Now showing items 66-85 of 247

    • The Dalton quantum chemistry program system 

      Aidas, Kestutis; Angeli, Celestino; Bak, Keld L.; Bakken, Vebjørn; Bast, Radovan; Boman, Linus; Christiansen, Ove; Cimiraglia, Renzo; Coriani, Sonja; Dahle, Pål; Dalskov, Erik K.; Ekström, Ulf Egil; Enevoldsen, Thomas; Eriksen, Janus J.; Ettenhuber, Patrick; Fernández, Berta; Ferrighi, Lara; Fliegl, Heike; Frediani, Luca; Hald, Kasper; Halkier, Asger; Hattig, Christof; Heiberg, Hanne; Helgaker, Trygve; Hennum, Alf Christian; Hettema, Hinne; Hjertenæs, Eirik; Høst, Stine; Høyvik, Ida Marie; Iozzi, Maria Francesca; Jansik, Brannislav; Jensen, Hans-Jørgen Aa.; Jonsson, Dan Johan; Jørgensen, Poul; Kauczor, Johanna; Kirpekar, Sheela; Kjærgaard, Thomas; Klopper, Wim; Knecht, Stefan; Kobayashi, Rika; Koch, Henrik; Kongsted, Jacob; Krapp, Andreas; Kristensen, Kasper; Ligabue, Andrea; Lutnæs, Ola B.; Melo, Juan I.; Mikkelsen, Kurt V.; Myhre, Rolf Heilemann; Neiss, Christian; Nielsen, Christian B.; Norman, Patrick; Olsen, Jeppe; Olsen, Jogvan Magnus H.; Osted, Anders; Packer, Martin J.; Pawlowski, Filip; Pedersen, Thomas Bondo; Provasi, Patricio F.; Reine, Simen Sommerfelt; Rinkevicius, Zilvinas; Ruden, Torgeir A.; Ruud, Kenneth; Rybkin, Vladimir V.; Salek, Pawel; Samson, Claire C. M.; Sanchez de Meras, Alfredo; Saue, Trond; Sauer, Stephan P. A.; Schimmelpfennig, Bernd; Sneskov, Kristian; Steindal, Arnfinn Hykkerud; Sylvester-Hvid, Kristian O.; Taylor, Peter R.; Teale, Andrew M.; Tellgren, Erik; Tew, David P.; Thorvaldsen, Andreas J.; Thøgersen, Lea; Vahtras, Olav; Watson, Mark A.; Wilson, David J. D.; Ziolkowski, Marcin; Ågren, Hans (Journal article; Tidsskriftartikkel; Peer reviewed, 2014-05)
      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, Møller–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 ...
    • Darmstadtium, roentgenium, and copernicium form strong bonds with cyanide 

      Demissie, Taye Beyene; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-05-05)
      We report the structures and properties of the cyanide complexes of three superheavy elements (darmstadtium, roentgenium, and copernicium) studied using two‐ and four‐component relativistic methodologies. The electronic and structural properties of these complexes are compared to the corresponding complexes of platinum, gold, and mercury. The results indicate that these superheavy elements form ...
    • Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR 

      Narayanan, Dilip; Gani, Osman; Gruber, Franz; Engh, Richard Alan (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-07-04)
      Drug design of protein kinase inhibitors is now greatly enabled by thousands of publicly available X-ray structures, extensive ligand binding data, and optimized scaffolds coming off patent. The extensive data begin to enable design against a spectrum of targets (polypharmacology); however, the data also reveal heterogeneities of structure, subtleties of chemical interactions, and apparent inconsistencies ...
    • A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges 

      Timmins, Joanna; Moe, Elin (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-04-27)
      The Deinococcus radiodurans bacterium is extremely resistant to ionising radiation and desiccation and can withstand a 200-fold higher radiation dose than most other bacteria with no loss of viability. The mechanisms behind this extreme resistance are not fully understood, but it is clear that several factors contribute to this phenotype. Efficient scavenging of reactive oxygen species and repair ...
    • Degradation of oil products in a soil from a Russian Barents hot‑spot during electrodialytic remediation 

      Pedersen, Kristine Bondo; Lejon, Tore; Jensen, Pernille E.; Ottosen, Lisbeth M. (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-02-24)
      A highly oil-polluted soil from Krasnoe in North-West Russia was used to investigate the degradation of organic pollutants during electrodialytic remediation. Removal efficiencies were up to 70 % for total hydrocarbons (THC) and up to 65 % for polyaromatic hydrocarbons (PAH). Relatively more of the lighter PAH compounds and THC fractions were degraded. A principal component analysis (PCA) revealed ...
    • Demetalation of copper undecaarylcorroles: Molecular structures of a free-base undecaarylisocorrole and a gold undecaarylcorrole 

      Capar, Jan; Zonneveld, Job; Berg, Steffen; Isaksson, Johan; Gagnon, Kevin J.; Kolle, Ekaney Thomas; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-06-27)
      Copper undecaarylcorroles were found to undergo acid-induced demetalation with unusual ease under both reductive and nonreductive conditions. The resulting free-base undecaarylcorroles were found to be rather reactive, readily photooxygenating to yield 5/10-hydroxyisocorroles and open-chain tetrapyrroles. The use of nonreductive conditions led to 50-75% yields of undecaarylisocorroles, a new class ...
    • Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization 

      Thakkar, Balmukund; Svendsen, John Sigurd Mjøen; Engh, Richard Alan (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-25)
      Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine ...
    • Design and Biological Evaluation of Antifouling Dihydrostilbene Oxime Hybrids 

      Moodie, Lindon W. K.; Cervin, Gunnar; Trepos, Rozenn; Labriere, Christophe; Hellio, Claire; Pavia, Henrik; Svenson, Johan (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-03-13)
      By combining the recently reported repelling natural dihydrostilbene scaffold with an oxime moiety found in many marine antifoulants, a library of nine antifouling hybrid compounds was developed and biologically evaluated. The prepared compounds were shown to display a low antifouling effect against marine bacteria but a high potency against the attachment and growth of microalgae down to MIC ...
    • Diagrammatic Coupled Cluster Monte Carlo 

      Scott, Charles J. C.; Di Remigio, Roberto; Crawford, T. Daniel; Thom, Alex J. W. (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-02-09)
      We propose a modified coupled cluster Monte Carlo algorithm that stochastically samples connected terms within the truncated Baker–Campbell–Hausdorff expansion of the similarity-transformed Hamiltonian by construction of coupled cluster diagrams on the fly. Our new approach—diagCCMC—allows propagation to be performed using only the connected components of the similarity-transformed Hamiltonian, ...
    • Differential Evolution-Based Weighted Combination of Distance Metrics for k-means Clustering 

      Muhammad Fuad, Muhammad Marwan (Journal article; Tidsskriftartikkel; Peer reviewed, 2014)
    • Differential expression profiling of ΔlitR and ΔrpoQ mutants reveals insight into QS regulation of motility, adhesion and biofilm formation in Aliivibrio salmonicida 

      Khider, Miriam; Hjerde, Erik; Hansen, Hilde; Willassen, Nils Peder (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-03-15)
      <i>Background</i>: The coordination of group behaviors in bacteria is achieved by a cell-cell signaling process called quorum sensing (QS). QS is an intercellular communication system, which synchronously controls expression of a vast range of genes in response to changes in cell density and is mediated by autoinducers that act as extracellular signals. <i>Aliivibrio salmonicida</i>, the causative ...
    • A Dihydride Mechanism Can Explain the Intriguing Substrate Selectivity of Iron-PNP-Mediated Hydrogenation 

      Hopmann, Kathrin Helen; Morello, Glenn Robert (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-07-24)
      Iron-PNP pincer complexes are efficient catalysts for the hydrogenation of aldehydes and ketones. A variety of hydrogenation mechanisms have been proposed for these systems, but there appears to be no clear consensus on a preferred pathway. We have employed high-level quantum chemical calculations to evaluate various mechanistic possibilities for iron-PNP catalysts containing either CH2, NCH3, ...
    • Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome 

      Jensen, Marianne Slang; Fredriksen, Lasse; Mackenzie, Alasdair; Pope, Phillip; Leiros, Ingar; Chylenski, Piotr; Williamson, Adele Kim; Christopeit, Tony; Østby, Heidi; Vaaje-Kolstad, Gustav; Eijsink, Vincent (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-24)
      Enzymatic depolymerization of recalcitrant polysaccharides plays a key role in accessing the renewable energy stored within lignocellulosic biomass, and natural biodiversities may be explored to discover microbial enzymes that have evolved to conquer this task in various environments. Here, a metagenome from a thermophilic microbial community was mined to yield a novel, thermostable cellulase, named ...
    • Discovery of Novel Inhibitor Scaffolds against the Metallo-beta-lactamase VIM-2 by Surface Plasmon Resonance (SPR) Based Fragment Screening 

      Christopeit, Tony; Carlsen, Trine Josefine Olsen; Helland, Ronny; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-10-17)
      Metallo-β-lactamase (MBL) inhibitors can restore the function of carbapenem antibiotics and therefore help to treat infections of antibiotic resistant bacteria. In this study, we report novel fragments inhibiting the clinically relevant MBL Verona integron-encoded metallo-β-lactamase (VIM-2). The fragments were identified from a library of 490 fragments using an orthogonal screening approach based ...
    • Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives 

      Thode, Sunniva Katharina; Rojek, Ewelina; Kozlowski, Mikolaj; Ahmad, Rafi; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02-14)
      Siderophores are small molecules synthesized and secreted by bacteria and fungi to scavenge iron. Extracellular ferri-siderohores are recognized by cognate receptors on the cell surface for transport over membranes. Several siderophore systems from <i>Vibrionaceae</i> representatives are known and well understood, e.g., the molecular structure of the siderophore, the biosynthesis gene cluster ...
    • DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases 

      Williamson, Adele Kim; Grgic, Miriam; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-07-11)
      DNA ligases join breaks in the phosphodiester backbone of DNA by catalysing the formation of bonds between opposing 5′P and 3′OH ends in an adenylation-dependent manner. Catalysis is accompanied by reorientation of two core domains to provide access to the active site for cofactor utilization and enable substrate binding and product release. The general paradigm is that DNA ligases engage their DNA ...
    • Dynamical models of mutated chronic myelogenous leukemia cells for a postimatinib treatment scenario: Response to dasatinib or nilotinib therapy 

      Woywod, Clemens Joachim; Gruber, Franz; Engh, Richard Alan; Flå, Tor (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-07-05)
      Targeted inhibition of the oncogenic BCR-ABL1 fusion protein using the ABL1 tyrosine kinase inhibitor imatinib has become standard therapy for chronic myelogenous leukemia (CML), with most patients reaching total and durable remission. However, a significant fraction of patients develop resistance, commonly due to mutated ABL1 kinase domains. This motivated development of second-generation drugs ...
    • 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 ...