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  • 1. Abbasi, Alireza
    et al.
    Skripkin, Mikhail Yu.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Torapava, Natallia
    Ambidentate coordination of dimethyl sulfoxide in rhodium(III) complexes2011In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 40, no 5, p. 1111-1118Article in journal (Refereed)
    Abstract [en]

    The two dimethyl sulfoxide solvated rhodium(III) compounds, [Rh(dmso-kappa O)(5)(dmso-kappa S)](CF(3)SO(3))(3) (1 & 1* at 298 K and 100 K, respectively) and [Rh(dmso-kappa O)(3)(dmso-kappa S)(2)Cl](CF(3)SO(3))(2) (2), crystallize with orthorhombic unit cells in the space group Pna2(1) (No. 33), Z = 4. In the [Rh(dmso)(6)](3+) complex with slightly distorted octahedral coordination geometry, the Rh-O bond distance is significantly longer with O trans to S, 2.143(6) angstrom (1) and 2.100(6) angstrom (1*), than the mean Rh-O bond distance with O trans to O, 2.019 angstrom (1) and 2.043 angstrom (1*). In the [RhCl(dmso)(5)](3+) complex, the mean Rh-O bond distance with O trans to S, 2.083 angstrom, is slightly longer than that for O trans to Cl, 2.067(4) angstrom, which is consistent with the trans influence DMSO-kappa S > Cl > DMSO-kappa O of the opposite ligands. Raman and IR absorption spectra were recorded and analyzed and a complete assignment of the vibrational bands was achieved with support by force field calculations. An increase in the Rh-O stretching vibrational frequency corresponded to a decreasing trans-influence from the opposite ligand. The Rh-O force constants obtained were correlated with the Rh-O bond lengths, also including previously obtained values for other M(dmso)(6)(3+) complexes with trivalent metal ions. An almost linear correlation was obtained for the MO stretching force constants vs. the reciprocal square of the MO bond lengths. The results show that the metal ion-oxygen bonding of dimethyl sulfoxide ligands is electrostatically dominated in those complexes and that the stretching force constants provide a useful measure of the relative trans-influence of the opposite ligands in hexa-coordinated Rh(III)-complexes.

  • 2. 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)
  • 3.
    Ahlford, Katrin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Asymmetric transfer hydrogenation of ketones: Catalyst development and mechanistic investigation2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The development of ligands derived from natural amino acids for asymmetric transfer hydrogenation (ATH) of prochiral ketones is described herein. In the first part, reductions performed in alcoholic media are examined, where it is found that amino acid-derived hydroxamic acids and thioamides, respectively, are simple and versatile ligands that in combination with [RhCp*Cl2]2 efficiently catalyze this particular transformation. Selectivities up to 97% ee of the corresponding secondary alcohols are obtained, and it is furthermore observed that the two different ligand classes, albeit based on the same amino acid scaffold, give rise to products of opposite configuration.

    The highly interesting enantioswitchable nature of the two abovementioned catalysts is studied in detail by mechanistic investigations. A structure/activity correlation analysis is performed, which reveals that the diverse behavior of the catalysts arise from different interactions between the ligands and the metal. Kinetic studies furthermore stress the catalyst divergence, since a difference in the rate determining step is established from initial rate measurements. In addition, rate constants are determined for each step of the overall reduction process.

    In the last part, catalyst development for ATH executed in water is discussed. The applicability of hydroxamic acid ligands is further extended, and catalysts based on these compounds are found to be efficient and compatible with aqueous conditions. The structurally even simpler amino acid amide is also evaluated as a ligand, and selectivities up to 90% ee are obtained in the reduction of a number of aryl alkyl ketones. The very challenging reduction of dialkyl ketones is moreover examined in the Rh-catalyzed aqueous ATH, where a modified surfactant-resembling sulfonylated diamine is used as ligand, and the reaction is carried out in the presence of SDS-micelles. A positive effect is to some extent found on the catalyst performance upon addition of phase-transfer components, especially regarding the catalytic activity in the reduction of more hydrophobic substrates.

  • 4.
    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.

  • 5.
    Ahlsten, Nanna
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Transition metal-catalysed enol formation from allylic alcohols: Isomerisation, C−C and C−F bond formations 2011Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes the isomerisation of allylic alcohols into enols and enolates catalysed by transition metal complexes. The transformation has been used to prepare both unsubstituted and α-substituted carbonyl compounds. Significant attention has been given to the mechanistic aspects of the reactions.

    In the first part of this thesis, an environmentally benign procedure for the redox isomerisation of allylic alcohols into ketones is described. The reaction takes place in water and at room temperature using a cationic rhodium complex in combination with water-soluble phosphines. A variety of allylic alcohols could be isomerised in high yields using this procedure.

    The second part describes the combination of an allylic alcohol isomerisation with a C−C bond formation, catalysed by a rhodium complex. In this way, allylic alcohols were coupled with aldehydes and N-tosyl imines forming aldol and Mannich-type products. In addition, homoallylic and bishomoallylic alcohols were for the first time isomerised into the corresponding enolates and coupled using this methodology.

    In the third part of this thesis, the isomerisation of allylic alcohols was coupled with a C−F bond formation using an iridium complex and electrophilic fluorinating reagents. This novel transformation was used to convert allylic alcohols into single regioisomers of α-fluoroketones. The reaction is tolerant to air and water and takes place at room temperature.

    All of the reactions described take place under mild conditions, are operationally simple, and utilise catalysts formed in situ from commercially available metal complexes and ligands.

  • 6.
    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.

  • 7.
    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.

  • 8.
    Bielawski, Marcin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Diaryliodonium Salts: Development of Synthetic Methodologies and α-Arylation of Enolates2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes novel reaction protocols for the synthesis of diaryliodonium salts and also provides an insight to the mechanism of α-arylation of carbonyl compounds with diaryliodonium salts.

     The first chapter gives a general introduction to the field of hypervalent iodine chemistry, mainly focusing on recent developments and applications of diaryliodonium salts.

    Chapter two describes the synthesis of electron-rich to electron-poor diaryliodonium triflates, in moderate to excellent yields from a range of arenes and iodoarenes.

    In chapter three, it is described that molecular iodine can be used together with arenes in a direct one-pot, three-step synthesis of symmetric diaryliodonium triflates. A large scale synthesis of bis(4-tert-butylphenyl)iodonium triflate is also described, controlled and verified by an external research group, further demonstrating the reliability of this methodology.

    The fourth chapter describes the development of a sequential one-pot synthesis of diaryliodonium salts from aryl iodides and boronic acids, furnishing symmetric and unsymmetric, electron-rich to electron-poor diaryliodonium tetrafluoroborates in moderate to excellent yields. This method was developed to overcome the regiochemical limitations imposed by the reaction mechanism in the protocols described in the preceding chapters.

    Chapter five describes a one-pot synthesis of heteroaromatic iodonium salts under similar conditions described in chapter two.

    The final chapter describes the reaction of enolates with chiral diaryliodonium salts or together with a phase transfer catalyst yielding racemic products. DFT calculations were performed, which revealed a low lying energy transition state (TS) between intermediates, which is believed to be responsible for the lack of selectivity observed in the experimental work. It is also proposed that a [2,3] rearrangement is preferred over a [1,2] rearrangement in the α-arylation of carbonyl compounds.

    The synthetic methodology described in this thesis is the most generally applicable, efficient and high-yielding to date for the synthesis of diaryliodonium salts, making these reagents readily available for various applications in synthesis.

  • 9.
    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.

  • 10.
    Buitrago, Elina
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lundberg, Helena
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Andersson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ryberg, Per
    Aztra Zeneca, Global Process R&D, Södertälje, Sweden.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Selective reduction of heteroaromatic ketones: A combinatorial approach2011Conference paper (Other academic)
    Abstract [en]

    The enantioselective reduction of prochiral ketones is a most productiveway towards enantio enriched secondary alcohols used in the preparation of biologically active compounds. There are numerous transition metal catalyzed methods for this transformation, particularly based on Ru(II)-and Rh(I)-complexes, but there is a demand for a larger substrate scope. Heteroaromatic ketones are traditionally more challenging substrates. Normally a catalyst is developed for one benchmark substrate, and asubstrate screen is made with the best performing catalyst. Using this methodology, there is a high probability that for different substrates, another catalyst could outperform the one used. We have executed a multiple screen, containing a variety of different ligands together with both Ru and Rh, and heteroaromatic ketones to fine-tune, and find the optimum catalyst depending on the substrate. The acquired information was used to synthesize known, biologically active compounds, where the key reduction steps were performed with high enantioselectivities and yields.

  • 11.
    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.

  • 12. 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.

  • 13. 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.

  • 14.
    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.

  • 15.
    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.

  • 16.
    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.

  • 17.
    Deiana, Luca
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhao, Gui-Ling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ibrahem, Ismail
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rios, Ramon
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Catalytic asymmetric aziridination of α, β- unsaturated aldehydes2011In: Abstracts of Papers, 242nd ACS National Meeting & Exposition, Denver, CO, United States, August 28-September 1, 2011, American Chemical Society , 2011Conference paper (Other academic)
    Abstract [en]

    The development, scope and application of the highly enantioselective organocatalytic aziridination of a, b- unsaturated aldehydes is presented. The aminocatalytic aziridination of a, b- unsaturated aldehydes enables the asymmetric formation of b-formylaziridines with up to >19:1 dr and 99% ee. The aminocatalytic aziridination of a-monosobstituted enals gives access to terminal a-substituted-a-formyl aziridines in high yields and up to 99% ee. In the case of the organocatalytic aziridination of disubstituted a, b-unsaturated aldehydes, the transformations gives nearly enantiomeric pure b-formyl-functionalized aziridine products. A higly enantioselective one-pot cascade sequence based on combination of asymmetric amine and N-heterocyclic carbene catalysis is also disclosed. This transformation gives the corresponding N-Boc and N-Cbz protected b-amino acid esters with ee´s ranging from 92-99%.

  • 18.
    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.

  • 19.
    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)
  • 20.
    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

  • 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.
    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.

  • 23.
    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.

  • 24.
    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.

  • 25. 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.

  • 26. 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)
  • 27. 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.

  • 28.
    Jalalian, Nazli
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ishikawa, Eloisa E.
    Universidade de Sao Paulo, Instituto de Quimica.
    Silva Jr., Luiz F.
    Universidade de Sao Paulo, Instituto de Quimica.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Room temperature, metal-free synthesis of diaryl ethers with use of diaryliodonium salts2011In: Abstracts of Papers, 242nd ACS National Meeting & Exposition, Denver, CO, United States, August 28-September 1, 2011, American Chemical Society , 2011Conference paper (Other academic)
    Abstract [en]

    Diaryl ethers are common structural features in numerous natural products and biol. active compds.  Despite more than a century of immense focus on finding efficient synthetic routes to this compd. class, diaryl ethers remain difficult to obtain.  Routes that are catalytic in copper have been developed, but high catalyst loadings, excess reagents, elevated temps. and long reaction times are still needed.  Pd-catalyzed cross-couplings of phenols and aryl halides at temps. up to 100 °C have recently been reported to give high yields of diaryl ethers.  Diaryliodonium salts are non-toxic alternatives to transition metals in the synthesis of diaryl ethers and we have recently developed effective synthetic routes to these salts.  Herein we report a fast, high-yielding synthesis of diaryl ethers.  The reaction conditions are mild, metal-free, and avoid the use of halogenated solvents, additives, or excess reagents.  Precautions to avoid air or moisture are not needed.  The scope includes ortho- and halo-substituted diaryl ethers, which are difficult to obtain by metal-catalyzed protocols .

  • 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.
    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.

  • 31. 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.

  • 32.
    Johnston, Eric
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    New Tools for Green Catalysis: Studies on a Biomimetic Hybrid Catalyst and a Novel Nanopalladium Catalyst2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The first part of this thesis describes an improved synthetic route to hybrid (hydroquinone-Schiff base)cobalt catalysts. Preparation of the 5-(2,5-hydroxyphenyl)salicylaldehyde building block was improved by altering the protective groups of the hydroquinone (HQ) starting material. Both protection and deprotection could be carried out under mild conditions, resulting in high yields. By optimizing the reaction conditions of the Suzuki cross-coupling, an efficient and inexpensive synthetic route with a good overall yield was developed.

    The second part describes the use of the hybrid catalyst as an electron transfer mediator (ETM) in the palladium-catalyzed aerobic carbocyclization of enallenes. By covalently linking the HQ to the cobalt Schiff-base complex the reaction proceeded at lower temperatures with a five-fold increase of the reaction rate compared to the previously reported system.

    The third part describes the application of the hybrid catalyst in the biomimetic aerobic oxidation of secondary alcohols. Due to the effi­ciency of the intramolecular electron transfer, the hybrid catalyst allowed for a lower catalytic loading and milder reaction conditions compared to the previous separate-component system. Benzylic alcohols as well as aliphatic alcohols were oxidized to the corresponding ketones in excellent yield and selectivity using this methodology.

    The fourth part describes the synthesis and characterization of highly dispersed palladium nanoparticles supported on aminopropyl-modified siliceous mesocellular foam. The Pd nanocatalyst showed excellent activity for the aerobic oxidation of a wide variety of alcohols under air atmosphere. Moreover, the catalyst can be recycled several times without any decrease in activity or leaching of the metal into solution.

    Finally, the fifth part describes the application of the Pd nanocatalyst in transfer hydrogenations and Suzuki coupling reactions. The catalyst was found to be highly efficient for both transformations, resulting in chemoselective reduction of various alkenes as well as coupling of a variety of aryl halides with various boronic acids in excellent yields. Performing the latter reaction under microwave irradiation significantly increased the reaction rate, compared to conventional heating. However, no significant increase in reaction rate was observed for the transfer hydrogenations, under microwave heating.

  • 33.
    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.

  • 34.
    Kalek, Marcin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of C(sp2)-P bonds by palladium-catalyzed reactions: Mechanistic investigations and synthetic studies2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on synthetic and mechanistic aspects of palladium-catalyzed C(sp2)-P bond-forming reactions, with the aim to develop mild and efficient methods for the synthesis of biologically active phosphorus compounds, e.g. DNA analogs.

    The first part of the thesis is devoted to detailed mechanistic investigations of the palladium-catalyzed C-P cross-coupling reaction, in order to fully understand the underlying chemistry and by rational design of the reaction conditions, improve the overall efficiency of the process and broaden its applicability. In particular influence of palladium coordination by different anions on the rate of ligand substitution and reductive elimination steps of the reaction was studied. It was found that coordination of acetate ion results in unprecedented acceleration of both of the mechanistic steps, what leads to remarkable shortening of the overall reaction times. In-depth kinetic investigations enabled to ascribe the observed effects to ability of the acetate ion to act as a bidentate ligand for palladium. This causes considerable alternation of the reaction mechanism, comparing to the reaction involving halide-containing complexes, and results in significant rate increase.

    Based on the above mechanistic studies an efficient method for the synthesis of arylphosphonates, using substoichiometric amounts of inorganic acetate additive and reduced amount of catalyst, was developed.

    In the next part of the thesis, efforts to further enhance the palladium-catalyzed cross-coupling efficiency by using a microwave-assisted synthesis are described. These explorations resulted in a successful development of two protocols, one for a cross-coupling of H-phosphonates and the other for H,H-phosphinates, under the microwave heating conditions. Application of this energy source resulted in extremely short reaction times, measured in minutes.

    The final chapter of this thesis deals with studies on palladium-catalyzed SN2’ propargylic substitution reaction with phosphorus nucleophiles, which leads to allene products. Efficient procedure for the synthesis of allenylphosphonates and related compounds was developed. The method enables full control of stereochemistry in the allene moiety and at the asymmetric phosphorus center. Some conclusions on the mechanism of the reaction were also drawn.

  • 35.
    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.

  • 36.
    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.

  • 37.
    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.

  • 38.
    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.

  • 39.
    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.

  • 40.
    Karlsson, Erik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Catalysts for Oxygen Production and Utilization: Closing the Oxygen Cycle: From Biomimetic Oxidation to Artificial Photosynthesis2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes the development and study of catalysts for redox reactions, which either utilize oxygen or hydrogen peroxide for the purpose of selectively oxidizing organic substrates, or produce oxygen as the necessary byproduct in the production of hydrogen by artificial photosynthesis.

    The first chapter gives a general introduction about the use of environmentally friendly oxidants in the field of organic synthesis, and about the field of artificial photosynthesis. The second chapter describes a computational study of the mechanism of palladium-catalyzed oxidative carbohydroxylation of allene-substituted conjugated dienes. The proposed mechanism, which was supported by DFT calculations, involves an unusual water attack on a (π-allyl)palladium complex. The third chapter describes a computational study of the oxidation of unfunctionalized hydrocarbons, ethers and alcohols with hydrogen peroxide, catalyzed by methyltrioxorhenium (MTO). The mechanism was found to proceed via rate-limiting hydride abstraction followed by hydroxide transfer in a single concerted, but highly asynchronous, step as shown by intrinsic reaction coordinate (IRC) scans. The fourth chapter describes the use of a new hybrid (hydroquinone-Schiff base)cobalt catalyst as electron transfer mediator (ETM) in the palladium-catalyzed aerobic carbocyclization of enallenes. Covalently linking the two ETMs gave a fivefold rate increase compared to the use of separate components. The fifth chapter describes an improved synthetic route to the (hydroquinone-Schiff base)cobalt catalysts. Preparation of the key intermediate 5-(2,5-hydroxyphenyl)salicylaldehyde was improved by optimization of the key Suzuki coupling and change of protecting groups from methyl ethers to easily cleaved THP groups. The catalysts could thus be prepared in good overall yield from inexpensive starting materials.

    Finally, the sixth chapter describes the preparation and study of two catalysts for water oxidation, both based on ligands containing imidazole groups, analogous to the histidine residues present in the oxygen evolving complex (OEC) and in many other metalloenzymes. The first, ruthenium-based, catalyst was found to catalyze highly efficient water oxidation induced by visible light. The second catalyst is, to the best of our knowledge, the first homogeneous manganese complex to catalyze light-driven water oxidation.

  • 41.
    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)
  • 42. 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

  • 43. Kuttel, Michelle
    et al.
    Mao, Yue
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lundborg, Magnus
    CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation2011In:  Proceedings - 2011 7th IEEE International Conference on eScience, eScience 2011, , art. no. 6123304, 2011, p. 395-402Conference paper (Refereed)
    Abstract [en]

    CarbBuilder is a software tool for building 3D structures of carbohydrates, which are the most structurally varied of all molecular classes. CarbBuilder was designed with the dual aims of portability and adaptability, using an iterative software development approach. CarbBuilder employs a simple algorithm, using heuristics based upon experimental data to convert a primary structure description of a carbohydrate molecule into a three-dimensional structure file. This straightforward approach means that CarbBuilder can be easily adapted: users can add additional monosaccharide building blocks or alter the conformational defaults to suit specific requirements. The output carbohydrate structure can be used for subsequent molecular simulation investigations. CarbBuilder is freely available and portable: it is a text-based stand-alone program that can run on Windows, Linux and MacOS X systems without installation.

  • 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. Küpper, Frithjof C.
    et al.
    Feiters, Martin C.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kaiho, Tatsuo
    Yanagida, Shozo
    Zimmermann, Michael B.
    Carpenter, Lucy J.
    Luther, George W., III
    Lu, Zunli
    Jonsson, Mats
    Kloo, Lars
    Commemorating Two Centuries of Iodine Research: An Interdisciplinary Overview of Current Research2011In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, no 49, p. 11598-11620Article, review/survey (Refereed)
    Abstract [en]

    Iodine was discovered as a novel element in 1811 during the Napoleonic Wars. To celebrate the bicentennial anniversary of this event we reflect on the history and highlight the many facets of iodine research that have evolved since its discovery. Iodine has an impact on many aspects of life on Earth as well as on human civilization. It is accumulated in high concentrations by marine algae, which are the origin of strong iodine fluxes into the coastal atmosphere which influence climatic processes, and dissolved iodine is considered a biophilic element in marine sediments. Iodine is central to thyroid function in vertebrates, with paramount implications for human health. Iodine can exist in a wide range of oxidation states and it features a diverse supramolecular chemistry. Iodine is amenable to several analytical techniques, and iodine compounds have found widespread use in organic synthesis. Elemental iodine is produced on an industrial scale and has found a wide range of applications in innovative materials, including semiconductorsin particular, in solar cells.

  • 46.
    Larsson, Johanna M
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-catalyzed C-H functionalization of alkenes under oxidative conditions2011Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The unique properties of high oxidation state palladium have been used to develop new catalytic alkene C-H functionalization reactions. A Heck-type coupling based on the reactivity of palladium catalysts and diaryliodonium salts has been developed with broad synthetic scope and tolerance for functional groups that are ordinarily reactive in Pd0/PdII catalysis, for example, allylic acetates and aryl bromides. Poisoning experiments and DFT studies suggest that a PdII/PdIV cycle is operating. The first catalytic allylic C-H silylation method has also been developed utilizing commercially available hexamethyldisilane as silyl source and iodine(III) reagents as oxidants.

  • 47.
    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.

  • 48.
    Li, Jia-Qi
    et al.
    Uppsala University, Sweden.
    Peters, Byron
    Uppsala University, Sweden.
    Andersson, Pher G.
    Uppsala University, Sweden; University of KwaZulu-Natal, South Africa.
    Highly Enantioselective Asymmetric Isomerization of Primary AllylicAlcohols with an Iridium–N,P Complex2011In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 17, p. 11143-11145Article in journal (Refereed)
    Abstract [en]

    Highly enantioselective asym. isomerization of a range of E- and Z- trisubstituted primary allylic alcs. to the corresponding chiral aldehydes catalyzed by a N,​P-​ligated iridium complex is reported.  Notably, the selectivity of this catalyst was less sensitive to steric effects in the asym. isomerization of Z-​trisubstituted allylic alcs. than E-​trisubstituted compds.

  • 49.
    Li, Xichen
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Chen, Guangju
    Schinzel, Sandra
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    A comparison between artificial and natural water oxidation2011In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 40, no 42, p. 11296-11307Article in journal (Refereed)
    Abstract [en]

    Two artificial water oxidation catalysts, the blue dimer and the Llobet catalyst, have been studied using hybrid DFT methods. The results are compared to those for water oxidation in the natural photosystem II enzyme. Studies on the latter system have now reached a high level of understanding, at present much higher than the one for the artificial systems. A recent high resolution X-ray structural investigation of PSII has confirmed the main features of the structure of the oxygen evolving complex (OEC) suggested by previous DFT cluster studies. The O-O bond formation mechanism suggested is of direct coupling (DC) type between an oxygen radical and a bridging oxo ligand. A similar DC mechanism is found for the Llobet catalyst, while an acid-base (AB) mechanism is preferred for the blue dimer. All of them require at least one oxygen radical. Full energy diagrams, including both redox and chemical steps, have been constructed illustrating similarities and differences to the natural system. Unlike previous DFT studies, the results of the present study suggest that the blue dimer is rate-limited by the initial redox steps, and the Llobet catalyst by O(2) release. The results could be useful for further improvement of the artificial systems.

  • 50.
    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

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