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  • 201. Coll, Mercedes
    et al.
    Pamies, Oscar
    Adolfsson, Hans
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Dieguez, Montserrat
    Second-Generation Amino Acid Furanoside Based Ligands from D-Glucose for the Asymmetric Transfer Hydrogenation of Ketones2013Ingår i: ChemCatChem, ISSN 1867-3880, E-ISSN 1867-3899, Vol. 5, nr 12, s. 3821-3828Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A novel series of modular amino acid thioamide ligands functionalized with carbohydrates were introduced and employed in the rhodium-catalyzed asymmetric transfer hydrogenation (ATH) of aryl alkyl ketones, including the less-studied heteroaromatic ketones. The ligands are based on amino acid hydroxyamides (pseudodipeptides), which are the most successful ligands previously used in asymmetric hydrogen transfer reactions. High enantioselectivities [up to 99% enantiomeric excess (ee)] were achieved in the ATH of a wide range of aryl alkyl ketones by using catalysts generated insitu from [RhCl2Cp*](2) (Cp*=C5Me5) and thioamide ligands comprising a 3-benzyl glucofuranoside backbone and a bulky isopropyl group in the -amino acid moiety. Interestingly, both enantiomers of the alcohol products can readily be obtained with high enantioselectivity by simply changing the absolute configuration of the -amino acid. The good performance can be extended to a very challenging class of industrially interesting heteroaromatic ketones (up to 99%ee).

  • 202. Coll, Mercedes
    et al.
    Pàmies, Oscar
    Adolfsson, Hans
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Diéguez, Montserrat
    Carbohydrate-based pseudo-dipeptides: new ligands for the highly enantioselective Ru-catalyzed transfer hydrogenation reaction2011Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 47, nr 44, s. 12188-12190Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ruthenium-complexes of novel carbohydrate based pseudo-dipeptide ligands effectively and selectively catalyze the reduction of a broad range of aryl–alkyl ketones under ATH conditions. Excellent enantioselectivities (>99% ee) are obtained using aminosugars as the sole source of chirality.

  • 203.
    Cordova, Armando
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Lin, Shuangzheng
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Tseggai, Abrehet
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Concise catalytic asymmetric total synthesis of biologically active tropane alkaloids2012Ingår i: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 354, nr 7, s. 1363-1372Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A general strategy for the total asymmetric synthesis of valuable tropane alkaloids by catalytic stereoselective transformations is disclosed. The power of this approach is exemplified by the concise catalytic enantioselective total syntheses of (+)-methylecgonine, (-)-cocaine and (+)-cocaine as well as the first catalytic asymmetric total syntheses of a cocaine C-1 derivative and (+)-ferruginine starting from 5-oxo-protected-a,beta-unsaturated enals using only two and three column chromatographic purification steps, respectively.

  • 204.
    Cortés González, Miguel A.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Nordeman, Patrik
    Bermejo Gómez, Antonio
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. AstraZeneca PET Centre at Karolinska Institutet, Sweden.
    Meyer, Denise N.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Antoni, Gunnar
    Schou, Magnus
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    [F-18]fluoro-benziodoxole: a no-carrier-added electrophilic fluorinating reagent. Rapid, simple radiosynthesis, purification and application for fluorine-18 labelling2018Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, nr 34, s. 4286-4289Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Operationally simple radiosynthesis and purification of [F-18]fluoro-benziodoxole was developed starting from a cyclotron produced [F-18]F- precursor, [F-18]TBAF, and tosyl-benziodoxole. The synthetic utility of [F-18]fluoro-benziodoxole was demonstrated by electrophilic fluorocyclization of o-styrilamides proceeding with high RCC (typically 50-90%) and high molar activity (up to 396 GBq mol(-1)).

  • 205. Cosner, Casey C.
    et al.
    Iska, Vijaya Bhaskara Reddy
    Chatterjee, Anamitra
    Markiewicz, John T.
    Corden, Steven J.
    Löfstedt, Joakim
    Ankner, Tobias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Richer, Joshua
    Hulett, Tyler
    Schauer, Douglas J.
    Wiest, Olaf
    Helquist, Paul
    Evolution of Concise and Flexible Synthetic Strategies for Trichostatic Acid and the Potent Histone Deacetylase Inhibitor Trichostatin A2013Ingår i: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, nr 1, s. 162-172Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    (R)-(+)-Trichostatic acid and (R)-(+)-trichostatin A (TSA) are natural products that have attracted considerable attention in the field of epigenetic therapies. TSA in particular is a naturally occurring hydroxamic acid having potent activity as a histone deacetylase inhibitor (HDACi) and having significant potential for treatment of a myriad of genetically based diseases. Development of TSA and other trichostatic acid derivatives into useful small-molecule therapies has been hindered by the low natural abundance and high cost associated with these compounds. We report herein our collective efforts towards the development of concise and scalable routes for the synthesis of trichostatic acid and TSA in both racemic and enantioenriched forms. Three independent synthetic pathways were developed with varying degrees of efficiency and convergency. In the first synthesis, the key step was a vinylogous Horner-Wadsworth-Emmons condensation. A Marshall propargylation reaction was used as the key step in the second synthesis, and Pd-catalyzed a-alkenylation of a ketone zinc enolate by using various functionalized alkenyl or dienyl halides was developed for the third synthesis. The second pathway proved to be readily amenable to an enantioselective modification, and both the second and third pathways were straightforwardly adapted for the facile preparation of new analogues of trichostatic acid and TSA.

  • 206.
    Cotton, Hanna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Chiral metallocene ligands for transition metal-catalysed reactions2004Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
  • 207. Cotton, Hanna K.
    et al.
    Norinder, Jakob
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Screening of Ligands in the Asymmetric Metallocenethiolatocopper(I)-Catalyzed Allylic Substitution with Grignard Reagents2006Ingår i: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 62, nr 24, s. 5632-5640Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Screening of metallocenethiolate ligands for copper(I)-catalyzed substitution of allylic acetates with Grignard reagents has been carried out. The previously used ligand, lithium (R,Sp)-2-(1-dimethylaminoethyl)ferrocenylthiolate (4a), possessing both central and planar chirality, was the starting point for the screening. It was found that the diastereomeric ligand lithium (R,Rp)-2-(1-dimethylaminoethyl)ferrocenylthiolate (4b) exhibiting reversed planar chirality gave increased enantioselectivity in the allylic substitution, at least when cinnamyl acetate was used as a substrate. The ruthenocene-based ligand lithium (R,Sp)-2-(1-dimethylaminoethyl)ruthenocenylthiolate (4c) gave an enhanced reaction rate, but lower chiral induction. The use of disulfide bis[(R,Sp)-2-(1-dimethylaminoethyl)ferrocenyl]disulfide (7a) as a ligand precursor worked well but resulted in lower enantioselectivity.

  • 208.
    Covarrubias, Adrian Suarez
    et al.
    Department of Cell and Molecular Biology, Uppsala University, Sweden.
    Högbom, Martin
    Department of Cell and Molecular Biology, Uppsala University, Sweden.
    Bergfors, Terese
    Department of Cell and Molecular Biology, Uppsala University, Sweden.
    Carroll, Paul
    Institute for Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London.
    Mannerstedt, Karin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Oscarson, Stefan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Parish, Tanya
    Institute for Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London.
    Jones, T Alwyn
    Department of Cell and Molecular Biology, Uppsala University, Sweden.
    Mowbray, Sherry L
    Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Center, Uppsala, Sweden.
    Structural, biochemical, and in vivo investigations of the threonine synthase from Mycobacterium tuberculosis.2008Ingår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 381, nr 3, s. 622-33Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Threonine biosynthesis is a general feature of prokaryotes, eukaryotic microorganisms, and higher plants. Since mammals lack the appropriate synthetic machinery, instead obtaining the amino acid through their diet, the pathway is a potential focus for the development of novel antibiotics, antifungal agents, and herbicides. Threonine synthase (TS), a pyridoxal-5-phosphate-dependent enzyme, catalyzes the final step in the pathway, in which L-homoserine phosphate and water are converted into threonine and inorganic phosphate. In the present publication, we report structural and functional studies of Mycobacterium tuberculosis TS, the product of the rv1295 (thrC) gene. The structure gives new insights into the catalytic mechanism of TSs in general, specifically by suggesting the direct involvement of the phosphate moiety of the cofactor, rather than the inorganic phosphate product, in transferring a proton from C4' to C(gamma) in the formation of the alphabeta-unsaturated aldimine. It further provides a basis for understanding why this enzyme has a higher pH optimum than has been reported elsewhere for TSs and gives rise to the prediction that the equivalent enzyme from Thermus thermophilus will exhibit similar behavior. A deletion of the relevant gene generated a strain of M. tuberculosis that requires threonine for growth; such auxotrophic strains are frequently attenuated in vivo, indicating that TS is a potential drug target in this organism.

  • 209. Cribiù, Riccardo
    et al.
    Borbas, K. Eszter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    On the synthesis of vinyl and phenyl C-furanosides by stereospecific debenzylative cycloetherification2009Ingår i: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 65, nr 10, s. 2022-2031Artikel i tidskrift (Refereegranskat)
  • 210.
    Cribiù, Riccardo
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stereospecific debenzylative cycloetherification of carbohydrate-derived allylic alcohols, ethers and esters to form vinyl C-furanosides2008Ingår i: Chemical Communications, ISSN 1359-7345, nr 10, s. 1246-1248Artikel i tidskrift (Refereegranskat)
  • 211. Crovetto, Luis
    et al.
    Paredes, Jose M.
    Rios, Ramon
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Talavera, Eva M.
    Avarez-Pez, Jose M.
    Photophysics of a xanthenic derivative dye useful as an ""On/Off"" fluorescence probe2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 51, s. 13311-13320Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The photophysical behavior of a new fluorescein derivative has been explored by using absorption and steady-state and time-resolved fluorescence measurements. The influence of ionic strength, as well as total buffer concentration, on both the absorbance and fluorescence has been investigated. The apparent acidity constant of the dye determined by absorbance is almost independent of the added buffer and salt concentrations. A semiempirical model is proposed to rationalize the variations in the apparent pK(a) values. The excited-state proton-exchange reaction around the physiological pH becomes reversible upon addition of phosphate buffer, inducing a pH-dependent change of the steady-state fluorescence and decay times. Fluorescence decay traces, collected as a function of total buffer concentration and pH, were analyzed by global compartmental analysis, yielding the following values of the rate constants describing excited-state dynamics: k(01) = 1.29 x 10(10) s(-1), k(02) = 4.21 x 10(8) s(-1), k(21)approximate to 3 x 10(6) M-1 s(-1), k(12)(B) = 6.40 x 10(8) M-1 s(-1), and k(21)(B) = 2.61 x 10(7) M-1 s(- 1). The decay rate constant values of k(01), k(21), and k(21)(B), along with the low molar absorption coefficient of the neutral form, mean that coupled decays are practically monoexponential at buffer concentrations higher than 0.02 M and any pH. Thus, the pH and buffer concentration can modulate the main lifetime of the dye.

  • 212.
    Csjernyik, Gábor
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Studies of Biomimtic Oxidations and Racemizations2004Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    This thesis deals with studies of ruthenium-catalyzed hydrogen transfer reactions for oxidations and racemization.

    Through optimisation of the substrate-selective redox catalyst, the electron and proton transfer mediator (a benzoquinone derivative), and the oxygen-activating metal macrocycle a highly efficient biomimetic oxidation of secondary alcohols was obtained. Several alcohols were subjected to the new oxidation protocol and the corresponding ketones were isolated in high yield.

    The deactivation of the oxygen-activating metal macrocycle retarded the aerobic oxidation of primary alcohols. Encapsulation of the metal macrocycle into zeolite, described in chapter 3, proved to be an efficient method to solve this problem and comparable conversion of alcohols was achieved. The immobilization of the oxygen-activating porphyrin to a surface can be an alternative approach to solve the deactivation problem. Therefore as the first step towards studies of immobilized porphyrins on a metal surface (of gold or silver), S-thioacetyl derivatized porphyrins were synthesized; two alternative syntheses are described in chapter 4.

    A new and effecient ruthenium-catalyzed racemization protocol was established by proper ligand tuning. The racemization of the enantiomerically pure alcohols was increased significantly; this work is reported in chapter 5.

  • 213.
    Csjernyik, Gábor
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bogár, Krisztián
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    New Efficient Ruthenium Catalysts for Racemization of Alcohols at Room Temperature2004Ingår i: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 45, nr 36, s. 6799-6802Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    5-Pentaphenylcyclopentadienyl)RuCl(CO)2 was found to catalyze efficiently the racemization of chiral alcohols such as (S)-1-phenylethanol, (S)-1-phenylpropan-2-ol, (S)-4-phenylbutan-2-ol and (S)-4-methoxy-1-phenylethanol at room temperature in the presence of a base. The catalytic activity of three other Ru(II) complexes was also investigated. The effects of halide and solvent were studied as well.

  • 214.
    Csjernyik, Gábor
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-Erling
    Notheisz, Ferenc
    Zsigmond, Ágnes
    Ruthenium-Catalyzed Aerobic Oxidation of Alcohols on Zeolite-Encapsulated Cobalt Salophen Catalyst2002Ingår i: Topics in catalysis, ISSN 1022-5528, Vol. 19, nr 1, s. 119-124Artikel i tidskrift (Refereegranskat)
  • 215.
    Csjernyik, Gábor
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-Erling
    Éll, Alida H
    Fadini, Luca
    Pugin, Benoit
    Efficient Ruthenium-Catalyzed Aerobic Oxidation of Alcohols Using a Biomimetic Coupled Catalytic System2002Ingår i: Journal of Organic Chemistry, ISSN 0022-3263, Vol. 67, nr 5, s. 1657-1662Artikel i tidskrift (Refereegranskat)
  • 216.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Intramolecular aglycon delivery2008Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 343, nr 10-11, s. 1553-1573Artikel, forskningsöversikt (Övrigt vetenskapligt)
  • 217.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Neodisaccharide diglycosyl compounds: Ethers, thioethers and selenoethers. A survey of their synthesis and biological activity2011Ingår i: Comptes rendus. Chimie, ISSN 1631-0748, E-ISSN 1878-1543, Vol. 14, nr 2-3, s. 274-285Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This article gives an account of the area of nonglycosidically linked neodisaccharide compounds consisting of two monosaccharides linked by formal condensation without using the anomeric centre, i.e. by ether bonds, and also their thioether and selenoether counterparts. Synthetic methods and biological relevance are covered.

  • 218.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    New oligosaccharide analogues: non-glycosidically linked thioether-bridged pseudodisaccharides2006Ingår i: Synlett, ISSN 0936-5214, nr 11, s. 1711-1714Artikel i tidskrift (Refereegranskat)
  • 219.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Short synthesis of a benzyl ether protected building block for the synthesis of carbocyclic galactopyranose mimics2010Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 345, nr 8, s. 1056-1060Artikel i tidskrift (Refereegranskat)
  • 220.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Synthesis of carbasugar-containing non-glycosidically linked pseudodisaccharides and higher pseudooligosaccharides2009Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, nr 17, s. 2285-2310Artikel, forskningsöversikt (Refereegranskat)
  • 221.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Agrawal, Santosh
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Borbas, K. Eszter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Martín-Matute, Belén
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Iridium-catalysed condensation of alcohols and amines as a method for aminosugar synthesis2011Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 47, nr 27, s. 7827-7829Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Primary carbohydrate amines at primary and secondary carbons are alkylated by alcohols in the presence of [Cp*IrCl2]2. When primary carbohydrate alcohols are used as the coupling partners and in the presence of Cs2CO3, amine-linked pseudodisaccharides are obtained. Secondary carbohydrate alcohols are unaffected under these conditions, which allows regioselective reactions.

  • 222.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Alonzi, Dominic S.
    Butters, Terry D.
    Carbasugar-thioether pseudodisaccharides related to N-glycan biosynthesis2009Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, nr 4, s. 454-459Artikel i tidskrift (Refereegranskat)
  • 223.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Eriksson, Lars
    Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Bis(methyl 2,4,6-tri-O-acetyl-beta-D-allofuranosid-3-yl)sulfane2007Ingår i: Acta Crystallographica Section E, ISSN 1600-5368, Vol. E63, s. o4197-Artikel i tidskrift (Refereegranskat)
  • 224.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Frigell, Jens
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Pershagen, Elias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Akhtar, Tashfeen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Moreno-Clavijo, Elena
    Robina, Inmaculada
    Alonzi, Dominic S.
    Butters, Terry D.
    Amine-linked diglycosides: Synthesis facilitated by the enhanced reactivity of allylic electrophiles, and glycosidase inhibition assays2011Ingår i: Beilstein Journal of Organic Chemistry, ISSN 2195-951X, E-ISSN 1860-5397, Vol. 7, s. 1-9Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Diglycose derivatives, consisting of two monosaccharides linked at non-anomeric positions by a bridging nitrogen atom, have been synthesised. Conversion of one of the precursor monosaccharide coupling components into an unsaturated derivative enhances its electrophilicity at the allylic position, facilitating coupling reactions. Mitsunobu coupling between nosylamides and 2,3-unsaturated-4-alcohols gave the 4-amino-pseudodisaccharides with inversion of configuration as single regio- and diastereoisomers. A palladium-catalysed coupling between an amine and a 2,3-unsaturated 4-trichloroacetimidate gave a 2-amino-pseudodisaccharide as the major product, along with other minor products. Derivatisation of the C=C double bond in pseudodisaccharides allowed the formation of Man(N4-6)Glc and Man(N4-6)Man diglycosides. The amine-linked diglycosides were found to show weak glycosidase inhibitory activity.

  • 225. Cumpstey, Ian
    et al.
    Frigell, jens
    Pershagen, Elias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Alonzi, D.S.
    Butters, T.D.
    N-linked neodisaccharides: Synthesis facilitated by the enhanced reactivity of allylic electrophiles, and glycosidase inhibitory activityManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Neodisaccharides consisting of two monosaccharides linked by a bridging nitrogen atom have been synthesised. Converting one of the monosaccharide coupling components into an unsaturated derivative enhances its electrophilicity at the allylic position, facilitating coupling reactions. Mitsunobu coupling between nosylamides and 2,3-unsaturated 4-alcohols gave the 4-amino pseudodisaccharides with inversion of configuration as single regio- and diastereoisomers. A palladium catalysed coupling between an amine and a 2,3-unsaturated 4-trichloroacetimidate gave a 2-amino pseudodisaccharide as the major product along with other minor products. Derivatisation of the C=C double bond in pseudodisaccharides allowed the formation of Man(N4–6)Glc and Man(N4–6)Man neodisaccharides. The inhibitory activity of some N-linked neodisaccharides against the enzyme α-Glucosidase II is reported.

  • 226.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Gehrke, Sebastian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Erfan, Sayeh
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cribiù, Riccardo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Studies on the synthesis of valienamine and 1-epi-valienamine starting from D-glucose or L-sorbose2008Ingår i: Carbohydrate Research, ISSN 0008-6215, Vol. 343, nr 10-11, s. 1675-1692Artikel i tidskrift (Refereegranskat)
  • 227.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ramstadius, Clinton
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Akhtar, Tashfeen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Goldstein, Irwin J
    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI .
    Winter, Harry C
    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI .
    Non-glycosidically linked pseudodisaccharides: thioethers, sulfoxides, sulfones, ethers, selenoethers, and their binding to lectins2010Ingår i: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, nr 10, s. 1951-1970Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Hydrolytically stable non-glycosidically linked tail-to-tail pseudodisaccharides are linked by a single bridging atom remote from the anomeric centre of the constituent monosaccharides. Some such pseudodisaccharides with sulfur or oxygen bridges were found to act as disaccharide mimetics in their binding to the Banana Lectin and to Concanavalin A. A versatile synthetic route to a small library of such compounds is described

  • 228.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ramstadius, Clinton
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Borbas, K. Eszter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Investigation of Coupling Reactions for the Synthesis of Valienamine Pseudodisaccharides2011Ingår i: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, nr 12, s. 1701-1704Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Amine-linked pseudodisaccharides based on valienamine were synthesised by C-N bond-forming reactions between valienol-derived C-1 electrophiles and carbohydrate nitrogen nucleophiles. Palladium-catalysed coupling with trichloroacetimidate leaving groups, Mitsunobu reactions with a nosylamide nucleophile, and alkylation of amines by C-1 bromides were investigated.

  • 229.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ramstadius, Clinton
    Borbas, K. Eszter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Alonzi, Dominic S.
    Butters, Terry D.
    Synthesis and alpha-Glucosidase II inhibitory activity of valienamine pseudodisaccharides relevant to N-glycan biosynthesis2011Ingår i: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1090-2120, Vol. 21, nr 18, s. 5219-5223Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Valienol-derived allylic C-1 bromides have been used as carbaglycosyl donors for alpha-xylo configured valienamine pseudodisaccharide synthesis. We synthesised valienamine analogues of the Glc(alpha 1 -> 3)Glc and Glc(alpha 1 -> 3) Man disaccharides representing the linkages cleaved by alpha-Glucosidase II in N-glycan biosynthesis. These (N1 -> 3)-linked pseudodisaccharides were found to have some alpha-Glucosidase II inhibitory activity, while two other (N1 -> 6)-linked valienamine pseudodisaccharides failed to inhibit the enzyme. (C)

  • 230.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ramstadius, Clinton
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Borbas, Katalin Eszter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Alonzi, Dominic
    Oxford University.
    Butters, Terry
    Oxford University.
    Coupling reactions of valienol C-1 electrophiles for valienamine pseudodisaccharide synthesis: synthesis and α-Glucosidase II inhibitory activity of pseudodisaccharides relevant to N-glycan biosynthesisManuskript (preprint) (Övrigt vetenskapligt)
  • 231. Córdova, A
    et al.
    Sundén, H
    Engqvist, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    The Direct Amino Acid-Catalyzed Asymmetric Incorporation of Molecular Oxygen to Organic Compounds2004Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, Vol. 126, nr 29, s. 8914-8915Artikel i tidskrift (Refereegranskat)
  • 232.
    Córdova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Asymmetric amino acid catalysis2008Ingår i: Recent Devlopments in Physical Chemistry, 3rd Mexican Meeting on Mathematical and Experimental Physics, 2008, s. 47-59Konferensbidrag (Refereegranskat)
  • 233.
    Córdova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Asymmetric bifunctional catalysis using heterobimetallic and multimetallic systems in enantioselective conjugate additions2010Ingår i: Catalytic Asymmetric Conjugate Reactions / [ed] Armando Córdova, Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA , 2010, 1, s. 169-190Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 234.
    Córdova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Catalytic Asymmetric Conjugate Reactions2010Samlingsverk (redaktörskap) (Övrigt vetenskapligt)
  • 235.
    Córdova, Armando
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Engqvist, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ibrahem, Ismail
    Casas, Jésus
    Sundén, Henrik
    Plausible origins of homochirality in the amino acid catalyzed neogenesis of carbohydrates2005Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 2005, s. 2047-2049Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The intrinsic ability of amino acids to catalyze the asymmetric formation of carbohydrates, which enzymes have mediated for millions of years, with significant amplification of enantiomeric excess suggests a plausible ancient catalytic process for the evolution of homochirality.

  • 236.
    Córdova, Armando
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ibrahem, Ismail
    Casas, Jesús
    Sundén, Henrik
    Engqvist, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Reyes, Efraim
    Amino Acid-Catalyzed Neogenesis of Carbohydrates: A Plausible Ancient Transformation2005Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 11, nr 16, s. 4772-4784Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Hexose sugars play a fundamental role in vital biochemical processes and their biosynthesis is achieved through enzyme-catalyzed pathways. Herein we disclose the ability of amino acids to catalyze the asymmetric neogenesis of carbohydrates by sequential cross-aldol reactions. The amino acids mediate the asymmetric de novo synthesis of natural L- and D-hexoses and their analogues with excellent stereoselectivity in organic solvents. In some cases, the four new stereocenters are assembled with almost absolute stereocontrol. The unique feature of these results is that, when an amino acid is employed as the catalyst, a single reaction sequence can convert a protected glycol aldehyde into a hexose in one step. For example, proline and its derivatives catalyze the asymmetric neogenesis of allose with >99 % ee in one chemical manipulation. Furthermore, all amino acids tested catalyzed the asymmetric formation of natural sugars under prebiotic conditions, with alanine being the smallest catalyst. The inherent simplicity of this catalytic process suggests that a catalytic prebiotic “gluconeogenesis” may occur, in which amino acids transfer their stereochemical information to sugars. In addition, the amino acid catalyzed stereoselective sequential cross-aldol reactions were performed as a two-step procedure with different aldehydes as acceptors and nucleophiles. The employment of two different amino acids as catalysts for the iterative direct aldol reactions enabled the asymmetric synthesis of deoxysugars with >99 % ee. In addition, the direct amino acid catalyzed C2+C2+C2 methodology is a new entry for the short, highly enantioselective de novo synthesis of carbohydrate derivatives, isotope-labeled sugars, and polyketide natural products. The one-pot asymmetric de novo syntheses of deoxy and polyketide carbohydrates involved a novel dynamic kinetic asymmetric transformation (DYKAT) mediated by an amino acid.

  • 237.
    Córdova, Armando
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Rios, Ramón
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Direct Catalytic Asymmetric Mannich Reactions and Surroundings2008Ingår i: Amino Group Chemistry. From Synthesis to the Life Sciences., Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim , 2008, s. 185-205Kapitel i bok, del av antologi (Refereegranskat)
  • 238.
    Córdova, Armando
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Rios, Ramón
    The University of Barcelona, Departament Química Orgànica.
    Highly Z- and enantioselective ring-opening/cross-metathesis reactions and Z-selective ring-opening metathesis polymerization2009Ingår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 48, nr 47, s. 8827-8831Artikel i tidskrift (Refereegranskat)
  • 239. Daikoku, S.
    et al.
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kanie, Y.
    Ito, Y.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kanie, O.
    Synthesis and structural investigation of a series of mannose-containing oligosaccharides using mass spectrometry2018Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 16, nr 2, s. 228-238Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A series of compounds associated with naturally occurring and biologically relevant glycans consisting of alpha-mannosides were prepared and analyzed using collision-induced dissociation (CID), energy-resolved mass spectrometry (ERMS), and H-1 nuclear magnetic resonance spectroscopy. The CID experiments of sodiated species of disaccharides and ERMS experiments revealed that the order of stability of mannosyl linkages was as follows: 6-linked > 4-linked >= 2-linked > 3-linked mannosyl residues. Analysis of linear trisaccharides revealed that the order observed in disaccharides could be applied to higher glycans. A branched trisaccharide showed a distinct dissociation pattern with two constituting disaccharide ions. The estimation of the content of this ion mixture was possible using the disaccharide spectra. The hydrolysis of mannose linkages at 3- and 6-positions in the branched trisaccharide revealed that the 3-linkage was cleaved twice as fast as the 6-linkage. It was observed that the solution-phase hydrolysis and gas-phase dissociation have similar energetics.

  • 240. Daikoku, Shusaku
    et al.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kanie, Osamu
    Analysis of a series of isomeric oligosaccharides by energy-resolved mass spectrometry: a challenge on homobranched trisaccharides2009Ingår i: Rapid Communications in Mass Spectrometry, ISSN 0951-4198, E-ISSN 1097-0231, Vol. 23, nr 23, s. 3713-3719Artikel i tidskrift (Refereegranskat)
  • 241.
    Das, Arindam
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wang, Dong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Belhomme, Marie-Charlotte
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Copper-Catalyzed Cross-Coupling of Allylboronic Acids with alpha-Diazoketones2015Ingår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 17, nr 19, s. 4754-4757Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Copper-catalyzed cross-coupling of substituted allylboronic acids with alpha-diazoketones was studied. This allylation reaction is highly regioselective, providing the branched allylic product. The process involves creation of a new C(sp(3))-C(sp(3)) bond by retaining the keto functional group of the alpha-diazoketone precursor.

  • 242. Das, Biswanath
    et al.
    Daver, Henrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Pyrkosz-Bulska, Monika
    Gumienna-Kontecka, Elzbieta
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Nordlander, Ebbe
    An Unsymmetric Ligand with a N5O2 Donor Set and Its Corresponding Dizinc Complex: A Structural and Functional Phosphoesterase Model2018Ingår i: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, nr 36, s. 4004-4013Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To mimic the active sites of the hydrolytic enzyme zinc phosphotriesterase, a new dinucleating unsymmetric ligand, PICIMP (2-{[2-hydroxy-5-methyl-3-({[(1-methyl-1H-imidazol-2-yl)methyl](pyridin-2-ylmethyl)amino}methyl)benzyl][(1-methyl-1H-imidazol-2-yl)methyl]amino}acetic acid), has been synthesized and characterized. The hydrolytic efficacy of the complex solution (PICIMP/ZnCl2 = 1:2) has been investigated using bis-(2,4-dinitrophenyl)phosphate (BDNPP), a DNA analogue substrate. Speciation studies were undertaken by potentiometric titrations at varying pH for both the ligand and the corresponding dizinc complex to elucidate the formation of the active hydrolysis catalyst; these studies reveal that the dinuclear zinc(II) complexes, [Zn-2(PICIMP)](2+) and [Zn-2(PICIMP)(OH)](+) predominate in solution above pH 4. The obtained pK(a) of 7.44 for the deprotonation of water suggests formation of a bridging hydroxide between the two Zn-II ions. Kinetic investigations of BDNPP hydrolysis over the pH range 5.5-10.5 have been performed. The cumulative results indicate the hydroxo-bridged dinuclear Zn-II complex [Zn-2(PICIMP)(mu-OH)](+) as the effective catalyst. Density functional theory calculations were performed to investigate the detailed reaction mechanism. The calculations suggest that the bridging hydroxide becomes terminally coordinated to one of the zinc ions before performing the nucleophilic attack in the reaction.

  • 243. Das, Biswanath
    et al.
    Daver, Henrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Pyrkosz-Bulska, Monika
    Persch, Elke
    Barman, Suman K.
    Mukherjee, Rabindranath
    Gumienna-Kontecka, Elzbieta
    Jarenmark, Martin
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Nordlander, Ebbe
    A dinuclear zinc(II) complex of a new unsymmetric ligand with an N(5)0(2) donor set; A structural and functional model for the active site of zinc phosphoesterases2014Ingår i: Journal of Inorganic Biochemistry, ISSN 0162-0134, E-ISSN 1873-3344, Vol. 132, s. 6-17Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The dinuclear complex [Zn-2(DPCPMP)(pivalate)](C10(4)), where DPCPMP is the new unsymmetrical ligand [2-(N-(3-((bis((pyridin-2-yl)methyl)amino)methyl)-2-hydroxy-5-methylbenzyl)-N-((pyridin2-y1)methyl)amino)acetic acid], has been synthesized and characterized. The complex is a functional model for zinc phosphoesterases with dinuclear active sites. The hydrolytic efficacy of the complex has been investigated using bis-(2,4-dinitrophenyl)phosphate(BDNPP), a DNA analog, as substrate. Speciation studies using potentiometric titrations have been performed for both the ligand and the corresponding dizinc complex to elucidate the formation of the active hydrolysis catalyst; they reveals that the dinuclear zinc(II) complexes, [Zn-2(DPCPMP)](2) and [Zn-2(DPCPMP)(OH)1 predominate the solution above pH 4. The relatively high pKa of 8.38 for water deprotonation suggests that a terminal hydroxide complex is formed. Kinetic investigations of BDNPP hydrolysis over the pH range 5.5-11.0 and with varying metal to ligand ratio (metal salt:ligand = 0.5:1 to 3:1) have been performed. Variable temperature studies gave the activation parameters triangle H double dagger = 95.6 kJ mol(-1), triangle S double dagger = 44.8 J mo1(-1) K-1, and 6,triangle G double dagger = 108.0 kJ mo1-1. The cumulative results indicate the hydroxido-bridged dinuclear Zn(II) complex [Zn-2(DPCPMP)(mu-OH)] (+) as the effective catalyst. The mechanism of hydrolysis has been probed by computational modeling using density functional theory (DFF). Calculations show that the reaction goes through one concerted step (S(N)2 type) in which the bridging hydroxide in the transition state becomes terminal and performs a nucleophilic attack on the BDNPP phosphorus; the leaving group dissociates simultaneously in an overall inner sphere type activation. The calculated free energy barrier is in good agreement with the experimentally determined activation parameters.

  • 244. Das, Biswanath
    et al.
    Daver, Henrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Singh, Amrendra
    Singh, Reena
    Haukka, Matti
    Demeshko, Serhiy
    Meyer, Franc
    Lisensky, George
    Jarenmark, Martin
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Nordlander, Ebbe
    A Heterobimetallic FeIIIMnII Complex of an Unsymmetrical Dinucleating Ligand: A Structural and Functional Model Complex for the Active Site of Purple Acid Phosphatase of Sweet Potato2014Ingår i: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, Vol. 2014, nr 13, s. 2204-2212Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The heterodinuclear mixed-valence complex [FeMn(ICIMP)(OAc)(2)Cl] (1) {H2ICIMP = 2-(N-carboxylmethyl)-[N-(N-methylimidazolyl-2-methyl)aminomethyl]-[6-(N-isopropylmethyl)-[N-(N-methylimidazolyl-2-methyl)]aminomethyl-4-methylphenol], an unsymmetrical N4O2 donor ligand} has been synthesized and fully characterized by several spectroscopic techniques as well as by X-ray crystallography. The crystal structure of the complex reveals that both metal centers in 1 are six-coordinate with the chloride ion occupying the sixth coordination site of the Mn-II ion. The phenoxide moiety of the ICIMP ligand and both acetate ligands bridge the two metal ions of the complex. Mossbauer spectroscopy shows that the iron ion in 1 is high-spin Fe-III. Two quasi-reversible redox reactions for the complex, attributed to the (FeMnII)-Mn-III/(FeMnII)-Mn-II (at -0.67 V versus Fc/Fc(+)) and (FeMnII)-Mn-III/(FeMnIII)-Mn-III (at 0.84 V), were observed by means of cyclic voltammetry. Complex 1, with an Fe-III-Mn-II distance of 3.58 angstrom, may serve as a model for the mixed-valence oxidation state of purple acid phosphatase from sweet potato. The capability of the complex to effect organophosphate hydrolysis (phosphatase activity) has been investigated at different pH levels (5.5-11) by using bis(2,4-dinitrophenyl)phosphate (BDNPP) as the substrate. Density functional theory calculations indicate that the substrate coordinates to the Mn-II ion. In the transition state, a hydroxide ion that bridges the two metal ions becomes terminally coordinated to the Fe-III ion and acts as a nucleophile, attacking the phosphorus center of BDNPP with the concomitant dissociation of the leaving group.

  • 245. Das, Biswanath
    et al.
    Lee, Bao-Lin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Karlsson, Erik A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Torbjörn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Shatskiy, Andrey
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Demeshko, Serhiy
    Liao, Rong-Zhen
    Laine, Tanja M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Haukka, Matti
    Zeglio, Erica
    Abdel-Magied, Ahmed F.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Meyer, Franc
    Kärkäs, Markus D.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Johnston, Eric V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Nordlander, Ebbe
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Water oxidation catalyzed by molecular di- and nonanuclear Fe complexes: importance of a proper ligand framework2016Ingår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 45, nr 34, s. 13289-13293Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The synthesis of two molecular iron complexes, a dinuclear iron(III,III) complex and a nonanuclear iron complex, based on the di-nucleating ligand 2,2'-(2-hydroxy-5-methyl-1,3-phenylene)bis(1H-benzo[d]imidazole-4-carboxylic acid) is described. The two iron complexes were found to drive the oxidation of water by the one-electron oxidant [Ru(bpy)(3)](3+).

  • 246.
    Daver, Henrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Quantum Chemical Modelling of Biomimetic Phosphoesterase Complexes2015Licentiatavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Phosphoesterases are a class of enzymes that catalyze hydrolysis of phosphoester bonds. They facilitate the modification of nucleic acid sequences, as well as the breakdown of rest products of warfare agents and insecticides. In this thesis, three biomimetic complexes that perform the same tasks are studied using density functional theory.

    Two of the catalysts contain a dizinc core while the third binds an Fe(III) ion and a Mn(II)ion. These complexes catalyze the hydrolysis of the phosphodiester substrate bis-(2,4)-dinitrophenyl phosphate (BDNPP). The substrate is analogous to the phosphoric link between two nucleotides in DNA, and the system is thus a model for cleaving bonds between nucleotides.

    By means of computational modelling, the reaction mechanisms are investigated in detail. Different binding modes of the substrates to the catalysts are considered and several mechanistic proposals are evaluated. Conclusions are drawn on the basis of free energy barriers calculated for the different mechanisms.

    In all studied reactions, a hydroxide bridging the metals becomes terminally coordinated to one of the zinc ions and then attacks the phosphorus center in a nucleophilic fashion. Leaving group dissociation takes place without a barrier.

    One of the catalysts was also studied binding a model substrate for RNA, namely hydroxy-2-isopropyl p-nitrophenyl phosphate (HPNP). The hydroxide was found to act as a base, activating the alcohol moiety of the substrate which in turn performs the nucleophilic attack on the phosphorus center.

    Common for all studied systems is that the catalyst-product complex is calculated to be the most stable species. Hence, this complex is suggested to be the resting state of the catalytic cycle. The free energy barriers of the reactions are associated with going from the catalystproduct complex of one catalytic cycle to the transition state for nucleophilic attack in the next. Calculated barriers are in good agreements with experiments.

  • 247.
    Daver, Henrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Algarra, Andrés G.
    Rebek, Jr., Julius
    Harvey, Jeremy N.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Toward Accurate Quantum Chemical Modeling of Water-Soluble Self-Assembled CapsulesManuskript (preprint) (Övrigt vetenskapligt)
  • 248.
    Daver, Henrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Algarra, Andrés G.
    Rebek, Julius
    Harvey, Jeremy N.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mixed Explicit-Implicit Solvation Approach for Modeling of Alkane Complexation in Water-Soluble Self-Assembled Capsules2018Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, nr 39, s. 12527-12537Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The host-guest binding properties of a water-soluble resorcinarene-based cavitand are examined using density functional theory methodology. Experimentally, the cavitand has been observed to self-assemble in aqueous solution into both 1:1 and 2:1 host/guest complexes with hydrophobic guests such as n-alkanes. For n-decane, equilibrium was observed between the 1:1 and 2:1 complexes, while 1:1 complexes are formed with shorter n-alkanes and 2:1 complexes are formed with longer ones. These findings are used to assess the standard quantum chemical methodology. It is first shown that a rather advanced com- putational protocol (B3LYP-D3(BJ)/6-311+G(2d,2p) with COSMO-RS and quasi-rigid-rotor-harmonic-oscillator) gives very large errors. Systematic examination of the various elements of the methodology shows that the error stems from the implicit solvation model. A mixed explicit-implicit solvation protocol is developed that involves a parametrization of the hydration free energy of water such that water cluster formation in water is predicted to be thermoneutral. This new approach is demonstrated to lead to a major improvement in the calculated binding free energies of n-alkanes, reproducing very well the 1:1 versus 2:1 host/guest binding trends.

  • 249.
    Daver, Henrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Das, Biswanath
    Nordlander, Ebbe
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Theoretical Study of Phosphodiester Hydrolysis and Transesterification Catalyzed by an Unsymmetric Biomimetic Dizinc Complex2016Ingår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 55, nr 4, s. 1872-1882Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Density functional theory calculations have been used to investigate the reaction mechanisms of phosphodiester hydrolysis and transesterification catalyzed by a dinuclear zinc complex of the 2-(N-isopropyl-N-((2-pyridyl)methyl)-aminomethyl)-6-(N-(carboxylmethyl)-N-((2-pyridyl)methyl)amino-methyl)-4-methylphenol (IPCPMP) ligand, mimicking the active site of zinc phosphotriesterase. The substrates bis(2,4)-dinitrophenyl phosphate (BDNPP) and 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) were employed as analogues of DNA and RNA, respectively. A number of different mechanistic proposals were considered, with the active catalyst harboring either one or two hydroxide ions. It is concluded that for both reactions the catalyst has only one hydroxide bound, as this option yields lower overall energy barriers. For BDNPP hydrolysis, it is suggested that the hydroxide acts as the nucleophile in the reaction, attacking the phosphorus center of the substrate. For HPNP transesterification, on the other hand, the hydroxide is proposed to act as a Bronsted base, deprotonating the alcohol moiety of the substrate, which in turn performs the nucleophilic attack. The calculated overall barriers are in good agreement with measured rates. Both reactions are found to proceed by essentially concerted associative mechanisms, and it is demonstrated that two consecutive catalytic cycles need to be considered in order to determine the rate-determining free energy barrier.

  • 250.
    Daver, Henrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Harvey, Jeremy N.
    Rebek, Jr., Julius
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Quantum Chemical Modeling of Cycloaddition Reaction in a Self-Assembled Capsule2017Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, nr 43, s. 15494-15503Artikel i tidskrift (Refereegranskat)
    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.

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