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  • 251. Barzegar, Hamid Reza
    et al.
    Nitze, Florian
    Malolepszy, Artur
    Stobinski, Leszek
    Tai, Cheuk-Wai
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wagberg, Thomas
    Water Assisted Growth of C-60 Rods and Tubes by Liquid-Liquid Interfacial Precipitation Method2012In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 17, no 6, p. 6840-6853Article in journal (Refereed)
    Abstract [en]

    C-60 nanorods with hexagonal cross sections are grown using a static liquid-liquid interfacial precipitation method in a system of C-60/m-dichlorobenzene solution and ethanol. Adding water to the ethanol phase leads instead to C-60 tubes where both length and diameter of the C-60 tubes can be controlled by the water content in the ethanol. Based on our observations we find that the diameter of the rods/tubes strongly depends on the nucleation step. We propose a liquid-liquid interface growth model of C-60 rods and tubes based on the diffusion rate of the good C-60 containing solvent into the poor solvent as well as on the size of the crystal seeds formed at the interface between the two solvents. The grown rods and tubes exhibit a hexagonal solvate crystal structure with m-dichlorobenzene solvent molecules incorporated into the crystal structure, independent of the water content. An annealing step at 200 degrees C at a pressure <1 kPa transforms the grown structures into a solvent-free face centered cubic structure. Both the hexagonal and the face centered cubic structures are very stable and neither morphology nor structure shows any signs of degradation after three months of storage.

  • 252.
    Barzegar, Hamid Reza
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Nitze, Florian
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Malolepszy, Artur
    Stobinski, Leszek
    Tai, Cheuk-Wai
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Water assisted growth of C-60 rods and tubes by liquid-liquid interfacial precipitation method2012In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 17, no 6, p. 6840-6853Article in journal (Refereed)
    Abstract [en]

    C-60 nanorods with hexagonal cross sections are grown using a static liquid-liquid interfacial precipitation method in a system of C-60/m-dichlorobenzene solution and ethanol. Adding water to the ethanol phase leads instead to C-60 tubes where both length and diameter of the C-60 tubes can be controlled by the water content in the ethanol. Based on our observations we find that the diameter of the rods/tubes strongly depends on the nucleation step. We propose a liquid-liquid interface growth model of C-60 rods and tubes based on the diffusion rate of the good C-60 containing solvent into the poor solvent as well as on the size of the crystal seeds formed at the interface between the two solvents. The grown rods and tubes exhibit a hexagonal solvate crystal structure with m-dichlorobenzene solvent molecules incorporated into the crystal structure, independent of the water content. An annealing step at 200 degrees C at a pressure <1 kPa transforms the grown structures into a solvent-free face centered cubic structure. Both the hexagonal and the face centered cubic structures are very stable and neither morphology nor structure shows any signs of degradation after three months of storage.

  • 253.
    Bashir, Tariq
    et al.
    University of Borås, School of Engineering.
    Bakare, Fatimat
    University of Borås, School of Engineering.
    Baghaei, Behnaz
    University of Borås, School of Engineering.
    Mehrjerdi, Adib Kalantar
    Skrifvars, Mikael
    University of Borås, School of Engineering.
    Influence of different organic solvents and oxidants on insulating and film-forming properties of PEDOT polymer2013In: Iranian polymer journal, ISSN 1026-1265, E-ISSN 1735-5265, Vol. 22, no 8, p. 599-611Article in journal (Refereed)
    Abstract [en]

    Processing of conjugate polymers has always been a challenge because of their poor solubility and infusibility in organic and inorganic solvents. The processibility and applications of intrinsically conductive polymers (ICPs) can be enhanced by producing their solutions or dispersions in different suitable solvents. It can also be achieved by preparing un-doped or electrically neutral polymers, which can further be transformed in semiconductor after oxidation/reduction reaction. The present study focuses on the preparation of active dispersions of poly (3,4-ethylenedioxythiophene) (PEDOT) conductive polymer in various organic solvents. For this purpose, the polymerization of 3,4-ethylenedioxythiophene (EDOT) monomer was carried out in three different organic solvents, ethanol, 1-butanol and acetonitrile with two commonly used oxidants, ferric (III) chloride (FeCl3) and ferric (III) p-toluenesulfonate (FepTS). In this regard, the oxidant and monomer solutions with variable molar concentrations (0.25, 0.5, 1.0 M) were prepared in particular solvents and then these solutions were mixed with different monomer/oxidant volume ratios. The obtained dispersions of PEDOT can readily be polymerized on the surface of different materials after solvent evaporation and a uniform film can be achieved. The effect of molar as well as volume concentrations of EDOT monomer and oxidant on insulating (undoped/neutral) and film forming properties of PEDOT was investigated. These dispersions were applied on a transparent PET film and cellulosic fibers (viscose), dried at room temperature and analyzed using scanning electron microscope (SEM), optical microscope and ATR-FTIR spectroscopic analysis. The electrical characterization of undoped PEDOT-coated fibers was performed on Keithly picoammeter. This study contributes to obtain a simpler and instantaneous polymerization method of PEDOT preparation and to enhance its application area.

  • 254.
    Bashir, Tariq
    et al.
    University of Borås, School of Engineering.
    Fast, Lars
    Skrifvars, Mikael
    University of Borås, School of Engineering.
    Persson, Nils-Krister
    University of Borås, Swedish School of Textiles.
    Electrical Resistance Measurement Methods and Electrical Characterization of Poly(3,4-ethylenedioxythiophene)- Coated Conductive Fibers2012In: Journal of Applied Polymer Science, ISSN 0021-8995, E-ISSN 1097-4628, Vol. 124, no 4, p. 2954-2961Article in journal (Refereed)
    Abstract [en]

    Textile fibers and yarns of high conductivity, and their integration into wearable textiles for different electronic applications, have become an important research field for many research groups throughout the world. We have produced novel electrically conductive textile yarns by vapor-phase polymerization (VPP) of a conjugated polymer, poly(3,4-ethylenedioxythiophene) (PEDOT), on the surface of commercially available textile yarns (viscose). In this article, we have presented a novel setup for electrical resistance measurements, which can be used not only for fibrous structures but also for woven structures of specific dimensions. We have reported a two-point resistance- measuring method using an already manufactured setup and also a comparison with the conventionally used method (so-called crocodile clip method). We found that the electrical properties of PEDOT-coated viscose fibers strongly depend on the concentration of oxidant (FeCl3)and the doping (oxidation) process of PEDOT. To evaluate the results, we used mass specific resistance values of PEDOT-coated viscose yarns instead of normal surface resistance values. The voltage–current (V–I) characteristics support the ohmic behavior of coated fibers to some extent. Monitoring of the charging effect of the flow of current through conductive fibers for prolonged periods of time showed that conductivity remains constant. The change in electrical resistance values with increase in the length of coated fibers was also reported. The resistance measuring setup employed could also be used for continuous measurement of resistance in the production of conductive fibers, as well as for four-point resistance measurement.

  • 255. Bassanini, Ivan
    et al.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Industrial Biotechnology. CNR, Italy.
    Riva, Sergio
    Dicarboxylic esters: Useful tools for the biocatalyzed synthesis of hybrid compounds and polymers2015In: Beilstein Journal of Organic Chemistry, ISSN 2195-951X, E-ISSN 1860-5397, Vol. 11, p. 1583-1595Article, review/survey (Refereed)
    Abstract [en]

    Dicarboxylic acids and their derivatives (esters and anhydrides) have been used as acylating agents in lipase-catalyzed reactions in organic solvents. The synthetic outcomes have been dimeric or hybrid derivatives of bioactive natural compounds as well as functionalized polyesters.

  • 256. Basu, Basudeb
    et al.
    Paul, Susmita
    Kundu, Samir
    Byström, Emil
    Irgum, Knut
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Organic Polymeric Resins Embedded with Pd NPs: Newly Designed, Efficient and Chemoselective Catalyst for Reduction of Nitrobenzenes2017In: Current Organocatalysis, ISSN 2213-3372, Vol. 4, no 1, p. 48-61Article in journal (Refereed)
    Abstract [en]

    Background: Organic polymer supported palladium nanoparticles (NPs) are important for use as heterogeneous catalyst in various organic reactions. This works describes Pd Nps immobilized on to polystyrene-based ion-exchange resin surface for use as catalyst in the reduction of nitrobenzenes. The heterogeneous catalyst was found useful for hydrogenation of nitro group under both catalytic transfer hydrogenation (CTH) as well as by using molecular hydrogen (H2).

    Methods: The catalyst was prepared from Amberlite IRA 900 Cl after rinsing with formic acid (10%) and subsequent treatment with Na2PdCl4 in DMF. The resulting Pd Nps immobilized resins was designated as VersaCat Pd and used for CTH of nitrobenzenes in the presence of H-donors (sodium formate, formic acid, hydrazine hydrate) and also for hydrogenation with H2 gas. The catalyst was characterized by FT-IR, MAS-NMR, SEM, TEM and XPS and surface morphologies were studied before and after the reaction.

    Results: Hydrogenations of nitrobenzenes under CTH using different H-source and direct use of H2 gas were achieved successfully with good to excellent yields. Reactions were performed under mild conditions and high degree of chemoselectivity was also observed. The catalyst was recyclable, used for six consecutive runs with appreciable conversions and showed higher activity (> 3 times) in terms of metalcontent than commercially available Pd/C (10%) in the hydrogenation of nitrobenzenes using H2 gas. The TEM images showed that Pd Nps are evenly distributed with size 50-200 mm on polymeric matrices and there was no significant changes observed after the first catalytic run. However, considerable rupture of the polymeric surface occurred after six runs, as seen from SEM studies.

    Conclusion: The present study establishes high catalytic efficiency and chemoselectivity of the newly developed organic polystyrene-based resin-soaked Pd NPs (VersaCat Pd) in the reduction of nitrobenzenes. Both CTH and hydrogenation using H2 gas were successfully done. Interestingly, hydrazine hydrate offered excellent control over chemoselectivity under CTH conditions and allowed clean conversion from nitro to amine, while keeping a chloro substitutent unaffected. Hydrogenation using molecular H2 gave maximum TOF. Easy preparation, high efficacy, TOF, chemoselectivity, and versatile applications are notable features for this heterogeneous palladium catalyst (VersaCat Pd). These features are often required in chemical industries.

  • 257. Battistel, Marcos D.
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Freedberg, Daron I.
    Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 17, p. 4860-4869Article in journal (Refereed)
    Abstract [en]

    We introduce the abundant hydroxyl groups of glycans as NMR handle's and structural probes to expand the repertoire of tools for structure function studies on glycans in solution. To this end, we present the facile detection and assignment of hydroxyl groups in a Wide range of sample concentrations (0.5-1700 mM) and temperatures, ranging from -5 to 25 degrees C.,We then exploit this information to directly detect hydrogen bonds, well-known for their importance in molecular structural determination through NMR. Via HSQC-TOCSY, we were able to determine the directionality; of these hydrogen bonds in sucrose Furthermore, by means Of molecular dynamics simulations in conjunction with NMR, we establish that one Out of the three detected hydrogen bonds arises from intermolecular interactions. This finding may shed light on glycan glycan interactions and glycan recognition by proteins.

  • 258.
    Baumann, Herbert
    Stockholm University, Faculty of Science.
    Synthesis of and NMR and conformational studies on some 3-O-, 4-O- and 3,4-di-O-glycopyranosyl-substituted methyl d-glycopyranosides1988Doctoral thesis, comprehensive summary (Other academic)
  • 259.
    Bedecs, Katarina
    Stockholm University, Faculty of Science, Department of Neurochemistry and Neurotoxicology.
    Galanin in the rat dorsal spinal cord: an inhibitor peptide in sensory processing1995Doctoral thesis, comprehensive summary (Other academic)
  • 260. Bedekar, Ashutosh V.
    et al.
    Andersson, Pher
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Chemistry. Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    A New Class of Bis-Oxazoline Ligands for the Cu-Catalysed Asymmetric Cyclopropanation of Olefins1996In: Tetrahedron Letters, Vol. 37, no 23, p. 4073-4076Article in journal (Refereed)
  • 261. Bedekar, Ashutosh V.
    et al.
    Koroleva, Elise B.
    Andersson, Pher
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Chemistry. Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    Investigation of the Effects of the Structure and Chelate Size of Bis-oxazoline Ligands in the Asymmetric Copper-Catalyzed Cyclopropanation of Olefins: Design of a New Class of Ligands1997In: J. Org. Chem., no 62, p. 2518-2526Article in journal (Refereed)
  • 262. Bedin, Michele
    et al.
    Karim, Alavi
    Reitti, Marcus
    Carlsson, Anna-Carin C
    Topić, Filip
    Cetina, Mario
    Pan, Fangfang
    Havel, Vaclav
    Al-Ameri, Fatima
    Sindelar, Vladimir
    Rissanen, Kari
    Gräfenstein, Jürgen
    Erdelyi, Mate
    Counterion influence on the N-I-N halogen bond.2015In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 6, no 7, p. 3746-3756Article in journal (Refereed)
    Abstract [en]

    A detailed investigation of the influence of counterions on the [N-I-N]+ halogen bond in solution, in the solid state and in silico is presented. Translational diffusion coefficients indicate close attachment of counterions to the cationic, three-center halogen bond in dichloromethane solution. Isotopic perturbation of equilibrium NMR studies performed on isotopologue mixtures of regioselectively deuterated and nondeuterated analogues of the model system showed that the counterion is incapable of altering the symmetry of the [N-I-N]+ halogen bond. This symmetry remains even in the presence of an unfavorable geometric restraint. A high preference for the symmetric geometry was found also in the solid state by single crystal X-ray crystallography. Molecular systems encompassing weakly coordinating counterions behave similarly to the corresponding silver(i) centered coordination complexes. In contrast, systems possessing moderately or strongly coordinating anions show a distinctly different behavior. Such silver(i) complexes are converted into multi-coordinate geometries with strong Ag-O bonds, whereas the iodine centered systems remain linear and lack direct charge transfer interaction with the counterion, as verified by 15N NMR and DFT computation. This suggests that the [N-I-N]+ halogen bond may not be satisfactorily described in terms of a pure coordination bond typical of transition metal complexes, but as a secondary bond with a substantial charge-transfer character.

  • 263. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Tian, Guangjun
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bartkowiak, Wojciech
    Nonempirical Simulations of Inhomogeneous Broadening of Electronic Transitions in Solution: Predicting Band Shapes in One- and Two-Photon Absorption Spectra of Chalcones2017In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 22, no 10, article id 1643Article in journal (Refereed)
    Abstract [en]

    We have examined several approaches relying on the Polarizable Embedding (PE) scheme to predict optical band shapes for two chalcone molecules in methanol solution. The PE-TDDFT and PERI-CC2 methods were combined with molecular dynamics simulations, where the solute geometry was kept either as rigid, flexible or partly-flexible (restrained) body. The first approach, termed RBMD-PE-TDDFT, was employed to estimate the inhomogeneous broadening for subsequent convolution with the vibrationally-resolved spectra of the molecule in solution determined quantum-mechanically (QM). As demonstrated, the RBMD-PE-TDDFT/QM-PCM approach delivers accurate band widths, also reproducing their correct asymmetric shapes. Further refinement can be obtained by the estimation of the inhomogeneous broadening using the RBMD-PERI-CC2 method. On the other hand, the remaining two approaches (FBMD-PE-TDDFT and ResBMD-PE-TDDFT), which lack quantum-mechanical treatment of molecular vibrations, lead to underestimated band widths. In this study, we also proposed a simple strategy regarding the rapid selection of the exchange-correlation functional for the simulations of vibrationally-resolved one-and two-photon absorption spectra based on two easy-to-compute metrics.

  • 264.
    Begnini, Fabio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Uppsala University.
    Development of Novel Macrocyclic Inhibitors of Protein-Protein Interactions: Applied to the Keap1-Nrf2 Complex2019Licentiate thesis, comprehensive summary (Other academic)
  • 265. Begum, Sartaz
    et al.
    Nyandoro, Stephen
    Buriyo, Amelia
    Makangara, John
    Munissi, Joan
    Duffy, Sandra
    Avery, Vicky
    Erdelyi, Mate
    University of Gothenburg.
    Bioactivities of extracts, debromolaurintrerol and fucosterol from Macroalgae species2018In: Tanzania Journal of Science, ISSN 2507-7961, Vol. 44, no 2, p. 104-116Article in journal (Refereed)
    Abstract [en]

    Parasitic diseases including malaria, and other numerous microbial infections and physiological diseases are threatening the global population. Tanzanian coast shores are endowed with a variety of macroalgae (seaweeds), hitherto unsystematically explored to establish their biomedical potentials. Thus, antiplasmodial activity using malarial imaging assay, antimicrobial activity using microplate dilution technique, antioxidant activity using DPPH radical scavenging method and cytotoxicity using brine shrimp test were carried out on crude extracts from the selected species of algae (Acanthophora spicifera, Cystoseira myrica, Cystoseira trinodis, Laurencia filiformis, Padina boryana, Sargassum oligocystum, Turbinaria crateriformis, Ulva fasciata and Ulva reticulata) occurring along the coast of Tanzania. The extracts showed antimicrobial activities with MIC ranging from 0.3- 5.0 µg/mL against Staphylococcus aureus, Streptococcus pyogenes, Pseudomonas aeruginosa, Escherichia coli, Candida albicans and Cryptococcus neoformans; DPPH radical scavenging activity at EC50 1.0- 100 µg/mL and cytotoxicity on brine shrimp larvae with LC50 value ranging from20 - 1000 µg/mL. The extracts from C. myrica and P. boryana inhibited growth of Plasmodium falciparum (3D7 strain) by 80 and 71%, respectively at 40 µg/mL while a sesquiterpene debromolaurinterol (1) which was chromatographically isolated from C. myrica exhibited antiplasmodial activity with IC50 20 µM whereas a sterol fucosterol (2) from P. boryana showed weak activity at 40 µM. Bioactivities portrayed by the investigated extracts indicate their ingredients as potential sources of bioactive agents that warrant further explorations.

  • 266.
    Beiroth, Femke
    et al.
    Christiana Albertina Univ Kiel, Otto Diels Inst Organ Chem, Otto Hahn Pl 3-4, D-24118 Kiel, Germany.
    Koudelka, Tomas
    Christiana Albertina Univ Kiel, Inst Expt Med, Systemat Prote & Bioanalyt, Niemannsweg 11, D-24105 Kiel, Germany.
    Overath, Thorsten
    Christiana Albertina Univ Kiel, Inst Expt Med, Systemat Prote & Bioanalyt, Niemannsweg 11, D-24105 Kiel, Germany.
    Knight, Stefan D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Biology.
    Tholey, Andreas
    Christiana Albertina Univ Kiel, Inst Expt Med, Systemat Prote & Bioanalyt, Niemannsweg 11, D-24105 Kiel, Germany.
    Lindhorst, Thisbe K.
    Christiana Albertina Univ Kiel, Otto Diels Inst Organ Chem, Otto Hahn Pl 3-4, D-24118 Kiel, Germany.
    Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH2018In: Beilstein Journal of Organic Chemistry, ISSN 2195-951X, E-ISSN 1860-5397, Vol. 14, p. 1890-1900Article in journal (Refereed)
    Abstract [en]

    Photoaffinity labeling is frequently employed for the investigation of ligand-receptor interactions in solution. We have employed an interdisciplinary methodology to achieve facile photolabeling of the lectin FimH, which is a bacterial protein, crucial for adhesion, colonization and infection. Following our earlier work, we have here designed and synthesized diazirine-functionalized mannosides as high-affinity FimH ligands and performed an extensive study on photo-crosslinking of the best ligand (mannoside 3) with a series of model peptides and FimH. Notably, we have employed high-performance mass spectrometry to be able to detect radiation results with the highest possible accuracy. We are concluding from this study that photolabeling of FimH with sugar diazirines has only very limited success and cannot be regarded a facile approach for covalent modification of FimH.

  • 267. Belda, O
    et al.
    Kaiser, N F
    Bremberg, U
    Larhed, M
    Hallberg, A
    Moberg, C
    Highly stereo- and regioselective allylations catalyzed by Mo-pyridylamide complexes: Electronic and steric effects of the ligand2000In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 65, no 18, p. 5868-5870Article in journal (Refereed)
  • 268. Beletskaya, I.P
    et al.
    Bregadze, V.I.
    Ivushkin, V.A.
    Petrovskii, P.V.
    Sivaev, I.B.
    Sjöberg, Stefan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Chemistry. Department of Biochemistry and Organic Chemistry, Organic Chemistry II. Organisk kemi.
    Zhigareva, G.B.
    New B-substituted derivatives of m-carborane, p-carborane, and cobalt bis(1,2-decarbollide) anion2004In: J. Organomet. Chem., no 689, p. 2920-Article in journal (Refereed)
  • 269.
    Belfrage, Anna Karin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Design and Synthesis of Hepatitis C Virus NS3 Protease Inhibitors: Targeting Different Genotypes and Drug-Resistant Variants2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Since the first approved hepatitis C virus (HCV) NS3 protease inhibitors in 2011, numerous direct acting antivirals (DAAs) have reached late stages of clinical trials. Today, several combination therapies, based on different DAAs, with or without the need of pegylated interferon-α injection, are available for chronic HCV infections. The chemical foundation of the approved and late-stage HCV NS3 protease inhibitors is markedly similar. This could partly explain the cross-resistance that have emerged under the pressure of NS3 protease inhibitors. The first-generation NS3 protease inhibitors were developed to efficiently inhibit genotype 1 of the virus and were less potent against other genotypes.

    The main focus in this thesis was to design and synthesize a new class of 2(1H)-pyrazinone based HCV NS3 protease inhibitors, structurally dissimilar to the inhibitors evaluated in clinical trials or approved, potentially with a unique resistance profile and with a broad genotypic coverage. Successive modifications were performed around the pyrazinone core structure to clarify the structure-activity relationship; a P3 urea capping group was found valuable for inhibitory potency, as were elongated R6 residues possibly directed towards the S2 pocket. Dissimilar to previously developed inhibitors, the P1’ aryl acyl sulfonamide was not essential for inhibition as shown by equally good inhibitory potency for P1’ truncated inhibitors. In vitro pharmacokinetic (PK) evaluations disclosed a marked influence from the R6 moiety on the overall drug-properties and biochemical evaluation of the inhibitors against drug resistant enzyme variants showed retained inhibitory potency as compared to the wild-type enzyme. Initial evaluation against genotype 3a displayed micro-molar potencies. Lead optimization, with respect to improved PK properties, were also performed on an advanced class of HCV NS3 protease inhibitors, containing a P2 quinazoline substituent in combination with a macro-cyclic proline urea scaffold with nano-molar cell based activities.

    Moreover, an efficient Pd-catalyzed C-N urea arylation protocol, enabling high yielding introductions of advanced urea substituents to the C3 position of the pyrazinone, and a Pd-catalyzed carbonylation procedure, to obtain acyl sulfinamides, were developed. These methods can be generally applicable in the synthesis of bioactive compounds containing peptidomimetic scaffolds and carboxylic acid bioisosteres.

  • 270.
    Belfrage, Anna Karin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Abdurakhmanov, Eldar
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Åkerblom, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Brandt, Peter
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Oshalim, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Gising, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Skogh, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Neyts, Johan
    Danielson, U. Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Sandström, Anja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Discovery of pyrazinone based compounds that potently inhibit the drug resistant enzyme variant R155K of the hepatitis C virus NS3 protease2016In: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 24, no 12, p. 2603-2620Article in journal (Refereed)
    Abstract [en]

    Herein, we present the design and synthesis of 2(1H)-pyrazinone based HCV NS3 protease inhibitors with variations in the C-terminus. Biochemical evaluation was performed using genotype 1a, both the wildtype and the drug resistant enzyme variant, R155K. Surprisingly, compounds without an acidic sulfonamide retained good inhibition, challenging our previous molecular docking model. Moreover, selected compounds in this series showed nanomolar potency against R155K NS3 protease; which generally confer resistance to all HCV NS3 protease inhibitors approved or in clinical trials. These results further strengthen the potential of this novel substance class, being very different to the approved drugs and clinical candidates, in the development of inhibitors less sensitive to drug resistance.

  • 271.
    Belfrage, Anna Karin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Gising, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Svensson, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Åkerblom, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Sköld, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Sandström, Anja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Efficient and Selective Palladium-Catalysed C-3 Urea Couplings to 3,5-Dichloro-2(1H)-pyrazinones2015In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 5, p. 978-986Article in journal (Refereed)
    Abstract [en]

    The development of a robust palladium-catalysed urea N-arylation protocol to install various ureas at the 3-position of the 2(1H)-pyrazinone scaffold is described. The method involves Pd(OAc)2 in combination with bidentate ligands, xantphos [4,5-bis(diphenylphosphino)-9,9-dimethylxanthene] in particular, and resulted in good to excellent coupling yields of aliphatic, aromatic, and sterically hindered ureas. Furthermore, the C-3 chlorine was shown to be selectively displaced in the presence of aryl halide ureas, and this finding was supported by density functional theory (DFT) calculations. This allows further diversification of the scaffold for the production of compound libraries. Overall, the protocol facilitates further exploitation of pyrazinones as beta-sheet-inducing scaffolds in the development of sophisticated peptidomimetics/protease inhibitors. This is exemplified here by the synthesis of a new pyrazinone-based hepatitis C virus (HCV) NS3 protease inhibitor.

  • 272. Belfrage, Anna Karin
    et al.
    Wakchaure, Prasad
    Larhed, Mats
    Sandström, Anja
    Palladium-catalyzed carbonylation of aryl iodides with sulfinamidesManuscript (preprint) (Other academic)
  • 273.
    Belfrage, Anna Karin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Wakchaure, Prasad
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Larhed, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Sandström, Anja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Palladium-Catalyzed Carbonylation of Aryl Iodides with Sulfinamides2015In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 32, p. 7069-7074Article in journal (Refereed)
    Abstract [en]

    A facile palladium(0)-catalyzed carbonylative protocol for the generation of new acyl-sulfinamides in moderate to good yields is described. Aliphatic and aromatic sulfinamides were exploited as hitherto unexplored nucleophiles in carbonylation chemistry, with use of CO gas generated ex situ from Mo(CO)6 in a sealed two-chamber system. Both electron-poor and electron-rich (hetero)aryl iodides were employed as electrophiles. The two-chamber system and the use of an inorganic base were essential for efficacious synthesis of acyl-sulfinamide products. Finally, it was demonstrated that a one-pot (or single-vial) synthesis of acyl-sulfinamides was feasible under CO at balloon pressure in the presence of Cs2CO3 as base.

  • 274.
    Belhomme, Marie-Charlotte
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Wang, Dong
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Formation of C(sp(3))-C(sp(3)) Bonds by Palladium Catalyzed Cross-Coupling of alpha-Diazoketones and Allylboronic Acids2016In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 18, no 10, p. 2503-2506Article in journal (Refereed)
    Abstract [en]

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

  • 275.
    Bellini, Rosalba
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Magre, Marc
    Biosca, Maria
    Norrby, Per-Ola
    Pamies, Oscar
    Dieguez, Montserrat
    Moberg, Christina
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Conformational Preferences of a Tropos Biphenyl Phosphinooxazoline-a Ligand with Wide Substrate Scope2016In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 6, no 3, p. 1701-1712Article in journal (Refereed)
    Abstract [en]

    Excellent enantioselectivities are observed in palladium-catalyzed allylic substitutions of a wide range of substrate types and nucleophiles using a bidentate ligand composed of oxazoline and chirally flexible biaryl phosphite elements. This unusually wide substrate scope is shown by experimental and theoretical studies of its eta(3)-allyl and eta(2)-olefin complexes not to be a result of configurational interconversion of the biaryl unit, since the ligand in all reactions adopts an S-a,S configuration on coordination to palladium, but rather the ability of the ligand to adapt the size of the substrate-binding pocket to the reacting substrate. This ability also serves as an explanation to its excellent performance in other types of catalytic processes.

  • 276.
    Bellissent-Funel, Marie-Claire
    et al.
    CEA Saclay, CNRS, Lab Leon Brillouin, F-91191 Gif Sur Yvette, France..
    Hassanali, Ali
    Abdus Salaam Int Ctr Theoret Phys, Condensed Matter & Stat Phys, I-34151 Trieste, Italy..
    Havenith, Martina
    Ruhr Univ Bochum, Fac Chem & Biochem, Univ Str 150 Bldg NC 7-72, D-44780 Bochum, Germany..
    Henchman, Richard
    Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England..
    Pohl, Peter
    Johannes Kepler Univ Linz, Gruberstr 40, A-4020 Linz, Austria..
    Sterpone, Fabio
    Inst Biol Physicochim, Lab Biochim Theor, 13 Rue Pierre & Marie Curie, F-75005 Paris, France..
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Xu, Yao
    Ruhr Univ Bochum, Fac Chem & Biochem, Univ Str 150 Bldg NC 7-72, D-44780 Bochum, Germany..
    Garcia, Angel E.
    Los Alamos Natl Lab, Ctr Non Linear Studies, Los Alamos, NM 87545 USA..
    Water Determines the Structure and Dynamics of Proteins2016In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 116, no 13, p. 7673-7697Article, review/survey (Refereed)
    Abstract [en]

    Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

  • 277. Bengtson, A
    et al.
    Hallberg, A
    Larhed, M
    Fast synthesis of aryl triflates with controlled microwave heating2002In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 4, no 7, p. 1231-1233Article in journal (Refereed)
    Abstract [en]

    [GRAPHICS] Synthesis of aryl triflates from phenols using N-phenyltriflimide requires only 6 min for completion when conducted with controlled microwave heating. The methodology was applied to both solution- and solid-phase conditions. Ten different aryl triflates were synthesized and isolated in good yields. Applications in high-throughput chemistry are suggested.

  • 278. Bengtson, A
    et al.
    Larhed, M
    Hallberg, A
    Protected indanones by a Heck-Aldol annulation reaction2002In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 67, no 16, p. 5854-5856Article in journal (Refereed)
    Abstract [en]

    Monoprotected 3-hydroxyindan-1-ones have been prepared in moderate to good yields by a new tandem reaction involving salicylaldehyde triflates and commercially available 2-hydroxyethyl vinyl ether. This one-pot annulation reaction proceeds in the presence of a palladium bidentate catalyst and results in the formation of two new ring systems.

  • 279.
    Bengtsson, Linda
    KTH, School of Chemical Science and Engineering (CHE).
    Odorant binding protein and olfactory receptors: plausible role as detectors in an odorant biosensor2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The development of an inexpensive, portable, stable, sensitive and selective biosensor for detection of odorants is a daunting task. Here, we hypothesized the development of a detector layer composed of the protein groups; the olfactory receptors (ORs) and the odorant binding proteins (OBPs), known to bind odorants in animal sensing. We report the design of 13 OR gene-vector constructs, and their subsequent transformation into

    Escherichia (E.) coli (BL21 (DE3)-STAR-pLysS) strain. Moreover, we report the expression of several ORs into an in vitro wheat germ extract using three separate detergent mixes for protein solubilization.

     

    In addition, we describe the design of an odorant binding protein from the Aenopheles gambiae mosquito PEST strain (OBP-PEST) gene-vector construct under an IPTG (Isopropyl β-D-1-thiogalactopyranoside) inducible promoter. OBP-PEST was heterologously expressed in E.coli with an 8 amino acid long sequence (WSPQFEK) attached C-terminally, via a thrombin cleavage site and a flexible linker (GSSG). The WSPQFEK sequence, commonly referred to as a Strep-tag, enabled subsequent affinity chromatography purification of the protein, via binding to an engineered Streptavidin equivalent. Surprisingly, the OBP-PEST was found to contain a signal sequence leading to its truncation and secretion when expressed in E.coli.

     

    Biophysical analyses were established using Circular Dichroism (CD) for the analysis of two lipocalins: Beta-lactoglobulin (BLG) and OBP-PEST. We studied the solubility, refoldability and the conformational transitions of BLG, as a result of change in solvent, pH and temperature. The secondary structure of OBP-PEST and its thermal stability was investigated.

     

    In conclusion, this thesis work has enabled biophysical analyses of OBP-PEST and future analogs of interest to the development of a stable protein detector layer. Although further experiments are needed to fully characterize the biophysical properties, and to find odorant substrates of OBP-PEST, it was found to be a suitable alternative to ORs in a biosensor detector layer application. More importantly, an inherent OBP-PEST signal sequence was found to mediate protein secretion when expressed heterologously in E.coli. To the best of our knowledge this is the first lipocalin discovered to be secreted upon heterologous expression in E.coli.

     

    We hypothesize that this signal peptide could be used as a means for targeted secretion and, hence, efficient protein purification.

  • 280.
    Benselfelt, Tobias
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Henschen, Jonatan
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Pettersson, Torbjörn
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Wågberg, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Polyelectrolyte multilayers on differently charged cellulose surfaces2016In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 251Article in journal (Other academic)
  • 281.
    Benyahia Erdal, Nejla
    et al.
    KTH, School of Chemical Science and Engineering (CHE). Royal Inst Technol, Sch Chem Sci & Engn, Stockholm, Sweden..
    Adolfsson, Karin H.
    KTH, School of Chemical Science and Engineering (CHE). Sch Chem Sci & Engn, Stockholm, Sweden..
    Hakkarainen, Minna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. Royal Inst Technol, Stockholm, Sweden..
    Silicone-hydrogel bandage lenses used in conjunction with pharmaceutical eye drops: An uptake and release study2016In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 251Article in journal (Other academic)
  • 282. Bergenstråhle-Wohlert, M.
    et al.
    Berglund, L.A.
    Brady, J.W.
    Larsson, P.T.
    RISE, Innventia.
    Westlund, P.-O.
    Wohlert, J.
    Concentration enrichment of urea at cellulose surfaces: Results from molecular dynamics simulations and NMR spectroscopy2012In: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, no 1, p. 1-12Article in journal (Refereed)
  • 283. Bergenstråhle-Wohlert, Malin
    et al.
    Angles d'Ortoli, Thibault
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sjöberg, Nils A.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Wohlert, Jakob
    On the anomalous temperature dependence of cellulose aqueous solubility2016In: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, Vol. 23, no 4, p. 2375-2387Article in journal (Refereed)
    Abstract [en]

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

  • 284.
    Berglin, Ewa
    et al.
    Umeå University, Faculty of Medicine, Department of Odontology, Oral Microbiology.
    Edlund, Maj-Britt K.
    Umeå University, Faculty of Medicine, Department of Odontology, Oral Microbiology.
    Nyberg, Göran K.
    Umeå University, Faculty of Medicine, Department of Odontology, Oral Microbiology.
    Carlsson, Jan
    Umeå University, Faculty of Medicine, Department of Odontology, Oral Microbiology.
    Potentiation by L-cysteine of the bactericidal effect of hydrogen peroxide in Escherichia coli1982In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 152, no 1, p. 81-88Article in journal (Refereed)
    Abstract [en]

    Under anaerobic conditions an exponentially growing culture of Escherichia coli K-12 was exposed to hydrogen peroxide in the presence of various compounds. Hydrogen peroxide (0.1 mM) together with 0.1 mM L-cysteine or L-cystine killed the organisms more rapidly than 10 mM hydrogen peroxide alone. The exposure of E. coli to hydrogen peroxide in the presence of L-cysteine inhibited some of the catalase. This inhibition, however, could not fully explain the 100-fold increase in hydrogen peroxide sensitivity of the organism in the presence of L-cysteine. Of other compounds tested only some thiols potentiated the bactericidal effect of hydrogen peroxide. These thiols were effective, however, only at concentrations significantly higher than 0.1 mM. The effect of L-cysteine and L-cystine could be annihilated by the metal ion chelating agent 2,2'-bipyridyl. DNA breakage in E. coli K-12 was demonstrated under conditions where the organisms were killed by hydrogen peroxide.

  • 285.
    Berglin, Ewa H.
    et al.
    Umeå University, Faculty of Medicine, Department of Odontology, Oral Microbiology.
    Carlsson, Jan
    Umeå University, Faculty of Medicine, Department of Odontology, Oral Microbiology.
    Potentiation by sulfide of hydrogen peroxide-induced killing of Escherichia coli1985In: Infection and Immunity, ISSN 0019-9567, E-ISSN 1098-5522, Vol. 49, no 3, p. 538-543Article in journal (Refereed)
    Abstract [en]

    L-Cysteine potentiates 100-fold the hydrogen peroxide-induced killing of a growing culture of Escherichia coli K-12 (Berglin et al., J. Bacteriol. 152:81-88). In the present study it is shown that hydrogen sulfide is formed from L-cysteine and that sodium sulfide could substitute for L-cysteine in the potentiation of hydrogen peroxide-induced killing of E. coli K-12. Addition of an amino acid, L-leucine, L-valine, or L-alanine, to an L-cysteine-containing medium with a growing culture of E. coli K-12 inhibited hydrogen sulfide formation and the potentiation of hydrogen peroxide-induced killing. These amino acids did not inhibit hydrogen sulfide formation from L-cysteine by a cell extract, and they did not inhibit the potentiation by sulfide of hydrogen peroxide-induced killing. This indicated that the amino acids protected the culture from L-cysteine-potentiated, hydrogen peroxide-induced killing by inhibiting the transport of L-cysteine into the cell. The potentiation by sodium sulfide of hydrogen peroxide-induced killing was abolished by the metal ion chelator 2,2'-bipyridyl. This indicated that metal ions, in addition to sulfide, were involved in the killing. Toxic effects of hydrogen peroxide are often presumed to be mediated by hydroxyl radicals formed in iron-catalyzed reactions. It was demonstrated that iron sulfide was more efficient than ferrous iron in catalyzing the formation of hydroxyl radicals from hydrogen peroxide. It was suggested that hydrogen sulfide formed in polymicrobial infections may play an important role in the host defense by potentiating the antimicrobial effect of hydrogen peroxide produced by phagocytic cells.

  • 286. Berglund, Jennie
    et al.
    Angles d'Ortoli, Thibault
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Vilaplana, Francisco
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bergenstråhle-Wohlert, Malin
    Lawoko, Martin
    Henriksson, Gunnar
    Lindström, Mikael
    Wohlert, Jakob
    A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility2016In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 88, no 1, p. 56-70Article in journal (Refereed)
    Abstract [en]

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

  • 287.
    Berglund, Jennie
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Bergenstråhle, Malin
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Vilaplana, Francisco
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Biotechnology (BIO), Glycoscience.
    d'Ortoli, Thibault Angles
    Stockholm Univ, Dept Organ Chem, Stockholm, Sweden..
    Widmalm, Goran
    Stockholm Univ, Dept Organ Chem, Stockholm, Sweden..
    Lawoko, Martin
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Henriksson, Gunnar
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Lindström, Mikael
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Wohlert, Jakob
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    How the flexibility properties of hemicelluloses are affected by the glycosidic bonds between different backbone sugars - A molecular dynamics study2016In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 251Article in journal (Other academic)
  • 288.
    Berglund, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Mechanical behavior of nanostructured cellulosic materials2016In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 251Article in journal (Other academic)
  • 289.
    Berglund, P.
    et al.
    Mid Sweden University.
    Holmquist, M.
    Hedenstrom, E.
    Hult, K.
    Hogberg, H. -E
    2-Methylalkanoic acids resolved by esterification catalysed by lipase from Candida rugosa: Alcohol chain length and enantioselectivity1993In: Tetrahedron Asymmetry, ISSN 09574166 (ISSN), Vol. 4, no 8, p. 1869-1878Article in journal (Refereed)
    Abstract [en]

    Enantiomerically pure (R)-2-methyldecanoic acid and (S)-2-methyl-1-decanol were prepared in a multi gram scale by esterification reactions catalysed by lipase from Candida rugosa. The enantiomeric ratios (E-values) were determined as a function of the chain length of the alcohol used as the complementary substrate in cyclohexane. In the resolution of 2-methyldecanoic acid the highest value (E = 37 ± 5) was obtained, when either 2-hexanol, 1-heptanol or 1-octanol were used. In contrast, when resolving 2-methyloctanoic acid, the E-values increased continually with increasing chain length of the alcohol used. 1-Hexadecanol gave the highest value: E > 100. The E-values were determined from the enantiomeric excess (ee) of the product at a conversion below 0.4. After two consecutive esterification reactions enantiomerically pure (R)-2-methyldecanoic acid, >99.8% ee, and after subsequent reduction of the ester produced, (S)-2-methyl-1-decanol, 96.7% ee, were obtained.

  • 290.
    Berglund, P.
    et al.
    Mid Sweden University.
    Holmquist, M.
    Hult, K.
    Hogberg, H. -E
    Alcohols as enantioselective inhibitors in a lipase catalysed esterification of a chiral acyl donor1995In: Biotechnology Letters, ISSN 01415492 (ISSN), Vol. 17, no 1, p. 55-60Article in journal (Refereed)
    Abstract [en]

    Increased reaction rates and increased enantioselectivities were observed with decreased concentrations of n-alkanols when resolving 2-methyldecanoic acid by esterification catalysed by immobilised lipase from Candida rugosa at controlled water activities in cyclohexane. The enantioselectivity was found to be independent of the water activity in the reaction medium at the n-heptanol concentrations investigated. However, when n-decanol was used as the acyl acceptor, not only the alcohol concentration but also the water activity in the reaction medium, influenced the enantioselectivity. The results obtained showed that the low enantioselectivity seen at a high alcohol concentration could be explained by the alcohol influencing the apparent V(max)(S) and V(max)(R) differently.

  • 291.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Asymmetric Organic Synthesis with Enzymes: Edited by Vicente Gotor, Ignacio Alfonso and Eduardo Garcia-Urdiales2008In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, no 35, p. 6514-6515Article, book review (Other academic)
  • 292.
    Berglund, Per
    KTH, Superseded Departments, Chemistry.
    Candida rugosa lipase as a catalyst in organic media: Enantioselectivity in kinetic resolutions of 2-methylalkanoic acids1995Doctoral thesis, comprehensive summary (Other academic)
  • 293.
    Berglund, Per
    et al.
    KTH, Superseded Departments, Biotechnology.
    Branneby, Cecilia
    Svedendahl Humble, Maria
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Carlqvist, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Magnusson, Anders
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Aldol and Michael additions catalyzed by a rationally redesigned hydrolytic enzyme2003In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 226, no 2, p. U155-U156Article in journal (Refereed)
  • 294. Bergman, J.
    et al.
    Pettersson, B.
    Hasimbegovic, V.
    Svensson, Per H.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry. AstraZeneca R&D, Pharmaceut Dev, Sweden.
    Thionations using a P4S10-pyridine complex in solvents such as acetonitrile and dimethyl sulfone2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 6, p. 1546-1553Article in journal (Refereed)
    Abstract [en]

    Tetraphosphorus decasulfide (P 4S 10) in pyridine has been used as a thionating agent for a long period of time. The moisture-sensitive reagent has now been isolated in crystalline form, and the detailed structure has been determined by X-ray crystallography. The thionating power of this storable reagent has been studied and transferred to solvents such as acetonitrile in which it has proven to be synthetically useful and exceptionally selective. Its properties have been compared with the so-called Lawesson reagent (LR). Particularly interesting are the results from thionations at relatively high temperatures (̃165 °C) in dimethyl sulfone as solvent. Under these conditions, for instance, acridone and 3-acetylindole could quickly be transformed to the corresponding thionated derivatives. Glycylglycine similarly gave piperazinedithione. At these temperatures, LR is inefficient due to rapid decomposition. The thionated products are generally cleaner and more easy to obtain because in the crystalline reagent, impurities which invariably are present in the conventional reagents, P 4S 10 in pyridine or LR, have been removed.

  • 295. Bergman, Jan
    et al.
    Arewang, Carl-Johan
    Svensson, Per H.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry. SP Process Development, Sweden .
    Oxidative Ring Expansion of Spirocyclic Oxindole Derivatives2014In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 79, no 19, p. 9065-9073Article in journal (Refereed)
    Abstract [en]

    Oxidation of the spirocyclic oxindole derivative, isamic acid 1, led to decarboxylation and ring expansion to quinazolino[4,5-b]quinazoline-6,8-dione 7 rather than, as previously believed, its isomer 6. The structure of 7 was confirmed by X-ray crystallography. Condensation of isatin (indole-2,3-dione) and 2-aminobenzamide led to the spirocyclic molecule, spiro[3H-indole-3,2'(1H)quinazoline]-2,4'(1H,3H)dione 8, which was also identified as an intermediate in the oxidation of isamic acid. Mild hydrolysis of 7 gave the 10-membered molecule 22. Isamic acid could easily be converted to N-nitrosoisamic acid, which when heated in ethanol underwent a ring expansion to a hydroximino derivative, 38, of compound 6. The structure of 38 was confirmed by X-ray crystallography.

  • 296.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Engqvist, Robert
    Karolinska Institute.
    Stålhandske, C
    Chemical Centre, Lund.
    Wallberg, H
    KTH.
    Studies of the reactions between indole-2,3-diones (isatins) and 2-aminobenzylamine2003In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 59, no 7, p. 1033-1048Article in journal (Refereed)
  • 297.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Janosik, T
    Koch, E
    Pelcman, B
    Acid-induced dimerization of 3-(1H-indol-3-yl)maleimides. Formation of cyclopentindole derivatives2000In: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 1, ISSN 1470-4358, no 16, p. 2615-2621Article in journal (Refereed)
    Abstract [en]

    Acid-induced dimerizations of 3-substituted maleimides have been investigated, leading to e.g. the cyclopentindole 9 and the deeply coloured spiro compounds 24 and 25 in good yields. 3-(1H-Indol-3-yl)maleimide 6b readily gave the cycloaddition products 13-15 on treatment with appropriate dienophiles. In addition, several related 3,3-di-(1H-indol-3-yl)succinimides have been prepared and studied.

  • 298.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Janosik, T
    Yudina, L
    Desarbre, E
    Lidgren, G
    Venemalm, L
    Reactions of 1,2-bis(1H-indol-2-yl)ethane: Formation of indolo[2,3-c]carbazole and cyclohept[1,2-b : 5,4-b ']bisindole derivatives2000In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 56, no 13, p. 1911-1916Article in journal (Refereed)
    Abstract [en]

    1,2-Bis(1H-indol-2-yl)ethane (9) has been prepared and converted into indolo[2,3-c]carbazole (8) using palladium acetate in refluxing acetic acid. Reaction of 9 with CoF3 in hot TFA led to isolation of cyclohept[1,2-b:5,4-b']bisindole derivatives 11 and 12, which could be elaborated into further derivatives. Treatment of 9 with orthoesters, aldehydes and ketones under acidic conditions afforded additional bisindoles containing a seven-membered ring.

  • 299.
    Bergman, Jan
    et al.
    Södertörn University, School of Life Sciences.
    Johnson, Ann-Louise
    A short synthesis of the carbazole alkaloid clausine E2006In: Organic preparations and procedures international, ISSN 0030-4948, E-ISSN 1945-5453, Vol. 38, no 6, p. 593-599Article in journal (Refereed)
  • 300.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Koch, E
    Pelcman, B
    Coupling reactions of indole-3-acetic acid derivatives. Synthesis of arcyriaflavin A2000In: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 1, ISSN 1470-4358, no 16, p. 2609-2614Article in journal (Refereed)
    Abstract [en]

    The bisindolesuccinic acid methyl ester 10 was obtained by an iodine-promoted coupling of the dianion 9. The diester was converted to the N-benzylimide 12, which was oxidatively cyclized to the indolo[2,3-a]pyrrolo[3,4-c]carbazole 15. The diester 10 could be directly transformed to the known indolocarbazole diester 27 via acid-induced intramolecular cyclization in TFA. The same methodology gave arcyriaflavin A 4 from the succinimide 18b.

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