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  • 451. Johansson, Mikael
    et al.
    Lindén, Auri
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Osmium-Catalyzed Dihydroxylaition of Alkenes by H2O2 in Room Temperature Ionic Liquid co-Catalyzed by VO(acac)2 or MeReO32005In: Journal of Organometallic Chemistry, ISSN 0022-328X, Vol. 690, no 15, p. 3614-3619Article in journal (Refereed)
  • 452.
    Johansson, Mikael
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Purse, Byron W.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Terasak, Osamu
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Aerobic Oxidations Catalyzed by Zeolite-Encapsulated Cobalt Salophen2008In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 350, no 11-12, p. 1807-1815Article in journal (Refereed)
    Abstract [en]

    Cobalt salophen was encapsulated in a series of zeolites with a wide variation of the silicon-to-aluminium atomic ratio and with different cations. The zeolite-cobalt salophen catalysts were prepared using the “ship-in-a-bottle technique” where the complex was synthesized in the super cage of the zeolite and therefore locked into the pocket. The encapsulated catalysts were then tested in the aerobic oxidation of hydroquinone to p-benzoquinone; the best encapsulated catalyst was shown to be an efficient electron-transfer mediator in a palladium-catalyzed aerobic oxidative carbocyclization.

  • 453.
    Johansson, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Borgström, Magnus
    Lomoth, Reiner
    Palmblad, Magnus
    Bergquist, Jonas
    Hammarström, Leif
    Sun, Licheng
    Åkermark, Björn
    Electron Donor-Acceptor Dyads Based on Ruthenium(II) Bipyridine and Terpyridine Complexes Bound to Naphthalenediimide2003In: Inorganic Chemistry, ISSN 0020-1669, Vol. 42, no 9, p. 2908-2918Article in journal (Refereed)
  • 454. Johansson, Olof
    et al.
    Wolpher, Henriette
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Borgström, Magnus
    Hammarström, Leif
    Bergquist, Jonas
    Sun, Licheng
    Åkermark, Björn
    Intramolecular charge separation in a hydrogen bonded tyrosine-ruthenium(II)-naphtalene diimide triad2004In: Chemical Communications, ISSN 1359-7345, no 2, p. 194-195Article in journal (Refereed)
  • 455.
    Johansson, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Wolpher, Henriette
    Borgström, Magnus
    Hammarström, Leif
    Bergquist, Jonas
    Sun, Licheng
    Åkermark, Björn
    Intramolecular charge separation in a hydrogen bonded tyrosune-ruthenium(II) baphthalene diimide triad2004In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, p. 194-195Article in journal (Refereed)
  • 456. Johansson, Per-Ola
    et al.
    Bäck, Marcus
    Kvarnström, Ingemar
    Jansson, Katarina
    Vrang, Lotta
    Hamelink, Elizabeth
    Hallberg, Anders
    Rosenquist, Åsa
    Samuelsson, Bertil
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Potent inhibitors of the hepatitis C virus NS3 protease: use of a novel P2 cyclopentane-derived template2006In: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, Vol. 14, p. 5136-5151Article in journal (Refereed)
  • 457.
    Johansson, Tommy
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kers, Annika
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    2-Pyridylphosphonates: A New type of Modification for Nucleotide Analogues2001In: Tetrahedron Letters, ISSN 0040-4039, Vol. 42, no 11, p. 2217-2220Article in journal (Refereed)
    Abstract [en]

    Suitably protected dithymidine H-phosphonates afforded the corresponding dinucleoside 2-pyridylphosphonates upon treatment with N-methoxypyridinium tosylate in acetonitrile in the presence of 1,8-diazabicylo[5.4.0]undec-7-ene (DBU). The reaction was rapid (ca. 5 min), practically quantitative and proceeded stereospecifically, most likely with retention of configuration at the phosphorus centre.

    A simple and efficient protocol for the preparation of a new type of oligonucleotide analogue bearing a 2-pyridylphosphonate internucleotide linkage was developed

  • 458.
    Johansson, Tommy
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nucleoside H-phosphonates.: Part 19. Efficient entry to novel nucleotide analogues with 2-pyridyl and 4-pyridylphosphonothioate internucleotide linkages2004In: Tetrahedron, ISSN 0040-4020, Vol. 60, no 2, p. 389-395Article in journal (Refereed)
    Abstract [en]

    Synthetic and 31P NMR spectroscopy studies resulted in the development of efficient protocols for the stereospecific synthesis of a novel type of nucleotide analogues, 2-pyridyl- and 4-pyridylphosphonothioates. The underlying chemistry involves formation of the P–C bond via a base-promoted reaction of suitably protected dithymidine H-phosphonothioates with N-methoxypyridinium tosylate in acetonitrile, or with trityl chloride in pyridine, to produce high yields of nucleotide analogues with a 2-pyridyl- or 4-pyridyl moiety directly bound to the phosphorus centre.

  • 459.
    Johansson, Tommy
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of Dinucleoside Pyridylphosphonates Involving Palladium(0)-catalysed Phosphorus-carbon Bond Formation as a Key Step2001In: Chemical Communications, ISSN 1359-7345, no 24, p. 2564-2565Article in journal (Refereed)
    Abstract [en]

    Dinucleoside 3-pyridylphosphonates, as well as their 2- and 4-pyridyl positional isomers, have been synthesised using a palladium(0)-catalysed cross coupling strategy

  • 460.
    Johansson, Tommy
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    The Case for Configurational Stability of H-Phosphonate Diesters in the Presence of Diazabicyclo[5.4.0]undec-7-ene (DBU)2001In: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, Vol. 9, no 9, p. 2315-2322Article in journal (Refereed)
    Abstract [en]

    Configurational stability of dinucleoside H-phosphonates and the stereochemical course of their sulfurisation in the presence of diazabicyclo[5.4.0]undec-7-ene (DBU) were investigated using 31P NMR spectroscopy. It was found that under the reaction conditions and irrespective of the type of protecting groups present in the nucleoside moieties, the H-phosphonate diesters investigated did not undergo any detectable epimerisation at the phosphorus centre, and their sulfurisation with elemental sulfur in the presence of DBU, proceeded stereospecifically. Thus, we could not confirm reports from another laboratory on a stereoselective course of sulfurisation of H-phosphonate diesters and the corresponding acylphosphonates in the presence of DBU.

  • 461.
    Johnston, Eric V
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bogár, Krisztián
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Enantioselective synthesis of (R)-bufuralol via dynamic kinetic resolution in the key step2010In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 75, no 13, p. 4596-4599Article in journal (Refereed)
    Abstract [en]

    An enantioselective synthesis of (R)-bufuralol via a ruthenium- and enzyme-catalyzed dynamic kinetic resolution (DKR) has been achieved. The synthesis starts from readily available 2-ethylphenol and provides (R)-bufuralol in high ee and a good overall yield of 31%.

  • 462.
    Johnston, Eric V.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Karlsson, Erik A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lindberg, Staffan A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Efficient reoxidation of palladium by a hybrid catalyst in aerobic palladium-catalyzed carbocyclization of enallenes2009In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 28, p. 6799-6801Article in journal (Refereed)
  • 463.
    Johnston, Eric V.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Karlsson, Erik A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tran, Lien-Hoa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Efficient aerobic ruthenium-catalyzed oxidation of secondary alcohols by the use of a hybrid electron transfer catalyst2010In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 10, p. 1971-1976Article in journal (Refereed)
    Abstract [en]

    Biomimetic aerobic oxidation of secondary alcohols has been performed using hybrid catalyst 1 and Shvo's catalyst 2. This combination allows mild reaction conditions and low catalytic loading, due to the efficiency of intramolecular electron transfer. By this method a wide range of different alcohols have been converted into their corresponding ketones. Oxidation of benzylic as well as aliphatic, electron-rich, electron-deficient and sterically hindered alcohols could be oxidized in excellent yield and selectivity. Oxidation of (S)-1-phenyl-ethanol showed that no racemization occurred during the course of the reaction, indicating that the hydride 2b adds to the quinone much faster than it re-adds to the ketone product. The kinetic deuterium isotope effect of the oxidation was determined by the use of 1-phenylethanol (3a) and 1-deuterio-1-phenylethanol (3a-d1) in parallel and competitive manner, which gave the same isotope effect within experimental error (k(H)/k(D) approximate to 2.8). This indicates that there is no strong coordination of the substrate to the catalyst.

  • 464.
    Johnston, Eric V.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Karlsson, Erik A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tran, Lien-Hoa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Efficient synthesis of hybrid (hydroquinone-Schiff base)cobalt oxidation catalysts2009In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 23, p. 3973-3976Article in journal (Refereed)
    Abstract [en]

    Hybrid catalysts A and B have recently been found to efficiently transfer electrons from a metal catalyst to molecular oxygen in biomimetic oxidations. In the present work hybrid catalysts A and B were synthesized in high yield from inexpensive starting materials. The key step is an efficient Suzuki cross-coupling, which allows the use of unprotected aldehyde 5. The new synthesis of the title hybrid catalysts is easy to carry out and can be scaled up.

  • 465.
    Johnston, Eric V.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Shakeri, Mozaffar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tai, Cheuk-Wai
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Palmgren, Pål
    Eriksson, Kristofer
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Oscarsson, Sven
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Highly dispersed palladium nanoparticles on mesocellular foam: an efficient and recyclable heterogeneous catalyst for alcohol oxidation2012In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 18, no 39, p. 12202-12206Article in journal (Refereed)
  • 466.
    Jonker, Sybrand J. T.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Diner, Colin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Schulz, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Iwamoto, Hiroaki
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Catalytic asymmetric propargyl- and allylboration of hydrazonoesters: a metal-free approach to sterically encumbered chiral alpha-amino acid derivatives2018In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, no 91, p. 12852-12855Article in journal (Refereed)
    Abstract [en]

    A new asymmetric catalytic propargyl- and allylboration of hydrazonoesters is reported. The reactions utilize allenyl- and allylboronic acids in the presence of the inexpensive parent BINOL catalyst. The reactions can be performed under mild conditions (0 degrees C) without any metal catalyst or other additives affording sterically encumbered chiral -amino acids. This is the first metal-free method for the asymmetric propargyl- and allylboration of hydrazonoesters.

  • 467.
    Jonsson, K. Hanna M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Methyl 4-O-benzoyl-2,3-O-isopropylidene-a-L-rhamnopyranoside2006In: Acta Crystallographica Section C: Crystal Structure Communications, ISSN 0108-2701, E-ISSN 1600-5759, Vol. 62, no 8, p. o447-o449Article in journal (Refereed)
    Abstract [en]

    The title compound, C17H22O6, having an ester group at O4 of the hexopyranosyl sugar residue shows for the exo-cyclic C=O bond a conformation that is eclipsed to the C4-H4 bond. The two related torsion angles are denoted by syn and cis conformations. The q1 torsion angle (H4-C4-O4-C10) is indicated to have a similar conformation in solution as analyzed by NMR spectroscopy and a Karplus-type relationship.

  • 468.
    Jonsson, K. Hanna M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    NMR analysis of conformationally dependent nJC,H and nJC,C in the trisaccharide α-L-Rhap-(1→2)[α-L-Rhap-(1→3)]-α-L-Rhap-OMe and a site-specifically labeled isotopologue thereof2011In: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 49, no 3, p. 117-124Article in journal (Refereed)
    Abstract [en]

    An array of NMR spectroscopy experiments have been carried out to obtain conformationally dependent 1H,13C- and 13C,13C-spin–spin coupling constants in the trisaccharide α-L-Rhap-(1 → 2)[α-L-Rhap-(1 → 3)]-α-L-Rhap-OMe. The trisaccharide was synthesized with 13C site-specific labeling at C2′ and C2″, i.e. in the rhamnosyl groups in order to alleviate 1H spectral overlap. This facilitated the measurement of a key trans-glycosidic proton–proton cross-relaxation rate using 1D 1H,1H-T-ROESY experiments as well as a 3JC, H coupling employing 1D 1H,13C-long-range experiments, devoid of potential interference from additional J coupling. By means of both the natural abundance compound and the 13C-labeled sample 2D 1H,13C-J-HMBC and 1H,13C-HSQC-HECADE NMR experiments, total line-shape analysis of 1H NMR spectra and 1D 13C NMR experiments were employed to extract 3JC, H, 2JC, H, 3JC, C, and 1JC, C coupling constants. The 13C site-specific labeling facilitates straightforward determination of nJC, C as the splitting of the 13C natural abundance resonances. This study resulted in eight conformationally dependent coupling constants for the trisaccharide and illustrates the use of 13C site-specific labeling as a valuable approach that extends the 1D and 2D NMR methods in current use to attain both hetero- and homonuclear spin–spin coupling constants that subsequently can be utilized for conformational analysis.

  • 469.
    Jonsson, K. Hanna M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Säwén, Elin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Studies on the conformational flexibility of alpha-L-rhamnose-containing oligosaccharides using C-13-site-specific labeling, NMR spectroscopy and molecular simulations: implications for the three-dimensional structure of bacterial rhamnan polysaccharides2012In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 10, no 12, p. 2453-2463Article in journal (Refereed)
    Abstract [en]

    Bacterial polysaccharides are comprised of a variety of monosaccharides, L-rhamnose (6-deoxy-L-mannose) being one of them. This sugar is often part of alpha-(1 -> 2)- and/or alpha-(1 -> 3)-linkages and we have therefore studied the disaccharide alpha-L-Rhap-(1 -> 2)-alpha-L-Rhap-OMe to obtain information on conformational preferences at this glycosidic linkage. The target disaccharide was synthesized with C-13 site-specific labeling at C1' and at C2', i.e., in the terminal group. 2D H-1, C-13-HSQC-HECADE and H-1, C-13-J-HMBC NMR experiments, 1D C-13 and H-1 NMR spectra together with total line-shape analysis were used to extract conformationally dependent hetero- and homonuclear spin-spin coupling constants. This resulted in the determination of (2)JC(2',H1'), (3)J(C1',C1), (3)J(C1',C3), (3)J(C2',C2), (2)J(C1',C2), (1)JC(1',C2'), and (1)J(C1',H1'). These data together with previously determined J(CH) and H-1, H-1 NOEs result in fourteen conformationally dependent NMR parameters that are available for analysis of glycosidic linkage flexibility and conformational preferences. A 100 ns molecular dynamics (MD) simulation of the disaccharide with explicit water molecules as solvent showed a major conformational state at phi(H) approximate to 40 degrees and psi(H) approximate to -35 degrees, consistent with experimental NMR data. In addition, MD simulations were carried out also for alpha-L-Rhap-(1 -> 3)-alpha-L-Rhap-OMe and a rhamnan hexasaccharide. The gathered information on the oligosaccharides was used to address conformational preferences for a larger structure, a 2- and 3-linked nonasaccharide, with implications for the 3D structure of rhamnan polysaccharides, which should be regarded as flexible polymers.

  • 470.
    Jonsson, K. Hanna M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural determination of the O-antigenic polysaccharide from Escherichia coli O742009In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, no 12, p. 1592-1595Article in journal (Refereed)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from Escherichia coli O74 has been determined. Component analysis, together with 1H and 13C NMR spectroscopy as well as 1H,15N-HSQC experiments were employed to elucidate the structure. Inter-residue correlations were determined by 1H,1H-NOESY and 1H,13C-heteronuclear multiple-bond correlation experiments. The PS is composed of tetrasaccharide repeating units with the following structure:

    Full-size image (5K)

    Cross-peaks of low intensity from an α-linked N-acetylglucosamine residue were present in the NMR spectra, and spectral analysis indicates that they originate from the penultimate residue in the polysaccharide. Consequently, the biological repeating unit has a 3-substituted N-acetyl-d-glucosamine residue at its reducing end. The 1H, 13C and 15N NMR chemical shifts of the α- and β-anomeric forms of d-Fucp3NAc are also reported. The repeating unit of the E. coli O74 O-antigen is identical to that of the capsular polysaccharide from E. coli K45.

  • 471.
    Jonsson, K. Hanna M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural studies of the O-antigenic polysaccharide from Shigella dysenteriae type 3 and Escherichia coli O124, a reinvestigation2006In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 341, p. 2986-2989Article in journal (Refereed)
  • 472. Kabeshov, Mikhail A.
    et al.
    Kysilka, Ondřej
    Rulíšek, Lubomír
    Suleimanov, Yury V.
    Bella, Marco
    Malkov, Andrei V.
    Kočovský, Pavel
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Czech Academy of Sciences, Czech Republic; Charles University Prague, Czech Republic.
    Cross-Aldol Reaction of Isatin with Acetone Catalyzed by Leucinol: A Mechanistic Investigation2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 34, p. 12026-12033Article in journal (Refereed)
    Abstract [en]

    Comprehensive mechanistic studies on the enantioselective aldol reaction between isatin (1a) and acetone, catalyzed by L-leucinol (3a), unraveled that isatin, apart from being a substrate, also plays an active catalytic role. Conversion of the intermediate oxazolidine 4 into the reactive syn-enamine 6, catalyzed by isatin, was identified as the rate-determining step by both the calculations (G=26.1kcalmol(-1) for the analogous L-alaninol, 3b) and the kinetic isotope effect (k(H)/k(D)=2.7 observed for the reaction using [D-6]acetone). The subsequent reaction of the syn-enamine 6 with isatin produces (S)-2a (calculated G=11.6kcalmol(-1)). The calculations suggest that the overall stereochemistry is controlled by two key events: 1)the isatin-catalyzed formation of the syn-enamine 6, which is thermodynamically favored over its anti-rotamer 7 by 2.3kcalmol(-1); and 2)the high preference of the syn-enamine 6 to produce (S)-2a on reaction with isatin (1a) rather than its enantiomer (G=2.6kcalmol(-1)).

  • 473. Kaderavek, Pavel
    et al.
    Zapletal, Vojtech
    Fiala, Radovan
    Srb, Pavel
    Padrta, Petr
    Precechtelova, Jana Pavlikova
    Soltesova, Maria
    Kowalewski, Jozef
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chmelik, Josef
    Sklenar, Vladimir
    Zidek, Lukas
    Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies2016In: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 266, p. 23-40Article in journal (Refereed)
    Abstract [en]

    Standard spectral density mapping protocols, well suited for the analysis of N-15 relaxation rates, introduce significant systematic errors when applied to C-13 relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and C-13 frequencies can be obtained from data acquired at three magnetic fields for uniformly C-13-labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

  • 474.
    Kadow, Maria
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Ernst Moritz Arndt Universitat Greifswald, Germany.
    Balke, Kathleen
    Willetts, Andrew
    Bornscheuer, Uwe T.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Functional assembly of camphor converting two-component Baeyer-Villiger monooxygenases with a flavin reductase from E-coli2014In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 98, no 9, p. 3975-3986Article in journal (Refereed)
    Abstract [en]

    The major limitation in the synthetic application of two-component Baeyer-Villiger monooxygenases was addressed by identifying the 28-kDa flavin-reductase Fre from Escherichia coli as a suitable supplier of reduced FMN for these enzymes. Coexpression of Fre with either 2,5- or 3,6-diketocamphane monooxygenase from Pseudomonas putida NCIMB 10007 significantly enhanced the conversion of camphor and norcamphor serving as representative ketones. With purified enzymes, full conversion was achieved, while only slight amounts of product were formed in the absence of this flavin reductase. Fusion of the genes of Fre and DKCMOs into single open reading frame constructs resulted in unstable proteins exhibiting flavin reducing, but poor oxygenating activity, which led to overall decreased conversion of camphor.

  • 475.
    Kahle, Maximilian
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Jareck, Sascha
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ädelroth, Pia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Insights into the mechanism of nitric oxide reductase from a Fe-B-depleted variant2019In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 593, no 12, p. 1351-1359Article in journal (Refereed)
    Abstract [en]

    A key step of denitrification, the reduction of toxic nitric oxide to nitrous oxide, is catalysed by cytochrome c-dependent NO reductase (cNOR). cNOR contains four redox-active cofactors: three hemes and a nonheme iron (Fe-B). Heme b(3) and Fe-B constitute the active site, but the specific mechanism of NO-binding events and reduction is under debate. Here, we used a recently constructed, fully folded and hemylated cNOR variant that lacks Fe-B to investigate the role of Fe-B during catalysis. We show that in the Fe-B-less cNOR, binding of both NO and O-2 to heme b(3) still occurs but further reduction is impaired, although to a lesser degree for O-2 than for NO. Implications for the catalytic mechanisms of cNOR are discussed.

  • 476.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bartoszewicz, Agnieszka
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of nucleoside phosphorothio-, phosphorodithio- and phosphoroselenoate diesters via oxidative esterification of the corresponding H-phosphonate analogues2008In: Nucleic Acids Symposium Series, ISSN 0261-3166, Vol. 52, p. 285-286Article in journal (Refereed)
  • 477.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. California Institute of Technology, United States; University of Warsaw, Poland.
    Fu, Gregory C.
    Caution in the Use of Nonlinear Effects as a Mechanistic Tool for Catalytic Enantioconvergent Reactions: Intrinsic Negative Nonlinear Effects in the Absence of Higher-Order Species2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 11, p. 4225-4229Article in journal (Refereed)
    Abstract [en]

    Investigation of the dependence of product enantiometric excess (ee) on catalyst ee is a widely used tool to probe the mechanism of an enantioselective reaction; in particular, the observation of a nonlinear relationship is usually interpreted as an indication of the presence of one or more species that contain at least two units of the chiral entity. In this report, we demonstrate that catalytic enantioconvergent reactions can display an intrinsic negative nonlinear effect that originates purely from the kinetic characteristics of certain enantioconvergent processes and is independent of possible aggregation of the chiral entity. Specifically, this intrinsic negative nonlinear effect can arise when there is a kinetic resolution of the racemic starting material, and its magnitude is correlated with the selectivity factor and the conversion; the dependence on conversion provides a ready means to distinguish it from a more conventional nonlinear effect. We support our analysis with experimental data for two distinct enantioconvergent processes, catalyzed by a chiral phosphine and the other by a chiral Pd/phosphine complex.

  • 478.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Combining Meyer-Schuster Rearrangement with Aldol and Mannich Reactions: Theoretical Study of the Intermediate Interception Strategy2012In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, no 46, p. 19159-19169Article in journal (Refereed)
    Abstract [en]

    Interception of the transient allenyl enolate intermediate of the vanadium-catalyzed Meyer-Schuster rearrangement with aldehydes and imines has been studied computationally using density functional theory. Mechanistic details of the catalytic cycles for each of the reaction variants are established. In particular, it is shown that the active form of I the catalyst contains two triphenylsiloxy ligands, the transesterification of vanadate occurs via sigma-bond metathesis, and vanadium enolate is directly involved in the key C-C bond formation. The calculations also provide support for the dissociative course of the key 1,3-shift step. The stereochemistry of the reaction is thoroughly investigated, and the obtained energy barriers reproduce and rationalize the experimentally observed (Z)-, (E)-selectivity. The calculated free energy profiles are analyzed in terms of efficiency of the intermediate enolate interception. It is shown that the investigated reactions represent borderline cases, in which the intermediate trapping is only slightly favored over the undesired isomerization pathway.

  • 479. Kalek, Marcin
    et al.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mechanism and Selectivity of Cooperatively Catalyzed Meyer-Schuster Rearrangement/Tsuji-Trost Allylic Substitution. Evaluation of Synergistic Catalysis by Means of Combined DFT and Kinetics Simulations2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 30, p. 10250-10266Article in journal (Refereed)
    Abstract [en]

    The reaction between propargylic alcohols and allylic carbonates, engaging vanadium and palladium catalysts, is an exemplary case of a cooperatively catalyzed process. This combined Meyer-Schuster rearrangement/Tsuji-Trost allylic substitution clearly illustrates the enormous advantages offered by the simultaneous use of two catalysts, but also the inherent challenges regarding selectivity associated with such a reaction design. These challenges originate from the fact that the desired product of the combined process is formed by a bimolecular coupling of the two substrates activated by the respective catalysts. However, these two processes may also occur in a detached way via the reactions of the catalytic intermediates with the starting propargylic alcohol present in the reaction mixture, leading to the formation of two side-products. Herein, we investigate the overall mechanism of this reaction using density functional theory (DFT) methodology. The mechanistic details of the catalytic cycles for all the individual processes are established. In particular, it is shown that the diphosphine ligand, dppm, used in the reaction promotes the formation of dinuclear palladium complexes, wherein only a single metal center is directly involved in the catalysis. Due to the complexity of the combined reaction network, kinetics simulation techniques are employed in order to analyze the overall selectivity. The simulations directly link the results of the DFT calculations with the experimental data and confirm that the computed free energy profiles indeed reproduce the observed selectivities. In addition, a sensitivity analysis is carried out to assess the importance of the individual steps on the product distribution. The observed behavior of the kinetic network is rationalized, and trends in the reaction outcome upon changing the initial conditions, such as the catalysts amounts and ratio, are discussed. The results provide a general framework for understanding the factors governing the selectivity of the cooperatively catalyzed reactions.

  • 480.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Jezowska, Martina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Preparation of arylphosphonates by palladium(0)-catalyzed cross-coupling in the presence of acetate additives: Synthetic and mechanistic studies2009In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 351, no 18, p. 3207-3216Article in journal (Refereed)
    Abstract [en]

    An efficient protocol for the synthesis of arylphosphonate diesters via a palladium-catalyzed cross-coupling of H-phosphonate diesters with aryl electrophiles, promoted by acetate ions, was developed. A significant shortening of the cross-coupling time in the presence of the added acetate ions was achieved for bidentate and monodentate supporting ligands, and for different aryl electrophiles (iodo, bromo and triflate derivatives). The reaction conditions were optimized in terms of amount of the catalyst, supporting ligands, and source of the acetate ion used. Various arylphosphonates, including those of potential biological significance, were synthesized using this newly developed protocol. Some mechanistic aspects of the investigated reactions are also discussed.

  • 481.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johansson, Tommy
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Jezowska, Martina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-catalyzed propargylic substitution with phosphorus nucleophiles: efficient, stereoselective synthesis of allenylphosphonates and related compounds2010In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 12, no 20, p. 4702-4704Article in journal (Refereed)
    Abstract [en]

    A new, efficient method is developed, based on a palladium(0)-catalyzed reaction of propargylic derivatives with various phosphorus nucleophiles, to produce allenylphosphonates and their analogues with defined stereochemistry in the allenic and the phosphonate moiety. 

  • 482.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Efficient synthesis of mono-and diarylphosphinic acids: a microwave-assisted palladium-catalyzed cross-coupling of aryl halides with phosphinate2009In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 65, no 50, p. 10406-10412Article in journal (Refereed)
    Abstract [en]

    A general, efficient method for the microwave-assisted synthesis of mono- and diarylphosphinic acids from anilinium phosphinate and aryl halides, using Pd(0) and Xantphos as a supporting ligand, was developed.

  • 483.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Novel, stereoselective and stereospecific synthesis of allenylphosphonates and related compounds via palladium-catalyzed propargylic substitution2011In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 353, no 10, p. 1741-1755Article in journal (Refereed)
    Abstract [en]

    We have developed a novel method for the synthesis of allenylphosphonates and related compounds based on a palladium(0)-catalyzed reaction of propargylic derivatives with H-phosphonate,H-phosphonothioate, H-phosphonoselenoate, and H-phosphinateesters. The reaction is stereoselective and stereospecific, and provides a convenient entry to a vast array of allenylphosphonates and their analogues with diverse substitution patterns in the allenic moiety and at the phosphorus center. Some mechanistic aspects of this new reaction were also investigated.

  • 484.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-catalyzed C-P bond formation: Mechanistic studies on the ligand substitution and the reductive elimination. An intramolecular catalysis by the acetate group in PdII complexes2008In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 27, no 22, p. 5876-5888Article in journal (Refereed)
    Abstract [en]

    Ligand substitution and reductive elimination of the palladium-catalyzed C−P bond forming cross-coupling were investigated in depth. It was found that for PhPdII(PPh3)2X (X = I, Br, Cl) complexes, a step commonly referred to as ligand substitution commenced with coordination of an H-phosphonate diester, followed by its deprotonation to form an equilibrium mixture of penta- and tetracoordinate palladiumphosphonate intermediates, from which reductive elimination of the product (diethyl phenylphosphonate) occurred. For the acetate counterpart, PhPdII(PPh3)2(OAc), the incorporation of a phosphonate moiety to the complex was preceded by a rate-determining removal of the supporting phosphine ligand, facilitated by an intramolecular catalysis by the acetate group. Both the reaction steps, i.e., formation of palladiumphosphonate intermediates and reductive elimination, were significantly faster for the acetate versus halides containing PdII complexes investigated. Similar observations were found to be true also for bidentate ligand complexes [(dppp)PdII(Ph)X]; however, in this instance, a single palladiumphosphonate intermediate, (dppp)PdII(Ph)(PO(OEt)2), could be observed by 31P NMR spectroscopy. The synthetic and kinetic studies on the cross-coupling reaction of diethyl H-phosphonate with phenyl halides permitted us to elucidate a crucial catalytic role of an acetate group in PdII complexes and to propose two distinctive catalytic cycles, which complemented traditional Pd0/PdII schemes, for the palladium-mediated C−P bond formation.

  • 485.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pd(0)-Catalyzed phosphorus-carbon bond formation: Mechanistic and synthetic studies on the role of the palladium sources and anionic additives2007In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 26, no 24, p. 5840-5847Article in journal (Refereed)
    Abstract [en]

    Pd(PPh3)4, Pd(dba)2, Pd(OAc)2, and PdCl2, have been evaluated as possible Pd(0) sources for the palladium-catalyzed P−C bond formation via a cross-coupling of aryl halides with H-phosphonate diesters. It was found that the most efficient catalytic system can be generated from Pd(OAc)2 with a key role being played by Pd(II) and Pd(0) species with coordinated acetate ions. The reactivity of differently ligated Pd(II) complexes was determined, and 31P NMR spectroscopy studies were carried out to provide mechanistic interpretations for the observed differences between the catalytic systems.

  • 486.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ziadi, Asraa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Microwave-assisted palladium-catalyzed cross-coupling of aryl and vinyl halides with H-phosphonate diesters2008In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 10, no 20, p. 4637-4640Article in journal (Refereed)
    Abstract [en]

    A general and efficient method for the microwave-assisted formation of the C−P bond was developed. Using a prevalent palladium catalyst, Pd(PPh3)4, a quantitative cross-coupling of various H-phosphonate diesters with aryl and vinyl halides was achieved in less than 10 min. The reactions occurred with retention of configuration at the phosphorus center and in the vinyl moiety. Using this protocol, several C-phosphonates, including those bearing nucleoside and cholesteryl moieties, were prepared in high yields.

  • 487.
    Kamerlin, Shina C. L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Vicatos, Spyridon
    Dryga, Anatoly
    Warshel, Arieh
    Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems2011In: Annual review of physical chemistry (Print), ISSN 0066-426X, E-ISSN 1545-1593, Vol. 62, p. 41-64Article in journal (Refereed)
    Abstract [en]

    Recent years have witnessed an explosion in computational power, leading toattempts to model ever more complex systems. Nevertheless, there remain cases for which the use of brute-force computer simulations is clearly not the solution. In such cases, great benefit can be obtained from the use of physically sound simplifications. The introduction of such coarse graining can be traced back to the early usage of a simplified model in studies of proteins. Since then, the field has progressed tremendously. In this review,we cover both key developments in the field and potential future directions. Additionally, particular emphasis is given to two general approaches, namely the renormalization and reference potential approaches, which allow one to move back and forth between the coarse-grained (CG) and full models, as these approaches provide the foundation for CG modeling of complex systems.

  • 488.
    Kamerlin, Shina C. L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Warshel, Arieh
    Multiscale modeling of biological functions2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 22, p. 10401-10411Article in journal (Refereed)
    Abstract [en]

    Recent years have witnessed a tremendous explosion in computational power, which in turn has resulted in great progress in the complexity of the biological and chemical problems that can be addressed by means of all-atom simulations. Despite this, however, our computational time is not infinite, and in fact many of the key problems of the field were resolved long before the existence of the current levels of computational power. This review will start by presenting a brief historical overview of the use of multiscale simulations in biology, and then present some key developments in the field, highlighting several cases where the use of a physically sound simplification is clearly superior to a brute-force approach. Finally, some potential future directions will be discussed.

  • 489.
    Kamerlin, Shina C. L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Warshel, Arieh
    The empirical valence bond model: theory and applications2011In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 1, no 1, p. 30-45Article in journal (Refereed)
    Abstract [en]

    Recent years have seen an explosion in computer power, allowing for the examination of ever more challenging problems. For instance, a recent simulation study, which was the first of its kind, was able to actually explore the dynamical nature of enzyme catalysis on a millisecond timescale (Pisliakov AV, Cao J, Kamerlin SCL, Warshel A. Proc Natl Acad Sci U S A 2009, 106:17359.), something that as recently as a year or two ago would have been considered impossible. However, the questions that need addressing are nevertheless very complex, and experimental approaches can unfortunately often be inconclusive (Åqvist J, Kolmodin K, Florián J, Warshel A, Chem Biol 1999, 6:R71.) in answering them. Therefore, it is essential to have an approach that is both reliable and able to capture complex systems in order to resolve long-standing controversies [particularly with regards to questions such as the origin of enzyme catalysis, where the relevant energy contributions cannot be separated without some computational models (Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM, Chem Rev 2006, 106:3210.)]. Herein, we will present the empirical valence bond (EVB) approach, which, at present, is arguably the most powerful tool for examining chemical reactivity in the condensed phase. We will illustrate the effectiveness of the EVB method when evaluating, for instance, catalytic effects and demonstrate that it is currently the optimal tool for elucidating challenging problems such as understanding the catalytic power of enzymes. Finally, the increasing appreciation of this approach can maybe best illustrated not only by its proliferation but also by attempts to capture its basic chemistry under a different name, as will be discussed in this work.

  • 490.
    Kamerlin, Shina C. L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Wilkie, John
    The effect of leaving group on mechanistic preference in phosphate monoesterhydrolysis2011In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 9, no 15, p. 5394-5406Article in journal (Refereed)
    Abstract [en]

    We present 2-dimensional potential energy surfaces and  transition states (TS) for water attack on a series of substituted phosphate monoester monoanions at the DFT level of theory, comparing a standard 6-31++g(d,p) basis set with a larger triple-zeta (augmented cc-pVTZ) basis set. Small fluorinated model compounds are used to simulate increasing leaving group stability without adding further geometrical complexity to the system. We demonstrate that whilst changing the leaving group causes little qualitative change in the potential energy surfaces (with the exception of the system with the most electron withdrawing leaving group, CF3O-, in which the associative pathway changes from a stepwise AN + DN pathway to a concerted ANDN pathway), there is a quantitative change in relative gas-phase and solution barriers for the two competing pathways. In line with previous studies, in the case of OCH3, the barriers for the associative and dissociative pathways are similar in solution, and the two pathways are equally viable and indistinguishable in solution. However, significantly increasing the stability of the leaving group (decreasing proton affinity, PA) results in the progressive favouring of a stepwise dissociative, DN + AN, mechanism over associative mechanisms.

  • 491.
    Kamerlin, Shina Caroline Lynn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical comparison of p-nitrophenyl phosphate and sulfate Hydrolysis in aqueous solution: implications for enzyme-catalyzed sulfuryl transfer2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 22, p. 9228-9238Article in journal (Refereed)
    Abstract [en]

    Both phosphoryl and sulfuryl transfers are ubiquitous in biology, being involved in a wide range of processes, ranging from cell division to apoptosis. Additionally, it is becoming increasingly clear that enzymes that can catalyze phosphoryl transfer can often cross-catalyze sulfuryl transfer (and vice versa). However, while there have been extensive experimental and theoretical studies performed on phosphoryl transfer, the body of available research on sulfuryl transfer is comparatively much smaller. The present work presents a direct theoretical comparison of p-nitrophenyl phosphate and sulfate monoester hydrolysis, both of which are considered prototype systems for probing phosphoryl and sulfuryl transfer, respectively. Specifically, free energy surfaces have been generated using density functional theory, by initial geometry optimization in PCM using the 6-31+G* basis set and the B3LYP density functional, followed by single-point calculations using the larger 6-311+G** basis set and the COSMO continuum model. The resulting surfaces have been then used to identify the relevant transition states, either by further unconstrained geometry optimization or from the surface itself where possible. Additionally, configurational entropies were evaluated using a combination of the quasiharmonic approximation and the restraint release approach and added to the calculated activation barriers as a correction. Finally, the overall activation entropy was estimated by approximating the solvent contribution to the total activation entropy using the Langevin dipoles solvation model. We have reproduced both the experimentally observed activation barriers and the observed trend in the activation entropies with reasonable accuracy, as well as providing a comparison of calculated and observed 15N and 18O kinetic isotope effects. We demonstrate that, counterintuitively, the hydrolysis of the p-nitrophenyl sulfate proceeds through a more expansive pathway than its phosphate analogue. Additionally, we show that the solvation effects upon moving from the ground state to the transition state are quite different for both reactions, suggesting that the enzymes that catalyze these reactions would need active sites with quite different electrostatic preorganization for the efficient catalysis of either reaction (despite which many enzymes can catalyze both phosphoryl and sulfuryl transfer). We believe that such a comparative study is an important foundation for understanding the molecular basis for phosphate–sulfate cross-promiscuity within members of the alkaline phosphatase superfamily.

  • 492. Kang, Yu
    et al.
    Gohlke, Ulrich
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hamark, Christoffer
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Scheidt, Tom
    Kunstrnann, Sonja
    Heinemann, Udo
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Santer, Mark
    Barbirz, Stefanie
    Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions2016In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 138, no 29, p. 9109-9118Article in journal (Refereed)
    Abstract [en]

    Understanding interactions of bacterial surface polysaccharides with receptor protein scaffolds is important for the development of antibiotic therapies. The corresponding protein recognition domains frequently form low-affinity complexes with polysaccharides that are difficult to address with experimental techniques due to the conformational flexibility of the polysaccharide. In this work, we studied the tailspike protein (TSP) of the bacteriophage Sf6. Sf6TSP binds and hydrolyzes the high-rhamnose, serotype Y O-antigen polysaccharide of the Gram-negative bacterium Shigella flexneri (S. flexneri) as a first step of bacteriophage infection. Spectroscopic analyses and enzymatic cleavage assays confirmed that Sf6TSP binds long stretches of this polysaccharide. Crystal structure analysis and saturation transfer difference (STD) NMR spectroscopy using an enhanced method to interpret the data permitted the detailed description of affinity contributions and flexibility in an Sf6TSP-octasaccharide complex. Dodecasaccharide fragments corresponding to three repeating units of the O-antigen in complex with Sf6TSP were studied computationally by molecular dynamics simulations. They showed that distortion away from the low-energy solution conformation found in the octasaccharide complex is necessary for ligand binding. This is in agreement with a weak-affinity functional polysaccharide protein contact that facilitates correct placement and thus hydrolysis of the polysaccharide close to the catalytic residues. Our simulations stress that the flexibility of glycan epitopes together with a small number of specific protein contacts provide the driving force for Sf6TSP-polysaccharide complex formation in an overall weak-affinity interaction system.

  • 493.
    Kapla, Jon
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wohlert, Jakob
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Maliniak, Arnold
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 34, p. 22438-22447Article in journal (Refereed)
    Abstract [en]

    The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.

  • 494.
    Kapla, Jon
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wohlert, Jakob
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Maliniak, Arnold
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Molecular Dynamics Simulations of Membrane-Sugar Interactions2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 22, p. 6667-6673Article in journal (Refereed)
    Abstract [en]

    It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range W-TRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane sugar interactions.

  • 495. Kapoor, Mili
    et al.
    Srinivas, Honnappa
    Kandiah, Eaazhisai
    Gemma, Emiliano
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ellgaard, Lars
    Oscarson, Stefan
    Helenius, Ari
    Surolia, Avadhesha
    Interactions of Substrate with Calreticulin, an Endoplasmic Reticulum Chaperone2003In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 278, no 8, p. 6194–6200-Article in journal (Refereed)
  • 496.
    Karlsson, Erik A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mechanism of the palladium-catalyzed carbohydroxylation of allene-substituted conjugated dienes: rationalization of the recently observed nucleophilic attack by water on a (pi-allyl)palladium intermediate2008In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 14, no 30, p. 9175-9180Article in journal (Refereed)
    Abstract [en]

    The mechanism of the palladium-catalyzed oxidative carbohydroxylation of allene-substituted 1,3-cyclohexadiene was studied by DFT calculations. All intermediates and transition states of the reaction were identified and their structures were calculated. The calculations confirm the mechanism previously proposed and show that the CC bond-forming step occurs via insertion of one of the double bonds of 1,3-cyclohexadiene into a Pdvinyl bond of a vinylpalladium intermediate. This reaction leads to a (π-allyl)palladium intermediate, and coordination of benzoquinone and a double bond in the molecule to Pd creates a highly reactive cationic π-allyl complex, which is readily attacked by water according to the calculations.

  • 497.
    Karlsson, Erik A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lee, Bao-Lin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Becerril, Valeria Saavedra
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Abrahamsson, Maria
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis and Electron-Transfer Processes in a New Family of Ligands for Coupled Ru-Mn2 Complexes2014In: ChemPlusChem, ISSN 2192-6506, Vol. 79, no 7, p. 936-950Article in journal (Refereed)
    Abstract [en]

    A series of [Ru(bpy)(3)](2+)-type (bpy= 2,2'-bipyridine) photosensitisers have been coupled to a ligand for Mn, which is expected to give a dinuclear complex that is active as a water oxidation catalyst. Unexpectedly, photophysical studies showed that the assemblies had very short lived excited states and that the decay patterns were complex and strongly dependent on pH. One dyad was prepared that was capable of catalysing chemical water oxidation by using [Ru(bpy)(3)](3+) as an oxidant. However, photochemical water oxidation in the presence of an external electron acceptor failed, presumably because the short excited-state lifetime precluded initial electron transfer to the added acceptor. The photophysical behaviour could be explained by the presence of an intricate excited-state manifold, as also suggested by time-dependent DFT calculations.

  • 498.
    Karlsson, Erik A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lee, Bao-Lin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hansson, Örjan
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Photosensitized water oxidation by use of a bioinspired manganese catalyst2011In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, no 49, p. 11715-11718Article in journal (Refereed)
  • 499.
    Karlsson, Erik A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Oxidation of ethers, alcohols, and unfunctionalized hydrocarbons by the methyltrioxorhenium/H2O2 system: a computational study on catalytic C-H bond activation2009In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 8, p. 1862-1869Article in journal (Refereed)
    Abstract [en]

    A concerted mechanism that does not involve an ionic intermediate was revealed by a DFT study on oxidation of ethers, alcohols, and unfunctionalized hydrocarbons by methyltrioxorhenium/H2O2. Instead, CH insertion occurs through hydride transfer and then turns into a hydroxide transfer/rebound in a concerted fashion. The picture shows selected frames from an intrinsic reaction coordinate scan from the transition state to the product for the oxidation of cis-1,2-dimethylcyclohexane.

    The potential-energy surfaces (PESs) of methyltrioxorhenium (MTO)-catalyzed CH insertion reactions in the presence of hydrogen peroxide were studied by accurate DFT methods for a series of substrates including unsaturated hydrocarbons, an ether, and an alcohol. Based on the comprehensive analysis of transition states and intrinsic reaction coordinate (IRC) scans, CH insertion was found to proceed by a concerted mechanism that does not require, as previously thought, a side-on or a butterfly-like transition state. We found that a typical transition state follows requirements of the SN2 reaction instead. Furthermore, by exploring the PESs of several CH insertion reactions, we discovered that no ionic intermediate is formed even in a polar solvent. The latter was modeled within the self-consistent reaction field approach in a polarizable continuum model (PB-SCRF/PCM). According to our study, CH insertion occurs by a concerted but highly asynchronous mechanism that first proceeds by hydride transfer and then turns into hydroxide transfer/rebound. For the oxidation of alcohols, CH bond cleavage occurs without formation of alkoxide intermediates on the dominant pathway. The computed deuterium kinetic isotope effect of 2.9 for the hydride-transfer transition state for alcohol oxidation is in good agreement with the experimental kH/kD ration of 3.2 reported by Zauche and Espenson. As confirmed by IRC and PES scans in different solvents, the OH-rebound phase of the CH insertion pathway demonstrates strong similarities with the rebound mechanism that was previously proposed for cytochrome P450 and metalloporphyrin-catalyzed oxidations.

  • 500. Karmakar, Anirban
    et al.
    Oliver, Clive L.
    Platero-Prats, Ana E.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Laurila, Elina
    Öhrström, Lars
    Crystal structures and hydrogen bond analysis of five amino acid conjugates of terephthalic and benzene-1,2,3-tricarboxylic acids2014In: CrystEngComm, ISSN 1466-8033, E-ISSN 1466-8033, Vol. 16, no 35, p. 8243-8251Article in journal (Refereed)
    Abstract [en]

    Four linear connecting amino acid derived ligands, 1-4, and one potentially three connecting, 5, were prepared by the reaction of the appropriate terephthaloyl dichloride or benzene-1,3,5-tricarbonyl trichloride with the methyl ester protected amino acid. Amino acids used here were alanine (1, 5), isoleucine (2), leucine (3) and valine (4). Crystalline forms of four amino acid substituted terephthalamides (2,2'-(terephthaloylbis(azanediyl))dipropanoic acid dihydrate 1; 2,2'-(terephthaloylbis(azanediyl)) bis(3-methylpentanoic acid) monohydrate 2; 2,2'-(terephthaloylbis(azanediyl))bis(4-methylpentanoic acid) dihydrate 3; 2,2'-(terephthaloylbis(azanediyl)) bis(3-methylbutanoic acid) dihydrate 4) and one benzene-1,3,5- tricarboxamide molecule (2,2',2 ''-((benzene-1,3,5-tricarbonyl)tris(azanediyl))tripropionic acid hemihydrate 5) were characterised and the single crystal structures were solved. All the compounds form hydrogen bonded 2D and 3D nets. Linear connecting amino acid derivatives can be categorised into three groups depending on the hydrogen bond patterns and final structures. Compounds 1 and 2 form 3D structures but the final structure is different due to the different hydrogen bond synthons. Compounds 3 and 4 are isostructural and form 2D hydrogen bonded structures while 5 forms a hydrogen bonded pcu-net. Intermolecular interactions have been analysed with Hirshfeld surfaces and graph set symbols.

78910111213 451 - 500 of 1217
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