Now showing items 41-60 of 551

    • 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; 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 ...
    • Bacterial extracellular vesicles: towards realistic models for bacterial membranes in molecular interaction studies by surface plasmon resonance 

      Brilkov, Maxim; Stenbakk, Victoria; Jakubec, Martin; Vasskog, Terje; Kristoffersen, Tone; Cavanagh, Jorunn Pauline; Ericson, Johanna Ulrica; Isaksson, Johan Mattias; Flaten, Gøril Eide (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-12-13)
      One way to mitigate the ongoing antimicrobial resistance crisis is to discover and develop new classes of antibiotics. As all antibiotics at some point need to either cross or just interact with the bacterial membrane, there is a need for representative models of bacterial membranes and efficient methods to characterize the interactions with novel molecules -both to generate new knowledge and to ...
    • Raman spectroscopy online monitoring of biomass production, intracellular metabolites and carbon substrates during submerged fermentation of oleaginous and carotenogenic microorganisms 

      Dzurendová, Simona; Olsen, Pernille Margrethe; Byrtusova, Dana; Tafintseva, Valeria; Shapaval, Volha; Horn, Svein Jarle; Kohler, Achim; Szotkowski, Martin; Marova, Ivana; Zimmermann, Boris (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-12-18)
      Background - Monitoring and control of both growth media and microbial biomass is extremely important for the development of economical bioprocesses. Unfortunately, process monitoring is still dependent on a limited number of standard parameters (pH, temperature, gasses etc.), while the critical process parameters, such as biomass, product and substrate concentrations, are rarely assessable in-line. ...
    • Radical Group Transfer of Vinyl and Alkynyl Silanes Driven by Photoredox Catalysis 

      Baussiere, Floriane; Haugland, Marius Myreng (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-08-15)
      Radical group transfer is a powerful tool for the formation of C−C bonds. These processes typically involve radical addition to C−C π bonds, followed by fragmentation of the resulting cyclic intermediate. Despite the advantageous lability of organosilanes in this context, silicon-tethered radical acceptor groups have remained underexplored in radical group transfer reactions. We report a general ...
    • Free-Base Corrole Anion 

      Tarai, Arup; Mallick, Jyotiprakash; Conradie, Jeanet; Kar, Sanjib; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-08-30)
      Free-base corroles have long been known to be acidic, readily undergoing deprotonation by mild bases and in polar solvents. The conjugate base, however, has not been structurally characterized until now. Presented here is a first crystal structure of a freebase corrole anion, derived from tris(p-cyanophenyl)corrole, as the tetrabuylammonium salt. The low-temperature (100 K) structure reveals ...
    • FAIR+E pathogen data for surveillance and research: lessons from COVID-19 

      Neves, Aitana; Cuesta, Isabel; Hjerde, Erik; Klemetsen, Terje; Salgado, David; van Helden, Jacques; Rahman, Nadim; Fatima, Nazeefa; Karathanasis, Nestoras; Zmora, Pawel; Åkerström, Wolmar Nyberg; Grellscheid, Sushma Nagaraja; Waheed, Zahra; Blomberg, Niklas (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-11-21)
      The COVID-19 pandemic has exemplified the importance of interoperable and equitable data sharing for global surveillance and to support research. While many challenges could be overcome, at least in some countries, many hurdles within the organizational, scientific, technical and cultural realms still remain to be tackled to be prepared for future threats. We propose to (i) continue supporting global ...
    • Jahn-Teller distortion in bis(terpyridine)nickel(III) – Elongation or compression? 

      Conradie, Jeanet (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-11-06)
      DFT methods were used to evaluate the type of Jahn-Teller distortion in the low spin d<sup>7</sup> bis(terpyridine)nickel (III) doublet. The strain of the tridentate terpyridine ligand in bis(terpyridine)nickel(III) leads to longer Ni(III)-N terminal bond lengths than the Ni(III)-N central bonds. In addition, in all DFT optimized bis(terpyridine)nickel (III) molecules, the one set of Ni(III)-N ...
    • Constrained DFT-based magnetic machine-learning potentials for magnetic alloys: a case study of Fe–Al 

      Tantardini, Christian; Kotykhov, Alexey S.; Gubaev, Konstantin; Hodapp, Max; Shapeev, Alexander V.; Novikov, van S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-11-13)
      We propose a machine-learning interatomic potential for multi-component magnetic materials. In this potential we consider magnetic moments as degrees of freedom (features) along with atomic positions, atomic types, and lattice vectors. We create a training set with constrained DFT (cDFT) that allows us to calculate energies of confgurations with non-equilibrium (excited) magnetic moments and, ...
    • Towards high-throughput screening (HTS) of polyhydroxyalkanoate (PHA) production via Fourier transform infrared (FTIR) spectroscopy of Halomonas sp. R5-57 and Pseudomonas sp. MR4-99 

      Christensen, Mikkel; Chiciudean, Iulia; Jablonski, Piotr; Tănase, Ana-Maria; Shapaval, Volha; Hansen, Hilde (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-03-08)