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  • 1.
    Abdel-Magied, Ahmed F.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Shatskiy, Andrey
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Liao, Rong-Zhen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Laine, Tanja M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Arafa, Wael A. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. University Fayoum, Egypt.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kärkäs, Markus D.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Bjorn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Johnston, Eric V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Chemical and Photochemical Water Oxidation Mediated by an Efficient Single-Site Ruthenium Catalyst2016Ingår i: ChemSusChem, ISSN 1864-5631, E-ISSN 1864-564X, Vol. 9, nr 24, s. 3448-3456Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Water oxidation is a fundamental step in artificial photosynthesis for solar fuels production. In this study, we report a single-site Ru-based water oxidation catalyst, housing a dicarboxylate-benzimidazole ligand, that mediates both chemical and light-driven oxidation of water efficiently under neutral conditions. The importance of the incorporation of the negatively charged ligand framework is manifested in the low redox potentials of the developed complex, which allows water oxidation to be driven by the mild one-electron oxidant [Ru(bpy)(3)](3+) (bpy = 2,2'-bipyridine). Furthermore, combined experimental and DFT studies provide insight into the mechanistic details of the catalytic cycle.

  • 2.
    Alam, Rauful
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Diner, Colin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Jonker, Sybrand
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Catalytic Asymmetric Allylboration of Indoles and Dihydroisoquinolines with Allylboronic Acids: Stereodivergent Synthesis of up to Three Contiguous Stereocenters2016Ingår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 55, nr 46, s. 14417-14421Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The catalytic asymmetric allylboration of cyclic imines with gamma,gamma-disubstituted allylboronic acids provides products with adjacent stereocenters in high yield and stereoselectivity. Various electrophiles, including 3,4-dihydroisoquinolines and indoles, were prenylated in a fully stereodivergent fashion by switching the E/Z geometry of the allylboronate and/or the enantiomer of the BINOL catalyst. 3-Methylindole provided products with three adjacent stereocenters with high stereoselectivity in one synthetic operation.

  • 3.
    Angles d'Ortoli, Thibault
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Assembling and Unraveling Carbohydrates Structures: Conformational analysis of synthesized branched oligosaccharides2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Advances in the elaboration of vaccines and enzyme inhibitors rely on acquiring more knowledge about protein-carbohydrate binding events. Furthermore, the relationships between biological function and the three-dimensional properties of large glycans can be studied by focusing on the structural components they contained, namely, by scaling down the system under analysis. Chemical methods are useful assets as they allow the isolation and determination of epitopes; these small and recognizable fragments that lead to very specific interactions. In this thesis, biologically relevant saccharides were obtained using recently developed concepts in carbohydrate synthesis and NMR spectroscopy was used to unravel their conformational preferences.

    In paper I, the convergent synthesis of the tetrasaccharide found in the natural product solaradixine is described. Reactivity enhanced disaccharide glycosyl donors were coupled to a disaccharide acceptor in a 2 + 2 fashion. The computer program CASPER was subsequently used to verify the synthesized structure.

    The conformation arming concept employed in paper I was further investigated in paper II. An NMR-based methodology enabled the determination of the ring conformations of a set of donors. Subsequently, glycosylation reactions were performed and yields were correlated to donors ring shapes. Perturbations in the rings shape caused by bulky silyl ether protective groups were sufficient to boost the potency of several donors. As a matter of fact, complex branched oligosaccharides could be obtained in good to excellent yields.

    In paper III, NMR spectroscopy observables were measured to elucidate the ring shape, the mutual orientation of the rings across the glycosidic bond and the positions of the side chains of 5 trisaccharides found in larger structures. With the aid of molecular dynamics simulations, their overall conformational propensities were revealed.

    Finally, the software CASPER prediction skills were improved by adding, inter alia, NMR information of synthesized mono- and disaccharides to its database. Unassigned chemical shifts from polysaccharides served as input to challenge its ability to solve large carbohydrate structures.

  • 4.
    Angles d'Ortoli, Thibault
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Synthesis of the tetrasaccharide glycoside moiety of Solaradixine and rapid NMR-based structure verification using the program CASPER2016Ingår i: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 72, nr 7, s. 912-927Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The major glycoalkaloid in the roots of Solanum laciniatum is Solaradixine having the branched tetrasaccharide beta-D-Glcp-(1 -> 2)-beta-D-Glcp-(1 -> 3)[alpha-L-Rhap-(1 -> 2)]-beta-D-Galp linked to O3 of the steroidal alkaloid Solasodine. We herein describe the synthesis of the methyl glycoside of the tetrasaccharide using a super-armed disaccharide as a donor molecule. A 2-(naphthyl)methyl protecting group was used in the synthesis of the donor since it was tolerant to a wide range of reaction conditions. The 6-O-benzylated-hexa-O-tert-butyldimethylsilyi-protected beta-D-Glcp-(1 -> 2)-beta-D-Glcp-SEt donor, which avoided 1,6-anydro formation, was successfully glycosylated at O3 of a galactoside acceptor molecule. However, subsequent glycosylation at O2 by a rhamnosyl donor was unsuccessful and instead a suitably protected alpha-L-Rhap(1 -> 2)-beta-D-Galp-OMe disaccharide was used as the acceptor molecule together with a super-armed beta-D-Glcp-(1 -> 2)-beta-D-Glcp-SEt donor in the glycosylation reaction, to give a tetrasaccharide in a yield of 55%, which after deprotection resulted in the target molecule, the structure of which was verified by the NMR chemical shift prediction program CASPER.

  • 5. Ashour, Radwa M.
    et al.
    Abdel-Magied, Ahmed F.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Nuclear Materials Authority, Egypt.
    Abdel-Khalek, Ahmed A.
    Helaly, O. S.
    Ali, M. M.
    Preparation and characterization of magnetic iron oxide nanoparticles functionalized by L-cysteine: Adsorption and desorption behavior for rare earth metal ions2016Ingår i: Journal of Environmental Chemical Engineering, ISSN 2160-6544, E-ISSN 2213-3437, Vol. 4, nr 3, s. 3114-3121Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this work, magnetic iron oxide nanoparticles functionalized with L-cysteine (Cys-Fe3O4 NPs) was synthesized and fully characterized by transmission electron microscopy (TEM), X-ray powder diffraction (XRD), Fourier transform infra-red (FTIR), thermogravimetric analysis (TGA) and zeta potential measurements. The synthesized Cys-Fe(3)O(4)NPs has been evaluated as a highly adsorbent for the adsorption of a mixture of four rare earths RE3+ ions (La3+, Nd3+, Gd3+ and Y3+) from digested monazite solutions. The influence of various factors on the adsorption efficiency such as, the contact time, sample pH, temperature, and concentration of the stripping solution were investigated. The results indicate that Cys-Fe3O4 NPs achieve high removal efficiency 96.7, 99.3, 96.5 and 87% for La3+, Nd3+, Gd3+ and Y3+ ions, respectively, at pH = 6 within 15 min, and the adsorbent affinity for metal ions was found to be in order of Nd3+ > La3+ > Gd3+ > Y3+ ions. Using the Langmuir model, a maximum adsorption capacity of La3+, Nd3+, Gd3+ and Y3+ at room temperature was found to be 71.5, 145.5, 64.5 and 13.6 mg g (1), respectively. The Langmuir isotherm and pseudo-second order model fitted much better than the other isotherms and kinetic models. The obtained results for the thermodynamic parameters confirmed the spontaneous and endothermic nature of the process. Moreover, the desorption was carried out with 0.1 M nitric acid solutions. In addition, Cys-Fe3O4 NPs can be used as a highly efficient adsorbent for the adsorption of La3+, Nd3+, Gd3+ and Y3+ ions from digested monazite solutions.

  • 6.
    Belhomme, Marie-Charlotte
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wang, Dong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Formation of C(sp(3))-C(sp(3)) Bonds by Palladium Catalyzed Cross-Coupling of alpha-Diazoketones and Allylboronic Acids2016Ingår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 18, nr 10, s. 2503-2506Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Palladium catalyzed cross-coupling of allylboronic acids with a-diazoketones was studied. The reaction selectively affords the linear allylic product. The reaction proceeds with formation of a new C(sp(3))-C(sp(3)) bond. The reaction was performed without an external oxidant, likely without the Pd-catalyst undergoing redox reactions.

  • 7. Bergenstråhle-Wohlert, Malin
    et al.
    Angles d'Ortoli, Thibault
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sjöberg, Nils A.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wohlert, Jakob
    On the anomalous temperature dependence of cellulose aqueous solubility2016Ingår i: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, Vol. 23, nr 4, s. 2375-2387Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The solubility of cellulose in water-based media is promoted by low temperature, which may appear counter-intuitive. An explanation to this phenomenon has been proposed that is based on a temperature-dependent orientation of the hydroxymethyl group. In this paper, this hypothesis is investigated using molecular dynamics computer simulations and NMR spectroscopy, and is discussed in conjunction with alternative explanations based on solvent–solute and solvent–solvent hydrogen bond formation respectively. It is shown that neither simulations nor experiments lend support to the proposed mechanism based on the hydroxymethyl orientation, whereas the two alternative explanations give rise to two distinct contributions to the hydration free energy of cellooligomers.

  • 8. Berglund, Jennie
    et al.
    Angles d'Ortoli, Thibault
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Vilaplana, Francisco
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bergenstråhle-Wohlert, Malin
    Lawoko, Martin
    Henriksson, Gunnar
    Lindström, Mikael
    Wohlert, Jakob
    A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility2016Ingår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 88, nr 1, s. 56-70Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by NMR spectroscopy. Three types of β-(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di- and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated and free energy maps of the φ - ψ space and hydrogen bonding patterns were obtained. The glycosidic linkage between Glc-Glc or Glc-Man (C-type) was the stiffest with mainly one probable conformation; the linkage from Man-Man or Man-Glc (M-type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl-units (X-type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of hemicelluloses’ function both in the cell wall and in technical products.

  • 9.
    Bermejo Gómez, Antonio
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Karolinska Universitetssjukhuset, Sweden; Karolinska Institutet, Sweden.
    Cortés González, Miguel A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Karolinska Institutet, Sweden.
    Lübcke, Marvin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Karolinska Institutet, Sweden.
    Johansson, Magnus J.
    Halldin, Christer
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Karolinska Insitutet, Sweden.
    Schou, Magnus
    Efficient DBU accelerated synthesis of F-18-labelled trifluoroacetamides2016Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 52, nr 97, s. 13963-13966Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nucleophilic F-18-fluorination of bromodifluoromethyl derivatives was performed using [F-18] Bu4NF in the presence of DBU(1,8-diazabicyclo[5.4.0]undec-7-ene). This novel procedure provided a diverse set of [F-18] trifluoroacetamides in good to excellent radiochemical conversions. A mechanism where DBU acts as organomediator in this transformation is proposed.

  • 10.
    Blomberg, Margareta R. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mechanism of Oxygen Reduction in Cytochrome c Oxidase and the Role of the Active Site Tyrosine2016Ingår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 55, nr 3, s. 489-500Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cytochrome c oxidase, the terminal enzyme in the respiratory chain, reduces molecular oxygen to water and stores the released energy through electrogenic chemistry and proton pumping across the membrane. Apart from the heme-copper binuclear center, there is a conserved tyrosine residue in the active site (BNC). The tyrosine delivers both an electron and a proton during the O-O bond cleavage step, forming a tyrosyl radical. The catalytic cycle then occurs in four reduction steps, each taking up one proton for the chemistry (water formation) and one proton to be pumped. It is here suggested that in three of the reduction steps the chemical proton enters the center of the BNC, leaving the tyrosine unprotonated with radical character. The reproprotonation of the tyrosine occurs first in the final reduction step before binding the next oxygen molecule. It is also suggested that this reduction mechanism and the presence of the tyrosine are essential for the proton pumping. Density functional theory calculations on large cluster models of the active site show that only the intermediates with the proton in the center of the BNC and with an unprotonated tyrosyl radical have a high electron affinity of similar size as the electron donor, which is essential for the ability to take up two protons per electron and thus for the proton pumping. This type of reduction mechanism is also the only one that gives a free energy profile in accordance with experimental observations for the amount of proton pumping in the working enzyme.

  • 11.
    Blomberg, Margareta R. A.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Improved free energy profile for reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR)2016Ingår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, nr 19, s. 1810-1818Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Quantum chemical calculations play an essential role in the elucidation of reaction mechanisms for redox-active metalloenzymes. For example, the cleavage and the formation of covalent bonds can usually not be described only on the basis of experimental information, but can be followed by the calculations. Conversely, there are properties, like reduction potentials, which cannot be accurately calculated. Therefore, computational and experimental data has to be carefully combined to obtain reliable descriptions of entire catalytic cycles involving electron and proton uptake from donors outside the enzyme. Such a procedure is illustrated here, for the reduction of nitric oxide (NO) to nitrous oxide and water in the membrane enzyme, cytochrome c dependent nitric oxide reductase (cNOR). A surprising experimental observation is that this reaction is nonelectrogenic, which means that no energy is conserved. On the basis of hybrid density functional calculations a free energy profile for the entire catalytic cycle is obtained, which agrees much better with experimental information on the active site reduction potentials than previous ones. Most importantly the energy profile shows that the reduction steps are endergonic and that the entire process is rate-limited by high proton uptake barriers during the reduction steps. This result implies that, if the reaction were electrogenic, it would become too slow when the gradient is present across the membrane. This explains why this enzyme does not conserve any of the free energy released.

  • 12.
    Bornschein, Christoph
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Universität Rostock, Germany.
    Gustafson, Karl P. J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Verho, Oscar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Beller, Matthias
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Evaluation of Fe and Ru Pincer-Type Complexes as Catalysts for the Racemization of Secondary Benzylic Alcohols2016Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 22, nr 33, s. 11583-11586Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fe and Ru pincer-type catalysts are used for the racemization of benzylic alcohols. Racemization with the Fe catalyst was achieved within 30 minutes under mild reaction conditions, with a catalyst loading as low as 2 mol %. This reaction constitutes the first example of an iron-catalyzed racemization of an alcohol. The efficiency for racemization of the Fe catalyst and its Ru analogue was evaluated for a wide range of sec-benzylic alcohols. The commercially available Ru complex proved to be highly robust and even tolerated the presence of water in the reaction mixture.

  • 13. Bunrit, Anon
    et al.
    Dahlstrand, Christian
    Srifa, Pemikar
    Olsson, Sandra K.
    Huang, Genping
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Tianjin University, China.
    Biswas, Srijit
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Samec, Joseph S. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Uppsala University, Sweden.
    Nucleophilic Substitution of the Hydroxyl Group in Stereogenic Alcohols with Chirality Transfer2016Ingår i: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, Vol. 27, nr 2, s. 173-176Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A brief overview of the development of direct substitution of the hydroxyl (OH) group of alcohols in our research group is presented. By applying a BrOnsted acid, an intramolecular substitution of the OH group in stereogenic alcohols with chirality transfer was achieved. Noteworthy, the intramolecular substitution has a wide scope in respect to both the nucleophile and also the nucleofuge. A mechanistic study by both experiments and DFT calculations revealed a unique reaction pathway in which the BrOnsted acid operates in a bifunctional manner to promote an S(N)2-type reaction mechanism.

  • 14.
    Bunrit, Anon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Uppsala University, Sweden.
    Sawadjoon, Supaporn
    Tšupova, Svetlana
    Sjöberg, Per J. R.
    Samec, Joseph S. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Uppsala University, Sweden.
    A General Route to beta-Substituted Pyrroles by Transition-Metal Catalysis2016Ingår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 81, nr 4, s. 1450-1460Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An atom-efficient route to pyrroles substituted in the beta-position has been achieved in four high yielding steps by a combination of Pd, Ru, and Fe catalysis with only water and ethene as side-products. The reaction is general and gives pyrroles substituted in the beta-position with linear and branched alkyl, benzyl, or aryl groups in overall good yields. The synthetic route includes a Pd-catalyzed monoallylation step of amines with substituted allylic alcohols that proceeds to yield the monoallylated products in moderate to excellent yields. In a second step, unsymmetrical diallylated aromatic amines are generated from the reaction of a second allylic alcohol with high selectivity in moderate to good yields by control of the reaction temperature. Ru-catalyzed ring-closing metathesis performed on the diallylated aromatic amines yields the pyrrolines substituted in the beta-position in excellent yields. By addition of ferric chloride to the reaction mixture, a selective aromatization to yield the corresponding pyrroles substituted in the beta-position was achieved. A reaction mechanism involving a palladium hydride, generated from insertion of palladium to O-H of an allyl alcohol, that is responsible for the C-O bond cleavage to generate the pi-allyl intermediate is proposed.

  • 15. Das, Biswanath
    et al.
    Lee, Bao-Lin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Karlsson, Erik A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Torbjörn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Shatskiy, Andrey
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Demeshko, Serhiy
    Liao, Rong-Zhen
    Laine, Tanja M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Haukka, Matti
    Zeglio, Erica
    Abdel-Magied, Ahmed F.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Meyer, Franc
    Kärkäs, Markus D.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Johnston, Eric V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Nordlander, Ebbe
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Water oxidation catalyzed by molecular di- and nonanuclear Fe complexes: importance of a proper ligand framework2016Ingår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 45, nr 34, s. 13289-13293Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The synthesis of two molecular iron complexes, a dinuclear iron(III,III) complex and a nonanuclear iron complex, based on the di-nucleating ligand 2,2'-(2-hydroxy-5-methyl-1,3-phenylene)bis(1H-benzo[d]imidazole-4-carboxylic acid) is described. The two iron complexes were found to drive the oxidation of water by the one-electron oxidant [Ru(bpy)(3)](3+).

  • 16.
    Daver, Henrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Das, Biswanath
    Nordlander, Ebbe
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Theoretical Study of Phosphodiester Hydrolysis and Transesterification Catalyzed by an Unsymmetric Biomimetic Dizinc Complex2016Ingår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 55, nr 4, s. 1872-1882Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Density functional theory calculations have been used to investigate the reaction mechanisms of phosphodiester hydrolysis and transesterification catalyzed by a dinuclear zinc complex of the 2-(N-isopropyl-N-((2-pyridyl)methyl)-aminomethyl)-6-(N-(carboxylmethyl)-N-((2-pyridyl)methyl)amino-methyl)-4-methylphenol (IPCPMP) ligand, mimicking the active site of zinc phosphotriesterase. The substrates bis(2,4)-dinitrophenyl phosphate (BDNPP) and 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) were employed as analogues of DNA and RNA, respectively. A number of different mechanistic proposals were considered, with the active catalyst harboring either one or two hydroxide ions. It is concluded that for both reactions the catalyst has only one hydroxide bound, as this option yields lower overall energy barriers. For BDNPP hydrolysis, it is suggested that the hydroxide acts as the nucleophile in the reaction, attacking the phosphorus center of the substrate. For HPNP transesterification, on the other hand, the hydroxide is proposed to act as a Bronsted base, deprotonating the alcohol moiety of the substrate, which in turn performs the nucleophilic attack. The calculated overall barriers are in good agreement with measured rates. Both reactions are found to proceed by essentially concerted associative mechanisms, and it is demonstrated that two consecutive catalytic cycles need to be considered in order to determine the rate-determining free energy barrier.

  • 17.
    Erbing, Elis
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Vazquez-Romero, Ana
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Gómez, Antonio Bermejo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Platero-Prats, Ana E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Carson, Fabian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Zou, Xiaodong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Tolstoy, Päivi
    Martín-Matute, Belén
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    General, Simple, and Chemoselective Catalysts for the Isomerization of Allylic Alcohols: The Importance of the Halide Ligand2016Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 22, nr 44, s. 15659-15663Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Remarkably simple Ir-III catalysts enable the isomerization of primary and sec-allylic alcohols under very mild reaction conditions. X-ray absorption spectroscopy (XAS) and mass spectrometry (MS) studies indicate that the catalysts, with the general formula [Cp*Ir-III], require a halide ligand for catalytic activity, but no additives or additional ligands are needed.

  • 18.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conde-Alvarez, Raquel
    Ståhle, Jonas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Holst, Otto
    Iriarte, Maite
    Zhao, Yun
    Arce-Gorvel, Vilma
    Hanniffy, Sean
    Gorvel, Jean-Pierre
    Moriyon, Ignacio
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural Studies of Lipopolysaccharide-defective Mutants from Brucella melitensis Identify a Core Oligosaccharide Critical in Virulence2016Ingår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 291, nr 14, s. 7727-7741Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The structures of the lipooligosaccharides from Brucella melitensis mutants affected in the WbkD and ManB(core) proteins have been fully characterized using NMR spectroscopy. The results revealed that disruption of wbkD gives rise to a rough lipopolysaccharide (R-LPS) with a complete core structure (beta-D-Glcp-(1 -> 4)-alpha-Kdop-(2 -> 4)[beta-D-GlcpN-(1 -> 6)-beta-D-GlcpN-(1 -> 4)[beta-D-GlcpN-(1 -> 6)]-beta-D-GlcpN-(1 -> 3)-alpha-D-Manp-(1 -> 5)]-alpha-Kdop-(2 -> 6)-beta-D-GlcpN3N4P-(1 -> 6)-alpha-D-GlcpN3N1P), in addition to components lacking one of the terminal beta-D-GlcpN and/or the beta-D-Glcp residues (48 and 17%, respectively). These structures were identical to those of the R-LPS from B. melitensis EP, a strain simultaneously expressing both smooth and R-LPS, also studied herein. In contrast, disruption of man-B-core gives rise to a deep-rough pentasaccharide core (beta-D-Glcp-(1 -> 4)-alpha-Kdop-(2 -> 4)-alpha-Kdop-(2 -> 6)-beta-D-GlcpN3N4P-(1 -> 6)-alpha-D-GlcpN3N1P) as the major component (63%), as well as a minor tetrasaccharide component lacking the terminal beta-D-Glcp residue (37%). These results are in agreement with the predicted functions of the WbkD (glycosyltransferase involved in the biosynthesis of the O-antigen) and ManB(core) proteins (phosphomannomutase involved in the biosynthesis of a mannosyl precursor needed for the biosynthesis of the core and O-antigen). We also report that deletion of B. melitensis wadC removes the core oligosaccharide branch not linked to the O-antigen causing an increase in overall negative charge of the remaining LPS inner section. This is in agreement with the mannosyltransferase role predicted for WadC and the lack of GlcpN residues in the defective core oligosaccharide. Despite carrying the O-antigen essential in B. melitensis virulence, the core deficiency in the wadC mutant structure resulted in a more efficient detection by innate immunity and attenuation, proving the role of the beta-D-GlcpN-(1 -> 6)-beta-D-GlcpN-(1 -> 4)[beta-D-GlcpN-(1 -> 6)]-beta-D-GlcpN-(1 -> 3)-alpha-D-Manp-(1 -> 5) structure in virulence.

  • 19.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zaccheus, Mona
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Ansaruzzaman, Mohammad
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of a polysaccharide from Vibrio parahaemolyticus strain AN-160002016Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 432, s. 41-49Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The structure of a polysaccharide from Vibrio parahaemolyticus strain AN-16000 has been investigated. The sugar and absolute configuration analysis revealed D-Glc, D-GalN, D-QuiN and L-FucN as major components. The PS was subjected to dephosphorylation with aqueous 40% HF to obtain an oligosaccharide that was analyzed by H-1 and C-13 NMR spectroscopy. The HR-MS spectrum of the oligosaccharide revealed a pentasaccharide composed of two Glc residues, one QuiNAc and one GalNAc, one FucNAc, as well as a glycerol moiety. The structure of the PS was determined using H-1, C-13, N-15 and P-31 NMR spectroscopy; inter-residue correlations were identified by H-1, C-13-heteronuclear multiple-bond correlation, H-1, H-1-NOESY and H-1, P-31-hetero-TOCSY experiments. The PS backbone has the following teichoic acid-like structure: -> 3)-D-Gro-(1-P-6)-beta-D-Glcp-(1 -> 4)-alpha-L-FucpNAc-(1 -> 3)-beta-D-QuipNAc-(1 -> with a side-chain consisting of alpha-D-Glcp-(1 -> 6)-alpha-D-GalpNAc-(1 -> linked to the O3 position of the FucNAc residue.

  • 20. Francois, Camille
    et al.
    Pourchet, Sylvie
    Boni, Gilles
    Fontaine, Stephane
    Gaillard, Yves
    Placet, Vincent
    Galkin, Maxim V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Orebom, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Samec, Joseph
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Plasseraud, Laurent
    Diglycidylether of iso-eugenol: a suitable lignin-derived synthon for epoxy thermoset applications2016Ingår i: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 6, nr 73, s. 68732-68738Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A novel lignin-based synthon, diglycidylether of iso-eugenol (DGE-isoEu) is used as a prepolymer for the preparation of thermosetting resins. DGE-isoEu is synthesized in a two-step procedure with a satisfactory yield from bio-based iso-eugenol (isoEu, 2-methoxy-4-(1-propenyl)phenol) catalytically fragmented from lignin in an organosolv process. DGE-isoEu was fully characterized by NMR, MS and FTIR. Curing of the DGE-isoEu monomer has then been investigated in the presence of several carboxylic acid derivatives hardeners. The thermal and mechanical properties of each material were recorded showing, in particular, a high T-g and instantaneous modulus values in the range of 78-120 degrees C and 4.6-5.5 GPa, respectively. The lignin derived new materials give very attractive thermo-mechanical properties comparable to that of common BPA-containing epoxy resins.

  • 21.
    Galkin, Maxim V.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Samec, Joseph S. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Lignin Valorization through Catalytic Lignocellulose Fractionation: A Fundamental Platform for the Future Biorefinery2016Ingår i: ChemSusChem, ISSN 1864-5631, E-ISSN 1864-564X, Vol. 9, nr 13, s. 1544-1558Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Current processes for the fractionation of lignocellulosic biomass focus on the production of high-quality cellulosic fibers for paper, board, and viscose production. The other fractions that constitute a major part of lignocellulose are treated as waste or used for energy production. The transformation of lignocellulose beyond paper pulp to a commodity (e.g., fine chemicals, polymer precursors, and fuels) is the only feasible alternative to current refining of fossil fuels as a carbon feedstock. Inspired by this challenge, scientists and engineers have developed a plethora of methods for the valorization of biomass. However, most studies have focused on using one single purified component from lignocellulose that is not currently generated by the existing biomass fractionation processes. A lot of effort has been made to develop efficient methods for lignin depolymerization. The step to take this fundamental research to industrial applications is still a major challenge. This review covers an alternative approach, in which the lignin valorization is performed in concert with the pulping process. This enables the fractionation of all components of the lignocellulosic biomass into valorizable streams. Lignocellulose fractions obtained this way (e.g., lignin oil and glucose) can be utilized in a number of existing procedures. The review covers historic, current, and future perspectives, with respect to catalytic lignocellulose fractionation processes.

  • 22.
    Galkin, Maxim V.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Smit, Arjan T.
    Subbotina, Elena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Artemenko, Konstantin A.
    Bergquist, Jonas
    Huijgen, Wouter J. J.
    Samec, Joseph S. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Hydrogen-free catalytic fractionation of woody biomass2016Ingår i: ChemSusChem, ISSN 1864-5631, E-ISSN 1864-564X, Vol. 9, nr 23, s. 3280-3287Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The pulping industry could become a biorefinery if the lignin and hemicellulose components of the lignocellulose are valorized. Conversion of lignin into well-defined aromatic chemicals is still a major challenge. Lignin depolymerization reactions often occur in parallel with irreversible condensation reactions of the formed fragments. Here, we describe a strategy that markedly suppresses the undesired condensation pathways and allows to selectively transform lignin into a few aromatic compounds. Notably, applying this strategy to woody biomass at organosolv pulping conditions, the hemicellulose, cellulose, and lignin were separated and in parallel the lignin was transformed into aromatic monomers. In addition, we were able to utilize a part of the lignocellulose as an internal source of hydrogen for the reductive lignin transformations. We hope that the presented methodology will inspire researchers in the field of lignin valorization as well as pulp producers to develop more efficient biomass fractionation processes in the future.

  • 23. Hammarström, Lars G. J.
    et al.
    Harmel, Robert K.
    Granath, Mikael
    Ringom, Rune
    Gravenfors, Ylva
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Färnegårdh, Katarina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Svensson, Per H.
    Wennman, David
    Lundin, Göran
    Roddis, Ylva
    Kitambi, Satish S.
    Bernlind, Alexandra
    Lehmann, Fredrik
    Ernfors, Patrik
    The Oncolytic Efficacy and in Vivo Pharmacokinetics of [2-(4-Chlorophenyl)quinolin-4-yl](piperidine-2-yl)methanol (Vacquinol-1) Are Governed by Distinct Stereochemical Features2016Ingår i: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 59, nr 18, s. 8577-8592Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Glioblastoma remains an incurable brain cancer. Drugs developed in the past 20 years have not improved the prognosis for patients, necessitating the development of new treatments. We have previously reported the therapeutic potential of the quinoline methanol Vacquinol-1 (1) that targets glioblastoma cells and induces cell death by catastrophic vacuolization. Compound 1 is a mixture of four stereoisomers due to the two adjacent stereogenic centers in the molecule, complicating further development in the preclinical setting. This work describes the isolation and characterization of the individual isomers of 1 and shows that these display stereospecific pharmacokinetic and pharmacodynamic features. In addition, we present a stereoselective synthesis of the active isomers, providing a basis for further development of this compound series into a novel experimental therapeutic for glioblastoma.

  • 24.
    Ilchenko, Nadia O.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cortes, Miguel A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Palladium-Catalyzed lodofluorination of Alkenes Using Fluorolodoxole Reagent2016Ingår i: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 6, nr 1, s. 447-450Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The application of an air- and moisture-stable fluoroiodane reagent was investigated in the palladium-catalyzed iodofluorination reaction of alkenes. Both the iodo and fluoro substituents arise from the fluoroiodane reagent. In the case of certain palladium catalysts, the alkene substrates undergo allylic rearrangement prior to the iodofluorination process. The reaction is faster for electron-rich alkenes than for electron-deficient ones.

  • 25.
    Jiang, Tuo
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Quan, Xu
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zhu, Can
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Andersson, Pher G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Palladium-Catalyzed Oxidative Synthesis of a-Acetoxylated Enones from Alkynes2016Ingår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 55, nr 19, s. 5824-5828Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report a palladium-catalyzed oxidative functionalization of alkynes to generate -acetoxylated enones in one step. A range of functional groups are well-tolerated in this reaction. Mechanistic studies, including the use of O-18-labeled DMSO, revealed that the ketone oxygen atom in the product originates from DMSO.

  • 26. Kaderavek, Pavel
    et al.
    Zapletal, Vojtech
    Fiala, Radovan
    Srb, Pavel
    Padrta, Petr
    Precechtelova, Jana Pavlikova
    Soltesova, Maria
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Chmelik, Josef
    Sklenar, Vladimir
    Zidek, Lukas
    Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies2016Ingår i: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 266, s. 23-40Artikel i tidskrift (Refereegranskat)
    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.

  • 27. Kang, Yu
    et al.
    Gohlke, Ulrich
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Hamark, Christoffer
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Scheidt, Tom
    Kunstrnann, Sonja
    Heinemann, Udo
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Santer, Mark
    Barbirz, Stefanie
    Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions2016Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 138, nr 29, s. 9109-9118Artikel i tidskrift (Refereegranskat)
    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.

  • 28. Kazemi, Masoud
    et al.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Aqvist, Johan
    Peptide Release on the Ribosome Involves Substrate-Assisted Base Catalysis2016Ingår i: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 6, nr 12, s. 8432-8439Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Termination of protein synthesis on the ribosome involves hydrolysis of the ester bond between the P-site tRNA and the nascent peptide chain. This reaction occurs in the peptidyl transferase center and is triggered by the class I release factors RF1 and RF2 in prokaryotes. Peptidyl-tRNA hydrolysis is pH-dependent, and experimental results suggest that an ionizable group with pK(a) > 9 is involved in the reaction. The nature of this group is, however, unknown. To resolve this problem, we conducted density functional theory calculations using a large cluster model of the peptidyl transferase center. Our calculations reveal that peptidyl-tRNA hydrolysis occurs via a base-catalyzed mechanism with a predicted activation energy of 15.8 kcal mol(-1), which is in good agreement with experimental data. In this mechanism, the P-site A76 2'-OH group is deprotonated and acts as the general base by activating the nucleophilic water molecule. The energy cost of deprotonating the 2'-hydroxyl group at pH 7.5 is estimated to be about 8 kcal mo1(-1), on the basis of its experimental plc in aqueous solution, and this step is predicted to be the source of the observed pH dependence. The proposed mechanism is consistent not only with experimentally derived activation energies but also with the observed kinetic solvent isotope effect.

  • 29. Kazemi, Masoud
    et al.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åqvist, Johan
    Enzyme catalysis by entropy without Circe effect2016Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, nr 9, s. 2406-2411Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Entropic effects have often been invoked to explain the extraordinary catalytic power of enzymes. In particular, the hypothesis that enzymes can use part of the substrate-binding free energy to reduce the entropic penalty associated with the subsequent chemical transformation has been very influential. The enzymatic reaction of cytidine deaminase appears to be a distinct example. Here, substrate binding is associated with a significant entropy loss that closely matches the activation entropy penalty for the uncatalyzed reaction inwater, whereas the activation entropy for the rate-limiting catalytic step in the enzyme is close to zero. Herein, we report extensive computer simulations of the cytidine deaminase reaction and its temperature dependence. The energetics of the catalytic reaction is first evaluated by density functional theory calculations. These results are then used to parametrize an empirical valence bond description of the reaction, which allows efficient sampling by molecular dynamics simulations and computation of Arrhenius plots. The thermodynamic activation parameters calculated by this approach are in excellent agreement with experimental data and indeed show an activation entropy close to zero for the rate-limiting transition state. However, the origin of this effect is a change of reaction mechanism compared the uncatalyzed reaction. The enzyme operates by hydroxide ion attack, which is intrinsically associated with a favorable activation entropy. Hence, this has little to do with utilization of binding free energy to pay the entropic penalty but rather reflects how a preorganized active site can stabilize a reaction path that is not operational in solution.

  • 30.
    Kessler, Simon N.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Iron-catalyzed Cross-Coupling of Propargyl Carboxylates and Grignard Reagents: Synthesis of Substituted Allenes2016Ingår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 55, nr 11, s. 3734-3738Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Presented herein is a mild, facile, and efficient iron-catalyzed synthesis of substituted allenes from propargyl carboxylates and Grignard reagents. Only 1-5mol% of the inexpensive and environmentally benign [Fe(acac)(3)] at -20 degrees C was sufficient to afford a broad range of substituted allenes in excellent yields. The method tolerates a variety of functional groups.

  • 31.
    Kessler, Simon N.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Hundemer, Fabian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Stockholm Univ, Arrhenius Lab, Dept Organ Chem, SE-10691 Stockholm, Sweden.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    A Synthesis of Substituted alpha-Allenols via Iron-Catalyzed Cross-Coupling of Propargyl Carboxylates with Grignard Reagents2016Ingår i: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 6, nr 11, s. 7448-7451Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    alpha-Allenols are attractive and versatile compounds whose preparation can be a nontrivial task. In this Letter, we provide a method for the prompt synthesis of substituted alpha-allenols via a catalytic cross-coupling reaction which makes use of a nontoxic and cost-effective iron catalyst. The catalyst loading is typically as low as 1-5 mol %. The mild reaction conditions (-20 degrees C) and the short reaction time (15 min) allow for the presence of a variety of functional groups. Moreover, the reaction was shown to be scalable up to gram scale and the propargyl substrates are readily accessible by a one-pot synthesis.

  • 32. Kim, Seonghoon
    et al.
    Patel, Dhilon-S.
    Park, Soohyung
    Slusky, Joanna
    Klauda, Jeffery B.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Im, Wonpil
    Bilayer Properties of Lipid A from Various Gram-Negative Bacteria2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 111, nr 8, s. 1750-1760Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Lipid A is the lipid anchor of a lipopolysaccharide in the outer leaflet of the outer membrane of Gram-negative bacteria. In general, lipid A consists of two phosphorylated N-acetyl glucosamine and several acyl chains that are directly linked to the two sugars. Depending on the bacterial species and environments, the acyl chain number and length vary, and lipid A can be chemically modified with phosphoethanolamine, aminoarabinose, or glycine residues, which are key to bacterial pathogenesis. In this work, homogeneous lipid bilayers of 21 distinct lipid A types from 12 bacterial species are modeled and simulated to investigate the differences and similarities of their membrane properties. In addition, different neutralizing ion types (Ca2+, K+, and Na+) are considered to examine the ion's influence on the membrane properties. The trajectory analysis shows that (1) the area per lipid is mostly correlated to the acyl chain number, and the area per lipid increases as a function of the acyl chain number; (2) the hydrophobic thickness is mainly determined by the average acyl chain length with slight dependence on the acyl chain number, and the hydrophobic thickness generally increases with the average acyl chain length; (3) a good correlation is observed among the area per lipid, hydrophobic thickness, and acyl chain order; and (4) although the influence of neutralizing ion types on the area per lipid and hydrophobic thickness is minimal, Ca2+ stays longer on the membrane surface than K+ or Na+, consequently leading to lower lateral diffusion and a higher compressibility modulus, which agrees well with available experiments.

  • 33. Kuttel, Michelle M.
    et al.
    Ståhle, Jonas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures2016Ingår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, nr 22, s. 2098-2105Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    CarbBuilder is a portable software tool for producing three-dimensional molecular models of carbohydrates from the simple text specification of a primary structure. CarbBuilder can generate a wide variety of carbohydrate structures, ranging from monosaccharides to large, branched polysaccharides. Version 2.0 of the software, described in this article, supports monosaccharides of both mammalian and bacterial origin and a range of substituents for derivatization of individual sugar residues. This improved version has a sophisticated building algorithm to explore the range of possible conformations for a specified carbohydrate molecule. Illustrative examples of models of complex polysaccharides produced by CarbBuilder demonstrate the capabilities of the software. CarbBuilder is freely available under the Artistic License 2.0.

  • 34.
    Kärkäs, Markus D.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Liao, Rong-Zhen
    Laine, Tanja M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Torbjörn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ghanem, Shams
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Molecular ruthenium water oxidation catalysts carrying non-innocent ligands: mechanistic insight through structure-activity relationships and quantum chemical calculations2016Ingår i: Catalysis Science & Technology, ISSN 2044-4753, E-ISSN 2044-4761, Vol. 6, nr 5, s. 1306-1319Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Robust catalysts that mediate H2O oxidation are of fundamental importance for the development of novel carbon-neutral energy technologies. Herein we report the synthesis of a group of single-site Ru complexes. Structure-activity studies revealed that the individual steps in the oxidation of H2O depended differently on the electronic properties of the introduced ligand substituents. The mechanistic details associated with these complexes were investigated experimentally along with quantum chemical calculations. It was found that O-O bond formation for the developed Ru complexes proceeds via high-valent Ru-VI species, where the capability of accessing this species is derived from the non-innocent ligand architecture. This cooperative catalytic involvement and the ability of accessing Ru-VI are intriguing and distinguish these Ru catalysts from a majority of previously reported complexes, and might generate unexplored reaction pathways for activation of small molecules such as H2O.

  • 35.
    Kärkäs, Markus D.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Catalytic Water Oxidation by Ruthenium Complexes Containing Negatively Charged Ligand Frameworks2016Ingår i: The chemical record, ISSN 1527-8999, E-ISSN 1528-0691, Vol. 16, nr 2, s. 940-963Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Artificial photosynthesis represents an attractive way of converting solar energy into storable chemical energy. The H2O oxidation half-reaction, which is essential for producing the necessary reduction equivalents, is an energy-demanding transformation associated with a high kinetic barrier. Herein we present a couple of efficient Ru-based catalysts capable of mediating this four-proton-four-electron oxidation. We have focused on the incorporation of negatively charged ligands, such as carboxylate, phenol, and imidazole, into the catalysts to decrease the redox potentials. This account describes our work in designing Ru catalysts based on this idea. The presence of the negatively charged ligands is crucial for stabilizing the metal centers, allowing for light-driven H2O oxidation. Mechanistic details associated with the designed catalysts are also presented.

  • 36.
    Kärkäs, Markus D.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Water oxidation using earth-abundant transition metal catalysts: opportunities and challenges2016Ingår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 45, nr 37, s. 14421-14461Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Catalysts for the oxidation of H2O are an integral component of solar energy to fuel conversion technologies. Although catalysts based on scarce and precious metals have been recognized as efficient catalysts for H2O oxidation, catalysts composed of inexpensive and earth-abundant element(s) are essential for realizing economically viable energy conversion technologies. This Perspective summarizes recent advances in the field of designing homogeneous water oxidation catalysts (WOCs) based on Mn, Fe, Co and Cu. It reviews the state of the art catalysts, provides insight into their catalytic mechanisms and discusses future challenges in designing bioinspired catalysts based on earth-abundant metals for the oxidation of H2O.

  • 37.
    Laine, Tanja M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Development of Ruthenium Catalysts for Water Oxidation2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    An increasing global energy demand requires alternative fuel sources. A promising method is artificial photosynthesis. Although, the artificial processes are different from the natural photosynthetic process, the basic principles are the same, i.e. to split water and to convert solar energy into chemical energy. The energy is stored in bonds, which can at a later stage be released upon combustion. The bottleneck in the artificial systems is the water oxidation. The aim of this research has been to develop catalysts for water oxidation that are stable, yet efficient. The molecular catalysts are comprised of organic ligands that ultimately are responsible for the catalyst structure and activity. These ligands are often based on polypyridines or other nitrogen-containing aromatic compounds. This thesis describes the development of molecular ruthenium catalysts and the evaluation of their ability to mediate chemical and photochemical oxidation of water. Previous work from our group has shown that the introduction of negatively charged groups into the ligand frameworks lowers the redox potentials of the metal complexes. This is beneficial as it makes it possible to drive water oxidation with [Ru(bpy)3]3+-type oxidants (bpy = 2,2’-bipyridine), which can be photochemically generated from the corresponding [Ru(bpy)3]2+ complex. Hence, all the designed ligands herein contain negatively charged groups in the coordination site for ruthenium.

    The first part of this thesis describes the development of two mononuclear ruthenium complexes and the evaluation of these for water oxidation. Both complexes displayed low redox potentials, allowing for water oxidation to be driven either chemically or photochemically using the mild one-electron oxidant [Ru(bpy)3]3+.

    The second part is a structure–activity relationship study on several analogues of mononuclear ruthenium complexes. The complexes were active for water oxidation and the redox potentials of the analogues displayed a linear relationship with the Hammet σmeta parameter. It was also found that the complexes form high-valent Ru(VI) species, which are responsible for mediating O–O bond formation.

    The last part of the thesis describes the development of a dinuclear ruthenium complex and the catalytic performance for chemical and photochemical water oxidation. It was found that the complex undergoes O–O bond formation via a bridging peroxide intermediate, i.e. an I2M–type mechanism.

  • 38. Li, Jia-Qi
    et al.
    Liu, Jianguo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Krajangsri, Suppachai
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Chumnanvej, Napasawan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Singh, Thishana
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Andersson, Pher G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Asymmetric Hydrogenation of Allylic Alcohols Using Ir-N,P-Complexes2016Ingår i: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 6, nr 12, s. 8342-8349Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study, a series of gamma,gamma-disubstituted and beta,gamma-disubstituted allylic alcohols were prepared and successfully hydrogenated using suitable N,P-based Ir complexes. High yields and excellent enantioselectivities were obtained for most of the substrates studied. This investigation also revealed the effect of the acidity of the N,P-Ir-complexes on the acid sensitive allylic alcohols. DFT Delta pK(a) calculations were used to explain the effect of the N,P-ligand on the acidity of the corresponding Ir-complex. The selectivity model of the reaction was used to accurately predict the absolute configuration of the hydrogenated alcohols.

  • 39. Liao, Rong-Zhen
    et al.
    Chen, Shi-Lu
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Unraveling the Mechanism and Regioselectivity of the B12-Dependent Reductive Dehalogenase PceA2016Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 22, nr 35, s. 12391-12399Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    PceA is a cobalamin-dependent reductive dehalogenase that catalyzes the dechlorination of perchloroethylene to trichloroethylene and then to cis-dichloroethylene as the sole final product. The reaction mechanism and the regioselectivity of this enzyme are investigated by using density functional calculations. Four different substrates, namely, perchloroethylene, trichloroethylene, cis-dichloroethylene, and chlorotheylene, have been considered and were found to follow the same reaction mechanism pattern. The reaction starts with the reduction of Co-II to Co-I through a proton-coupled electron transfer process, with the proton delivered to a Tyr246 anion. This is followed by concerted C-Cl bond heterolytic cleavage and proton transfer from Tyr246 to the substrate carbon atom, generating a Co-III-Cl intermediate. Subsequently, a one-electron transfer leads to the formation of the Co-II-Cl product, from which the chloride and the dehalogenated product can be released from the active site. The substrate reactivity follows the trend perchloroethylene>trichloroethylene >> cis-dichloroethylene >> chlorotheylene. The barriers for the latter two substrates are significantly higher compared with those for perchloroethylene and trichloroethylene, implying that PceA does not catalyze their degradation. In addition, the formation of cis-dichloroethylene has a lower barrier by 3.8kcalmol(-1) than the formation of trans-dichloroethylene and 1,1-dichloroethylene, reproducing the regioselectivity. These results agree quite well with the experimental findings, which show cis-dichloroethylene as the sole product in the PceA-catalyzed dechlorination of perchloethylene and trichloroethylene.

  • 40. Liao, Rong-Zhen
    et al.
    Santoro, Stefano
    Gotsev, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Marcelli, Tommaso
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Origins of Stereoselectivity in Peptide-Catalyzed Kinetic Resolution of Alcohols2016Ingår i: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 6, nr 2, s. 1165-1171Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The origin of the stereoselectivity of the tetrapeptide-catalyzed kinetic resolution of trans-2-N-acetamidocyclohexanol is investigated by means of density functional theory calculations. Transition states for the functionalization of both (R,R) and (S,S) substrates were optimized considering all possible conformers. Due to the flexibility of the peptidic catalyst, a large number of transition states had to be located, and analysis of the geometries and energies allowed for the identification of the main factors that control the stereo selectivity.

  • 41.
    Lind, Maria E. S.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Quantum Chemical Modeling of Enantioconvergency in Soluble Epoxide Hydrolase2016Ingår i: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 6, nr 12, s. 8145-8155Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Soluble epoxide hydrolases (sEHs) catalyze the hydrolysis of epoxides to their corresponding vicinal diols. One property of a number of these enzymes is that they can catalyze the hydrolysis of some racemic substrates in an enantioconvergent one-enzyme fashion. Here, we have used the dispersion-corrected B3LYP-D3 density functional theory method to investigate the enantioconvergent conversion of styrene oxide (SO) by sEH from Solanum tuberosum (StEH1). A large cluster model of the active site, consisting of 279 atoms, is designed on the basis of the X-ray crystal structure of StEH1 in complex with the competitive inhibitor valpromide. Different substrate orientations of the two enantiomers of SO are examined, and the full reaction mechanisms for epoxide opening at the two carbons are calculated, including both the alkylation and hydrolysis half-reactions. The calculated overall reaction energy profiles show that the rate-determining step is associated with the dissociation of the covalent intermediate, which is the second step of the hydrolysis half-reaction. The calculations reproduce the experimentally observed regioselectivities for the two enantiomers of the substrate, in that both (S)-SO and (R)-SO are calculated to yield the same (R)-diol product. The obtained energy profiles indicate that the transition states for both the alkylation and hydrolysis half-reactions have to be taken into account in order to understand the stereochemical outcome of the reaction. The transition state structures are analyzed in detail, and several factors that contribute to the selectivity control are identified. In addition, the mechanistic scenario in which the active site His300 residue is in the protonated form is also considered and the implications on the energies and enantioselection are discussed. The current calculations demonstrate the applicability of the quantum chemical cluster methodology in reproducing and rationalizing experimental enantioselectivities, lending further support to its usefulness as a tool in asymmetric biocatalysis. The results presented here can be helpful in the rational engineering of sEHs to obtain variants with refined biocatalytic properties.

  • 42.
    Lindstedt, Erik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stridfeldt, Elin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Olofsson, Berit
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mild Synthesis of Sterically Congested Alkyl Aryl Ethers2016Ingår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 18, nr 17, s. 4234-4237Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An efficient and transition-metal-free method is presented to access tertiary alkyl aryl ethers by arylation of tertiary alcohols with ortho-substituted diaryliodonium salts. The scope covers cyclic and acyclic aliphatic, benzylic, allylic, and propargylic tertiary alcohols as well as primary and secondary fluorinated alcohols. The methodology gives access to alkyl aryl ethers of previously unprecedented steric congestion. Furthermore, the versatility of the developed procedure was demonstrated by arylation of the pro-drug mestranol.

  • 43.
    Lundberg, Helena
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Adolfsson, Hans
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Catalytic α-Alkylation/Reduction of Ketones with Primary Alcohols To Furnish Secondary Alcohols2016Ingår i: Synthesis (Stuttgart), ISSN 0039-7881, E-ISSN 1437-210X, Vol. 48, nr 5, s. 644-652Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    The formation of secondary alcohol products via a tandem -alkylation/transfer hydrogenation of ketones with primary alcohols is a little explored reaction with unrealized potential for green synthesis. This review covers the current literature in the field, including asymmetric versions of the reaction, and outlines future possibilities and challenges for the methodology. 1 Introduction 2 Formation of Racemic Alcohols 3 Formation of Enantiomerically Enriched Alcohols 4 Conclusions

  • 44. Margalef, Jèssica
    et al.
    Slagbrand, Tove
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Tinnis, Fredrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Adolfsson, Hans
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Umeå University, Sweden.
    Diéguez, Montserrat
    Pàmies, Oscar
    Third-Generation Amino Acid Furanoside-Based Ligands from d-Mannose for the Asymmetric Transfer Hydrogenation of Ketones: Catalysts with an Exceptionally Wide Substrate Scope2016Ingår i: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 358, nr 24, s. 4006-4018Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A modular ligand library of -amino acid hydroxyamides and thioamides was prepared from 10 different N-tert-butyloxycarbonyl-protected -amino acids and three different amino alcohols derived from 2,3-O-isopropylidene--d-mannofuranoside. The ligand library was evaluated in the half-sandwich ruthenium- and rhodium-catalyzed asymmetric transfer hydrogenation of a wide array of ketone substrates, including simple as well as sterically demanding aryl alkyl ketones, aryl fluoroalkyl ketones, heteroaromatic alkyl ketones, aliphatic, conjugated and propargylic ketones. Under the optimized reaction conditions, secondary alcohols were obtained in high yields and in enantioselectivities up to >99%. The choice of ligand/catalyst allowed for the generation of both enantiomers of the secondary alcohols, where the ruthenium-hydroxyamide and the rhodium-thioamide catalysts act complementarily towards each other. The catalytic systems were also evaluated in the tandem isomerization/asymmetric transfer hydrogenation of racemic allylic alcohols to yield enantiomerically enriched saturated secondary alcohols in up to 98% ee. Furthermore, the catalytic tandem -alkylation/asymmetric transfer hydrogenation of acetophenones and 3-acetylpyridine with primary alcohols as alkylating and reducing agents was studied. Secondary alcohols containing an elongated alkyl chain were obtained in up to 92% ee.

  • 45.
    Martinez-Erro, Samuel
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sanz-Marco, Amparo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Gómez, Antonio Bermejo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Vazquez-Romero, Ana
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ahlquist, Mårten S. G.
    Martin-Matute, Belén
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Base-Catalyzed Stereospecific Isomerization of Electron-Deficient Allylic Alcohols and Ethers through Ion-Pairing2016Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 138, nr 40, s. 13408-13414Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A mild base-catalyzed strategy for the isomerization of allylic alcohols and allylic ethers has been developed. Experimental and computational investigations indicate that transition metal catalysts are not required when basic additives are present. As in the case of using transition metals under basic conditions, the isomerization catalyzed solely by base also follows a stereospecific pathway. The reaction is initiated by a rate-limiting deprotonation. Formation of an intimate ion pair between an allylic anion and the conjugate acid of the base results in efficient transfer of chirality. Through this mechanism, stereochemical information contained in the allylic alcohols is transferred to the ketone products. The stereospecific isomerization is also applicable for the first time to allylic ethers, yielding synthetically valuable enantioenriched (up to 97% ee) enol ethers.

  • 46.
    Mendoza, Abraham
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Colas, Kilian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Suarez-Pantiga, Samuel
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Götz, Daniel C. G.
    Johansson, Magnus J.
    Chemical Innovation through Ligand Total Synthesis2016Ingår i: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, Vol. 27, nr 12, s. 1753-1759Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Natural products are an abundant source of synthetic challenges that foster crucial breakthroughs in organic chemistry. Despite the superior complexity of these targets, ligand total synthesis can inspire solutions to unsolved chemical problems and provide access to creative catalyst designs. This Synpacts article presents a comparative analysis of natural and ligand total synthesis to provide a context for our recent research and motivate the importance of future undertakings in this area.

  • 47. Miralles, Nuria
    et al.
    Alam, Rauful
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Fernandez, Elena
    Transition-Metal-Free Borylation of Allylic and Propargylic Alcohols2016Ingår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 55, nr 13, s. 4303-4307Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The base-catalyzed allylic borylation of tertiary allylic alcohols allows the synthesis of 1,1-disubstituted allyl boronates, in moderate to high yield. The unexpected tandem performance of the Lewis acid-base adduct, [Hbase](+)[MeO-B(2)pin(2)](-) favored the formation of 1,2,3-triborylated species from the tertiary allylic alcohols and 1-propargylic cyclohexanol at 90 degrees C.

  • 48.
    Muheim, Claudio
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Bakali, Amin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wieslander, Åke
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Daley, Daniel O.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Identification of a Fragment-Based Scaffold that Inhibits the Glycosyltransferase WaaG from Escherichia coli2016Ingår i: Antibiotics, ISSN 0066-4774, E-ISSN 2079-6382, Vol. 5, nr 1Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    WaaG is a glycosyltransferase that is involved in the biosynthesis of lipopolysaccharide in Gram-negative bacteria. Inhibitors of WaaG are highly sought after as they could be used to inhibit the biosynthesis of the core region of lipopolysaccharide, which would improve the uptake of antibiotics. Herein, we establish an activity assay for WaaG using C-14-labeled UDP-glucose and LPS purified from a increment waaG strain of Escherichia coli. We noted that addition of the lipids phosphatidylglycerol (PG) and cardiolipin (CL), as well as the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) increased activity. We then use the assay to determine if three molecular scaffolds, which bind to WaaG, could inhibit its activity in vitro. We show that 4-(2-amino-1,3-thiazol-4-yl)phenol inhibits WaaG (IC50 1.0 mM), but that the other scaffolds do not. This study represents an important step towards an inhibitor of WaaG by fragment-based lead discovery.

  • 49.
    Nagendiran, Anuja
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Pascanu, Vlad
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bermejo Gómez, Antonio
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    González Miera, Greco
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Tai, Cheuk-Wai
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Verho, Oscar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Martín-Matute, Belén
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mild and Selective Catalytic Hydrogenation of the C=C Bond in a,b-Unsaturated Carbonyl Compounds Using Supported Palladium Nanoparticles2016Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 22, nr 21, s. 7184-7189Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Chemoselective reduction of the C=C bond in a variety of α,β-unsaturated carbonyl compounds using supported palladium nanoparticles is reported. Three different heterogeneous catalysts were compared using 1 atm of H2: 1) nano-Pd on a metal–organic framework (MOF: Pd0-MIL-101-NH2(Cr)), 2) nano-Pd on a siliceous mesocellular foam (MCF: Pd0-AmP-MCF), and 3) commercially available palladium on carbon (Pd/C). Initial studies showed that the Pd@MOF and Pd@MCF nanocatalysts were superior in activity and selectivity compared to commercial Pd/C. Both Pd0-MIL-101-NH2(Cr) and Pd0-AmP-MCF were capable of delivering the desired products in very short reaction times (10–90 min) with low loadings of Pd (0.5–1 mol %). Additionally, the two catalytic systems exhibited high recyclability and very low levels of metal leaching.

  • 50.
    Nagendiran, Anuja
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sörensen, Henrik
    Johansson, Magnus J.
    Tai, Cheuk-Wai
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Nanopalladium-catalyzed conjugate reduction of Michael acceptors - application in flow2016Ingår i: Green Chemistry, ISSN 1463-9262, E-ISSN 1463-9270, Vol. 18, nr 9, s. 2632-2637Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A continuous-flow approach towards the selective nanopalladium-catalyzed hydrogenation of the olefinic bond in various Michael acceptors, which could lead to a greener and more sustainable process, has been developed. The nanopalladium is supported on aminofunctionalized mesocellular foam. Both aromatic and aliphatic substrates, covering a variation of functional groups such as acids, aldehydes, esters, ketones, and nitriles were selectively hydrogenated in high to excellent yields using two different flow-devices (H-Cube (R) and Vapourtec). The catalyst was able to hydrogenate cinnamaldehyde continuously for 24 h (in total hydrogenating 19 g cinnanmaldehyde using 70 mg of catalyst in the H-cube (R)) without showing any significant decrease in activity or selectivity. Furthermore, the metal leaching of the catalyst was found to be very low (ppb amounts) in the two flow devices.

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