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  • 1.
    Abdel-Magied, Ahmed F.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Arafa, Wael A. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Laine, Tanja M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Shatskiy, Andrey
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Substituent Effects in Molecular Ruthenium Water Oxidation Catalysts Based on Amide Ligands2017In: ChemCatChem, ISSN 1867-3880, E-ISSN 1867-3899, Vol. 9, no 9, p. 1583-1587Article in journal (Refereed)
    Abstract [en]

    The production of clean and sustainable energy is considered as one of the most urgent issues for our society. Mastering the oxidation of water to dioxygen is essential for the production of solar fuels. A study of the influence of the substituents on the catalytic activity of a series of mononuclear Ru complexes (2a-e) based on a tetradentate ligand framework is presented. At neutral pH, using [Ru(bpy)(3)](PF6)(3) (bpy=2,2'-bipyridine) as the terminal oxidant, a good correlation between the turnover frequency (TOF) and the Hammett sigma(meta) parameters was obtained. Additionally, a general pathway for the deactivation of Ru-based catalysts 2a-e during the catalytic oxidation of water through poisoning by carbon monoxide was demonstrated. These results highlight the importance of ligand design for fine-tuning the catalytic activity of water oxidation catalysts.

  • 2.
    Alfredsson, Maria
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry.
    Synthesis and Characterization of Acrylfentanyl Metabolites2017Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Acrylfentanyl is a synthetic opioid that has been widely used in the last year. To help in the fight against synthetic drugs two potential metabolites of acrylfentanyl, one monohydroxy and one dihydroxy were synthesized. These metabolites will hopefully later be implemented in the analytical methods for metabolites of acrylfentanyl in urine by the Swedish National Board of Forensic Medicine.

    To have metabolites for analysis are very important as they are the main target in drug testing.

    The method used to synthesize the metabolites is a five-step synthesis with an additional 6th step for the dihydroxy metabolite. The methods used in the synthesis includes protection of amine with tert-butyloxycarbonyl, reductive amination with sodium triaceto boronhydride, alkylation and demethylation with boron tribromide. The methods used produced good results with high yields in nearly all steps.

  • 3.
    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.

  • 4. Andersson, Hanna
    et al.
    Danelius, Emma
    University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.
    Jarvoll, Patrik
    University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.
    Niebling, Stephan
    University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.
    Hughes, Ashley J
    University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.
    Westenhoff, Sebastian
    University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.
    Brath, Ulrika
    University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.
    Erdélyi, Máté
    The Swedish NMR Centre, Medicinaregatan 5c, SE-413 96 Gothenburg, Sweden.
    Assessing the Ability of Spectroscopic Methods to Determine the Difference in the Folding Propensities of Highly Similar β-Hairpins2017In: ACS omega, ISSN 2470-1343, Vol. 2, no 2, p. 508-516Article in journal (Refereed)
    Abstract [en]

    We have evaluated the ability of nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopies to describe the difference in the folding propensities of two structurally highly similar cyclic β-hairpins, comparing the outcome to that of molecular dynamics simulations. NAMFIS-type NMR ensemble analysis and CD spectroscopy were observed to accurately describe the consequence of altering a single interaction site, whereas a single-site 13C NMR chemical shift melting curve-based technique was not.

  • 5.
    Andersson, Hanna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. University of Gothenburg, SE-412 96 Gothenburg, Sweden.
    Gräfenstein, Jürgen
    National Sun Yat-Sen University, Kaohsiung, Taiwan.
    Isobe, Minoru
    National Sun Yat-Sen University, Kaohsiung, Taiwan.
    Erdélyi, Máté
    University of Gothenburg, SE-412 96 Gothenburg, Sweden; The Swedish NMR Centre, SE-413 96 Gothenburg, Sweden.
    Sydnes, Magne O
    University of Stavanger, NO-4036 Stavanger, Norway.
    Photochemically Induced Aryl Azide Rearrangement: Solution NMR Spectroscopic Identification of the Rearrangement Product2017In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, no 3, p. 1812-1816Article in journal (Refereed)
    Abstract [en]

    Photolysis of ethyl 3-azido-4,6-difluorobenzoate at room temperature in the presence of oxygen results in the regioselective formation of ethyl 5,7-difluoro-4-azaspiro[2.4]hepta-1,4,6-triene-1-carboxylate, presumably via the corresponding ketenimine intermediate which undergoes a photochemical four-electron electrocyclization followed by a rearrangement. The photorearrangement product was identified by multinuclear solution NMR spectroscopic techniques supported by DFT calculations.

  • 6.
    Angles d'Ortoli, Thibault
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hamark, Christoffer
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structure-Reactivity Relationships of Conformationally Armed Disaccharide Donors and Their Use in the Synthesis of a Hexasaccharide Related to the Capsular Polysaccharide from Streptococcus pneumoniae Type 372017In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, no 15, p. 8123-8140Article in journal (Refereed)
    Abstract [en]

    To advance the field of glycobiology, efficient synthesis methods of oligosaccharides and glycoconjugates are a requisite. In glycosylation reactions using superarmed donors, both selectivity and reactivity issues must be considered, and we herein investigate these aspects for differently protected beta-linked 2-O-glycosylated glucosyl donors carrying bulky tert-butyldimethylsilyl groups to different extents. The acceptors in reactions being secondary alcohols presents a challenging situation with respect to steric crowding. Conformational pyranose ring equilibria of the superarmed disaccharide donors with axial-rich substituents contained skew and boat conformations, and three-state models were generally assumed. With NIS/TfOH as the promotor, 2,6-di-tert-butyl-4-methylpyridine as the base, and a dichloromethane/toluene solvent mixture, ethyl 1-thio-beta-d-glucosyl disaccharide donors having 6-O-benzyl group(s) besides tert-butyldimethylsilyl groups were efficiently coupled at -40 degrees C to the hydroxyl group at position 3 of glucopyranosyl acceptors to form beta-(1 -> 2),beta-(1 -> 3)-linked trisaccharides, isolated in excellent 95% yield. The more axial-rich donors in skew and boat conformations are thus preorganized closer to the assumed transition state in these glycosylation reactions. The developed methodology was subsequently applied in the synthesis of a multibranched hexasaccharide related to the capsular polysaccharide from Streptococcus pneumoniae type 37, which consists of a beta-(1 -> 3)-linked backbone and a beta-(1 -> 2)-linked side chain of D-glucosyl residues in disaccharide repeating units.

  • 7. Arafa, Wael A. A.
    et al.
    Mohamed, Ashraf M.
    Abdel-Magied, Ahmed F.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    ULTRASOUND-MEDIATED THREE-COMPONENT REACTION ON-WATER PROTOCOL FOR THE SYNTHESIS OF NOVEL MONO- AND BIS-1,3-THIAZIN-4-ONE DERIVATIVES2017In: Heterocycles, ISSN 0385-5414, E-ISSN 1881-0942, Vol. 94, no 8, p. 1439-1455Article in journal (Refereed)
    Abstract [en]

    Green synthetic and catalyst-free strategy towards the synthesis of novel mono- and bis-1,3-thiazin-4-one scaffolds through a one pot, reaction of carbon disulfide, monoacetylenic esters and amines under ultrasonication has been reported. The merits of this protocol comprise no need for tedious workup steps and afforded the desired products in excellent yields make this synthetic protocol more efficient and worthy of further attentiveness. Moreover, the method exhibited excellent score in a number of green metrics.

  • 8. Arafa, Wael Abdelgayed Ahmed
    et al.
    Abdel-Magied, Ahmed Fawzy
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Nuclear Material Authority, Egypt.
    Utilization of ultrasonic irradiation as green and effective one-pot protocol to prepare a novel series of bis-2-amino-1,3,4-oxa(thia) diazoles and bis-tetrazoles2017In: ARKIVOC, ISSN 1551-7004, E-ISSN 1551-7012, p. 327-340Article in journal (Refereed)
    Abstract [en]

    In an effective and straightforward conversion, bis-semicarbazones and bis-thiosemicarbazones are transformed into a diversity of novel substituted bis-2-amino-1,3,4-oxadiazoles and bis-2-amino-1,3,4-thiadiazoles, respectively under ultrasonic irradiation. Bis-tetrazoles are obtained from the dialdehydes by sequential reaction with hydroxylamine hydrochloride, phosphorus pentoxide and sodium azide without isolation of the intermediates oximes and nitriles. All the reactions proceed cleanly and smoothly under mild conditions, with short reaction times and broad functional groups possibility. No side reactions were observed. [GRAPHICS]

  • 9. Atilaw, Yoseph
    et al.
    Duffy, Sandra
    Heydenreich, Matthias
    Muiva-Mutisya, Lois
    Avery, Vicky M
    Erdelyi, Mate
    Yenesew, Abiy
    Three Chalconoids and a Pterocarpene from the Roots of Tephrosia aequilata.2017In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 22, no 2, article id E318Article in journal (Refereed)
    Abstract [en]

    In our search for new antiplasmodial agents, the CH₂Cl₂/CH₃OH (1:1) extract of the roots of Tephrosia aequilata was investigated, and observed to cause 100% mortality of the chloroquine-sensitive (3D7) strain of Plasmodium falciparum at a 10 mg/mL concentration. From this extract three new chalconoids, E-2',6'-dimethoxy-3',4'-(2'',2''-dimethyl)pyranoretrochalcone (1, aequichalcone A), Z-2',6'-dimethoxy-3',4'-(2'',2''-dimethyl)pyranoretrochalcone (2, aequichalcone B), 4''-ethoxy-3''-hydroxypraecansone B (3, aequichalcone C) and a new pterocarpene, 3,4:8,9-dimethylenedioxy-6a,11a-pterocarpene (4), along with seven known compounds were isolated. The purified compounds were characterized by NMR spectroscopic and mass spectrometric analyses. Compound 1 slowly converts into 2 in solution, and thus the latter may have been enriched, or formed, during the extraction and separation process. The isomeric compounds 1 and 2 were both observed in the crude extract. Some of the isolated constituents showed good to moderate antiplasmodial activity against the chloroquine-sensitive (3D7) strain of Plasmodium falciparum.

  • 10. Atilaw, Yoseph
    et al.
    Muiva-Mutisya, Lois
    Ndakala, Albert
    Akala, Hoseah M
    Yeda, Redemptah
    Wu, Yu J
    Coghi, Paolo
    Wong, Vincent K W
    Erdelyi, Mate
    Yenesew, Abiy
    Four Prenylflavone Derivatives with Antiplasmodial Activities from the Stem of Tephrosia purpurea subsp. leptostachya.2017In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 22, no 9, article id E1514Article in journal (Refereed)
    Abstract [en]

    Four new flavones with modified prenyl groups, namely (E)-5-hydroxytephrostachin (1), purleptone (2), (E)-5-hydroxyanhydrotephrostachin (3), and terpurlepflavone (4), along with seven known compounds (5-11), were isolated from the CH₂Cl₂/MeOH (1:1) extract of the stem of Tephrosia purpurea subsp. leptostachya, a widely used medicinal plant. Their structures were elucidated on the basis of NMR spectroscopic and mass spectrometric evidence. Some of the isolated compounds showed antiplasmodial activity against the chloroquine-sensitive D6 strains of Plasmodium falciparum, with (E)-5-hydroxytephrostachin (1) being the most active, IC50 1.7 ± 0.1 μM, with relatively low cytotoxicity, IC50 > 21 μM, against four cell-lines.

  • 11.
    Ayub, Rabia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Excited State Aromaticity and Antiaromaticity: Fundamental Studies and Applications2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The central theme of this thesis is the ability to tune various molecular properties by controlling and utilizing aromaticity and antiaromaticity in the lowest electronically excited states. This investigation is based on qualitative theory, quantum chemical (QC) calculations and experimental work.

    Baird's rule tells that the π-electron count for aromaticity and antiaromaticity is reversed in the ππ* triplet (T1) state when compared to Hückel's rule for the singlet ground state. The excited state aromatic character of [4n]annulenes is probed by usage of two structural moieties, the cyclopropyl (cPr) group and the silacyclobutene (SCB) ring. The results of QC calculations and photoreactivity experiments showed that the cPr group and the SCB ring remained closed when attached to or fused with [4n]annulenes so as to preserve T1 aromatic stabilization. In contrast, both moieties ring-opened when attached to or fused with [4n+2]annulenes as a means for alleviation of T1 antiaromaticity. These two structural moieties are shown to indicate T1 aromatic character of [4n]annulenes except in a limited number of cases.

    The T1 antiaromatic character of compounds with 4n+2 π-electrons was utilized for photo(hydro)silylations and photohydrogenations. QC calculations showed that due to T1 antiaromaticity, benzene is able to abstract hydrogen atoms from trialkylsilanes. The photoreactions occurred under mild conditions for benzene and certain polycyclic aromatic hydrocarbons. In contrast, COT was found to be unreactive under similar conditions.

    It is further revealed that various properties of molecules can be tailored by rational design using Baird’s rule. Three modes of connectivity (linear, bent, and cyclic) of polycyclic conjugated hydrocarbons (PCH) were explored by DFT calculations. When the PCHs contain a central [4n]unit and 4nπ-electron perimeter, bent isomers have lower triplet state energies than linear ones due to increased T1 aromaticity in the bent isomers. With regard to the cyclic connectivity, macrocyclic compounds are designed by modifying the C20 monocycle through incorporation of monocyclic units (all-carbon as well as heterocyclic) and the impact of macrocyclic T1 aromaticity upon insertion of different units is examined through QC calculations. The results provide insights on excited state aromaticity in macrocyclic systems.

  • 12.
    Ayub, Rabia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    El Bakouri, Ouissam
    Univ Girona, IQCC, C Maria Aurelia Capmany 6, Girona 17003, Catalonia, Spain..
    Jorner, Kjell
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Sola, Miguel
    Univ Girona, IQCC, C Maria Aurelia Capmany 6, Girona 17003, Catalonia, Spain..
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Can Baird's and Clar's Rules Combined Explain Triplet State Energies of Polycyclic Conjugated Hydrocarbons with Fused 4n pi- and (4n+2)pi-Rings?2017In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, no 12, p. 6327-6340Article in journal (Refereed)
    Abstract [en]

    Compounds that can be labeled as "aromatic chameleons" are pi-conjugated compounds that are able to adjust their pi-electron distributions so as to comply with the different rules of aromaticity in different electronic states. We used quantum chemical calculations to explore how the fusion of benzene rings onto aromatic chameleonic units represented by biphenylene, dibenbzocyclooctatetraene, and dibenzo[a,e]pentalene modifies the first triplet excited states (T-1) of the compounds. Decreases in T-1 energies are observed when going from isomers with linear connectivity of the fused benzene rings to those with cis- or transbent connectivities. The T-1 energies decreased down to those of the parent (isolated) 4n pi-electron units. Simultaneously, we observe an increased influence of triplet State aromaticity of the central 4n ring as given by Baird's rule and evidenced by geometric, magnetic, and electron density based aromaticity indices (HOMA, NICS-XY, ACID, and FLU). Because of an influence of,triplet state aromaticity in the central 4n pi-electron units,, the most stabilized, compounds, retain the triplet excitation in Baird pi-quartets or octets, enabling the outer benzene rings to adapt closed-shell singlet Clar pi-sextet character. Interestingly, the T-1 energies go down as the total number of aromatic cycles within a molecule in the T-1 state increases.

  • 13.
    Ayub, Rabia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. uppsala university.
    El Bakouri, Ouissam
    Univ Girona, IQCC, C Maria Aurelia Capmany 6, Girona 17003, Catalonia, Spain.
    Jorner, Kjell
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. uppsala university.
    Sola, Miquel
    Univ Girona, IQCC, C Maria Aurelia Capmany 6, Girona 17003, Catalonia, Spain.
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. uppsala university.
    Can Baird’s and Clar’s Rules Combined Explain Triplet State Energies of Polycyclic Conjugated Hydrocarbons with Fused 4nπ- and (4n + 2)π-Rings?2017In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, no 12, p. 6327-6340Article in journal (Refereed)
  • 14.
    Ayub, Rabia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Papadakis, Raffaello
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Jorner, Kjell
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. uppsala university.
    Zietz, Burkhard
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. uppsala university.
    Cyclopropyl Group: An Excited-State Aromaticity Indicator?2017In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 23, no 55, p. 13684-13695Article in journal (Refereed)
    Abstract [en]

    The cyclopropyl (cPr) group, which is a well-known probe for detecting radical character at atoms to which it is connected, is tested as an indicator for aromaticity in the first * triplet and singlet excited states (T-1 and S-1). Baird's rule says that the -electron counts for aromaticity and antiaromaticity in the T-1 and S-1 states are opposite to Huckel's rule in the ground state (S-0). Our hypothesis is that the cPr group, as a result of Baird's rule, will remain closed when attached to an excited-state aromatic ring, enabling it to be used as an indicator to distinguish excited-state aromatic rings from excited-state antiaromatic and nonaromatic rings. Quantum chemical calculations and photoreactivity experiments support our hypothesis; calculated aromaticity indices reveal that openings of cPr substituents on [4n]annulenes ruin the excited-state aromaticity in energetically unfavorable processes. Yet, polycyclic compounds influenced by excited-state aromaticity (e.g., biphenylene), as well as 4n-electron heterocycles with two or more heteroatoms represent limitations.

  • 15.
    Balliu, Aleksandra
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Exploring molecular interactions between polypeptide conjugates and protein targets: Manipulating affinity by chemical modifications2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis molecular interactions between polypeptide conjugates and protein targets were investigated. Polypeptides were derivatized with small organic molecules, peptides and oligonucleotides. New strategies were developed with the aim to increase affinities for proteins of biological interest.

    A 42-residue polypeptide (4-C15L8) conjugated to a small organic molecule 3,5-bis[[bis(2-pyridylmethyl)amino]methyl]benzoic acid (PP1), was shown to bind glycogen phosphorylase a (GPa) in the presence of zinc ions. Under the assumption that hydrophobic interactions dominated the binding energy, the hydrophobic residues of 4-C15L8-PP1 were systematically replaced in order to study their contribution to the affinity enhancement. The replacement of the Nle, Ile and Leu residues by Ala amino acids reduced affinities. The introduction of non-natural L-2-aminooctanoic acid (Aoc) residues into the peptide sequence enhanced the binding affinity for GPa. A decreased KD of 27nM was obtained when Nle5, Ile9 and Leu12 were replaced by Aoc residues, in comparison to the KD value of 280nM obtained for the unmodified 4-C15L8-PP1. It is evident that there are non-obvious hydrophobic binding sites on the surfaces of proteins that could be identified by introducing the more hydrophobic and conformationally flexible Aoc residues. The downsizing of the 42-mer peptide to an 11-mer and the incorporation of three Aoc residues gave rise to a KD of 550 nM, comparable to that of  4-C15L8-PP1 suggesting that bioactive peptides can be downsized by the introduction of Aoc.

    Aiming to improve in vivo stability, the affinity for human serum albumin (HSA) of hydrophobic, positively and negatively charged polypeptide-PP1 conjugates was evaluated. Increased hydrophobicity due to the introduction of Aoc residues did not significantly increase the affinity for HSA. No binding was observed in the case of the most negatively charged polypeptides whereas the slightly negatively and positively charged polypeptides conjugated to PP1 bound HSA with affinities that increased with the positive charge. It was found that polypeptide-PP1 conjugates target the zinc binding site of the HSA. Affinity enhancement was obtained due to the incorporation of PP1 and increased by charge to charge interactions between the positively charged amino acids of the polypeptide and the negatively charged residues of HSA, in close proximity to the HSA zinc binding site. The survival times of the peptide-PP1 conjugates in human serum were extended as a result of binding to HSA. Zn2+ ion chelating agents can be incorporated in potential peptide therapeutics with a short plasma half-life, without increasing their molecular weights.

  • 16.
    Barrozo, Alexandre
    et al.
    Univ Southern Calif, Dept Chem, Los Angeles, CA 90089 USA..
    Blaha-Nelson, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Williams, Nicholas H.
    Univ Sheffield, Dept Chem, Sheffield S3 7HF, S Yorkshire, England..
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    The effect of magnesium ions on triphosphate hydrolysis2017In: Pure and Applied Chemistry, ISSN 0033-4545, E-ISSN 1365-3075, Vol. 89, no 6, p. 715-727Article in journal (Refereed)
    Abstract [en]

    The role of metal ions in catalyzing phosphate ester hydrolysis has been the subject of much debate, both in terms of whether they change the transition state structure or mechanistic pathway. Understanding the impact of metal ions on these biologically critical reactions is central to improving our understanding of the role of metal ions in the numerous enzymes that facilitate them. In the present study, we have performed density functional theory studies of the mechanisms of methyl triphosphate and acetyl phosphate hydrolysis in aqueous solution to explore the competition between solvent-and substrate-assisted pathways, and examined the impact of Mg2+ on the energetics and transition state geometries. In both cases, we observe a clear preference for a more dissociative solvent-assisted transition state, which is not significantly changed by coordination of Mg2+. The effect of Mg2+ on the transition state geometries for the two pathways is minimal. While our calculations cannot rule out a substrate-assisted pathway as a possible solution for biological phosphate hydrolysis, they demonstrate that a significantly higher energy barrier needs to be overcome in the enzymatic reaction for this to be an energetically viable reaction pathway.

  • 17. 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.

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

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

  • 19.
    Bergman, Sara
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Brandt, Peter
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Nordeman, Patrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Larhed, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Odell, Luke R.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Eriksson, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Synthesis of 11C-Labelled Ureas by Palladium(II)-Mediated Oxidative Carbonylation2017In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 22, no 10, article id 1688Article in journal (Refereed)
    Abstract [en]

    Positron emission tomography is an imaging technique with applications in clinical settings as well as in basic research for the study of biological processes. A PET tracer, a biologically active molecule where a positron-emitting radioisotope such as carbon-11 has been incorporated, is used for the studies. Development of robust methods for incorporation of the radioisotope is therefore of the utmost importance. The urea functional group is present in many biologically active compounds and is thus an attractive target for incorporation of carbon-11 in the form of [C-11] carbon monoxide. Starting with amines and [C-11] carbon monoxide, both symmetrical and unsymmetrical C-11-labelled ureas were synthesised via a palladium(II)-mediated oxidative carbonylation and obtained in decay-corrected radiochemical yields up to 65%. The added advantage of using [C-11] carbon monoxide was shown by the molar activity obtained for an inhibitor of soluble epoxide hydrolase (247 GBq/mu mol-319 GBq/mu mol). DFT calculations were found to support a reaction mechanism proceeding through an C-11-labelled isocyanate intermediate.

  • 20.
    Bergström, Maria
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Ganji, Suresh
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Naidu Veluru, Ramesh
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Unelius, C. Rikard
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    N-Iodosuccinimide (NIS) in Direct Aromatic Iodination2017In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 22, p. 3234-3239Article in journal (Refereed)
    Abstract [en]

    N-Iodosuccinimide (NIS) in pure trifluoroacetic acid (TFA) offers a time-efficient and general method for the iodination of a wide range of mono-and disubstituted benzenes at room temperature, as demonstrated in this paper. The starting materials were generally converted into mono-iodinated products in less than 16 hours at room temperature, without byproducts. A few deactivated substrates needed addition of sulfuric acid to increase the reaction rate. Another exception was methoxybenzenes that preferentially were iodinated by NIS in acetonitrile with only catalytic amounts of TFA.

  • 21. 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.

  • 22.
    Bornhof, Anna-Bea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Xiong, Ruisheng
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Borbas, K. Eszter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Rational Synthesis of 2-Bromoporphyrins and 2,12-Dibromoporphyrins2017In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, no 23, p. 12908-12913Article in journal (Refereed)
    Abstract [en]

    Bromoporphyrins were prepared by the metal-mediated self-condensation of brominated 1-formyldipyrromethanes. Depending on the conditions, Mg(II)-2,12-dibromoporphyrin and Mg(II)-2-bromoporphyrin could be obtained in up to 11% and 17% isolated yield, respectively. Zn(II) was also a viable templating metal. The positions of the bromine substituents were confirmed by 2D-NMR spectroscopic analysis and the X-ray crystal structure of a derivative. Suzuki and Sonogashira reactions of the bromoporphyrins yielded 2-substituted or 2,12-disubstituted porphyrins with red-shifted absorption and emission spectra. This method provides access to the minimalist core of beta-mono- and beta,beta'-disubstituted porphyrins from readily available starting materials.

  • 23.
    Bunrit, Anon
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Stockholm University.
    Direct Catalytic Nucleophilic Substitution of Non-Derivatized Alcohols2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on the development of methods for the activation of the hydroxyl group in non-derivatized alcohols in substitution reactions. The thesis is divided into two parts, describing three different catalytic systems.

    The first part of the thesis (Chapter 2) describes nucleophilic allylation of amines with allylic alcohols, using a palladium catalyst to generate unsymmetrical diallylated amines. The corresponding amines were further transformed by a one-pot ring-closing metathesis and aromatization reaction to afford β-substituted pyrroles with linear and branched alkyl, benzyl, and aryl groups in overall moderate to good yields.

    The second part (Chapters 3 and 4) describes the direct intramolecular stereospecific nucleophilic substitution of the hydroxyl group in enantioenriched alcohols by Lewis acid and Brønsted acid/base catalysis.

    In Chapter 3, the direct intramolecular substitution of non-derivatized alcohols has been developed using Fe(OTf)3 as catalyst. The hydroxyl groups of aryl, allyl, and alkyl alcohols were substituted by the attack of O- and N-centered nucleophiles, to provide five- and six-membered heterocycles in up to excellent yields with high enantiospecificities. Experimental studies showed that the reaction follows first-order dependence with respect to the catalyst, the internal nucleophile, and the internal electrophile of the substrate. Competition and catalyst-substrate interaction experiments demonstrated that this transformation proceeds via an SN2-type reaction pathway.

    In Chapter 4, a Brønsted acid/base catalyzed intramolecular substitution of non-derivatized alcohols was developed. The direct intramolecular and stereospecific substitution of different alcohols was successfully catalyzed by phosphinic acid (H3PO2). The hydroxyl groups of aryl, allyl, propargyl, and alkyl alcohols were substituted by O-, N-, and S-centered nucleophiles to generate five- and six-membered heterocycles in good to excellent yields with high enantiospecificities. Mechanistic studies (both experiments and density functional theory calculations) have been performed on the reaction forming five-membered heterocyclic compounds. Experimental studies showed that phosphinic acid does not promote SN1 reactivity. Rate-order determination indicated that the reaction follows first-order dependence with respect to the catalyst, the internal nucleophile, and the internal electrophile. DFT calculations corroborated with a reaction pathway in which the phosphinic acid has a dual activation mode and operates as a bifunctional Brønsted acid/Brønsted base to simultaneously activate both the nucleophile and nucleofuge, resulting in a unique bridging transition state in an SN2-type reaction mechanism.

  • 24.
    Cedervall, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Magnetic Materials for Cool Applications: Relations between Structure and Magnetism in Rare Earth Free Alloys2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    New and more efficient magnetic materials for energy applications are a big necessity for sustainable future. Whether the application is energy conversion or refrigeration, materials based on sustainable elements should be used, which discards all rare earth elements. For energy conversion, permanent magnets with high magnetisation and working temperature are needed whereas for refrigeration, the entropy difference between the non-magnetised and magnetised states should be large. For this reason, magnetic materials have been synthesised with high temperature methods and structurally and magnetically characterised with the aim of making a material with potential for large scale applications. To really determine the cause of the physical properties the connections between structure (crystalline and magnetic) and, mainly, the magnetic properties have been studied thoroughly.

    The materials that have been studied have all been iron based and exhibit properties with potential for the applications in mind. The first system, for permanent magnet applications, was Fe5SiB2. It was found to be unsuitable for a permanent magnet, however, an interesting magnetic behaviour was studied at low temperatures. The magnetic behaviour arose from a change in the magnetic structure which was solved by using neutron diffraction. Substitutions with phosphorus (Fe5Si1-xPxB2) and cobalt (Fe1-xCox)5PB2 were then performed to improve the permanent magnet potential. While the permanent magnetic potential was not improved with cobalt substitutions the magnetic transition temperature could be greatly controlled, a real benefit for magnetic refrigeration. For this purpose AlFe2B2 was also studied, and there it was found, conclusively, that the material undergoes a second order transition, making it unsuitable for magnetic cooling. However, the magnetic structure was solved with two different methods and was found to be ferromagnetic with all magnetic moments aligned along the crystallographic a-direction. Lastly, the origin of magnetic cooling was studied in Fe2P, and can be linked to the interactions between the magnetic and atomic vibrations.

  • 25.
    Chow, Shiao Y.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Odell, Luke R.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Eriksson, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Low-Pressure Radical 11C-Aminocarbonylation of Alkyl Iodides through Thermal Initiation2017In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, Vol. 2017, no 8, p. 1236-1236Article in journal (Refereed)
  • 26.
    Cirera, B.
    et al.
    IMDEA Nanosci, Spain.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Otero, R.
    IMDEA Nanosci, Spain; University of Autonoma Madrid, Spain.
    Gallego, J. M.
    CSIC, Spain.
    Miranda, R.
    IMDEA Nanosci, Spain; University of Autonoma Madrid, Spain.
    Ecija, D.
    IMDEA Nanosci, Spain.
    Efficient Lanthanide Catalyzed Debromination and Oligomeric Length-Controlled Ullmann Coupling of Aryl Halides2017In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 121, no 14, p. 8033-8041Article in journal (Refereed)
    Abstract [en]

    Lanthanide elements play a vital role in a broad range of high-tech applications, and there is an increasing interest in their catalytic activity, particularly in organo-metallics. However, their catalytic role on surfaces remains unexplored. Here, we present a scanning tunneling microscopy and density functional theory study of the debromination, contacting, and coupling of dibromine terphenyl species with Dy (f-block element) and Ag (d-block element) adatoms, respectively. We show that Dy debrominates the targeted species more efficiently than Ag adatoms at room temperature, promoting the formation of unprecedented C-Dy-C organo-metallic supramolecules versus C-Ag-C parallel chains for the Ag case. DFT calculations corroborate our results showing an almost spontaneous debromination process with Dy compared to Ag. Upon annealing, for samples containing Dy, the formation of C-Ag-C organometallic bonds and concomitant C-C coupling is inhibited, giving rise to a self-assembly of debrominated monomers, showing only a minority number of covalent dimes species. For samples without Dy covalent chains of irregular length are promoted. Our studies open new avenues for using lanthanide elements as efficient dehalogenation catalysts. Furthermore, we illustrate their potential as inhibitors of uncontrolled C-C coupling reactions, of great relevance for fine-tuning the length of polymeric compounds.

  • 27.
    Colas, Kilian
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martín-Montero, Raúl
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mendoza, Abraham
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Intermolecular Pummerer Coupling with Carbon Nucleophiles in Non-Electrophilic Media2017In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 56, no 50, p. 16042-16046Article in journal (Refereed)
    Abstract [en]

    A new Pummerer-type C-C coupling protocol is introduced based on turbo-organomagnesium amides, which unlike traditional Pummerer reactions, does not require strong electrophilic activators, engages a broad range of C(sp(3))-, C(sp(2))-, and C(sp)-nucleophiles, and seamlessly integrates with C-H and C-X magnesiation. Given the central character of sulfur compounds in organic chemistry, this protocol allows access to unrelated carbonyls, olefins, organometallics, halides, and boronic esters through a single strategy.

  • 28.
    Crespo, Abel
    et al.
    Univ Santiago de Compostela, Ctr Singular Invest Quim Biol & Mat Mol CIQUS, Santiago De Compostela 1578, Spain.;Univ Santiago de Compostela, Fac Farm, Dept Quim Organ, Santiago De Compostela 1578, Spain..
    El Maatougui, Abdelaziz
    Univ Santiago de Compostela, Ctr Singular Invest Quim Biol & Mat Mol CIQUS, Santiago De Compostela 1578, Spain.;Univ Santiago de Compostela, Fac Farm, Dept Quim Organ, Santiago De Compostela 1578, Spain..
    Azuaje, Jhonny
    Univ Santiago de Compostela, Ctr Singular Invest Quim Biol & Mat Mol CIQUS, Santiago De Compostela 1578, Spain.;Univ Santiago de Compostela, Fac Farm, Dept Quim Organ, Santiago De Compostela 1578, Spain..
    Escalante, Luz
    Univ Santiago de Compostela, Ctr Singular Invest Quim Biol & Mat Mol CIQUS, Santiago De Compostela 1578, Spain.;Univ Santiago de Compostela, Fac Farm, Dept Quim Organ, Santiago De Compostela 1578, Spain..
    Majellaro, Maria
    Univ Santiago de Compostela, Ctr Singular Invest Quim Biol & Mat Mol CIQUS, Santiago De Compostela 1578, Spain.;Univ Santiago de Compostela, Fac Farm, Dept Quim Organ, Santiago De Compostela 1578, Spain..
    Loza, Maria Isabel
    Univ Santiago de Compostela, Ctr Singular Invest Med Mol & Enfermedades Cron C, Santiago De Compostela 1578, Spain..
    Brea, Jose
    Univ Santiago de Compostela, Ctr Singular Invest Med Mol & Enfermedades Cron C, Santiago De Compostela 1578, Spain..
    Isabel Cadavid, Mara
    Univ Santiago de Compostela, Ctr Singular Invest Med Mol & Enfermedades Cron C, Santiago De Compostela 1578, Spain..
    Gutiérrez-de-Terán, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Sotelo, Eddy
    Univ Santiago de Compostela, Ctr Singular Invest Quim Biol & Mat Mol CIQUS, Santiago De Compostela 1578, Spain.;Univ Santiago de Compostela, Fac Farm, Dept Quim Organ, Santiago De Compostela 1578, Spain..
    Exploring the influence of the substituent at position 4 in a series of 3,4-dihydropyrimidin-2(1H)-one A(2B) adenosine receptor antagonists2017In: Chemistry of Heterocyclic Compounds, ISSN 0009-3122, E-ISSN 1573-8353, Vol. 53, no 3, p. 316-321Article in journal (Refereed)
    Abstract [en]

    In the context of a program to identify selective adenosine A(2B) receptor antagonists, we have obtained a focused library of 4-substituted 3,4-dihydropyrimidin-2(1H)-ones and its affinity for the four human adenosine receptor subtypes was determined. The synthesis was accomplished by using an experimentally simple and efficient Biginelli approach. The biological evaluation of the library revealed that all the documented derivatives exhibit low or negligible affinity for the A(2B) receptor, thus highlighting the critical importance of the substituent at position 4 of the 3,4-dihydropyrimidin-2(1H)-one chemotype.

  • 29.
    Dahl, Kenneth
    et al.
    Karolinska Institute, Stockholm, Sweden.
    Nordeman, Patrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    11C-Acetylation of Amines with [11C]Methyl Iodide with Bis(cyclopentadienyldicarbonyliron) as the CO Source2017In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 38, p. 5785-5788Article in journal (Refereed)
    Abstract [en]

    We describe herein a novel approach for the direct 11C-acetylation of amines. The carbonylative protocol is palladium-mediated, uses bis(cyclopentadienyldicarbonyliron) as the CO source, and [11C]methyl iodide or [11C]methyl iodide-D3 as a radioactive precursor. A set of functionalized primary and secondary amines was 11C-labelled in radiochemical yields ranging from 7–85 %. The potential use of this method for positron emission tomography radiotracer production was additionally demonstrated by the radiosynthesis of [11C]lacosamide, [11C]melatonine, and [11C]acecainide in 44–55 % RCY.

  • 30.
    Dahl, Kenneth
    et al.
    Karolinska Insititute, Ctr Psychiat Res, Karolinska Hosp, Dept Clin Neurosci, SE-17176 Stockholm, Sweden..
    Nordeman, Patrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    C-11-Carbonylation through in Situ Generated C-11-Benzoyl Chlorides with Tetrabutylammonium Chloride as Chloride Source2017In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 18, p. 2648-2651Article in journal (Refereed)
    Abstract [en]

    Aromatic C-11-containing acids, amides, esters, and aldehydes were obtained through a novel C-11-carbonylative reaction. In the two-step process, aryl iodides are first reacted with (CO)-C-11 and tetrabutylammonium chloride in a palladium-mediated reaction to yield C-11-benzoyl chlorides in situ. The crude mixture is then further treated with either a hydroxide, amine, alcohol, or a hydride in a second vial to furnish the final C-11-carbonyl product. The monodentate ligand tri-tert-butylphosphonium tetrafluoroborate was proven to be crucial for obtaining high radiochemical yields (RCY). A wide range of C-11-containing carbonyl compounds were successfully radiolabeled in moderate to excellent RCYs, ranging from 41-93%. The synthetic retinoic acid tamibarotene was obtained in a RCY of 89%, whereas the Boc-protected procainamide was labelled in 68% RCY, which is a significantly increase (2-3 fold) in RCY compared to other published methods.

  • 31.
    Danelius, Emma
    et al.
    University of Gothenburg, SE-41296 Gothenburg, Sweden.
    Andersson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. University of Gothenburg, SE-41296 Gothenburg, Sweden.
    Jarvoll, Patrik
    University of Gothenburg, SE-41296 Gothenburg, Sweden.
    Lood, Kajsa
    University of Gothenburg, SE-41296 Gothenburg, Sweden.
    Gräfenstein, Jürgen
    University of Gothenburg, SE-41296 Gothenburg, Sweden.
    Erdélyi, Máté
    University of Gothenburg, SE-41296 Gothenburg, Sweden.
    Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation2017In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Biochemistry, ISSN 0006-2960, Vol. 56, no 25, p. 3265-3272Article in journal (Refereed)
    Abstract [en]

    Halogen bonding is a weak chemical force that has so far mostly found applications in crystal engineering. Despite its potential for use in drug discovery, as a new molecular tool in the direction of molecular recognition events, it has rarely been assessed in biopolymers. Motivated by this fact, we have developed a peptide model system that permits the quantitative evaluation of weak forces in a biologically relevant proteinlike environment and have applied it for the assessment of a halogen bond formed between two amino acid side chains. The influence of a single weak force is measured by detection of the extent to which it modulates the conformation of a cooperatively folding system. We have optimized the amino acid sequence of the model peptide on analogues with a hydrogen bond-forming site as a model for the intramolecular halogen bond to be studied, demonstrating the ability of the technique to provide information about any type of weak secondary interaction. A combined solution nuclear magnetic resonance spectroscopic and computational investigation demonstrates that an interstrand halogen bond is capable of conformational stabilization of a β-hairpin foldamer comparable to an analogous hydrogen bond. This is the first report of incorporation of a conformation-stabilizing halogen bond into a peptide/protein system, and the first quantification of a chlorine-centered halogen bond in a biologically relevant system in solution.

  • 32.
    Daniel, Quentin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Water oxidation: From Molecular Systems to Functional Devices2017Doctoral thesis, monograph (Other academic)
    Abstract [en]

    The production of hydrogen gas, through the process of water splitting,is one of the most promising concepts for the production of clean andrenewable fuel.The introduction of this thesis provides a brief overview of fossil fuelsand the need for an energy transition towards clean and renewable energy.Hydrogen gas is presented as a possible candidate fuel with its productionthrough artificial photosynthesis, being described. However, the highlykinetically demanding key reaction of the process – the water oxidationreaction – requires the use of a catalyst. Hence, a short presentation of differentmolecular water oxidation catalysts previously synthesized is also provided.The second part of the thesis focuses on ruthenium-based molecularcatalysis for water oxidation. Firstly, the design and the catalytic performancefor a new series of catalysts are presented. Secondly, a further study onelectron paramagnetic resonance of a catalyst shows the coordination of awater molecule to a ruthenium centre to generate a 7-coordinated complex atRuIII state. Finally, in an electrochemical study, coupled with nuclear magneticresonance analysis, mass spectrometry and X-ray diffraction spectroscopy, wedemonstrate the ability of a complex to perform an in situ dimerization of twounits in order to generate an active catalyst.The final part of this thesis focuses on immobilisation of first rowtransition metal catalysts on the surface of electrodes for electrochemical wateroxidation. Initially, a copper complex was designed and anchored on a goldsurface electrode. Water oxidation performance was studied byelectrochemistry, while deactivation of the electrode was investigated throughX-ray photoelectron spectroscopy, revealing the loss of the copper complexfrom the electrode during the reaction. Finally, we re-investigated cobaltporphyrin complexes on the surface of the electrode. Against the backgroundof previous report, we show that the decomposition of cobalt porphyrin intocobalt oxide adsorbed on the surface is responsible for the catalytic activity.This result is discussed with regard to the detection limit of various spectroscopic methods.

  • 33.
    Daniel, Quentin
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Huang, Ping
    Fan, Ting
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Duan, Lele
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Wang, Lei
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Li, Fusheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mamedov, Fikret
    Styring, Stenbjörn
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Rearranging from 6-to 7-coordination initiates the catalytic activity: An EPR study on a Ru-bda water oxidation catalyst2017In: Coordination chemistry reviews, ISSN 0010-8545, E-ISSN 1873-3840, Vol. 346, p. 206-215Article in journal (Refereed)
    Abstract [en]

    The coordination of a substrate water molecule on a metal centered catalyst for water oxidation is a crucial step involving the reorganization of the ligand sphere. This process can occur by substituting a coordinated ligand with a water molecule or via a direct coordination of water onto an open site. In 2009, we reported an efficient ruthenium-based molecular catalyst, Ru-bda, for water oxidation. Despite the impressive improvement in catalytic activity of this type of catalyst over the past years, a lack of understanding of the water coordination still remains. Herein, we report our EPR and DFT studies on Ru-bda (triethylammonium 3-pyridine sulfonate)(2) (1) at its Ru-III oxidation state, which is the initial state in the catalytic cycle for the O-O bond formation. Our investigation suggests that at this III-state, there is already a rearrangement in the ligand sphere where the coordination of a water molecule at the 7th position (open site) takes place under acidic conditions (pH = 1.0) to form a rare 7-coordinated Ru-III species.

  • 34.
    Daver, Henrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Modeling of Phosphoesterase Mimics and Chemistry in Confined Spaces2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, density functional theory is employed in the study of two kinds of systems that can be considered to be biomimetic in their own ways. First, three binuclear metal complexes, synthesized by the group of Prof. Ebbe Nordlander, have been investigated. The complexes are designed to resemble the active sites of phosphatase enzymes and have been examined in complexes where either two Zn(II) ions or one Fe(III) and one Mn(II) ion are bound. These dinuclear compounds were studied as catalysts for the hydrolysis of bis(2,4-dinitrophenyl) phosphate and the transesterification of 2-hydroxypropyl p-nitrophenyl phosphate, which are model systems for the same reactions occurring in DNA or RNA. It was found that the two reactions take place in similar ways: a hydroxide ion that is terminally bound to one of the metal centers acts either as a nucleophile in the hydrolysis reaction or as a base in the transesterification. The leaving groups depart in an effectively concerted manner, and the formed catalyst-product complexes are predicted to be the resting states of the catalytic cycles. The rate-determining free energy barriers are identified from the catalyst-product complex in one catalytic cycle to the transition state of nucleophilic attack in the next.

    Another type of biomimetic modeling is made with an aim of imitating the conceptual features of selective binding of guests and screening them from solute-solvent interactions. Such features are found in so-called nanocontainers, and this thesis is concerned with studies of two capsules synthesized by the group of Prof. Julius Rebek, Jr. First, the cycloaddition of phenyl acetylene and phenyl azide has experimentally been observed to be accelerated in the presence of a capsule. Computational studies were herein performed on this system, and a previously unrecognized structure of the capsule is discovered. Two main factors are then identified as sources of the rate acceleration compared to the uncatalyzed reaction, namely the reduction of the entropic component and the selective destabilization of the reactant supercomplex over the transition state.

    In the second capsule study, the alkane binding trends of a water-soluble cavitand was studied. It is found that implicit solvation models fail severely in reproducing the experimental equilibrium observed between binding of n-decane by the cavitand monomer and encapsulation in the capsule dimer. A mixed explicit/implicit solvation protocol is developed to better quantify the effect of hydrating the cavitand, and a simple correction to the hydration free energy of a single water molecule is proposed to remedy this. The resulting scheme is used to predict new hydration free energies of the cavitand complexes, resulting in significant improvement vis-à-vis experiments.

    The computational results presented in this thesis show the usefulness of the quantum chemical calculations to develop understanding of experimental trends observed for substrate binding and catalysis. In particular, the methodology is shown to be versatile enough such that experimental observations can be reproduced for such diverse systems as studied herein.

  • 35.
    Daver, Henrik
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Harvey, Jeremy N.
    Rebek, Jr., Julius
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Modeling of Cycloaddition Reaction in a Self-Assembled Capsule2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 43, p. 15494-15503Article in journal (Refereed)
    Abstract [en]

    Dispersion-corrected density functional theory is used to study the cycloaddition reaction between phenyl acetylene and phenyl azide inside a synthetic, self-assembled capsule. The capsule is first characterized computationally and a previously unrecognized structure is identified as being the most stable. Next, an examination of the free energies of host-guest complexes is conducted, considering all possible reagent, solvent and solvent impurity combinations as guests. The experimentally observed relative stabilities of host-guest complexes are quite well reproduced, when the experimental concentrations are taken into account. Experimentally, the presence of the host capsule has been shown to accelerate the cycloaddition reaction and to yield exclusively the 1,4-regioisomer product. Both these observations are reproduced by the calculations. A detailed energy decomposition analysis shows that reduction of the entropic cost of bringing together the reactants along with a geometric destabilization of the reactant supercomplex are the major contributors to the rate acceleration compared to the background reaction. Finally, a sensitivity analysis is conducted to assess the stability of the results with respect to the choice of methodology.

  • 36.
    Denisova, Aleksandra
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Hyperconjugation in Group 14 Organic Compounds: Design and Property Investigations2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Nowadays π-conjugated molecules are widely used as materials for devices in organic and molecular electronics. This is due to the ability of such molecules to conduct electricity. However, π-conjugation leads to molecular rigidness and associated lower solubility, which limits possible applications. Meanwhile, there are other types of conjugation that do not cause molecular rigidness but still provide conductivity. One of them is so called hyperconjugation. While π-conjugation involves only p atomic orbitals, hyperconjugation is characterized by interaction of π and σ orbitals. Hyperconjugation is normally weaker than π-conjugation, thus, in order to get strongly hyperconjugated molecules they should be enhanced in some way.

    In this thesis, I describe methods for design of strongly hyperconjugated molecules. It is possible to increase the strength of hyperconjugation by various methods and some of them are discussed. We performed quantum chemical calculations in order to investigate optical and geometric properties of the hyperconjugated molecules and evaluate the relative strength of hyperconjugation. In some cases, results of calculations were compared with experimental results aiming to confirm the relevance of the calculations. First, we have investigated how the change of group 14 elements in the 1,4-ditetrelocyclohexa-2,5-dienes influence the hyperconjugation strength. Next, the substituent effect was considered in fulvenes and their hyperconjugated analogs. We showed this effect from the perspective of the substituents influence on the aromatic properties of molecules in the ground and first electronically excited states. Further, the gradual shift when going from monomer to oligomers were investigated. For this hyperconjugated oligomers were constructed from 1,4-disilacyclohexa-2,5-diene and cyclobutadisilole fragments. Additionally we showed the influence of electron withdrawing and electron donating groups on hyperconjugation in siloles and 1,4-disilacyclohexa-2,5-dienes. Finally, hyperconjugation was investigated in a set of silicon-containing omni-hyperconjugated compounds.

    The results obtained from this research showed that hyperconjugation strength can be increased significantly up to levels comparable to purely π-conjugated molecules. We hope that these results will be useful in development of other hyperconjugated small molecules, oligomers, and polymers, which can be further used as material for electronic devices.

  • 37.
    Devaraj, Karthik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Ruthenium-catalyzed C-H Functionalization of (Hetero)arenes2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis concerned about the Ru-catalyzed C-H functionalizations on the synthesis of 2-arylindole unit, silylation of heteroarenes and preparation of aryne precursor.

    In the first project, we developed the Ru-catalyzed C2-H arylation of N-(2-pyrimidyl) indoles and pyrroles with nucleophilic arylboronic acids under oxidative conditions. Wide variety of arylboronic acids afforded the desired product in excellent yield regardless of the substituents or functional group electronic nature. Electron-rich heteroarenes are well suited for this method than electron-poor heteroarenes. Halides such as bromide and iodide also survived, further derivatisation of the halide is shown by Heck alkenylation. In order to find catalytic on-cycle intermediate extensive mechanistic experiments have been carried out by preparing presumed ruthenacyclic complexes and C-H/D exchange reactions. It suggested that para-cymene ligand is not present in the catalytic on-cycle intermediate and we suspect that metalation occurs with electrophilic ruthenium center via SEAr mechanism.

    In the second project, we developed the Ru-catalyzed silylation of gramine, tryptamine and their congeners using silanes as coupling partner. The transformation worked well with many different silanes. Regarding directing group, nitrogen atom containing directing groups are more favoured than the oxygen containing directing groups. Wide range of gramines and tryptamines also yielded the desired product in poor to excellent yield. At higher temperature, albeit in low yield, undirected silylation occurred. In order to get some insights about the reaction pathway of the silylation C-H/D exchange experiments were performed, and it revealed the possibility of C4-H activation of gramines by an electron rich metal- Si-H/D experiments showed Si-H activation by Ru is easy.

    In the final project, we presented the closely related aryne precursors from arylboronic acids via Ru-catalyzed C-H silylation of arylboronates and their selective oxidation. Worthy of note, the aryne capture products obtained from arylboronic acids in a single purification.

  • 38. Deyou, Tsegaye
    et al.
    Marco, Makungu
    Heydenreich, Matthias
    Pan, Fangfang
    Gruhonjic, Amra
    Fitzpatrick, Paul A
    Koch, Andreas
    Derese, Solomon
    Pelletier, Jerry
    Rissanen, Kari
    Yenesew, Abiy
    Erdelyi, Mate
    Isoflavones and Rotenoids from the Leaves of Millettia oblata ssp. teitensis.2017In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 80, no 7, p. 2060-2066Article in journal (Refereed)
    Abstract [en]

    A new isoflavone, 8-prenylmilldrone (1), and four new rotenoids, oblarotenoids A-D (2-5), along with nine known compounds (6-14), were isolated from the CH2Cl2/CH3OH (1:1) extract of the leaves of Millettia oblata ssp. teitensis by chromatographic separation. The purified compounds were identified by NMR spectroscopic and mass spectrometric analyses, whereas the absolute configurations of the rotenoids were established on the basis of chiroptical data and in some cases by single-crystal X-ray crystallography. Maximaisoflavone J (11) and oblarotenoid C (4) showed weak activity against the human breast cancer cell line MDA-MB-231 with IC50 values of 33.3 and 93.8 μM, respectively.

  • 39.
    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.

  • 40.
    Elgland, Mathias
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Nordeman, P.
    Uppsala University, Sweden.
    Fyrner, Timmy
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Antoni, G.
    Uppsala University, Sweden.
    Nilsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Konradsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    beta-Configured clickable [F-18] FDGs as novel F-18-fluoroglycosylation tools for PET2017In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, no 18, p. 10231-10236Article in journal (Refereed)
    Abstract [en]

    In oncology and neurology the F-18-radiolabeled glucose analogue 2-deoxy-2-[F-18]fluoro-D-glucose ([F-18]FDG) is by far the most commonly employed metabolic imaging agent for positron emission tomography (PET). Herein, we report a novel synthetic route to beta-configured mannopyranoside precursors and a chemoselective F-18-fluoroglycosylation method that employ two b-configured [F-18]FDG derivatives equipped with either a terminal azide or alkyne aglycon respectively, for use as a CuAAC clickable tool set for PET. The b-configured precursors provided the corresponding [F-18]FDGs in a radiochemical yield of 77-88%. Further, the clickability of these [F-18]FDGs was investigated by click coupling to the suitably functionalized Fmoc-protected amino acids, Fmoc-N-(propargyl)-glycine and Fmoc-3-azido-L-alanine, which provided the F-18-fluoroglycosylated amino acid conjugates in radiochemical yields of 75-83%. The F-18-fluoroglycosylated amino acids presented herein constitute a new and interesting class of metabolic PET radiotracers.

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

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

  • 42. Erdelyi, Mate
    Application of the Halogen Bond in Protein Systems.2017In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 56, no 22, p. 2759-2761Article, review/survey (Refereed)
  • 43. Erdelyi, Mate
    et al.
    Metrangolo, Pierangelo
    Introduction to the special issue on halogen bonding.2017In: Acta Crystallographica. Section B: Structural Science, Crystal Engineering and Materials, ISSN 2052-5192, E-ISSN 2052-5206, Vol. 73, no Pt 2, article id 135Article, review/survey (Refereed)
  • 44.
    Esfandiarfard, Keyhan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Uppsala University.
    Novel Organophosphorus Compounds for Materials and Organic Synthesis2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is devoted to the development of new organophosphorus compounds for potential uses in material science and as reagents in Organic Chemistry. Organophosphorus compounds in a single molecule or organic electronics context are appealing as the phosphorous centers perturb the electronic properties of the π-conjugated systems while at the same time provide synthetic handles for subsequent synthetic modifications. As such, new synthetic methodology to such compounds and the exploration of new building blocks is of considerable interest. In a different study, novel organophosphorus compounds are synthesized and shown to promote a reaction in Organic Chemistry that has previously not been possible, i.e. the stereoselective reductive coupling of aldehydes to alkenes. Such developments enlarge the toolkit of reactions that are available to Organic Chemists, and may impact the synthetic routes to pharmaceuticals and other important commodity chemicals.

    A general introduction of the key structural unit of this thesis, phosphaalkenes, is given in the first chapter. The synthesis, reactivity, properties and applications of these P=C double bond containing compounds are highlighted. The Wittig reaction and its variations as well as the phosphorus analogues that produce phosphaalkenes are outlined in detail.

    The second chapter is dedicated to the synthesis of a precursor that is used for the preparation of novel π-conjugated, organophosphorus compounds. C,C-Dibromophosphaalkenes are prepared and the halide substituents are used for the selective introduction of acetylene units. Besides the phosphaalkenes, the successful syntheses of two new diphosphenes is presented, indicating a broad applicability of the precursors.

    The third chapter is dedicated to the isolation of a metal-free phosphanylphosphonate that transforms aldehydes quantitatively to their corresponding E-phosphaalkenes in a transition metal-free phospha-HWE (Horner-Wadsworth-Emmons) reaction. The reaction benefits from mild conditions, high E-stereoselectivity, and a broad substrate scope.

    In the last chapter, a novel method for the reductive coupling of aldehydes to olefins is introduced. The reaction, which is a vast improvement over the McMurry coupling, allows for the selective synthesis of symmetrical and most importantly unsymmetrical E-alkenes. The phosphanylphosphonate mentioned above is the reagent that facilitates the coupling of the aldehydes via a phosphaalkene intermediate. This one-pot reaction benefits from mild conditions, good conversions, and high E-stereoselectivity.

    In summary, the thesis presents novel aspects of organophosphorus chemistry. These include the preparations and exploration of interesting precursors for the construction of π-conjugated organophosphorus compounds, and the use of organophosphorus reagents for unprecedented transformations in Organic Chemistry.

  • 45.
    Fan, Ke
    et al.
    KTH, School of Chemical Science and Engineering (CHE).
    Ji, Yongfei
    Zou, Haiyuan
    Zhang, Jinfeng
    Zhu, Bicheng
    Chen, Hong
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Daniel, Quentin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Luo, Yi
    Yu, Jiaguo
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Hollow Iron-Vanadium Composite Spheres: A Highly Efficient Iron-Based Water Oxidation Electrocatalyst without the Need for Nickel or Cobalt2017In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 56, no 12, p. 3289-3293Article in journal (Refereed)
    Abstract [en]

    Noble-metal-free bimetal-based electrocatalysts have shown high efficiency for water oxidation. Ni and/or Co in these electrocatalysts are essential to provide a conductive, high-surface area and a chemically stable host. However, the necessity of Ni or Co limits the scope of low-cost electrocatalysts. Herein, we report a hierarchical hollow FeV composite, which is Ni- and Co-free and highly efficient for electrocatalytic water oxidation with low overpotential 390 mV (10 mA cm(-2) catalytic current density), low Tafel slope of 36.7 mV dec(-1), and a considerable durability. This work provides a novel and efficient catalyst, and greatly expands the scope of low-cost Fe-based electrocatalysts for water splitting without need of Ni or Co.

  • 46.
    Farag, Mohamed A.
    et al.
    Cairo Univ, Pharmacognosy Dept, Coll Pharm, Kasr el Aini St,PB 11562, Cairo, Egypt..
    Ali, Sara E.
    German Univ Cairo, Fac Pharm & Biotechnol, Dept Pharmaceut Biol, PB 11835, Cairo, Egypt..
    Hodaya, Rashad H.
    Desert Res Ctr, Plant Prod Dept, PB 11714, Cairo, Egypt..
    El-Seedi, Hesham R.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Menoufia Univ, Fac Sci, Dept Chem, Shibin Al Kawm 32512, Egypt..
    Sultani, Haider N.
    Leibniz Inst Plant Biochem, Dept Bioorgan Chem, Weinberg 3, D-06120 Halle, Saale, Germany..
    Laub, Annegret
    Leibniz Inst Plant Biochem, Dept Bioorgan Chem, Weinberg 3, D-06120 Halle, Saale, Germany..
    Eissa, Tarek E.
    Modern Sci & Arts Univ, Coll Pharm, Pharmacognosy Dept, PB 12566, Cairo, Egypt..
    Abou-Zaid, Fouad O. F.
    Desert Res Ctr, Plant Prod Dept, PB 11714, Cairo, Egypt..
    Wessjohann, Ludger A.
    Leibniz Inst Plant Biochem, Dept Bioorgan Chem, Weinberg 3, D-06120 Halle, Saale, Germany..
    Phytochemical Profiles and Antimicrobial Activities of Allium cepa Red cv. and A. sativum Subjected to Different Drying Methods: A Comparative MS-Based Metabolomics2017In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 22, no 5, article id 761Article in journal (Refereed)
    Abstract [en]

    Plants of the Allium genus produce sulphur compounds that give them a characteristic (alliaceous) flavour and mediate for their medicinal use. In this study, the chemical composition and antimicrobial properties of Allium cepa red cv. and A. sativum in the context of three different drying processes were assessed using metabolomics. Bulbs were dried using either microwave, air drying, or freeze drying and further subjected to chemical analysis of their composition of volatile and non-volatile metabolites. Volatiles were collected using solid phase micro-extraction (SPME) coupled to gas chromatography-mass spectrometry (GC/MS) with 42 identified volatiles including 30 sulphur compounds, four nitriles, three aromatics, and three esters. Profiling of the polar non-volatile metabolites via ultra-performance liquid chromatography coupled to high resolution MS (UPLC/MS) annotated 51 metabolites including dipeptides, flavonoids, phenolic acids, and fatty acids. Major peaks in GC/MS or UPLC/MS contributing to the discrimination between A. sativum and A. cepa red cv. were assigned to sulphur compounds and flavonoids. Whereas sulphur conjugates amounted to the major forms in A. sativum, flavonoids predominated in the chemical composition of A. cepa red cv. With regard to drying impact on Allium metabolites, notable and clear separations among specimens were revealed using principal component analysis (PCA). The PCA scores plot of the UPLC/MS dataset showed closer metabolite composition of microwave dried specimens to freeze dried ones, and distant from air dried bulbs, observed in both A. cepa and A. sativum. Compared to GC/MS, the UPLC/MS derived PCA model was more consistent and better in assessing the impact of drying on Allium metabolism. A phthalate derivative was found exclusively in a commercial garlic preparation via GC/MS, of yet unknown origin. The freeze dried samples of both Allium species exhibited stronger antimicrobial activities compared to dried specimens with A. sativum being in general more active than A. cepa red cv.

  • 47.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bastos, Erick L.
    Bechara, Etelvino J. H.
    Baader, Wilhelm J.
    Four‐membered cyclic peroxides: Carriers of chemical energy2017In: Journal of Physical Organic Chemistry, ISSN 0894-3230, E-ISSN 1099-1395, p. 1-18Article in journal (Refereed)
    Abstract [en]

    Four‐membered cyclic peroxides are high‐energy compounds often associated tocold light emission, but whose chemical and biological roles are still matters ofdebate. The often‐dangerous synthesis of 1,2‐dioxetanes, achieved around 50 yearsago, has been mastered over the years to a point where some derivatives are commerciallyavailable. This fact does not imply that 1,2‐dioxetanes can be convenientlyprepared in the gram scale or that the synthesis of analogous 1,2‐dioxetanones andthe elusive 1,2‐dioxetanedione are simple. Important questions on the mechanism ofchemiluminescence and bioluminescence reactions are under experimental and theoreticalscrutiny. The available data have contributed to relate structural and mediumeffects to the quantum efficiency of these compounds to produce excited states.Consequently, such peroxides have been suggested to produce biologically relevantelectronically excited species in vivo in the absence of light. The connection of thishypothesis with melanin‐mediated photodamage in the dark has renewed the interestin such cyclic peroxides. This reviewgives some insight on the synthesis, chemiluminescencemechanism, and biological relevance of 1,2‐dioxetanes, 1,2‐dioxetanones,and 1,2‐dioxetanedione and provides practical protocols for those interested inengaging this field.

  • 48.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Oliveira, Marcelo
    Fdez. Galvan, Ignacio
    Baader, Wilhelm J.
    A combined theoretical and experimental study onthe mechanism of spiro-adamantyl-1,2-dioxetanone decomposition2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, p. 17462-17472Article in journal (Refereed)
    Abstract [en]

    1,2-Dioxetanones have been considered as model compounds for bioluminescence processes. Theunimolecular decomposition of these prototypes leads mainly to the formation of triplet excited stateswhereas in the catalysed decomposition of these peroxides singlet states are formed preferentially.Notwithstanding, these cyclic peroxides are important models to understand the general principles ofchemiexcitation as they can be synthesised, purified and characterised. We report here results ofexperimental and theoretical approaches to investigating the decomposition mechanism of spiroadamantyl-1,2-dioxetanone. The activation parameters in the unimolecular decomposition of thisderivative have been determined by isothermal kinetic measurements (30–70 C) and thechemiluminescence activation energy calculated from the correlation of emission intensities. Theactivation energy for peroxide decomposition proved to be considerably lower than thechemiluminescence activation energy indicating the existence of different reaction pathways for groundand excited state formation. These experimental results are compared with the calculations at thecomplete active space second-order perturbation theory (CASPT2), which reveal a two-step biradicalmechanism starting by weak peroxide bond breakage followed by carbon–carbon elongation. Thetheoretical findings also indicate different transition state energies on the excited and ground statesurfaces during the C–C bond cleavage in agreement with the experimental activation parameters.

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

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

  • 50. 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.

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