Endre søk
Begrens søket
123 1 - 50 of 107
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Treff pr side
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
Merk
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 1. Agasti, Soumitra
    et al.
    Maity, Soham
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maiti, Debabrata
    Palladium-Catalyzed Synthesis of 2,3-Disubstituted Benzofurans: An Approach Towards the Synthesis of Deuterium Labeled Compounds2015Inngår i: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 357, nr 10, s. 2331-2338Artikkel i tidsskrift (Fagfellevurdert)
    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
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Catalytic Regio- and Stereoselective Reactions for the Synthesis of Allylic and Homoallylic Compounds2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis is focused on two main areas of organic synthesis, palladium-catalyzed functionalization of alkenes and allylic alcohols, as well as development of new allylboration reactions.

    We have developed a palladium-catalyzed selective allylic trifluoroacetoxylation reaction based on C−H functionalization. Allylic trifluoroacetates were synthesized from functionalized olefins under oxidative conditions. The reactions proceed under mild conditions with a high level of diastereoselectivity. Mechanistic studies of the allylic C−H trifluoroacetoxylation indicate that the reaction proceeds via (η3-allyl)palladium(IV) intermediate.

    Palladium-catalyzed regio- and stereoselective synthesis of allylboronic acids from allylic alcohols has been demonstrated. Diboronic acid B2(OH)4 was used as the boron source in this process.

    The reactivity of the allylboronic acids were studied in three types of allylboration reactions: allylboration of ketones, imines and acyl hydrazones. All three processes are conducted under mild conditions without any additives. The reactions proceeded with remarkably high regio- and stereoselectivity.

    An asymmetric version of the allylboration of ketones was also developed. In this process chiral BINOL derivatives were used as catalysts. The reaction using γ-disubstituted allylboronic acids and various aromatic and aliphatic ketones afforded homoallylic alcohols bearing two adjacent quaternary stereocenters with excellent regio-, diastereo- and enantioselectivity (up to 97:3 er) in high yield. The stereoselectivity in the allylboration reactions could be rationalized on the basis of the Zimmerman-Traxler TS model.

  • 3.
    Alam, Rauful
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Vollgraff, Tobias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Synthesis of Adjacent Quaternary Stereocenters by Catalytic Asymmetric Allylboration2015Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, nr 35, s. 11262-11265Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 4.
    Algarra, Andres G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Computational Insights into the Isomerism of Hexacoordinate Metal-Sarcophagine Complexes: The Relationship between Structure and Stability2015Inngår i: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, nr 3, s. 503-511Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 5.
    Angles d'Ortoli, Thibault
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sjöberg, Nils A.
    Vasiljeva, Polina
    Lindman, Jonas
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bergenstråhle-Wohlert, Malin
    Wohlert, Jakob
    Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers2015Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, nr 30, s. 9559-9570Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model.

  • 6.
    Bartoszewicz, Agnieszka
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    González Miera, Greco
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Marcos, Rocio
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Norrby, Per-Ola
    Martín-Matute, Belén
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mechanistic Studies on the Alkylation of Amines with Alcohols Catalyzed by a Bifunctional Iridium Complex2015Inngår i: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 5, nr 6, s. 3704-3716Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The mechanism of the N-alkylation of amines with alcohols catalyzed by an iridium complex containing an N-heterocyclic carbene (NHC) ligand with a tethered alcohol/alkoxide functionality was investigated by a combination of experimental and computational methods. The catalyst resting state is an iridium hydride species containing the amine substrate as a ligand, and decoordination of the amine, followed by coordination of the imine intermediate to the iridium center, constitute the rate-determining step (rds) of the catalytic process. The alcohol/alkoxide that is tethered to the NHC participates in every step of the catalytic cycle by accepting or releasing protons and forming hydrogen bonds with the reacting species. Thus, the iridium complex with the alcohol/alkoxide tethered to the N-heterocyclic carbene ligand acts as a bifunctional catalyst.

  • 7. Bejhed, Rebecca S.
    et al.
    Tian, Bo
    Eriksson, Kristofer
    Brucas, Rimantas
    Oscarsson, Sven
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Strömberg, Mattias
    Svedlindh, Peter
    Gunnarsson, Klas
    Magnetophoretic Transport Line System for Rapid On-Chip Attomole Protein Detection2015Inngår i: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 31, nr 37, s. 10296-10302Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 8. Biosca, Maria
    et al.
    Paptchikhine, Alexander
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Pàmies, Oscar
    Andersson, Pher G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Diéguez, Montserrat
    Extending the Substrate Scope of Bicyclic P-Oxazoline/Thiazole Ligands for Ir-Catalyzed Hydrogenation of Unfunctionalized Olefins by Introducing a Biaryl Phosphoroamidite Group2015Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, nr 8, s. 3455-3464Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This study identifies a series of Ir-bicyclic phosphoroamidite-oxazoline/thiazole catalytic systems that can hydrogenate a wide range of minimally functionalized olefins (including E-and Z-tri- and disubstituted substrates, vinylsilanes, enol phosphinates, tri- and disubstituted alkenylboronic esters, and alpha,beta-unsaturated enones) in high enantioselectivities (ee values up to 99%) and conversions. The design of the new phosphoroamidite-oxazoline/thiazole ligands derives from a previous successful generation of bicyclic N-phosphane-oxazoline/thiazole ligands, by replacing the N-phosphane group with a pi-acceptor biaryl phosphoroamidite moiety. A small but structurally important family of Ir-phosphoroamidite-oxazoline/thiazole precatalysts has thus been synthesized by changing the nature of the N-donor group (either oxazoline or thiazole) and the configuration at the biaryl phosphoroamidite moiety. The substitution of the N-phosphane by a phosphoroamidite group in the bicyclic N-phosphane-oxazoline/thiazole ligands extended the range of olefins that can be successfully hydrogenated.

  • 9.
    Blomberg, Margareta R. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    How Quantum Chemistry Can Solve Fundamental Problems in Bioenergetics2015Inngår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 115, nr 18, s. 1197-1201Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 10.
    Blomberg, Margareta R. A.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradient2015Inngår i: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1847, nr 3, s. 364-376Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 11.
    Blomberg, Margareta R. A.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Protonation of the binuclear active site in cytochrome c oxidase decreases the reduction potential of Cu-B2015Inngår i: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1847, nr 10, s. 1173-1180Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 12. Brown, Michael
    et al.
    Delorme, Marion
    Malmedy, Florence
    Malmgren, Joel
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Olofsson, Berit
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wirth, Thomas
    Synthesis of New Chiral Diaryliodonium Salts2015Inngår i: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, Vol. 26, nr 11, s. 1573-1577Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A structurally diverse range of chiral diaryliodonium salts have been synthesised which have potential application in metal-free stereoselective arylation reactions.

  • 13. Bunrit, Anon
    et al.
    Dahlstrand, Christian
    Olsson, Sandra K.
    Srifa, Pemikar
    Huang, Genping
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Orthaber, Andreas
    Sjöberg, Per J. R.
    Biswas, Srijit
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Samec, Joseph S. M.
    Brønsted Acid-Catalyzed Intramolecular Nucleophilic Substitution of the Hydroxyl Group in Stereogenic Alcohols with Chirality Transfer2015Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, nr 14, s. 4646-4649Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 14. Bustelo, Emilio
    et al.
    Gushchin, Artem L.
    Fernandez-Trujillo, M. Jesus
    Basallote, Manuel G.
    Algarra, Andres G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    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 Theory2015Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, nr 42, s. 14823-14833Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 15.
    Carson, Fabian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Martínez-Castro, Elisa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Marcos, Rocio
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    González Miera, Greco
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Jansson, Kjell
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Zou, Xiaodong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Martin-Matute, Belén
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Effect of the functionalisation route on a Zr-MOF with an Ir-NHC complex for catalysis2015Inngår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 51, nr 54, s. 10864-10867Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new iridium N-heterocyclic carbene (NHC) metallolinker has been synthesised and introduced into a metal-organic framework (MOF), for the first time, via two different routes: direct synthesis and postsynthetic exchange (PSE). The two materials were compared in terms of the Ir loading and distribution using X-ray energy dispersive spectroscopy (EDS), the local Ir structure using X-ray absorption spectroscopy (XAS) and the catalytic activity. The materials showed good activity and recyclability as catalysts for the isomerisation of an allylic alcohol.

  • 16.
    Carson, Fabian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Pascanu, Vlad
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bermejo Gómez, Antonio
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zhang, Yi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Platero-Prats, Ana E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zou, Xiaodong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Martín-Matute, Belén
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Influence of the Base on Pd@MIL-101-NH2(Cr) as Catalyst for the Suzuki-Miyaura Cross-Coupling Reaction2015Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, nr 30, s. 10896-10902Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The chemical stability of metal-organic frameworks (MOFs) is a major factor preventing their use in industrial processes. Herein, it is shown that judicious choice of the base for the Suzuki-Miyaura cross-coupling reaction can avoid decomposition of the MOF catalyst Pd@MIL-101-NH2(Cr). Four bases were compared for the reaction: K2CO3, KF, Cs2CO3 and CsF. The carbonates were the most active and achieved excellent yields in shorter reaction times than the fluorides. However, powder XRD and N-2 sorption measurements showed that the MOF catalyst was degraded when carbonates were used but remained crystalline and porous with the fluorides. XANES measurements revealed that the trimeric chromium cluster of Pd@MIL-101-NH2(Cr) is still present in the degraded MOF. In addition, the different countercations of the base significantly affected the catalytic activity of the material. TEM revealed that after several catalytic runs many of the Pd nanoparticles (NPs) had migrated to the external surface of the MOF particles and formed larger aggregates. The Pd NPs were larger after catalysis with caesium bases compared to potassium bases.

  • 17.
    Das, Arindam
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wang, Dong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Belhomme, Marie-Charlotte
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Copper-Catalyzed Cross-Coupling of Allylboronic Acids with alpha-Diazoketones2015Inngår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 17, nr 19, s. 4754-4757Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 18.
    Daver, Henrik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Quantum Chemical Modelling of Biomimetic Phosphoesterase Complexes2015Licentiatavhandling, med artikler (Annet vitenskapelig)
    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.

  • 19.
    Deng, Hong-Ping
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wang, Dong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Direct Allylation of Quinones with Allylboronates2015Inngår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 80, nr 6, s. 3343-3348Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 20.
    Dey, Chandan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Lindstedt, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Olofsson, Berit
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Wallenberg Research Centre at Stellenbosch University, South Africa.
    Metal-Free C-Arylation of Nitro Compounds with Diaryliodonium Salts2015Inngår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 17, nr 18, s. 4554-4557Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An efficient, mild, and metal-free arylation of nitro-alkanes with diaryliodonium salts has been developed, giving easy access to tertiary nitro compounds. The reaction proceeds in high yields without the need for excess reagents and can be extended to alpha-arylation of nitroesters. Nitroalkanes were selectively C-arylated in the presence of other easily arylated functional groups, such as phenols and aliphatic alcohols.

  • 21.
    Engelmark Cassimjee, Karim
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Manta, Bianca
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    A quantum chemical study of the ω-transaminase reaction mechanism2015Inngår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, nr 31, s. 8453-8464Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 22.
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Exploring the Molecular Behavior of Carbohydrates by NMR Spectroscopy: Shapes, motions and interactions2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Carbohydrates are essential biomolecules that decorate cell membranes and proteins in organisms. They are important both as structural elements and as identification markers. Many biological and pathogenic processes rely on the identification of carbohydrates by proteins, thereby making them attractive as molecular blueprints for drugs. This thesis describes how NMR spectroscopy can be utilized to study carbohydrates in solution at a molecular level. This versatile technique facilitates for investigations of (i) shapes, (ii) motions and (iii) interactions.

    A conformational study of an E. coli O-antigen was performed by calculating atomic distances from NMR NOESY experiments. The acquired data was utilized to validate MD simulations of the LPS embedded in a membrane. The agreement between experimental and calculated data was good and deviations were proven to arise from spin-diffusion. In another study presented herein, both the conformation and the dynamic behavior of amide side-chains linked to derivatives of D-Fucp3N, a sugar found in the O-antigen of bacteria, were investigated. J-couplings facilitated a conformational analysis and 13C saturation transfer NMR experiments were utilized to measure rate constants of amide cis-trans isomerizations.

    13C NMR relaxation and 1H PFG diffusion measurements were carried out to explore and describe the molecular motion of mannofullerenes. The dominating motions of the mannofullerene spectral density were found to be related to pulsating motions of the linkers rather than global rotational diffusion. The promising inhibition of Ebola viruses identified for a larger mannofullerene can thus be explained by an efficient rebinding mechanism that arises from the observed flexibility in the linker.

    Molecular interactions between sugars and caffeine in water were studied by monitoring chemical shift displacements in titrations. The magnitude of the chemical shift displacements indicate that the binding occurs by a face to face stacking of the aromatic plane of caffeine to the ring plane of the sugar, and that the interaction is at least partly driven by solvation effects. Also, the binding of a Shigella flexneri serotype Y octasaccharide to a bacteriophage Sf6 tail spike protein was investigated. This interaction was studied by 1H STD NMR and trNOESY experiments. A quantitative analysis of the STD data was performed employing a newly developed method, CORCEMA-ST-CSD, that is able to simulate STD data more accurately since the line broadening of protein resonances are accounted for in the calculations.

  • 23.
    Engström, Olof
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Muñoz, Antonio
    Illescas, Beatriz M.
    Martin, Nazario
    Ribeiro-Viana, Renato
    Rojo, Javier
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Investigation of glycofullerene dynamics by NMR spectroscopy2015Inngår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, nr 32, s. 8750-8755Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Glycofullerenes, in which carbohydrate molecules are attached via a linker to a [60]fullerene core, facilitate spherical presentation of glyco-based epitopes. We herein investigate the dynamics of two glycofullerenes, having 12 and 36 mannose residues at their periphery, by NMR translational diffusion and quantitative C-13 relaxation studies employing a model-free approach for their interpretation. The sugar residues are shown to be highly flexible entities with S-2 < 0.2 in both compounds. Notably, the larger glycofullerene with longer linkers shows faster internal dynamics and higher flexibility than its smaller counterpart. The dynamics and flexibility as well as the slower translational diffusion of the larger glycofullerene, thereby favoring rebinding to a receptor, may together with its spatial extension explain why it is better than the smaller one at blocking the DC-SIGN receptor and inhibiting the infection by pseudotyped Ebola virus particles.

  • 24.
    Eriksson, Kristofer
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Verho, Oscar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Nyholm, Leif
    Oscarsson, Sven
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Dispersed Gold Nanoparticles Supported in the Pores of Siliceous Mesocellular Foam: A Catalyst for Cycloisomerization of Alkynoic Acids to gamma-Alkylidene Lactones2015Inngår i: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, nr 10, s. 2250-2255Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 25.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Li, Shengyu
    Yang, Zhennai
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the exopolysaccharide from Lactobacillus plantarum C88 using NMR spectroscopy and the program CASPER2015Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 402, s. 87-94Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Some lactic acid bacteria, such as those of the Lactobacillus genus, have the ability to produce exopolysaccharides (EPSs) that confer favorable physicochemical properties to food and/or beneficial physiological effects on human health. In particular, the EPS of Lactobacillus plantarum C88 has recently demonstrated in vitro antioxidant activity and, herein, its structure has been investigated using NMR spectroscopy and the computer program CASPER (Computer Assisted Spectrum Evaluation of Regular polysaccharides). The pentasaccharide repeating unit of the O-deacetylated EPS consists of a trisaccharide backbone, -> 4)-alpha-DGalp-(1 -> 2)-alpha-D-Glcp-(1 -> 3)-beta-D-Glcp-(1 ->, with terminal D-Glc and D-Gal residues (1.0 and 0.8 equiv per repeating unit, respectively) extending from O3 and O6, respectively, of the -> 4)-alpha-D-Galp-(1 -> residue. In the native EPS an O-acetyl group is present, 0.85 equiv per repeating unit, at O2 of the alpha-linked galactose residue; thus the repeating unit of the EPS has the following structure: -> 4)[beta-D-Glcp-(1 -> 3)][beta-D-Galp-(1 -> 6)]alpha-D-Galp2Ac-(1 -> 2)-alpha-D-Glcp-(1 -> 3)-beta-D-Glcp-(1 ->. These structural features, and the chain length (similar to 10(3) repeating units on average, determined in a previous study), are expected to play an important role in defining the physicochemical properties of the polymer.

  • 26.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural Elucidation of the O-Antigen Polysaccharide from Escherichia coli O1812015Inngår i: ChemistryOpen, ISSN 2191-1363, Vol. 4, nr 1, s. 47-55Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Shiga-toxin-producing Escherichia coli (STEC) is an important pathogen associated to food-borne infection in humans; strains of E.coli O181, isolated from human cases of diarrhea, have been classified as belonging to this pathotype. Herein, the structure of the O-antigen polysaccharide (PS) from E.coli O181 has been investigated. The sugar analysis showed quinovosamine (QuiN), glucosamine (GlcN), galactosamine (GalN), and glucose (Glc) as major components. Analysis of the high-resolution mass spectrum of the oligosaccharide (OS), obtained by dephosphorylation of the O-deacetylated PS with aqueous 48% hydrofluoric acid, revealed a pentasaccharide composed of two QuiNAc, one GlcNAc, one GalNAc, and one Glc residue. The H-1 and (CNMR)-C-13 chemical shift assignments of the OS were carried out using 1D and 2D NMR experiments, and the OS was sequenced using a combination of tandem mass spectrometry (MS/MS) data and NMR (CNMR)-C-13 glycosylation shifts. The structure of the native PS was determined using NMR spectroscopy, and it consists of branched pentasaccharide repeating units joined by phosphodiester linkages: -> 4)[alpha-L-QuipNAc-(1 -> 3)]-alpha-D-GalpNAc6Ac-(1 -> 6)-alpha-D-Glcp-(1 -> P-4)-alpha-L-QuipNAc-(1 -> 3)-beta-D-GlcpNAc-(1 ->; the O-acetyl groups represent 0.4 equivalents per repeating unit. Both the OS and PSs exhibit rare conformational behavior since two of the five anomeric proton resonances could only be observed at an elevated temperature.

  • 27.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies and biosynthetic aspects of the O-antigen polysaccharide from Escherichia coli O422015Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 403, s. 174-181Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from Escherichia coli O42 has been investigated by NMR spectroscopy as the main method, which was complemented with sugar analysis, mass spectrometry, and analysis of biosynthetic information. The O-specific chain of the O-deacylated lipopolysaccharide (LPS-OH) consists of branched tetrasaccharide-glycerol repeating units joined by phosphodiester linkages. The lipid-free polysaccharide contains 0.8 equiv of O-acetyl groups per repeating unit and has the following teichoic acid-like structure: Based on biosynthetic aspects, this should also be the biological repeating unit. This O-antigen structure is remarkably similar to that of E. coli O28ac, differing only in the presence or absence, respectively, of a glucose residue at the branching point. The structural similarity explains the serological cross-reactivity observed between strains of these two serogroups, and also their almost identical O-antigen gene cluster sequences. -> 2)-(R)-Gro-(1-P-4)-beta-D-GlcpNAc-(1 -> 3)-beta-D-Galf2Ac-(1 -> 3)-alpha-D-GlcpNAc-(1 -> vertical bar a-D-Glcp-(1 -> 3)

  • 28.
    Gigant, Nicolas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Université Paris-Sud, France.
    Quintin, Francois
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Preparation of Tetrasubstituted Olefins Using Mono or Double Aerobic Direct C-H Functionalization Strategies: Importance of Steric Effects2015Inngår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 80, nr 5, s. 2796-2803Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 29. Girgis, Adel S.
    et al.
    Mabied, Ahmed F.
    Stawinski, Jacek
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Hegazy, Lamees
    George, Riham F.
    Farag, Hanaa
    Shalaby, ElSayed M.
    Farag, I. S. Ahmed
    Synthesis and DFT studies of an antitumor active spiro-oxindole2015Inngår i: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 39, nr 10, s. 8017-8027Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 30.
    Hamark, Christoffer
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    The sweet side of molecular structure: NMR spectroscopic studies of glycans and their interactions with proteins2015Doktoravhandling, med artikler (Annet vitenskapelig)
    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.  

  • 31.
    Huang, Genping
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kalek, Marcin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Liao, Rong-Zhen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mechanism, reactivity, and selectivity of the iridium-catalyzed C(sp(3))-H borylation of chlorosilanes2015Inngår i: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 6, nr 3, s. 1735-1746Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 32.
    Janson, Pär G.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ilchenko, Nadia O.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Diez-Varga, Alberto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Szabó, Kálmán J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Effects of B(2)pin(2) and PCy3 on copper-catalyzed trifluoromethylation of substituted alkenes and alkynes with the Togni reagent2015Inngår i: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 71, nr 6, s. 922-931Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 33.
    Jiang, Tuo
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bartholomeyzik, Teresa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mazuela, Javier
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Willersinn, Jochen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Palladium(II)/Bronsted Acid-Catalyzed Enantioselective Oxidative Carbocyclization-Borylation of Enallenes2015Inngår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 54, nr 20, s. 6024-6027Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 34. Kabeshov, Mikhail A.
    et al.
    Kysilka, Ondřej
    Rulíšek, Lubomír
    Suleimanov, Yury V.
    Bella, Marco
    Malkov, Andrei V.
    Kočovský, Pavel
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Czech Academy of Sciences, Czech Republic; Charles University Prague, Czech Republic.
    Cross-Aldol Reaction of Isatin with Acetone Catalyzed by Leucinol: A Mechanistic Investigation2015Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, nr 34, s. 12026-12033Artikkel i tidsskrift (Fagfellevurdert)
    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)).

  • 35.
    Kapla, Jon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stevensson, Baltzar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Wohlert, Jakob
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 34, s. 22438-22447Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.

  • 36.
    Kerdphon, Sutthichat
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    N-Heterocyclic Carbene-Phosphine Iridium Catalyzed Alkylation Reactions and Asymmetric Hydrogenation of Ketones2015Licentiatavhandling, med artikler (Annet vitenskapelig)
    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%).

  • 37.
    Kerdphon, Sutthichat
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Xu, Quan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Parihar, Vijay Singh
    Andersson, Pher G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    C-N Coupling of Amides with Alcohols Catalyzed by N-Heterocyclic Carbene-Phosphine Iridium Complexes2015Inngår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 80, nr 22, s. 11529-11537Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    N-heterocyclic carbene-phosphine iridium complexes (NHC-Ir) were developed/found to be a highly reactive catalyst for N-monoalkylation of amides with alcohols via hydrogen transfer. The reaction produced the desired product in high isolated yields using a wide range of substrates with low catalyst loading and short reaction times.

  • 38.
    Kocovsky, Pavel
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Academy of Sciences of the Czech Republic, Czech Republic; Charles University, Czech Republic.
    Bäckvall, Jan-E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    The syn/anti-Dichotomy in the Palladium-Catalyzed Addition of Nucleophiles to Alkenes2015Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, nr 51, s. 36-56Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 39.
    Kovalenko, Oleksandr O.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Adolfsson, Hans
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Highly Efficient and Chemoselective Zinc-Catalyzed Hydrosilylation of Esters under Mild Conditions2015Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, nr 7, s. 2785-2788Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 40.
    Kovalenko, Oleksandr O.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Volkov, Alexey
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Adolfsson, Hans
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mild and Selective Et2Zn-Catalyzed Reduction of Tertiary Amides under Hydrosilylation Conditions2015Inngår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 17, nr 3, s. 446-449Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 41.
    Laine, Tanja M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kärkäs, Markus D.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Liao, Rong-Zhen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Huazhong University of Science & Technology, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    A Dinuclear Ruthenium-Based Water Oxidation Catalyst: Use of Non-Innocent Ligand Frameworks for Promoting Multi-Electron Reactions2015Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, nr 28, s. 10039-10048Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 42.
    Laine, Tanja M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kärkäs, Markus D.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Liao, Rong-Zhen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Huazhong University of Science & Technology, People's Republic of China.
    Åkermark, Torbjörn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Lee, Bao-Lin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Karlsson, Erik A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Efficient photochemical water oxidation by a dinuclear molecular ruthenium complex2015Inngår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 51, nr 10, s. 1862-1865Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 43.
    Li, Xichen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Beijing Normal University, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Alternative mechanisms for O-2 release and O-O bond formation in the oxygen evolving complex of photosystem II2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 18, s. 12168-12174Artikkel i tidsskrift (Fagfellevurdert)
    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).

  • 44. Li, Xichen
    et al.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Water Oxidation for Simplified Models of the Oxygen-Evolving Complex in Photosystem II2015Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 21, nr 51, s. 18821-18827Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 45. Li, Xichen
    et al.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ryde, Ulf
    Simulation of the isotropic EXAFS spectra for the S-2 and S-3 structures of the oxygen evolving complex in photosystem II2015Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, nr 13, s. 3979-3984Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 46. Liao, Rong-Zhen
    et al.
    Chen, Shi-Lu
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Which Oxidation State Initiates Dehalogenation in the B12-Dependent Enzyme NpRdhA: Co-II, COI or Co-0?2015Inngår i: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 5, nr 12, s. 7350-7358Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 47.
    Liao, Rong-Zhen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kärkäs, Markus D.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Lee, Bao-Lin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Åkermark, Björn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Photosystem II Like Water Oxidation Mechanism in a Bioinspired Tetranuclear Manganese Complex2015Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 54, nr 1, s. 342-351Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 48.
    Liao, Rong-Zhen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Huazhong University of Science & Technology, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mechanism and selectivity of the dinuclear iron benzoyl-coenzyme A epoxidase BoxB2015Inngår i: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 6, nr 5, s. 2754-2764Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 49.
    Liao, Rong-Zhen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Huazhong University of Science & Technology, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mechanism for O-O bond formation in a biomimetic tetranuclear manganese cluster - A density functional theory study2015Inngår i: Journal of Photochemistry and Photobiology. B: Biology, ISSN 1011-1344, E-ISSN 1873-2682, Vol. 152, nr Part A, s. 162-172Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 50.
    Liao, Rong-Zhen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Phosphate Hydrolysis by the Fe-2-Ca-3-Dependent Alkaline Phosphatase PhoX: Mechanistic Insights from DFT calculations2015Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 54, nr 24, s. 11941-11947Artikkel i tidsskrift (Fagfellevurdert)
    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.

123 1 - 50 of 107
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf