Now showing items 124-143 of 525

    • The crystal structure of haemoglobin from Atlantic cod 

      Helland, Ronny; Bjørkeng, Eva katrin; Rothweiler, Ulli; Sydnes, Magne Olav; Pampanin, Daniela Maria (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-07-16)
      The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 A˚ resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.
    • Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans 

      Niiranen, Laila; Lian, Kjersti; Johnson, Kenneth A; Moe, Elin (Journal article; Tidsskriftartikkel, 2015-02-27)
      Background: Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding ...
    • The crystal structure of the tetrameric DABA-aminotransferase EctB, a rate-limiting enzyme in the ectoine biosynthesis pathway 

      Hillier, Heidi Therese; Altermark, Bjørn; Leiros, Ingar (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-02-29)
      L‐2,4‐diaminobutyric acid (DABA) aminotransferases can catalyze the formation of amines at the distal ω‐position of substrates, and is the intial and rate‐limiting enzyme in the biosynthesis pathway of the cytoprotecting molecule (S)‐2‐methyl‐1,4,5,6‐tetrahydro‐4‐pyrimidine carboxylic acid (ectoine). Although there is an industrial interest in the biosynthesis of ectoine, the DABA aminotransferases ...
    • Cyclic Voltammetric Study of 2-Hydroxybenzophenone (HBP) Derivatives and the Correspondent Change in the Orbital Energy Levels in Different Solvents 

      Adeniyi, Adebayo A.; Ngake, Tankiso L.; Conradie, Jeanet (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-07-14)
      The experimental UV and CV of five substituted 2-hydroxybenzophenones in solvents acetonitrile, n-dimethylformamide and dimethylsulfoxide are presented. Results obtained were used to determine their experimental highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and the results were compared to their theoretical model. The derivatives with an electron withdrawing ...
    • D3.3 (M18) - Report on curation in core ELIXIR registries (an ELIXIR Norway ELIXIR3 deliverable) 

      Bösl, Korbinian Michael; Fatima, Nazeefa; Gundersen, Sveinung; Klemetsen, Terje; Petters, Sebastian; Åberg, Espen (Research report; Forskningsrapport, 2023-10-01)
      This report serves as an update on the progress of WP3 Task 3.4 in ELIXIR3, in support of curation efforts on content in repositories of metadata, datasets, tools, training, workflows, and other resources, in line with the ELIXIR Platforms. The report documents progress made, methods used, and plans for the near future as of month 18 of a 48-month timeline. ELIXIR Norway extends support to numerous ...
    • Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems 

      Olsen, Jógvan Magnus Haugaard; Reine, Simen Sommerfelt; Vahtras, Olav; Kjellgren, Erik; Reinholdt, Peter; Dundas, Karen O.H; Li, Xin; Cukras, Janusz; Ringholm, Magnus; Hedegård, Erik Donovan; Di Remigio, Roberto; List, Nanna H.; Faber, Rasmus; Tenorio, Bruno Nunes Cabral; Bast, Radovan; Pedersen, Thomas Bondo; Rinkevicius, Zilvinas; Sauer, Stephan P. A.; Mikkelsen, Kurt V.; Kongsted, Jacob; Coriani, Sonia; Ruud, Kenneth; Helgaker, Trygve; Jensen, Hans Jørgen Aa.; Norman, Patrick (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-06-05)
      The <i>Dalton Project</i> provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to ...
    • 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 ...
    • Data to Understand the Nature of Non-Covalent Interactions in the Thiophene Clusters 

      Malloum, Alhadji; Conradie, Jeanet (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-01-10)
      We have reported herein the data to understand the nature and number of non-covalent interactions that stabilize the structures of the thiophene clusters. In addition, we have also provided the optimized Cartesian coordinates of all the structures of the investigated thiophene clusters. Initially, the geometries have been generated using the ABCluster code which performs a global optimization to ...
    • 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 ...
    • Demystifying the Origin of Vibrational Coherence Transfer Between the S1 and T1 States of the Pt-pop Complex 

      Karak, Pijush; Ruud, Kenneth; Chakrabarti, Swapan (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-10-01)
      We demonstrate that spin-vibronic coupling is the most significant mechanism in vibrational coherence transfer (VCT) from the singlet (S<sub>1</sub>) to the triplet (T<sub>1</sub>) state of the [Pt<sub>2</sub>(P<sub>2</sub>O<sub>5</sub>H<sub>2</sub>)<sub>4</sub>]<sup>4–</sup> complex. Our time-dependent correlation function-based study shows that the rate of intersystem crossing (<i>k</i><sub>ISC</sub>) ...
    • 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 ...
    • Description of the uEMEP_v5 downscaling approach for the EMEP MSC-W chemistry transport model 

      Denby, Bruce; Gauss, Michael; Wind, Peter; Mu, Qing; Wærsted, Eivind Grøtting; Fagerli, Hilde; Valdebenito Bustamante, Alvaro Moises; Klein, Heiko (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-12-11)
      A description of the new air quality downscaling model – the urban EMEP (uEMEP) and its combination with the EMEP MSC-W model (European Monitoring and Evaluation Programme Meteorological Synthesising Centre West) – is presented. uEMEP is based on well-known Gaussian modelling principles. The uniqueness of the system is in its combination with the EMEP MSC-W model and the “local fraction” calculation ...
    • 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 ...
    • Development of potent cholinesterase inhibitors based on a marine pharmacophore 

      Elumalai, Vijayaragavan; Trobec, Tomaz; Grundner, Maja; Labriere, Christophe; Frangez, Robert; Sepcic, Kristina; Hansen, Jørn H; Svensson, Johan (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-07-01)
      The management of neurological disorders such as dementia associated with Alzheimer's or Parkinson's disease includes the use of cholinesterase inhibitors. These compounds can slow down the progression of these diseases and can also be used in the treatment of glaucoma and myasthenia gravis. The majority of the cholinesterase inhibitors used in the clinic are derived from natural products and our ...
    • DFT studies of the redox behavior of oligo(aza)pyridines and experimental CVs of 4′-substituted terpyridines 

      Mateyise, Nandisiwe Ghandi Sibongile; Conradie, Marrigje M.; Conradie, Jeanet (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-11-17)
      The cyclic voltammograms of a series of substituted terpyridine ligands are presented, showing that reduction occur generally below −2 V versus the redox potential of ferrocene. Density functional theory (DFT) calculated energies and the theoretically calculated reduction potentials of a large series of substituted oligo(aza)pyridine ligands (terpyridine, bipyridine and phenanthroline) are determined ...
    • 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, ...