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  • 1.
    Agrawal, Santosh
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martínez-Castro, Elisa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Marcos, Rocio
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martín-Matute, Belén
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Readily Available Ruthenium Complex for Efficient Dynamic Kinetic Resolution of Aromatic alpha-Hydroxy Ketones2014In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 16, no 8, p. 2256-2259Article in journal (Refereed)
    Abstract [en]

    A ruthenium complex formed from commercially available [Ru(p-cymene)Cl-2](2) and 1,4-bis(diphenylphosphino)butane catalyzes the racemization of aromatic alpha-hydroxy ketones very efficiently at room temperature. The racemization is fully compatible with a kinetic resolution catalyzed by a lipase from Pseudomonas stutzeri. This is the first example of dynamic kinetic resolution of alpha-hydroxy ketones at ambient temperature in which the metal and enzyme catalysts work in concert in one pot at room temperature to give quantitative yields of esters of alpha-hydroxy ketones with very high enantioselectivity.

  • 2.
    Alam, Rauful
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-catalyzed Allylic C-H and C-OH Functionalization. Reactions of the Obtained Allylboronic Acids2014Licentiate thesis, monograph (Other academic)
    Abstract [en]

    This thesis is focused on the studies of two major transformations. The first transformation deals with the development of palladium-catalyzed selective allylic trifluoroacetoxylation reactions based on C-H functionalization, whereas the second comprises the synthesis and isolation of allylboronic acids using diboronic acid B2(OH)4 as boron source. Both reactions proceed with a very high regio- and stereoselectivity. The mechanistic studies of the allylic C-H trifluoroacetoxylation indicate that the reaction proceeds via (η3-allyl)palladium intermediate.

    The reactivity of the allylboronic acids was studied with ketone and imine substrates. Unlikeother boronates (such as allyl-Bpin derivatives), allylboronic acids react with ketones and imines without any additives under neutral and mild conditions (typically at room temperature). The regio- and stereoselectivity of this reaction is remarkably high. Using functionalized allylboronic acids (prepared in the above mentioned Pd-catalyzed reactions) homoallylic alcohols and amines with adjacent tertiary and quaternary centers could be obtained with high selectivity. Interestingly, both the ketones and the imines reacted with anti-stereoselectivity. This was surprising for the imines. Our mechanistic study has shown that the acyclic aldimines undergo cis/trans isomerization prior to the allylation reaction.

  • 3.
    Alam, Rauful
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Das, Arindam
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Huang, Genping
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stereoselective allylboration of imines and indoles under mild conditions. An in situ E/Z isomerization of imines by allylboroxines2014In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 5, no 7, p. 2732-2738Article in journal (Refereed)
    Abstract [en]

    Direct allylboration of various acyclic and cyclic aldimine, ketimine and indole substrates was performed using allylboronic acids. The reaction proceeds with very high anti-stereoselectivity for both E and Z imines. The allylboroxines formed by dehydration of allylboronic acids have a dual effect: promoting E/Z isomerization of aldimines and triggering the allylation by efficient electron withdrawal from the imine substrate.

  • 4.
    Alamsetti, Santosh Kumar
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Persson, Andreas K. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-Catalyzed Intramolecular Hydroamination of Propargylic Carbamates and Carbamothioates2014In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 16, no 5, p. 1434-1437Article in journal (Refereed)
    Abstract [en]

    An efficient and simple methodology was developed for the synthesis of oxazolidinones, oxazolidinthiones, imidazolidinthiones, and imidazolidinones from the corresponding propargylic starting materials using Pd(OAc)(2) and n-Bu4NOAc as catalysts in DCE at room temperature.

  • 5. Anderson, Mattias
    et al.
    Afewerki, Samson
    Berglund, Per
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mid Sweden University, Sweden.
    Total Synthesis of Capsaicin Analogues from Lignin-Derived Compounds by Combined Heterogeneous Metal, Organocatalytic and Enzymatic Cascades in One Pot2014In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 356, no 9, p. 2113-2118Article in journal (Refereed)
    Abstract [en]

    The total synthesis of capsaicin analogues was performed in one pot, starting from compounds that can be derived from lignin. Heterogeneous palladium nanoparticles were used to oxidise alcohols to aldehydes, which were further converted to amines by an enzyme cascade system, including an amine transaminase. It was shown that the palladium catalyst and the enzyme cascade system could be successfully combined in the same pot for conversion of alcohols to amines without any purification of intermediates. The intermediate vanillyl-amine, prepared with the enzyme cascade system, could be further converted to capsaicin analogues without any purification using either fatty acids and a lipase, or Schotten-Baumann conditions, in the same pot. An aldol compound (a simple lignin model) could also be used as starting material for the synthesis of capsaicin analogues. Using l-alanine as organocatalyst, vanillin could be obtained by a retro-aldol reaction. This could be combined with the enzyme cascade system to convert the aldol compound to vanillylamine in a one-step one-pot reaction.

  • 6.
    Arafa, Wael A. A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    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 Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Berends, Hans-Martin
    Messinger, Johannes
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dinuclear manganese complexes for water oxidation: evaluation of electronic effects and catalytic activity2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 24, p. 11950-11964Article in journal (Refereed)
    Abstract [en]

    During recent years significant progress has been made towards the realization of a sustainable and carbon-neutral energy economy. One promising approach is photochemical splitting of H2O into O-2 and solar fuels, such as H-2. However, the bottleneck in such artificial photosynthetic schemes is the H2O oxidation half reaction where more efficient catalysts are required that lower the kinetic barrier for this process. In particular catalysts based on earth-abundant metals are highly attractive compared to catalysts comprised of noble metals. We have now synthesized a library of dinuclear Mn-2 (II,III) catalysts for H2O oxidation and studied how the incorporation of different substituents affected the electronics and catalytic efficiency. It was found that the incorporation of a distal carboxyl group into the ligand scaffold resulted in a catalyst with increased catalytic activity, most likely because of the fact that the distal group is able to promote proton-coupled electron transfer (PCET) from the high-valent Mn species, thus facilitating O-O bond formation.

  • 7.
    Bartholomeyzik, Teresa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium(II)-Catalyzed Oxidative Carbocyclization/Functionalization of Allenynes2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The selective formation of carbon-carbon bonds constitutes a key transformation in organic synthesis with useful applications in pharmaceutical or material industry. A particularly versatile tool for carbon-carbon as well as carbon-heteroatom bond formation is palladium catalysis, which allows for mild and selective routes even towards complex structures.

    The work in this thesis describes the development and the mechanistic investigation of a palladium(II)-catalyzed oxidative carbocyclization/functionalization methodology, which converts 1,5-allenynes into either arylated or borylated carbocycles. To this end, either boronic acids or B2pin2 are employed and 1,4-benzoquinone serves as the stoichiometric oxidant. These protocols provide access to two products, a cyclic triene and a cyclic vinylallene. Their formation is dependent on the substrate structure as the latter product requires a propargylic C–H bond to be present in the substrate. Based on kinetic isotope effects, mechanisms involving either an initial allenic or propargylic C–H abstraction, respectively, were proposed. Full control of product selectivity to give either trienes or vinylallenes was achieved by modifying the reaction conditions with additives. Using substoichiometric amounts of BF3·OEt2 leads selectively to borylated or arylated vinylallenes. Under arylating conditions the reaction is zero order in allenyne and oxidant, and first order in phenylboronic acid. Transmetalation and, to some extent, propargylic C–H cleavage were found to be turnover-limiting. The selective reaction towards functionalized trienes was achieved by addition of either substoichiometric LiOAc·2H2O (borylation) or excess amounts of H2O (arylation). For the latter case, a kinetic study revealed an unusually slow catalyst activation. Lower concentrations of H2O gave product mixtures, and it was shown that vinylallenes are formed with either boronic acid or boroxine, whereas the formation of trienes requires boronic acid.

  • 8.
    Bartholomeyzik, Teresa
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mazuela, Javier
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Deng, Youqian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-Catalyzed Oxidative Arylating Carbocyclization of Allenynes: Control of Selectivity and Role of H2O2014In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 53, no 33, p. 8696-8699Article in journal (Refereed)
    Abstract [en]

    Highly selective protocols for the carbocyclization/arylation of allenynes using arylboronic acids are reported. Arylated vinylallenes are obtained with the use of BF3 center dot Et2O as an additive, whereas addition of water leads to arylated trienes. These conditions provide the respective products with excellent selectivities (generally > 97:3) for a range of boronic acids and different allenynes. It has been revealed that water plays a crucial role for the product distribution.

  • 9.
    Bermejo Gómez, Antonio
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Holmberg, Pär
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martin-Matute, Belén
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Transition metal-catalyzed redox isomerization of codeine and morphine in water2014In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 4, no 74, p. 39519-39522Article in journal (Refereed)
    Abstract [en]

    A water-soluble rhodium complex formed from commercially available [Rh(COD)(CH3CN)(2)]BF4 and 1,3,5-triaza-7-phosphaadamantane (PTA) catalyzes the isomerization of both codeine and morphine into hydrocodone and hydromorphone with very high efficiency. The reaction is performed in water, allowing isolation of the final products by simple filtration, which results in very high isolated yields. The reactions can be easily scaled up to 100 g.

  • 10.
    Blomberg, Margareta R. A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Borowski, Tomasz
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Studies of Mechanisms for Metalloenzymes2014In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 114, no 7, p. 3601-3658Article, review/survey (Refereed)
  • 11.
    Blomberg, Margareta R. A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Proton pumping in cytochrome c oxidase: Energetic requirements and the role of two proton channels2014In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1837, no 7, p. 1165-1177Article in journal (Refereed)
    Abstract [en]

    Cytochrome c oxidase is a superfamily of membrane bound enzymes catalyzing the exergonic reduction of molecular oxygen to water, producing an electrochemical gradient across the membrane. The gradient is formed both by the electrogenic chemistry, taking electrons and protons from opposite sides of the membrane, and by proton pumping across the entire membrane. In the most efficient subfamily, the A-family of oxidases, one proton is pumped in each reduction step, which is surprising considering the fact that two of the reduction steps most likely are only weakly exergonic. Based on a combination of quantum chemical calculations and experimental information, it is here shown that from both a thermodynamic and a kinetic point of view, it should be possible to pump one proton per electron also with such an uneven distribution of the free energy release over the reduction steps, at least up to half the maximum gradient. A previously suggested pumping mechanism is developed further to suggest a reason for the use of two proton transfer channels in the A-family. Since the rate of proton transfer to the binuclear center through the D-channel is redox dependent, it might become too slow for the steps with low exergonicity. Therefore, a second channel, the K-channel, where the rate is redox-independent is needed. A redox-dependent leakage possibility is also suggested, which might be important for efficient energy conservation at a high gradient. A mechanism for the variation in proton pumping stoichiometry over the different subfamilies of cytochrome oxidase is also suggested. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.

  • 12. Both, P.
    et al.
    Green, A. P.
    Gray, C. J.
    Sardzik, R.
    Voglmeir, J.
    Fontana, Carolina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Austeri, M.
    Rejzek, M.
    Richardson, D.
    Field, R. A.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Flitsch, S. L.
    Eyers, C. E.
    Discrimination of epimeric glycans and glycopeptides using IM-MS and its potential for carbohydrate sequencing2014In: Nature Chemistry, ISSN 1755-4330, E-ISSN 1755-4349, Vol. 6, no 1, p. 65-74Article in journal (Refereed)
    Abstract [en]

    Mass spectrometry is the primary analytical technique used to characterize the complex oligosaccharides that decorate cell surfaces. Monosaccharide building blocks are often simple epimers, which when combined produce diastereomeric glycoconjugates indistinguishable by mass spectrometry. Structure elucidation frequently relies on assumptions that biosynthetic pathways are highly conserved. Here, we show that biosynthetic enzymes can display unexpected promiscuity, with human glycosyltransferase pp-a-GanT2 able to utilize both uridine diphosphate N-acetylglucosamine and uridine diphosphate N-acetylgalactosamine, leading to the synthesis of epimeric glycopeptides in vitro. Ion-mobility mass spectrometry ( IM-MS) was used to separate these structures and, significantly, enabled characterization of the attached glycan based on the drift times of the monosaccharide product ions generated following collision-induced dissociation. Finally, ion-mobility mass spectrometry following fragmentation was used to determine the nature of both the reducing and non-reducing glycans of a series of epimeric disaccharides and the branched pentasaccharide Man3 glycan, demonstrating that this technique may prove useful for the sequencing of complex oligosaccharides.

  • 13.
    Bouma, M. J.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    7.07 α-Oxygenation of Carbonyl Compounds2014In: Comprehensive Organic Synthesis II (Second Edition) / [ed] Paul Knochel and Gary A. Molander, Amsterdam: Oxford: Elsevier , 2014, 2nd, p. 213-241Chapter in book (Refereed)
    Abstract [en]

    Abstract The chapter describes synthetically useful strategies for α-oxygenation of carbonyl compounds, with special emphasis on recent methods for catalytic and asymmetric reactions. The oxidation of enolates, enols, enol ethers, and α,β-unsaturated compounds is discussed in detail. Classical oxidation reagents like metal oxides, molecular oxygen, peroxides, and peracids are covered, with asymmetric dihydroxylation of enol ethers giving the highest enantioselectivities together with organocatalytic methods using peroxides. Oxaziridines, nitrosoarenes, and hypervalent iodine compounds are more recently developed α-oxygenation alternatives that allow metal-free oxidations under mild conditions. The combination of nitrosoarenes with organocatalysis is currently the best method for enantioselective α-oxygenations. The area of asymmetric α-oxygenations with hypervalent iodine compounds is currently under development, and high enantioselectivities have only been achieved in intramolecular reactions and epoxidations.

  • 14. Bratt, Emma
    et al.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johansson, Magnus J.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    A General Suzuki Cross-Coupling Reaction of Heteroaromatics Catalyzed by Nanopalladium on Amino-Functionalized Siliceous Mesocellular Foam2014In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 79, no 9, p. 3946-3954Article in journal (Refereed)
    Abstract [en]

    Suzuki-Miyaura cross-coupling reactions of heteroaromatics catalyzed by palladium supported in the cavities of amino-functionalized siliceous mesocellular foam are presented. The nanopalladium catalyst effectively couples not only heteroaryl halides with boronic acids but also heteroaryl halides with boronate esters, potassium trifluoroborates, MIDA boronates, and triolborates, producing a wide range of heterobiaryls in good to excellent yields. Furthermore, the heterogeneous palladium nanocatalyst can easily be removed from the reaction mixture by filtration and recycled several times with minimal loss in activity. This catalyst provides an alternative, environmentally friendly, low-leaching process for the preparation of heterobiaryls.

  • 15. Chen, Mo
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Brady, John W.
    Wohlert, Jakob
    Molecular Dynamics Simulations of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Chloride and Its Binary Mixtures with Ethanol2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 10, p. 4465-4479Article in journal (Refereed)
    Abstract [en]

    Room temperature ionic liquids (ILs) of the imidazolium family have attracted much attention during the past decade for their capability to dissolve biomass. Besides experimental work, numerous compuational studies have been concerned with the physical properties of both neat ILs and their interactions with different solutes, in particular, carbohydrates. Many classical force fields designed specifically for ILs have been found to yield viscosities that are too high for the liquid state, which has been attributed to the fact that the effective charge densities are too high due to the lack of electronic polarizability. One solution to this problem has been uniform scaling of the partial charges by a scale factor in the range 0.6-0.9, depending on model. This procedure has been shown to improve the viscosity of the models, and also to positively affect other properties, such as diffusion constants and ionic conductivity. However, less attention has been paid to how this affects the overall thermodynamics of the system, and the problems it might create when the IL models are combined with other force fields (e.g., for solutes). In the present work, we employ three widely used IL force fields to simulate 1-n-buty1-3-methyl-imidazolium chloride in both the crystal and the liquid state, as well as its binary mixture with ethanol. Two approaches are used: one in which the ionic charge is retained at its full integer value and one in which the partial charges are uniformly reduced to 85%. We investigate and calculate crystal and liquid structures, molar heat capacities, heats of fusion, self-diffusion constants, ionic conductivity, and viscosity for the neat IL, and ethanol activity as a function of ethanol concentration for the binary mixture. We show that properties of the crystal are less affected by charge scaling compared to the liquid. In the liquid state, transport properties of the neat IL are generally improved by scaling, whereas values for the heat of fusion are unaffected, and results for the heat capacity are ambiguous. Neither full nor reduced charges could reproduce experimental ethanol activities for the whole range of compositions.

  • 16. Chow, Winnie W. Y.
    et al.
    Herwik, Stanislav
    Kisban, Sebastian
    Ruther, Patrick
    Neves, Herc
    Oscarsson, Sven
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Gothelid, Emmanuelle
    Influence of bio-coatings on the recording performance of neural electrodes2014In: Biomedizinische Technik (Berlin. Zeitschrift), ISSN 1862-278X, E-ISSN 0013-5585, Vol. 59, no 4, p. 315-322Article in journal (Refereed)
    Abstract [en]

    Neural probes are complex devices consisting of metallic (often Pt based) electrodes, spread over an insolating/dielectric backbone. Their functionality is often limited in time because of the formation of scaring tissues around the implantation tracks. Functionalization of the probes surface can be used to limit the glial scar reaction. This is however challenging, as this treatment has to be equally efficient on all probe surfaces (metallic as well as dielectric) and should not influence the electrodes performances. This paper presents a novel technique to functionalize recording neural probes with hyaluronic acid (HyA), a major component of the extracellular matrix (ECM). HyA and the probe surface are both modified to make the reaction feasible: HyA is chemically functionalized with SS-pyridine groups while the probe surfaces are silanized. The thiol groups thus introduced on the probe surface can then react with the HyA SS-pyridine group, resulting in a covalent bonding of the latter on the former. The electrodes are protected by introducing a pretreatment step, namely an additional hyaluronic acid layer on the platinum electrode, prior to the silanization process, which was found to be effective in reducing electrode impedance under optimized conditions.

  • 17.
    Das, Arindam
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Alam, Rauful
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stereocontrol in Synthesis of Homoallylic Amines. Syn Selective Direct Allylation of Hydrazones with Allylboronic Acids2014In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 16, no 14, p. 3808-3811Article in journal (Refereed)
    Abstract [en]

    Allylboronic acids directly react with acyl hydrazones, affording homoallylic amine derivatives. The reaction proceeds with very high syn selectivity, which is the opposite of the stereochemistry observed for allylboration of imines. The reaction can be carried out with both aromatic and aliphatic acyl hydrazones. Based on our studies the excellent syn stereochemistry can be explained by chelation control of the acyl hydrazone and the B(OH)(2) moiety.

  • 18. Das, Biswanath
    et al.
    Daver, Henrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pyrkosz-Bulska, Monika
    Persch, Elke
    Barman, Suman K.
    Mukherjee, Rabindranath
    Gumienna-Kontecka, Elzbieta
    Jarenmark, Martin
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nordlander, Ebbe
    A dinuclear zinc(II) complex of a new unsymmetric ligand with an N(5)0(2) donor set; A structural and functional model for the active site of zinc phosphoesterases2014In: Journal of Inorganic Biochemistry, ISSN 0162-0134, E-ISSN 1873-3344, Vol. 132, p. 6-17Article in journal (Refereed)
    Abstract [en]

    The dinuclear complex [Zn-2(DPCPMP)(pivalate)](C10(4)), where DPCPMP is the new unsymmetrical ligand [2-(N-(3-((bis((pyridin-2-yl)methyl)amino)methyl)-2-hydroxy-5-methylbenzyl)-N-((pyridin2-y1)methyl)amino)acetic acid], has been synthesized and characterized. The complex is a functional model for zinc phosphoesterases with dinuclear active sites. The hydrolytic efficacy of the complex has been investigated using bis-(2,4-dinitrophenyl)phosphate(BDNPP), a DNA analog, as substrate. Speciation studies using potentiometric titrations have been performed for both the ligand and the corresponding dizinc complex to elucidate the formation of the active hydrolysis catalyst; they reveals that the dinuclear zinc(II) complexes, [Zn-2(DPCPMP)](2) and [Zn-2(DPCPMP)(OH)1 predominate the solution above pH 4. The relatively high pKa of 8.38 for water deprotonation suggests that a terminal hydroxide complex is formed. Kinetic investigations of BDNPP hydrolysis over the pH range 5.5-11.0 and with varying metal to ligand ratio (metal salt:ligand = 0.5:1 to 3:1) have been performed. Variable temperature studies gave the activation parameters triangle H double dagger = 95.6 kJ mol(-1), triangle S double dagger = 44.8 J mo1(-1) K-1, and 6,triangle G double dagger = 108.0 kJ mo1-1. The cumulative results indicate the hydroxido-bridged dinuclear Zn(II) complex [Zn-2(DPCPMP)(mu-OH)] (+) as the effective catalyst. The mechanism of hydrolysis has been probed by computational modeling using density functional theory (DFF). Calculations show that the reaction goes through one concerted step (S(N)2 type) in which the bridging hydroxide in the transition state becomes terminal and performs a nucleophilic attack on the BDNPP phosphorus; the leaving group dissociates simultaneously in an overall inner sphere type activation. The calculated free energy barrier is in good agreement with the experimentally determined activation parameters.

  • 19. Das, Biswanath
    et al.
    Daver, Henrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Singh, Amrendra
    Singh, Reena
    Haukka, Matti
    Demeshko, Serhiy
    Meyer, Franc
    Lisensky, George
    Jarenmark, Martin
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nordlander, Ebbe
    A Heterobimetallic FeIIIMnII Complex of an Unsymmetrical Dinucleating Ligand: A Structural and Functional Model Complex for the Active Site of Purple Acid Phosphatase of Sweet Potato2014In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, Vol. 2014, no 13, p. 2204-2212Article in journal (Refereed)
    Abstract [en]

    The heterodinuclear mixed-valence complex [FeMn(ICIMP)(OAc)(2)Cl] (1) {H2ICIMP = 2-(N-carboxylmethyl)-[N-(N-methylimidazolyl-2-methyl)aminomethyl]-[6-(N-isopropylmethyl)-[N-(N-methylimidazolyl-2-methyl)]aminomethyl-4-methylphenol], an unsymmetrical N4O2 donor ligand} has been synthesized and fully characterized by several spectroscopic techniques as well as by X-ray crystallography. The crystal structure of the complex reveals that both metal centers in 1 are six-coordinate with the chloride ion occupying the sixth coordination site of the Mn-II ion. The phenoxide moiety of the ICIMP ligand and both acetate ligands bridge the two metal ions of the complex. Mossbauer spectroscopy shows that the iron ion in 1 is high-spin Fe-III. Two quasi-reversible redox reactions for the complex, attributed to the (FeMnII)-Mn-III/(FeMnII)-Mn-II (at -0.67 V versus Fc/Fc(+)) and (FeMnII)-Mn-III/(FeMnIII)-Mn-III (at 0.84 V), were observed by means of cyclic voltammetry. Complex 1, with an Fe-III-Mn-II distance of 3.58 angstrom, may serve as a model for the mixed-valence oxidation state of purple acid phosphatase from sweet potato. The capability of the complex to effect organophosphate hydrolysis (phosphatase activity) has been investigated at different pH levels (5.5-11) by using bis(2,4-dinitrophenyl)phosphate (BDNPP) as the substrate. Density functional theory calculations indicate that the substrate coordinates to the Mn-II ion. In the transition state, a hydroxide ion that bridges the two metal ions becomes terminally coordinated to the Fe-III ion and acts as a nucleophile, attacking the phosphorus center of BDNPP with the concomitant dissociation of the leaving group.

  • 20.
    Deiana, Luca
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ghisu, Lorenza
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Afewerki, Samson
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hedin, Niklas
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Bacsik, Zoltan
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mid-Sweden University, Sweden.
    Enantioselective Heterogeneous Synergistic Catalysis for Asymmetric Cascade Transformations2014In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 356, no 11-12, p. 2485-2492Article in journal (Refereed)
    Abstract [en]

    A modular design for a novel heterogeneous synergistic catalytic system, which simultaneously activates the electrophile and nucleophile by the combined activation modes of a separate metal and non-metal catalyst, for asymmetric cascade transformations on a solid surface is disclosed. This modular catalysis strategy generates carbocycles (up to 97.5: 2.5 er) as well as spirocyclic oxindoles (97.5: 2.5 to > 99: 0.5 er), containing all-carbon quaternary centers, in a highly enantioselective fashion via a one-pot dynamic relay process.

  • 21.
    Engelmark Cassimjee, Karim
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kadow, Maria
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Wikmark, Ylva
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Svedendahl Humble, Maria
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rothstein, M. L.
    Rothstein, D. M.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    A general protein purification and immobilization method on controlled porosity glass: biocatalytic applications2014In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 50, no 65, p. 9134-9137Article in journal (Refereed)
    Abstract [en]

    A general combined purification and immobilization method to facilitate biocatalytic process development is presented. The support material, EziG (TM), is based on controlled porosity glass (CPG) or polymer-coated versions thereof (HybCPG) and binds protein affinity tags. Biocatalytic reactions in aqueous and organic media with seven enzymes of biocatalytic interest are shown.

  • 22.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kovacs, Helena
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    NMR structure analysis of uniformly 13C-labeled carbohydrates2014In: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 59, no 2, p. 95-110Article in journal (Refereed)
    Abstract [en]

    In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of C-13-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly C-13-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-C-13)-sucrose, 342 Da] and one compound of medium molecular weight (C-13-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, similar to 10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The C-13 resonances are traced using C-13-C-13 correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the C-13 resonances, the H-1 chemical shifts are derived in a straightforward manner using one-bond H-1-C-13 correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the (1) J (CC) splitting of the C-13 resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either C-13 or H-1 detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T-2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the H-1-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the C-13-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with N-15 at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and C-13-detected (H)CACO spectra.

  • 23.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lundborg, Magnus
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rapid structural elucidation of polysaccharides employing predicted functions of glycosyltransferases and NMR data: Application to the O-antigen of Escherichia coli O592014In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 24, no 5, p. 450-457Article in journal (Refereed)
    Abstract [en]

    A computerized method that uses predicted functions of glycosyltransferases (GTs) in conjunction with unassigned NMR data has been developed for the structural elucidation of bacterial polysaccharides (PSs). In this approach, information about the action of GTs (consisting of possible sugar residues used as donors and/or acceptors, as well as the anomeric configuration and/or substitution position in the respective glycosidic linkages) is extracted from the Escherichia coli O-antigen database and is submitted, together with the unassigned NMR data, to the CASPER program. This time saving methodology, which alleviates the need for chemical analysis, was successfully implemented in the structural elucidation of the O-antigen PS of E. coli O59. The repeating unit of the O-specific chain was determined using the O-deacylated PS and has a branched structure, namely, -> 6)[alpha-d-GalpA3Ac/4Ac-(1 -> 3)]-alpha-d-Manp-(1 -> 3)-alpha-d-Manp-(1 -> 3)-beta-d-Manp-(1 -> 3)-alpha-d-GlcpNAc-(1 ->. The identification of the O-acetylation positions was efficiently performed by comparison of the H-1,C-13 HSQC NMR spectra of the O-deacylated lipopolysaccharide and the lipid-free PS in conjunction with chemical shift predictions made by the CASPER program. The side-chain d-GalpA residue carries one equivalent of O-acetyl groups at the O-3 and O-4 positions distributed in the LPS in a 3:7 ratio, respectively. The presence of O-acetyl groups in the repeating unit of the E. coli O59 PS is consistent with the previously proposed acetyltransferase WclD in the O-antigen gene cluster.

  • 24.
    Ghosh, Raju
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lindstedt, Erik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Jalalian, Nazli
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Room Temperature, Metal-Free Arylation of Aliphatic Alcohols2014In: ChemistryOpen, ISSN 2191-1363, Vol. 3, no 2, p. 54-57Article in journal (Refereed)
    Abstract [en]

    Diaryliodonium salts are demonstrated as efficient arylating agents of aliphatic alcohols under metal-free conditions. The reaction proceeds at room temperature within 90min to give alkyl aryl ethers in good to excellent yields. Aryl groups with electron-withdrawing substituents are transferred most efficiently, and unsymmetric iodonium salts give chemoselective arylations. The methodology has been applied to the formal synthesis of butoxycaine.

  • 25.
    Ghosh, Raju
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Metal-Free Synthesis of N-Aryloxyimides and Aryloxyamines2014In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 16, no 6, p. 1830-1832Article in journal (Refereed)
    Abstract [en]

    N-Hydroxyphthalimide and N-hydroxysuccinimide have been arylated with diaryliodonium salts to provide N-aryloxyimides in excellent yields in short reaction times. A novel hydrolysis under mild and hydrazine-free conditions yielded aryloxyamines, which are valuable building blocks in the synthesis of oxime ethers and benzofurans.

  • 26.
    Ghosh, Raju
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stridfeldt, Elin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Metal-Free One-Pot Synthesis of Benzofurans2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 29, p. 8888-8892Article in journal (Refereed)
    Abstract [en]

    Ethyl acetohydroxamate was efficiently arylated with diaryliodonium salts at room temperature under transition-metal-free conditions. The obtained O-arylated products were reacted in situ with ketones under acidic conditions to yield substituted benzo[b]furans through oxime formation, [3,3]-rearrangement, and cyclization in a fast and operationally simple one-pot fashion without using excess reagents. Alternatively, the O-arylated products could be isolated or transformed in situ to aryloxyamines or O-arylaldoximes. The methodology was applied to the synthesis of Stemofuran A and the formal syntheses of Coumestan, Eupomatenoid 6, and (+)-machaeriol B.

  • 27.
    Gigant, Nicolas
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Access to Cinnamyl Derivatives from Arenes and Allyl Esters by a Biomimetic Aerobic Oxidative Dehydrogenative Coupling2014In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 16, no 6, p. 1664-1667Article in journal (Refereed)
    Abstract [en]

    An efficient biomimetic aerobic oxidative dehydrogenative alkenylation of arenes with allyl esters is presented. The reaction proceeds under an ambient pressure of oxygen with relatively low catalyst loading of palladium acetate, employing catalytic amounts of electron-transfer mediators (ETMs). This study represents a new environmentally friendly method for the synthesis of cinnamyl derivatives.

  • 28.
    Gigant, Nicolas
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Aerobic Direct C-H Arylation of Nonbiased Olefins2014In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 16, no 17, p. 4432-4435Article in journal (Refereed)
    Abstract [en]

    An efficient ligand-promoted biomimetic aerobic oxidative dehydrogenative cross-coupling between arenes and nonbiased olefins is presented. Acridine as a ligand was found to significantly enhance the rate, the yield, and the scope of the reaction under ambient oxygen pressure, providing a variety of alkenylarenes via an environmentally friendly procedure.

  • 29.
    Gigant, Nicolas
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Aerobic Double Dehydrogenative Cross Coupling between Cyclic Saturated Ketones and Simple Arenes2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 20, p. 5890-5894Article in journal (Refereed)
    Abstract [en]

    The synthesis of 3-aryl-2-cyclohexenones is a topic of current interest as they are not only privileged structures in bioactive molecules, but they are also relevant feedstocks for the synthesis of substituted phenols or anilines, which are ubiquitous structural elements both in drug design and medicinal chemistry. A simple and sustainable one-pot aerobic double dehydrogenative reaction under mild conditions for the introduction of arenes in the -position of cyclic ketones has been developed. Starting from the corresponding saturated ketone, this reaction sequence proceeds under relatively low Pd catalyst loading and involves catalytic amounts of electron-transfer mediators (ETMs) under ambient oxygen pressure.

  • 30.
    Gustafson, Karl P. J.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lihammar, Richard
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Engström, Karin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chemoenzymatic Dynamic Kinetic Resolution of Primary Amines Using a Recyclable Palladium Nanoparticle Catalyst Together with Lipases2014In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 79, no 9, p. 3747-3751Article in journal (Refereed)
    Abstract [en]

    A catalyst consisting of palladium nanoparticles supported on amino-functionalized siliceous mesocellular foam (Pd-AmP-MCF) was used in chemoenzymatic dynamic kinetic resolution (DKR) to convert primary amines to amides in high yields and excellent ee's. The efficiency of the nanocatalyst at temperatures below 70 degrees C enables reaction conditions that are more suitable for enzymes. In the present study, this is exemplified by subjecting 1-phenylethylamine (1a) and analogous benzylic amines to DKR reactions using two commercially available lipases, Novozyme-435 (Candida antartica Lipase B) and Amano Lipase PS-C1 (lipase from Burkholderia cepacia) as biocatalysts. The latter enzyme has not previously been used in the DKR of amines because of its low stability at temperatures over 60 degrees C. The viability of the heterogeneous Pd-AmP-MCF was further demonstrated in a recycling study, which shows that the catalyst can be reused up to five times.

  • 31.
    Hamark, Christoffer
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Landström, Jens
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    SEAL by NMR: Glyco-Based Selenium-Labeled Affinity Ligands Detected by NMR Spectroscopy2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 43, p. 13905-13908Article in journal (Refereed)
    Abstract [en]

    We report a method for the screening of interactions between proteins and selenium-labeled carbohydrate ligands. SEAL by NMR is demonstrated with selenoglycosides binding to lectins where the selenium nucleus serves as an NMR-active handle and reports on binding through Se-77 NMR spectroscopy. In terms of overall sensitivity, this nucleus is comparable to C-13 NMR, while the NMR spectral width is ten times larger, yielding little overlap in Se-77 NMR spectroscopy, even for similar compounds. The studied ligands are singly selenated bioisosteres of methyl glycosides for which straightforward preparation methods are at hand and libraries can readily be generated. The strength of the approach lies in its simplicity, sensitivity to binding events, the tolerance to additives and the possibility of having several ligands in the assay. This study extends the increasing potential of selenium in structure biology and medicinal chemistry. We anticipate that SEAL by NMR will be a beneficial tool for the development of selenium-based bioactive compounds, such as glycomimetic drug candidates.

  • 32.
    Ilchenko, Nadia
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Development of Catalytic ElectrophilicTrifluoromethylation and Fluorination Methods2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is focused on development of new catalytic, electrophilic fluorination and trifluoromethylation methods of alkenes. These reactions were carried out using hypervalent trifluoromethyl and fluoroiodine reagents.

    The first project involved copper catalyzed oxytrifluoromethylation of terminal alkenes and alkynes. In this reaction the employed hypervalent iodine underwent a formal addition to C-C multiple bonds. Subsequently, we have also shown that under similar reaction conditions in the presence of B2pin2 as additive quinones can smoothly undergo C-H trifluoromethylation.

    We also developed a cyanotrifluoromethylation reaction of styrenes, which proceds in the presence of copper cyanide and PCy3 as additive. This reaction allows addition of both trifluoromethyl and cyanofunctionality to the styrene, creating two new carbon-carbon bonds.

    The interesting substituent effects and the acceleration of B2pin2 and PCy3 additives inspired us to further investigate the mechanism for the above trifluoromethylation reactions. The Hammett studies showed that the oxytrifluoromethylation reactions are slightly accelerated by electron donor substituents. The C-H trifluoromethylation does not show deuterium isotope effect. Both B2pin2 and PCy3 accelerated the trifluoromethylation reactions but the extent of the acceleration was dependent on the reaction type and on the substituent effects.

    Inspired by our trifluoromethylation results, we have also studied the silver-mediated difluorination of styrenes in the presence of an electrophilic hypervalent iodine based fluorine source. We obtained over 50% of the difluorinated product which suggests that one fluorine atom comes from the fluoroiodine reagent and the other one from BF4-. A phenonium ion intermediate has been proposed to be involved in the mechanism of the difluorination reaction.

  • 33.
    Ilchenko, Nadia O.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tasch, Boris O. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mild Silver-Mediated Geminal Difluorination of Styrenes Using an Air- and Moisture-Stable Fluoroiodane Reagent2014In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 53, no 47, p. 12897-12901Article in journal (Refereed)
    Abstract [en]

    An air-and moisture-stable fluoroiodane in the presence of AgBF4 is suitable for selective geminal difluorination of styrenes under mild reaction conditions. One of the C-F bonds is formed by transfer of electrophilic fluorine from the hypervalent iodine reagent, while the other one arises from the tetrafluoroborate counterion of silver. Deuterium-isotope-labelling experiments and rearrangement of methyl styrene substrates suggest that the reaction proceeds through a phenonium ion intermediate.

  • 34. Jakhetia, Richa
    et al.
    Marri, Aruna
    Ståhle, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verma, Naresh K.
    Serotype-conversion in Shigella flexneri: identification of a novel bacteriophage, Sf101, from a serotype 7a strain2014In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 15, p. 742-Article in journal (Refereed)
    Abstract [en]

    Background: Shigella flexneri is the major cause of bacillary dysentery in the developing countries. The lipopolysaccharide (LPS) O-antigen of S. flexneri plays an important role in its pathogenesis and also divides S. flexneri into 19 serotypes. All the serotypes with an exception for serotype 6 share a common O-antigen backbone comprising of N-acetylglucosamine and three rhamnose residues. Different serotypes result from modification of the basic backbone conferred by phage-encoded glucosyltransferase and/or acetyltransferase genes, or plasmid-encoded phosphoethanolamine transferase. Recently, a new site for O-acetylation at positions 3 and 4 of Rha(III), in serotypes 1a, 1b, 2a, 5a and Y was shown to be mediated by the oacB gene. Additionally, this gene was shown to be carried by a transposon-like structure inserted upstream of the adrA region on the chromosome. Results: In this study, a novel bacteriophage Sf101, encoding the oacB gene was isolated and characterised from a serotype 7a strain. The complete sequence of its 38,742 bp genome encoding 66 open reading frames (orfs) was determined. Comparative analysis revealed that phage Sf101 has a mosaic genome, and most of its proteins were >90% identical to the proteins from 12 previously characterised lambdoid phages. In addition, the organisation of Sf101 genes was found to be highly similar to bacteriophage Sf6. Analysis of the Sf101 OacB identified two amino acid substitutions in the protein; however, results obtained by NMR spectroscopy confirmed that Sf101-OacB was functional. Inspection of the chromosomal integration site of Sf101 phage revealed that this phage integrates in the sbcB locus, thus unveiling a new site for integration of serotype-converting phages of S. flexneri, and determining an alternative location of oacB gene in the chromosome. Furthermore, this study identified oacB gene in several serotype 7a isolates from various regions providing evidence of O-acetyl modification in serotype 7a. Conclusions: This is the first report on the isolation of bacteriophage Sf101 which contains the S. flexneri O-antigen modification gene oacB. Sf101 has a highly mosaic genome and was found to integrate in the sbcB locus. These findings contribute an advance in our current knowledge of serotype converting phages of S. flexneri.

  • 35.
    Janson, Pär
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Oxidative Trifluoromethylation and other Functionalization Reactions of Alkenes and Alkynes2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis concerns the use of various potent oxidants in organic synthesis. The main focus is directed at selectively introducing trifluoromethyl groups into compounds containing double or triple bonds. All reactions proceed under mild conditions and can in most cases be performed on the bench-top.

    We have developed three different procedures for transformations of activated alkenes and alkynes as well as quinones. In paper I the selective introduction of a trifluoromethyl group together with an oxygen functionality to double and triple bonds is demonstrated.

    Paper II is focused on the related chemoselective cyanotrifluoromethylation in which a cyano group is added instead of the oxygen functionality.

    Paper III describes a new procedure for C–H trifluoromethylation of quinones. Our studies on the mechanistic aspects of the above reactions are described in Paper IV. In these studies we investigated the ligand and substituent effects in Cu-catalyzed reactions.

    Paper V is focused on a conceptually new palladium-catalyzed allylic C–H acyloxylation of olefins under oxidative conditions. The procedure uses an inexpensive, safe and environmentally benign oxidant, sodium perborate, which is activated with acetic anhydride.

  • 36.
    Jiang, Liying
    et al.
    Stockholm University, Faculty of Science, Department of Analytical Chemistry.
    Dziedzic, Pawel
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Spacil, Zdenek
    Stockholm University, Faculty of Science, Department of Analytical Chemistry. University of Washington, USA.
    Zhao, Gui-Ling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nilsson, Lennart
    Ilag, Leopold L.
    Stockholm University, Faculty of Science, Department of Analytical Chemistry.
    Cordova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mid-Sweden University, Sweden.
    Abiotic synthesis of amino acids and self-crystallization under prebiotic conditions2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, article id 6769Article in journal (Refereed)
    Abstract [en]

    Building on previous research on the origin and homochirality of life, this study focuses on analyses profiling important building blocks of life: the natural amino acids. The spark discharge variation of the iconic Miller experiment was performed with a reducing gas mixture of ammonia, methane, water and hydrogen. Amino acid analysis using liquid chromatography coupled with tandem mass spectrometry after pre-column derivatizaiton revealed the generation of several amino acids including those essential for life. Re-crystallization of the synthetic products and enantiomeric ratio analysis were subsequently performed. Results from liquid chromatography coupled with either fluorescent detector or tandem mass spectrometry after pre-column derivatization with chiral reagent revealed spontaneous and effective asymmetric resolution of serine and alanine. This work describes a useful analytical platform for investigation of hypotheses regarding the origin and homochirality of amino acids under prebiotic conditions. The formation of numerous amino acids in the electric discharge experiment and the occurrence of high enantiomeric ratios of amino acids in re-crystallization experiment give valuable implications for future studies in unraveling fundamental questions regarding origins and evolution of life.

  • 37.
    Jiang, Tuo
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium(II)-Catalyzed Oxidative Carbocyclization: Stereoselective Formation of C–C and C–B Bonds2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Transition metal catalysis has emerged as one of the most versatile methods for the selective formation of carbon–carbon and carbon–heteroatom bonds. In particular, oxidative carbon–carbon bond forming reactions have been widely studied due to their atom economic feature. This thesis has been focused on the development of new palladium(II)-catalyzed carbocyclization reactions under oxidative conditions.

    The first part of the thesis describes the palladium(II)-catalyzed oxidative carbocyclization-borylation and -arylation of enallenes. In these reactions, the (σ-alkyl)palladium(II) intermediate, which was shown previously to undergo β-hydride elimination, could be trapped in situ by organoboron reagents (B2pin2 and arylboronic acids) to form new carbon–boron and carbon–carbon bonds. Through these two protocols, a range of borylated and arylated carbocycles were obtained as single diastereomers in high yields.

    The second part deals with a palladium(II)-catalyzed oxidative diarylative carbocyclization of enynes. The reaction was proposed to start with a syn-arylpalladation of an alkyne, followed by insertion of the coordinated alkene. Subsequent arylation afforded a series of valuable diarylated tetrahydrofuran and tetrahydropyran products.

    The final part of the thesis advances the previously developed palladium(II)-catalyzed oxidative carbocyclization-borylation of enallenes in an enantioselective manner. C2-symmetric chiral phosphoric acids were used as the novel co-catalyst to trigger the enantioselective formation of intramolecular carbon–carbon bonds. By using this chiral anion strategy, a number of enallenes were converted to the borylated carbocycles with high to excellent enantioselectivity.

  • 38.
    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.

  • 39.
    Kovalenko, Oleksandr O.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lundberg, Helena
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Huebner, Dennis
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tandem alpha-Alkylation/Asymmetric Transfer Hydrogenation of Acetophenones with Primary Alcohols2014In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 30, p. 6639-6642Article in journal (Refereed)
    Abstract [en]

    A tandem -alkylation/asymmetric transfer hydrogenation of acetophenones with primary alcohols, mediated by a single ruthenium catalyst, is described. Under optimized reaction conditions and with use of [Ru(p-cymene)Cl-2](2) in combination with an amino acid hydroxyamide ligand, the chiral secondary alcohol products were isolated in moderate yields and in moderate to good enantiomeric excess (up to 89% ee).

  • 40.
    Kärkäs, Markus D.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Artificial Photosynthesis: Molecular Systems for Catalytic Water Oxidation2014In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 114, no 24, p. 11863-12001Article, review/survey (Refereed)
  • 41.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Li, Xi-Chen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Reaction Mechanism of Water Oxidation Catalyzed by Iron Tetraamido Macrocyclic Ligand Complexes - A DFT Study2014In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, no 4, p. 728-741Article in journal (Refereed)
    Abstract [en]

    Density functional calculations are used to elucidate the reaction mechanism of water oxidation catalyzed by iron tetra-amido macrocyclic ligand (TAML) complexes. The oxidation of the starting TAML-Fe3+-OH2 complex by removing three electrons and two protons leads to the formation of a key intermediate, TAML-Fe5+=O, which can undergo nucleophilic attack by either a water molecule or a nitrate ion. Both pathways involve attack on the oxo group and lead to the production of O-2. The water attack is more favoured and has a total barrier of 15.4 kcal/mol. The alternative nitrate attack pathway has a barrier of 19.5 kcal/mol. Nitrate functions as a cocatalyst by first donating an oxygen atom to the oxo group to form O-2 and a nitrite ion, which can then be reoxidized to regenerate a nitrate ion. Three possible competing pathways result in ligand modification, namely, water and nitrate attack on the ligand, as well as ligand amide oxidation. The water attack on the ligand has a low barrier of only 10.9 kcal/mol and leads to the opening of the benzene ring, which explains the observation of fast catalyst degradation. The lack of activity or lower activity of other catalysts with different substituents is also rationalized.

  • 42.
    Lihammar, Richard
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Enzyme- and Transition Metal-Catalyzed Asymmetric Transformations: Application of Enzymatic (D)KR in Enantioselective Synthesis2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Dynamic kinetic resolution (DKR) is a powerful method for obtaining compounds with high optical purity. The process relies on the combination of a kinetic resolution with an in situ racemization. In this thesis, a combination of an immobilized hydrolase and a transition metal-based racemization catalyst was employed in DKR to transform racemic alcohols and amines into enantioenriched esters and amides, respectively.

    In the first part the DKR of 1,2-amino alcohols with different rings sizes and N-protecting groups is described. We showed that the immobilization method used to support the lipase strongly influenced the stereoselectivity of the reaction.

    The second part deals with the DKR of C3-functionalized cyclic allylic alcohols affording the corresponding allylic esters in high yields and high ee’s. The protocol was also extended to include carbohydrate derivatives, leading to inversion of a hydroxyl substituted chiral center on the carbohydrate.

    The third part focuses on an improved method for obtaining benzylic primary amines. By using a novel, recyclable catalyst composed of Pd nanoparticles on amino-functionalized mesocellular foam, DKR could be performed at 50 °C. Moreover, Lipase PS was for the first time employed in the DKR of amines.

    In the fourth part DKR was applied in the total synthesis of Duloxetine, a compound used in the treatment of major depressive disorder. By performing a six-step synthesis, utilizing DKR in the enantiodetermining step, Duloxetine could be isolated in an overall yield of 37% and an ee >96%.

    In the final part we investigated how the enantioselectivty of reactions catalyzed by Candida Antarctica lipase B for δ-substituted alkan-2-ols are influenced by water. The results showed that the enzyme displays much higher enantioselectivity in water than in anhydrous toluene. The effect was rationalized by the creation of a water mediated hydrogen bond in the active site that helps the enzyme form enantiodiscriminating binding modes.

  • 43.
    Lihammar, Richard
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rönnols, Jerk
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Epimerization of Glycal Derivatives by a Cyclopentadienylruthenium Catalyst: Application to Metalloenzymatic DYKAT2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 45, p. 14756-14762Article in journal (Refereed)
    Abstract [en]

    Epimerization of a non-anomeric stereogenic center in carbohydrates is an important transformation in the synthesis of natural products. In this study an epimerization procedure of the allylic alcohols of glycals by cyclopentadienylruthenium catalyst 1 is presented. The epimerization of 4,6-O-benzylidene-D-glucal 4 in toluene is rapid, and an equlibrium with its D-allal epimer 5 is established within 5min at room temperature. Exchange rates for allal and glucal formation were determined by 1D H-1 EXSY NMR experiments to be 0.055s(-1) and 0.075s(-1), respectively. For 4-O-benzyl-L-rhamnal 8 the epimerization was less rapid and four days of epimerization was required to achieve equilibration of the epimers at room temperature. The epimerization methodology was subsequently combined with acylating enzymes in a dynamic kinetic asymmetric transformation (DYKAT), giving stereoselective acylation to the desired stereoisomers 12, 13, and 15. The net effect of this process is an inversion of a stereogenic center on the glycal, and yields ranging from 71% to 83% of the epimer were obtained.

  • 44.
    Lind, Maria E. S.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical Study of Reaction Mechanism and Stereoselectivity of Arylmalonate Decarboxylase2014In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 4, no 11, p. 4153-4160Article in journal (Refereed)
    Abstract [en]

    The reaction mechanism of arylmalonate decarboxylase is investigated using density functional theory calculations. This enzyme catalyzes the asymmetric decarboxylation of prochiral disubstituted malonic acids to yield the corresponding enantiopure carboxylic acids. The quantum chemical cluster approach is employed, and two different models of the active site are designed: a small one to study the mechanism and characterize the stationary points and a large one to study the enantioselectivity. The reactions of both α-methyl-α-phenylmalonate and α-methyl-α-vinylmalonate are considered, and different substrate binding modes are assessed. The calculations overall give strong support to the suggested mechanism in which decarboxylation of the substrate first takes place, followed by a stereoselective protonation by a cysteine residue. The enediolate intermediate and the transition states are stabilized by a number of hydrogen bonds that make up the dioxyanion hole, resulting in feasible energy barriers. It is further demonstrated that the enantioselectivity in the case of α-methyl-α-phenylmalonate substrate is dictated already in the substrate binding, because only one binding mode is energetically accessible, whereas in the case of the smaller α-methyl-α-vinylmalonate substrate, both the binding and the following transition states contribute to the enantioselectivity.

  • 45.
    Liu, Jianguo
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Asymmetric hydrogenation of allylic alcoholsusing iridium catalysts2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The first part of this thesis is focussed on the enantioselective iridium catalyzeda symmetric hydrogenation of allylic alcohols. The study involved the preparation of a range of allylic alcohols. These allylic alcohols were then hydrogenated, using iridium catalysts that have been previously prepared, to produce chiral alcohols with high yields and excellent enantioselectivity. The selectivity model of the reaction was used to accurately predict the absolute configuration of the hydrogenated products.

    The second part of the thesis was directed on the application of iridium catalyzed asymmetric hydrogenation of allylic alcohols in the synthesis of a late-stage intermediate of Aliskiren. A total of three synthetic routes were evaluated. The best synthesis relies on asymmetric hydrogenation of an allylic ester and an allylic alcohol as key-steps. Full conversion and 94% ee for the allylic alcohol were achieved. The late-stage intermediate of Aliskiren was successfully synthesized in eight steps.

  • 46.
    Lundberg, Helena
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tinnis, Fredrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Selander, Nicklas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Catalytic amide formation from non-activated carboxylic acids and amines2014In: Chemical Society Reviews, ISSN 0306-0012, E-ISSN 1460-4744, Vol. 43, no 8, p. 2714-2742Article, review/survey (Refereed)
    Abstract [en]

    The amide functionality is found in a wide variety of biological and synthetic structures such as proteins, polymers, pesticides and pharmaceuticals. Due to the fact that synthetic amides are still mainly produced by the aid of coupling reagents with poor atom-economy, the direct catalytic formation of amides from carboxylic acids and amines has become a field of emerging importance. A general, efficient and selective catalytic method for this transformation would meet well with the increasing demands for green chemistry procedures. This review covers catalytic and synthetically relevant methods for direct condensation of carboxylic acids and amines. A comprehensive overview of homogeneous and heterogeneous catalytic methods is presented, covering biocatalysts, Lewis acid catalysts based on boron and metals as well an assortment of other types of catalysts.

  • 47. Malkov, Andrei V.
    et al.
    Lee, Darren S.
    Barlog, Maciej
    Elsegood, Mark R. J.
    Kocovsky, Pavel
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-Catalyzed Stereoselective Intramolecular Oxidative Amidation of Alkenes in the Synthesis of 1,3-and 1,4-Amino Alcohols and 1,3-Diamines2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 17, p. 4901-4905Article in journal (Refereed)
    Abstract [en]

    An efficient and practical Pd-catalyzed intramolecular oxidative allylic amidation provides facile access to derivatives of 1,3- and 1,4-amino alcohols and 1,3-diamines. The method operates under mild reaction conditions (RT) with molecular oxygen (1atm) as the sole reoxidant of Pd. Excellent diastereoselectivities were attained with substrates bearing a secondary stereogenic center

  • 48.
    Malmgren, Joel
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Iodonium Salts: Preparation, Chemoselectivity and Metal-Catalyzed Applications2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis concerns the preparation and use of diaryliodonium salts. In Project I various unsymmetrical diaryliodonium salts were reacted with three different nucleophiles in order to study the chemoselectivity of the reactions of the salts. The main focus of this project was to gain a deeper understanding of the underlying factors that affect the chemoselectivity in transition metal-free arylation reactions. They were found to be very nucleophile-dependent. Some nucleophiles were very sensitive to electronic effects, whereas others were sensitive to steric factors. Ultimately, some arenes are never transferred. A very interesting scrambling reaction was also observed under the reaction conditions, where unsymmetrical diaryliodonium salts form symmetrical salts in situ.

    Project II details the preparation of N-heteroaryliodonium salts via a one-pot procedure. The salts were designed so that the N-heteroaryl moiety was selectively transferred in applications both with and without transition metals. The chemoselectivity was demonstrated by selective transfer of the pyridyl group onto two different nucleophiles.

    The third project in the thesis discusses the synthesis of alkynyl(aryl)iodonium salts and alkynylbenziodoxolones from arylsilanes. This protocol could potentially be a very useful complement to the existing procedures, in which boronic acids are used.

    The last part of the thesis (Project IV) describes a C-2 selective arylation of indoles where diaryliodonium salts were used in combination with hetero-geneous palladium catalysis. This transformation was performed in water at ambient temperature to 50 °C, and tolerated variations of both the indole and the diaryliodonium salt. Importantly, several N-H indoles could be arylated. The MCF-supported Pd-catalyst showed very little leaching and it was demonstrated that the main part of the reaction occurred via heterogeneous catalysis.

  • 49.
    Malmgren, Joel
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nagendiran, Anuja
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tai, Cheuk-Wai
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    C-2 Selective Arylation of Indoles with Heterogeneous Nanopalladium and Diaryliodonium Salts2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 42, p. 13531-13535Article in journal (Refereed)
    Abstract [en]

    A simple and efficient method to prepare synthetically useful 2-arylindoles is presented, using a heterogeneous Pd catalyst and diaryliodonium salts in water under mild conditions. A remarkably low leaching of metal catalyst was observed under the applied conditions. The developed protocol is highly C-2 selective and tolerates structural variations both in the indole and in the diaryliodonium salt. Arylations of both NH indoles and N-protected indoles with ortho-substituted, electron-rich, electron-deficient, or halogenated diaryliodonium salts were achieved to give the desired products in high to excellent isolated yields within 6 to 15 h at room temperature or 40 °C.

  • 50.
    Manta, Bianca
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Studies of Enzymatic Reaction Mechanisms: Investigations of Cytosine Deaminase and ω-Transaminase2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, density functional theory is used to study the reaction mechanisms of two dierent enzymes. Quantum chemical cluster models of the active sites were designed using available crystal structures. In this approach only the active site residues are considered and the effects of the surroundings are accounted for by a coordinate-locking scheme and a polarizable continuum model.

    The enzymes studied are cytosine deaminase (CDA) from Escherichia coli and ω-transaminase from Chromobacterium violaceum (Cv-ωTA). CDA is a zinc-dependentenzyme that catalyzes the hydrolytic deamination of cytosine into uracil and ammonia. Cv-ωTA carries out the interchange of amino and keto groups by utilizing the cofactor pyridoxal-5’-phosphate (PLP). The calculations provide optimized geometries and energies of transition states and intermediates, which are analyzed and used to construct a potential energy prole for the reaction and to identify the rate-limiting step. Each theoretical investigation provides a detailed description of the catalytic mechanism and establishes the roleof important active site residues.

    In the rst study (Paper I), it was found that a glutamate and an aspartate residue assist in the proton transfer events throughout the reaction. In the second study (Paper II), it was found that the lysine residue, which in the holo enzyme binds the cofactor PLP, assists in several proton transfer events once it has been replaced by the amino substrate. It was also found that the water substrate can be utilized as a proton shuttle before it is consumed at a later stage in the reaction mechanism.

    Apart from the detailed chemical insight, the results in this thesis confirmthat density functional theory together with cluster models of active sites is a very useful approach for studying diverse enzymatic reaction mechanisms.

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