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  • 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 ...
  • Biological Evaluations, NMR Analyses, Molecular Modeling Studies, and Overview of the Synthesis of the Marine Natural Product (−)-Mucosin 

    Nolsøe, Jens Mortansson Jelstrup; Underhaug, Jarl; Sørskår, Åshild Moi; Antonsen, Simen; Malterud, Karl Egil; Gani, Osman; Fan, Qiong; Hjorth, Marit; Sæther, Thomas; Hansen, Trond Vidar; H. Stenstrøm, Yngve (Journal article; Tidsskriftartikkel; Peer reviewed, 2024-02-24)
    Natural products obtained from marine organisms continue to be a rich source of novel structural architecture and of importance in drug discovery, medicine, and health. However, the success of such endeavors depends on the exact structural elucidation and access to sufficient material, often by stereoselective total synthesis, of the isolated natural product of interest. (−)-Mucosin (1), a fatty ...
  • Preventing E. coli Biofilm Formation with Antimicrobial Peptide-Functionalized Surface Coatings: Recognizing the Dependence on the Bacterial Binding Mode Using Live-Cell Microscopy 

    Hansson, Adam; Karlsen, Eskil André; Stensen, Wenche Gunvor B; Svendsen, John Sigurd Mjøen; Berglin, Mattias; Lundgren, Anders (Journal article; Tidsskriftartikkel; Peer reviewed, 2024-01-31)
    Antimicrobial peptides (AMPs) can kill bacteria by destabilizing their membranes, yet translating these molecules’ properties into a covalently attached antibacterial coating is challenging. Rational design efforts are obstructed by the fact that standard microbiology methods are ill-designed for the evaluation of coatings, disclosing few details about why grafted AMPs function or do not ...
  • Quantitative at-line monitoring of enzymatic hydrolysis using benchtop diffusion nuclear magnetic resonance spectroscopy 

    McCarney, Evan R.; Kristoffersen, Kenneth Aase; Anderssen, Kathryn Elizabeth (Journal article; Tidsskriftartikkel; Peer reviewed, 2024-01-18)
    Benchtop diffusion nuclear magnetic resonance (NMR) spectroscopy was used to perform quantitative monitoring of enzymatic hydrolysis. The study aimed to test the feasibility of the technology to characterize enzymatic hydrolysis processes in real time. Diffusion ordered spectroscopy (DOSY) was used to measure the signal intensity and apparent self-diffusion constant of solubilized protein in ...
  • A Mechanistic Study of the Cu-catalyzed N-arylation of Hydantoin with Aryl(TMP)iodonium Salts 

    Nova Flores, Ainara; Berntsen, Linn Neerbye (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-10-16)
    The use of diaryliodonium salts in organic reactions has rapidly increased in the last decade because of their efficiency in arylation reactions. Despite this, mechanistic investigations are still scarce, particularly for copper catalyzed N-arylation reactions. Recently, we published the use of the unsymmetrical aryl(TMP)iodonium salts (TMP=2,4,6-trimethoxyphenyl) for the selective Cu-catalyzed ...
  • Preparation of a Compound with a SiII−SiIV−SiII Bonding Arrangement 

    Kushvaha, Saroj Kumar; Kallenbach, Paula; Gorantla, Sai Manoj N. V. T.; Herbst-Irmer, Regine; Stalke, Dietmar; Roesky, Herbert W. (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-11-07)
    Herein, we report the synthesis of a rare bis-silylene, 1, in which two Si<sup>II</sup>atoms are bridged by a Si<sup>IV</sup> atom. Compound 1 contains an unusual Si<sup>II</sup> SiI<sup>V</sup> Si<sup>II</sup> bonding arrangement with Si<sup>II</sup> Si<sup>IV</sup> bond distances of 2.4212(8) and 2.4157(7) Å. Treatment of 1 with Fe(CO)<sub>5</sub> afforded a dinuclear Fe<sup>0</sup>S complex 2 ...
  • From Diaminosilylenes to Silapyramidanes: Making Sense of the Stability of Divalent Silicon Compounds 

    Torstensen, Kristian; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-11-07)
    Since the discovery of decamethylsilicocene over three decades ago, chemists have successfully isolated a variety of divalent silicon compounds by orchestrating steric and electronic effects to their advantage. Two broad strategies of electronic stabilization appear to have been widely deployed, namely, π-conjugation as in diaminosilylenes and π-complexation as in decamethylsilicocene and ...
  • Label-free measurement of antimicrobial peptide interactions with lipid vesicles and nanodiscs using microscale thermophoresis 

    Rainsford, Philip Ben; Rylandsholm, Fredrik G.; Jakubec, Martin; Silk, Mitchell; Juskewitz, Eric; Ericson, Johanna Ulrica; Svendsen, John Sigurd Mjøen; Engh, Richard Alan; Isaksson, Johan Mattias (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-08-03)
    One strategy to combat antimicrobial resistance is the discovery of new classes of antibiotics. Most antibiotics will at some point interact with the bacterial membrane to either interfere with its integrity or to cross it. Reliable and efficient tools for determining the dissociation constant for membrane binding (K<sub><i>D</sub></i>) and the partitioning coefficient between the aqueous- and ...
  • Comparative analysis of HiSeq3000 and BGISEQ-500 sequencing platform with shotgun metagenomic sequencing data 

    Kumar, Animesh; Robertsen, Espen Mikal; Willassen, Nils Peder; Fu, Juan; Hjerde, Erik (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-12-29)
    Recent advances in sequencing technologies and platforms have enabled to generate metagenomics sequences using different sequencing platforms. In this study, we analyzed and compared shotgun metagenomic sequences generated by HiSeq3000 and BGISEQ-500 platforms from 12 sediment samples collected across the Norwegian coast. Metagenomics DNA sequences were normalized to an equal number of bases for ...
  • Full Breit Hamiltonian in the Multiwavelets Framework 

    Tantardini, Christian; Remigio, Roberto Di; Bjørgve, Magnar; Jensen, Stig Rune; Frediani, Luca (Journal article; Tidsskriftartikkel; Peer reviewed, 2024-01-01)
    New techniques in core–electron spectroscopy are necessary to resolve the structures of oxides of f-elements and other strongly correlated materials that are present only as powders and not as single crystals. Thus, accurate quantum chemical methods must be developed to calculate core spectroscopic properties in such materials. In this contribution, we present an important development in this ...
  • Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations 

    Wilkins, Ryan Scott; Lund, Bjarte Aarmo; Isaksen, Geir Villy; Åqvist, Johan Lennart Gösta; Brandsdal, Bjørn Olav (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-12-19)
    Chorismate mutase (CM) enzymes have long served as model systems for benchmarking new methods and tools in computational chemistry. Despite the enzymes’ prominence in the literature, the extent of the roles that activation enthalpy and entropy play in catalyzing the conversion of chorismate to prephenate is still subject to debate. Knowledge of these parameters is a key piece in fully understanding ...
  • Scalar Relativistic Effects with Multiwavelets: Implementation and Benchmark 

    Brakestad, Anders; Jensen, Stig Rune; Tantardini, Christian; Pitteloud, Quentin Gregoire; Wind, Peter Ariaan; Užulis, Jānis; Gulans, Andris; Hopmann, Kathrin Helen; Frediani, Luca (Journal article; Tidsskriftartikkel; Peer reviewed, 2024-01-05)
    The importance of relativistic effects in quantum chemistry is widely recognized, not only for heavier elements but throughout the periodic table. At the same time, relativistic effects are strongest in the nuclear region, where the description of electrons through a linear combination of atomic orbitals becomes more challenging. Furthermore, the choice of basis sets for heavier elements is ...
  • Room Temperature-Stable Magnesium Electride via Ni(II) Reduction 

    Do, Cuong Dat; Day, Craig S.; Odena, Carlota; Benet-Buchholz, Jordi; Xu, Liang; Foroutan-Nejad, Cina; Hopmann, Kathrin Helen; Martin, Ruben (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-07-13)
    Herein, we report the synthesis of highly reduced bipyridyl magnesium complexes and the first example of a stable organic magnesium electride supported by quantum mechanical computations and X-ray diffraction. These complexes serve as unconventional homogeneous reductants due to their high solubility, modular redox potentials, and formation of insoluble, non-coordinating byproducts. The applicability ...
  • Understanding the Influence of Lewis Acids on CO2 Hydrogenation: The Critical Effect Is on Formate Rotation 

    Pavlovic, Ljiljana; Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-10-11)
    Lewis acids (LAs) have been shown to accelerate hydrogenation of C0<sub>2</sub>, but the underlying mechanistic details remain to be elucidated. We have employed computational methods to investigate how LAs affect CO<sub>2</sub> hydrogenation with a range of known metal-hydrides (L<sub>n</sub>Ir–H, L<sub>n</sub>Ru–H, L<sub>n</sub>Mn–H, L<sub>n</sub>Co–H). Our results show that LAs can alter the ...
  • The Transition from Unfolded to Folded G-Quadruplex DNA Analyzed and Interpreted by Two-Dimensional Infrared Spectroscopy 

    Soenarjo, A Larasati; Lan, Zhihao; Sazanovich, Igor V.; Chan, Yee San; Ringholm, Magnus; Jha, Ajay; Klug, David R. (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-08-30)
    A class of DNA folds/structures known collectively as G-quadruplexes (G4) commonly forms in guanine-rich areas of genomes. G4-DNA is thought to have a functional role in the regulation of gene transcription and telomerase-mediated telomere maintenance and, therefore, is a target for drugs. The details of the molecular interactions that cause stacking of the guanine-tetrads are not well-understood, ...
  • Structure/function studies of the NAD<sup>+</sup>-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding 

    Fernandes, Andreia; Williamson, Adele Kim; Matias, Pedro M.; Moe, Elin (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-09-15)
    Bacterial NAD<sup>+</sup>-dependent DNA ligases (LigAs) are enzymes involved in replication, recombination, and DNA-repair processes by catalyzing the formation of phosphodiester bonds in the backbone of DNA. These multidomain proteins exhibit four modular domains, that are highly conserved across species, with the BRCT (breast cancer type 1 C-terminus) domain on the C-terminus of the enzyme. In ...
  • Local Oxidation States in {FeNO}<sup>6-8</sup> Porphyrins: Insights from DMRG/CASSCF-CASPT2 Calculations 

    Phung, Quan Manh; Nam, Ho Ngoc; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-11-27)
    A first DMRG/CASSCF–CASPT2 study of a series of paradigmatic {FeNO}<sup>6</sup>, {FeNO}<sup>7</sup>, and {FeNO}<sup>8</sup> heme–nitrosyl complexes has led to substantial new insight as well as uncovered key shortcomings of the DFT approach. By virtue of its balanced treatment of static and dynamic correlation, the calculations have provided some of the most authoritative information available to ...
  • Cavity-Free Continuum Solvation: Implementation and Parametrization in a Multiwavelet Framework 

    Gerez Sazo, Gabriel Adolfo; Remigio Eikås, Roberto Di; Jensen, Stig Rune; Bjørgve, Magnar; Frediani, Luca (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-03-18)
    We present a multiwavelet-based implementation of a quantum/classical polarizable continuum model. The solvent model uses a diffuse solute–solvent boundary and a position-dependent permittivity, lifting the sharp-boundary assumption underlying many existing continuum solvation models. We are able to include both surface and volume polarization effects in the quantum/classical coupling, with guaranteed ...
  • A Theoretical Search for Stable Terminal Carbides 

    Ghosh, Abhik; Conradie, Jeanet (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-11-20)
    xploratory scalar-relativistic density functional theory (B3LYP*-D3/ZORA-STO-TZ2P) calculations have been used to examine the stability and bonding of pseudotetrahedral Group 8 (Fe, Ru, and Os) and Group 9 (Co, Rh, and Ir) terminal carbide complexes with dδ4 ground states and tripodal tris(N-heterocyclic-carbene) supporting ligands. The calculations predict relatively low adiabatic ionization ...
  • Enhanced teaching and learning outcomes from restructuring a basic organic chemistry course 

    Hansen, Jørn Hedløy; Bayer, Annette; Haugland, Marius Myreng (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-05-10)
    The first course in organic chemistry is tough for many students, and motivation may be an additional serious problem if you are taking the course as a part of your study program but do not intend to become a chemist. The combination of long, speedy traditional lectures, complicated material and the use of an important new language (electron flow arrows) does not contribute to easing the cognitive ...

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