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  • 1.
    Agnemo, Roland
    Umeå University, Faculty of Science and Technology.
    Ligniners reaktioner med alkalisk väteperoxid1981Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Under alkaline conditions hydrogen peroxide can be used either as a 1ignin-degrading or a 1ignin-preserving bleaching agent. If heavy metal ions are present and/or silicate is absent in the reaction medium, hydrogen peroxide decomposes via hydroxyl radicals and superoxide ions to oxygen and water. These decomposition products are able to react for example with phenolic lignin structures and thereby cause a partial degradation of lignin. In such a system peroxide could act as a bleaching and delignifying agent at the same time and these properties can be utilized for the bleaching of chemical pulps.In order to elucidate the factors which influence the degradation of phenolic structures by oxidation with alkaline hydrogen peroxide the lignin model compounds-methylsyringyl alcohol was studied.By determining the first order reaction rate constants for the oxidation, the main results which were obtained indicate that phenolic lignin structures can be efficiently degraded especially if:A. The pH in the bleaching liquor is close to the pK -valueàfor hydrogen peroxide.B. The ionic strength in the bleaching medium is as high as possible.C. A fixed amount of heavy metal ions (manganese) is added to the bleaching liquor.In the presence of silicate and diethylentriaminepenta-acetic acid (DTPA) hydrogen peroxide is stabilized against decomposition. Under these conditions alkaline hydrogen peroxide is able to react only with lignin units containing conjugated carbonyl groups such as quinone, aryl-oe-carbonyl and cinnamaldehyd structures, leading to an elimination of the chromophoric structures without any substantial dissolution of lignin. In this part of work we have elucidated the kinetic behavior and the reaction products from lignin model compounds of the aryl-of- carbonyl and cinnamaldehyde types.1,2-Diarylpropan-1,3,-diol structures constitute an important building unit in native lignins. We have demonstrated that under hydrogen peroxide bleaching conditions the model compound 2,3--bis(4-hydroxy-3-methoxyphenyl)-3-ethoxy-propanol was converted to stilbenes, ûe. structures which when present in pulps may contribute to a rapid yellowing. The results obtained with model compounds under simulated lignin retaining bleaching conditions demonstrate that there are possibilities to improve the bleaching of mechanical pulps with hydrogen peroxide if:A. The remaining heavy metal ions complexed with DTPA are present in their lowest valence states.B. The concentration of hydroperoxy ions can be maintained at a high level at the lowest possible pH-value.

  • 2. Aguilera, Adriana Freites
    et al.
    Tolvanen, Pasi
    Heredia, Shuyana
    Muñoz, Marta González
    Samson, Tina
    Oger, Adrien
    Verove, Antoine
    Eränen, Kari
    Leveneur, Sebastien
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Industrial Chemistry & Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Salmi, Tapio
    Epoxidation of fatty acids and vegetable oils assisted by microwaves catalyzed by a cation exchange resin2018In: Industrial & Engineering Chemistry Research, ISSN 0888-5885, E-ISSN 1520-5045, Vol. 57, no 11, p. 3876-3886Article in journal (Refereed)
    Abstract [en]

    Epoxidation of oleic acid and cottonseed oil was conducted in a semibatch reactor with in-situ-formed percarboxylic acid (peracetic acid or perpropionic acid), using hydrogen peroxide as an oxidizing agent and carboxylic acid (acetic acid or propionic acid) as oxygen carriers. Amberlite IR-120 was implemented as the catalyst. The system was comprised of a loop reactor, where the mixture was pumped through a single-mode cavity in which microwave irradiation was introduced. A heat exchanger was integrated into the system to replace microwave heating, to compare the results obtained via microwave heating versus conventional heating. The catalyst loading effect was studied, as well as the influence of microwave irradiation and the implementation of the SpinChem rotating bed reactor (RBR), in hopes of decreasing the influence of the internal mass transfer. The application of microwave irradiation results in an improvement of the reaction yield in the absence of a catalyst.

  • 3.
    Albers, Michael Franz
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Synthesis and investigation of bacterial effector molecules2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During infections, bacterial microorganisms initiate profound interactions with mammalian host cells. Usually defense mechanisms of the host destroy intruding bacteria in rapid manner. However, many bacterial pathogens have evolved in a way to avoid these mechanisms. By use of effector molecules, which can be small organic molecules or proteins with enzymatic activity, the host is manipulated on a molecular level. Effectors mediating post-translational modifications (PTMs) are employed by many pathogens to influence the biological activity of host proteins. In the presented thesis, two related PTMs are investigated in detail: Adenylylation, the covalent transfer of an adenosine monophosphate group from adenosine triphosphate onto proteins, and phosphocholination, the covalent transfer of a phosphocholine moiety onto proteins. Over the past years, enzymes mediating these modifications have been discovered in several pathogens, especially as a mechanism to influence the signaling of eukaryotic cells by adenylylating or phosphocholinating small GTPases. However, the development of reliable methods for the isolation and identification of adenylylated and phosphocholinated proteins remains a vehement challenge in this field of research. This thesis presents general procedures for the synthesis of peptides carrying adenylylated or phosphocholinated tyrosine, threonine and serine residues. From the resulting peptides, mono-selective polyclonal antibodies against adenylylated tyrosine and threonine have been raised. The antibodies were used as tools for proteomic research to isolate unknown substrates of adenylyl transferases from eukaryotic cells. Mass spectrometric fragmentation techniques have been investigated to ease the identification of adenylylated proteins. Furthermore, this work presents a new strategy to identify adenylylated proteins. Additionally, small effector molecules are involved in the regulation of infection mechanisms. In this work, the small molecule LAI-1 (Legionella autoinducer 1) from the pathogen Legionella pneumophila, the causative agent of the Legionnaire’s disease, was synthesised together with its amino-derivatives. LAI-1 showed are a clear pharmacological effect on the regulation of the life cycle of L. pneumophila, initiating transmissive traits like motility and virulence. Furthermore, LAI-1 was shown to have an effect on eukaryotic cells as well. Directed motility of the eukaryotic cells was significantly reduced and the cytoskeletal architecture was reorganised, probably by interfering with the small GTPase Cdc42.

  • 4. Almroth, Bethanie M. Carney
    et al.
    Gunnarsson, Lina M.
    Cuklev, Filip
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kristiansson, Erik
    Larsson, D. G. Joakim
    Waterborne beclomethasone dipropionate affects the physiology of fish while its metabolite beclomethasone is not taken up2015In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 511, p. 37-46Article in journal (Refereed)
    Abstract [en]

    Asthma is commonly treated with inhalable glucocorticosteroids, including beclomethasone dipropionate (BDP). This is a synthetic prodrug which is metabolized to the more active monopropionate (BMP) and free beclomethasone in humans. To evaluate potential effects of residual drugs on fish, we conducted a 14 day flow-through exposure experiment with BDP and beclomethasone using rainbow trout, and analyzed effects on plasma glucose, hepatic glutathione and catalase activity together with water and body concentrations of the BDP, BMP and beclomethasone. We also analyzed hepatic gene expression in BDP-exposed fish by micro-array and quantitative PCR Beclomethasone (up to 0.65 mu g/L) was not taken up in the fish while BDP (0.65 and 0.07 mu g/L) resulted in accumulation of both beclomethasone, BMP and BDP in plasma, reaching levels up to those found in humans during therapy. Accordingly, exposure to 0.65 mu g/L of BDP significantly increased blood glucose as well as oxidized glutathione levels and catalase activity in the liver. Exposure to beclomethasone or the low concentration of BDP had no effect on these endpoints. Both exposure concentrations of BDP resulted in significantly higher transcript abundance of phosphoenolpyruvate carboxykinase involved in gluconeogenesis, and of genes involved in immune responses. As only the rapidly metabolized prodrug was potent in fish, the environmental risks associated with the use of BDP are probably small. However, the observed physiological effects in fish of BDP at plasma concentrations known to affect human physiology provides valuable input to the development of read-across approaches in the identification of pharmaceuticals of environmental concern.

  • 5.
    Andersson, Barbro
    Umeå University, Faculty of Science and Technology.
    Analysis of plant growth regulating substances1982Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Natural plant growth regulators (phytohormones) are a group of organic compounds which, in very small amounts, act as regulators of physiological processes in plants.Methods were developed for the analysis of phytohormones in samples from Norway spruce (Picea abies (L.) Karst.) and Scots pine (Pinus sylvestris (L.) Karst»). Identification of abscisic acid, 3-indoleacetic acid, gibbe-rellin Ag and the conjugate N-(3-indoleacetyl)aspartic acid was performed by GC-MS as their methyl esters. A quantitative determination of abscisic acid was made by GC-ECD and this method was also applied to anther samples of Anemone canadensis. 3-Indole-acetic acid and N-(3-indoleacetyl)aspartic acid were quantified by reversed-phase HPLC and spectrofluorimetric detection. Dichlorophene, used as a growth regulator in containerized seedlings of pine and spruce, was analysed by GC-MID in peat and paper.

  • 6.
    Andersson, David C.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Martinez, N.
    Zeller, D.
    Rondahl, S. H.
    Koza, M. M.
    Frick, B.
    Ekstrom, F.
    Peters, J.
    Linusson, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Changes in dynamics of alpha-chymotrypsin due to covalent inhibitors investigated by elastic incoherent neutron scattering2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 37, p. 25369-25379Article in journal (Refereed)
    Abstract [en]

    An essential role of enzymes is to catalyze various chemical reactions in the human body and inhibition of the enzymatic activity by small molecules is the mechanism of action of many drugs or tool compounds used to study biological processes. Here, we investigate the effect on the dynamics of the serine protease alpha-chymotrypsin when in complex with two different covalently bound inhibitors using elastic incoherent neutron scattering. The results show that the inhibited enzyme displays enhanced dynamics compared to the free form. The difference was prominent at higher temperatures (240-310 K) and the type of motions that differ include both small amplitude motions, such as hydrogen atom rotations around a methyl group, and large amplitude motions, such as amino acid side chain movements. The measurements were analyzed with multivariate methods in addition to the standard univariate methods, allowing for a more in-depth analysis of the types of motions that differ between the two forms. The binding strength of an inhibitor is linked to the changes in dynamics occurring during the inhibitor-enzyme binding event and thus these results may aid in the deconvolution of this fundamental event and in the design of new inhibitors.

  • 7.
    Andersson, Hans
    Umeå University, Faculty of Science and Technology, Chemistry.
    Reaction Between Grignard reagents and Heterocyclic N-oxides: Synthesis of Substituted Pyridines, Piperidines and Piperazines2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes the development of new synthetic methodologies for preparation of bioactive interesting compounds, e.g. substituted pyridines, piperidines or piparazines. Thesecompounds are synthesized from commercially available, cheap and easily prepared reagents, videlicet the reaction between Grignard reagents and heterocyclic N-oxides.

     The first part of this thesis deals with an improvement for synthesis of dienal-oximes and substituted pyridines. This was accomplished by a rapid addition of Grignard reagents to pyridine N-oxides at rt. yielding a diverse set of substituted dienal-oximes. During these studies, it was observed that the obtained dienal-oxmies are prone to ring-close upon heating. By taking advantage of this, a practical synthesis of substituted pyridines was developed.

    In the second part, an ortho-metalation of pyridine N-oxides using Grignard reagents is discussed. The method can be used for incorporation of a range of different electrophiles, including aldehydes, ketones and halogens. Furthermore, the importance for incorporation of halogens are exemplified through a Suzuki–Miyaura coupling reaction of 2-iodo pyridine N-oxides and different boronic acids. Later it was discovered that if the reaction temperature is kept below -20 °C, the undesired ringopening can be avoided. Thus, the synthesis of 2,3-dihydropyridine N-oxide, by reacting Grignard reagents with pyridine N-oxides at -40 °C followed by sequential addition of aldehyde or ketone, was accomplished. The reaction provides complete regio- and stereoselectivity yielding trans-2,3-dihydropyridine N-oxides in good yields. These intermediate products could then be used for synthesis of either substituted piperidines, by reduction, or reacted in a Diels–Alder cycloaddtion to give the aza-bicyclo compound.

    In the last part of this thesis, the discovered reactivity for pyridine N-oxides, is applied on pyrazine N-oxides in effort to synthesize substituted piperazines. These substances are obtained by the reaction of Grignard reagents and pyrazine N-oxides at -78 °C followed by reduction and protection, using a one-pot procedure. The product, a protected piperazine, that easily can be orthogonally deprotected, allowing synthetic modifications at either nitrogens in a fast and step efficient manner. Finally, an enantioselective procedure using a combination of PhMgCl and (-)-sparteine is discussed, giving opportunity for a stereoselective synthesis of substituted piperazines.

  • 8.
    Andersson, Ida E.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Modified Glycopeptides Targeting Rheumatoid Arthritis: Exploring molecular interactions in class II MHC/glycopeptide/T-cell receptor complexes2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Rheumatoid arthritis (RA) is an autoimmune inflammatory disease that leads to degradation of cartilage and bone mainly in peripheral joints. In collagen-induced arthritis (CIA), a mouse model for RA, activation of autoimmune CD4+ T cells depends on a molecular recognition system where T-cell receptors (TCRs) recognize a complex between the class II MHC Aq protein and CII259-273, a glycopeptide epitope from type II collagen (CII). Interestingly, vaccination with the Aq/CII259-273 complex can relieve symptoms and cause disease regression in mice. This thesis describes the use of modified glycopeptides to explore interactions important for binding to the Aq protein and recognition by autoimmune T-cell hybridomas obtained from mice with CIA.

    The CII259-273 glycopeptide was modified by replacement of backbone amides with different amide bond isosteres, as well as substitution of two residues that anchor the glycopeptide in prominent pockets in the Aq binding site. A three-dimensional structure of the Aq/glycopeptide complex was modeled to provide a structural basis for interpretation of the modified glycopeptide’s immunological activities. Overall, it was found that the amide bond isosteres affected Aq binding more than could be explained by the static model of the Aq/glycopeptide complex. Molecular dynamics (MD) simulations, however, revealed that the introduced amide bond isosteres substantially altered the hydrogen-bonding network formed between the N-terminal 259-265 backbone sequence of CII259-273 and Aq. These results indicated that the N-terminal hydrogen-bonding interactions follow a cooperative model, where the strength and presence of individual hydrogen bonds depended on the neighboring interactions.

    The two important anchor residues Ile260 and Phe263 were investigated using a designed library of CII259-273 based glycopeptides with substitutions by different (non-)natural amino acids at positions 260 and 263. Evaluation of binding to the Aq protein showed that there was scope for improvement in position 263 while Ile was preferred in position 260. The obtained SAR understanding provided a valuable basis for future development of modified glycopeptides with improved Aq binding. Furthermore, the modified glycopeptides elicited varying T-cell responses that generally could be correlated to their ability to bind to Aq. However, in several cases, there was a lack of correlation between Aq binding and T-cell recognition, which indicated that the interactions with the TCRs were determined by other factors, such as presentation of altered epitopes and changes in the kinetics of the TCR’s interaction with the Aq/glycopeptide complex.

    Several of the modified glycopeptides were also found to bind well to the human RA-associated DR4 protein and elicit strong responses with T-cell hybridomas obtained from transgenic mice expressing DR4 and the human CD4 co-receptor. This encourages future investigations of modified glycopeptides that can be used to further probe the MHC/glycopeptide/TCR recognition system and that also constitute potential therapeutic vaccines for treatment of RA. As a step towards this goal, three modified glycopeptides presented in this thesis have been identified as candidates for vaccination studies using the CIA mouse model.

  • 9.
    Badea, Silviu-Laurentiu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Danet, Andrei-Florin
    Enantioselective stable isotope analysis (ESIA) - A new concept to evaluate the environmental fate of chiral organic contaminants2015In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 514, p. 459-466Article in journal (Refereed)
    Abstract [en]

    Since 2011, the enantiospecific stable carbon isotope analysis (ESIA) has emerged as an innovative technique to assess the environmental fate of chiral emerging compounds by combining in one experimental technique both compound specific isotope analysis (CSIA) and enantioselective analysis. To date, the ESIA was applied for four classes of compounds: alpha-hexachlorocyclohexane (alpha-HCH), polar herbicides (phenoxy acids), synthetic polycyclic musk galaxolide (HHCB), and phenoxyalkanoic methyl herbicides. From an analytical point of view there are factors that are hindering the application of ESIA methods for the field samples: (i.e. amounts of target analyte, matrix effects, GC resolution) and overcoming these factors is challenging. While ESIA was shown as a mature technique for the first three abovementioned class of compounds, no isotope analysis of individual enantiomers could be performed for phenoxyalkanoic methyl herbicides. With respect to field studies, one study showed that ESIA might be a promising tool to distinguish between biotic and abiotic transformation pathways of chiral organic contaminants and even to differentiate between their aerobic and anaerobic biotransformation pathways. The development of ESIA methods for new chiral emerging contaminants in combination with development of multi-element isotope analysis will contribute to a better characterization of transformation pathways of chiral organic contaminants. (C) 2015 Elsevier B.V. All rights reserved.

  • 10.
    Barange, Deepak Kumar
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Johnson, Magnus T.
    Cairns, Andrew G.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Olsson, Roger
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Regio- and Stereoselective Alkylation of Pyridine-N-oxides: Synthesis of Substituted Piperidines and Pyridines2016In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 18, no 24, p. 6228-6231Article in journal (Refereed)
    Abstract [en]

    Regio- and stereoselective addition of alkyl Grignard reagents to pyridine-N-oxides gave C2-alkylated N-hydroxy-1,2,5,6-tetrahydropyridines and trans-2,3-disubstituted N-hydroxy-1,2,5,6-tetrahydropyridines in good to excellent yields. These intermediates were aromatized or alternatively reduced in one-pot methodologies for efficient syntheses of alkylpyridines or piperidines, respectively. These reactions have a broad substrate scope and short reaction times.

  • 11.
    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.

  • 12. 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.

  • 13.
    Bergqvist, Per-Anders
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Zaliauskiene, Audrone
    Field study considerations in the use of passive sampling devices in water monitoring2007In: Passive Sampling Techniques in Environmental Monitoring / [ed] R. Greenwood, G. Mills and B. Vrana, Amsterdam: Elsevier, 2007, p. 311-328Chapter in book (Other academic)
    Abstract [en]

    Semipermeable membrane devices (SPMDs) are passive monitors that are being increasingly used by monitoring agencies and wastewater dischargers to measure the contents of lipophilic organic chemicals that may adversely affect water quality. This chapter addresses the most frequently asked questions regarding the use of SPMDs for water monitoring and other questions related to the field application of SPMDs. It provides a sound understanding of the applicability and limitations of SPMDs for obtaining reliable monitoring data. The chapter discusses under field study considerations: pre-exposure considerations; SPMD storage considerations; and precautions/procedures during deployment and retrieval of SPMDs. In environmental monitoring projects using SPMDs, quality control (QC) procedures for sampling and analysis are applied to ensure that the data are of high quality. Appropriate QC samples are prepared to quantify possible sampler contamination during transport, deployment, retrieval, storage, processing, enrichment, fractionation operations and analyte recovery. In general, two groups of quality assurance measures are implemented: replicate QC and sampling device control.

  • 14.
    Bidleman, Terry Frank
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Air Quality Processes Research Section, Environment Canada.
    Jantunen, L. M.
    Hung, H.
    Ma, J.
    Stern, G. A.
    Rosenberg, B.
    Racine, J.
    Annual cycles of organochlorine pesticide enantiomers in Arctic air suggest changing sources and pathways2015In: Atmospheric Chemistry And Physics, ISSN 1680-7316, E-ISSN 1680-7324, Vol. 15, no 3, p. 1411-1420Article in journal (Refereed)
    Abstract [en]

    Air samples collected during 1994-2000 at the Canadian Arctic air monitoring station Alert (82 degrees 30'N, 62 degrees 20'W) were analysed by enantiospecific gas chromatography-mass spectrometry for alpha-hexachlorocyclohexane (alpha-HCH), trans-chlordane (TC) and cis-chlordane (CC). Results were expressed as enantiomer fractions (EF = peak areas of (+)/[(+) + (-)] enantiomers), where EFs = 0.5, <0.5 and >0.5 indicate racemic composition, and preferential depletion of (+) and (-) enantiomers, respectively. Long-term average EFs were close to racemic values for alpha-HCH (0.504 +/- 0.004, n = 197) and CC (0.505 +/- 0.004, n = 162), and deviated farther from racemic for TC (0.470 +/- 0.013, n = 165). Digital filtration analysis revealed annual cycles of lower alpha-HCH EFs in summer-fall and higher EFs in winter-spring. These cycles suggest volatilization of partially degraded alpha-HCH with EF < 0.5 from open water and advection to Alert during the warm season, and background transport of alpha-HCH with EF > 0.5 during the cold season. The contribution of sea-volatilized alpha-HCH was only 11% at Alert, vs. 32% at Resolute Bay (74.68 degrees N, 94.90 degrees W) in 1999. EFs of TC also followed annual cycles of lower and higher values in the warm and cold seasons. These were in phase with low and high cycles of the TC / CC ratio (expressed as F-TC = TC/(TC + CC)), which suggests greater contribution of microbially "weathered" TC in summer-fall versus winter-spring. CC was closer to racemic than TC and displayed seasonal cycles only in 1997-1998. EF profiles are likely to change with rising contribution of secondary emission sources, weathering of residues in the environment, and loss of ice cover in the Arctic. Enantiomer-specific analysis could provide added forensic capability to air monitoring programs.

  • 15.
    Blomberg, David
    Umeå University, Faculty of Science and Technology, Chemistry.
    Synthesis of β-turn and pyridine based peptidomimetics2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Despite the unfavorable pharmacokinetic properties associated with peptides, they are still of great interest in drug development due to a multitude of interesting biological functions. The development of peptidomimetics strives to maintain or improve the biological activity of a peptide concurrently with removing the unwanted properties. This thesis describes two synthetic approaches to peptidomimetics with particular emphasis on secondary structure mimetics.

    First the design, synthesis and evaluation of two beta-turn mimetics incorporated in the endorphin Leu-enkephalin is presented. The beta-turn mimetics were stabilized by replacement of the intramolecular hydrogen bond with an ethylene bridge, and the amide bond between Tyr and Gly was replaced with an ether linkage. Linear analogues of the two mimetics were also synthesized. The peptidomimetics and their linear analogues were evaluated in a competitive binding assay at two opiate receptors, my and delta. One of the cyclized beta-turn mimetics was found to be a delta receptor antagonist with an IC50 value of 160 nM.

    Second a synthetic strategy to a beta-strand mimetic using 2-fluoro-4-iodopyridine as scaffold is described. The synthesis involved a Grignard exchange reaction on the pyridine scaffold using an amino acid derivative as electrophile followed by an SNAr reaction using an amine as nucleophile. The synthesis of a tripeptidomimetic of Leu-Gly-Gly and attempts to introduce chiral building blocks at the C-terminal, as well as studies towards elongated mimetics are presented.

    Two additional studies deal with the synthesis of two classes of potential thrombin inhibitors based on the pyridine scaffold. The first class contain pyridine as central fragment (P2 residue) substituted with a para-amidinobenzylamine group as P1 residue and various benzoyl groups as P3 residues. Three potential thrombin inhibitors were synthesized and found to be microM inhibitors in an enzymatic assay. In the second class, the pyridine ring serves as P3 residue. This class also lacks a strongly basic group in the P1 position. A small library of eight compounds were synthesized and evaluated in the enzymatic assay. Unfortunately, these compounds lacked inhibitory activity.

  • 16. Borah, Raju Kumar
    et al.
    Raul, Prasanta Kumar
    Mahanta, Abhijit
    Shchukarev, Andrey
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Industrial Chemistry & Reaction Engineering, Åbo Akademi University, Åbo-Turku, Finland.
    Thakur, Ashim Jyoti
    Copper Oxide Nanoparticles as a Mild and Efficient Catalyst for N-Arylation of Imidazole and Aniline with Boronic Acids at Room Temperature2017In: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, Vol. 28, no 10, p. 1177-1182Article in journal (Refereed)
    Abstract [en]

    The present work describes the excellent catalytic activity of copper(II) oxide nanoparticles (NPs) towards N-arylation of aniline and imidazole at room temperature. The copper(II) oxide NPs were synthesized by a thermal refluxing technique and characterized by FT-IR spectroscopy; powder XRD, SEM, EDX, TEM, TGA, XPS, BET surface area analysis, and particle size analysis. The size of the NPs was found to be around 12 nm having a surface area of 164.180 m(2) g(-1). The catalytic system was also found to be recyclable and could be reused in subsequent catalytic runs without a significant loss of activity.

  • 17. Bui, Hue T B
    et al.
    Vo, Duy D
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Chau, Yen N T
    Tu, Cuc T K
    Mai, Hieu V
    Truong, Kiet V
    Facile Synthesis of 4-Oxo-4H-quinolizine-2-carboxamide Derivatives2015In: Synthetic Communications, ISSN 0039-7911, E-ISSN 1532-2432, Vol. 45, no 24, p. 2861-2868Article in journal (Refereed)
    Abstract [en]

    A facile synthetic method for the construction of 2-substituted-4-oxo-4H-quinolizine-based core structure has been successfully developed. The synthesis made use of a one-pot Stobbe condensation followed by cyclization starting from the commercially available 2-pyridinecarbaldehyde. The structure of the formed 4-oxo-4H-quinolizine-2-carboxylate was fully confirmed by mass spectra, H-1 NMR and C-13 NMR, correlation spectrography, heteronuclear multiple bond correlation, and heteronuclear single quantum coherence (HSQC) spectra. The ethyl carboxylate moiety was then further functionalized via direct aminolysis by a range of amines to afford the corresponding 4-oxo-4H-quinolizine-2-carboxamides 4a-i in moderate to good yields.

  • 18. Bui, Hue Thi Buu
    et al.
    Ha, Quy Thi Kim
    Oh, Won Keun
    Vo, Duy Duc
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Chau, Yen Nguyen Tram
    Tu, Cuc Thi Kim
    Pham, Em Canh
    Tran, Phuong Thao
    Tran, Loan Thi
    Mai, Hieu Van
    Microwave assisted synthesis and cytotoxic activity evaluations of new benzimidazole derivatives2016In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 57, no 8, p. 887-891Article in journal (Refereed)
    Abstract [en]

    Twelve new 2-quinolizinylbenzimidazole and 2-naphthalylbenzimidazole derivatives with various 5- and 6-positioned substituents (aza, H, CH3, Cl, NO2, NH2, OCH3), have been synthesized in moderate to excellent yields via the condensation of 4-oxo-4H-quinolizinecarbaldehyde or naphthalenecarbaldehyde with substituted o-phenylenediamines, o-nitroaniline, and 2,3-pyridinediamine using sodium metabisulfite or sodium hydrosulfite under microwave irradiation. The new benzimidazole derivatives were screened for their cytotoxic activity against the human breast cancer cell line (MCF-7). The results showed on one hand that 2-(substituted quinolizinyl)-1H-benzimidazoles (12bf) were less active (3–6 fold) than the positive control Tamoxifen (CC50 = 6.52 μM), and on the other hand, among the 2-(substituted naphthalyl)-1H-benzimidazoles series (13af), compounds 6,7,8-trimethoxy-3-(5-chloro-1H-benzo[d]imidazol-2-yl)naphthalen-1-ol (13c) (CC50 = 7.48 μM) and 6,7,8-trimethoxy-3-(5-methoxy-1H-benzo[d]imidazol-2-yl)naphthalen-1-ol (13f) (CC50 = 6.43 μM) were found to be as active as Tamoxifen.

  • 19.
    Carlsson, Marcus
    Umeå University, Faculty of Science and Technology, Chemistry.
    Synthesis and optical characterization of optical power limiting platinum(II) acetylides2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Interactions between light and a molecule can result in reversible or irreversible changes in properties of both the light and the molecule. Of the many known interactions, nonlinear absorption is a process in which an intense light signal, for instance from a laser, can be moderated. This can be manifested either in a marked lowering of the light’s intensity or in reductions in fluctuations of its intensity. Such an effect is often termed ‘optical power limiting’ (OPL).

    High power lasers can be very dangerous since their high intensity can damage or destroy eyes and optical sensors. However, there are currently no adequate protective measures against lasers that cover the entire visible region and there is an increasing demand for new or improved OPL materials. Some of the most promising optical power limiting materials are substances that combine nonlinear optical properties with high transparency in normal light, but after activation by a laser beam, their light transmittance falls extremely rapidly via so-called self-activating mechanisms. The platinum(II) acetylides comprise one class of compounds with such properties.

    In this study, various OPL Pt(II) acetylides were synthesized and their nonlinear optical properties were characterized. The emphasis of the work was on preparation of the compounds, but in order to design organoplatinum chromophores for OPL, attempts were also made to obtain insight into the mechanisms of nonlinear absorption.

    The work was divided into two main parts. In the first the goal was to find compounds that are good optical limiters in solution. The possibility of isolating the chromophore site by dendron shielding and the effects of incorporating a thiophene ring into the organic molecular system were also explored. In addition, a new route for synthesizing these compounds was developed. The second part was focused on incorporating the most interesting compounds into solid materials. The preparation and characterization of Pt(II) acetylides with molecular groups for covalent attachment to a silica matrix via the solution gel approach is described.

  • 20.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Regulation of the scp Genes in the Cyanobacterium Synechocystis sp PCC 6803-What is New?2015In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 20, no 8, p. 14621-14637Article in journal (Refereed)
    Abstract [en]

    In the cyanobacterium Synechocystis sp. PCC 6803 there are five genes encoding small CAB-like (SCP) proteins, which have been shown to be up-regulated under stress. Analyses of the promoter sequences of the scp genes revealed the existence of an NtcA binding motif in two scp genes, scpB and scpE. Binding of NtcA, the key transcriptional regulator during nitrogen stress, to the promoter regions was shown by electrophoretic mobility shift assay. The metabolite 2-oxoglutarate did not increase the affinity of NtcA for binding to the promoters of scpB and scpE. A second motif, the HIP1 palindrome 5' GGCGATCGCC 3', was detected in the upstream regions of scpB and scpC. The transcription factor encoded by sll1130 has been suggested to recognize this motif to regulate heat-responsive genes. Our data suggest that HIP1 is not a regulatory element within the scp genes. Further, the presence of the high light regulatory (HLR1) motif was confirmed in scpB-E, in accordance to their induced transcriptions in cells exposed to high light. The HLR1 motif was newly discovered in eight additional genes.

  • 21.
    Chorell, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pilicides and Curlicides: Design, synthesis, and evaluation of novel antibacterial agents targeting bacterial virulence2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    New strategies are needed to counter the growing problem of bacterial resistance to antibiotics. One such strategy is to design compounds that target bacterial virulence, which could work separately or in concert with conventional bacteriostatic or bactericidal antibiotics. Pilicides are a class of compounds based on a ring-fused 2-pyridone scaffold that target bacterial virulence by blocking the chaperone/usher pathway in E. coli and thereby inhibit the assembly of pili. This thesis describes the design, synthesis, and biological evaluation of compounds based on the pilicide scaffold with the goal of improving the pilicides and expanding their utility. Synthetic pathways have been developed to enable the introduction of substituents at the C-2 position of the pilicide scaffold. Biological evaluation of these compounds demonstrated that some C-2 substituents give rise to significant increases in potency. X-ray crystallography was used to elucidate the structural basis of this improved biological activity. Furthermore, improved methods for the preparation of oxygen-analogues and C-7 substituted derivatives of the pilicide scaffold have been developed. These new methods were used in combination with existing strategies to decorate the pilicide scaffold as part of a multivariate design approach to improve the pilicides and generate structure activity relationships (SARs).

    Fluorescent pilicides were prepared using a strategy where selected substituents were replaced with fluorophores having similar physicochemical properties as the original substituents. Many of the synthesized fluorescent compounds displayed potent pilicide activities and can thus be used to study the complex interactions between pilicide and bacteria. For example, when E. coli was treated with fluorescent pilicides, it was found that the compounds were not uniformly distributed throughout the bacterial population, suggesting that the compounds are primarily associated to bacteria with specific properties.

    Finally, by studying compounds designed to inhibit the aggregation of Aβ, it was found that some compounds based on the pilicide scaffold inhibit the formation of the functional bacterial amyloid fibers known as curli; these compounds are referred to as 'curlicides'. Some of the curlicides also prevent the formation of pili and thus exhibit dual pilicide-curlicide activity. The potential utility of such 'dual-action' compounds was highlighted by a study of one of the more potent dual pilicide-curlicides in a murine UTI model were the compound was found to significantly attenuate virulence in vivo.

  • 22.
    Chorell, Erik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Bengtsson, Christoffer
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sainte-Luce Banchelin, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Das, Pralay
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Uvell, Hanna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sinha, Arun K
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pinkner, Jerome S
    Department of Molecular Microbiology, Washington University, School of Medicine, St. Louis, Missouri 63110, USA.
    Hultgren, Scott J
    Department of Molecular Microbiology, Washington University, School of Medicine, St. Louis, Missouri 63110, USA.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Synthesis and application of a bromomethyl substituted scaffold to be used for efficient optimization of anti-virulence activity2011In: European Journal of Medicinal Chemistry, ISSN 0223-5234, E-ISSN 1768-3254, Vol. 46, no 4, p. 1103-1116Article in journal (Refereed)
    Abstract [en]

    Pilicides are a class of compounds that attenuate virulence in Gram negative bacteria by blocking the chaperone/usher pathway in Escherichia coli. It has also been shown that compounds derived from the peptidomimetic scaffold that the pilicides are based on can prevent both Aβ aggregation and curli formation. To facilitate optimizations towards the different targets, a new synthetic platform has been developed that enables fast and simple introduction of various substituents in position C-7 on the peptidomimetic scaffold. Importantly, this strategy also enables introduction of previously unattainable heteroatoms in this position. Pivotal to the synthetic strategy is the synthesis of a C-7 bromomethyl substituted derivative of the ring-fused dihydrothiazolo 2-pyridone pilicide scaffold. From this versatile and reactive intermediate various heteroatom-linked substituents could be introduced on the scaffold including amines, ethers, amides and sulfonamides. In addition, carbon-carbon bonds could be introduced to the sp(3)-hybridized bromomethyl substituted scaffold by Suzuki-Miyaura cross couplings. Evaluation of the 24 C-7 substituted compounds in whole-bacterial assays provided important structure-activity data and resulted in the identification of a number of new pilicides with activity as good or better than those developed previously.

  • 23.
    Chorell, Erik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Chorell, Elin
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Medicine.
    Efficient Synthesis of 2-Substituted Phthalimides from Phthalic Acids in One Step2013In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, Vol. 2013, no 33, p. 7512-7516Article in journal (Refereed)
    Abstract [en]

    Efficient procedures for synthesizing 2-substituted phthalimide (isoindole-1,3-dione) analogues starting from phthalic acids have been developed by using experimental design. The phthalimide central fragment frequently appears in biologically active compounds, materials, catalysts, and fluorescent probes, and therefore the development of general, fast, and convenient synthetic methods to this scaffold under neutral, acidic, and basic conditions would be attractive. After an initial screening, the use of acetonitrile, acetic acid, or pyridine in combination with microwave heating proved most promising. Experimental design was applied to these conditions to optimize the time, temperature, and concentration. This strategy has successfully generated synthetic methods that have been used to synthesize a series of phthalimides from phthalic acids and various amines or anilines in excellent yields. The developed methods have proven to be general, fast, convenient, and economic, and thus are expected to have broad utility to efficiently construct novel compounds for future biological and chemical applications.

  • 24.
    Chorell, Erik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pinkner, Jerome S.
    Department of Molecular Microbiology, Washington University, School of Medicine, St. Louis, Missouri 63110, USA.
    Bengtsson, Christoffer
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Edvinsson, Sofie
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Cusumano, Corinne K.
    Rosenbaum, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Johansson, Lennart B-Å
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hultgren, Scott J.
    Department of Molecular Microbiology, Washington University, School of Medicine, St. Louis, Missouri 63110, USA.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Design and synthesis of fluorescently labeled pilicides and curlicides: bioactive tools to study bacterial virulence mechanismsManuscript (preprint) (Other academic)
    Abstract [en]

    Pilicides and curlicides block formation of the E. coli virulence factors pili and curli. To facilitate studies of the interaction between these compounds and the pili and curli assembly systems, fluorescent pilicides and curlicides have been synthesized. This was achieved using a strategy where key pilicide and curlicide substituents were replaced by fluorophores having similar physicochemical properties. The resulting fluorescent compounds had improved anti-virulence activities as measured in pili- and curli-dependent biofilm assays. We created fluorescent pilicides and curlicides by introducing both coumarin and 4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) fluorophores at two positions on the peptidomimetic pilicide and curlicide scaffold. Fluorescence images of the uropathogenic Escherichia coli (UPEC) strain UTI89 grown in the presence of these compounds shows that the compounds are strongly associated to the bacteria and seem to discriminate between different bacteria in a population.

  • 25. Colak, Burcu
    et al.
    Da Silva, Julio C. S.
    Soares, Thereza A.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Departament of Fundamental Chemistry, CCEN, Federal University of Pernambuco, Cidade Universitaria, Brazil.
    Gautrot, Julien E.
    Impact of the Molecular Environment on Thiol-Ene Coupling For Biofunctionalization and Conjugation2016In: Bioconjugate chemistry, ISSN 1043-1802, E-ISSN 1520-4812, Vol. 27, no 9, p. 2111-2123Article in journal (Refereed)
    Abstract [en]

    Thiol-ene radical coupling is increasingly used for the biofunctionalization of biomaterials and the formation of 3D hydrogels enabling cell encapsulation. Indeed, thiol-ene chemistry presents interesting features that are particularly attractive for platforms requiring specific reactions of peptides or proteins, in particular, in situ, during cell culture or encapsulation. Despite such interest, little is known about the factors impacting thiol-ene chemistry in situ, under biologically relevant conditions. Here we explore some of the molecular parameters controlling photoinitiated thiol-ene couplings with a series of alkenes and thiols, including peptides, in buffered conditions. H-1 NMR and HPLC were used to quantify the efficiency of couplings and the impact of the pH of the buffer, as well as the molecular structure and local microenvironment close to alkenes and thiols to be coupled. Some of these observations are supported by molecular dynamics and quantum mechanics calculations. An important finding of our work is that the plc of thiols (and its variation upon changes in molecular structure) have a striking impact on coupling efficiencies. Similarly, positively charged and aromatic amino acids are found to have some impact on thiol-ene couplings. Hence, our study demonstrates that molecular design should be carefully selected in order to achieve high biofunctionalization levels in biomaterials with peptides or promote the efficient formation of peptide-based hydrogels.

  • 26.
    Dahlgren, Markus
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Statistical molecular design, QSAR modeling, and scaffold hopping – Development of type III secretion inhibitors in Gram negative bacteria2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Type III secretion is a virulence system utilized by several clinically important Gram-negative pathogens. Computational methods have been used to develop two classes of type III secretion inhibitors, the salicylidene acylhydrazides and the acetylated salicylanilides. For these classes of compounds, quantitative structure-activity relationship models have been constructed with data from focused libraries obtained by statistical molecular design. The models have been validated and shown to provide useful predictions of untested compounds belonging to these classes. Scaffold hopping of the salicylidene acylhydrazides have resulted in a number of synthetic targets that might mimic the scaffold of the compounds. The synthesis of two libraries of analogs to two of these scaffolds and the biological evaluation of them is presented.

  • 27.
    Dang, Hung The
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Chorell, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, USA.
    Uvell, Hanna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pinkner, Jerome S.
    Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, USA.
    Hultgren, Scott J.
    Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, USA.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Syntheses and biological evaluation of 2-amino-3-acyl-tetrahydrobenzothiophene derivatives: antibacterial agents with antivirulence activity2014In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 12, no 12, p. 1942-1956Article in journal (Refereed)
    Abstract [en]

    Developing new compounds targeting virulence factors (e.g., inhibition of pilus assembly by pilicides) is a promising approach to combating bacterial infection. A high-throughput screening campaign of a library of 17 500 small molecules identified 2-amino-3-acyl-tetrahydrobenzothiophene derivatives (hits 2 and 3) as novel inhibitors of pili-dependent biofilm formation in a uropathogenic Escherichia coli strain UTI89. Based on compounds 2 and 3 as the starting point, we designed and synthesized a series of structurally related analogs and investigated their activity against biofilm formation of E. coli UTI89. Systematic structural modification of the initial hits provided valuable information on their SARs for further optimization. In addition, small structural changes to the parent molecules resulted in low micromolar inhibitors (20-23) of E. coli biofilm development without an effect on bacterial growth. The hit compound 3 and its analog 20 were confirmed to prevent pili formation in a hemagglutination (HA) titer assay and electron microscopy (EM) measurements. These findings suggest that 2-amino-3-acyl-tetrahydrobenzothiophenes may serve as a new class of compounds for further elaboration as antibacterial agents with antivirulence activity.

  • 28. de Araujo Filho, Cesar Augusto
    et al.
    Salmi, Tapio Olavi
    Bernas, Andreas
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kinetic model for homogeneously catalyzed halogenation of glycerol2013In: Industrial & Engineering Chemistry Research, ISSN 0888-5885, E-ISSN 1520-5045, Vol. 52, no 4, p. 1523-1530Article in journal (Refereed)
    Abstract [en]

    A new kinetic model for the halogenation of polyalcohols, e.g. chlorination of glycerol with gaseous HCl in the presence of homogeneous acid catalysts was developed. The model is based on a reaction mechanism, which includes esterification and epoxidation steps followed by halogenation steps. The principle of quasi-steady state was applied to the ester and ionic intermediates appearing in the model and rate equations were derived. Furthermore, some simplified cases of the rate equations were considered, such as immediate water removal from the reaction mixture and analytical solutions for the simplified kinetic models were derived. The model was verified against experimental data obtained from laboratory-scale semibatch reactors. The conclusion is that the model worked very well, predicting correctly the glycerol conversion and the product distribution of α-, β-, α,β- and α,γ-chlorinated products. The kinetic model can be used for design of reactors for homogeneously catalyzed halogenation.

  • 29.
    Edo Gimenez, Mar
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Skoglund, Nils
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics. Energy Engineering, Department of Engineering Sciences & Mathematics, Luleå University of Technology, Luleå, Sweden.
    Gao, Qiuju
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Persson, Per-Erik
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Fate of metals and emissions of organic pollutants from torrefaction of waste wood, MSW, and RDF2017In: Waste Management, ISSN 0956-053X, E-ISSN 1879-2456, Vol. 68, p. 646-652Article in journal (Refereed)
    Abstract [en]

    Torrefaction of municipal solid waste (MSW), refuse-derived fuel (RDF), and demolition and construction wood (DC) was performed at 220°C and a residence time of 90 min in a bench-scale reactor. The levels of toxic polychlorinated dibenzo-p-dioxins (PCDD) and dibenzofurans (PCDF) contained in emission from the torrefaction process were evaluated. In addition, main ash-forming elements and trace metals in the raw feedstock and char were determined. The use of MSW in fuel blends with DC resulted in lower PCDD and PCDF emissions after torrefaction, compared with the RDF blends. The migration of chlorine from the feedstock to the gas phase reduces the chlorine content of the char which may reduce the risk of alkali chloride-corrosion in char combustion. However, trace metals catalytically active in the formation of PCDD and PCDF remain in the char, thereby may promote PCDD and PCDF formation during subsequent char combustion for energy recovery; this formation is less extensive than when the feedstock is used.

  • 30.
    Edo Giménez, Mar
    et al.
    Umeå University.
    Ortuño,, N
    Conesa, J.A
    Persson, P-E
    Jansson, S
    Emissions from co-combustion of demolition and construction wood and household waste fuel blendsManuscript (preprint) (Other academic)
  • 31.
    Edvinsson, Sofie
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Johansson, Susanne
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, Andreas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    An efficient procedure for the synthesis of formylacetic esters2012In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 53, no 50, p. 6819-6821Article in journal (Refereed)
    Abstract [en]

    An efficient synthesis of formylacetic esters via ozonolysis of trans-beta-hydromuconic esters followed by a solid-supported triphenylphosphine reduction has been developed. In addition, an extension toward formylacetic amides and a one-pot preparation of more stable intermediates which can be used for further transformations are also described.

  • 32.
    Emtenäs, Hans
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Synthesis and biological evaluation of Bicyclic β-Lactams and 2-Pyridinones: Pilicides Targeting Pilus Biogenesis in Pathogenic Bacteria2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    New methods have been developed for the synthesis of bicyclic β-lactams and 2-pyridinones by combining acyl Meldrum’s acids and Δ2-thiazolines. The 2-pyridinones were synthesised both in solution using conventional heating or microwave assisted heating as well as by solid supported chemistry.

    The compounds (pilicides) were designed to interfere with the assembly of pili in uropathogenic E. coli by inhibiting the periplasmic chaperones. The affinity of the pilicides to the chaperones was investigated with surface plasmon resonance technique (Biacore) and with relaxation-edited 1H NMR spectroscopy experiments. Finally, the pilicides were investigated for their ability to inhibit pili formation in uropathogenic E. coli in a hemagglutination assay, where members of the 2-pyridinone family proved to be able to cause depiliation.

  • 33.
    Engdahl, Cecilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Knutsson, Sofie
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ekström, Fredrik
    Linusson, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Discovery of selective inhibitors targeting acetylcholinesterase 1 from disease-transmitting mosquitoes2016In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 59, no 20, p. 9409-9421Article in journal (Other academic)
    Abstract [en]

    Vector control of disease-transmitting mosquitoes is increasingly important due to the re-emergence and spread of infections such as malaria and dengue. We have conducted a high throughput screen (HTS) of 17,500 compounds for inhibition of the essential AChE1 enzymes from the mosquitoes Anopheles gambiae and Aedes aegypti. In a differential HTS analysis including the human AChE, several structurally diverse, potent, and selective noncovalent AChE1 inhibitors were discovered. For example, a phenoxyacetamide-based inhibitor was identified with a 100-fold selectivity for the mosquito over the human enzyme. The compound also inhibited a resistance conferring mutant of AChE1. Structure-selectivity relationships could be proposed based on the enzymes' 3D structures; the hits' selectivity profiles appear to be linked to differences in two loops that affect the structure of the entire active site. Noncovalent inhibitors of AChE1, such as the ones presented here, provide valuable starting points toward insecticides and are complementary to existing and new covalent inhibitors.

  • 34.
    Eriksson, Lennart
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    A strategy for ranking environmentally occuring chemicals1991Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A systematic methodology for quantitative structure-activity relationship (QSAR) development in environmental toxicology is provided. The methodology is summarized in a strategy with six sequential steps.

    The strategy rests on two cornerstones, namely (1) the use of statistical design to select a series of representative compounds (the so-called training set) on which to base a QSAR, and (2) the multivariate modelling of the relationship between physicochemical and biological properties of the training set compounds.

    The first step of the strategy is the division of chemicals into classes of structurally similar compounds. Briefly, steps 2 to 6 are: (2) physico-chemical and structural characterization of the compounds in a class, (3) selection of a training set of representative compounds, (4) biological testing of the selected training set, (5) QSAR model development, and (6) experimental validation of the QSAR and predictions for non-tested compounds.

    The thesis summarizes the results obtained from the application of the strategy to the class of halogenated aliphatic compounds. Biological measurements were made in four biological test systems, reflecting acute toxicity, mutagenicity, relative cytotoxicity and genotoxicity. QSARs were developed relating each biological endpoint to the structural descriptors of the compounds. Multivariate PLS modelling was used in the data analysis. The developed QSARs were used for predicting the biological activity pattern of the non-tested compounds in the class. These predictions may be used as a starting point for a priority ranking for further biological testing of these compounds.

    The strategy has not been developed solely for establishing QSARs for the halogenated aliphatics class. On the contrary, this work is intended to demonstrate a generally applicable QSAR methodology.

  • 35. Forsum, Oskar
    et al.
    Näsholm, Torgny
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Transformation of Plants with D-Amino Acid Resistance Selectable Markers2009In: D-Amino Acids: Practical Methods and Protocols, Volume 4: Enzymes Involved in the Metabolism of D-Amino Acids / [ed] Ryuichi Konno, Hans Brückner, Antimo D'Aniello, George H. Fisher, Noriko Fujii and Hiroshi Homma, Hauppauge: Nova Science Publishers, Inc., 2009, p. 73-79Chapter in book (Other academic)
  • 36.
    Gabrielsson, Jon
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Multivariate methods in tablet formulation2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes the application of multivariate methods in a novel approach to the formulation of tablets for direct compression. It begins with a brief historical review, followed by a basic introduction to key aspects of tablet formulation and multivariate data analysis. The bulk of the thesis is concerned with the novel approach, in which excipients were characterised in terms of multiple physical or (in most cases) spectral variables. By applying Principal Component Analysis (PCA) the descriptive variables are summarized into a few latent variables, usually termed scores or principal properties (PP’s). In this way the number of descriptive variables is dramatically reduced and the excipients are described by orthogonal continuous variables. This means that the PP’s can be used as ordinary variables in a statistical experimental design. The combination of latent variables and experimental design is termed multivariate design or experimental design in PP’s. Using multivariate design many excipients can be included in screening experiments with relatively few experiments.

    The outcome of experiments designed to evaluate the effects of differences in excipient composition of formulations for direct compression is, of course, tablets with various properties. Once these properties, e.g. disintegration time and tensile strength, have been determined with standardised tests, quantitative relationships between descriptive variables and tablet properties can be established using Partial Least Squares Projections to Latent Structures (PLS) analysis. The obtained models can then be used for different purposes, depending on the objective of the research, such as evaluating the influence of the constituents of the formulation or optimisation of a certain tablet property.

    Several examples of applications of the described methods are presented. Except in the first study, in which the feasibility of this approach was first tested, the disintegration time of the tablets has been studied more carefully than other responses. Additional experiments have been performed in order to obtain a specific disintegration time. Studies of mixtures of excipients with the same primary function have also been performed to obtain certain PP’s. Such mixture experiments also provide a straightforward approach to additional experiments where an interesting area of the PP space can be studied in more detail. The robustness of a formulation with respect to normal batch-to-batch variability has also been studied.

    The presented approach to tablet formulation offers several interesting alternatives, for both planning and evaluating experiments.

  • 37.
    Gandla, Madhavi Latha
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Derba-Maceluch, Marta
    Liu, Xiaokun
    Gerber, Lorenz
    Master, Emma R.
    Mellerowicz, Ewa J.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Expression of a fungal glucuronoyl esterase in Populus: Effects on wood properties and saccharification efficiency2015In: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700, Vol. 112, p. 210-220Article in journal (Refereed)
    Abstract [en]

    The secondary walls of angiosperms contain large amounts of glucuronoxylan that is thought to be covalently linked to lignin via ester bonds between 4-O-methyl-alpha-D-glucuronic acid (4-O-Me-GlcA) moieties in glucuronoxylan and alcohol groups in lignin. This linkage is proposed to be hydrolysed by glucuronoyl esterases (GCEs) secreted by wood-degrading fungi. We report effects of overexpression of a GCE from the white-rot basidiomycete Phanerochaete carnosa, PcGCE, in hybrid aspen (Populus tremula L. x tremuloides Michx.) on the wood composition and the saccharification efficiency. The recombinant enzyme, which was targeted to the plant cell wall using the signal peptide from hybrid aspen cellulase PttCel9B3, was constitutively expressed resulting in the appearance of GCE activity in protein extracts from developing wood. Diffuse reflectance FT-IR spectroscopy and pyrolysis-GC/MS analyses showed significant alternation in wood chemistry of transgenic plants including an increase in lignin content and S/G ratio, and a decrease in carbohydrate content Sequential wood extractions confirmed a massive (+43%) increase of Klason lignin, which was accompanied by a ca. 5% decrease in cellulose, and ca. 20% decrease in wood extractives. Analysis of the monosaccharide composition using methanolysis showed a reduction of 4-O-Me-GlcA content without a change in Xyl contents in transgenic lines, suggesting that the covalent links between 4-O-Me-GlcA moieties and lignin protect these moieties from degradation. Enzymatic saccharification without pretreatment resulted in significant decreases of the yields of Gal, Glc, Xyl and Man in transgenic lines, consistent with their increased recalcitrance caused by the increased lignin content In contrast, the enzymatic saccharification after acid pretreatment resulted in Glc yields similar to wild-type despite of their lower cellulose content. These data indicate that whereas PcGCE expression in hybrid aspen increases lignin deposition, the inhibitory effects of lignin are efficiently removed during acid pretreatment, and the extent of wood cellulose conversion during hydrolysis after acid pretreatment is improved in the transgenic lines possible due to reduced cell wall cross-links between cell wall biopolymers by PcGCE. 

  • 38.
    Gao, Qiuju
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dioxins and dioxin-like compounds in thermochemical conversion of biomass: formation, distribution and fingerprints2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In the transition to a sustainable energy supply there is an increasing need to use biomass for replacement of fossil fuel. A key challenge is to utilize biomass conversion technologies in an environmentally sound manner. Important aspects are to minimize potential formation of persistent organic pollutants (POPs) such as dioxins and dioxin-like compounds.

    This thesis involves studies of formation characteristics of polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and naphthalenes (PCNs) in microwave-assisted pyrolysis (MAP) and torrefaction using biomass as feedstock. The research focuses are on their levels, distributions, fingerprints (homologue profiles and isomer patterns) and the underlying formation pathways. The study also included efforts to optimize methods for extracting chlorinated aromatic compounds from thermally treated biomass. The overall objective was to contribute better understanding on the formation of dioxins and dioxin-like compounds in low temperature thermal processes.

    The main findings include the following:

    • Pressurized liquid extraction (PLE) is applicable for simultaneous extraction of PCDDs, PCDFs, PCNs, polychlorinated phenols and benzenes from thermally treated wood. The choice of solvent for PLE is critical, and the extraction efficiency depends on the degrees of biomass carbonization.
    • In MAP experiments PCDDs, PCDFs and PCNs were predominantly found in pyrolysis oils, while in torrefaction experiments they were mainly retained in solid chars with minor fractions in volatiles. In both cases, highly chlorinated congeners with low volatility tended to retain on particles whereas the less chlorinated congeners tended to volatize into the gas phase.
    • Isomer patterns of PCDDs, PCDFs and PCNs generated in MAP were more selective than those reported in combustion processes. The presence of isomers with low thermodynamic stability suggests that the pathway of POPs formation in MAP may be governed not only by thermodynamic stabilities but also by kinetic factors.
    • Formation of PCDDs, PCDFs and PCNs depends not only on the chlorine contents in biomass but also the presence of metal catalysts and organic/metal-based preservatives.

    Overall, the results provide information on the formation characteristics of PCDDs, PCDFs and PCNs in MAP and torrefaction. The obtained knowledge is useful regarding management and utilization of thermally treated biomass with minimum environmental impact.

  • 39.
    Gao, Qiuju
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Budarin, Vitaliy L.
    Cieplik, Mariusz
    Gronnow, Mark
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    PCDDs, PCDFs and PCNs in products of microwave-assisted pyrolysis of woody biomass: Distribution among solid, liquid and gaseous phases and effects of material composition2016In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 145, p. 193-199Article in journal (Refereed)
    Abstract [en]

    Microwave-assisted pyrolysis (MAP) of lignocellulosic biomass is a technique that could potentially be used to produce and upgrade renewable energy carriers. However, there is no available information about the formation of dioxins and other organic pollutants in MAP treatment of woody biomass. In this study, MAP experiments were conducted in lab-scale using virgin softwood, bark, and impregnated wood as feedstocks. The non-condensable gas, liquid (fractionated into aqueous and oil phases), and char fractions generated during pyrolysis were collected and analysed for polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and naphthalenes (PCNs). The concentrations of PCDDs, PCDFs and PCNs in the pyrolysis products ranged from 0.52 to 43.7 ng kg(-1). All investigated compound groups were most abundant in the oil fraction, accounting for up to 68% (w/w) of the total concentrations. The highest PCDD, PCDF and PCN concentrations were found from the pyrolysis of bark, which has relatively high contents of chlorine and mineral matter, followed by impregnated wood, which contains organic and metal-based preservatives. The homologue profiles of all three compound groups were dominated by the less chlorinated homologues. The homologue abundance decreased as the degree of chlorination increased. This trend was observed for all three feedstocks.

  • 40.
    Gao, Qiuju
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Cieplik, Mariusz K
    Budarin, Vitaliy L
    Gronnow, Mark
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mechanistic evaluation of polychlorinated dibenzo-p-dioxin, dibenzofuran and naphthalene isomer fingerprints in microwave pyrolysis of biomass2016In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 150, p. 168-175Article in journal (Refereed)
    Abstract [en]

    Isomer distribution patterns of polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and naphthalenes (PCNs) were investigated in microwave-assisted pyrolysis (MAP) products of woody biomass. The feedstocks included bark and impregnated wood. The results indicated that isomer distributions in MAP are more selective compared to those reported from wood burning and waste incineration. Favored formation of 4-MoCDF and highly selective chlorine substitution at the 2,4-position observed during MAP suggested a preferred formation pathway of PCDFs involving (chloro)phenol precursors followed by subsequent chlorination. The PCDD distribution was dominated by isomers typically formed from chlorophenol condensation at relatively low temperature. The PCN isomer distributions showed a tendency for sequential chlorination from non-substituted naphthalene at successive positions. The presence of isomers such as 1-MoCDD, 4-MoCDF, 1,2,3-TriCN with low thermodynamic stability indicates that kinetic factors may be important in the MAP process.

  • 41.
    Gao, Qiuju
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Edo, M
    Larsson, S. H.
    Collina, E
    Rudolfsson, M
    Gallina, M
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Physical transformation and formation of PCDDs and PCDFs in torrefaction of biomass with different chemical compositionManuscript (preprint) (Other academic)
  • 42.
    Gao, Qiuju
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pommer, Linda
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Evaluation of solvent for pressurized liquid extraction of PCDD, PCDF, PCN, PCBz, PCPh and PAH in torrefied woody biomass2015In: Fuel, ISSN 0016-2361, E-ISSN 1873-7153, Vol. 154, p. 52-58Article in journal (Refereed)
    Abstract [en]

    Biomass torrefaction for sustainable energy production has gained an increasing interest. However, there is a lack of information on the thermal formation of persistent organic pollutants such as dioxins in the torrefied solid product. In this paper, we investigated the applicability of pressurized liquid extraction (PLE) for simultaneous extraction of a number of polychlorinated planar aromatic compounds from torrefied wood. The targeted compounds included polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), naphthalenes (PCNs), benzenes (PCBz), phenols (PCPhs) and PAHs. PLE tests were conducted on torrefied and non-torrefied (i.e. raw) eucalyptus wood chips using 5 single solvents (n-hexane, toluene, dichloromethane, acetone and methanol) and a mixture of n-hexane/toluene (1:1, v/v). The performance of each solvent was evaluated in terms of recoveries of spiked internal standards and the amount of co-extracted sample matrix. High polarity solvents such as methanol and acetone resulted in poor recoveries from torrefied wood for most of the target compounds, probably due to the high co-extraction of thermally degraded lignocellulosic compounds. Raw wood was less solvent-dependent and comparable results were obtained for polar and non-polar solvents. Toluene showed the best performance of the investigated solvents, with average recoveries of 79 +/- 14% and 66 +/- 9% for raw and torrefied wood, respectively. The method was validated using pentachlorophenol-tainted spruce wood chips. The proposed PLE method was compared to the traditional Soxhlet method. Results show that PLE gave equivalent or better extraction for all target compounds.

  • 43. Garcia, Ariel
    et al.
    Lopez, Yoney
    Karimi, Keikhosro
    Benitez, Agustin
    Lundin, Magnus
    Taherzadeh, Mohammad
    Martín, Carlos
    Umeå University, Faculty of Science and Technology, Department of Chemistry. *Department of Chemistry and Chemical Engineering, University of Matanzas, Matanzas 44740, Cuba.
    Chemical and physical characterization and acid hydrolysis of a mixture of Jatropha Curcas shells and husks2015In: Cellulose Chemistry and Technology, ISSN 0576-9787, Vol. 49, no 9-10, p. 737-744Article in journal (Refereed)
    Abstract [en]

    Jatropha curcas L. is a tropical plant with considerable potential for producing biodiesel and other products of high economic and social interest. During the biodiesel production process from J. curcas different residues, such as shells and husks are generated. In this work, the physical characterization of J. curcas fruits was performed, and the chemical composition of a mixture of shells and husks was determined. The physical characterization revealed that shells and husks account, respectively, for 25.0 and 27.8% of the fruit weight. The compositional analyses of the material showed a quite high content of glucans (32.8% w/w) and xylans (16.4% w/w), which indicates the potential of J. curcas shells and husks for production of ethanol, xylitol and other glucose- and xylose-derived products. Acid hydrolysis was applied to a mixture of shells and husks under different sulphuric acid concentrations (from 0.5 to 4.5%), temperatures (170-220 degrees C) and time (10-20 min), and the hydrolytic conversion of xylan was evaluated. A zone of experimental conditions giving maximal xylan conversion was identified at around 4% H2SO4, 180 degrees C and reaction time below 10 min.

  • 44. Gentili, Francesco G.
    et al.
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Algal cultivation in urban wastewater: an efficient way to reduce pharmaceutical pollutants2017In: Journal of Applied Phycology, ISSN 0921-8971, E-ISSN 1573-5176, Vol. 29, no 1, p. 255-262Article in journal (Refereed)
    Abstract [en]

    The purpose of this study was to investigate whether pharmaceutical pollutants in urban wastewater can be reduced during algal cultivation. A mixed population of wild freshwater green algal species was grown on urban wastewater influent in a 650 L photobioreactor under natural light and with the addition of flue gases. Removal efficiencies were very high (> 90 %), moderate (50-90 %), low (10-50 %), and very low or non-quantifiable (< 10 %) for 9, 14, 11, and 18 pharmaceuticals, respectively, over a 7-day period. High reduction was found in the following pharmaceuticals: the beta-blockers atenolol, bispropol, and metoprolol; the antibiotic clarithromycine; the antidepressant bupropion; the muscle relaxant atracurium; hypertension drugs diltiazem and terbutaline used to relive the symptoms of asthma. Regression analysis did not detect any relationship between the reduction in pharmaceutical contents and light intensity reaching the water surface of the algal culture. However, the reduction was positively correlated with light intensity inside the culture and stronger when data collected during the night were excluded. Algae cultivation can remove partially or totally pharmaceutical pollutants from urban wastewater, and this opens up new possibilities for treating urban wastewater.

  • 45. Gisbert, Patricia
    et al.
    Trillo, Paz
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Organic Chemistry Dpt. and Instituto de Sintesis Organica (ISO).
    Pastor, Isidro M.
    Comparative Study of Catalytic Systems Formed by Palladium and Acyl-Substituted Imidazolium Salts2018In: CHEMISTRYSELECT, ISSN 2365-6549, Vol. 3, no 3, p. 887-893Article in journal (Refereed)
    Abstract [en]

    Amino amides, which are readily accessible from amino acids, were used in the preparation of both monoamido and diamido functionalized imidazolium salts in very straightforward protocols. Different catalytic systems formed with palladium(II) acetate and acyl functionalized imidazolium salts were tested in the Matsuda-Heck reaction. The comparative study revealed that the presence of one carbamoyl moiety in the N-heterocyclic carbene precursor is more beneficial during the catalytic process. Thus, better activity was observed with the catalytic system formed using 3-benzyl-1-(N-phenylcarbamoyl-methyl)imidazolium chloride in a 1:1 metal/ligand ratio. Moreover, this fact was evidenced by means of UV/vis studies.

  • 46. Gomes, Claudio M
    et al.
    Wittung-Stafshede, Pernilla
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Protein folding and metal ions: mechanisms, biology and disease2010Book (Other academic)
    Abstract [en]

    The role of metal ions in protein folding and structure is a critical topic to a range of scientists in numerous fields, particularly those working in structural biology and bioinorganic chemistry, those studying protein folding and disease, and those involved in the molecular and cellular aspects of metals in biological systems. Protein Folding and Metal Ions: Mechanisms, Biology and Disease presents the contributions of a cadre of international experts who offer a comprehensive exploration of this timely subject at the forefront of current research. Divided into four sections, this volume: Provides case study examples of protein folding and stability studies in particular systems or proteins that comprise different metal ions of co-factors Reviews the proteins that shuttle metal ions in the cell to a particular target metalloprotein Illustrates how metal binding can be connected to pathological protein conformations in unrelated diseases, from cancer to protein deposition disorders such as Parkinson's disease Addresses protein redesign of metal-containing proteins by computational methods, folding simulation studies, and work on model peptides -- dissecting the relative energetic contribution of metals sites to protein folding and stability Together, the 13 chapters in this text cogently describe the state of the science today, illuminate current challenges, propose future possibilities, and encourage further study in this area that offers much promise especially with regard to novel approaches to the treatment of some of the most challenging and tragic diseases.  

  • 47.
    Grahn, Hans
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Paramagnetic relaxation reagents: nuclear magnetic resonance studies of preferential solvation1986Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The interactions between neutral paramagnetic relaxation reagents (PARR's) and certain aromatic compounds have been studied by 1H and 13 C spin-lattice relaxation time measurements. In media such as cyclohexane and carbon tetrachloride, Cr(acac)3 becomes preferentially solvated by aromatic solutes. The solvation is significantly suppressed in a more interacting solvent like dichloromethane. Paramagnetic induced chemical shifts of the aromatic outer sphere ligand indicate in addition to relaxation data, a preferential orientation caused by dipole-dipole interactions. For benzene or for several alkylated benzenes which have small or no permanent dipole moments, the interaction is electrostatic, i.e. of a dipole-dipole induced type and where the easily polarizable aromatic ring is preferred in the solvation sphere.

    Carbon tetrachloride is shewn to have a specific PARR interaction. If co-ordination number, solution structure etc., are to be determined using weakly interacting substrates, this solvent should be avoided.

    A multivariate statistical approach is also reported, where 13 C electron-nuclear relaxation data and induced shifts of monosubstituted arcmatics have been related to different physical descriptors. Most of the variance in relaxation and shift data is best described by the dipole moment. The results support a dipole-dipole interaction as the preferred solvation mechanism.

    The preferential solvation of several organic substrates with the diamagnetic Co(acac)3 is studied by varying the substrate concentration in cyclohexane. By the use of 59 Co shift, it is shown that proton donating solutes such as chloroform and methanol have a specific solvation. The order of preference is close to that obtained in Cr(acac)3 solutions.

  • 48. Greene, Sarah E.
    et al.
    Pinkner, Jerome S.
    Chorell, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dodson, Karen W.
    Shaffer, Carrie L.
    Conover, Matt S.
    Livny, Jonathan
    Hadjifrangiskou, Maria
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Hultgren, Scott J.
    Pilicide ec240 Disrupts Virulence Circuits in Uropathogenic Escherichia coli2014In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 5, no 6, p. UNSP e02038-Article in journal (Refereed)
    Abstract [en]

    Chaperone-usher pathway (CUP) pili are extracellular organelles produced by Gram-negative bacteria that mediate bacterial pathogenesis. Small-molecule inhibitors of CUP pili, termed pilicides, were rationally designed and shown to inhibit type 1 or P piliation. Here, we show that pilicide ec240 decreased the levels of type 1, P, and S piliation. Transcriptomic and proteomic analyses using the cystitis isolate UTI89 revealed that ec240 dysregulated CUP pili and decreased motility. Paradoxically, the transcript levels of P and S pilus genes were increased during growth in ec240, even though the level of P and S piliation decreased. In contrast, the most downregulated transcripts after growth in ec240 were from the type 1 pilus genes. Type 1 pilus expression is controlled by inversion of the fimS promoter element, which can oscillate between phase on and phase off orientations. ec240 induced the fimS phase off orientation, and this effect was necessary for the majority of ec240's inhibition of type 1 piliation. ec240 increased levels of the transcriptional regulators SfaB and PapB, which were shown to induce the fimS promoter phase off orientation. Furthermore, the effect of ec240 on motility was abolished in the absence of the SfaB, PapB, SfaX, and PapX regulators. In contrast to the effects of ec240, deletion of the type 1 pilus operon led to increased S and P piliation and motility. Thus, ec240 dysregulated several uropathogenic Escherichia coli (UPEC) virulence factors through different mechanisms and independent of its effects on type 1 pilus biogenesis and may have potential as an antivirulence compound. IMPORTANCE CUP pili and flagella play active roles in the pathogenesis of a variety of Gram-negative bacterial infections, including urinary tract infections mediated by UPEC. These are extremely common infections that are often recurrent and increasingly caused by antibiotic-resistant organisms. Preventing piliation and motility through altered regulation and assembly of these important virulence factors could aid in the development of novel therapeutics. This study increases our understanding of the regulation of these virulence factors, providing new avenues by which to target their expression.

  • 49.
    Gustafsson, Tomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Asymmetric Synthesis of C-Glycosylated Amino Acids: Incorporation in Collagen Glycopeptides and Evaluation in a Model for Rheumatoid Arthritis2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes stereoselective syntheses of four amino acids, three of which are C-glycosidic analogues of glycosylated amino acids. The overall goal of the project was to probe the interactions between MHC molecules, glycopeptide antigens and T cell receptors, that are essential for development of collagen induced arthritis. Collagen induced arthritis is a frequently used mouse model for rheumatoid arthritis, an autoimmune disease that attacks joint cartilage and leads to a painful and eventually crippling condition.

    The thesis is based on four studies. The first study describes the synthesis of hydroxylysine, an amino acid that is found in collagen and is an important constituent of the glycopeptide proposed as an antigen in collagen induced arthritis. During the synthesis of hydroxylysine some new insight into the mechanism of the reductive opening of p-methoxybenzylidene acetals was obtained.

    The remaining three studies deals with the synthesis of C-glycosidic analogues of glycosylated amino acids, hydroxy norvaline, threonine and hydroxylysine.The synthesis of each amino acid required control of several stereogenic centra and utilizes a variety of approaches such as use of stereoselective reactions, chiral auxilaries, chiral templates and asymmetric catalysis.

    The C-glycosidic analogues of galactosylated hydroxynorvaline and hydroxylysine were incorporated in glycopeptides from type II collagen and evaluated in T cell response assays. It was found that the T cells were stimulated by the C-glycopeptides, but that higher concentrations were required than for the native O-glycopeptide

  • 50.
    Hainzl, Tobias
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sauer-Eriksson, A. Elisabeth
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Signal-sequence induced conformational changes in the signal recognition particle2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7163Article in journal (Refereed)
    Abstract [en]

    Co-translational protein targeting is an essential, evolutionarily conserved pathway for delivering nascent proteins to the proper cellular membrane. In this pathway, the signal recognition particle (SRP) first recognizes the N-terminal signal sequence of nascent proteins and subsequently interacts with the SRP receptor. For this, signal sequence binding in the SRP54 M domain must be effectively communicated to the SRP54 NG domain that interacts with the receptor. Here we present the 2.9 angstrom crystal structure of unbound- and signal sequence bound SRP forms, both present in the asymmetric unit. The structures provide evidence for a coupled binding and folding mechanism in which signal sequence binding induces the concerted folding of the GM linker helix, the finger loop, and the C-terminal alpha helix alpha M6. This mechanism allows for a high degree of structural adaptability of the binding site and suggests how signal sequence binding in the M domain is coupled to repositioning of the NG domain.

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