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  • 1. Afewerki, Samson
    et al.
    Breistein, Palle
    Deiana, Luca
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dziedzic, Pawel
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ibrahem, Ismail
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Catalytic enantioselective β -alkylation of α,β-unsaturated aldehydes by combination of transition-metal- and aminocatalysis: Total synthesis of bisabolane sesquiterpenes2011In: Chemistry: a European Journal, ISSN 0947-6539, Vol. 17, no 32, p. 8784-8788Article in journal (Refereed)
  • 2.
    Ahlford, Katrin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Amino acid-derived amides and hydroxamic acids as ligands for asymmetric transfer hydrogenation in aqueous media2011In: Catalysis communications, ISSN 1566-7367, E-ISSN 1873-3905, Vol. 12, no 12, p. 1118-1121Article in journal (Refereed)
    Abstract [en]

    Amides and hydroxamic acids derived from α-amino acids were evaluated as ligands in combination with rhodium and iridium half-sandwich complexes in asymmetric transfer hydrogenation (ATH) of ketones. The reactions were performed in aqueous media using lithium formate as hydride source. The catalyst systems turned out to be highly efficient and ees up to 90% were obtained.

  • 3.
    Ahlsten, Nanna
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bartoszewicz, Agnieszka
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Agrawal, Santosh
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martin-Matute, Belen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    A facile synthesis of α-fluoro ketones catalyzed by [Cp*IrCl2](2)2011In: Synthesis (Stuttgart), ISSN 0039-7881, E-ISSN 1437-210X, no 16, p. 2600-2608Article in journal (Refereed)
    Abstract [en]

    Allylic alcohols are isomerized into enolates (enols) by [Cp*IrCl2]2. The enolates react with Selectfluor present in the reaction media. This method produces α-fluoro ketones as single constitutional isomers in high yields.

  • 4.
    Ahlsten, Nanna
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martin-Matute, Belen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ir-catalysed formation of C-F bonds. From allylic alcohols to α-fluoroketones2011In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 47, no 29, p. 8331-8333Article in journal (Refereed)
    Abstract [en]

    A novel iridium-catalysed tandem isomerisation/C-F bond formation from allylic alcohols and Selectfluor® to prepare α-fluorinated ketones as single constitutional isomers is reported.

  • 5. Ai, Yue-Jie
    et al.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chen, Shi-Lu
    Hua, Wei-Jie
    Fang, Wei-Hai
    Luo, Yi
    Repair of DNA Dewar Photoproduct to (6-4) Photoproduct in (6-4) Photolyase2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 37, p. 10976-10982Article in journal (Refereed)
    Abstract [en]

    Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.

  • 6. Ai, Yue-jie
    et al.
    Tian, Guangjun
    Liao, Rong-zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhang, Qiong
    Fang, Wei-hai
    Luo, Yi
    Intrinsic Property of Flavin Mononucleotide Controls its Optical Spectra in Three Redox States2011In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, no 16, p. 2899-2902Article in journal (Refereed)
  • 7.
    Bacsik, Zoltan
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Ahlsten, Nanna
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ziadi, Asraa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhao, Guoying
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Garcia-Bennett, Alfonso E.
    Uppsala universitet.
    Martin-Matute, Belen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hedin, Niklas
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Mechanisms and Kinetics for Sorption of CO(2) on Bicontinuous Mesoporous Silica Modified with n-Propylamine2011In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 27, no 17, p. 11118-11128Article in journal (Refereed)
    Abstract [en]

    We studied equilibrium adsorption and uptake kinetics and identified molecular species that formed during sorption of carbon dioxide on amine-modified silica. Bicontinuous silicas (AMS-6 and MCM-48) were postsynthetically modified with (3-aminopropyl)triethoxysilane or (3-aminopropyl)methyldiethoxysilane, and amine-modified AMS-6 adsorbed more CO(2) than did amine-modified MCM-48. By in situ FTIR spectroscopy, we showed that the amine groups reacted with CO(2) and formed ammonium carbamate ion pairs as well as carbamic acids under both dry and moist conditions. The carbamic acid was stabilized by hydrogen bonds, and ammonium carbamate ion pairs formed preferably on sorbents with high densities of amine groups. Under dry conditions, silylpropylcarbamate formed, slowly, by condensing carbamic acid and silanol groups. The ratio of ammonium carbamate ion pairs to silylpropylcarbamate was higher for samples with high amine contents than samples with low amine contents. Bicarbonates or carbonates did not form under dry or moist conditions. The uptake of CO(2) was enhanced in the presence of water, which was rationalized by the observed release of additional amine groups under these conditions and related formation of ammonium carbamate ion pairs. Distinct evidence for a fourth and irreversibly formed moiety was observed under sorption of CO(2) under dry conditions. Significant amounts of physisorbed, linear CO(2) were detected at relatively high partial pressures of CO(2), such that they could adsorb only after the reactive amine groups were consumed.

  • 8.
    Bogár, Krisztián
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Krumlinde, Patrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bacsik, Zoltán
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hedin, Niklas
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Bäckvall, Jan E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Heterogenized Wilkinson's Catalyst for Transfer Hydrogenation of Carbonyl Compounds2011In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 23, p. 4409-4414Article in journal (Refereed)
    Abstract [en]

    Wilkinson’s catalyst [RhCl(PPh3)3] was heterogenized on common silica by the use of a grafting/anchoring technique. The immobilized catalyst showed high activity and selectivity in transfer hydrogenation reactions of a range of carbonyl compounds in 2-propanol. Reactions carried out in 2-propanol at reflux afforded the corresponding alcohols in high yields in short reaction times. The heterogeneous feature ofthe catalyst allows for easy recovery and efficient reuse in the same reaction up to 5 times without any detectible loss of catalytic activity.

  • 9.
    Buitrago, Elina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zani, Lorenzo
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Selective hydrosilylation of ketones catalyzed by in situ-generated iron NHC complexes2011In: Applied organometallic chemistry, ISSN 0268-2605, E-ISSN 1099-0739, Vol. 25, no 10, p. 748-752Article in journal (Refereed)
    Abstract [en]

    Aryl alkyl-, heteroaryl alkyl- and dialkyl ketones were readily reduced to their corresponding secondary alcohols in high yields, using the commercially available and inexpensive polymeric silane polymethylhydrosiloxane (PMHS), as reducing agent. The reaction is catalyzed by an in situ-generated iron complex, conveniently generated from iron(II) acetate and the commercially available N-heterocyclic carbene (NHC) precursor IPr·HCl.

  • 10. Chojnacka, Kinga
    et al.
    Santoro, Stefano
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Awartani, Radi
    Richards, Nigel G. J.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Aponick, Aaron
    Synthetic studies on the solanacol ABC ring system by cation-initiated cascade cyclization: implications for strigolactone biosynthesis2011In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 9, no 15, p. 5350-5353Article in journal (Refereed)
    Abstract [en]

    We report a new method for constructing the ABC ringsystem of strigolactones, in a single step from a simple linearprecursor by acid-catalyzed double cyclization. The reactionproceeds with a high degree of stereochemical control, whichcan be qualitatively rationalized usingDFT calculations. Ourconcise synthetic approach offers a new model for thinkingabout the (as yet) unknown chemistry that is employed in thebiosynthetic pathways leading to this class of plant hormones.

  • 11. Coll, Mercedes
    et al.
    Pàmies, Oscar
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Diéguez, Montserrat
    Carbohydrate-based pseudo-dipeptides: new ligands for the highly enantioselective Ru-catalyzed transfer hydrogenation reaction2011In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 47, no 44, p. 12188-12190Article in journal (Refereed)
    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.

  • 12.
    Cumpstey, Ian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Neodisaccharide diglycosyl compounds: Ethers, thioethers and selenoethers. A survey of their synthesis and biological activity2011In: Comptes rendus. Chimie, ISSN 1631-0748, E-ISSN 1878-1543, Vol. 14, no 2-3, p. 274-285Article in journal (Refereed)
    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.

  • 13.
    Cumpstey, Ian
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Agrawal, Santosh
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Borbas, K. Eszter
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martín-Matute, Belén
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Iridium-catalysed condensation of alcohols and amines as a method for aminosugar synthesis2011In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 47, no 27, p. 7827-7829Article in journal (Refereed)
    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.

  • 14.
    Cumpstey, Ian
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Frigell, Jens
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pershagen, Elias
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Akhtar, Tashfeen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    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 assays2011In: Beilstein Journal of Organic Chemistry, ISSN 2195-951X, E-ISSN 1860-5397, Vol. 7, p. 1-9Article in journal (Refereed)
    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.

  • 15.
    Cumpstey, Ian
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ramstadius, Clinton
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Borbas, K. Eszter
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Investigation of Coupling Reactions for the Synthesis of Valienamine Pseudodisaccharides2011In: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, no 12, p. 1701-1704Article in journal (Refereed)
    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.

  • 16.
    Cumpstey, Ian
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ramstadius, Clinton
    Borbas, K. Eszter
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Alonzi, Dominic S.
    Butters, Terry D.
    Synthesis and alpha-Glucosidase II inhibitory activity of valienamine pseudodisaccharides relevant to N-glycan biosynthesis2011In: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1090-2120, Vol. 21, no 18, p. 5219-5223Article in journal (Refereed)
    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)

  • 17.
    Deiana, Luca
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dziedzic, Pawel
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhao, Gui-Ling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Vesely, Jan
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ibrahem, Ismail
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rios, Ramón
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry, Structural Chemistry.
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Catalytic asymmetric aziridination of α,β-unsaturated aldehydes2011In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 17, no 28, p. 7904-7917Article in journal (Refereed)
    Abstract [en]

    The development, scope, and application of the highly enantioselective organocatalytic aziridination of α,β-unsaturated aldehydes is presented. The aminocatalytic azirdination of α,β-unsaturated aldehydes enables the asymmetric formation of β-formyl aziridines with up to >19:1 d.r. and 99% ee. The aminocatalytic aziridination of α-monosubstituted enals gives access to terminal α-substituted-α-formyl aziridines in high yields and upto 99% ee. In the case of the organocatalytic aziridination of disubstituted α,β-unsaturated aldehydes, the transformations were highly diastereo- and enantioselective and give nearly enantiomerically pure β-formyl-functionalized aziridine products (99% ee). A highly enantioselective one-pot cascade sequence based on the combination of asymmetric amine and N-heterocycliccarbene catalysis (AHCC) is also disclosed. This one-pot three-component co-catalytic transformation between α,β-unsaturated aldehydes, hydroxylamine derivatives, and alcohols gives the corresponding N-tert-butoxycarbonyl and N-carbobenzyloxy-protected β-amino acid esters with ee values ranging from 92–99%. The mechanisms and stereochemistry of all these catalytic transformations are also discussed.

  • 18.
    Endo, Yoshinori
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Aerobic Lactonization of Diols by Biomimetic Oxidation2011In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 17, no 45, p. 12596-12601Article in journal (Refereed)
  • 19.
    Engström, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Shakeri, Mozaffar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dynamic Kinetic Resolution of β-Amino Esters by a Heterogeneous System of a Palladium Nanocatalyst and Candida antarctica Lipase A2011In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 10, p. 1827-1830Article in journal (Refereed)
    Abstract [en]

    A dynamic kinetic resolution (DKR) of β-amino esters have been developed by the use of a heterogeneous racemization catalyst and an immobilized enzyme that accepts aromatic, heteroaromatic and aliphatic substrates. The reaction conditions were optimized to yield an efficient catalytic system without by-product formation. The products are obtained in 96–99 % ee and high yields

  • 20.
    Engström, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Vallin, Michaela
    Syrén, Per-Olof
    Hult, Karl
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mutated variant of Candida antarctica lipase B in (S)-selective dynamickinetic resolution of secondary alcohols2011In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 9, no 1, p. 81-82Article in journal (Refereed)
    Abstract [en]

    An (S)-selective dynamic kinetic resolution of secondaryalcohols, employing a mutated variant of Candida antarcticalipase B (CalB) gave products in 84–88% yield and in 90–97%ee.

  • 21. Foster, R. A.
    et al.
    Carlin, N. I. A.
    Majcher, M.
    Tabor, H.
    Ng, L.-K.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural elucidation of the O-antigen of the Shigella flexneri provisionalserotype 88-893: structural and serological similarities with S. flexneri provisional serotype Y394 (1c)2011In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, no 6, p. 872-876Article in journal (Refereed)
    Abstract [en]

    The structure of the repeating unit of the O-antigen polysaccharide from Shigella flexneri provisional serotype 88-893 has been determined. 1H and 13C NMR spectroscopy as well as 2D NMR experiments were employed to elucidate the structure. The carbohydrate part of the hexasaccharide repeating unit is identical to the previously elucidated structure of the O-polysaccharide from S. flexneri prov. serotype Y394. The O-antigen of S. flexneri prov. serotype 88-893 carries 0.7 mol O-acetyl group per repeating unit located at O-2 of the 3-substituted rhamnosyl residue, as identified by H2BC and BS-CT-HMBC NMR experiments. The O-antigen polysaccharide is composed of hexasaccharide repeating units with the following structure: →2)-α-l-Rhap-(1→2)-α-l-Rhap-(1→3)-α-l-Rhap2Ac-(1→3)[α-d-Glcp-(1→2)-α-d-Glcp-(1→4)]-β-d-GlcpNAc-(1→. Serological studies showed that type antigens for the two provisional serotypes are identical; in addition 88-893 expresses S. flexneri group factor 6 antigen. We propose that provisional serotypes Y394 and 88-893 be designated as two new serotypes 7a and 7b, respectively, in the S. flexneri typing scheme.

  • 22.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Cumpstey, Ian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Carbasugar analogues of galactofuranosides: beta-O-linked derivatives and towards beta-S-linked derivatives2011In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, no 11, p. 1277-1290Article in journal (Refereed)
    Abstract [en]

    A selectively protected carbasugar analogue of beta-galactofuranose was synthesised from glucose using ring-closing metathesis as the key step. The carbasugar was converted into an alpha-galacto configured 1,2-epoxide, which was an effective electrophile in Lewis acid catalysed coupling reactions with alcohols. The epoxide was opened with regioselective attack at C-1 to give beta-galacto configured C-1 ethers. Using carbohydrates as nucleophiles, we synthesised a number of pseudodisaccharides. The epoxide was also regioselectively opened at C-1 with a sulfur nucleophile under basic conditions to give a beta-galacto configured C-1 thioether.

  • 23.
    Frigell, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pearcey, Jean A.
    Lowary, Todd L.
    Cumpstey, Ian
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Carbasugar Analogues of Galactofuranosides: Pseudodisaccharide Mimics of Fragments of Mycobacterial Arabinogalactan2011In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 7, p. 1367-1375Article in journal (Refereed)
    Abstract [en]

    A partially protected carbasugar analogue of beta-galactofuranose was converted into an alpha-galacto-configured 1,2-epoxide, which was opened by alcohols under Lewis acid catalysis with regioselective attack at C-1 to give beta-galacto-configured C-1 ethers. Using OH-5 and OH-6 carbagalactofuranose derivatives as nucleophiles, we synthesised pseudodisaccharide analogues of substructures of the arabinogalactan from M. tuberculosis. The dicarba analogue of the disaccharide Galf(beta 1 -> 5) Galf was found to moderately inhibit the action of GlfT2 galactofuranosyl transferase from M. tuberculosis.

  • 24.
    Gao, Weiming
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Li, Mingrun
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Romare, Kristina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Licheng
    Royal Institute of Technology (KTH), Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of a [3Fe2S] cluster with low redox potential from [2Fe2S] hydrogenase models: electrochemical and photochemical generation of hydrogen2011In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, Vol. 2011, no 7, p. 1100-1105Article in journal (Refereed)
    Abstract [en]

    In the attempted replacement of carbon monoxide by the bis(phosphane) dppv in a dinuclear [2Fe2S] complex, a trinuclear [3Fe2S] complex with two bis(phosphane) ligands was unexpectedly obtained. On protonation, this gave a bridged hydride complex with an unusually low potential for the reduction of protons to molecular hydrogen. The redox potential also appears sufficiently positive for direct electron transfer from an excited [Ru(bpy)(3)](2+) sensitizer.

  • 25.
    Goncalves, Sylvie
    et al.
    Universite de Strasbourg, Faculte de Pharmacie UMR/CNRS 7199, Laboratoire des Systemes Chimiques Fonctionnels, Illkirch, France.
    Santoro, Stefano
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nicolas, Marc
    Les Laboratoires Pierre Fabre, Centre de Developpement Chimique et Industriel, Gaillac, France.
    Wagner, Alain
    Universite de Strasbourg, Faculte de Pharmacie UMR/CNRS 7199, Laboratoire des Systemes Chimiques Fonctionnels, Illkirch, France.
    Maillos, Philippe
    Les Laboratoires Pierre Fabre, Centre de Developpement Chimique et Industriel, Gaillac, France.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Baati, Rachid
    Universite de Strasbourg, Faculte de Pharmacie UMR/CNRS 7199, Laboratoire des Systemes Chimiques Fonctionnels, Illkirch, France.
    Cationic cyclization of 2-alkenyl-1,3-dithiolanes: DiastereoselectiveSynthesis of trans-decalins2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 9, p. 3274-3285Article in journal (Refereed)
    Abstract [en]

    An unprecedented and highly diastereoselective 6-endo-trig cyclization of 2-alkenyl-1,3-dithiolanes has beendeveloped yielding trans-decalins, an important scaffold present in numerous di- and triterpenes. The novelty of this 6-endo-trigc yclization stands in the stepwise mechanism involving 2-alkenyl-1,3-dithiolane, acting as a novel latent initiator. It is suggested that the thioketal opens temporarily under the influence of TMSOTf, triggering the cationic 6-endo-trig cyclization, andcloses after C−C bond formation and diastereoselective protonation to terminate the process. DFT calculations confirm this mechanistic proposal and provide a rationale for the observed diastereoselectivity. The reaction tolerates a wide range of functionalities and nucleophilic partners within the substrate. We have also shown that the one-pot 6-endo-trig cyclization followedby in situ 1,3-dithiolane deprotection afford directly the corresponding ketone. This improvement allowed the achievement of the shortest total synthesis of triptophenolide and the shortest formal synthesis of triptolide.

  • 26. Hatcher, Elizabeth
    et al.
    Säwén, Elin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    MacKerell, Jr., Alexander D.
    Conformational properties of methyl β-maltoside and methyl α- and β-cellobioside disaccharides2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 3, p. 597-608Article in journal (Refereed)
    Abstract [en]

    An investigation of the conformational properties of methyl β-maltoside, methyl α-cellobioside, and methyl β-cellobioside disaccharides using NMR spectroscopy and molecular dynamics (MD) techniques, is presented. Emphasis is placed on validation of a recently presented force field for hexopyranose disaccharides followed by elucidation of the conformational properties of two different types of glycosidic linkages, α-(1 → 4) and β-(1 → 4). Both gas-phase and aqueous-phase simulations are performed to gain insight into the effect of solvent on the conformational properties. A number of transglycosidic J-coupling constants and proton−proton distances are calculated from the simulations and are used to identify the percent sampling of the three glycosidic conformations (syn, anti-, and anti-ψ) and, in turn, describe the flexibility around the glycosidic linkage. The results show the force field to be in overall good agreement with experiment, although some very small limitations are evident. Subsequently, a thorough hydrogen bonding analysis is performed to obtain insights into the conformational properties of the disaccharides. In methyl β-maltoside, competition between HO2′−O3 intramolecular hydrogen bonding and intermolecular hydrogen bonding of those groups with solvent leads to increased sampling of syn, anti-, and anti-ψ conformations and better agreement with NMR J-coupling constants. In methyl α- and β-cellobioside, O5′−HO6 and HO2′−O3 hydrogen bonding interactions are in competition with intermolecular hydrogen bonding involving the solvent molecules. This competition leads to retention of the O5′−HO3 hydrogen bond and increased sampling of the syn region of the /ψ map. Moreover, glycosidic torsions are correlated to the intramolecular hydrogen bonding occurring in the molecules. The present results verify that in the β-(1 → 4)-linkage intramolecular hydrogen bonding in the aqueous phase is due to the decreased ability of water to successfully compete for the O5′ and HO3 hydrogen bonding moieties, in contrast to that occurring between the O5′ and HO6 atoms in this α-(1 → 4)-linkage.

  • 27. Ibrahem, Ismail
    et al.
    Breistein, Palle
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    One-Pot Three-Component Catalytic Enantioselective Synthesis of Homoallylboronates2011In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, no 50, p. 12036-12041Article in journal (Refereed)
  • 28. Ibrahem, Ismail
    et al.
    Santoro, Stefano
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Enantioselective conjugate silyl additions to α,β-unsaturated aldehydes catalyzed by combination of transition metal and chiral amine catalysts2011In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 353, no 2+3, p. 245-252Article in journal (Refereed)
    Abstract [en]

    We report that transition metal-catalyzed nucleophilic activation can be combined with chiral amine-catalyzed iminium activation as exemplified by the unprecedented enantioselective conjugate addition of a dimethylsilanyl group to α,β-unsaturated aldehydes. These reactions proceed with excellent 1,4-selectivity to afford the corresponding β-silyl aldehyde products 3 in high yields and up to 97:3 er using inexpensive bench stable copper salts and simple chiral amine catalysts. The reaction canalso generate a quaternary stereocenter with goodenantioselectivity. Density functional calculations are performed to elucidate the reaction mechanism and the origin of enantioselectivity.

  • 29.
    Jalalian, Nazli
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ishikawa, Eloisa E.
    Silva Jr., Luiz F.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Room temperature, metal-free synthesis of diaryl ethers with use of diaryliodonium salts2011In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 13, no 6, p. 1552-1555Article in journal (Refereed)
    Abstract [en]

    A fast, high-yielding synthesis of diaryl ethers with use of mild and metal-free conditions has been developed. The scope includes bulky orthosubstituteddiaryl ethers, which are difficult to obtain by metal-catalyzed protocols. Halo-substituents, racemization-prone amino acid derivatives,and heteroaromatics are also tolerated. The methodology is expected to be of high utility in the synthesis of complex molecules and in thepharmaceutical industry.

  • 30.
    Jalilian, Ehsan
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Brismar, Hjalmar
    Laurell, Fredrik
    Lidin, Sven
    Luminescence properties of the Cu4I62- cluster2011In: CrystEngComm, ISSN 1466-8033, E-ISSN 1466-8033, Vol. 13, no 14, p. 4729-4734Article in journal (Refereed)
    Abstract [en]

    Two new solvates were prepared in the system Cu(I)I using a solvolysis reaction. The structures for both of them were solved by X-ray crystllaography, showing that they constitute two modifications of the same compound with the net formula [Cu4I6](P(C6H5)4)2·2OC(CH3)2. Both types of crystals show vivid fluorescence when exposed to UV light. The formation of the first modification (I) seems to be preferred by kinetics and on ageing in the mother liquor it converts to modification (II). The Cu positions in (I) are disordered while those in (II) are fully ordered. The luminescent properties of both crystals were characterized using a confocal microscope and an excitation wavelength of 405 nm, resulting in fluorescence spectra with the intensities of 1.22 and 0.52 relative to the reference (fluorescein 10 µM). Density functional theory calculations on the ordered Cu4I62− core of modification (II) show that the de-excitation from LUMO to HOMO is responsible for the luminescence. The calculated emission spectrum has a maximum at 531 nm in good agreement with the results from confocal microscopy.

  • 31.
    Jalilian, Ehsan
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lidin, Sven
    Luminescence properties of monoclinic Cu4I4(Piperidine)42011In: Materials research bulletin, ISSN 0025-5408, E-ISSN 1873-4227, Vol. 46, no 8, p. 1192-1196Article in journal (Refereed)
    Abstract [en]

    A new modification of Cu4I4Pip4 has been synthesized under hydrothermal conditions. X-ray crystallography revealed that this compound crystallized in the monoclinic system and consists of a tetrahedral core with composition Cu4I4, in which each Cu atom is coordinated by a piperidine molecule via the N atom. In contrast to a previously reported modification of Cu4I4Pip4, the present modification shows luminescent properties when exposed to UV-light. In addition, we have used time-dependent density functional theory calculations to characterize both compounds in term of both absorption and emission.

  • 32.
    Jiang, Tuo
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Persson, Andreas K. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-Catalyzed Oxidative Carbocyclization/Arylation of Enallenes2011In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 13, no 21, p. 5838-5841Article in journal (Refereed)
    Abstract [en]

    A stereoselective palladium-catalyzed oxidative carbocyclization/arylation of enallenes is described. The reaction shows wide tolerance toward highly functionalized arylboronic acids and results In a cis addition of two carbon moieties to an olefin in good to excellent yields.

  • 33.
    Jimenez-Halla, J. Oscar C.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bickelhaupt, F. Matthias
    Sola, Miquel
    Organomagnesium clusters: Structure, stability, and bonding in archetypal models2011In: Journal of Organometallic Chemistry, ISSN 0022-328X, E-ISSN 1872-8561, Vol. 696, no 25, p. 4104-4111Article in journal (Refereed)
    Abstract [en]

    We have studied the molecular structure and the nature of the chemical bond in the monomers and tetramers of the Grignard reagent CH(3)MgCl as well as MgX(2) (X = H, Cl, and CH(3)) at the BP86/TZ2P level of theory. For the tetramers, we discuss the stability of three possible molecular structures of C(2h), D(2h), and T(d) symmetry. The most stable structure for (MgCl(2))(4) is D(2h), the one for (MgH(2))(4) is C(2h), and that of (CH(3)MgCl)(4) is T(d). The latter is 38 kcal/mol more stable with chlorines in bridge positions and methyl groups coordinated to a Mg vertex than vice versa. We find through a quantitative energy decomposition analysis (EDA) that the tetramerization energy is predominantly composed of electrostatic attraction Delta V(elstat) (60% of all bonding terms Delta V(elstat) + Delta E(oi)) although the orbital interaction Delta E(oi) also provides an important contribution (40%).

  • 34. Johannessen, Christian
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hecht, Lutz
    Barron, Laurence D.
    Glycan structure of a high-mannose glycoprotein from Raman optical activity2011In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, no 23, p. 5349-5351Article in journal (Refereed)
    Abstract [en]

    A revealing signature: The glycan structure of intact yeast external invertase, a high-mannose glycoprotein used as biocatalyst, was investigated by using Raman optical activity (ROA) spectroscopy. The conformational preferences present in mannose-containing di- and trisaccharides were found to be preserved in the glycan chains, with secondary polpeptide backbone structure suppressed.

  • 35.
    Jonsson, K. Hanna M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    NMR analysis of conformationally dependent nJC,H and nJC,C in the trisaccharide α-L-Rhap-(1→2)[α-L-Rhap-(1→3)]-α-L-Rhap-OMe and a site-specifically labeled isotopologue thereof2011In: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 49, no 3, p. 117-124Article in journal (Refereed)
    Abstract [en]

    An array of NMR spectroscopy experiments have been carried out to obtain conformationally dependent 1H,13C- and 13C,13C-spin–spin coupling constants in the trisaccharide α-L-Rhap-(1 → 2)[α-L-Rhap-(1 → 3)]-α-L-Rhap-OMe. The trisaccharide was synthesized with 13C site-specific labeling at C2′ and C2″, i.e. in the rhamnosyl groups in order to alleviate 1H spectral overlap. This facilitated the measurement of a key trans-glycosidic proton–proton cross-relaxation rate using 1D 1H,1H-T-ROESY experiments as well as a 3JC, H coupling employing 1D 1H,13C-long-range experiments, devoid of potential interference from additional J coupling. By means of both the natural abundance compound and the 13C-labeled sample 2D 1H,13C-J-HMBC and 1H,13C-HSQC-HECADE NMR experiments, total line-shape analysis of 1H NMR spectra and 1D 13C NMR experiments were employed to extract 3JC, H, 2JC, H, 3JC, C, and 1JC, C coupling constants. The 13C site-specific labeling facilitates straightforward determination of nJC, C as the splitting of the 13C natural abundance resonances. This study resulted in eight conformationally dependent coupling constants for the trisaccharide and illustrates the use of 13C site-specific labeling as a valuable approach that extends the 1D and 2D NMR methods in current use to attain both hetero- and homonuclear spin–spin coupling constants that subsequently can be utilized for conformational analysis.

  • 36.
    Kalek, Marcin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Novel, stereoselective and stereospecific synthesis of allenylphosphonates and related compounds via palladium-catalyzed propargylic substitution2011In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 353, no 10, p. 1741-1755Article in journal (Refereed)
    Abstract [en]

    We have developed a novel method for the synthesis of allenylphosphonates and related compounds based on a palladium(0)-catalyzed reaction of propargylic derivatives with H-phosphonate,H-phosphonothioate, H-phosphonoselenoate, and H-phosphinateesters. The reaction is stereoselective and stereospecific, and provides a convenient entry to a vast array of allenylphosphonates and their analogues with diverse substitution patterns in the allenic moiety and at the phosphorus center. Some mechanistic aspects of this new reaction were also investigated.

  • 37.
    Kamerlin, Shina C. L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Vicatos, Spyridon
    Dryga, Anatoly
    Warshel, Arieh
    Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems2011In: Annual review of physical chemistry (Print), ISSN 0066-426X, E-ISSN 1545-1593, Vol. 62, p. 41-64Article in journal (Refereed)
    Abstract [en]

    Recent years have witnessed an explosion in computational power, leading toattempts to model ever more complex systems. Nevertheless, there remain cases for which the use of brute-force computer simulations is clearly not the solution. In such cases, great benefit can be obtained from the use of physically sound simplifications. The introduction of such coarse graining can be traced back to the early usage of a simplified model in studies of proteins. Since then, the field has progressed tremendously. In this review,we cover both key developments in the field and potential future directions. Additionally, particular emphasis is given to two general approaches, namely the renormalization and reference potential approaches, which allow one to move back and forth between the coarse-grained (CG) and full models, as these approaches provide the foundation for CG modeling of complex systems.

  • 38.
    Kamerlin, Shina C. L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Warshel, Arieh
    Multiscale modeling of biological functions2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 22, p. 10401-10411Article in journal (Refereed)
    Abstract [en]

    Recent years have witnessed a tremendous explosion in computational power, which in turn has resulted in great progress in the complexity of the biological and chemical problems that can be addressed by means of all-atom simulations. Despite this, however, our computational time is not infinite, and in fact many of the key problems of the field were resolved long before the existence of the current levels of computational power. This review will start by presenting a brief historical overview of the use of multiscale simulations in biology, and then present some key developments in the field, highlighting several cases where the use of a physically sound simplification is clearly superior to a brute-force approach. Finally, some potential future directions will be discussed.

  • 39.
    Kamerlin, Shina C. L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Warshel, Arieh
    The empirical valence bond model: theory and applications2011In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 1, no 1, p. 30-45Article in journal (Refereed)
    Abstract [en]

    Recent years have seen an explosion in computer power, allowing for the examination of ever more challenging problems. For instance, a recent simulation study, which was the first of its kind, was able to actually explore the dynamical nature of enzyme catalysis on a millisecond timescale (Pisliakov AV, Cao J, Kamerlin SCL, Warshel A. Proc Natl Acad Sci U S A 2009, 106:17359.), something that as recently as a year or two ago would have been considered impossible. However, the questions that need addressing are nevertheless very complex, and experimental approaches can unfortunately often be inconclusive (Åqvist J, Kolmodin K, Florián J, Warshel A, Chem Biol 1999, 6:R71.) in answering them. Therefore, it is essential to have an approach that is both reliable and able to capture complex systems in order to resolve long-standing controversies [particularly with regards to questions such as the origin of enzyme catalysis, where the relevant energy contributions cannot be separated without some computational models (Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM, Chem Rev 2006, 106:3210.)]. Herein, we will present the empirical valence bond (EVB) approach, which, at present, is arguably the most powerful tool for examining chemical reactivity in the condensed phase. We will illustrate the effectiveness of the EVB method when evaluating, for instance, catalytic effects and demonstrate that it is currently the optimal tool for elucidating challenging problems such as understanding the catalytic power of enzymes. Finally, the increasing appreciation of this approach can maybe best illustrated not only by its proliferation but also by attempts to capture its basic chemistry under a different name, as will be discussed in this work.

  • 40.
    Kamerlin, Shina C. L.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Wilkie, John
    The effect of leaving group on mechanistic preference in phosphate monoesterhydrolysis2011In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 9, no 15, p. 5394-5406Article in journal (Refereed)
    Abstract [en]

    We present 2-dimensional potential energy surfaces and  transition states (TS) for water attack on a series of substituted phosphate monoester monoanions at the DFT level of theory, comparing a standard 6-31++g(d,p) basis set with a larger triple-zeta (augmented cc-pVTZ) basis set. Small fluorinated model compounds are used to simulate increasing leaving group stability without adding further geometrical complexity to the system. We demonstrate that whilst changing the leaving group causes little qualitative change in the potential energy surfaces (with the exception of the system with the most electron withdrawing leaving group, CF3O-, in which the associative pathway changes from a stepwise AN + DN pathway to a concerted ANDN pathway), there is a quantitative change in relative gas-phase and solution barriers for the two competing pathways. In line with previous studies, in the case of OCH3, the barriers for the associative and dissociative pathways are similar in solution, and the two pathways are equally viable and indistinguishable in solution. However, significantly increasing the stability of the leaving group (decreasing proton affinity, PA) results in the progressive favouring of a stepwise dissociative, DN + AN, mechanism over associative mechanisms.

  • 41.
    Kamerlin, Shina Caroline Lynn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical comparison of p-nitrophenyl phosphate and sulfate Hydrolysis in aqueous solution: implications for enzyme-catalyzed sulfuryl transfer2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 22, p. 9228-9238Article in journal (Refereed)
    Abstract [en]

    Both phosphoryl and sulfuryl transfers are ubiquitous in biology, being involved in a wide range of processes, ranging from cell division to apoptosis. Additionally, it is becoming increasingly clear that enzymes that can catalyze phosphoryl transfer can often cross-catalyze sulfuryl transfer (and vice versa). However, while there have been extensive experimental and theoretical studies performed on phosphoryl transfer, the body of available research on sulfuryl transfer is comparatively much smaller. The present work presents a direct theoretical comparison of p-nitrophenyl phosphate and sulfate monoester hydrolysis, both of which are considered prototype systems for probing phosphoryl and sulfuryl transfer, respectively. Specifically, free energy surfaces have been generated using density functional theory, by initial geometry optimization in PCM using the 6-31+G* basis set and the B3LYP density functional, followed by single-point calculations using the larger 6-311+G** basis set and the COSMO continuum model. The resulting surfaces have been then used to identify the relevant transition states, either by further unconstrained geometry optimization or from the surface itself where possible. Additionally, configurational entropies were evaluated using a combination of the quasiharmonic approximation and the restraint release approach and added to the calculated activation barriers as a correction. Finally, the overall activation entropy was estimated by approximating the solvent contribution to the total activation entropy using the Langevin dipoles solvation model. We have reproduced both the experimentally observed activation barriers and the observed trend in the activation entropies with reasonable accuracy, as well as providing a comparison of calculated and observed 15N and 18O kinetic isotope effects. We demonstrate that, counterintuitively, the hydrolysis of the p-nitrophenyl sulfate proceeds through a more expansive pathway than its phosphate analogue. Additionally, we show that the solvation effects upon moving from the ground state to the transition state are quite different for both reactions, suggesting that the enzymes that catalyze these reactions would need active sites with quite different electrostatic preorganization for the efficient catalysis of either reaction (despite which many enzymes can catalyze both phosphoryl and sulfuryl transfer). We believe that such a comparative study is an important foundation for understanding the molecular basis for phosphate–sulfate cross-promiscuity within members of the alkaline phosphatase superfamily.

  • 42.
    Karlsson, Erik A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lee, Bao-Lin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hansson, Örjan
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Photosensitized water oxidation by use of a bioinspired manganese catalyst2011In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, no 49, p. 11715-11718Article in journal (Refereed)
  • 43. Kleimark, Jonatan
    et al.
    Johansson, Charlotte
    Olsson, Susanne
    Håkansson, Mikael
    Hansson, Sverker
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Norrby, Per-Ola
    Sterically goverend selectivity in palladium-assisted allylic alkylation2011In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 30, p. 230-238Article in journal (Refereed)
    Abstract [en]

    The selectivity in the Pd-assisted allylic alkylation has been investigated in a system with a ligand tethered to the allylic moiety. Isolation of (η3-allyl)Pd complexes and stoichiometric reaction with malonate nucleophiles allowed separation of various factors influencing the regioselectivity in a system that cannot undergo apparent rotation. Unexpectedly, trans effects were found to have only a minor influence on the selectivity, whereas changing the tether length could shift the preference from favored internal to dominant terminal attack. DFT-assisted analysis revealed that the dominant selectivity-determiningfactors are the forced rotation of the allylic moiety and an important steric repulsion from a syn-alkyl substituent

  • 44.
    Kärkäs, Markus D.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Karlsson, Erik A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lee, Bao-Lin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Shariatgorji, Mohammadreza
    Ilag, Leopold
    Stockholm University, Faculty of Science, Department of Analytical Chemistry.
    Hansson, Örjan
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Light-Induced Water Oxidation by a Ru-complex Containing a Bio-Inspired Ligand2011In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 17, no 28, p. 7953-7959Article in journal (Refereed)
    Abstract [en]

    The new Ru-complex 8 containing the bio-inspired ligand 7 was successfully synthesized and characterized. Complex 8 could efficiently catalyze water oxidation using CeIV and RuIII as chemical oxidants. More importantly, this complex has sufficiently low overpotential to utilize ruthenium polypyridyl-type complexes as photosensitizers.

  • 45.
    Larsson, Johanna M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhao, Tony S. N.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-Catalyzed Oxidative Allylic C-H Silylation2011In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 13, no 7, p. 1888-1891Article in journal (Refereed)
    Abstract [en]

    Palladium-catalyzed allylic C−H silylation was performed with use of hexamethyldisilane as the silyl source. These C−H functionalization reactions occur only in the presence of hypervalent iodine reagents or other strong oxidants and proceed with excellent regioselectivity, providing the linear allylic isomer of the allylsilane products. In demonstrating the first oxidative allylic C−H silylation of alkenes, this study marks an important advance for the catalytic C−H functionalization method.

  • 46.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Georgieva, Polina
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Yu, Jian-Guo
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mechanism of mycolic acid cyclopropane synthase: A theoretical study2011In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 50, no 9, p. 1505-1513Article in journal (Refereed)
    Abstract [en]

    The reaction mechanism of mycolic acid cyclopropane synthase is investigated using hybrid density functional theory. The direct methylation mechanism is examined with a large model of the active site constructed on the basis of the crystal structure of the native enzyme. The important active site residue Glu140 is modeled in both ionized and neutral forms. We demonstrate that the reaction starts via the transfer of a methyl to the substrate double bond, followed by the transfer of a proton from the methyl cation to the bicarbonate present in the active site. The first step is calculated to be rate-limiting, in agreement with experimental kinetic results. The protonation state of Glu140 has a rather weak influence on the reaction energetics. In addition to the natural reaction, a possible side reaction, namely a carbocation rearrangement, is also considered and is shown to have a low barrier. Finally, the energetics for the sulfur ylide proposal, which has already been ruled out, is also estimated, showing a large energetic penalty for ylide formation.

  • 47.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical study of the chemoselectivity of tungsten-dependent acetylene hydratase2011In: ACS Catalysis, ISSN 2155-5435, Vol. 1, no 8, p. 937-944Article in journal (Refereed)
    Abstract [en]

    The tungsten-dependent enzyme acetylene hydratase catalyzes the hydration of acetylene to acetaldehyde. Very recently, we proposed a reaction mechanism for this enzyme based on density functional calculations (Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 22523). The mechanism involves direct coordination of the substrate to the tungsten ion, followed by a nucleophilic attack by a water molecule concerted with a proton transfer to a second-shell aspartate, which then reprotonates the substrate. Here, we use the same methodology to investigate the factors involved in the control of the chemoselectivity of this enzyme. The hydration reactions of three representative compounds (propyne, ethylene, and acetonitrile) are investigated using a large model of the active site. The energy of substrate binding to the metal ion and the barrier for the following nucleophilic attack are used to rationalize the experimental observations. It is shown that all three compounds have higher barriers for hydration compared with acetylene. In addition, propyne is shown to have a larger binding energy, explaining its behavior as a competitive inhibitor. Taken together, the results provide further corroboration of our suggested mechanism for acetylene hydratase

  • 48.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Yu, Jian-Guo
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum chemical modeling of enzymatic reactions: The case of decarboxylation2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 07, no 05, p. 1494-1501Article in journal (Refereed)
    Abstract [en]

    We present a systematic study of the decarboxylation step of the enzyme aspartate decarboxylase with the purpose of assessing the quantum chemical cluster approach for modeling this important class of decarboxylase enzymes. Active site models ranging in size from 27 to 220 atoms are designed, and the barrier and reaction energy of this step are evaluated. To model the enzyme surrounding, homogeneous polarizable medium techniques are used with several dielectric constants. The main conclusion is that when the active site model reaches a certain size, the solvation effects from the surroundings saturate. Similar results have previously been obtained from systematic studies of other classes of enzymes, suggesting that they are of a quite general nature.

  • 49.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Yu, Jian-Guo
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tungsten-dependent formaldehyde ferredoxin oxidoreductase: Reaction mechanism from quantum chemical calculations2011In: Journal of Inorganic Biochemistry, ISSN 0162-0134, E-ISSN 1873-3344, Vol. 105, no 7, p. 927-936Article in journal (Refereed)
    Abstract [en]

    Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus is a tungsten-dependent enzyme thatcatalyzes the oxidation of formaldehyde to formic acid. In the present study, quantum chemical calculationsare used to elucidate the reaction mechanism of this enzyme. Several possible mechanistic scenarios areinvestigated with a large model of the active site designed on the basis of the X-ray crystal structure of thenative enzyme. Based on the calculations, we propose a new mechanism in which the formaldehyde substratebinds directly to the tungsten ion.WVI=O then performs a nucleophilic attack on the formaldehyde carbon toform a tetrahedral intermediate. In the second step, which is calculated to be rate limiting, a proton istransferred to the second-shell Glu308 residue, coupled with a two-electron reduction of the tungsten ion.The calculated barriers for the mechanism are energetically very feasible and in relatively good agreementwith experimental rate constants. Three other second-shell mechanisms, including one previously proposedbased on experimental findings, are considered but ruled out because of their high barriers.

  • 50.
    Lihammar, Richard
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Millet, Renaud
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    An Efficient Dynamic Kinetic Resolution of N-Heterocyclic 1,2-Amino Alcohols2011In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 353, no 13, p. 2321-2327Article in journal (Refereed)
    Abstract [en]

    A chemoenzymatic dynamic kinetic resolution (DKR) of N-heterocyclic amino alcohols is described. Various lipases were studied as biocatalysts for the kinetic resolution of N-heterocyclic 1,2-amino alcohols. The influence of the support of the enzymes on the enantioselectivity in the resolution of different substrates is highlighted. Various 3-acetoxypyrrolidines and -piperidines were obtained in high yield and high enantiomeric excess in efficient DKR reactions.

12 1 - 50 of 96
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