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  • 201.
    Engqvist, Magnus
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Direct Amino Acid-Catalyzed Enantioselective α-Oxidation Reactions and Asymmetric de novo Synthesis of Carbohydrates2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The ability of amino acids to form nucleophilic enamines with aldehydes and ketones has been used in the development of asymmetric α-oxidation reactions with electrophilic oxidizing agents. Singlet molecular oxygen has for the first time been asymmetrically incorporated into aldehydes and ketones, and the products were isolated as their corresponding diols in good yields and ee’s. Organocatalytic α-oxidations of cyclic ketones with iodosobenzene and N-sulfonyloxaziridine were also possible and furnished after reduction the product diols in generally low yields and in low to good ee’s. Amino acids have also been shown to catalyze the formation of carbohydrates by sequential aldol reactions. For example, proline and hydroxy proline mediate a highly selective trimerisation of α-benzyloxyacetaldehyde into allose, which was obtained in >99 % ee. Non linear effect studies of this reaction revealed the largest permanent nonlinear effect observed in a proline-catalyzed reaction to date. Moreover, polyketides were also assembled in a similar fashion by an amino acid-catalyzed one-pot reaction, and was successful for the trimerisation of propionaldehyde, however the sequential cross aldol reactions suffered from lower selectivities. This problem was overcome by the development of a two-step synthesis that enabled the formation of a range of polyketides with excellent selectivities from a variety of aldehydes. The method furnishes the polyketides via the shortest route reported and in comparable product yields to most multi-step synthesis. All polyketides were isolated as single diastereomers with >99 % ee. Based on the observed amino acid-catalysis, amino acids are thought to have taken part in the prebiotic formation of tetroses and hexoses.

  • 202.
    Engström, Karin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Enantioselective biotransformations using engineered lipases from Candida antarctica2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Enzymes are attractive catalysts in organic synthesis since they are efficient, selective and environmentally friendly. A large number of enzyme-catalyzed transformations have been described in the literature. If no natural enzyme can carry out a desirable reaction, one possibility is to modify an existing enzyme by protein engineering and thereby obtain a catalyst with the desired properties. In this thesis, the development of enantioselective enzymes and their use in synthetic applications is described. 

    In the first part of this thesis, enantioselective variants of Candida antarctica lipase A (CALA) towards α-substituted p-nitrophenyl esters were developed by directed evolution. A highly selective variant of CALA towards p-nitrophenyl 2-phenylpropanoate was developed by pairwise randomization of amino acid residues close to the active site. The E value of this variant was 276 compared to 3 for the wild type.

    An approach where nine residues were altered simultaneously was used to discover another highly enantioselective CALA variant (E = 100) towards an ibuprofen ester. The sterical demands of this substrate made it necessary to vary several residues at the same time in order to reach a variant with improved properties.

    In the second part of the thesis, a designed variant of Candida antarctica lipase B (CALB) was employed in kinetic resolution (KR) and dynamic kinetic resolution (DKR) of secondary alcohols. The designed CALB variant (W104A) accepts larger substrates compared to the wild type, and by the application of CALB W104A, the scope of these resolutions was extended.

    First, a DKR of phenylalkanols was developed using CALB W104A. An enzymatic resolution was combined with in situ racemization of the substrate, to yield the products in up to 97% ee. Secondly, the KR of diarylmethanols with CALB W104A was developed. By the use of diarylmethanols with two different aryl groups, highly enantioselective transformations were achieved.

  • 203.
    Engström, Karin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Protein engineering of enzymes for improved enantioselectivity and application of engineered enzymes in organic synthesis2010Licentiate thesis, comprehensive summary (Other academic)
  • 204.
    Engström, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Gustafson, Karl P. J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Shakeri, Mozaffar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tai, Cheuk-Wai
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Co-immobilization of an Enzyme and a Metal into the Compartments of Mesoporous Silica for Cooperative Tandem Catalysis: An Artificial Metalloenzyme2013In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 52, no 52, p. 14006-14010Article in journal (Refereed)
    Abstract [en]

    Surpassing nature: A hybrid catalyst in which Candida antarctica lipase B and a nanopalladium species are co-immobilized into the compartments of mesoporous silica is presented. The metal nanoparticles and the enzyme are in close proximity to one another in the cavities of the support. The catalyst mimics a metalloenzyme and was used for dynamic kinetic resolution of a primary amine in high yield and excellent enantioselectivity.

  • 205.
    Engström, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nyhlén, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sandström, Anders G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Directed evolution of an enantioselective lipase with broad substrate scope for hydrolysis of α-substituted esters2010In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 132, no 20, p. 7038-7042Article in journal (Refereed)
    Abstract [en]

    A variant of Candida antarctica lipase A (CalA) was developed for the hydrolysis of α-substituted p-nitrophenyl esters by directed evolution. The E values of this variant for 7 different esters was 45−276, which is a large improvement compared to 2−20 for the wild type. The broad substrate scope of this enzyme variant is of synthetic use, and hydrolysis of the tested substrates proceeded with an enantiomeric excess between 95−99%. A 30-fold increase in activity was also observed for most substrates. The developed enzyme variant shows (R)-selectivity, which is reversed compared to the wild type that is (S)-selective for most substrates.

  • 206.
    Engström, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nyhlén, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sandström, Anders G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Enantioselective Kinetic Resolution of p-Nitrophenyl 2-Phenylpropanoate by a Variant of Candida antarctica Lipase A Developed by Directed Evolution2010In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 132, no 20, p. 7038-7042Article in journal (Refereed)
    Abstract [en]

    A variant of Candida antarctica lipase A (CalA) was developed for the hydrolysis of α-substituted p-nitrophenyl esters by directed evolution. The E values of this variant for 7 different esters was 45−276, which is a large improvement compared to 2−20 for the wild type. The broad substrate scope of this enzyme variant is of synthetic use, and hydrolysis of the tested substrates proceeded with an enantiomeric excess between 95−99%. A 30-fold increase in activity was also observed for most substrates. The developed enzyme variant shows (R)-selectivity, which is reversed compared to the wild type that is (S)-selective for most substrates.

  • 207.
    Engström, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Shakeri, Mozaffar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dynamic Kinetic Resolution of β-Amino Esters by a Heterogeneous System of a Palladium Nanocatalyst and Candida antarctica Lipase A2011In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 10, p. 1827-1830Article in journal (Refereed)
    Abstract [en]

    A dynamic kinetic resolution (DKR) of β-amino esters have been developed by the use of a heterogeneous racemization catalyst and an immobilized enzyme that accepts aromatic, heteroaromatic and aliphatic substrates. The reaction conditions were optimized to yield an efficient catalytic system without by-product formation. The products are obtained in 96–99 % ee and high yields

  • 208.
    Engström, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Vallin, Michaela
    Hult, Karl
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kinetic resolution of diarylmethanols using a mutated variant of lipase CALB2012In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 68, no 37, p. 7613-7618Article in journal (Refereed)
    Abstract [en]

    An enzymatic kinetic resolution of diarylmethanols via acylation has been developed. This was achieved by the use of a mutated variant of CALB that accepts larger substrates compared to the wild type. By the use of diarylmethanols with two differently sized aryl groups, enantioselective transformations were achieved. A larger size-difference led to a higher enantioselectivity. In addition, substrates with electronically different aryl groups, such as phenyl and pyridyl, also gave an enantioselective reaction. The highest E value was observed with a substrate where steric and electronic effects were combined.

  • 209.
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Carbohydrate dynamics and interactions studied by NMR spectroscopy2013Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The combination of NMR spectroscopy and molecular dynamics (MD) simulations are powerful tools in the studying of bioorganic molecules in solution. In this thesis two such studies are presented with focus on the NMR aspect. The caffeine association to sugars (D-glucose and sucrose) was investigated by NMR titrations and NOESY experiments in paper I. The observations from the NMR experiments confirmed MD simulations showing that the binding occurs by a face-to-face interaction between the aromatic surface of the caffeine and axial protons of the sugar ring. Different sugar molecules and residues have different preferences regarding which side of the sugar ring that are involved in the binding. The sucrose residues bind with only one ring face each whereas β-D-glucopyranose has two sides of similar binding probability and the α-D-glucopyranose has something in between. The MD simulations showed that the driving force of the binding is partly driven by hydration effects that favor the enthalpy of the system. A new approach to calculate NMR relaxation parameters (that is dependent on molecular motions) from computational simulations is presented in paper II. Each sugar residue is assumed to be a rigid unit connected by flexible joints in the approach, thus the name diffusive chain model (DCM). The simplified model together with a stochastic simulation approach lowers the computational cost which makes it possible to acquire long enough trajectories to the calculations of spin relaxation parameters. Two case studies with slightly different methodologies are presented. In one of them, spin relaxation parameters are reproduced for the human milk oligosaccharide LNF-1 in a feasible way by the use of Brownian dynamics.

  • 210.
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Exploring the Molecular Behavior of Carbohydrates by NMR Spectroscopy: Shapes, motions and interactions2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Carbohydrates are essential biomolecules that decorate cell membranes and proteins in organisms. They are important both as structural elements and as identification markers. Many biological and pathogenic processes rely on the identification of carbohydrates by proteins, thereby making them attractive as molecular blueprints for drugs. This thesis describes how NMR spectroscopy can be utilized to study carbohydrates in solution at a molecular level. This versatile technique facilitates for investigations of (i) shapes, (ii) motions and (iii) interactions.

    A conformational study of an E. coli O-antigen was performed by calculating atomic distances from NMR NOESY experiments. The acquired data was utilized to validate MD simulations of the LPS embedded in a membrane. The agreement between experimental and calculated data was good and deviations were proven to arise from spin-diffusion. In another study presented herein, both the conformation and the dynamic behavior of amide side-chains linked to derivatives of D-Fucp3N, a sugar found in the O-antigen of bacteria, were investigated. J-couplings facilitated a conformational analysis and 13C saturation transfer NMR experiments were utilized to measure rate constants of amide cis-trans isomerizations.

    13C NMR relaxation and 1H PFG diffusion measurements were carried out to explore and describe the molecular motion of mannofullerenes. The dominating motions of the mannofullerene spectral density were found to be related to pulsating motions of the linkers rather than global rotational diffusion. The promising inhibition of Ebola viruses identified for a larger mannofullerene can thus be explained by an efficient rebinding mechanism that arises from the observed flexibility in the linker.

    Molecular interactions between sugars and caffeine in water were studied by monitoring chemical shift displacements in titrations. The magnitude of the chemical shift displacements indicate that the binding occurs by a face to face stacking of the aromatic plane of caffeine to the ring plane of the sugar, and that the interaction is at least partly driven by solvation effects. Also, the binding of a Shigella flexneri serotype Y octasaccharide to a bacteriophage Sf6 tail spike protein was investigated. This interaction was studied by 1H STD NMR and trNOESY experiments. A quantitative analysis of the STD data was performed employing a newly developed method, CORCEMA-ST-CSD, that is able to simulate STD data more accurately since the line broadening of protein resonances are accounted for in the calculations.

  • 211.
    Engström, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mobarak, Hani
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ståhle, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Conformational Dynamics and Exchange Kinetics of N-Formyl and N-Acetyl Groups Substituting 3-Amino-3,6-dideoxy-alpha-D-galactopyranose, a Sugar Found in Bacterial O-Antigen Polysaccharides2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 41, p. 9487-9497Article in journal (Refereed)
    Abstract [en]

    Three dimensional shape and conformation of. carbohydrates are important factors in molecular recognition events and the N-acetyl group of a monosaccharide residue can function as a conformational gatekeeper whereby it influences the overall shape of the oligosaccharide. NMR spectroscopy and quantum mechanics (QM) calculations are used herein to investigate both the conformational preferences and the dynamic behavior of N-acetyl and N-formyl substituents of 3-amino-3,6-dideoxy-alpha-D-galactopyranose, a sugar and substitution pattern found in bacterial O-antigen polysaccharides. QM calculations suggest that the amide oxygen can be involved in hydrogen bonding with the axial OH4 group primarily but also with the equatorial OH2 group. However, an NMR J coupling analysis indicates that the 01 torsion angle, adjacent to the sugar ring, prefers an ap conformation where conformations <180 degrees also are accessible, but does not allow for intramolecular hydrogen bonding. In the formyl-substituted compound (4)J(HH) coupling constants to the exo-cyclic group were detected and analyzed. A van't Hoff analysis revealed that the trans conformation at the amide bond is favored by Delta G degrees approximate to - 0.8 kcal.mol(-1) in the formyl-containing compound and with Delta G degrees approximate to -2.5 kcal.mol(-1) when the N-acetyl group is the substituent. In both cases the enthalpic term dominates to the free energy, irrespective of water or DMSO as solvent, with only a small contribution from the entropic term. The cis-trans isomerization of the theta(2) torsion angle, centered at the amide bond, was also investigated by employing H-1 NMR line shape analysis and C-13 NMR saturation transfer experiments. The extracted transition rate constants were utilized to calculate transition energy barriers that were found to be about 20 kcal.mol(-1) in both DMSO-d(6) and D2O. Enthalpy had a higher contribution to the energy barriers in DMSO-d(6) compared to in D2O, where entropy compensated for the loss of enthalpy.

  • 212.
    Engström, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mobarak, Hani
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ståhle, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Conformational dynamics and exchange kinetics of N-formyl and N-acetyl groups substituting 3-amino-3,6-dideoxy-α-D-galactopyranose, a sugar found in bacterial O-antigen polysaccharidesManuscript (preprint) (Other academic)
  • 213.
    Engström, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Muñoz, Antonio
    Illescas, Beatriz M.
    Martin, Nazario
    Ribeiro-Viana, Renato
    Rojo, Javier
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Investigation of glycofullerene dynamics by NMR spectroscopy2015In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 32, p. 8750-8755Article in journal (Refereed)
    Abstract [en]

    Glycofullerenes, in which carbohydrate molecules are attached via a linker to a [60]fullerene core, facilitate spherical presentation of glyco-based epitopes. We herein investigate the dynamics of two glycofullerenes, having 12 and 36 mannose residues at their periphery, by NMR translational diffusion and quantitative C-13 relaxation studies employing a model-free approach for their interpretation. The sugar residues are shown to be highly flexible entities with S-2 < 0.2 in both compounds. Notably, the larger glycofullerene with longer linkers shows faster internal dynamics and higher flexibility than its smaller counterpart. The dynamics and flexibility as well as the slower translational diffusion of the larger glycofullerene, thereby favoring rebinding to a receptor, may together with its spatial extension explain why it is better than the smaller one at blocking the DC-SIGN receptor and inhibiting the infection by pseudotyped Ebola virus particles.

  • 214.
    Ericsson, Daniel J.
    et al.
    1Department of Cell and Molecular Biology, Uppsala University, Biomedical Center.
    Kasrayan, Alex
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johansson, Patrik
    1Department of Cell and Molecular Biology, Uppsala University, Biomedical Center.
    Bergfors, Terese
    1Department of Cell and Molecular Biology, Uppsala University, Biomedical Center.
    Sandström, Anders G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mowbray, Sherry L.
    Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Center.
    X-Ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation2008In: Journal of Molecular Biology, ISSN 0022-2836, Vol. 376, no 1, p. 109-119Article in journal (Refereed)
    Abstract [en]

    In nature, lipases (EC 3.1.1.3) catalyze the hydrolysis of triglycerides to form glycerol and fatty acids. Under the appropriate conditions, the reaction is reversible, and so biotechnological applications commonly make use of their capacity for esterification as well as for hydrolysis of a wide variety of compounds. In the present paper, we report the X-ray structure of lipase A from Candida antarctica, solved by single isomorphous replacement with anomalous scattering, and refined to 2.2-Å resolution. The structure is the first from a novel family of lipases. Contrary to previous predictions, the fold includes a well-defined lid as well as a classic α/β hydrolase domain. The catalytic triad is identified as Ser184, Asp334 and His366, which follow the sequential order considered to be characteristic of lipases; the serine lies within a typical nucleophilic elbow. Computer docking studies, as well as comparisons to related structures, place the carboxylate group of a fatty acid product near the serine nucleophile, with the long lipid tail closely following the path through the lid that is marked by a fortuitously bound molecule of polyethylene glycol. For an ester substrate to bind in an equivalent fashion, loop movements near Phe431 will be required, suggesting the primary focus of the conformational changes required for interfacial activation. Such movements will provide virtually unlimited access to solvent for the alcohol moiety of an ester substrate. The structure thus provides a basis for understanding the enzyme's preference for acyl moieties with long, straight tails, and for its highly promiscuous acceptance of widely different alcohol and amine moieties. An unconventional oxyanion hole is observed in the present structure, although the situation may change during interfacial activation

  • 215.
    Eriksson, Kristofer
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Gothelid, Emmanuelle
    Puglia, Carla
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Oscarsson, Sven
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Performance of a biomimetic oxidation catalyst immobilized on silica particles2013In: Journal of Catalysis, ISSN 0021-9517, E-ISSN 1090-2694, Vol. 303, p. 16-21Article in journal (Refereed)
    Abstract [en]

    A biomimetic oxidation catalyst, cobalt porphyrin with thiol linkers, was chemically conjugated to silica particles and utilized in the oxidation of hydroquinone to benzoquinone. The cobalt porphyrin/silica particle catalyst was characterized with Inductively Coupled Plasma (ICP) and X-ray Photoelectron Spectroscopy (XPS). The catalytic performance of the cobalt porphyrin molecules was compared to previous results for the same catalyst grafted to a gold surface and on silicon wafers. The measured catalytic activity, after background correction, was 100 times higher than that of its homogeneous counterpart, 10 times higher than that on a silicon wafer, and almost the same as that on a gold surface. The turnover frequency rates after 400 h are still comparable with initial rates reported for homogeneous porphyrins and salophens, whereas the use of particles as support increases the active surface area, which removes the limitations for scale-up associated with the previously used silicon wafers and gold surfaces.

  • 216. Eriksson, Kristofer L.E.
    et al.
    Chow, Winnie W.Y.
    Puglia, Carla
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Göthelid, Emmanuelle
    Oscarsson, Sven
    Performance of a biomimetic oxidation catalyst immobilized on silicon wafers: comparison with its gold congener2010In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 26, no 21, p. 16349-16354Article in journal (Refereed)
    Abstract [en]

    With the aim of extending the usefulness of an existing biomimetic catalytic system, cobalt porphyrin catalytic units with thiol linkers were heterogenized via chemical grafting to silicon wafers and utilized for the catalytic oxidation of hydroquinone to p-benzoquinone. Atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) were used to analyze the morphology and composition of the heterogeneous catalyst. The results of the catalytic oxidation of hydroquinone obtained with porphyrins grafted on silicon were compared with those obtained earlier with the same catalyst in homogeneous phase and immobilized on gold. It was found that the catalysis could run over 400 h, without showing any sign of deactivation. The measured catalytic activity is at least 10 times higher than that measured under homogeneous conditions, but also 10 times lower than that observed with the catalytic unit immobilized on gold. The reasons of this discrepancy are discussed in term of substrate influence and overlayer organization. The silicon-immobilized catalyst has potential as an advanced functional material with applications in oxidative heterogeneous catalysis of organic reactions, as it combines long-term relatively high activity with low cost.

  • 217.
    Eriksson, Lars
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Methyl 3-O-α-l-fucopyranosyl β-d-glucopyranoside tetrahydrate2012In: Acta Crystallographica Section E: Structure Reports Online, ISSN 1600-5368, E-ISSN 1600-5368, Vol. 68, p. o3180-o3181Article in journal (Refereed)
    Abstract [en]

    The title compound, C13H24O10·4H2O, is the methyl glycoside of a disaccharide structural element present in the backbone of the capsular polysaccharide from Klebsiella K1, which contains only three sugars and a substituent in the polysaccharide repeating unit. The conformation of the title disaccharide is described by the glycosidic torsion angles ϕH = 51.1 (1)° and ψH = 25.8 (1)°. In the crystal, a number of O—HO hydrogen bonds link the methyl glycoside and water mol­ecules, forming a three-dimensional network. One water mol­ecule is disordered over two positions with occupancies of 0.748 (4) and 0.252 (4).

  • 218. Eriksson, Lars
    et al.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Methyl α-l-rhamnosyl-(1→2)[α-l-rhamnosyl-(1→3)]-α-l-rhamnoside penta­hydrate: synchrotron study2012In: Acta Crystallographica Section E: Structure Reports Online, ISSN 1600-5368, E-ISSN 1600-5368, Vol. 68, no 7, p. o2221-o2222Article in journal (Refereed)
    Abstract [en]

    The title hydrate, C19H34O13·5H2O, contains a vicinally disubstituted tris­accharide in which the two terminal rhamnosyl sugar groups are positioned adjacent to each other. The conformation of the tris­accharide is described by the glycosidic torsion angles ϕ2 = 48 (1)°, ψ2 = −29 (1)°, ϕ3 = 44 (1)° and ψ3 = 4 (1)°, whereas the ψ2 torsion angle represents a conformation from the major state in solution, the ψ3 torsion angle conformation may have been caught near a potential energy saddle-point when compared to its solution structure, in which at least two but probably three conformational states are populated. Extensive inter­molecular O—HO hydrogen bonding is present in the crystal and a water-containing channel is formed along the b-axis direction.

  • 219.
    Fontana, Carolina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    NMR spectroscopy in structural and conformational analysis of bacterial polysaccharides2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Carbohydrates constitute one of the three major classes of biomolecules found in all living cells and, unlike nucleic acids and proteins, their polymeric structures are not based on a template. The structural diversity of these molecules confers them an enormous capacity to encode information in biological systems, acting as efficient mediators in the interaction of the cell with the environment. In order to understand the roles of glycans in biological processes it is of key importance to have a detailed understanding of their structures and conformational preferences, and NMR spectroscopy is one of most powerful techniques for the study of these molecules in solution.

    This thesis is focused on the structural and conformational analysis of lipopolysaccharides from Gram-negative bacteria. In the first two projects (Chapter 2 and 3) the structural analyses of the biological repeating units of the O-antigen polysaccharides from E. coli O174ab and O115 are described; in both cases a combination of NMR spectroscopy and gas chromatography techniques were used. Special emphasis was made in the characterization of the O-acetylation patterns observed in the native O-antigen polysaccharide from E. coli O115. Chapter 4 describes the development of a new methodology for the determination of the absolute configuration of monosaccharide components of glycans. This methodology was used in the structural elucidation of the O-antigen PS of E. coli O155 (Chapter 5) that was carried out in a semi-automated manner using the program CASPER and unassigned NMR data. The conformational preferences of O-antigen PS of E. coli O5ac and O5ab are analyzed in Chapter 6, using a combination of NMR spectroscopy and molecular modeling methods. In Chapter 7 the structural analysis is focused on the core region of the LPS, and the structures of the deacylated lipooligosaccharides of three rough mutants of B. melitesis are reported. In several of the aforementioned chapters, the biosynthetic aspects behind the assembly of the respective PSs were examined on the bases of genetic information available in the NCBI and ECODAB databases.  Finally, in Chapter 8, different NMR pulse sequences available for the study of proteins and nucleic acids were evaluated and optimized for the structural analysis of 13C uniformly-labeled oligo- and polysaccharides.

  • 220.
    Fontana, Carolina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural studies of glycans by NMR spectroscopy2012Licentiate thesis, comprehensive summary (Other academic)
  • 221.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Conde-Alvarez, Raquel
    Ståhle, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Holst, Otto
    Iriarte, Maite
    Zhao, Yun
    Arce-Gorvel, Vilma
    Hanniffy, Sean
    Gorvel, Jean-Pierre
    Moriyon, Ignacio
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural Studies of Lipopolysaccharide-defective Mutants from Brucella melitensis Identify a Core Oligosaccharide Critical in Virulence2016In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 291, no 14, p. 7727-7741Article in journal (Refereed)
    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.

  • 222.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Holst, Otto
    Moriyón, Ignacio
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural studies of the rough lipopolysaccharides of Brucella melitensis mutants affected in the biosynthesis of the core and O-antigen polysaccharideManuscript (preprint) (Other academic)
  • 223.
    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.
    13C-based NMR spectroscopy for Structure Analysis of Uniformly 13C-labeled Oligo- and PolysaccharidesManuscript (preprint) (Other academic)
  • 224.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Li, Shengyu
    Yang, Zhennai
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural studies of the exopolysaccharide from Lactobacillus plantarum C88 using NMR spectroscopy and the program CASPER2015In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 402, p. 87-94Article in journal (Refereed)
    Abstract [en]

    Some lactic acid bacteria, such as those of the Lactobacillus genus, have the ability to produce exopolysaccharides (EPSs) that confer favorable physicochemical properties to food and/or beneficial physiological effects on human health. In particular, the EPS of Lactobacillus plantarum C88 has recently demonstrated in vitro antioxidant activity and, herein, its structure has been investigated using NMR spectroscopy and the computer program CASPER (Computer Assisted Spectrum Evaluation of Regular polysaccharides). The pentasaccharide repeating unit of the O-deacetylated EPS consists of a trisaccharide backbone, -> 4)-alpha-DGalp-(1 -> 2)-alpha-D-Glcp-(1 -> 3)-beta-D-Glcp-(1 ->, with terminal D-Glc and D-Gal residues (1.0 and 0.8 equiv per repeating unit, respectively) extending from O3 and O6, respectively, of the -> 4)-alpha-D-Galp-(1 -> residue. In the native EPS an O-acetyl group is present, 0.85 equiv per repeating unit, at O2 of the alpha-linked galactose residue; thus the repeating unit of the EPS has the following structure: -> 4)[beta-D-Glcp-(1 -> 3)][beta-D-Galp-(1 -> 6)]alpha-D-Galp2Ac-(1 -> 2)-alpha-D-Glcp-(1 -> 3)-beta-D-Glcp-(1 ->. These structural features, and the chain length (similar to 10(3) repeating units on average, determined in a previous study), are expected to play an important role in defining the physicochemical properties of the polymer.

  • 225.
    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.

  • 226.
    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.
    Structural studies and biosynthetic aspects of the o antigen polysaccharide from Escherichia coli o1742012In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 354, p. 102-105Article in journal (Refereed)
    Abstract [en]

    The structure of the repeating unit of the O-antigenic polysaccharide (PS) from Escherichia coli O174 has been determined. Component analysis together with H-1 and C-13 NMR spectroscopy experiments were employed to elucidate the structure. Inter-residue correlations were determined by H-1, C-13-heteronuclear multiple-bond correlation and H-1, H-1-NOESY experiments. The PS is composed of tetrasaccharide repeating units with the following structure: -> 4)-beta-D-GlcpA-(1 -> 3)-beta-D-Galp-(1 -> 3)-beta-D-GalpNAc-(1 -> vertical bar beta-D-GlcpNAc-(1 -> 2) Cross-peaks of low intensity were present in the NMR spectra consistent with a beta-D-GlcpNAc-(1 -> 2)-beta-D-GlcpA(1 -> structural element at the terminal part of the polysaccharide, which on average is composed of similar to 15 repeating units. Consequently the biological repeating unit has a 3-substituted N-acetyl-D-galactosamine residue at its reducing end.

  • 227.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ramström, Kristoffer
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural studies of the O-antigen polysaccharide from Escherichia coli O115 and biosynthetic aspects thereof2013In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 23, no 3, p. 354-362Article in journal (Refereed)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) of Escherichia coliO115 has been investigated using a combination of component analysis and 1D and 2D nuclear magnetic resonance (NMR) spectroscopy experiments. The repeating unit of the O-antigen was elucidated using the O-deacetylated PS and has the following branched pentasaccharide structure: →3)[β-L-Rhap-(1 → 4)]-β-D-GlcpNAc-(1 → 4)-α-D-GalpA-(1 → 3)-α-D-Manp-(1 → 3)-β-D-GlcpNAc-(1→. Cross-peaks of low intensity, corresponding to a β-L-Rhap-(1 → 4)-β-D-GlcpNAc-(1→ structural element, were present in the NMR spectra and attributed to the terminal part of the PS; this information defines the biological repeating unit of the O-antigen by having a 3-substituted N-acetyl-D-glucosamine (GlcNAc) residue at its reducing end. Analysis of the NMR spectra of the native PS revealed O-acetyl groups distributed over different positions of theL-Rhap residue (∼0.70 per repeating unit) as well as at O-2 and O-3 of the D-GalpA residue (∼0.03 and ∼0.25 per repeating unit, respectively), which is in agreement with the presence of two acetyltransferases previously identified in the O-antigen gene cluster (Wang Q, Ruan X, Wei D, Hu Z, Wu L, Yu T, Feng L, Wang L. 2010. Mol Cell Probes. 24:286–290.). In addition, the four glycosyltransferases initially identified in the O-antigen gene cluster of E. coli O115 were analyzed using BLAST, and the function of two of them predicted on the basis of similarities with glycosyltransferases from Shigella dysenteriae type 5 and 12, as well as E. coli O58 and O152.

  • 228.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Karolinska Institute.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Facile Structural Elucidation of Glycans Using NMR Spectroscopy Data and the Program CASPER: Application to the O-Antigen Polysaccharide of Escherichia coli O1552013In: ChemPlusChem, ISSN 2192-6506, Vol. 78, no 11, p. 1327-1329Article in journal (Refereed)
    Abstract [en]

    The program CASPER was successfully employed to rapidly elucidate a new O-antigen polysaccharide structure (obtained from a strain of Escherichia coli serogroup O155), using solelyunassigned NMR spectroscopy data as input information. Thus, what is considered the most tedious and time-consuming part of the structural elucidation process has been reduced from several hours (or even days) of manual interpretation to about four minutes of automated analysis.

  • 229.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural studies and biosynthetic aspects of the O-antigen polysaccharide from Escherichia coli O422015In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 403, p. 174-181Article in journal (Refereed)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from Escherichia coli O42 has been investigated by NMR spectroscopy as the main method, which was complemented with sugar analysis, mass spectrometry, and analysis of biosynthetic information. The O-specific chain of the O-deacylated lipopolysaccharide (LPS-OH) consists of branched tetrasaccharide-glycerol repeating units joined by phosphodiester linkages. The lipid-free polysaccharide contains 0.8 equiv of O-acetyl groups per repeating unit and has the following teichoic acid-like structure: Based on biosynthetic aspects, this should also be the biological repeating unit. This O-antigen structure is remarkably similar to that of E. coli O28ac, differing only in the presence or absence, respectively, of a glucose residue at the branching point. The structural similarity explains the serological cross-reactivity observed between strains of these two serogroups, and also their almost identical O-antigen gene cluster sequences. -> 2)-(R)-Gro-(1-P-4)-beta-D-GlcpNAc-(1 -> 3)-beta-D-Galf2Ac-(1 -> 3)-alpha-D-GlcpNAc-(1 -> vertical bar a-D-Glcp-(1 -> 3)

  • 230.
    Fontana, Carolina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zaccheus, Mona
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Weintraub, Andrej
    Ansaruzzaman, Mohammad
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural studies of a polysaccharide from Vibrio parahaemolyticus strain AN-160002016In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 432, p. 41-49Article in journal (Refereed)
    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.

  • 231. Foster, R. A.
    et al.
    Carlin, N. I. A.
    Majcher, M.
    Tabor, H.
    Ng, L.-K.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural elucidation of the O-antigen of the Shigella flexneri provisionalserotype 88-893: structural and serological similarities with S. flexneri provisional serotype Y394 (1c)2011In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, no 6, p. 872-876Article in journal (Refereed)
    Abstract [en]

    The structure of the repeating unit of the O-antigen polysaccharide from Shigella flexneri provisional serotype 88-893 has been determined. 1H and 13C NMR spectroscopy as well as 2D NMR experiments were employed to elucidate the structure. The carbohydrate part of the hexasaccharide repeating unit is identical to the previously elucidated structure of the O-polysaccharide from S. flexneri prov. serotype Y394. The O-antigen of S. flexneri prov. serotype 88-893 carries 0.7 mol O-acetyl group per repeating unit located at O-2 of the 3-substituted rhamnosyl residue, as identified by H2BC and BS-CT-HMBC NMR experiments. The O-antigen polysaccharide is composed of hexasaccharide repeating units with the following structure: →2)-α-l-Rhap-(1→2)-α-l-Rhap-(1→3)-α-l-Rhap2Ac-(1→3)[α-d-Glcp-(1→2)-α-d-Glcp-(1→4)]-β-d-GlcpNAc-(1→. Serological studies showed that type antigens for the two provisional serotypes are identical; in addition 88-893 expresses S. flexneri group factor 6 antigen. We propose that provisional serotypes Y394 and 88-893 be designated as two new serotypes 7a and 7b, respectively, in the S. flexneri typing scheme.

  • 232. Fourniere, Viviane
    et al.
    Skantz, Linnea
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sajtos, Ferenc
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Oscarson, Stefan
    Lahmann, Martina
    Synthesis of the Lewis b pentasaccharide and a HSA-conjugate thereof2010In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 66, no 39, p. 7850-7855Article in journal (Refereed)
    Abstract [en]

    Helicobacter pylori, a gastric pathogen, binds to various blood group antigens, including the Lewis types, present in the gastric tissue and a relation between the presentation of the ligands and the overall strength of binding has been assumed. Synthetic Lewis b tetra- and hexasaccharide conjugates are available but not the analogous pentasaccharide. An efficient synthesis of the amino spacer equipped Lewis b pentasaccharide, 3-aminopropyl alpha-L-fucopyranosyl-(1 -> 2)-beta-D-galactopyranosyl-(1 3)-[alpha-L-fucopyranosyl-(1 -> 4)]-2-acetamido-2-deoxy-beta-D-glucopyranosyl-(1 -> 3)-beta-D-galactopyranoside, is presented to enable further investigation of the carbohydrate recognition process of H. pylori.

  • 233.
    Fournière, Viviane
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Cumpstey, Ian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of non-glycosidically linked selenoether pseudodisaccharides2010In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 51, no 16, p. 2127-2129Article in journal (Refereed)
    Abstract [en]

    Non-glycosidically linked disaccharide mimetics with a selenoether functionality linking the two monosaccharide residues have been synthesised. Protected Glc(Se3–3)Glc, Glc(Se3–6)Glc and Glc(Se3–6)Man structures were obtained. Selenium was introduced by displacement of carbohydrate sulfonates with a selenobenzoate anion. Conversion into diselenides by methanolysis of the benzoate and aerial oxidation was followed by reduction of the diselenides to selenolates, and in situ displacement of a second carbohydrate sulfonate in an SN2 reaction to give selenoethers. Glc(Se3–3)Glc and Glc(Se3–6)Glc were also obtained in deprotected form.

  • 234.
    Fransson, Ann-Britt L.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Deracemization of Functionalized Alcohols via Combined Ruthenium and Enzyme Catalysis2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The major part of this thesis describes the synthesis of enantiopure alcohols and diols by combining ruthenium-catalyzed racemization or epimerization and lipase-catalyzed asymmetric transformations. A minor part of this thesis is focused on ruthenium-catalyzed redox reactions for transfer hydrogenation of 1,3-cycloalkanediketones.

    Kinetic resolution of racemic γ-hydroxy acid derivatives was performed via Pseudomonas cepacia lipase (PS-C)-catalyzed transesterification. γ-Hydroxy esters and γ-hydroxy amides were studied showing in higher selec-tivity and yields for the γ-hydroxy amides. The enzyme PS-C tolerates both variation in the chain length and different functionalities giving good to high enantioselectivity. Combining enzymatic kinetic resolution with a ruthenium-catalyzed racemization led to a dynamic kinetic resolution (DKR). The use of 2,4-dimethyl-3-pentanol as a hydrogen source to suppress ketone formation in the dynamic kinetic resolution increased the yields of the acetate product. The synthetic utility of this procedure was illustrated by the practical synthesis of the γ-lactone (R)-5-methyltetrahydrofuran-2-one.

    A distereoselective transformation of cis/trans-1,3-cyclohexandiol using Candida antarctica lipase B (CALB)-catalyzed transesterification was of interest. Desymmetrization of cis-1,3-cyclohexanediol to the (R-monoacetate was successfully accomplished. Enantiopure (R,R)-diacetate was obtained from the (R)-monoacetate in a DYKAT process at room tem-perature. Metal- and enzyme-catalyzed transformation of cis/trans-1,3-cyclohexanediol using PS-C, gives a high diastereoselectivity for cis-diacetate. The (S)-mono-acetate was obtained from cis-diacetate by CALB-catalyzed hydrolysis. In addition, it was shown, by the use of deuterium-labeling that intramolecular acyl migration does not occur in the transformation of cis-monoacetate to the cis-diacetate.

    Ruthenium-catalyzed transfer hydrogenation of 1,3-cyclohexanedione under microwave heating was developed as an efficient and fast method for the preparation of 1,3-cycloalkandiols.

  • 235.
    Fransson, Ann-Britt L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Borén, Linnéa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pàmies, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kinetic Resolution and Chemoenzymatic Dynamic Kinetic Resolution of Functionalized γ-Hydroxy Amides2005In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 70, no 7, p. 2582-2587Article in journal (Refereed)
    Abstract [en]

    An efficient kinetic resolution of racemic gamma-hydroxy amides 1 was performed via Pseudomas cepacia lipase (PS-C)-catalyzed transesterification. The enzyme PS-C tolerates both variation in the chain length and different functionalities giving good to high enantioselectivity (E values of up to > 250). The combination of enzymatic kinetic resolution with a ruthenium-catalyzed racemization led to a dynamic kinetic resolution. The use of 2,4-dimethyl-3-pentanol as a hydrogen source to suppress ketone formation in the dynamic kinetic resolution yields the corresponding acetates in good yield and good to high enantioselectivity (ee's up to 98%). The synthetic utility of this procedure was illustrated by the practical synthesis of the versatile intermediate gamma-lactone (R)-5-methyltetrahydrofuran-2-one.

  • 236.
    Fransson, Ann-Britt L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Xu, Yongmei
    Leijondahl, Karin
    Bäckvall, Jan-Erling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Enzymatic Resolution, Desymmetrization and Dynamic Kinetic Asym-metric Transformation of 1,3-Cycloalkanediols2006In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 71, no 17, p. 6309-6316Article in journal (Refereed)
    Abstract [en]

    An efficient desymmetrization of cis-1,3-cyclohexanediol to (1S,3R)-3-(acetoxy)-1-cyclohexanol ((R,S)-2a) was performed via Candida antarctica lipase B (CALB)-catalyzed transesterification, in high yield (up to 93%) and excellent enantioselectivity (ee's up to >99.5%). (R,R)-Diacetate ((R,R)-3a) was obtained in a DYKAT process at room temperature from (1S,3R)-3-acetoxy-1-cyclohexanol ((R,S)-2a), in a high trans/cis ratio (91:9) and in excellent enantioselectivity of >99%. Metal- and enzyme-catalyzed dynamic transformation of cis/trans-1,3-cyclohexanediol using PS-C gave a high diastereoselectivity for cis-diacetate (cis/trans = 97:3). The (1R,3S)-3-acetoxy-1-cyclohexanol (ent-(R,S)-2a) was obtained from cis-diacetate by CALB-catalyzed hydrolysis in an excellent yield (97%) and selectivity (>99% ee). By deuterium labeling it was shown that intramolecular acyl migration does not occur in the transformation of cis-monoacetate to the cis-diacetate.

  • 237.
    Franzén, Johan
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-Catalyzed Carbocyclizations of Allenes with Unsaturated Hydrocarbons2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Palladium-catalyzed reactions of unsaturated hydrocarbons are important processes in organic chemistry especially for the generation of ring systems. This thesis describes the development and mechanistic studies of carbocyclization reactions of allenes with olefins, allyls or 1,3-dienes catalyzed by palladium(0)- and palladium(II)-complexes. These reactions generally exhibit high stereo- and regioselectivity and give rise to stereodefined [n,3,0] bicyclic systems (n=3,4,5,6) in good to excellent yields. The mechanisms for these reactions were investigated with special attention directed to the intramolecular reaction of (π-allyl)palladium(II)-complexes and (π-1,3-diene)palladium(II)-complexes with allenes. It was demonstrated that the carbon-carbon bond formation occurred by nucleophilic attack of the middle carbon atom of the allene on the face of the allyl or 1,3-diene opposite to that of the palladium atom. Further, two new types of oxidative palladium(II)-catalyzed reactions between allenes and olefins or 1,3-dienes have been developed. These cyclizations constitute a new type of carbon-carbon bond forming reaction and there are support for a palladium(II)-catalyzed C-H activation at the allenic moiety rendering a vinylidienepalladium-intermediate followed by carbon-carbon bond formation via insertion of the olefin or 1,3-diene.

  • 238. François, Camille
    et al.
    Pourchet, Sylvie
    Boni, Gilles
    Rautiainen, Sari
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Samec, Joseph
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Fournier, Lucie
    Robert, Carine
    Thomas, Christophe M.
    Fontaine, Stephane
    Gaillard, Yves
    Placet, Vincent
    Plasseraud, Laurent
    Design and synthesis of biobased epoxy thermosets from biorenewable resources2017In: Comptes rendus. Chimie, ISSN 1631-0748, E-ISSN 1878-1543, Vol. 20, no 11-12, p. 1006-1016Article in journal (Refereed)
    Abstract [en]

    Biobased diepoxy synthons derived from isoeugenol, eugenol or resorcinol (DGE-isoEu, DGE-Eu and DGER, respectively) have been used as epoxy monomers in replacement of the diglycidyl ether of bisphenol A (DGEBA). Their curing with six different biobased anhydride hardeners leads to fully biobased epoxy thermosets. These materials exhibit interesting thermal and mechanical properties comparable to those obtained with conventional petrosourced DGEBA-based epoxy resins cured in similar conditions. In particular, a high T-g in the range of 90-130 degrees C and instantaneous moduli higher than 4.3 GPa have been recorded. These good performances are very encouraging, making these new fully biobased epoxy thermosets compatible with the usual structural application of epoxy materials.

  • 239.
    Frigell, Jens
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of O-linked Carbasugar Analogues of Galactofuranosides and N-linked Neodisaccharides2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, carbohydrate mimicry is investigated through the syntheses of carbohydrate analogues and evaluation of their inhibitory effects on carbohydrate-processing enzymes.

    Galactofuranosides are interesting structures because they are common motifs in pathogenic microorganisms but not found in mammals. M.tuberculosis, responsible for the disease tuberculosis, has a cell wall containing a repeating unit of alternating (1→5)- and (1→6)-linked β-D-galactofuranosyl residues. Synthetic inhibitors of the enzymes involved in the biosynthesis of the cell wall could find great therapeutic use.

    The first part of this thesis describes the first synthesis of the hydrolytically stable carbasugar analogue of galactofuranose, 4a-carba-β-D-Galf, and the synthetic work of synthesising β-linked pseudodisaccharides containing carba-Galf, which were tested for glycosyltransferease inhibitory activity. The pseudodisaccharide carba-Galf-(β1→5)-carba-Galf was found to be a moderate inhibitor of the glycosyltransferase GlfT2 of M.tuberculosis. The thesis also describes how a general method towards biologically relevant α-linked carba-Galf ethers was developed.

    The final part of this thesis is focussed on the formation of nitrogen-linked monosaccharides without the participation of the anomeric centre. Such a mode of coupling is called tail-to-tail neodisaccharide formation. The couplings of carbohydrate derivatives via the Mitsunobu reaction are successfully reported herein. The method describes the key introduction of an allylic alcohol in the electrophile and the subsequent functionalisation of the alkene to obtain the neodisaccharide. Two synthesised neodisaccharides presented in this thesis have been sent to be tested for glycosidase inhibitory activity.

  • 240.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Cumpstey, Ian
    Carbasugar analogues of galactofuranose: α-O-linked derivativesManuscript (preprint) (Other academic)
    Abstract [en]

    Using an indirect method, we have synthesised α-linked carbasugar analogues of galactofuranosides for the first time. Opening of a β-talo configured carbasugar 1,2-epoxide by alcohol nucleophiles under Lewis acidic conditions proceeded with very good regioselectivity to give α-talo configured C-1-substituted ethers with OH-2 free. Inversion of configuration at OH-2 by an oxidation–reduction sequence gave the α-galacto configured carbahexofuranose C-1 ethers. A carbadisaccharide corresponding to the Galf(α1→3)Manp substructure from Apodus deciduus galactomannan was synthesised to exemplify the method.

  • 241.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Cumpstey, Ian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Carbasugar analogues of galactofuranosides: alpha-O-linked derivatives2010In: BEILSTEIN J ORG CHEM, ISSN 1860-5397, Vol. 6, p. 1127-1131Article in journal (Refereed)
    Abstract [en]

    Using an indirect method, we have synthesised alpha-linked carbasugar analogues of galactofuranosides for the first time. Ring opening of a beta-talo configured carbasugar 1,2-epoxide by alcohol nucleophiles under Lewis acidic conditions proceeded with very good regioselectivity to give alpha-talo configured C1-substituted ethers with a free OH-group at the C2 position. Inversion of configuration at C2 by an oxidation-reduction sequence gave the alpha-galacto configured carbahexofuranose C1 ethers. A carbadisaccharide corresponding to the Galf(alpha 1 -> 3)Manp substructure from Apodus deciduus galactomannan was synthesised to exemplify the method.

  • 242.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Cumpstey, Ian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    First synthesis of 4a-carba-beta-D-galactofuranose2007In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 48, no 52, p. 9073-9076Article in journal (Refereed)
  • 243.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Cumpstey, Ian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of carbadisaccharide mimics of galactofuranosides2009In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 50, no 36, p. 5142-5144Article in journal (Refereed)
  • 244.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Cumpstey, Ian
    Carbasugar analogues of galactofuranosides: β-O-linked derivativesManuscript (preprint) (Other academic)
    Abstract [en]

    A selectively protected carbasugar analogue of β-galactofuranose was synthesised from glucose using ring-closing metathesis as the key step. The carbasugar was converted into an α-galacto configured 1,2-epoxide, which was an effective electrophile in Lewis acid catalysed coupling reactions with alcohols. The epoxide was opened with regioselective attack at C-1 to give β-galacto configured C-1 ethers. Using carbohydrates as nucleophiles, we synthesised a number of pseudodisaccharides.

  • 245.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pearcey, J.A.
    Lowary, T.
    Cumpstey, Ian
    Carbasugar Analogues of Galactofuranose: Pseudodisaccharide Mimics of Fragments of Mycobacterial ArabinogalactanManuscript (preprint) (Other academic)
    Abstract [en]

    A partially protected carbasugar analogue of β-galactofuranose was converted into an α-galacto configured 1,2-epoxide, which was was opened by alcohols under Lewis acid catalysis with regioselective attack at C-1 to give β-galacto configured C-1 ethers. Using OH-5 and OH-6 carbagalactofuranose derivatives as nucleophiles, we synthesised pseudodisaccharide analogues of substructures of the arabinogalactan from M. tuberculosis. The dicarba analogue of the disaccharide Galf(β1→5)Galf was found to moderately inhibit the action of GlfT2 galactofuranosyl transferase from M. tuberculosis.

  • 246.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pearcey, Jean A.
    Lowary, Todd L.
    Cumpstey, Ian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Carbasugar Analogues of Galactofuranosides: Pseudodisaccharide Mimics of Fragments of Mycobacterial Arabinogalactan2011In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 7, p. 1367-1375Article in journal (Refereed)
    Abstract [en]

    A partially protected carbasugar analogue of beta-galactofuranose was converted into an alpha-galacto-configured 1,2-epoxide, which was opened by alcohols under Lewis acid catalysis with regioselective attack at C-1 to give beta-galacto-configured C-1 ethers. Using OH-5 and OH-6 carbagalactofuranose derivatives as nucleophiles, we synthesised pseudodisaccharide analogues of substructures of the arabinogalactan from M. tuberculosis. The dicarba analogue of the disaccharide Galf(beta 1 -> 5) Galf was found to moderately inhibit the action of GlfT2 galactofuranosyl transferase from M. tuberculosis.

  • 247.
    Gao, Weiming
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Li, Mingrun
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Romare, Kristina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Licheng
    Royal Institute of Technology (KTH), Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of a [3Fe2S] cluster with low redox potential from [2Fe2S] hydrogenase models: electrochemical and photochemical generation of hydrogen2011In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, Vol. 2011, no 7, p. 1100-1105Article in journal (Refereed)
    Abstract [en]

    In the attempted replacement of carbon monoxide by the bis(phosphane) dppv in a dinuclear [2Fe2S] complex, a trinuclear [3Fe2S] complex with two bis(phosphane) ligands was unexpectedly obtained. On protonation, this gave a bridged hydride complex with an unusually low potential for the reduction of protons to molecular hydrogen. The redox potential also appears sufficiently positive for direct electron transfer from an excited [Ru(bpy)(3)](2+) sensitizer.

  • 248.
    Gao, Weiming
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry, Structural Chemistry.
    Åkermark, Torbjörn
    Li, Mingrun
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry, Structural Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry, Structural Chemistry.
    Sun, Licheng
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Attachment of a hydrogen-bonding carboxylate side chain to an [FeFe]-hydrogenase model complex: Influence on the catalytic mechanism2010In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 16, no 8, p. 2537-2546Article in journal (Refereed)
    Abstract [en]

    Azapropanedithiolate (adt)-bridged model complexes of [FeFe]-hydrogenase bearing a carboxylic acid functionality have been designed with the aim of decreasing the potential for reduction of protons to hydrogen. Protonation of the bisphosphine complexes 46 has been studied by in situ IR and NMR spectroscopy, which revealed that protonation with triflic acid most likely takes place first at the N-bridge for complex 4 but at the FeFe bond for complexes 5 and 6. Using an excess of acid, the diprotonated species could also be observed, but none of the protonated species was sufficiently stable to be isolated in a pure state. Electrochemical studies have provided an insight into the catalytic mechanisms under strongly acidic conditions, and have also shown that complexes 3 and 6 are electro-active in aqueous solution even in the absence of acid, presumably due to hydrogen bonding. Hydrogen evolution, driven by visible light, has been observed for three-component systems consisting of [Ru(bpy)3]2+, complex 1, 2, or 3, and ascorbic acid in CH3CN/D2O solution by on-line mass spectrometry.

  • 249.
    Gao, Yan
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Liu, Jianhui
    Sun, Licheng
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nucleophilic attack of hydroxide on a MnV oxo complex: a model of the O-O bond formation in the oxygen evolving complex of photosystem II2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 25, p. 8726-8727Article in journal (Refereed)
  • 250.
    Gemma, Emiliano
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of Oligosaccharides for Interaction Studies with Various Lectins2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, the syntheses of oligosaccharides for interaction studies with various lectins are described. The first section reports the syntheses of tetra, tri- and disaccharides corresponding to truncated versions of the glucosylated arm of Glc1Man9(GlcNAc)2, found in the biosynthesis of N-glycans. The thermodynamic parameters of their interaction with calreticulin, a lectin assisting and promoting the correct folding of newly synthesised glycoproteins, were established by isothermal titration calorimetry. In the second section, a new synthetic pathway leading to the same tetra- and trisaccharides is discussed. Adoption of a convergent strategy and of a different protecting group pattern resulted in significantly increased yields of the target structures. The third section describes the syntheses of a number of monodeoxy-trisaccharides related to the above trisaccharide Glc-α-(1→3)-Man-α-(1→2)-Man-α-OMe. Differentsynthetic approaches were explored and the choice of early introduction of the deoxy functionality proved the most beneficial. In the last section, the synthesis of spacer-linked LacNAc dimers as substrates for the lectins galectin-1 and -3 is presented. This synthesis was realized by glycosidation of a number diols with peracetylated LacNAc-oxazoline. Pyridinium triflate was tested as a new promoter, affording the target dimers in high yields. This promoter in combination with microwave irradiation gave even higher yields and also shortened the reaction times.

2345678 201 - 250 of 959
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