Viser treff 184-203 av 527

    • Exact two-component Hamiltonians for relativistic quantum chemistry: Two-electron picture-change corrections made simple 

      Knecht, Stefan; Repisky, Michal; Jensen, Hans Jørgen Aagaard; Saue, Trond (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-09-19)
      Based on self-consistent field (SCF) atomic mean-field (amf) quantities, we present two simple yet computationally efficient and numerically accurate matrix-algebraic approaches to correct both scalar-relativistic and spin–orbit two-electron picture-change effects (PCEs) arising within an exact two-component (X2C) Hamiltonian framework. Both approaches, dubbed amfX2C and e(xtended)amfX2C, allow us ...
    • Exact Two-Component TDDFT with Simple Two-Electron Picture-Change Corrections: X-ray Absorption Spectra Near L- and M-Edges of Four-Component Quality at Two-Component Cost 

      Konecny, Lukas; Komorovsky, Stanislav; Vicha, Jan; Ruud, Kenneth; Repisky, Michal (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-02-01)
      X-ray absorption spectroscopy (XAS) has gained popularity in recent years as it probes matter with high spatial and elemental sensitivities. However, the theoretical modeling of XAS is a challenging task since XAS spectra feature a fine structure due to scalar (SC) and spin–orbit (SO) relativistic effects, in particular near L and M absorption edges. While full four-component (4c) calculations of ...
    • Excitation Energies from Real-Time Propagation of the Four-Component Dirac–Kohn–Sham Equation 

      Repisky, Michal; Konecny, Lukas; Kadek, Marius; Komorovsky, Stanislav; Malkina, Olga L.; Malkin, Vladimir G.; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-01-21)
      We report the first implementation of real-time time-dependent density functional theory (RT-TDDFT) at the relativistic four-component level of theory. In contrast to the perturbative linear-response TDDFT approach (LR-TDDFT), the RT-TDDFT approach performs an explicit time propagation of the Dirac–Kohn–Sham density matrix, offering the possibility to simulate molecular spectroscopies involving ...
    • Experimental and four-component relativistic DFT studies of tungsten carbonyl complexes 

      Demissie, Taye Beyene; Kostenko, Nataliya; Komorovsky, Stanislav; Repisky, Michal; Isaksson, Johan; Bayer, Annette; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-07-24)
      We present a theoretical and experimental study of the structure and nuclear magnetic resonance (NMR) parameters of the pentacarbonyltungsten complexes of η<sup>1</sup>-2-(trimethylstannyl)-4,5-dimethylphosphinine, η<sup>2</sup>-norbornene, and imidazolidine-2-thione. The three complexes have a pseudo-octahedral molecular structure with the six ligands bonded to the tungsten atom. The η<sup>1</sup ...
    • Exploration of New Biomass-Derived Solvents: Application to Carboxylation Reactions 

      Gevorgyan, Ashot; Hopmann, Kathrin Helen; Bayer, Annette (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-01-07)
      A range of hitherto unexplored biomass‐derived chemicals have been evaluated as new sustainable solvents for a large variety of CO<sub>2</sub>‐based carboxylation reactions. Known biomass‐derived solvents (biosolvents) are also included in the study and the results are compared with commonly used solvents for the reactions. Biosolvents can be efficiently applied in a variety of carboxylation reactions, ...
    • Exploring the role of L209 residue in the active site of NDM-1 a metallo-β-lactamase 

      Marcoccia, Francesca; Leiros, Hanna-Kirsti S.; Aschi, Massimiliano; Amicosante, Gianfranco; Perilli, Mariagrazia (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-01-02)
      Background:<br> New Delhi Metallo-β-Lactamase (NDM-1) is one of the most recent additions to the β-lactamases family. Since its discovery in 2009, NDM-1 producing Enterobacteriaceae have disseminated globally. With few effective antibiotics against NDM-1 producers, there is an urgent need to design new drug inhibitors through the help of structural and mechanistic information available from ...
    • Exploring the transcriptome of luxI- and ΔainS mutants and the impact of N-3-oxo-hexanoyl-L- and N-3-hydroxy- decanoyl-L-homoserine lactones on biofilm formation in Aliivibrio salmonicida 

      Khider, Miriam; Hansen, Hilde; Hjerde, Erik; Johansen, Jostein A; Willassen, Nils Peder (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-04-30)
      <i>Background</i>: Bacterial communication through quorum sensing (QS) systems has been reported to be important in coordinating several traits such as biofilm formation. In <i>Aliivibrio salmonicida</i> two QS systems the LuxI/R and AinS/R, have been shown to be responsible for the production of eight acyl-homoserine lactones (AHLs) in a cell density dependent manner. We have previously ...
    • Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida 

      Hansen, Geir Åsmund; Ahmad, Rafi; Hjerde, erik; Fenton, Christopher Graham; Willassen, Nils Peder; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)
      Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria. One member of this family, Aliivibrio ...
    • 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 ...
    • Facile Supramolecular Engineering of Porphyrin cis Tautomers: The Case of β-Octabromo-meso-tetraarylporphyrins 

      Thomas, Kolle E.; Slebodnick, Carla; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-04-02)
      A porphyrin cis tautomer, where the two central NH protons are on adjacent pyrrole rings, has long been invoked as an intermediate in porphyrin tautomerism. Only recently, however, has such a species been isolated and structurally characterized. Thus, single-crystal X-ray structure determinations of two highly saddled free-base porphyrins, β-heptakis(trifluoromethyl)-meso-tetrakis(p-fluorophenyl)porphyrin, ...
    • 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 ...
    • 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 ...
    • First-Principles Calculation of 1H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics 

      Castro, Abril C; Balcells, David; Repisky, Michal; Helgaker, Trygve; Cascella, Michele (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-11-23)
      <sup>1</sup>H NMR spectroscopy has become an important technique for the characterization of transition-metal hydride complexes, whose metal-bound hydrides are often difficult to locate by X-ray diffraction. In this regard, the accurate prediction of <sup>1</sup>H NMR chemical shifts provides a useful, but challenging, strategy to help in the interpretation of the experimental spectra. In this work, ...
    • Five-Photon Absorption and Selective Enhancement of Multiphoton Absorption Processes 

      Friese, Daniel Henrik; Bast, Radovan; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-05-12)
      We study one-, two-, three-, four- and five-photon absorption of three centrosymmetric molecules using density functional theory. These calculations are the first ab initio calculations of five-photon absorption. Even- and odd-order absorption processes show different trends in the absorption cross sections. The behaviour of all even-and odd-photon absorption properties shows a semi-quantitative ...
    • A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design 

      Ahkter, Sundus; Lund, Bjarte Aarmo; Ismael, Aya; Langer, Manuel; Isaksson, Johan; Christopeit, Tony; Leiros, Hanna-Kirsti S.; Bayer, Annette (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02-10)
      β-Lactam antibiotics are of utmost importance when treating bacterial infections in the medical community. However, currently their utility is threatened by the emergence and spread of β-lactam resistance. The most prevalent resistance mechanism to β-lactam antibiotics is expression of β-lactamase enzymes. One way to overcome resistance caused by β-lactamases, is the development of β-lactamase ...
    • Formal C-H carboxylation of unactivated arenes with carbon dioxide 

      Gevorgyan, Ashot; Hopmann, Kathrin Helen; Bayer, Annette (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-01-31)
      A formal C−H carboxylation of unactivated arenes using CO<sub>2</sub> in green solvents is described. The present strategy combines a sterically controlled Ir‐catalyzed C−H borylation followed by a Cu‐catalyzed carboxylation of the in situ generated organoboronates. The reaction is highly regioselective for the C−H carboxylation of 1,3‐disubstituted and 1,2,3‐trisubstituted benzenes, 1,2‐ or ...
    • Formative and Summative Automated Assessment with Multiple-Choice Question Banks 

      Beerepoot, Maarten (Journal article; Tidsskriftartikkel, 2023-07-18)
      Digital automated assessment is a valuable and time-efficient tool for educators to provide immediate and objective feedback to learners. Automated assessment, however, puts high demands on the quality of the questions, alignment with the intended learning outcomes, and the quality of the feedback provided to the learners. We here describe the development and use of a large number (N > 180) of ...
    • The four-component DFT method for the calculation of the EPR g-tensor using a restricted magnetically balanced basis and London atomic orbitals 

      Misenkova, Debora; Lemken, Florian; Repisky, Michal; Noga, Jozef; Malkina, Olga L.; Komorovsky, Stanislav (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-09-28)
      ABSTRACT Four-component relativistic treatments of the electron paramagnetic resonance g-tensor have so far been based on a common gauge origin and a restricted kinetically balanced basis. The results of such calculations are prone to exhibit a dependence on the choice of the gauge origin for the vector potential associated with uniform magnetic field and a related dependence on the basis set ...
    • Four-component relativistic 31P NMR calculations for: Trans -platinum(ii) complexes: Importance of the solvent and dynamics in spectral simulations 

      Castro, Abril C.; Fliegl, Heike; Cascella, Michele; Helgaker, Trygve; Repisky, Michal; Komorovsky, Stanislav; Medrano, María Ángeles; Quiroga, Adoración G.; Swart, Marcel (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-03-18)
      We report a combined experimental-theoretical study on the 31P NMR chemical shift for a number of trans-platinum(II) complexes. Validity and reliability of the 31P NMR chemical shift calculations are examined by comparing with the experimental data. A successful computational protocol for the accurate prediction of the 31P NMR chemical shifts was established for trans-[PtCl2(dma)PPh3] (dma = ...
    • Four-Component Relativistic Calculations in Solution with the Polarizable Continuum Model of Solvation: Theory, Implementation and Application to the Group 16 Dihydrides H2X (X= O, S, Se, Te, Po) 

      Di Remigio, Roberto; Bast, Radovan; Frediani, Luca; Saue, Trond (Journal article; Tidsskriftartikkel; Peer reviewed, 2014-11-20)