Now showing items 100-119 of 247

    • 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 ...
    • A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design 

      Ahkter, Sundus; Lund, Bjarte Aarmo; Ismael, Aya; Langer, Manuel; Isaksson, Johan; Christopeit, Tony; Leiros, Hanna-Kirsti S.; Bayer, Annette (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02-10)
      β-Lactam antibiotics are of utmost importance when treating bacterial infections in the medical community. However, currently their utility is threatened by the emergence and spread of β-lactam resistance. The most prevalent resistance mechanism to β-lactam antibiotics is expression of β-lactamase enzymes. One way to overcome resistance caused by β-lactamases, is the development of β-lactamase ...
    • Four-Component Relativistic Calculations in Solution with the Polarizable Continuum Model of Solvation: Theory, Implementation and Application to the Group 16 Dihydrides H2X (X= O, S, Se, Te, Po) 

      Di Remigio, Roberto; Bast, Radovan; Frediani, Luca; Saue, Trond (Journal article; Tidsskriftartikkel; Peer reviewed, 2014-11-20)
    • Four-Component Relativistic Density Functional Theory Calculations of EPR g- and Hyperfine-Coupling Tensors Using Hybrid Functionals: Validation on Transition-Metal Complexes with Large Tensor Anisotropies and Higher-Order Spin-Orbit Effects 

      Gohr, Sebastian; Hrobárik, Peter; Repisky, Michal; Komorovsky, Stanislav; Ruud, Kenneth; Kaupp, Martin (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-12-04)
      The four-component matrix Dirac-Kohn-Sham (mDKS) implementation of EPR g- and hyperfine A-tensor calculations within a restricted kinetic balance framework in the ReSpect code has been extended to hybrid functionals. The methodology is validated for an extended set of small 4d1 and 5d1 [MEXn] q systems, and for a series of larger Ir(II) and Pt(III) d7 complexes (S=1/2) with particularly ...
    • Four-component relativistic density functional theory with the polarisable continuum model: application to EPR parameters and paramagnetic NMR shifts 

      Di Remigio, Roberto; Repisky, Michal; Komorovsky, Stanislav; Hrobárik, Peter; Frediani, Luca; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-01-01)
      The description of chemical phenomena in solution is as challenging as it is im- portant for the accurate calculation of molecular properties. Here, we present the implementation of the polarizable continuum model (PCM) in the four-component Dirac–Kohn–Sham density functional theory framework, o ↵ ering a cost-e ↵ ective way to concurrently model solvent and relativistic e ↵ ects. The ...
    • Four-Component Relativistic Density-Functional Theory Calculations of Nuclear Spin-Rotation Constants: Relativistic Effects in p-Block Hydrides 

      Komorovsky, Stanislav; Repisky, Michal; Malkin, Elena; Demissie, Taye Beyene; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-07-01)
      We present an implementation of the nuclear spin–rotation (SR) constants based on the relativistic four-component Dirac–Coulomb Hamiltonian. This formalism has been implemented in the framework of the Hartree–Fock and Kohn–Sham theory, allowing assessment of both pure and hybrid exchange–correlation functionals. In the density-functional theory (DFT) implementation of the response equations, a ...
    • Fragment-Based Drug Discovery 

      Lund, Bjarte Aarmo (Journal article; Tidsskriftartikkel, 2015-06-13)
    • Fully Polarizable QM/Fluctuating Charge Approach to Two-Photon Absorption of Aqueous Solutions 

      Di Remigio, Roberto; Giovannini, Tommaso; Ambrosetti, Matteo; Cappelli, Chiara; Frediani, Luca (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-06-05)
      We present the extension of the quantum/classical polarizable fluctuating charge model to the calculation of single residues of quadratic response functions, as required for the computational modeling of two-photon absorption cross sections. By virtue of a variational formulation of the quantum/classical polarizable coupling, we are able to exploit an atomic orbital-based quasienergy formalism to ...
    • Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis 

      Klemetsen, Terje; Willassen, Nils Peder; Karlsen, Christian René (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-07-04)
      Understanding fish‐microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, ...
    • Gauge-origin independent calculations of electric-field-induced second-harmonic generation circular intensity difference using London atomic orbitals 

      Anelli, Marco; Ringholm, Magnus; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2017)
      We present the first gauge-origin independent calculations of the circular intensity difference (CID) in electric-field-induced second-harmonic generation (EFISHG), including all contributions up to the electric-quadrupole–magnetic-dipole level. A recursive, open-ended response theory framework in combination with the use of London atomic orbitals allows us to ensure gauge-origin independent results. ...
    • Gauge-origin independent calculations of Jones birefringence 

      Shcherbin, Dmitri; Thorvaldsen, Andreas johan; Jonsson, Dan Johan; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2011)
      We present the first gauge-origin independent formulation of Jones birefringence at the Hartree–Fock level of theory. Gauge-origin independence is achieved through the use of London atomic orbitals. The implementation is based on a recently proposed atomic orbital-based response theory formulation that allows for the use of both time- and perturbation-dependent basis sets [Thorvaldsen, Ruud, Kristensen, ...
    • Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat 

      Juhasz, Angela; Belova, Tatiana; Florides, Chris G; Maulis, Csaba; Fischer, Iris; Gell, Gyongyver; Birinyi, Zsofia; Ong, Jamie; Keeble-Gagnere, Gabriel; Maharajan, Amudha Deepalakshmi; Ma, Wujun; Gibson, Peter; Jia, Jizeng; Lang, Daniel; Mayer, Klaus F X; Spannagl, Manuel; Tye-Din, Jason A.; Appels, Rudi; Olsen, Odd-Arne (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-08-17)
      Wheat is an important staple grain for humankind globally because of its end-use quality and nutritional properties and its adaptability to diverse climates. For a small proportion of the population, specific wheat proteins can trigger adverse immune responses and clinical manifestations such as celiac disease, wheat allergy, baker’s asthma, and wheat-dependent exercise-induced anaphylaxis (WDEIA). ...
    • Geometric Energy Derivatives at the Complete Basis Set Limit: Application to the Equilibrium Structure and Molecular Force Field of Formaldehyde 

      Morgan, W. James; Matthews, Devin A; Ringholm, Magnus; Agarwal, Jay; Gong, Justin Z; Ruud, Kenneth; Allen, Wesley D.; Stanton, John F.; Schaefer, Henry F. III (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02-23)
      Geometric energy derivatives which rely on core-corrected focal-point energies extrapolated to the complete basis set (CBS) limit of coupled cluster theory with iterative and noniterative quadruple excitations, CCSDTQ and CCSDT(Q), are used as elements of molecular gradients and, in the case of CCSDT(Q), expansion coefficients of an anharmonic force field. These gradients are used to determine the ...
    • A Haar Wavelet-based Multi-resolution Representation Method of Time Series Data 

      Muhammad Fuad, Muhammad Marwan (Peer reviewed; Journal article; Tidsskriftartikkel, 2015-01-10)
      Similarity search of time series can be efficiently handled through a multi-resolution representation scheme which offers the possibility to use pre-computed distances that are calculated and stored at indexing time and then utilized at query time together with filters in the form of exclusion conditions which speed up the search. In this paper we introduce a new multi-resolution representation ...
    • Heterocyclic cellular lipid peroxidation inhibitors inspired by the marine antioxidant barettin 

      Labriere, Christophe; Andersen, Jeanette hammer; Albrigtsen, Marte; Hansen, Jørn H; Svenson, Johan (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-11-22)
      The marine environment remains a rich source for the discovery and development of novel bioactive compounds. The present paper describes the design, synthesis and biological evaluation of a library of small molecule heterocyclic mimetics of the marine 2,5-diketopiperazine barettin which is a powerful natural antioxidant. By mainly focusing on the influence from the brominated indole and heterocyclic ...
    • High quality draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a sea squirt in Northern Norway 

      Bjerga, Gro Elin Kjæreng; Hjerde, Erik; De Santi, Concetta; Williamson, Adele Kim; Smalås, Arne O.; Willassen, Nils Peder; Altermark, Bjørn (Journal article; Tidsskriftartikkel; Peer reviewed, 2014)
    • A high-throughput, restriction-free cloning and screening strategy based on ccdB-gene replacement 

      Bjerga, Gro Elin Kjæreng; Lund, Bjarte Aarmo; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2014)
      Background In high-throughput demanding fields, such as biotechnology and structural biology, molecular cloning is an essential tool in obtaining high yields of recombinant protein. Here, we address recently developed restriction-free methods in cloning, and present a more cost-efficient protocol that has been optimized to improve both cloning and clone screening. Results In our case study, ...
    • How accurate is DFT for iridium-mediated chemistry? 

      Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-09-27)
      Iridium chemistry is versatile and widespread, with superior performance for reaction types such as enantioselective hydrogenation and C−H activation. In order to gain insight into the mechanistic details of such systems, density functional theory (DFT) studies are often employed. But how accurate is DFT for modeling iridium-mediated transformations in solution? We have evaluated how well DFT ...
    • How does relativity affect magnetically induced currents? 

      Berger, Raphael Johann Friedrich; Repisky, Michal; Komorovsky, Stanislav (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-07-23)
      Magnetically induced probability currents in molecules are studied in relativistic theory. Spin–orbit coupling (SOC) enhances the curvature and gives rise to a previously unobserved current cusp in AuH or small bulge-like distortions in HgH2 at the proton positions. The origin of this curvature is magnetically induced spin-density arising from SOC in the relativistic description.