Now showing items 84-103 of 253

    • Effect of donor–acceptor orientation on solvent-dependent three-photon activity in through-space charge-transfer systems – case study of [2,2]-paracyclophane derivatives 

      Alam, MD Mehboob; Chattopadhyaya, Mausumi; Chakrabarti, Swapan; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2013)
      We study the effect of donor–acceptor orientation on solvent-dependent three-photon transition probabilities (δ3PA) of representative through-space charge-transfer (TSCT) systems, namely, doubly positively charged [2,2]-paracyclophane derivatives. Our cubic response calculations reveal that the value of δ3PA may be as high as 106 a.u., which can further be increased by a specific orientation of the ...
    • An efficient pseudo-spectral method for the description of atomic electronic wave functions – Application to the hydrogen atom in a uniform magnetic field 

      Woywod, Clemens; Roy, Susmita; Maiti, Kiran; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-27)
      <p>The mapping of an electronic state on a real-space support lattice may offer advantages over a basis set ansatz in cases where there are linear dependences due to basis set overcompleteness or when strong internal or external fields are present. Such discretization methods are also of interest because they allow for the convenient numerical integration of matrix elements of local operators. We ...
    • Electron and nuclear spin polarization in Rb-Xe spin-exchange optical hyperpolarization 

      Hanni, Matti; Lantto, Perttu; Repiský, Michal; Mareš, Jiří; Saam, Brian; Vaara, Juha (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-03)
      Spin-exchange optical hyperpolarization of <sup>129</sup>Xe gas enhances the signal-to-noise ratio in nuclear magnetic resonance experiments. The governing parameter of the Rb-Xe spin-exchange process, the so-called enhancement factor, was recently reevaluated experimentally. However, the underlying hyperfine coupling and atomic interaction potential as functions of the internuclear distance of the ...
    • Electronic structure of small surfactants: a continuum solvation study 

      Mozgawa, Krzysztof; Frediani, Luca (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-07-18)
      The e ect of surfaces and interfaces on the structure and properties of molecules is of a great interest in a number of biological and technological applications. Nevertheless, such an investigation is extremely challenging from an experimental point of view, due to the bidimensionality of the environment. In recent years, we have developed a framework to study molecules at surfaces ...
    • The Elephant in the Room of Density Functional Theory Calculations 

      Jensen, Stig Rune; Saha, Santanu; Flores-Livas, Jose A; Huhn, William; Blum, Volker; Goedecker, Stefan; Frediani, Luca (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-03-14)
      Using multiwavelets, we have obtained total energies and corresponding atomization energies for the GGA-PBE and hybrid-PBE0 density functionals for a test set of 211 molecules with an unprecedented and guaranteed μHartree accuracy. These quasi-exact references allow us to quantify the accuracy of standard all-electron basis sets that are believed to be highly accurate for molecules, such as Gaussian-type ...
    • The EMEP MSC-W chemical transport model - technical description 

      Simpson, David; Benedictow, Anna; Berge, Halldis; Bergström, Robert; Emberson, Lisa D.; Fagerli, Hilde; Flechard, Chris R.; Hayman, Garry D.; Gauss, Michael; Jonson, Jan Eiof; Jenkin, Michael E.; Nyiri, Agnes; Richter, Cornelia; Semeena, Valiyavetil S.; Tsyro, Svetlana; Tuovinen, Juha Pekka; Valdebenito, Alvaro; Wind, Peter (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      The Meteorological Synthesizing Centre-West (MSC-W) of the European Monitoring and Evaluation Programme (EMEP) has been performing model calculations in support of the Convention on Long Range Transboundary Air Pollution (CLRTAP) for more than 30 years. The EMEP MSC-W chemical transport model is still one of the key tools within European air pollution policy assessments. Traditionally, the model ...
    • Enantioselective incorporation of CO2: status and potential 

      Vaitla, Janakiram; Guttormsen, Yngve; Mannisto, Jere K.; Nova, Ainara; Repo, Timo; Bayer, Annette; Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-09-09)
      CO<sub>2</sub> is a promising and sustainable carbon feedstock for organic synthesis. New catalytic protocols for efficient incorporation of CO<sub>2</sub>into organic molecules are continuously being reported. However, little progress has been made in the enantioselective conversion of CO<sub>2</sub>to form enantioenriched molecules. In order to allow CO<sub>2</sub>to become a versatile carbon ...
    • Energetics of saddling versus ruffling in metalloporphyrins: Unusual ruffled dodecasubstituted porphyrins 

      Conradie, Jeanet; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-10-13)
      Presented herein is a first major density functional theory (BP86/D3/STO-TZ2P) survey of the energetics of saddling versus ruffling for a wide range of dodecasubstituted metalloporphyrins with M = Ni, Cu, Zn, Pd, and Pt. For the majority of X<sub>8</sub>TPP (i.e., β-octasubstituted-meso-tetraphenylporphyrin), the calculations indicated a clear preference for the saddled conformation, consistent with ...
    • Engineering low-temperature expression systems for heterologous production of cold-adapted enzymes 

      Bjerga, Gro Elin Kjæreng; Lale, Rahmi; Williamson, Adele Kim (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-02-26)
      Production of psychrophilic enzymes in the commonly used mesophilic expression systems is hampered by low intrinsic stability of the recombinant enzymes at the optimal host growth temperatures. Unless strategies for low-temperature expression are advanced, research on psychrophilic enzymes may end up being biased toward those that can be stably produced in commonly used mesophilic host systems. Two ...
    • Entropy and Enzyme Catalysis 

      Åqvist, Johan; Kazemi, Masoud; Isaksen, Geir Villy; Brandsdal, Bjørn Olav (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-02-07)
      The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed cases where the activation free energy is reduced by around 10 kcal/mol due to entropic effects, corresponding to a rate enhancement of ∼107 compared to the uncatalyzed reaction. However, despite substantial efforts from both the experimental ...
    • Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface 

      Williamson, Adele Kim; Rothweiler, Ulli; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2014-11-01)
      DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, ...
    • EURODELTA-Trends, a multi-model experiment of air quality hindcast in Europe over 1990-2010 

      Colette, Augustin; Andersson, Camilla; Manders, Astrid; Mar, Kathleen; Mircea, Mihaela; Pay, Maria-Teresa; Raffort, Valentin; Tsyro, Svetlana G.; Cuvelier, Cornelius; Adani, Mario; Bessagnet, Bertrand; Bergström, Robert; Briganti, Gino; Butler, Tim; Cappelletti, Andrea; Couvidat, Florian; D'Isidoro, Massimo; Doumbia, Thierno; Fagerli, Hilde; Granier, Claire; Heyes, Chris; Klimont, Zig; Ojha, Narendra; Otero, Noelia; Schaap, Martijn; Sindelarova, Katarina; Stegehuis, Annemiek I.; Roustan, Yelva; Vautard, Robert; Van Meijgaard, Erik; Garcia Vivanco, Marta; Wind, Peter Ariaan (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-09-05)
      The EURODELTA-Trends multi-model chemistry-transport experiment has been designed to facilitate a better understanding of the evolution of air pollution and its drivers for the period 1990–2010 in Europe. The main objective of the experiment is to assess the efficiency of air pollutant emissions mitigation measures in improving regional-scale air quality. <br>The present paper formulates the ...
    • Excitation Energies from Real-Time Propagation of the Four-Component Dirac–Kohn–Sham Equation 

      Repisky, Michal; Konecny, Lukas; Kadek, Marius; Komorovsky, Stanislav; Malkina, Olga L.; Malkin, Vladimir G.; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-01-21)
      We report the first implementation of real-time time-dependent density functional theory (RT-TDDFT) at the relativistic four-component level of theory. In contrast to the perturbative linear-response TDDFT approach (LR-TDDFT), the RT-TDDFT approach performs an explicit time propagation of the Dirac–Kohn–Sham density matrix, offering the possibility to simulate molecular spectroscopies involving ...
    • Experimental and four-component relativistic DFT studies of tungsten carbonyl complexes 

      Demissie, Taye Beyene; Kostenko, Nataliya; Komorovsky, Stanislav; Repisky, Michal; Isaksson, Johan; Bayer, Annette; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-07-24)
      We present a theoretical and experimental study of the structure and nuclear magnetic resonance (NMR) parameters of the pentacarbonyltungsten complexes of η<sup>1</sup>-2-(trimethylstannyl)-4,5-dimethylphosphinine, η<sup>2</sup>-norbornene, and imidazolidine-2-thione. The three complexes have a pseudo-octahedral molecular structure with the six ligands bonded to the tungsten atom. The η<sup>1</sup ...
    • Exploring the role of L209 residue in the active site of NDM-1 a metallo-β-lactamase 

      Marcoccia, Francesca; Leiros, Hanna-Kirsti S.; Aschi, Massimiliano; Amicosante, Gianfranco; Perilli, Mariagrazia (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-01-02)
      Background:<br> New Delhi Metallo-β-Lactamase (NDM-1) is one of the most recent additions to the β-lactamases family. Since its discovery in 2009, NDM-1 producing Enterobacteriaceae have disseminated globally. With few effective antibiotics against NDM-1 producers, there is an urgent need to design new drug inhibitors through the help of structural and mechanistic information available from ...
    • Exploring the transcriptome of luxI- and ΔainS mutants and the impact of N-3-oxo-hexanoyl-L- and N-3-hydroxy- decanoyl-L-homoserine lactones on biofilm formation in Aliivibrio salmonicida 

      Khider, Miriam; Hansen, Hilde; Hjerde, Erik; Johansen, Jostein A; Willassen, Nils Peder (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-04-30)
      <i>Background</i>: Bacterial communication through quorum sensing (QS) systems has been reported to be important in coordinating several traits such as biofilm formation. In <i>Aliivibrio salmonicida</i> two QS systems the LuxI/R and AinS/R, have been shown to be responsible for the production of eight acyl-homoserine lactones (AHLs) in a cell density dependent manner. We have previously ...
    • 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 ...
    • Extreme Scalability of DFT-based QM/MM MD Simulations Using MiMiC 

      Bolnykh, Viacheslav; Olsen, Jógvan Magnus Haugaard; Meloni, Simone; Bircher, Martin Peter; Ippoliti, Emiliano; Carloni, Paolo; Rothlisberger, Ursula (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-09-09)
      We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD ...
    • Features and structure of a cold active N-acetylneuraminic acid lyase 

      Gurung, Man Kumari; Altermark, Bjørn; Helland, Ronny; Smalås, Arne O.; Ræder, Inger Lin Uttakleiv (Journal article; Peer reviewed, 2019-06-11)
      N-acetylneuraminate lyases (NALs) are enzymes that catalyze the reversible cleavage and synthesis of sialic acids. They are therefore commonly used for the production of these high-value sugars. This study presents the recombinant production, together with biochemical and structural data, of the NAL from the psychrophilic bacterium Aliivibrio salmonicida LFI1238 (AsNAL). Our characterization shows ...
    • Five-Photon Absorption and Selective Enhancement of Multiphoton Absorption Processes 

      Friese, Daniel Henrik; Bast, Radovan; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-05-12)
      We study one-, two-, three-, four- and five-photon absorption of three centrosymmetric molecules using density functional theory. These calculations are the first ab initio calculations of five-photon absorption. Even- and odd-order absorption processes show different trends in the absorption cross sections. The behaviour of all even-and odd-photon absorption properties shows a semi-quantitative ...