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  • 1. Agasti, Soumitra
    et al.
    Maity, Soham
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Maiti, Debabrata
    Palladium-Catalyzed Synthesis of 2,3-Disubstituted Benzofurans: An Approach Towards the Synthesis of Deuterium Labeled Compounds2015In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 357, no 10, p. 2331-2338Article in journal (Refereed)
    Abstract [en]

    Palladium-catalyzed oxidative annulations between phenols and alkenylcarboxylic acids produced a library of benzofuran compounds. Depending on the nature of the substitution of the phenol precursor, either 2,3-dialkylbenzofurans or 2-alkyl-3-methylene-2,3-dihydrobenzofurans can be synthesized with excellent regioselectivity. Reactions between conjugated 5-phenylpenta-2,4-dienoic acids and phenol gave 3-alkylidenedihydrobenzofuran alkaloid motifs while biologically active 7-arylbenzofuran derivatives were prepared by starting from 2-phenylphenols. More interestingly, selective incorporation of deuterium from D2O has been discovered, which offers an attractive one-step method to access deuterated compounds.

  • 2.
    Alam, Rauful
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Vollgraff, Tobias
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of Adjacent Quaternary Stereocenters by Catalytic Asymmetric Allylboration2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 35, p. 11262-11265Article in journal (Refereed)
    Abstract [en]

    Allylboration of ketones with gamma-disubstituted allylboronic acids is performed in the presence of chiral BINOL derivatives. The reaction is suitable for single-step creation of adjacent quaternary stereocenters with high selectivity. We show that, with an appropriate choice of the chiral catalyst and the stereoisomeric prenyl substrate, full control of the stereo- and enantioselectivity is possible in the reaction.

  • 3.
    Algarra, Andres G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Computational Insights into the Isomerism of Hexacoordinate Metal-Sarcophagine Complexes: The Relationship between Structure and Stability2015In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, no 3, p. 503-511Article in journal (Refereed)
    Abstract [en]

    The hexacoordinate complexes that the macrobicyclic ligands {(NH3)(2)sar)(2+) and {NMe3)(2)sar}(2+) (sar = 3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane) form with transition metals such as Co-III, Co-II and Cu-II can adopt several isomeric structures. In this article, we have firstly employed DFT methods lo compute the relative stability of their Delta-ob(3), Delta-ob(2)lel, Delta-lel(2)ob and Delta-lel(3) isomers, as well as the activation barriers for their interconversion. In agreement with the experimental data, the results show that, in general, the different isomers of the Co-III and Co-II complexes present similar free energies, whereas the Cu-II complexes show a strong tendency towards the lel(3) form. In addition, the interplay between the structure and stability of these species has been studied by combining shape maps with a distortion/interaction energy analysis. In contrast to the geometries close to the ideal octahedron that all the studied Co complexes present, the le)3 structures of [Cu{(NH3)(2)sar}](4+) and [Cu{(NMe3)(2)sar](4+) are better described. as trigonal prisms. In such structures the ligand adopts a conformation significantly more stable than in the other isomers, and this drives the formation of lel(3)-[Cu{(NH3)(2)sar}](4+) and lel(3)-[Cu{(NNe3)(2)sar}](4+). Overall, the results show a clear relationship between the stability of a given isomer and its degree of distortion with respect to the ideal octahedron (or trigonal prism), with the latter being ultimately dependent on the transition metal and its radius.

  • 4. Bejhed, Rebecca S.
    et al.
    Tian, Bo
    Eriksson, Kristofer
    Brucas, Rimantas
    Oscarsson, Sven
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Strömberg, Mattias
    Svedlindh, Peter
    Gunnarsson, Klas
    Magnetophoretic Transport Line System for Rapid On-Chip Attomole Protein Detection2015In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 31, no 37, p. 10296-10302Article in journal (Refereed)
    Abstract [en]

    A lab-on-a-chip traveling wave magnetophoresis approach for sensitive and rapid protein detection is reported. In this method, a chip-based magnetic microarray comprising lines of micrometer-sized thin film magnetic elements was used to control the movement of magnetic beads (MBs). The MBs and the chip were functionalized, forming a sandwich-type assay. The MBs were transported across a detection area, and the presence of target molecules resulted in the immobilization of MBs within this area. Target quantification was accomplished by MB counting in the detection area using an optical microscope. In order to demonstrate the versatility of the microarray, biotinylated antiavidin was selected as the target protein. In this case, avidin-functionalized MBs and an avidin-functionalized detection area were used. With a total assay time of 1 to 1.5 h (depending on the labeling approach used), a limit of detection in the attomole range was achieved. Compared to on-chip surface plasmon resonance biodetection systems, our method has a larger dynamic range and is about a factor of 500 times more sensitive. Furthermore, our MB transportation system can operate in any chip-based biosensor platform, thereby significantly improving traditional biosensors.

  • 5.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    How Quantum Chemistry Can Solve Fundamental Problems in Bioenergetics2015In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 115, no 18, p. 1197-1201Article in journal (Refereed)
    Abstract [en]

    Three different enzymes are discussed, cytochrome c oxidase, involved in aerobic respiration, cytochrome c dependent nitric oxide reductase, involved in denitrification (anaerobic respiration), and photosystem II, involved in photosynthesis. For all three systems, free energy profiles for the entire catalytic cycle are obtained from quantum mechanical calculations on large cluster models of the active sites, using hybrid density functional theory with the B3LYP* functional. The free energy pro-files are used to solve different fundamental problems concerning energy conservation, enzymatic reaction mechanisms and structure, and also to explain experimental results that seem to be in conflict with each other. Possible future applications to related problems using similar methodology are suggested.

  • 6.
    Blomberg, Margareta R. A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradient2015In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1847, no 3, p. 364-376Article in journal (Refereed)
    Abstract [en]

    Experiments have shown that the A-family cytochrome c oxidases pump four protons per oxygen molecule, also at a high electrochemical gradient. This has been considered a puzzle, since two of the reduction potentials involved, Cu(II) and Fe(III), were estimated from experiments to be too low to afford proton pumping at a high gradient The present quantum mechanical study (using hybrid density functional theory) suggests a solution to this puzzle. First, the calculations show that the charge compensated Cu(II) potential for Cu-B is actually much higher than estimated from experiment, of the same order as the reduction potentials for the tyrosyl radical and the ferryl group, which are also involved in the catalytic cycle. The reason for the discrepancy between theory and experiment is the very large uncertainty in the experimental observations used to estimate the equilibrium potentials, mainly caused by the lack of methods for direct determination of reduced Cu-B. Second, the calculations show that a high energy metastable state, labeled E-H, is involved during catalytic turnover. The E-H state mixes the low reduction potential of Fe(III) in heme a(3) with another, higher potential, here suggested to be that of the tyrosyl radical, resulting in enough exergonicity to allow proton pumping at a high gradient In contrast, the corresponding metastable oxidized state, O-H, is not significantly higher in energy than the resting state, O. Finally, to secure the involvement of the high energy E-H state it is suggested that only one proton is taken up via the K-channel during catalytic turnover.

  • 7.
    Blomberg, Margareta R. A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Protonation of the binuclear active site in cytochrome c oxidase decreases the reduction potential of Cu-B2015In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1847, no 10, p. 1173-1180Article in journal (Refereed)
    Abstract [en]

    One of the remaining mysteries regarding the respiratory enzyme cytochrome c oxidase is how proton pumping can occur in all reduction steps in spite of the low reduction potentials observed in equilibrium titration experiments for two of the active site cofactors, CUB(II) and Fe-a3(III). It has been speculated that, at least the copper cofactor can acquire two different states, one metastable activated state occurring during enzyme turnover, and one relaxed state with lower energy, reached only when the supply of electrons stops. The activated state should have a transiently increased Cu-B(II) reduction potential, allowing proton pumping. The relaxed state should have a lower reduction potential, as measured in the titration experiments. However, the structures of these two states are not known. Quantum mechanical calculations show that the proton coupled reduction potential for Cu-B is inherently high in the active site as it appears after reaction with oxygen, which explains the observed proton pumping. It is suggested here that, when the flow of electrons ceases, a relaxed resting state is formed by the uptake of one extra proton, on top of the charge compensating protons delivered in each reduction step. The extra proton in the active site decreases the proton coupled reduction potential for Cu-B by almost half a volt, leading to agreement with titration experiments. Furthermore, the structure for the resting state with an extra proton is found to have a hydroxo-bridge between Cu-B(II) and Fe-a3(III), yielding a magnetic coupling that can explain the experimentally observed EPR silence.

  • 8. Bunrit, Anon
    et al.
    Dahlstrand, Christian
    Olsson, Sandra K.
    Srifa, Pemikar
    Huang, Genping
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Orthaber, Andreas
    Sjöberg, Per J. R.
    Biswas, Srijit
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Samec, Joseph S. M.
    Brønsted Acid-Catalyzed Intramolecular Nucleophilic Substitution of the Hydroxyl Group in Stereogenic Alcohols with Chirality Transfer2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 14, p. 4646-4649Article in journal (Refereed)
    Abstract [en]

    The hydroxyl group of enantioenriched benzyl, propargyl, allyl, and alkyl alcohols has been intramolecularly displaced by uncharged O-, N-, and S-centered nucleophiles to yield enantioenriched tetrahydrofuran, pyrrolidine, and tetrahydrothiophene derivatives with phosphinic acid catalysis. The five-membered heterocyclic products are generated in good to excellent yields, with high degree of chirality transfer, and water as the only side-product. Racemization experiments show that phosphinic acid does not promote S(N)1 reactivity. Density functional theory calculations corroborate a reaction pathway where the phosphinic acid operates as a bifunctional catalyst in the intramolecular substitution reaction. In this mechanism, the acidic proton of the phosphinic acid protonates the hydroxyl group, enhancing the leaving group ability. Simultaneously, the oxo group of phosphinic acid operates as a base abstracting the nucleophilic proton and thus enhancing the nucleophilicity. This reaction will open up new atom efficient techniques that enable alcohols to be used as nucleofuges in substitution reactions in the future.

  • 9. Bustelo, Emilio
    et al.
    Gushchin, Artem L.
    Fernandez-Trujillo, M. Jesus
    Basallote, Manuel G.
    Algarra, Andres G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    On the Critical Effect of the Metal (Mo vs. W) on the [3+2] Cycloaddition Reaction of M3S4 Clusters with Alkynes: Insights from Experiment and Theory2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 42, p. 14823-14833Article in journal (Refereed)
    Abstract [en]

    Whereas the cluster [Mo3S4(acac)(3)(py)(3)](+) ([1](+), acac=acetylacetonate, py=pyridine) reacts with a variety of alkynes, the cluster [W3S4(acac)(3)(py)(3)](+) ([2](+)) remains unaffected under the same conditions. The reactions of cluster [1]+ show polyphasic kinetics, and in all cases clusters bearing a bridging dithiolene moiety are formed in the first step through the concerted [3+2] cycloaddition between the C equivalent to C atoms of the alkyne and a Mo(mu-S)(2) moiety of the cluster. A computational study has been conducted to analyze the effect of the metal on these concerted [3+ 2] cycloaddition reactions. The calculations suggest that the reactions of cluster [2](+) with alkynes feature Delta G(+) values only slightly larger than its molybdenum analogue, however, the differences in the reaction free energies between both metal clusters and the same alkyne reach up to approximately 10 kcal mol(-1), therefore indicating that the differences in the reactivity are essentially thermodynamic. The activation strain model (ASM) has been used to get more insights into the critical effect of the metal center in these cycloadditions, and the results reveal that the change in reactivity is entirely explained on the basis of the differences in the interaction energies E-int between the cluster and the alkyne. Further decomposition of the E-int values through the localized molecular orbital-energy decomposition analysis (LMO-EDA) indicates that substitution of the Mo atoms in cluster [1](+) by W induces changes in the electronic structure of the cluster that result in weaker intra-and inter-fragment orbital interactions.

  • 10.
    Das, Arindam
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Wang, Dong
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Belhomme, Marie-Charlotte
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Copper-Catalyzed Cross-Coupling of Allylboronic Acids with alpha-Diazoketones2015In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 17, no 19, p. 4754-4757Article in journal (Refereed)
    Abstract [en]

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

  • 11.
    Daver, Henrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Modelling of Biomimetic Phosphoesterase Complexes2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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

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

  • 12.
    Deng, Hong-Ping
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Wang, Dong
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Direct Allylation of Quinones with Allylboronates2015In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 80, no 6, p. 3343-3348Article in journal (Refereed)
    Abstract [en]

    Allylboronates undergo C-H allylation of unsubstituted or monosubstituted benzoquinone and naphthoquinone substrates. In the case of 2,5- or 2,6-disubstituted quinones addition involving the substituted carbon takes place. Allylation with stereodefined allylboronates occurs with retention of the configuration.

  • 13.
    Engelmark Cassimjee, Karim
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Manta, Bianca
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    A quantum chemical study of the ω-transaminase reaction mechanism2015In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 31, p. 8453-8464Article in journal (Refereed)
    Abstract [en]

    ω-Transaminases are valuable tools in biocatalysis due to their stereospecificity and their broad substrate range. In the present study, the reaction mechanism of Chromobacterium violaceum ω-transaminase is investigated by means of density functional theory calculations. A large active site model is designed based on the recent X-ray crystal structure. The detailed energy profile for the half-transamination of (S)-1-phenylethylamine to acetophenone is calculated and the involved transition states and intermediates are characterized. The model suggests that the amino substrate forms an external aldimine with the coenzyme pyridoxal-5′-phosphate (PLP), through geminal diamine intermediates. The external aldimine is then deprotonated in the rate-determining step, forming a planar quinonoid intermediate. A ketimine is then formed, after which a hemiaminal is produced by the addition of water. Subsequently, the ketone product is obtained together with pyridoxamine-5′-phosphate (PMP). In the studied half-transamination reaction the ketone product is kinetically favored. The mechanism presented here will be valuable to enhance rational and semi-rational design of engineered enzyme variants in the development of ω-transaminase chemistry.

  • 14.
    Eriksson, Kristofer
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nyholm, Leif
    Oscarsson, Sven
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dispersed Gold Nanoparticles Supported in the Pores of Siliceous Mesocellular Foam: A Catalyst for Cycloisomerization of Alkynoic Acids to gamma-Alkylidene Lactones2015In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 10, p. 2250-2255Article in journal (Refereed)
    Abstract [en]

    A versatile approach for the production of dispersed thiol-stabilized gold nanoparticles in the pores of siliceous mesocellular foam (MCF) is described. The reported method is based on an electrochemical oxidation of a gold surface generating oxidative Au-III species, which give rise to a surface-confined redox reaction yielding MCF-supported Au-I thiolates. By reducing the corresponding Au-I-S-MCF species with sodium borohydride, thiol-stabilized gold nanoparticles in the size range of 1-8 nm were obtained as determined by transmission electron microscopy. Elemental analysis indicated an Au loading of 3% (w/w) on the MCF. The surface-confined Au nanoparticles were used to catalyze the cycloisomerization of alkynoic acids to the corresponding -alkylidene lactones in high efficiency and complete 5-exo-dig selectivity under mild reaction conditions.

  • 15.
    Gigant, Nicolas
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Université Paris-Sud, France.
    Quintin, Francois
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Preparation of Tetrasubstituted Olefins Using Mono or Double Aerobic Direct C-H Functionalization Strategies: Importance of Steric Effects2015In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 80, no 5, p. 2796-2803Article in journal (Refereed)
    Abstract [en]

    A novel protocol for the synthesis of tetrasubstituted olefins through a biomimetic approach has been explored. Both mono- and diarylations were performed under ambient oxygen pressure, giving a range of highly hindered tetrasubstituted alkenes. For diarylation of disubstituted substrates, it was demonstrated that the second arylation is the rate-limiting step of the overall transformation.

  • 16. Girgis, Adel S.
    et al.
    Mabied, Ahmed F.
    Stawinski, Jacek
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hegazy, Lamees
    George, Riham F.
    Farag, Hanaa
    Shalaby, ElSayed M.
    Farag, I. S. Ahmed
    Synthesis and DFT studies of an antitumor active spiro-oxindole2015In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 39, no 10, p. 8017-8027Article in journal (Refereed)
    Abstract [en]

    An anti-oncological active spiro-oxindole 7 was synthesized regioselectively via a [3+2]-cycloaddition reaction of azomethine ylide to exocyclic olefinic linkage of 4-piperidone 6, exhibiting properties against diverse tumor cell lines including leukemia, melanoma and cancers of the lung, colon, brain, ovary, breast, prostate, and kidney. Compound 7 crystallizes in the monoclinic system and P21/c space group with four molecules in the unit cell. The structure was also studied by AM1, PM3 and DFT techniques. DFT studies support the stereochemical selectivity of the reaction and determine the molecular electrostatic potential and frontier molecular orbitals.

  • 17.
    Hamark, Christoffer
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    The sweet side of molecular structure: NMR spectroscopic studies of glycans and their interactions with proteins2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, within the topic of bioorganic chemistry, the molecular structure of carbohydrates has been studied. Carbohydrates, or glycans, are ubiquitous biomolecules exhibiting a wide range of biological roles. The specific functions of these molecules are largely determined by their interactions with proteins and molecular structure ultimately governs such specialized recognition events.

    Glycan-binding proteins, such as lectins or enzymes, often interact with their sweet ligands in a transient fashion and nuclear magnetic resonance spectroscopy (NMR) is a viable technique to probe these complexes. In particular, ligand-based NMR techniques have been employed, typically in combination with other biophysical as well as biochemical and computational methods. The aim of this work has been to gain new insights about specific biological systems, to develop methods and to devise protocols for their studies.

    The first two papers cover NMR-interaction studies of native ligands as well as inhibitor glycans with the enzyme hen egg-white lysozyme and the lectin botulinum neurotoxin type A. Screening experiments were performed to investigate ligand affinities and selectivities. Solution models in combination with X-ray crystal structures were compared in order to evaluate their agreement and the details of interactions.

    A method for application in carbohydrate ligand NMR-screening was developed in paper three. The heteronucleus selenium was exploited as a reporter of selenoglycosides binding to lectins. 77Se NMR spectroscopy proved sensitive to binding events and the presented approach should be useful in large screenings of glycomimetic inhibitors.  In order to obtain sufficient amounts of glycans for bioorganic studies their production often relies on chemical synthesis. In the last paper, the structure of some conformationally highly activated glycosyl donors was thoroughly investigated and related to their reactivity in synthetic glycosylation reactions.  

  • 18.
    Huang, Genping
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kalek, Marcin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mechanism, reactivity, and selectivity of the iridium-catalyzed C(sp(3))-H borylation of chlorosilanes2015In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 6, no 3, p. 1735-1746Article in journal (Refereed)
    Abstract [en]

    The iridium-catalyzed C(sp(3))-H borylation of methylchlorosilanes is investigated by means of density functional theory, using the B3LYP and M06 functionals. The calculations establish that the resting state of the catalyst is a seven-coordinate Ir(V) species that has to be converted into an Ir(III)tris(boryl) complex in order to effect the oxidative addition of the C-H bond. This is then followed by a C-B reductive elimination to yield the borylated product, and the catalytic cycle is finally completed by the regeneration of the active catalyst over two facile steps. The two employed functionals give somewhat different conclusions concerning the nature of the rate-determining step, and whether reductive elimination occurs directly or after a prior isomerization of the Ir(V) hydride intermediate complex. The calculations reproduce quite well the experimentally-observed trends in the reactivities of substrates with different substituents. It is demonstrated that the reactivity can be correlated to the Ir-C bond dissociation energies of the corresponding Ir(V) hydride intermediates. The effect of the chlorosilyl group is identified to originate from the alpha-carbanion-stabilizing effect of the silicon, which is further reinforced by the presence of an electron-withdrawing chlorine substituent. Furthermore, the source of selectivity for the borylation of primary over secondary C(sp(3))-H can be explained on a steric basis, by repulsion between the alkyl group and the Ir/ligand moiety. Finally, the difference in the reactivity between C(sp(3))-H and C(sp(2))-H borylation is investigated and rationalized in terms of distortion/interaction analysis.

  • 19.
    Janson, Pär G.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ilchenko, Nadia O.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Diez-Varga, Alberto
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Effects of B(2)pin(2) and PCy3 on copper-catalyzed trifluoromethylation of substituted alkenes and alkynes with the Togni reagent2015In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 71, no 6, p. 922-931Article in journal (Refereed)
    Abstract [en]

    The copper-catalyzed oxytrifluoromethylation of phenylacetylenes and C-H trifluoromethylation of quinones were studied. It was found that both reactions are accelerated by B(2)pin(2) and PCy3 additives. The two reactions have different substituent effects. The oxytrifluoromethylation is faster in the presence of electron-donating groups, while the C-H trifluoromethylation is faster with electron-withdrawing substituents. The Hammett plot for oxytrifluoromethylation gave a rho value of 0.76 indicating electron demand in the rate determining step of the reaction. According to the absolute value of rho the reaction probably does not proceed through a rate determining formation of a carbocation intermediate. The kinetic isotope effect measurements indicate that in C-H trifluoromethylation of quinones the cleavage of the C-H bond is not the rate determining step of the reaction.

  • 20.
    Jiang, Tuo
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bartholomeyzik, Teresa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mazuela, Javier
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Willersinn, Jochen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium(II)/Bronsted Acid-Catalyzed Enantioselective Oxidative Carbocyclization-Borylation of Enallenes2015In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 54, no 20, p. 6024-6027Article in journal (Refereed)
    Abstract [en]

    An enantioselective oxidative carbocyclization-borylation of enallenes that is catalyzed by palladium(II) and a Bronsted acid was developed. Biphenol-type chiral phosphoric acids were superior co-catalysts for inducing the enantioselective cyclization. A number of chiral borylated carbocycles were synthesized in high enantiomeric excess.

  • 21. Kabeshov, Mikhail A.
    et al.
    Kysilka, Ondřej
    Rulíšek, Lubomír
    Suleimanov, Yury V.
    Bella, Marco
    Malkov, Andrei V.
    Kočovský, Pavel
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Czech Academy of Sciences, Czech Republic; Charles University Prague, Czech Republic.
    Cross-Aldol Reaction of Isatin with Acetone Catalyzed by Leucinol: A Mechanistic Investigation2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 34, p. 12026-12033Article in journal (Refereed)
    Abstract [en]

    Comprehensive mechanistic studies on the enantioselective aldol reaction between isatin (1a) and acetone, catalyzed by L-leucinol (3a), unraveled that isatin, apart from being a substrate, also plays an active catalytic role. Conversion of the intermediate oxazolidine 4 into the reactive syn-enamine 6, catalyzed by isatin, was identified as the rate-determining step by both the calculations (G=26.1kcalmol(-1) for the analogous L-alaninol, 3b) and the kinetic isotope effect (k(H)/k(D)=2.7 observed for the reaction using [D-6]acetone). The subsequent reaction of the syn-enamine 6 with isatin produces (S)-2a (calculated G=11.6kcalmol(-1)). The calculations suggest that the overall stereochemistry is controlled by two key events: 1)the isatin-catalyzed formation of the syn-enamine 6, which is thermodynamically favored over its anti-rotamer 7 by 2.3kcalmol(-1); and 2)the high preference of the syn-enamine 6 to produce (S)-2a on reaction with isatin (1a) rather than its enantiomer (G=2.6kcalmol(-1)).

  • 22.
    Kerdphon, Sutthichat
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    N-Heterocyclic Carbene-Phosphine Iridium Catalyzed Alkylation Reactions and Asymmetric Hydrogenation of Ketones2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is focused on hydrogen transfer reactions using N-heterocyclic carbenephosphine iridium catalysts and is divided in two parts. The first part describes the use of achiral N-heterocyclic carbene-phosphine iridium complexes catalyzing the methylation of ketones and alkylation of amides using alcohols as the electrophile. In Chapter 2, the N-heterocyclic carbene-phosphine iridium complexes that have been developed in the Andersson group was employed as catalysts for the methylation of ketones. These reactions were found to take place under mild conditions with low catalyst loading (1.0 mol%) to furnish the desired methylated products in up to 98% isolated yield. The achiral N-heterocyclic carbene-phosphine iridium complexes were also found to catalyze the N-alkylation of amides with alcohols, as presented in Chapter 3. It was discovered that the reactivity of the catalysts was highly dependent on the structure of the catalyst. At optimum reaction conditions, the best catalyst could be used with a wide range of substrates at low catalyst loading (0.5 mol%) to afford the desired product up to 98% isolated yield.

    The second part of this thesis details the preparation of chiral N-heterocyclic carbenephosphine iridium complexes and their use in the asymmetric hydrogenation of ketones (Chapter 4). These catalysts were successfully used in the asymmetric hydrogenation of ketones at room temperature under base-free conditions and led to full conversion of chiral alcohol products in 30 min with high enantiomeric excess (up to 96%).

  • 23.
    Kocovsky, Pavel
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Academy of Sciences of the Czech Republic, Czech Republic; Charles University, Czech Republic.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    The syn/anti-Dichotomy in the Palladium-Catalyzed Addition of Nucleophiles to Alkenes2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 51, p. 36-56Article in journal (Refereed)
    Abstract [en]

    In this review the stereochemistry of palladium-catalyzed addition of nucleophiles to alkenes is discussed, and examples of these reactions in organic synthesis are given. Most of the reactions discussed involve oxygen and nitrogen nucleophiles; the Wacker oxidation of ethylene has been reviewed in detail. An anti-hydroxypalladation in the Wacker oxidation has strong support from both experimental and computational studies. From the reviewed material it is clear that anti-addition of oxygen and nitrogen nucleophiles is strongly favored in intermolecular addition to olefin-palladium complexes even if the nucleophile is coordinated to the metal. On the other hand, syn-addition is common in the case of intramolecular oxy- and amidopalladation as a result of the initial coordination of the internal nucleophile to the metal.

  • 24.
    Kovalenko, Oleksandr O.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Highly Efficient and Chemoselective Zinc-Catalyzed Hydrosilylation of Esters under Mild Conditions2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 7, p. 2785-2788Article in journal (Refereed)
    Abstract [en]

    A mild and highly efficient catalytic hydrosilylation protocol for room-temperature ester reductions has been developed using diethylzinc as the catalyst. The methodology is operationally simple, displays high functional group tolerance and provides for a facile access to a broad range of different alcohols in excellent yields.

  • 25.
    Kovalenko, Oleksandr O.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Volkov, Alexey
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mild and Selective Et2Zn-Catalyzed Reduction of Tertiary Amides under Hydrosilylation Conditions2015In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 17, no 3, p. 446-449Article in journal (Refereed)
    Abstract [en]

    Diethylzinc (Et2Zn) can be used as an efficient and chemoselective catalyst for the reduction of tertiary amides under mild reaction conditions employing cost-effective polymeric silane (PMHS) as the hydride source. Crucial for the catalytic activity was the addition of a substoichiometric amount of lithium chloride to the reaction mixture. A series of amides containing different additional functional groups were reduced to their corresponding amines, and the products were isolated in good-to-excellent yields.

  • 26.
    Laine, Tanja M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Huazhong University of Science & Technology, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    A Dinuclear Ruthenium-Based Water Oxidation Catalyst: Use of Non-Innocent Ligand Frameworks for Promoting Multi-Electron Reactions2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 28, p. 10039-10048Article in journal (Refereed)
    Abstract [en]

    Insight into how H2O is oxidized to O-2 is envisioned to facilitate the rational design of artificial water oxidation catalysts, which is a vital component in solar-to-fuel conversion schemes. Herein, we report on the mechanistic features associated with a dinuclear Ru-based water oxidation catalyst. The catalytic action of the designed Ru complex was studied by the combined use of high-resolution mass spectrometry, electrochemistry, and quantum chemical calculations. Based on the obtained results, it is suggested that the designed ligand scaffold in Ru complex 1 has a non-innocent behavior, in which metal-ligand cooperation is an important part during the four-electron oxidation of H2O. This feature is vital for the observed catalytic efficiency and highlights that the preparation of catalysts housing non-innocent molecular frameworks could be a general strategy for accessing efficient catalysts for activation of H2O.

  • 27.
    Laine, Tanja M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Huazhong University of Science & Technology, People's Republic of China.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lee, Bao-Lin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Karlsson, Erik A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Efficient photochemical water oxidation by a dinuclear molecular ruthenium complex2015In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 51, no 10, p. 1862-1865Article in journal (Refereed)
    Abstract [en]

    Herein is described the preparation of a dinuclear molecular Ru catalyst for H2O oxidation. The prepared catalyst mediates the photochemical oxidation of H2O with an efficiency comparable to state-of-the-art catalysts.

  • 28.
    Li, Xichen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Beijing Normal University, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Alternative mechanisms for O-2 release and O-O bond formation in the oxygen evolving complex of photosystem II2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 18, p. 12168-12174Article in journal (Refereed)
    Abstract [en]

    In a previous detailed study of all the steps of water oxidation in photosystem II, it was surprisingly found that O-2 release is as critical for the rate as O-O bond formation. A new mechanism for O-2 release has now been found, which can be described as an opening followed by a closing of the interior of the oxygen evolving complex. A transition state for peroxide rotation forming a superoxide radical, missed in the previous study, and a structural change around the outside manganese are two key steps in the new mechanism. However, O-2 release may still remain rate-limiting. Additionally, for the step forming the O-O bond, an alternative, experimentally suggested, mechanism was investigated. The new model calculations can rule out the precise use of that mechanism. However, a variant with a rotation of the ligands around the outer manganese by about 301 will give a low barrier, competitive with the old DFT mechanism. Both these mechanisms use an oxyl-oxo mechanism for O-O bond formation involving the same two manganese atoms and the central oxo group (O5).

  • 29. Li, Xichen
    et al.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Water Oxidation for Simplified Models of the Oxygen-Evolving Complex in Photosystem II2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 51, p. 18821-18827Article in journal (Refereed)
    Abstract [en]

    For the main parts of the mechanism for water oxidation in photosystem II there has recently been very strong experimental support for the mechanism suggested by theoretical model studies. The question addressed in the present study is to what extent this knowledge can be used for the design of artificial catalysts. A major requirement for a useful artificial catalyst is that it is small enough to be synthesized. Small catalysts also have the big advantage that they could improve the catalysis per surface area. To make the mechanism found for PSII useful in this context, it needs to be analyzed in detail. A small model system was therefore used and the ligands were replaced one by one by water-derived ligands. Only the main chemical step of O-O bond formation was investigated in this initial study. The energetics for this small model and the larger one previously used for PSII are remarkably similar, which is the most important result of the present study. This shows that small model complexes have a potential for being very good water oxidation catalysts. It was furthermore found that there is a clear correlation between the barrier height for O-O bond formation and the type of optimal structure for the S-3 state. The analysis shows that a flexible central part of the complex is the key for efficient water oxidation.

  • 30. Li, Xichen
    et al.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ryde, Ulf
    Simulation of the isotropic EXAFS spectra for the S-2 and S-3 structures of the oxygen evolving complex in photosystem II2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 13, p. 3979-3984Article in journal (Refereed)
    Abstract [en]

    Most of the main features of water oxidation in photosystem II are now well understood, including the mechanism for O-O bond formation. For the intermediate S-2 and S-3 structures there is also nearly complete agreement between quantum chemical modeling and experiments. Given the present high degree of consensus for these structures, it is of high interest to go back to previous suggestions concerning what happens in the S-2-S-3 transition. Analyses of extended X-ray adsorption fine structure (EXAFS) experiments have indicated relatively large structural changes in this transition, with changes of distances sometimes larger than 0.3 angstrom and a change of topology. In contrast, our previous density functional theory (DFT)(B3LYP) calculations on a cluster model showed very small changes, less than 0.1 angstrom. It is here found that the DFT structures are also consistent with the EXAFS spectra for the S2 and S3 states within normal errors of DFT. The analysis suggests that there are severe problems in interpreting EXAFS spectra for these complicated systems.

  • 31. Liao, Rong-Zhen
    et al.
    Chen, Shi-Lu
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Which Oxidation State Initiates Dehalogenation in the B12-Dependent Enzyme NpRdhA: Co-II, COI or Co-0?2015In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 5, no 12, p. 7350-7358Article in journal (Refereed)
    Abstract [en]

    The quantum chemical cluster approach was used to elucidate the reaction mechanism of debromination catalyzed by the B12-dependent reductive dehalogenase NpRdliA. Various pathways, involving different oxidation states of the cobalt ion and different protonation states of the model, have been analyzed in order to find the most favorable one. We find that the reductive C Br cleavage takes place exclusively at the Co' state via a heterolytic pathway in the singlet state. Importantly, the C-H bond formation and the C Br bond cleavage proceeds via a concerted transition state, as opposed to the stepwise pathway suggested before. C Br cleavage at the Coll state has a very high barrier, and the reduction of Co' to Co is associated with a very negative potential; thus, reductive dehalogenation at Coll and Co can be safely ruled out. Examination of substrate with different halogen substitutions (F, Cl, Br, I) shows that the dehalogenation reactivity follows the order C I > C Br > C-C1 > C-F, and the barrier for defluorination is so high that NpRdhA cannot catalyze that reaction.

  • 32.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lee, Bao-Lin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Photosystem II Like Water Oxidation Mechanism in a Bioinspired Tetranuclear Manganese Complex2015In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 54, no 1, p. 342-351Article in journal (Refereed)
    Abstract [en]

    The synthesis of Mn-based catalysts to mimic the structural and catalytic properties of the oxygen-evolving complex in photosystem II is a long-standing goal for researchers. An interesting result in this field came with the synthesis of a Mn complex that enables water oxidation driven by the mild single-electron oxidant [Ru(bpy)(3)](3+). On the basis of hybrid density functional calculations, we herein propose a water oxidation mechanism for this bioinspired Mn catalyst, where the crucial O-O bond formation proceeds from the formal Mn-4(IV,IV,IV,V) state by direct coupling of a Mn-IV-bound terminal oxyl radical and a di-Mn bridging oxo group, a mechanism quite similar to the presently leading suggestion for the natural system. Of importance here is that the designed ligand is shown to be redox-active and can therefore store redox equivalents during the catalytic transitions, thereby alleviating the redox processes at the Mn centers.

  • 33.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Huazhong University of Science & Technology, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mechanism and selectivity of the dinuclear iron benzoyl-coenzyme A epoxidase BoxB2015In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 6, no 5, p. 2754-2764Article in journal (Refereed)
    Abstract [en]

    Benzoyl-CoA epoxidase is a dinuclear iron enzyme that catalyzes the epoxidation reaction of the aromatic ring of benzoyl-CoA with chemo-, regio- and stereo-selectivity. It has been suggested that this enzyme may also catalyze the deoxygenation reaction of epoxide, suggesting a unique bifunctionality among the diiron enzymes. We report a density functional theory study of this enzyme aimed at elucidating its mechanism and the various selectivities. The epoxidation is suggested to start with the binding of the O-2 molecule to the diferrous center to generate a diferric peroxide complex, followed by concerted O-O bond cleavage and epoxide formation. Two different pathways have been located, leading to (2S,3R)-epoxy and (2R,3S)-epoxy products, with barriers of 17.6 and 20.4 kcal mol(-1), respectively. The barrier difference is 2.8 kcal mol(-1), corresponding to a diastereomeric excess of about 99 : 1. Further isomerization from epoxide to phenol is found to have quite a high barrier, which cannot compete with the product release step. After product release into solution, fast epoxide-oxepin isomerization and racemization can take place easily, leading to a racemic mixture of (2S,3R) and (2R,3S) products. The deoxygenation of epoxide to regenerate benzoyl-CoA by a diferrous form of the enzyme proceeds via a stepwise mechanism. The C2-O bond cleavage happens first, coupled with one electron transfer from one iron center to the substrate, to form a radical intermediate, which is followed by the second C3-O bond cleavage. The first step is rate-limiting with a barrier of only 10.8 kcal mol(-1). Further experimental studies are encouraged to verify our results.

  • 34.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Huazhong University of Science & Technology, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mechanism for O-O bond formation in a biomimetic tetranuclear manganese cluster - A density functional theory study2015In: Journal of Photochemistry and Photobiology. B: Biology, ISSN 1011-1344, E-ISSN 1873-2682, Vol. 152, no Part A, p. 162-172Article in journal (Refereed)
    Abstract [en]

    Density functional theory calculations have been used to study the reaction mechanism of water oxidation catalyzed by a tetranuclear Mn-oxo cluster Mn4O4L6 (L = (C6H4)(2)PO4-). It is proposed that the O-O bond formation mechanism is different in the gas phase and in a water solution. In the gas phase, upon phosphate ligand dissociation triggered by light absorption, the O-O bond formation starting with both the Mn-4(III,III,IV,IV) and Mn-4(III,IV,IV,IV) oxidation states has to take place via direct coupling of two bridging oxo groups. The calculated barriers are 42.3 and 37.1 kcal/mol, respectively, and there is an endergonicity of more than 10 kcal/mol. Additional photons are needed to overcome these large barriers. In water solution, water binding to the two vacant sites of the Mn ions, again after phosphate dissociation triggered by light absorption, is thermodynamically and kinetically very favorable. The catalytic cycle is suggested to start from the Mn-4(III,III,III,IV) oxidation state. The removal of three electrons and three protons leads to the formation of a Mn-4(III,IV,IV,IV)-oxyl radical complex. The O-O bond formation then proceeds via a nucleophilic attack of water on the Mn-IV-oxyl radical assisted by a Mn-bound hydroxide that abstracts a proton during the attack. This step was calculated to be rate-limiting with a total barrier of 29.2 kcal/mol. This is followed by proton-coupled electron transfer, O-2 release, and water binding to start the next catalytic cycle.

  • 35.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Phosphate Hydrolysis by the Fe-2-Ca-3-Dependent Alkaline Phosphatase PhoX: Mechanistic Insights from DFT calculations2015In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 54, no 24, p. 11941-11947Article in journal (Refereed)
    Abstract [en]

    PhoX is a pentanudear metalloenzyme that employs two ferric ions and three calcium ions to catalyze the hydrolysis of phosphomonoesters. On the basis of the X-ray structure of PhoX (Science 2014, 34S, 1170-1173), a model of the active site is designed, and quantum chemical calculations are used to investigate the reaction mechanism of this enzyme. The calculations support the experimental suggestion, in which the two high spin ferric ions interact in an antiferromagnetic fashion. The two step mechanism proposed by experimentalists has been investigated. The nudeophilic attack of a trinudear bridging oxo group on the phosphorus center was calculated to be the first step, which is concomitant with the departure of the phenolate, which is stabilized by a calcium ion. The second step is a reverse attack by a water molecule activated by a calciumbound hydroxide, leading to the regeneration of the bridging oxo group. The second step was calculated to have a barrier of 27.6 kcal/mol. The high barrier suggests that the alternative mechanism involving phosphate release directly from the active site seems to be more likely. All five metal ions are involved in the catalysis by stabilizing the pentacoordinated trigonal bipyramidal transition states.

  • 36. Liao, Rong-Zhen
    et al.
    Wang, Mei
    Sun, Licheng
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    The mechanism of hydrogen evolution in Cu(bztpen)-catalysed water reduction: a DFT study2015In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 44, no 21, p. 9736-9739Article in journal (Refereed)
    Abstract [en]

    The mechanism of water reduction catalysed by a mononuclear copper complex Cu(bztpen) (bztpen = N-benzyl-N, N', N'-tris(pyridine-2-ylmethyl) ethylenediamine) has been elucidated by DFT calculations, revealing that hydrogen evolution proceeds via coupling of a Cu(II)-hydride and a pendant pyridinium, and providing important implications for the future design of new catalytic systems for water reduction.

  • 37.
    Lindstedt, Erik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of Aryl Ethers: Metal-Free Arylation of Alcohols using Diaryliodonium Salts2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis contains two parts showing different metal-free methods to synthesize aryl ethers using hypervalent iodine reagents, more specifically diaryliodonium salts. The first part describes arylation of benzylic and allylic alcohols and phenols in water using the easily accessible base sodium hydroxide. Chemoselectivity of phenols in aqueous media is discussed and limitations of the reaction are presented.

    The second part describes an arylation of aliphatic alcohols at room temperature with short reaction time and no excess of reagents are required. The scope of the methodology was investigated and showed that electron-deficient iodonium salts worked efficiently, but unfortunately electron-rich was not compatible with the reaction conditions. The methodology was applied in a formal synthesis of Butoxycaine.

  • 38.
    Lundberg, Helena
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hans, Adolfsson
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hafnium-Catalyzed Direct Amide Formation at Room Temperature2015In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 5, no 6, p. 3271-3277Article in journal (Refereed)
    Abstract [en]

    Herein, the first example of a metal-catalyzed protocol for direct amidation of non-activated carboxylic acids at ambient temperature (26 °C) is presented. The mild reaction conditions give rise to high yields of a range of amides in reaction times as short as 90 minutes, employing a commercial hafnium complex, [Hf(Cp)2Cl2], as catalyst. Amino acids are transformed into their corresponding amides without racemization, and the catalyst displays full selectivity for the amidation of carboxylic acids over esters. Electronic properties of the carboxylic acids were found to have a strong influence on the rate of the amidation reaction, and the need for a balanced amount of molecular sieves was observed to be highly important for optimal reaction outcome.

  • 39.
    Mazuela, Javier
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Banerjee, Debasis
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium(II)-Catalyzed Tandem Oxidative Acetoxylation/ortho C-H Activation/Carbocyclization of Arylallenes2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 30, p. 9559-9562Article in journal (Refereed)
    Abstract [en]

    Herein we report an example of tandem. oxidative acetoxylation/carbocyclization of arylallenes 1 using Pd(OAc)(2). The catalytic protocol is highly selective and provides access to new C-C and C-O bonds leading to a carbocyclization. The reaction proceeds via C-H activation by Pd. Mechanistic investigations show that the C-H activation is not the rate-limiting step and indicate that the reaction proceeds via acetoxylation of the allene.

  • 40. Olsen, Esben P. K.
    et al.
    Singh, Thishana
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Uppsala University, Sweden.
    Harris, Pernille
    Andersson, Pher G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Madsen, Robert
    Experimental and Theoretical Mechanistic Investigation of the Iridium-Catalyzed Dehydrogenative Decarbonylation of Primary Alcohols2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 2, p. 834-842Article in journal (Refereed)
    Abstract [en]

    The mechanism for the iridium-BINAP catalyzed dehydrogenative decarbonylation of primary alcohols with the liberation of molecular hydrogen and carbon monoxide was studied experimentally and computationally. The reaction takes place by tandem catalysis through two catalytic cycles involving dehydrogenation of the alcohol and decarbonylation of the resulting aldehyde. The square planar complex IrCl(CO)(rac-BINAP) was isolated from the reaction between [Ir(cod)Cl](2), rac-BINAP, and benzyl alcohol. The complex was catalytically active and applied in the study of the individual steps in the catalytic cycles. One carbon monoxide ligand was shown to remain coordinated to iridium throughout the reaction, and release of carbon monoxide was suggested to occur from a dicarbonyl complex. IrH2Cl(CO)(rac-BINAP) was also synthesized and detected in the dehydrogenation of benzyl alcohol. In the same experiment, IrHCl2(CO)(rac-BINAP) was detected from the release of HCl in the dehydrogenation and subsequent reaction with IrCl(CO)(rac-BINAP). This indicated a substitution of chloride with the alcohol to form a square planar iridium alkoxo complex that could undergo a beta-hydride elimination. A KIE of 1.0 was determined for the decarbonylation and 1.42 for the overall reaction. Electron rich benzyl alcohols were converted faster than electron poor alcohols, but no electronic effect was found when comparing aldehydes of different electronic character. The lack of electronic and kinetic isotope effects implies a rate-determining phosphine dissociation for the decarbonylation of aldehydes.

  • 41.
    Peters, Byron K.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liu, Jianguo
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Margarita, Cristiana
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Andersson, Pher G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Formal Total Synthesis of Aliskiren2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 19, p. 7292-7296Article in journal (Refereed)
    Abstract [en]

    The efficient and selective formal total synthesis of aliskiren is described. Aliskiren, a renin inhibitor drug, has received considerable attention, primarily because it is the first of the renin inhibitor drugs to be approved by the FDA. Herein, the formal synthesis of aliskiren by iridium-catalyzed asymmetric hydrogenation of two allylic alcohol fragments is reported. Screening a number of N,P-ligated iridium catalysts yielded two catalysts that gave the highest enantioselectivity in the hydrogenation, which gave the saturated alcohols in 97 and 93% ee. In only four steps after hydrogenation, the fragments were combined by using the Julia-Kocienski reaction to produce late-stage intermediate in an overall yield of 18%.

  • 42. Pino-Chamorro, Jose Ángel
    et al.
    Gushchin, Artem L.
    Fernandez-Trujillo, M. Jesus
    Hernandez-Molina, Rita
    Vicent, Cristian
    Algarra, Andres G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Basallote, Manuel G.
    Mechanism of [3+2] Cycloaddition of Alkynes to the [Mo3S4(acac)(3)(py)(3)][PF6] Cluster2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 7, p. 2835-2844Article in journal (Refereed)
    Abstract [en]

    A study, involving kinetic measurements on the stopped-flow and conventional UV/Vis timescales, ESI-MS, NMR spectroscopy and DFT calculations, has been carried out to understand the mechanism of the reaction of [Mo3S4(acac)(3)(py)(3)][PF6] ([1]PF6; acac = acetylacetonate, py = pyridine) with two RC equivalent to CR alkynes (R = CH2OH (btd), COOH (adc)) in CH3CN. Both reactions show polyphasic kinetics, but experimental and computational data indicate that alkyne activation occurs in a single kinetic step through a concerted mechanism similar to that of organic [3+2] cycloaddition reactions, in this case through the interaction with one Mo(mu-S)(2) moiety of [1](+). The rate of this step is three orders of magnitude faster for adc than that for btd, and the products initially formed evolve in subsequent steps into compounds that result from substitution of py ligands or from reorganization to give species with different structures. Activation strain analysis of the [3+2] cycloaddition step reveals that the deformation of the two reactants has a small contribution to the difference in the computed activation barriers, which is mainly associated with the change in the extent of their interaction at the transition-state structures. Subsequent frontier molecular orbital analysis shows that the carboxylic acid substituents on adc stabilize its HOMO and LUMO orbitals with respect to those on btd due to better electron-withdrawing properties. As a result, the frontier molecular orbitals of the cluster and alkyne become closer in energy; this allows a stronger interaction.

  • 43.
    Pu, Maoping
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ab Initio Molecular Dynamics with Explicit Solvent Reveals a Two-Step Pathway in the Frustrated Lewis Pair Reaction2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 49, p. 17708-17720Article in journal (Refereed)
    Abstract [en]

    The role solvent plays in reactions involving frustrated Lewis pairs (FLPs)-for example, the stoichiometric mixture of a bulky Lewis acid and a bulky Lewis base-still remains largely unexplored at the molecular level. For a reaction of the phosphorus/boron FLP and dissolved CO2 gas, first principles (Born-Oppenheimer) molecular dynamics with explicit solvent reveals a hitherto unknown two-step reaction pathway-one that complements the concerted (one-step) mechanism known from the minimum-energy-path calculations. The rationalization of the discovered reaction pathway-that is, the stepwise formation of P-C and O-B bonds-is that the environment (typical organic solvents) stabilizes an intermediate which results from nucleophilic attack of the phosphorus Lewis base on CO2. This finding is significant because presently the concerted reaction-path paradigm predominates in the rationalization of FLP reactivity. Herein we point out how to attain experimental proof of our results.

  • 44.
    Pu, Maoping
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chemistry of Intermolecular Frustrated Lewis Pairs in Motion: Emerging Perspectives and Prospects2015In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 55, no 2, p. 179-195Article, review/survey (Refereed)
    Abstract [en]

    This feature article describes the chemistry in motion of frustrated Lewis pairs (FLPs). With state-of-the-art ab initio molecular dynamics (AIMD) simulations supplemented by minimum energy path (MEP) and potential energy surface (PES) calculations, we examine the binding of CO2 and the heterolytic cleavage of H-2 by a Lewis base (LB), tBu(3)P, and a Lewis acid (LA), B(C6F5)(3). We strive to uncover and understand mechanistic implications of the physical laws that govern the behavior of a LB and a LA when they react with a third species (e.g., CO2 or H-2) at finite temperature. The approximation that we necessarily must make at present is to forgo the quantization of the movement of atoms in favor of the Born-Oppenheimer molecular dynamics (BOMD), which unfold according to the classical (Newton's) laws of motion. However, strict quantum chemical theory is used to compute all of the forces that govern the dynamics of the macromolecular FLP system. Using physical reasoning and innovative computer simulations, we show that multi-scale motion is the predominant mechanistic aspect in reactions of the tBu(3)P/B(C6F5)(3) FLP, as well as, conceivably, those of other similar intermolecular FLPs. Insight achieved thus far leads to a novel activity model for intermolecular FLPs and specific predictions, which could be useful for future experimental and theoretical studies of FLP and other chemistries.

  • 45. Pàmies, Oscar
    et al.
    Diéguez, Montserrat
    Bäckvall, Jan-E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Artificial Metalloenzymes in Asymmetric Catalysis: Key Developments and Future Directions2015In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 357, no 8, p. 1567-1586Article in journal (Refereed)
    Abstract [en]

    Artificial metalloenzymes combine the excellent selective recognition/binding properties of enzymes with transition metal catalysts, and therefore many asymmetric transformations can benefit from these entities. The search for new successful strategies in the construction of metal-enzyme hybrid catalysts has therefore become a very active area of research. This review discusses all the developed strategies and the latest advances in the synthesis and application in asymmetric catalysis of artificial metalloenzymes with future directions for their design, synthesis and application (Sections 2-4). Finally, advice is presented (to the non-specialist) on how to prepare and use artificial metalloenzymes (Section 5).

  • 46.
    Rabten, Wangchuk
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Development of Ruthenium Complexes for Water Oxidation2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Development of a methodology to combat the world energy crisis can be one of the greatest challenges now facing mankind. Our research is focused on the development of versatile catalysts (WOCs) that oxidize water into molecular oxygen at neutral pH, driven by the mild one-electron oxidant [Ru(bpy)3]3+, using natural photosynthesis a sa model.

    The first part of the thesis describes the unexpected generation of a mononuclear Ru complex from a hexadentate ligand, which was envisioned to accommodate two metal atoms. The study of this mononuclear catalyst clearly demonstrated the importance of having strongly electron donating functional groups and their effect on catalytic water oxidation.

    The second part of thesis presents the preparation of a mononuclear Ru complex, which contains two amide groups in the ligand scaffold and the superior reactivity of this complex in catalytic water oxidation under neutral condition. When mild one-electronoxidant [Ru(bpy)3]3+ was employed, TONs of ∼ 6000 and TOFs of ∼20s-1 were achieved, which are the highest values reported so far, using this type of oxidant

  • 47.
    Rabten, Wangchuk
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chen, Hong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Liao, Rong-Zhen
    Tinnis, Fredrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Andersson, Pher G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Catalytic Water Oxidation by a Molecular Ruthenium Complex: Unexpected Generation of a Single-Site Water Oxidation Catalyst2015In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 54, no 10, p. 4611-4620Article in journal (Refereed)
    Abstract [en]

    The increasing energy demand calls for the development of sustainable energy conversion processes. Here, the splitting of H2O to O-2 and H-2, or related fuels, constitutes an excellent example of solar-to-fuel conversion schemes. The critical component in such schemes has proven to be the catalyst responsible for mediating the four-electron oxidation of H2O to O-2. Herein, we report on the unexpected formation of a single-site Ru complex from a ligand envisioned to accommodate two metal centers. Surprising N-N bond cleavage of the designed dinuclear ligand during metal complexation resulted in a single-site Ru complex carrying a carboxylate amide motif. This ligand lowered the redox potential of the Ru complex sufficiently to permit H2O oxidation to be carried out by the mild one-electron oxidant [Ru(bpy)(3)](3+) (bpy = 2,2'-bipyridine). The work thus highlights that strongly electron-donating ligands are important elements in the design of novel, efficient H2O :oxidation catalysts.

  • 48. Romanini, Simone
    et al.
    Galletti, Emilio
    Caruana, Lorenzo
    Mazzanti, Andrea
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Santoro, Stefano
    Fochi, Mariafrancesca
    Bernardi, Luca
    Catalytic Asymmetric Reactions of 4-Substituted Indoles with Nitroethene: A Direct Entry to Ergot Alkaloid Structures2015In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, no 49, p. 17578-17582Article in journal (Refereed)
    Abstract [en]

    A domino Friedel-Crafts/nitro-Michael reaction between 4-substituted indoles and nitroethene is presented. The reaction is catalyzed by BINOL-derived phosphoric acid catalysts, and delivers the corresponding 3,4-ring-fused indoles with very good results in terms of yields and diastereo- and enantioselectivities. The tricyclic benzo[c-d] indole products bear a nitro group at the right position to serve as precursors of ergot alkaloids, as demonstrated by the formal synthesis of 6,7-secoagroclavine from one of the adducts. DFT calculations suggest that the outcome of the reaction stems from the preferential evolution of a key nitronic acid intermediate through a nucleophilic addition pathway, rather than to the expected quenching through protonation.

  • 49.
    Santoro, Stefano
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Marcelli, Tommaso
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hammar, Peter
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical Study of Mechanism and Stereoselectivity of Catalytic Kinugasa Reaction2015In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 80, no 5, p. 2649-2660Article in journal (Refereed)
    Abstract [en]

    The mechanism of the catalytic Kinugasa reaction is investigated by means of density functional theory calculations. Different possible mechanistic scenarios are presented using phenanthroline as a ligand, and it is shown that the most reasonable one in terms of energy barriers involves two copper ions. The reaction starts with the formation of a dicopper-acetylide that undergoes a stepwise cycloaddition with the nitrone, generating a five-membered ring intermediate. Protonation of the nitrogen of the metalated isoxazoline intermediate results in ring opening and the formation of a ketene intermediate. This then undergoes a copper-catalyzed cyclization by an intramolecular nucleophilic attack of the nitrogen on the ketene, affording a cyclic copper enolate. Catalyst release and tautomerization gives the final beta-lactamic product. A comprehensive study of the enantioselective reaction was also performed with a chiral bis(azaferrocene) ligand. In this case, two different reaction mechanisms, involving either the scenario with the two copper ions or a direct cycloaddition of the parent alkyne using one copper ion, were found to have quite similar barriers. Both mechanisms reproduced the experimental enantioselectivity, and the current calculations can therefore not distinguish between the two possibilities.

  • 50.
    Shatskiy, Andrey
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kivijärvi, Tove
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lundberg, Helena
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tinnis, Fredrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ruthenium-Catalyzed Asymmetric Transfer Hydrogenation of Propargylic Ketones2015In: ChemCatChem, ISSN 1867-3880, E-ISSN 1867-3899, Vol. 7, no 23, p. 3818-3821Article in journal (Refereed)
    Abstract [en]

    The asymmetric transfer hydrogenation of alpha,beta-propargyl ketones catalyzed by an in situ formed ruthenium-hydroxyamide complex was explored. The acetylenic alcohols were isolated in good to excellent yields with excellent ee values (typically >90%) after short reaction times at room temperature.

12 1 - 50 of 68
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