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  • Insight into the fluorescence quenching of Trp214 at HSA by the Dimetridazole ligand from simulation 

    Pomogaev, Valdimir A; Ramazanov, Ruslan R; Ruud, Kenneth; Artyukhov, Victor Ya (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-08-24)
    Spectroscopy is an important tool for detecting drug binding to amino acid sequences. One such important spectroscopic process is the fluorescence quenching due to charge transfer (CT) processes between a drug molecule and the chromophore center of Human Serum Albumin (HSA). We present a theoretical investigation of the CT occurring upon electronic excitation when a dimetridazole (Dmz) molecule ...
  • Iron‐Catalyzed Carbenoid Transfer Reactions of Vinyl Sulfoxonium Ylides: An Experimental and Computational Study 

    Vaitla, Janakiram; Bayer, Annette; Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-10-15)
    A method for the generation of unprecedented vinyl carbenoids from sulfoxonium ylides has been developed and applied in the synthesis of a diverse array of heterocycles such as indolizines, pyrroles, 3‐pyrrolin‐2‐ones, and furans. The reactions proceed by FeBr<sub>2</sub> catalysis under mild reaction conditions with a broad substrate scope. A reaction pathway involving iron carbenoids is proposed ...
  • Rhodium-Catalyzed Hydrocarboxylation: Mechanistic Analysis Reveals Unusual Transition State for Carbon–Carbon Bond Formation 

    Pavlovic, Ljiljana; Vaitla, Janakiram; Bayer, Annette; Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-03-12)
    The mechanism of rhodium-COD-catalyzed hydrocarboxylation of styrene derivatives and α,β-unsaturated carbonyl compounds with CO<sub>2</sub> has been investigated using density functional theory (PBE-D2/IEFPCM). The calculations support a catalytic cycle as originally proposed by Mikami and co-workers including β-hydride elimination, insertion of the unsaturated substrate into a rhodium–hydride bond, ...
  • Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition 

    Bjerga, Gro Elin Kjæreng; Larsen, Øivind; ARSIN, Hasan; Williamson, Adele Kim; Garcia-Moyano, Antonio; Leiros, Ingar; Puntervoll, Pål (Journal article; Tidsskriftartikkel; Preprint; Manuskript, 2018-06-16)
    Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading activity may have adverse effects inside a cell, but little is known about their regulatory mechanism. Until now, ISPs have mostly been described from <i>Bacillus</i> species, with structural data from a single homolog. Here, we study a ...
  • Biochemical characterization of ParI, an orphan C5-DNA methyltransferase from Psychrobacter arcticus 273-4 

    Grgic, Miriam; Williamson, Adele Kim; Bjerga, Gro Elin Kjæreng; Altermark, Bjørn; Leiros, Ingar (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-25)
    <p>Cytosine-specific DNA methyltransferases are important enzymes in most living organisms. In prokaryotes, most DNA methyltransferases are members of the type II restriction-modification system where they methylate host DNA, thereby protecting it from digestion by the accompanying restriction endonucleases. DNA methyltransferases can also act as solitary enzymes having important roles in controlling ...
  • 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 ...
  • Unraveling the Microscopic Origin of Triplet Lasing from Organic Solids 

    Paul, Lopa; Banerjee, Ambar; Paul, Ankan; Ruud, Kenneth; Chakrabarti, Swapan (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-07-16)
    We present a heuristic mechanism for the origin of the unusual triplet lasing from (E)-3-(((4-nitrophenyl)imino)methyl)-2H-thiochroman-4-olate·BF<sub>2</sub>. We demonstrate that whereas the moderate lifetime (1.03 μs) of the first triplet state (T<sub>1</sub>) prohibits triplet–triplet annihilation, the relatively faster S<sub>1</sub> → T<sub>1</sub> intersystem crossing and the 10<sup>4</sup> times ...
  • Resolution-of-identity accelerated relativistic two- and four-component electron dynamics approach to chiroptical spectroscopies 

    Konecny, Lukas; Kadek, Marius; Komorovsky, Stanislav; Ruud, Kenneth; Repisky, Michal (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-11-27)
    We present an implementation and application of electron dynamics based on real-time time-dependent density functional theory (RT-TDDFT) and relativistic 2-component X2C and 4-component Dirac–Coulomb (4c) Hamiltonians to the calculation of electron circular dichroism and optical rotatory dispersion spectra. In addition, the resolution-of-identity approximation for the Coulomb term (RI-J) is introduced ...
  • Rare and Nonexistent Nitrosyls: Periodic Trends and Relativistic Effects in Ruthenium and Osmium Porphyrin-Based {MNO}7 Complexes 

    Demissie, Taye Beyene; Conradie, Jeanet; Vazquez-Lima, Hugo; Ruud, Kenneth; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-12-14)
    Relativistic and nonrelativistic density functional theory calculations were used to investigate rare or nonexistent ruthenium and osmium analogues of nitrosylhemes. Strong ligand field effects and, to a lesser degree, relativistic effects were found to destabilize {RuNO}<sup>7</sup> porphyrins relative to their {FeNO}<sup>7</sup> analogues. Substantially stronger relativistic effects account for ...
  • Heterocyclic cellular lipid peroxidation inhibitors inspired by the marine antioxidant barettin 

    Labriere, Christophe; Andersen, Jeanette hammer; Albrigtsen, Marte; Hansen, Jørn H; Svenson, Johan (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-11-22)
    The marine environment remains a rich source for the discovery and development of novel bioactive compounds. The present paper describes the design, synthesis and biological evaluation of a library of small molecule heterocyclic mimetics of the marine 2,5-diketopiperazine barettin which is a powerful natural antioxidant. By mainly focusing on the influence from the brominated indole and heterocyclic ...
  • Cobalt-Catalysed Alkene Hydrogenation: A Metallacycle Can Explain the Hydroxyl Activating Effect and the Diastereoselectivity 

    Morello, Glenn Robert; Zhong, Hongyu; Chirik, Paul J.; Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-04)
    Bis(phosphine)cobalt dialkyl complexes have been reported to be highly active in the hydrogenation of tri-substituted alkenes bearing hydroxyl substituents. Alkene substrates containing ether, ester, or ketone substituents show minimal reactivity, indicating an activating effect of the hydroxyl group. The mechanistic details of bis(phosphine)cobalt-catalysed hydrogenation were recently evaluated ...
  • Stepwise Deoxygenation of Nitrite as a Route to Two Families of Ruthenium Corroles: Group 8 Periodic Trends and Relativistic Effects 

    Alemayehu, Abraham; Vazquez Lima, Hugo; Gagnon, Kevin J.; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-04-19)
    Given the many applications of ruthenium porphyrins, the rarity of ruthenium corroles and the underdeveloped state of their chemistry are clearly indicative of an area ripe for significant breakthroughs. The tendency of ruthenium corroles to form unreactive metal–metal-bonded dimers has been recognized as a key impediment in this area. Herein, by exposing free-base meso-tris(p-X-phenyl)corroles, ...
  • 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 ...
  • Comparative conformational analyses and molecular dynamics studies of glycylglycine methyl ester and glycylglycine N -methylamide 

    Thakkar, Balmukund S.; Engh, Richard Alan (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-01-24)
    Compared to their amide analogs, peptidic esters have a lower propensity for intramolecular hydrogen bonding, and thus most likely quite different stable geometries. On the other hand, their similarity and facile conversion to peptides has led to their broad use in synthetic and biological applications. This dichotomy creates a need to understand their conformational properties. Here, we study the ...
  • 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 ...
  • Modeled deposition of nitrogen and sulfur in Europe estimated by 14 air quality model systems: evaluation, effects of changes in emissions and implications for habitat protection 

    Vivanco, Marta García; Theobald, Mark R.; García-Gómez, Héctor; Garrido, Juan Luis; Prank, Marje; Aas, Wenche; Adani, Mario; Aluyz, Ummugulsum; Andersson, Camilla; Bellasio, Roberto; Bessagnet, Bertrand; Bianconi, Fabio; Bieser, Johannes; Brandt, Jørgen; Briganti, Gino; Cappelletti, Andrea; Curci, Gabriele; Christensen, Jesper H.; Colette, Augustin; Couvidat, Florian; Cuvelier, Cornelis; D'Isidoro, Massimo; Flemming, Johannes; Fraser, Andrea; Geels, Camilla; Hansen, Kaj M.; Hogrefe, Christian; Im, Ulas; Jorba, Oriol; Kitwiroon, Nutthida; Manders, Astrid; Mircea, Mihaela; Otero, Noelia; Pay, Maria-Teresa; Pozzoli, Luca; Solazzo, Efisio; Tsyro, Svetlana; Unal, Alper; Wind, Peter; Galmarini, Stefano (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-07-17)
    <p>The evaluation and intercomparison of air quality models is key to reducing model errors and uncertainty. The projects AQMEII3 and EURODELTA-Trends, in the framework of the Task Force on Hemispheric Transport of Air Pollutants and the Task Force on Measurements and Modelling, respectively (both task forces under the UNECE Convention on the Long Range Transport of Air Pollution, LTRAP), have brought ...
  • Enantioselective incorporation of CO2: status and potential 

    Vaitla, Janakiram; Guttormsen, Yngve; Mannisto, Jere K.; Nova, Ainara; Repo, Timo; Bayer, Annette; Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-09-09)
    CO<sub>2</sub> is a promising and sustainable carbon feedstock for organic synthesis. New catalytic protocols for efficient incorporation of CO<sub>2</sub>into organic molecules are continuously being reported. However, little progress has been made in the enantioselective conversion of CO<sub>2</sub>to form enantioenriched molecules. In order to allow CO<sub>2</sub>to become a versatile carbon ...
  • Geometric Energy Derivatives at the Complete Basis Set Limit: Application to the Equilibrium Structure and Molecular Force Field of Formaldehyde 

    Morgan, W. James; Matthews, Devin A; Ringholm, Magnus; Agarwal, Jay; Gong, Justin Z; Ruud, Kenneth; Allen, Wesley D.; Stanton, John F.; Schaefer, Henry F. III (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02-23)
    Geometric energy derivatives which rely on core-corrected focal-point energies extrapolated to the complete basis set (CBS) limit of coupled cluster theory with iterative and noniterative quadruple excitations, CCSDTQ and CCSDT(Q), are used as elements of molecular gradients and, in the case of CCSDT(Q), expansion coefficients of an anharmonic force field. These gradients are used to determine the ...
  • A multi-model comparison of meteorological drivers of surface ozone over Europe 

    Otero, Noelia; Sillmann, Jana; Mar, Kathleen; Rust, Henning W.; Solberg, Sverre; Andersson, Camilla; Engardt, Magnuz; Bergström, Robert; Bessagnet, Bertrand; Colette, Augustin; Couvidat, Florian; Cuvelier, Cornelius; Tsyro, Svetlana; Fagerli, Hilde; Schaap, Martijn; Manders, Astrid; Mircea, Mihaela; Briganti, Gino; Cappelletti, Andrea; Adani, Mario; D'Isidoro, Massimo; Pay, María Teresa; Theobald, Mark; Vivanco, Marta G.; Wind, Peter Ariaan; Ojha, Narendra; Raffort, Valentin; Butler, Tim (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-08-24)
    The implementation of European emission abatement strategies has led to a significant reduction in the emissions of ozone precursors during the last decade. Ground-level ozone is also influenced by meteorological factors such as temperature, which exhibit interannual variability and are expected to change in the future. The impacts of climate change on air quality are usually investigated through ...
  • Benchmarking the Performance of Exchange-Correlation Functionals for Predicting Two-Photon Absorption Strengths 

    Beerepoot, Maarten; Alam, MD Mehboob; Bednarska, Joanna; Bartkowiak, Wojciech; Ruud, Kenneth; Zaleśny, Robert (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-31)
    The present work investigates the performance of exchange–correlation functionals in the prediction of two-photon absorption (2PA) strengths. For this purpose, we considered six common functionals used for studying 2PA processes and tested these on six organoboron chelates. The set consisted of two semilocal (PBE and BLYP), two hybrid (B3LYP and PBE0), and two range-separated (LC-BLYP and CAM-B3LYP) ...

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