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  • 51. Jouve, Karine
    et al.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Oxidative cyclization of N-methyl- and N-benzoylpyridylthioureas. Preparation of new thiazolo[4,5-b] and [5,4-b]pyridine derivatives2003In: Journal of Heterocyclic Chemistry, ISSN 0022-152X, E-ISSN 1943-5193, Vol. 40, no 2, p. 261-268Article in journal (Refereed)
  • 52. Jää-Aro, Kai-Mikael
    et al.
    Ihrén, Johan
    Zetterling, Fredrik
    Laaksonen, Aatto
    Visual Interactive Molecular Simulation1999In: Proceedings of the High-Performance Computing Symposium - HPC '99: 1999 Advanced Simulation Technologies Conference : San Diego, California, April 11-15, 1999, Hyatt Islandia Hotel / [ed] Adrian Michel Tentner, San Diego: Society for Computer Simulation International , 1999, p. 43-46Conference paper (Refereed)
  • 53. Li, Jianjun
    et al.
    Dzieciatkowska, Monika
    Hood, Derek W.
    Cox, Andrew D.
    Schweda, Elke K. H.
    Södertörn University, School of Life Sciences.
    Moxon, E. Richard
    Richards, James C.
    Structural characterization of sialylated glycoforms of H-influenzae by electrospray mass spectrometry: fragmentation of protonated and sodiated O-deacylated lipopolysaccharides2007In: Rapid Communications in Mass Spectrometry, ISSN 0951-4198, E-ISSN 1097-0231, Vol. 21, no 6, p. 952-960Article in journal (Refereed)
    Abstract [en]

    Sialylated lipopolysaccharide (LPS) glycoforms from Haemophilus influenzae were characterized by tandem mass spectrometry using a new generation hyphenated mass spectrometer which combines a triple quadrupole and a linear ion trap (Q-Trap). The fragmentation of both protonated and sodiated molecular ions from O-deacylated LPS (LPS-OH) obtained in MS2 experiments in the positive mode was studied. The MS2 spectra of protonated ions provided unambiguous evidence for the presence and sequence of sialylated lactosamine present in lacto-N-neotetraose oligosaccharide extensions but not for sialyl-lactose structures whilst fragmentation of sodiated adducts, [M+Na](+), afforded information diagnostic of mono- and disialylated lactose extensions. To study this we used a highly sialylated LPS from a H. influenzae strain capable of sialyl-lactose expression only. We then applied the method to the H. influenzae genome strain, Rd, in which glycoforms containing both sialyl-lactose and sialyl-lacto-N-neotetraose were detected from diagnostic B-ions at m/z 638.2 ([Neu5Ac(1) Hex(2)+ Na](+)) and 657.2 ([Neu5Ac(1) Hex(1) HexNAc(1)+H](+)). Unique fragmentation patterns provided the locations and sequences of these oligosaccharide extensions. This is the first time both sialylated lactose and sialylated lacto-N-neotetraose units have been detected and characterized by tandem mass spectrometry in the same molecule. This methodology is of general applicability for determination of common sialylated oligosaccharide extension in bacterial LPS.

  • 54.
    Lindberg, Marie
    Södertörn University College, School of Life Sciences.
    Cloning, overexpression and biophysical characterization of grd/grl/wrt domains from Caenorhabditis elegans in Escherichia coli2008Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Hedgehog related genes have been shown to play a major role in development in all deuterostomes. In C.elegans, such genes have been found where the similarity is restricted to the C-terminal domain. This work has focused on the hedgehog related C.elegans proteins called ground (grd), ground-like (grl), and wart (wrt) which appear to form a unique structural family.These proteins are cysteine rich and have conserved cysteine patterns which, together with thethought that they are secreted, are expected to be in disulfide form. Since the extracellular environment is very oxidizing and due to the conserved cysteine pattern, disulfide bonds are thought to play a big part in the folding and stabilization of these proteins. The stability of the protein and the formation of a disulfide bond are related through a thermodynamic cycle, which insures that the stabilization of the protein by the disulfide is reflected by the identical stabilization of the disulfide by the protein. Practically, there are numerous parameters that can be used to try to achieve the correct disulfide bonds and folding, when doing in vitro trials, some of which were used in this project. C.elegans proteins grd-5, grd-13, grl-24, wrt-3 and wrt-5 were studied in this project. All of the proteins were expressed and purified with success, with theexception of grl-24. All constructs formed inclusion bodies. Some refolding attempts were performed on grd-13 and wrt-3. The presence of a disulfide bond in refolded grd-13 was demonstrated using chemical fragmentation. In general, these attempts did not give correctly folded proteins but provide a foundation to continue experiments aimed at producing a native-like protein for structural and functional studies.

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  • 55.
    Lundin, Evelina
    Södertörn University, Teacher Education.
    Säger en bild mer än tusen ord?: En multimodal textanalys av ett tradtionellt och ett digitalt läromedel i kemi2017Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The purpose with this thesis is to analyze how written text and images interact in a traditional and digital learning component in chemistry.

    • How does text and images interact in a traditional and digital teaching material for grades 4-6 in the field of water characteristics and circuits?

    • What are the multimodal similarities and differences between the two teaching tools?

    To answer the questions, a quality multimodal text analysis has been used together with a model that focuses on the text's overall structure and the interaction between the text's parts. The result showed that there was interaction between text and images in all the teaching materials. The properties and circuits of the water are reinforced through pictures and accompanying text in both study units. The difference was in the traditional teaching medium, where there were more pictures and shorter text, while in the digital learning medium there were long information-proof texts.

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  • 56. Nordling, M M
    et al.
    Nygren, Jonas
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Sundberg, K
    Rafter, J J
    Toxicological characterization of a novel in vivo benzo[a]lpyrene metabolite, 7-oxo-benz[d]anthracene-3,4-dicarboxylic acid anhydride2002In: Chemical Research in Toxicology, ISSN 0893-228X, E-ISSN 1520-5010, Vol. 15, no 10, p. 1274-1280Article in journal (Refereed)
    Abstract [en]

    Recently, we described a new in vivo pathway in the metabolism of benzo[a]pyrene (BP) that involves an opening of the aromatic ring system. One of the products of this pathway, isolated from rat urine, was the anhydride of 7-oxo-benz[d]anthracene-3,4-dicarboxylic acid (ABADA). We have now investigated the effect of ABADA on several cellular targets, known to be important in tumor formation. ABADA was as efficient as BP-7,8-diol-9,10-epoxide in inducing direct strand breaks but not alkali labile sites in DNA in HT-29 cells and exhibited weak mutagenic activity in Salmonella typhimurium strain TA 102. The cytotoxicity of ABADA to HCT 116 cells appeared to be due to apoptosis, as caspase-3 activity and poly-ADP-ribose polymerase (PARP) cleavage was observed. COX-2 promoter activity was induced by ABADA in HCT 116 cells. In conclusion, this novel metabolic pathway may also be contributing to the carcinogenicity of BP.

  • 57. Okwakol, J
    et al.
    Grivas, Spiros
    Södertörn University, School of Life Sciences.
    5H-[1,2,5]selenadiazolo[3,4-f]indole as a masked form of 5,6-diaminoindole2005In: Heterocycles, ISSN 0385-5414, E-ISSN 1881-0942, Vol. 65, no 8, p. 1939-1946Article in journal (Refereed)
    Abstract [en]

    6-Nitroindoline (9) was converted into 1-acetyl-5,6-aminoindoline (12) which was then transformed via selenadiazoles (13-15) to the title selenadiazoloindole (4) by two alternative 3-step synthetic sequences in 38-.42% overall yield from 12. The unstable 5,6-diaminoindole (16) was then obtained by reductive deselenation of 4. Fully assigned H-1, C-13 and Se-17 NMR spectral data for the title indole (4) and Se-77 NMR spectral data for the intermediate selenadiazoles (13-15) are presented.

  • 58.
    Okwakol, Jealux
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Grivas, Spiros
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Synthesis of thienoindoles via the vicarious nucleophilic substitution of nitrobenzo[b]thiopenes2006In: Heterocyclic Communications, ISSN 0793-0283, E-ISSN 2191-0197, Vol. 12, no 3-4, p. 173-178Article in journal (Refereed)
    Abstract [en]

    The 8H-thieno[3,2-g]indole (12) and 6H-thieno[3,2-e]indole (16) were easily obtained by the reductive cyclisation of (5-amino-1-benzothien-4-yl)acetonitrile (15) and (7-amino-1-benzothien-6-yl)acetonitrile (11), the latter synthesised via cyanomethylation of 5- and 7-nitrobenzo[b]thiophienes.

  • 59. Rehn, Stanley
    et al.
    Bergman, Jan
    Södertörn University, School of Life Sciences. Karolinska Institute.
    The reaction between 3-aminocrotonates and oxindole-3-ylidene derivatives: synthesis of highly substituted pyrroles2005In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 61, no 12, p. 3115-3123Article in journal (Refereed)
    Abstract [en]

    The reaction between 3-aminocrotonates and 3-acetonylideneoxindole in refluxing toluene resulted in 2-pyrrolo-3 '-yloxindoles in high yields (around 90%). At room temperature the 2-pyrrolo-3 '-yioxindoles exists as keto-enol tautomers. Treatment with POCl3 yielded the 2-chloro-3-pyrrolyl indole, which gave the pyrrolo annulated indolopyran-2-one upon basic hydrolysis of 2-chloro-3-pyrrolyl indole methyl ester.

  • 60.
    Rehn, Stanley
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Stensland, B
    The three-component reaction between isatin, alpha-amino acids, and dipolarophiles2004In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 2, p. 413-418Article in journal (Refereed)
    Abstract [en]

    3-Spiro[pyrrolidino-oxindoles] were prepared in high yields from a three-component reaction between isatin, an alpha-amino acid, and a dipolarophile. Both N-substituted and N-unsubstituted alpha-amino acids were used as the amine component.

  • 61. Rewcastle, G W
    et al.
    Janosik, Tomasz
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Reactions of 2-lithiated indoles with elemental sulfur. Formation of pentathiepino[6,7-b]indoles and indoline-2-thiones2001In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 57, no 33, p. 7185-7189Article in journal (Refereed)
    Abstract [en]

    The reactions of 2-lithiated indole and 1-methylindole with elemental sulfur have been studied, leading e.g. to a rational approach to pentathiepino[6,7-b]indoles 5 and 10. Notable amounts of the previously known tetrathiocino[5,6-b:8,7-b ' ]diindole 11 could be observed as a side reaction in the preparation of 10. Treatment of the anions of indoline-2-thiones 6 or 7 with sulfur also gave the pentathiepins 5 or 10, respectively. In addition, a convenient and clean lithiation route to indoline-2-thione (6) has been developed.

  • 62. Ruda, M C
    et al.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Koehler, K
    Liu, Y
    A solution-phase procedure for the preparation of 4-azasteroid numetics2003In: Heterocyclic Communications, ISSN 0793-0283, E-ISSN 2191-0197, Vol. 9, no 6, p. 571-574Article in journal (Refereed)
  • 63. Ruda, M C
    et al.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Wu, J
    Preparation of N-alkylated pyridones via selective N-alkylation of 2-alkoxypyridines on solid phase2002In: Journal of combinatorial chemistry, ISSN 1520-4766, E-ISSN 1520-4774, Vol. 4, no 5, p. 530-535Article in journal (Refereed)
    Abstract [en]

    Regioselective solid-phase synthesis of N-alkylated 2-pyridones has been carried out starting from 2-halopyridines. Variously substituted 2-halopyridines were linked to a Wang resin in quantitative yields to afford 2-alkoxypyridines. The coupled products were then reacted with a variety of alkyl halides, resulting in tandem alkylation and cleavage from the resin to generate N-alkylated pyridones With no detectable traces of O-alkylated products. The scope and limitations of this exceptionally selective reaction have been studied.

  • 64. Ruda, M
    et al.
    Kann, N
    Gordon, S
    Bergman, Jan
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Nelson, W
    Agback, P
    Hagberg, L
    Koehler, K F
    Solid-phase synthesis of a 6-phenylquinolin-2(1H)-one library directed toward nuclear hormone receptors2005In: Journal of combinatorial chemistry, ISSN 1520-4766, E-ISSN 1520-4774, Vol. 7, no 4, p. 567-573Article in journal (Refereed)
    Abstract [en]

    A library of 6-phenylquinolin-2(1H)-ones with diversity at position I and the ortho, meta, and para positions of the pendant phenyl ring has been synthesized using solid-phase parallel synthetic techniques. A key step in the synthesis of the library is a tandem alkylation cleavage in which diversity can be introduced at position 1 simultaneously to the cleavage from the resin. The yields of this step were significantly improved over what has previously been reported by addition of cesium carbonate to scavenge the acid that is formed during the reaction. Furthermore, we have shown that the solid support linkage is tolerant to Suzuki coupling and etherification reaction conditions and that selective cleavage of the linkage can take place in the presence of esters. The resulting 6-phenylquinolin-2(1H)-one library was screened against a panel of nuclear hormone receptors (androgen, estrogen alpha and beta isoforms, glucocorticoid, mineralocorticoid, and progesterone). Certain members of this library display moderate affinity for several of these receptors, and consequently, the 6-phenylquinolin-2(1H)-one core of the library may be considered a privileged structure for nuclear hormone receptors. In contrast, other members of the library display high selectivity for a particular receptor. The highest affinity ligand (9{2,1,1}) possesses an affinity of 330 nM for the androgen receptor, whereas the most selective ligand (9{2,4,1}) displays an affinity of 900 nM for the androgen receptor and a selectivity of 140-fold over the next highest affinity receptor.

  • 65.
    Schweda, Elke K H
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Li, J J
    Moxon, E R
    Richards, J C
    Structural analysis of lipopolysaccharide oligosaccharide epitopes expressed by non-typeable Haemophilus influenzae strain 1762002In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 337, no 5, p. 409-420Article in journal (Refereed)
    Abstract [en]

    The structure of the lipopolysaccharide (LPS) from non-typeable Haemophilus influenzae strain 176 has been investigated. Electrospray ionization-mass spectrometry (ESIMS) on O-deacylated LPS (LPS-OH) and core oligosaccharide (OS) samples obtained after mild-acid hydrolysis of LPS provided information on the composition and relative abundance of the glycoforms. ESIMS tandem-mass spectrometry on LPS-OH confirmed the presence of minor sialylated and disialylated glycoforms. Oligosaccharide samples were studied in detail using high-field NMR techniques. It was found that the LPS contains the common inner-core element of H. influenzae. L-alpha-D-Hepp-(1-->2)-[PEtn-->6]-L-alpha-D-Hepp-(1-->3)-[beta-D-Glep-(1 -->4)]-L-alpha-D-Hepp-(1-->5)[PPEtn-->4]-alpha-Kdop-(2-->6)-Lipid A having glycosyl substitution at the O-3 position of the terminal heptose as recently observed for non-typeable H. influenzae strain 486 [Mansson, M.: Bauer. S. H. J.: Hood, D. W.; Richards, J. C. Moxon, E. R. Schweda. E. K. H., Eur. J. Biochem. 2001. 268. 2148-2159]. The following LPS structures were identified as the major glycoforms. the most significant being indicated with an asterisk (*) (glycoforms are partly substituted with Gly at the terminal Hep): [GRAPHICS].

  • 66. Shirani, Hamid
    et al.
    Stensland, Birgitta
    Bergman, Jan
    Södertörn University, School of Life Sciences.
    Janosik, Tomasz
    New routes to 3-(Arylthio)indoles: Application to the synthesis of the 3,3 '-bis(indolyl) sulfone core of the marine alkaloid echinosulfone A2006In: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, no 15, p. 2459-2463Article in journal (Refereed)
    Abstract [en]

    A new approach to 3-(arylthio)indoles and related compounds has been developed, based on the reactions of aryl Grignard reagents or lithiated heteroaroinatics with a phenylsulfonyl-protected 3,3'-bis(indolyl) disulfide. In addition, a rational approach to the 3,3'-bis(indolyl) sulfone core of the alkaloid echinosulfone A has been accomplished, involving treatment of a 3-lithioindole with bis(phenylsulfonyl) sulfide as the key step.

  • 67.
    Slätt, Johnny
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Cyanoacetylation of indoles, pyrroles and amines, and synthetic uses of these products2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on an organic synthetic project aimed towards development of small molecules acting on the P2 receptor as well as development of synthetic methods to such molecules (primarily indoles and featuring isatogens in particular). The new methodology includes cyanoacetylation of indoles, pyrroles, amines, and enamines using cyanoacetic acid in acetic anhydride. The molecules obtained (e.g. 3-cyanoacetylindole) could be further functionalized by nitrosation followed by reduction. Cyanoacetylated anilines carrying an appropriate substituent (e.g NO2) could be cyclized to quinoxaline-N-oxides, a class of molecules which have been considered as analogues to isatogens. The molecule 2,2'-pyridylisatogen tosylate (PIT) is particularly interesting within this class because of its documented interaction with the P2 receptor.

  • 68.
    Slätt, Johnny
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Oxygenation of 2,3-dihydroindoles2002In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 58, no 45, p. 9187-9191Article in journal (Refereed)
    Abstract [en]

    Isatogens (3-oxo-3H-indole 1-oxides) possess interesting biological properties and development of a general method to construct these derivatives has now been developed. Indolines (2,3-dihydroindoles) and isatogens have been prepared in an efficient route starting from indoles substituted in position 2. Reduction of the 2-substituted indoles was performed with tin and hydrochloric acid to give racemic indolines, which were converted to isatogens by 3-chloroperoxybenzoic acid (m-CPBA).

  • 69.
    Slätt, Johnny
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Reinvestigation of a synthesis of quinoxaline-N-oxidesManuscript (preprint) (Other academic)
  • 70.
    Slätt, Johnny
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Beslic, Senad
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Stensland, Birgitta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Intitutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Functionalizations of 3-(cyanoacetyl)indole and 2-(cyanoacetyl)pyrroleManuscript (preprint) (Other academic)
  • 71.
    Slätt, Johnny
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Janosik, Tomasz
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Wahlström, Niklas
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthetic applications of 3-(cyanoacetyl)indoles and related compounds2005In: Journal of Heterocyclic Chemistry, ISSN 0022-152X, E-ISSN 1943-5193, Vol. 42, no 1, p. 141-145Article in journal (Refereed)
    Abstract [en]

    Various synthetic applications of 3-(cyanoacetyl)indoles, as well as syntheses of some related indoles, have been investigated. Diethyl 2-(1H-indol-3-yl)-2-oxoethylphosphonate and a methyl derivative thereof have been prepared in one step from indole. Moreover, it was demonstrated that 3-(cyanoacetyl)indoles are useful starting materials for the preparation of for example 3-(1H-indol-3-yl)-3-oxopropanamides, 3-heteroarylindoles or 3-heteroaroylindoles.

  • 72.
    Slätt, Johnny
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Romero, Ivan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Cyanoacetylation of indoles, pyrroles and aromatic amines with the combination cyanoacetic acid and acetic anhydride2004In: Synthesis (Stuttgart), ISSN 0039-7881, E-ISSN 1437-210X, no 16, p. 2760-2765Article in journal (Refereed)
    Abstract [en]

    Cyanoacetic acid was activated with acetic anhydride and when heated this reagent reacted with a variety of both activated and deactivated pyrroles, indoles and aniline derivatives.

  • 73. Tinnert, A S
    et al.
    Månsson, Martin
    Södertörn University, School of Life Sciences.
    Yildirim, Håkan H
    Södertörn University, School of Life Sciences.
    Hood, D W
    Schweda, Elke K H
    Södertörn University, School of Life Sciences.
    Structural investigation of lipopolysaccharides from nontypeable Haemophilus influenzae: investigation of inner-core phosphoethanolamine addition in NTHi strain 9812005In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 340, no 11, p. 1900-1907Article in journal (Refereed)
    Abstract [en]

    LPS of NTHi comprises a conserved tri-L-glycero-D-manno-heptosyl inner-core moiety (L-alpha-D-Hepp-(1 -> 2)-[PEtn -> 6]-L-alpha-D-Hepp-(1 -> 3)-[beta-D-Glcp-(1 -> 4)]-L-alpha-D-Hepp-(1 -> 5)-alpha-Kdop) in which addition of PEtn to the central heptose (HepII) in strain Rd is controlled by the gene lpt6. It was recently shown that NTHi strain 981 contains an additional PEtn linked to O-3 of the terminal heptose of the inner-core moiety (HepIII). In order to establish whether lpt6 is also involved in adding PEtn to HepIII, lpt6 in strain 981 was inactivated. The structure of the LPS of the resulting mutant strain 981lpt6 was investigated by MS and NMR techniques by which it was confirmed that the lpt6 gene product is responsible for addition of PEtn to O-6 of HepII in strain 981. However, it is not responsible for adding PEtn to O-3 of HepIII since the 981lpt6 mutant still had full substitution with PEtn at HepIII

  • 74.
    Wahlström, Niklas
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Synthesis of 2,3 '-biindolyls and indolo[3,2-a]carbazoles2004In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 45, no 39, p. 7273-7275Article in journal (Refereed)
    Abstract [en]

    Several highly activated 2,3'-biindolyls were prepared from methyl 5,6-dimethoxyindole-2-carboxylate and oxindoles. The 2,3'-biindolyls were further transformed into a hydroxy indolo[3,2-a]carbazole and a bisindole amde.

  • 75.
    Wahlström, Niklas
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Romero, I
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Synthesis of metabolites of the Ah receptor ligand 6-formylindolo[3,2-b]carbazole2004In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 12, p. 2593-2602Article in journal (Refereed)
    Abstract [en]

    Synthesis of the five mono- and di-hydroxylated metabolites of the aryl hydrocarbon receptor high affinity ligand 6-formylindolo[3,2-b]carbazole is described. The structures of the metabolites were unequivocally established as 2-hydroxy-, 8-hydroxy-, 2,10-dihydroxy-, 4,8-dihydroxy- and 2,8-dihydroxyindolo[3,2-b]carbazole-6-carboxaldehyde.

  • 76.
    Wahlström, Niklas
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Stensland, B
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthesis of 2,3 '-diindolylmethanes and substituted indolo[3,2-b]carbazoles2004In: Synthesis (Stuttgart), ISSN 0039-7881, E-ISSN 1437-210X, no 8, p. 1187-1194Article in journal (Refereed)
    Abstract [en]

    Three different synthetic routes to substituted 2,3'-diindolylmethanes, and the syntheses of substituted indolo[3,2-b]carbazoles are described. The first rigid proof of an acylation in the 2-position of a 1,3-unsubstituted indole is also presented in the form of an X-ray structure.

  • 77.
    Wahlström, Niklas
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Stensland, B
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Synthesis of the marine alkaloid caulersin2004In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 60, no 9, p. 2147-2153Article in journal (Refereed)
    Abstract [en]

    A three-step synthesis of caulersin (3) from indole-2-acetic acid methyl ester and indole-2-carbonyl chloride is described. As the spectral data of the synthetic sample differed from those reported for the natural product, the structure was determined by X-ray crystallography.

  • 78.
    Wiklund, Per
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthesis of heterocycles from anthranilic acid and its derivatives2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Anthranilic acid (2-aminobenzoic acid, Aa) is the biochemical precursor to the amino acid tryptophan, as well as a catabolic product of tryptophan in animals. It is also integrated into many alkaloids isolated from plants. Aa is produced industrially for production of dyestuffs and pharmaceuticals. The dissertation gives a historical background and a short review on the reactivity of Aa. The synthesis of several types of nitrogen heterocycles from Aa is discussed. Treatment of anthranilonitrile (2-aminobenzonitrile, a derivative of Aa) with organomagnesium compounds gave deprotonation and addition to the nitrile triple bond to form amine-imine complexed dianions. Capture of these intermediate with acyl halides normally gave aromatic quinazolines, a type of heterocyclic compounds that is considered to be highly interesting as scaffolds for development of new drugs. When the acyl halide was a tertiary 2-haloacyl halide, the reaction instead gave 1,4-benzodiazepine-3-ones via rearrangement. These compounds are isomeric to the common benzodiazepine drugs (such as diazepam, Valium®) which are 1,4-benzodiazepine-2-ones. Capture of the dianions with aldehydes or ketones, led to 1,2-dihydroquinazolines. Unsubstituted imine anions could be formed by treatment of anthranilonitrile with diisobutylaluminium hydride. Also in this case capture with aldehydes gave 1,2-dihydroquinazolines. Several different dicarboxylic acid derivatives of Aa were treated with dehydrating reagents, and the resulting products were more or less complex 1,3-benzoxazinones, one of which required X-ray crystallography confirm its structure. During the work on preparation of N-substituted derivatives of Aa, necessary for synthesis of 1,4-benzodiazepine-3,5-diones, it was noted that many of the obtained products were in fact not N-substituted, but O-substituted. This challenged the established notion that Aa reacts nucleophilically at the N-terminal under most conditions. Several grave errors in the recent literature were revealed. In 1976 researchers from the group that originally developed the common benzodiazepine drugs published a retraction of a claim of synthesis of a benzodiazepine by Gärtner in 1904. They found that the method actually gave a 6-membered ring system, not a 7-membered 1,4-benzodiazepine-3,5-dione as originally claimed. Because the 1,4-benzodiazepine skeleton is highly interesting as a scaffold for development of new drugs, a few publications on synthesis of this target has appeared. However, repetition of several of the described syntheses failed to yield the poorly described products. Studies on how to ring close N-carbamoyl derivatives of Aa were undertaken. It became clear that Umpolung of the substrates by N-derivatisation was a necessary prerequisite for ring closure. The introduction of the N-nitroso group was developed to this end, leading to N1-nitroso substituted 1,4-benzodiazepine-3,5-diones. The nitroso group could be removed after ring closure. Heating of one of these compounds induced a ring contraction rearrangement. A proposed mechanism involves elimination of HNO (nitrosyl) and proton mediated loss of CO.

  • 79.
    Wiklund, Per
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Alkylation and acylation of basic salts of anthranilic acid2004In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 45, no 5, p. 969-972Article in journal (Refereed)
    Abstract [en]

    The O-nucleophilicity of basic anthranilic acid salts was documented, analyzed, and utilized in synthesis. Specifically substitutions leading to esters instead of secondary amines, and formation of anthranilic acid anhydrides were studied.

  • 80.
    Wiklund, Per
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Ring forming reactions of imines of 2-aminobenzaldehyde and related compounds2003In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 1, no 2, p. 367-372Article in journal (Refereed)
  • 81.
    Wiklund, Per
    et al.
    Södertörn University, School of Life Sciences.
    Bergman, Jan
    Södertörn University, School of Life Sciences.
    The chemistry of anthranilic acid2006In: CURRENT ORGANIC SYNTHESIS, ISSN 1570-1794, Vol. 3, no 3, p. 379-402Article in journal (Refereed)
    Abstract [en]

    Anthranilic acid (2-aminobenzoic acid, AA) is a versatile and low cost starting material for synthesis of benzofused heterocycles. It also plays a vital part in the biosynthesis of tryptophan and its derivatives, as well as in several types of alkaloids. Therefore the chemistry of anthranilic acid is of importance in medicinal and biological chemistry. The main emphasis of this review article is on the use of anthranilic acid as a starting material for synthesis of heterocycles, but it also covers the history, synthesis and reactivity, as well as a short account of the medicinal chemistry and biochemistry of anthranilic acids.

  • 82.
    Wiklund, Per
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Rogers-Evans, M
    F. Hoffmann-La Roche Ltd, Basel, Switzerland .
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthesis of 1,4-benzodiazepine-3,5-diones2004In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 69, no 19, p. 6371-6376Article in journal (Refereed)
    Abstract [en]

    Even though benzodiazepines have a strong position in medicinal chemistry, very few synthetic routes to 1H-1,4-benzodiazepine-3,5(2H,4H)-diones have ever been published and the claimed products have often been poorly characterized. Through the present work several 1H-1,4-benzodiazepine-3,5(2H,4H)-diones have become available from N-carbamoylmethylanthranilic acids. The required ring closures were achieved only when the amino groups of the starting materials were substituted with electron withdrawing groups such as acetyl, alkyloxycarbonyl, or nitroso. During the synthetic work a novel ring contraction rearrangement from a 1-nitroso-1H-1,4-benzodiazepine-3,5(2H,4H)-dione to a 3H-quinazoline-4-one was observed. The proposed mechanism involves elimination of HNO followed by a proton-mediated loss of CO. The 1-nitrosated 1,4-benzodiazepinediones could be separately denitrosated to the corresponding amino compounds.

  • 83.
    Wiklund, Per
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Romero, Ivan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Products from dehydration of dicarboxylic acids derived from anthranilic acid2003In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 1, no 19, p. 3396-3403Article in journal (Refereed)
  • 84. Witt, A
    et al.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Recent developments in the field of quinazoline chemistry2003In: Current organic chemistry, ISSN 1385-2728, E-ISSN 1875-5348, Vol. 7, no 7, p. 659-677Article in journal (Refereed)
    Abstract [en]

    Recent developments in the chemistry of quinazolines and quinazolinones are discussed. The chemistry of quinazoline alkaloids is reviewed featuring chrysogine, luotonin A, tryptanthrin, febrifugine. and rutaecarpine.

  • 85. Witt, A
    et al.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap.
    Synthesis and reactions of some 2-vinyl-3H-quinazolin-4-ones2000In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 56, no 37, p. 7245-7253Article in journal (Refereed)
    Abstract [en]

    A simple, high-yielding synthesis of 2-vinyl-3H-quinazolin-4-one, 2-(1-chlorovinyl)-3H-quinazolin-4-one and 2-(1-bromovinyl)-3H-quinazolin-4-one. The 2-vinylquinazolinones 11a and 14 participate readily in nucleophilic addition reactions. Treatment with both carbon and nitrogen nucleophiles results in a clean conversion into a variety of 2-substituted 3H-quinazolin-4-one derivatives. The 2-(1-halovinyl)-3H-quinazolin-4-ones 11b and Ile reacted with carbon nucleophiles to give several derivatives of 2-substituted 3H-quinazolin-4-one, such as dihydrofurancarboxylic ethyl ester 23.

  • 86. Witt, A
    et al.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Total syntheses of the benzodiazepine alkaloids circumdatin F and circumdatin C2001In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 66, no 8, p. 2784-2788Article in journal (Refereed)
    Abstract [en]

    Total syntheses of circumdatin F and circumdatin C, which both possess a 3H-quinazolin-4-one as well as a 1,4-benzodiazepin-5-one moiety, are described. A tripeptide derivative was synthesized as a key intermediate and dehydrated to a benzoxazine by reaction with triphenylphosphine, iodine, and a tertiary amine. The natural products were attained via rearrangements to an amidine intermediate, deprotection with 45% HBr in acetic acid, and cyclization on silica gel.

  • 87. Witt, A
    et al.
    Gustavsson, A
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Studies towards the synthesis of the benzodiazepine alkaloid auranthine. Synthesis of an acetylated derivative2003In: Journal of Heterocyclic Chemistry, ISSN 0022-152X, E-ISSN 1943-5193, Vol. 40, no 1, p. 29-35Article in journal (Refereed)
  • 88.
    Yada, S.
    et al.
    KTH Royal Institute of Technology.
    Bagheri, S.
    KTH Royal Institute of Technology.
    Hansson, J.
    KTH Royal Institute of Technology.
    Do-Quang, M.
    KTH Royal Institute of Technology.
    Lundell, F.
    KTH Royal Institute of Technology.
    Van Der Wijngaart, W.
    KTH Royal Institute of Technology.
    Amberg, Gustav
    Södertörn University. KTH Royal Institute of Technology.
    Droplet leaping governs microstructured surface wetting2019In: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 15, no 46, p. 9528-9536Article in journal (Refereed)
    Abstract [en]

    Microstructured surfaces that control the direction of liquid transport are not only ubiquitous in nature, but they are also central to technological processes such as fog/water harvesting, oil-water separation, and surface lubrication. However, a fundamental understanding of the initial wetting dynamics of liquids spreading on such surfaces is lacking. Here, we show that three regimes govern microstructured surface wetting on short time scales: spread, stick, and contact line leaping. The latter involves establishing a new contact line downstream of the wetting front as the liquid leaps over specific sections of the solid surface. Experimental and numerical investigations reveal how different regimes emerge in different flow directions during wetting of periodic asymmetrically microstructured surfaces. These insights improve our understanding of rapid wetting in droplet impact, splashing, and wetting of vibrating surfaces and may contribute to advances in designing structured surfaces for the mentioned applications.

  • 89.
    Yildirim, Håkan H
    et al.
    Södertörn University, School of Life Sciences. Karolinska institutet.
    Li, J J
    National Research Council, Ottawa, Canada.
    Richards, J C
    National Research Council, Ottawa, Canada.
    Hood, D W
    John Radcliffe Hospital, Oxford, UK.
    Moxon, E R
    John Radcliffe Hospital, Oxford, UK.
    Schweda, Elke K H
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Complex O-acetylation in non-typeable Haemophilus influenzae lipopolysaccharide: evidence for a novel site of O-acetylation2005In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 340, no 17, p. 2598-2611Article in journal (Refereed)
    Abstract [en]

    The structure of the lipopolysaccharide (LPS) of non-typeable Haemophilus influenzae strain 723 has been elucidated using NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS) on O-deacylated LPS and core oligosaccharide material (OS), as well as ESI-MSn on permethylated dephosphorylated OS. It was found that the LPS contains the common structural element of H. influenzae, L-alpha-D-Hepp-(1 -> 2)-[PEtn -> 6]-L-alpha-D-Hepp-(1 -> 3)-[beta-D-Glcp-(1 -> 4)]-L-alpha-D-Hepp-(1 -> 5)-[PPEtn -> 4]-alpha-Kdo-(2 -> 6)-Lipid A, in which the beta-D-Glcp residue (GlcI) is substituted by phosphocholine at O-6 and the distal heptose residue (HepIII) by PEW at O-3, respectively. In a subpopulation of glycoforms O-2 of HepIII was substituted by beta-D-Galp-(1 -> 4)-beta-D-Glcp-(1 -> or beta-D-Glcp-(1 ->. Considerable heterogeneity of the LPS was due to the extent of substitution by O-acetyl groups (Ac) and ester-linked glycine of the core oligosaccharide. The location for glycine was found to be at Kdo. Prominent acetylation sites were found to be at GlcI, HepIII, and the proximal heptose (HepI) residue of the triheptosyl moiety. Moreover, GlcI was acetylated at O-3 and/or O-4 and HepI was acetylated at O-2 as evidenced by capillary electrophoresis ESI-MS" in combination with NMR analyses. This is the first study to show that an acetyl group can substitute HepI of the inner-core region of H. influenzae LPS.

  • 90. Yudina, Larisa N
    et al.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Synthesis and alkylation of indolo[3,2-b]carbazoles2003In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 59, no 8, p. 1265-1275Article in journal (Refereed)
12 51 - 90 of 90
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