Recent additions

  • Four-component relativistic time-dependent density-functional theory using a stable noncollinear DFT ansatz applicable to both closed- and open-shell systems 

    Komorovsky, Stanislav; Cherry, Peter J.; Repisky, Michal (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-11-14)
    We present a formulation of relativistic linear response time-dependent density functional theory for the calculation of electronic excitation energies in the framework of the four-component Dirac-Coulomb Hamiltonian. This approach is based on the noncollinear <i>ansatz</i> originally developed by Scalmani and Frisch [J. Chem. Theory Comput. 8, 2193 (2012)] and improves upon the past treatment of ...
  • Relativistic four-component linear damped response TDDFT for electronic absorption and circular dichroism calculations 

    Konecny, Lukas; Repisky, Michal; Ruud, Kenneth; Komorovsky, Stanislav (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-11-21)
    We present a detailed theory, implementation, and a benchmark study of a linear damped response time-dependent density functional theory (TDDFT) based on the relativistic four-component (4c) Dirac–Kohn–Sham formalism using the restricted kinetic balance condition for the small-component basis and a noncollinear exchange–correlation kernel. The damped response equations are solved by means of a ...
  • The quantitative level of T315I mutated BCR-ABL predicts for major molecular response to second-line nilotinib or dasatinib treatment in patients with chronic myeloid leukemia 

    Lange, Thoralf; Ernst, Thomas; Gruber, Franz; Maier, Jacqueline; Cross, Michael; Müller, Martin C.; Niederwieser, Dietger; Hochhaus, Andreas; Pfirrmann, Markus (Journal article; Tidsskriftartikkel; Peer reviewed, 2013-05)
    The BCR-ABL T315I mutation causes resistance to imatinib, nilotinib and dasatinib in chronic myeloid leukemia. Forty BCR-ABL positive patients with imatinib resistance were analyzed for T315I mutated clones after six months on nilotinib or dasatinib treatment by quantitative allele-specific ligation polymerase chain reaction with a sensitivity of 0.05%. Ligation polymerase chain reaction revealed ...
  • 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 ...
  • Caesium Fluoride-Mediated Hydrocarboxylation of Alkenes and Allenes: Scope and Mechanistic Insights 

    Gevorgyan, Ashot; Obst, Marc; Guttormsen, Yngve; Maseras, Feliu; Hopmann, Kathrin Helen; Bayer, Annette (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-09-11)
    A caesium fluoride-mediated hydrocarboxylation of olefins is disclosed that does not rely on precious transition metal catalysts and ligands. The reaction occurs at atmospheric pressures of CO<sub>2</sub> in the presence of 9-BBN as a stoichiometric reductant. Stilbenes, β-substituted styrenes and allenes could be carboxylated in good yields. The developed methodology can be used for preparation of ...
  • Catalytic Intermolecular Functionalization of Benzimidazoles 

    Hansen, Jørn H; Fjellaksel, Richard (Peer reviewed; Chapter; Bokkapittel, 2019-06-25)
    This chapter describes contemporary strategies for selective catalytic intermolecular functionalization of the benzimidazole scaffold. Functionalization at nitrogen and position C-2 is well developed employing copper, palladium, rhodium, nickel, and cobalt catalysis. Direct CH activation is the predominant approach to C-2 functionalization. Nickel-based catalysts can activate C—O bonds in conjunction ...
  • Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) 

    Le Doujet, Typhaine; De Santi, Concetta; Klemetsen, Terje; Hjerde, Erik; Willassen, Nils Peder; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-04-17)
    <p><i>Background - </i>The population of Atlantic cod (<i>Gadus morhua</i>), also known as Northeast Arctic cod, migrating Atlantic cod, or simply “skrei,” lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world’s largest population of Atlantic cod, and the population is distinct from the ...
  • CPPE: An Open-Source C++ and Python Library for Polarizable Embedding 

    Scheurer, Maximilian; Reinholdt, Peter; Kjellgren, Erik Rosendahl; Olsen, Jógvan Magnus Haugaard; Dreuw, Andreas; Kongsted, Jacob (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-10-03)
    We present a modular open-source library for polarizable embedding (PE) named CPPE. The library is implemented in C++, and it additionally provides a Python interface for rapid prototyping and experimentation in a high-level scripting language. Our library integrates seamlessly with existing quantum chemical program packages through an intuitive and minimal interface. Until now, CPPE has been ...
  • Norcorrole as a Delocalized, Antiaromatic System 

    Conradie, Jeanet; Foroutan-Nejad, Cina; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-03-19)
    Nickel norcorrole provides an unusual example of a molecule that is strongly antiaromatic according to the magnetic criterion, but which exhibits, according to high-quality DFT calculations, a symmetric, delocalized structure with no difference in bond length between adjacent C<sub>meso</sub>-C<sub>α</sub> bonds. A fragment molecular orbital analysis suggests that these discordant observations are ...
  • Antimicrobial activity of amphipathic α,α-disubstituted β-amino amide derivatives against ESBL–CARBA producing multi-resistant bacteria; effect of halogenation, lipophilicity and cationic character 

    Paulsen, Marianne Hagensen; Ausbacher, Dominik; Bayer, Annette; Engqvist, Magnus; Hansen, Terkel; Haug, Tor; Anderssen, Trude; Andersen, Jeanette Hammer; Sollid, Johanna U. Ericson; Strøm, Morten B. (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-09-06)
    The rapid emergence and spread of multi-resistant bacteria have created an urgent need for new antimicrobial agents. We report here a series of amphipathic α,α-disubstituted β-amino amide derivatives with activity against 30 multi-resistant clinical isolates of Gram-positive and Gram-negative bacteria, including isolates with extended spectrum β-lactamase – carbapenemase (ESBL-CARBA) production. A ...
  • Characterization of an intertidal zone metagenome oligoribonuclease and the role of the intermolecular disulfide bond for homodimer formation and nuclease activity 

    Piotrowski, Yvonne; Berg, Kristel; Klebl, David Paul; Leiros, Ingar; Larsen, Atle Noralf (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-08-17)
    The gene encoding MG Orn has been identified from a metagenomic library created from the intertidal zone in Svalbard and encodes a protein of 184 amino acid residues. The <i>mg orn</i> gene has been cloned, recombinantly expressed in <i>Escherichia coli</i>, and purified to homogeneity. Biochemical characterization of the enzyme showed that it efficiently degrades short RNA oligonucleotide substrates ...
  • 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 ...
  • Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation 

    Williamson, Adele Kim; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-07-17)
    DNA ligases join adjacent 5′ phosphate (5′P) and 3′ hydroxyl (3′OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures ...
  • 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, ...
  • Improved CRISPR/Cas9 gene editing by fluorescence activated cell sorting of green fluorescence protein tagged protoplasts 

    Petersen, Bent Larsen; Möller, Svenning Rune; Mravec, Jozef; Jørgensen, Bodil; Christensen, Mikkel; Liu, Ying; Wandall, Hans H.; Bennett, Eric Paul; Yang, Zhang (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-06-17)
    <i>Background</i>: CRISPR/Cas9 is widely used for precise genetic editing in various organisms. CRISPR/Cas9 editing may in many plants be hampered by the presence of complex and high ploidy genomes and inefficient or poorly controlled delivery of the CRISPR/Cas9 components to gamete cells or cells with regenerative potential. Optimized strategies and methods to overcome these challenges are ...
  • 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 ...
  • All-electron fully relativistic Kohn-Sham theory for solids based on the Dirac-Coulomb Hamiltonian and Gaussian-type functions 

    Kadek, Marius; Repisky, Michal; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-05-03)
    We present the first full-potential method that solves the fully relativistic four-component Dirac-Kohn-Sham equation for materials in the solid state within the framework of atom-centered Gaussian-type orbitals (GTOs). Our GTO-based method treats one-, two-, and three-dimensional periodic systems on an equal footing, and allows for a seamless transition to the methodology commonly used in studies ...
  • Response properties of embedded molecules through the polarizable embedding model 

    Steinmann, Casper; Reinholdt, Peter; Nørby, Morten Steen; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-04)
    The polarizable embedding (PE) model is a fragment‐based quantum‐classical approach aimed at accurate inclusion of environment effects in quantum‐mechanical response property calculations. The aim of this tutorial review is to give insight into the practical use of the PE model. Starting from a set of molecular structures and until you arrive at the final property, there are many crucial details to ...
  • MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry 

    Olsen, Jógvan Magnus Haugaard; Bolnykh, Viacheslav; Meloni, Simone; Ippoliti, Emiliano; Bircher, Martin Peter; Carloni, Paolo; Rothlisberger, Ursula (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-04-18)
    We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. This allows exploiting the existing parallelization strategies used by the coupled programs while maintaining a ...
  • 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 ...

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