crystallography. The structure of MopE* revealed a unique high affinity copper binding site consisting of two histidine imidazoles and one kynurenine, the latter ...
    • (3aS,4S,6S,7aR)-hexahydro-3a,5,5-trimethyl-2-phenyl-4,6-methano-1,3,2-benzodioxaborole 

      Lejon, Tore; Gozhina, Olga Vladimirovna; Khrustalev, Victor N. (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      The molecule of the title compound, C16H21BO2, comprises a chiral fused tricyclic system containing five-membered (1,3,2-dioxaborolane), six-membered (cyclohexane) and four-membered (cyclobutane) rings. The 1,3,2-dioxaborolane ring is almost planar (r.m.s. deviation = 0.035 Å), and the syn H and Me substituents at this ring are in an eclipsed conformation. The cyclohexane and cyclobutane rings adopt ...
    • Potassium [(1S )-1-azido-2-phenylethyl]trifluoridoborate 

      Lejon, Tore; Gorovoy, Alexey Sergeevich; Khrustalev, Victor N. (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      The title compound, K+·C8H8BF3N3-, is a salt containing the chiral organic trifluoridoborate anion. The organic anions and potassium cations are tightly bound to each other by the coordination K-F [2.654 (3)-3.102 (3) Å] and K-N [2.951 (4)-3.338 (4) Å] interactions. Thus, the potassium cation adopts a nine-vertex coordination polyhedron, which can be described as a distorted monocapped tetragonal ...
    • Anomalous dispersion analysis of inhibitor flexibility : a case study of the kinase inhibitor H-89 

      Pflug, Alexander; Johnson, Kenneth; Engh, Richard Alan (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      With its ability to show the interactions between drug-target proteins and small-molecule ligands, X-ray crystallography is an essential tool in drug-discovery programmes. However, its usefulness can be limited by crystallization artifacts or by the data resolution, and in particular when assumptions of unimodal binding (and isotropic motion) do not apply. Discrepancies between the modelled crystal ...
    • A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein 

      Steindal, Arnfinn Hykkerud; Olsen, Jógvan Magnus Haugaard; Ruud, Kenneth; Frediani, Luca; Kongsted, Jacob (Journal article; Tidsskriftartikkel; Peer reviewed, 2012-02-01)
      We present for the first time a QM/MM study of the one- and two-photon absorption spectra of the GFP chromophore embedded in the full protein environment described by an advanced quantum mechanically derived polarizable force field. The calculations are performed on a crystal structure of the green fluorescent protein (GFP) using the polarizable embedding density functional theory (PE-DFT) scheme. ...
    • The complex structures of isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila support a new active site locking mechanism 

      Leiros, Hanna-Kirsti S.; Fedøy, Anita-Elin; Leiros, Ingar; Steen, Ida Helene (Journal article; Tidsskriftartikkel; Peer reviewed, 2012-07-07)
      Isocitrate dehydrogenase (IDH) catalyzes the oxidative NAD(P)+ -dependent decarboxylation of isocitrate into a-ketoglutarate and CO2 and is present in organisms spanning the biological range of temperature. We have solved two crystal structures of the thermophilic Clostridium thermocellum IDH (CtIDH), a native open apo CtIDH to 2.35 Å and a quaternary complex of CtIDH with NADP+ , isocitrate and ...
    • A thermally stable {FeNO}(8) complex: properties and biological reactivity of reduced MNO systems 

      Patra, Ashis K.; Dube, Koustubh S.; Sanders, Brian C.; Papaefthymiou, Georgia C.; Conradie, Jeanet; Ghosh, Abhik; Harrop, Todd C. (Journal article; Tidsskriftartikkel; Peer reviewed, 2012-10-06)
      Reduced nitrogen oxide ligands such as NO<sup>−</sup>/HNO or nitroxyl participate in chemistry distinct from nitric oxide (NO). Nitroxyl has been proposed to form at heme centers to generate the Enemark–Feltham designated {FeNO}<sup>8</sup> system. The synthesis of a thermally stable {FeNO}<sup>8</sup> species namely, [Co(Cp<sup>*</sup>)<sub>2</sub>][Fe(LN<sub>4</sub>)(NO)] (3), housed in a heme-like ...
    • Pyrazine excited states revisited using the extended multi-state complete active space second-order perturbation method 

      Shiozaki, Toru; Woywod, Clemens Joachim; Werner, Hans-Joachim (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      We demonstrate that the recently developed extended multi-state complete active space second-order perturbation theory (XMS-CASPT2) [Shiozaki et al., J. Chem. Phys., 2011, 135, 081106] provides qualitatively correct potential energy surfaces for low-lying excited singlet states of pyrazine, while the potential energy surfaces of the standard MS-CASPT2 methods are ill-behaved near the crossing ...
    • Spin-rotation and NMR shielding constants in HCl 

      Jaszunski, Michal; Repisky, Michal; Demissie, Taye B.; Komorovsky, Stanislav; Malkin, Elena; Ruud, Kenneth; Garbacz, Piotr; Jackowski, Karol; Makulski, W (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      The spin-rotation and nuclear magnetic shielding constants are analysed for both nuclei in the HCl molecule. Nonrelativistic ab initio calculations at the CCSD(T) level of approximation show that it is essential to include relativistic effects to obtain spin-rotation constants consistent with accurate experimental data. Our best estimates for the spin-rotation constants of 1H35Cl are CCl =−53.914 ...
    • Role of zero-point vibrational corrections to carbon hyperfine coupling constants in organic pi radicals 

      Chen, Xiao; Rinkevicius, Zilvinas; Ruud, Kenneth; Ågren, Hans (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      By analyzing a set of organic π radicals, we demonstrate that zero-point vibrational corrections give significant contributions to carbon hyperfine coupling constants, in one case even inducing a sign reversal for the coupling constant. We discuss the implications of these findings for the computational analysis of electron paramagnetic spectra based on hyperfine coupling constants evaluated at the ...
    • Perturbed atoms in molecules and solids:the PATMOS model 

      Røeggen, Inge; Gao, Bin (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      A new computational method for electronic-structure studies of molecules and solids is presented. The key element in the new model – denoted the perturbed atoms in molecules and solids model – is the concept of a perturbed atom in a complex. The basic approximation of the new model is unrestricted Hartree Fock (UHF). The UHF orbitals are localized by the Edmiston-Ruedenberg procedure. The perturbed ...
    • Ab initio studies of two pyrimidine derivatives as possible photo-switch systems 

      Csehi, András; Woywod, Clemens Joachim; Halász, Gábor J.; Vibok, Agnes (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      The six lowest lying electronic singlet states of 8-(pyrimidine-2-yl)quinolin-ol and 2-(4-nitropyrimidine-2- yl)ethenol have been studied theoretically using the complete active space self-consistent-field (CASSCF) and Møller-Plesset second-order perturbation theory (MP2) methods. Both molecules can be viewed as consisting of a frame and a crane component. As a possible mechanism for the excited-state ...
    • MabCent: Arctic marine bioprospecting in Norway 

      Svenson, Johan (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      The deep waters surrounding the coastline of the northern parts of Norway represent an exciting biotope for marine exploration. Dark and cold Arctic water generates a hostile environment where the ability to adapt is crucial to survival. These waters are nonetheless bountiful and a diverse plethora of marine organisms thrive in these extreme conditions, many with the help of specialised ...
    • Structural and thermodynamic insight into phenylalanine hydroxylase from the human pathogen Legionella pneumophila 

      Leiros, Hanna-Kirsti S.; Flydal, Marte Innselset; Martinez, Aurora (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      Phenylalanine hydroxylase from Legionella pneumophila (lpPAH) has a major functional role in the synthesis of the pigment pyomelanin, which is a potential virulence factor. We present here the crystal structure of lpPAH, which is a dimeric enzyme that shows high thermostability, with a midpoint denat- uration temperature of 79 ◦C, and low substrate affinity. The structure revealed a dimerization ...
    • When Optimization Is Just an Illusion 

      Muhammad Fuad, Muhammad Marwan (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      Bio-inspired optimization algorithms have been successfully applied to solve many problems in engineering, science, and economics. In computer science bio-inspired optimization has different applications in different domains such as software engineering, networks, data mining, and many others. However, some applications may not be appropriate or even correct. In this paper we study this phenomenon ...
    • A Pre-initialization Stage of Population-Based Bio-inspired Metaheuristics for Handling Expensive Optimization Problems 

      Muhammad Fuad, Muhammad Marwan (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      Metaheuristics are probabilistic optimization algorithms which are applicable to a wide range of optimization problems. Bio-inspired, also called nature-inspired, optimization algorithms are the most widely-known metaheuristics. The general scheme of bio-inspired algorithms consists in an initial stage of randomly generated solutions which evolve through search operations, for several generations, ...
    • Analytic evaluation of the dipole Hessian matrix in coupled-cluster theory 

      Jagau, TC; Gauss, J; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      The general theory required for the calculation of analytic third energy derivatives at the coupled-cluster level of theory is presented and connected to preceding special formulations for hyperpolarizabilities and polarizability gradients. Based on our theory, we have implemented a scheme for calculating the dipole Hessian matrix in a fully analytical manner within the coupled-cluster singles and ...