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  • 1.
    Alam, Rauful
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-catalyzed Allylic C-H and C-OH Functionalization. Reactions of the Obtained Allylboronic Acids2014Licentiate thesis, monograph (Other academic)
    Abstract [en]

    This thesis is focused on the studies of two major transformations. The first transformation deals with the development of palladium-catalyzed selective allylic trifluoroacetoxylation reactions based on C-H functionalization, whereas the second comprises the synthesis and isolation of allylboronic acids using diboronic acid B2(OH)4 as boron source. Both reactions proceed with a very high regio- and stereoselectivity. The mechanistic studies of the allylic C-H trifluoroacetoxylation indicate that the reaction proceeds via (η3-allyl)palladium intermediate.

    The reactivity of the allylboronic acids was studied with ketone and imine substrates. Unlikeother boronates (such as allyl-Bpin derivatives), allylboronic acids react with ketones and imines without any additives under neutral and mild conditions (typically at room temperature). The regio- and stereoselectivity of this reaction is remarkably high. Using functionalized allylboronic acids (prepared in the above mentioned Pd-catalyzed reactions) homoallylic alcohols and amines with adjacent tertiary and quaternary centers could be obtained with high selectivity. Interestingly, both the ketones and the imines reacted with anti-stereoselectivity. This was surprising for the imines. Our mechanistic study has shown that the acyclic aldimines undergo cis/trans isomerization prior to the allylation reaction.

  • 2.
    Algarra, Andres G.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Aullon, Gabriel
    Bemhardt, Paul V.
    Martinez, Manuel
    Computational Insights on the Geometrical Arrangements of Cu(II) with a Mixed-Donor N3S3 Macrobicyclic Ligand2014In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 53, no 1, p. 512-521Article in journal (Refereed)
    Abstract [en]

    The macrobicyclic mixed-donor N3S3 cage ligand AMME-N(3)S(3)sar (1-methyl-8-amino-3,13,16-trithia-6,10,19-triazabicyclo[6.6.6]eicosane) can form complexes with Cu(II) in which it acts as hexadentate (N3S3) or tetradentate (N2S2) donor. These two complexes are in equilibrium that is strongly influenced by the presence of halide ions (Br- and Cl-) and the nature of the solvent (DMSO, MeCN, and H2O). In the absence of halides the hexadentate coordination mode of the ligand is preferred and the encapsulated complex (Cu-in(2+)) is formed. Addition of halide ions in organic solvents (DMSO or MeCN) leads to the tetradentate complex (Cu-out(+)) in a polyphasic kinetic process, but no Cu-out(+) complex is formed when the reaction is performed in water. Here we applied density functional theory calculations to study the mechanism of this interconversion as well as to understand the changes in the reactivity associated with the presence of water. Calculations were performed at the B3LYP/(SDD,6-31G**) level, in combination with continuum (MeCN) or discrete-continuum (H2O) solvent models. Our results show that formation of Cu-out(+) in organic media is exergonic and involves sequential halide-catalyzed inversion of the configuration of a N-donor of the macrocycle, rapid halide coordination, and inversion of the configuration of a S-donor. In aqueous solution the solvent is found to have an effect on both the thermodynamics and the kinetics of the reaction. Thermodynamically, the process becomes endergonic mainly due to the preferential solvation of halide ions by water, while the kinetics is influenced by formation of a network of H-bonded water molecules that surrounds the complex.

  • 3. Anderson, Mattias
    et al.
    Afewerki, Samson
    Berglund, Per
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mid Sweden University, Sweden.
    Total Synthesis of Capsaicin Analogues from Lignin-Derived Compounds by Combined Heterogeneous Metal, Organocatalytic and Enzymatic Cascades in One Pot2014In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 356, no 9, p. 2113-2118Article in journal (Refereed)
    Abstract [en]

    The total synthesis of capsaicin analogues was performed in one pot, starting from compounds that can be derived from lignin. Heterogeneous palladium nanoparticles were used to oxidise alcohols to aldehydes, which were further converted to amines by an enzyme cascade system, including an amine transaminase. It was shown that the palladium catalyst and the enzyme cascade system could be successfully combined in the same pot for conversion of alcohols to amines without any purification of intermediates. The intermediate vanillyl-amine, prepared with the enzyme cascade system, could be further converted to capsaicin analogues without any purification using either fatty acids and a lipase, or Schotten-Baumann conditions, in the same pot. An aldol compound (a simple lignin model) could also be used as starting material for the synthesis of capsaicin analogues. Using l-alanine as organocatalyst, vanillin could be obtained by a retro-aldol reaction. This could be combined with the enzyme cascade system to convert the aldol compound to vanillylamine in a one-step one-pot reaction.

  • 4.
    Arafa, Wael A. A.
    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, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Berends, Hans-Martin
    Messinger, Johannes
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dinuclear manganese complexes for water oxidation: evaluation of electronic effects and catalytic activity2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 24, p. 11950-11964Article in journal (Refereed)
    Abstract [en]

    During recent years significant progress has been made towards the realization of a sustainable and carbon-neutral energy economy. One promising approach is photochemical splitting of H2O into O-2 and solar fuels, such as H-2. However, the bottleneck in such artificial photosynthetic schemes is the H2O oxidation half reaction where more efficient catalysts are required that lower the kinetic barrier for this process. In particular catalysts based on earth-abundant metals are highly attractive compared to catalysts comprised of noble metals. We have now synthesized a library of dinuclear Mn-2 (II,III) catalysts for H2O oxidation and studied how the incorporation of different substituents affected the electronics and catalytic efficiency. It was found that the incorporation of a distal carboxyl group into the ligand scaffold resulted in a catalyst with increased catalytic activity, most likely because of the fact that the distal group is able to promote proton-coupled electron transfer (PCET) from the high-valent Mn species, thus facilitating O-O bond formation.

  • 5.
    Bartholomeyzik, Teresa
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium(II)-Catalyzed Oxidative Carbocyclization/Functionalization of Allenynes2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The selective formation of carbon-carbon bonds constitutes a key transformation in organic synthesis with useful applications in pharmaceutical or material industry. A particularly versatile tool for carbon-carbon as well as carbon-heteroatom bond formation is palladium catalysis, which allows for mild and selective routes even towards complex structures.

    The work in this thesis describes the development and the mechanistic investigation of a palladium(II)-catalyzed oxidative carbocyclization/functionalization methodology, which converts 1,5-allenynes into either arylated or borylated carbocycles. To this end, either boronic acids or B2pin2 are employed and 1,4-benzoquinone serves as the stoichiometric oxidant. These protocols provide access to two products, a cyclic triene and a cyclic vinylallene. Their formation is dependent on the substrate structure as the latter product requires a propargylic C–H bond to be present in the substrate. Based on kinetic isotope effects, mechanisms involving either an initial allenic or propargylic C–H abstraction, respectively, were proposed. Full control of product selectivity to give either trienes or vinylallenes was achieved by modifying the reaction conditions with additives. Using substoichiometric amounts of BF3·OEt2 leads selectively to borylated or arylated vinylallenes. Under arylating conditions the reaction is zero order in allenyne and oxidant, and first order in phenylboronic acid. Transmetalation and, to some extent, propargylic C–H cleavage were found to be turnover-limiting. The selective reaction towards functionalized trienes was achieved by addition of either substoichiometric LiOAc·2H2O (borylation) or excess amounts of H2O (arylation). For the latter case, a kinetic study revealed an unusually slow catalyst activation. Lower concentrations of H2O gave product mixtures, and it was shown that vinylallenes are formed with either boronic acid or boroxine, whereas the formation of trienes requires boronic acid.

  • 6.
    Bermejo Gómez, Antonio
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ahlsten, Nanna
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Platero-Prats, Ana E.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martín-Matute, Belén
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis of 4,5-disubstituted 2-aminothiazoles from a,b-unsaturated ketones: Preparation of 5-benzyl-4-methyl-2-aminothiazolium hydrochloride salt2014In: Organic Syntheses, ISSN 0078-6209, Vol. 91, p. 185-200Article in journal (Refereed)
  • 7.
    Blomberg, Margareta R. A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Borowski, Tomasz
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Studies of Mechanisms for Metalloenzymes2014In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 114, no 7, p. 3601-3658Article, review/survey (Refereed)
  • 8.
    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.
    Proton pumping in cytochrome c oxidase: Energetic requirements and the role of two proton channels2014In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1837, no 7, p. 1165-1177Article in journal (Refereed)
    Abstract [en]

    Cytochrome c oxidase is a superfamily of membrane bound enzymes catalyzing the exergonic reduction of molecular oxygen to water, producing an electrochemical gradient across the membrane. The gradient is formed both by the electrogenic chemistry, taking electrons and protons from opposite sides of the membrane, and by proton pumping across the entire membrane. In the most efficient subfamily, the A-family of oxidases, one proton is pumped in each reduction step, which is surprising considering the fact that two of the reduction steps most likely are only weakly exergonic. Based on a combination of quantum chemical calculations and experimental information, it is here shown that from both a thermodynamic and a kinetic point of view, it should be possible to pump one proton per electron also with such an uneven distribution of the free energy release over the reduction steps, at least up to half the maximum gradient. A previously suggested pumping mechanism is developed further to suggest a reason for the use of two proton transfer channels in the A-family. Since the rate of proton transfer to the binuclear center through the D-channel is redox dependent, it might become too slow for the steps with low exergonicity. Therefore, a second channel, the K-channel, where the rate is redox-independent is needed. A redox-dependent leakage possibility is also suggested, which might be important for efficient energy conservation at a high gradient. A mechanism for the variation in proton pumping stoichiometry over the different subfamilies of cytochrome oxidase is also suggested. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.

  • 9.
    Bouma, M. J.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    7.07 α-Oxygenation of Carbonyl Compounds2014In: Comprehensive Organic Synthesis II (Second Edition) / [ed] Paul Knochel and Gary A. Molander, Amsterdam: Oxford: Elsevier , 2014, 2nd, p. 213-241Chapter in book (Refereed)
    Abstract [en]

    Abstract The chapter describes synthetically useful strategies for α-oxygenation of carbonyl compounds, with special emphasis on recent methods for catalytic and asymmetric reactions. The oxidation of enolates, enols, enol ethers, and α,β-unsaturated compounds is discussed in detail. Classical oxidation reagents like metal oxides, molecular oxygen, peroxides, and peracids are covered, with asymmetric dihydroxylation of enol ethers giving the highest enantioselectivities together with organocatalytic methods using peroxides. Oxaziridines, nitrosoarenes, and hypervalent iodine compounds are more recently developed α-oxygenation alternatives that allow metal-free oxidations under mild conditions. The combination of nitrosoarenes with organocatalysis is currently the best method for enantioselective α-oxygenations. The area of asymmetric α-oxygenations with hypervalent iodine compounds is currently under development, and high enantioselectivities have only been achieved in intramolecular reactions and epoxidations.

  • 10. Chen, Shi-Lu
    et al.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    An investigation of possible competing mechanisms for Ni-containing methyl-coenzyme M reductase2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 27, p. 14029-14035Article in journal (Refereed)
    Abstract [en]

    Ni-containing methyl-coenzyme M reductase (MCR) is capable of catalyzing methane formation from methyl-coenzyme M (CH3-SCoM) and coenzyme B (CoB-SH), and also its reverse reaction (methane oxidation). Based on extensive experimental and theoretical investigations, it has turned out that a mechanism including an organometallic methyl-Ni(III)F-430 intermediate is inaccessible, while another mechanism involving a methyl radical and a Ni(II)-SCoM species currently appears to be the most acceptable one for MCR. In the present paper, using hybrid density functional theory and an active-site model based on the X-ray crystal structure, two other mechanisms were studied and finally also ruled out. One of them, involving proton binding on the CH3-SCoM substrate, which should facilitate methyl-Ni(III)F-430 formation, is demonstrated to be quite unfavorable since the substrate has a much smaller proton affinity than the F-430 cofactor. Another one (oxidative addition mechanism) is also shown to be unfavorable for the MCR reaction, due to the large endothermicity for the formation of the ternary intermediate with side-on C-S (for CH3-SCoM) or C-H (for methane) coordination to Ni.

  • 11. Chen, Shi-Lu
    et al.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Phosphate Monoester Hydrolysis by Trinuclear Alkaline Phosphatase; DFT Study of Transition States and Reaction Mechanism2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 11, p. 2321-2330Article in journal (Refereed)
    Abstract [en]

    Alkaline phosphatase (AP) is a trinuclear metalloenzyme that catalyzes the hydrolysis of a broad range of phosphate monoesters to form inorganic phosphate and alcohol (or phenol). In this paper, by using density functional theory with a model based on a crystal structure, the AP-catalyzed hydrolysis of phosphate monoesters is investigated by calculating two substrates, that is, methyl and p-nitrophenyl phosphates, which represent alkyl and aryl phosphates, respectively. The calculations confirm that the AP reaction employs a ping-pong mechanism involving two chemical displacement steps, that is, the displacement of the substrate leaving group by a Ser102 alkoxide and the hydrolysis of the phosphoseryl intermediate by a Zn2-bound hydroxide. Both displacement steps proceed via a concerted associative pathway no matter which substrate is used. Other mechanistic aspects are also studied. Comparison of our calculations with linear free energy relationships experiments shows good agreement.

  • 12. Chow, Winnie W. Y.
    et al.
    Herwik, Stanislav
    Kisban, Sebastian
    Ruther, Patrick
    Neves, Herc
    Oscarsson, Sven
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Gothelid, Emmanuelle
    Influence of bio-coatings on the recording performance of neural electrodes2014In: Biomedizinische Technik (Berlin. Zeitschrift), ISSN 1862-278X, E-ISSN 0013-5585, Vol. 59, no 4, p. 315-322Article in journal (Refereed)
    Abstract [en]

    Neural probes are complex devices consisting of metallic (often Pt based) electrodes, spread over an insolating/dielectric backbone. Their functionality is often limited in time because of the formation of scaring tissues around the implantation tracks. Functionalization of the probes surface can be used to limit the glial scar reaction. This is however challenging, as this treatment has to be equally efficient on all probe surfaces (metallic as well as dielectric) and should not influence the electrodes performances. This paper presents a novel technique to functionalize recording neural probes with hyaluronic acid (HyA), a major component of the extracellular matrix (ECM). HyA and the probe surface are both modified to make the reaction feasible: HyA is chemically functionalized with SS-pyridine groups while the probe surfaces are silanized. The thiol groups thus introduced on the probe surface can then react with the HyA SS-pyridine group, resulting in a covalent bonding of the latter on the former. The electrodes are protected by introducing a pretreatment step, namely an additional hyaluronic acid layer on the platinum electrode, prior to the silanization process, which was found to be effective in reducing electrode impedance under optimized conditions.

  • 13. Das, Biswanath
    et al.
    Daver, Henrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pyrkosz-Bulska, Monika
    Persch, Elke
    Barman, Suman K.
    Mukherjee, Rabindranath
    Gumienna-Kontecka, Elzbieta
    Jarenmark, Martin
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nordlander, Ebbe
    A dinuclear zinc(II) complex of a new unsymmetric ligand with an N(5)0(2) donor set; A structural and functional model for the active site of zinc phosphoesterases2014In: Journal of Inorganic Biochemistry, ISSN 0162-0134, E-ISSN 1873-3344, Vol. 132, p. 6-17Article in journal (Refereed)
    Abstract [en]

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

  • 14. Das, Biswanath
    et al.
    Daver, Henrik
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Singh, Amrendra
    Singh, Reena
    Haukka, Matti
    Demeshko, Serhiy
    Meyer, Franc
    Lisensky, George
    Jarenmark, Martin
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nordlander, Ebbe
    A Heterobimetallic FeIIIMnII Complex of an Unsymmetrical Dinucleating Ligand: A Structural and Functional Model Complex for the Active Site of Purple Acid Phosphatase of Sweet Potato2014In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, Vol. 2014, no 13, p. 2204-2212Article in journal (Refereed)
    Abstract [en]

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

  • 15.
    Deiana, Luca
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ghisu, Lorenza
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Afewerki, Samson
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hedin, Niklas
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Bacsik, Zoltan
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mid-Sweden University, Sweden.
    Enantioselective Heterogeneous Synergistic Catalysis for Asymmetric Cascade Transformations2014In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 356, no 11-12, p. 2485-2492Article in journal (Refereed)
    Abstract [en]

    A modular design for a novel heterogeneous synergistic catalytic system, which simultaneously activates the electrophile and nucleophile by the combined activation modes of a separate metal and non-metal catalyst, for asymmetric cascade transformations on a solid surface is disclosed. This modular catalysis strategy generates carbocycles (up to 97.5: 2.5 er) as well as spirocyclic oxindoles (97.5: 2.5 to > 99: 0.5 er), containing all-carbon quaternary centers, in a highly enantioselective fashion via a one-pot dynamic relay process.

  • 16.
    Deiana, Luca
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ghisu, Lorenza
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Cordova, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Afewerki, Samson
    Zhang, Renyun
    Cordova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mittuniversitetet, Sundsvall.
    Efficient and Highly Enantioselective Aerobic Oxidation-Michael-Carbocyclization Cascade Transformations by Integrated Pd(0)-CPG Nanoparticle/Chiral Amine Relay Catalysis2014In: Synthesis (Stuttgart), ISSN 0039-7881, E-ISSN 1437-210X, Vol. 46, no 10, p. 1303-1310Article in journal (Refereed)
    Abstract [en]

    A series of highly diastereo- and enantioselective aerobic oxidation-Michael-carbocyclization cascade transformations by integrated heterogeneous Pd(0)-CPG nanoparticle/chiral amine relay catalysis are disclosed. The heterogeneous Pd(0)-CPG nanoparticle catalysts were efficient for both the sequential aerobic oxidation and dynamic kinetic asymmetric Michael-carbocyclization transformations, resulting in 1) oxidation of a variety of allylic alcohols to enals and 2) formation of cyclopentenes containing an all-carbon quaternary stereocenter in good to high yields with up to 20:1 dr and 99.5:0.5 er.

  • 17.
    Deiana, Luca
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Jiang, Yan
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palo-Nieto, Carlos
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Afewerki, Samson
    Incerti-Pradillos, Celia A.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tai, Cheuk-Wai
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mid Sweden University, Sweden.
    Combined Heterogeneous Metal/Chiral Amine: Multiple Relay Catalysis for Versatile Eco-Friendly Synthesis2014In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 53, no 13, p. 3447-3451Article in journal (Refereed)
    Abstract [en]

    Herein is described a versatile and broad synergistic strategy for expansion of chemical space and the synthesis of valuable molecules (e.g. carbocycles and heterocycles), with up to three quaternary stereocenters, in a highly enantioselective fashion from simple alcohols (31examples, 95:5 to >99.5:0.5 e.r.) using integrated heterogeneous metal/chiral amine multiple relay catalysis and air/O-2 as the terminal oxidant. A novel highly 1,4-selective heterogeneous metal/amine co-catalyzed hydrogenation of enals was also added to the relay catalysis sequences.

  • 18.
    Ghosh, Raju
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Stridfeldt, Elin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Metal-Free One-Pot Synthesis of Benzofurans2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 29, p. 8888-8892Article in journal (Refereed)
    Abstract [en]

    Ethyl acetohydroxamate was efficiently arylated with diaryliodonium salts at room temperature under transition-metal-free conditions. The obtained O-arylated products were reacted in situ with ketones under acidic conditions to yield substituted benzo[b]furans through oxime formation, [3,3]-rearrangement, and cyclization in a fast and operationally simple one-pot fashion without using excess reagents. Alternatively, the O-arylated products could be isolated or transformed in situ to aryloxyamines or O-arylaldoximes. The methodology was applied to the synthesis of Stemofuran A and the formal syntheses of Coumestan, Eupomatenoid 6, and (+)-machaeriol B.

  • 19.
    Ilchenko, Nadia
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Development of Catalytic ElectrophilicTrifluoromethylation and Fluorination Methods2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is focused on development of new catalytic, electrophilic fluorination and trifluoromethylation methods of alkenes. These reactions were carried out using hypervalent trifluoromethyl and fluoroiodine reagents.

    The first project involved copper catalyzed oxytrifluoromethylation of terminal alkenes and alkynes. In this reaction the employed hypervalent iodine underwent a formal addition to C-C multiple bonds. Subsequently, we have also shown that under similar reaction conditions in the presence of B2pin2 as additive quinones can smoothly undergo C-H trifluoromethylation.

    We also developed a cyanotrifluoromethylation reaction of styrenes, which proceds in the presence of copper cyanide and PCy3 as additive. This reaction allows addition of both trifluoromethyl and cyanofunctionality to the styrene, creating two new carbon-carbon bonds.

    The interesting substituent effects and the acceleration of B2pin2 and PCy3 additives inspired us to further investigate the mechanism for the above trifluoromethylation reactions. The Hammett studies showed that the oxytrifluoromethylation reactions are slightly accelerated by electron donor substituents. The C-H trifluoromethylation does not show deuterium isotope effect. Both B2pin2 and PCy3 accelerated the trifluoromethylation reactions but the extent of the acceleration was dependent on the reaction type and on the substituent effects.

    Inspired by our trifluoromethylation results, we have also studied the silver-mediated difluorination of styrenes in the presence of an electrophilic hypervalent iodine based fluorine source. We obtained over 50% of the difluorinated product which suggests that one fluorine atom comes from the fluoroiodine reagent and the other one from BF4-. A phenonium ion intermediate has been proposed to be involved in the mechanism of the difluorination reaction.

  • 20. Jakhetia, Richa
    et al.
    Marri, Aruna
    Ståhle, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verma, Naresh K.
    Serotype-conversion in Shigella flexneri: identification of a novel bacteriophage, Sf101, from a serotype 7a strain2014In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 15, p. 742-Article in journal (Refereed)
    Abstract [en]

    Background: Shigella flexneri is the major cause of bacillary dysentery in the developing countries. The lipopolysaccharide (LPS) O-antigen of S. flexneri plays an important role in its pathogenesis and also divides S. flexneri into 19 serotypes. All the serotypes with an exception for serotype 6 share a common O-antigen backbone comprising of N-acetylglucosamine and three rhamnose residues. Different serotypes result from modification of the basic backbone conferred by phage-encoded glucosyltransferase and/or acetyltransferase genes, or plasmid-encoded phosphoethanolamine transferase. Recently, a new site for O-acetylation at positions 3 and 4 of Rha(III), in serotypes 1a, 1b, 2a, 5a and Y was shown to be mediated by the oacB gene. Additionally, this gene was shown to be carried by a transposon-like structure inserted upstream of the adrA region on the chromosome. Results: In this study, a novel bacteriophage Sf101, encoding the oacB gene was isolated and characterised from a serotype 7a strain. The complete sequence of its 38,742 bp genome encoding 66 open reading frames (orfs) was determined. Comparative analysis revealed that phage Sf101 has a mosaic genome, and most of its proteins were >90% identical to the proteins from 12 previously characterised lambdoid phages. In addition, the organisation of Sf101 genes was found to be highly similar to bacteriophage Sf6. Analysis of the Sf101 OacB identified two amino acid substitutions in the protein; however, results obtained by NMR spectroscopy confirmed that Sf101-OacB was functional. Inspection of the chromosomal integration site of Sf101 phage revealed that this phage integrates in the sbcB locus, thus unveiling a new site for integration of serotype-converting phages of S. flexneri, and determining an alternative location of oacB gene in the chromosome. Furthermore, this study identified oacB gene in several serotype 7a isolates from various regions providing evidence of O-acetyl modification in serotype 7a. Conclusions: This is the first report on the isolation of bacteriophage Sf101 which contains the S. flexneri O-antigen modification gene oacB. Sf101 has a highly mosaic genome and was found to integrate in the sbcB locus. These findings contribute an advance in our current knowledge of serotype converting phages of S. flexneri.

  • 21.
    Jiang, Liying
    et al.
    Stockholm University, Faculty of Science, Department of Analytical Chemistry.
    Dziedzic, Pawel
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Spacil, Zdenek
    Stockholm University, Faculty of Science, Department of Analytical Chemistry. University of Washington, USA.
    Zhao, Gui-Ling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Nilsson, Lennart
    Ilag, Leopold L.
    Stockholm University, Faculty of Science, Department of Analytical Chemistry.
    Cordova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mid-Sweden University, Sweden.
    Abiotic synthesis of amino acids and self-crystallization under prebiotic conditions2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, article id 6769Article in journal (Refereed)
    Abstract [en]

    Building on previous research on the origin and homochirality of life, this study focuses on analyses profiling important building blocks of life: the natural amino acids. The spark discharge variation of the iconic Miller experiment was performed with a reducing gas mixture of ammonia, methane, water and hydrogen. Amino acid analysis using liquid chromatography coupled with tandem mass spectrometry after pre-column derivatizaiton revealed the generation of several amino acids including those essential for life. Re-crystallization of the synthetic products and enantiomeric ratio analysis were subsequently performed. Results from liquid chromatography coupled with either fluorescent detector or tandem mass spectrometry after pre-column derivatization with chiral reagent revealed spontaneous and effective asymmetric resolution of serine and alanine. This work describes a useful analytical platform for investigation of hypotheses regarding the origin and homochirality of amino acids under prebiotic conditions. The formation of numerous amino acids in the electric discharge experiment and the occurrence of high enantiomeric ratios of amino acids in re-crystallization experiment give valuable implications for future studies in unraveling fundamental questions regarding origins and evolution of life.

  • 22.
    Karlsson, Erik A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lee, Bao-Lin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Becerril, Valeria Saavedra
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Abrahamsson, Maria
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Synthesis and Electron-Transfer Processes in a New Family of Ligands for Coupled Ru-Mn2 Complexes2014In: ChemPlusChem, ISSN 2192-6506, Vol. 79, no 7, p. 936-950Article in journal (Refereed)
    Abstract [en]

    A series of [Ru(bpy)(3)](2+)-type (bpy= 2,2'-bipyridine) photosensitisers have been coupled to a ligand for Mn, which is expected to give a dinuclear complex that is active as a water oxidation catalyst. Unexpectedly, photophysical studies showed that the assemblies had very short lived excited states and that the decay patterns were complex and strongly dependent on pH. One dyad was prepared that was capable of catalysing chemical water oxidation by using [Ru(bpy)(3)](3+) as an oxidant. However, photochemical water oxidation in the presence of an external electron acceptor failed, presumably because the short excited-state lifetime precluded initial electron transfer to the added acceptor. The photophysical behaviour could be explained by the presence of an intricate excited-state manifold, as also suggested by time-dependent DFT calculations.

  • 23. Karmakar, Anirban
    et al.
    Oliver, Clive L.
    Platero-Prats, Ana E.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Laurila, Elina
    Öhrström, Lars
    Crystal structures and hydrogen bond analysis of five amino acid conjugates of terephthalic and benzene-1,2,3-tricarboxylic acids2014In: CrystEngComm, ISSN 1466-8033, E-ISSN 1466-8033, Vol. 16, no 35, p. 8243-8251Article in journal (Refereed)
    Abstract [en]

    Four linear connecting amino acid derived ligands, 1-4, and one potentially three connecting, 5, were prepared by the reaction of the appropriate terephthaloyl dichloride or benzene-1,3,5-tricarbonyl trichloride with the methyl ester protected amino acid. Amino acids used here were alanine (1, 5), isoleucine (2), leucine (3) and valine (4). Crystalline forms of four amino acid substituted terephthalamides (2,2'-(terephthaloylbis(azanediyl))dipropanoic acid dihydrate 1; 2,2'-(terephthaloylbis(azanediyl)) bis(3-methylpentanoic acid) monohydrate 2; 2,2'-(terephthaloylbis(azanediyl))bis(4-methylpentanoic acid) dihydrate 3; 2,2'-(terephthaloylbis(azanediyl)) bis(3-methylbutanoic acid) dihydrate 4) and one benzene-1,3,5- tricarboxamide molecule (2,2',2 ''-((benzene-1,3,5-tricarbonyl)tris(azanediyl))tripropionic acid hemihydrate 5) were characterised and the single crystal structures were solved. All the compounds form hydrogen bonded 2D and 3D nets. Linear connecting amino acid derivatives can be categorised into three groups depending on the hydrogen bond patterns and final structures. Compounds 1 and 2 form 3D structures but the final structure is different due to the different hydrogen bond synthons. Compounds 3 and 4 are isostructural and form 2D hydrogen bonded structures while 5 forms a hydrogen bonded pcu-net. Intermolecular interactions have been analysed with Hirshfeld surfaces and graph set symbols.

  • 24.
    Kovalenko, Oleksandr O.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lundberg, Helena
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Huebner, Dennis
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Tandem alpha-Alkylation/Asymmetric Transfer Hydrogenation of Acetophenones with Primary Alcohols2014In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 30, p. 6639-6642Article in journal (Refereed)
    Abstract [en]

    A tandem -alkylation/asymmetric transfer hydrogenation of acetophenones with primary alcohols, mediated by a single ruthenium catalyst, is described. Under optimized reaction conditions and with use of [Ru(p-cymene)Cl-2](2) in combination with an amino acid hydroxyamide ligand, the chiral secondary alcohol products were isolated in moderate yields and in moderate to good enantiomeric excess (up to 89% ee).

  • 25.
    Kärkäs, Markus D.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Artificial Photosynthesis: Photosynthesis: From Nanosecond Electron Transfer to Catalytic Water Oxidation2014In: Accounts of Chemical Research, ISSN 0001-4842, E-ISSN 1520-4898, Vol. 47, no 1, p. 100-111Article, review/survey (Refereed)
    Abstract [en]

    Human society faces a fundamental challenge as energy consumption is projected to increase due to population and economic growth as fossil fuel resources decrease. Therefore the transition to alternative and sustainable energy sources is of the Utmost importance. The conversion of solar energy into chemical energy, by splitting H2O to generate molecular O-2 and H-2, could contribute to solving the global energy problem. Developing such a system will require the combination of several complicated processes, such as light-harvesting, charge separation, electron transfer, H2O oxidation, and reduction of the generated protons. The primary processes of charge separation and catalysis, which occur in the natural photosynthetic machinery, provide us with an excellent blueprint for the design of such systems. This Account describes our efforts to construct supramolecular assemblies capable of carrying out photoinduced electron transfer and to develop artificial water oxidation catalysts (WOCs). Early work in our group focused on linking a ruthenium chromophore to a manganese-based oxidation catalyst. When we incorporated a tyrosine unit into these supramolecular assemblies, we could observe fast intramolecular electron transfer from the manganese centers, via the tyrosine moiety, to the photooxidized ruthenium center, which clearly resembles the processes occurring in the natural system. Although we demonstrated multi-electron transfer in our artificial systems, the bottleneck proved to be the stability of the WOCs. Researchers have developed a number of WOCs, but the majority can only catalyze H2O oxidation in the presence of strong oxidants such as Ce-IV, which is difficult to generate photochemically. By contrast, illumination of ruthenium(II) photosensitizers in the presence of a sacrificial acceptor generates [Ru(bpy)(3)](3+)-type oxidants. Their oxidation potentials are significantly lower than that of Ce-IV, but our group recently showed that incorporating negatively charged groups into the ligand backbone could decrease the oxidation potential of the catalysts and, at the same time, decrease the potential for H2O oxidation. This permitted us to develop both ruthenium- and manganese-based WOCs that can operate under neutral conditions, driven by the mild oxidant [Ru(bpy)(3)](3+). Many hurdles to the development of viable systems for the production of solar fuels remain. However, the combination of important features from the natural photosynthetic machinery and novel artificial components adds insights into the complicated catalytic processes that are involved in splitting H2O.

  • 26.
    Kärkäs, Markus D.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Verho, Oscar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnston, Eric V.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Artificial Photosynthesis: Molecular Systems for Catalytic Water Oxidation2014In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 114, no 24, p. 11863-12001Article, review/survey (Refereed)
  • 27.
    Liao, Rong-Zhen
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Li, Xi-Chen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Reaction Mechanism of Water Oxidation Catalyzed by Iron Tetraamido Macrocyclic Ligand Complexes - A DFT Study2014In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, no 4, p. 728-741Article in journal (Refereed)
    Abstract [en]

    Density functional calculations are used to elucidate the reaction mechanism of water oxidation catalyzed by iron tetra-amido macrocyclic ligand (TAML) complexes. The oxidation of the starting TAML-Fe3+-OH2 complex by removing three electrons and two protons leads to the formation of a key intermediate, TAML-Fe5+=O, which can undergo nucleophilic attack by either a water molecule or a nitrate ion. Both pathways involve attack on the oxo group and lead to the production of O-2. The water attack is more favoured and has a total barrier of 15.4 kcal/mol. The alternative nitrate attack pathway has a barrier of 19.5 kcal/mol. Nitrate functions as a cocatalyst by first donating an oxygen atom to the oxo group to form O-2 and a nitrite ion, which can then be reoxidized to regenerate a nitrate ion. Three possible competing pathways result in ligand modification, namely, water and nitrate attack on the ligand, as well as ligand amide oxidation. The water attack on the ligand has a low barrier of only 10.9 kcal/mol and leads to the opening of the benzene ring, which explains the observation of fast catalyst degradation. The lack of activity or lower activity of other catalysts with different substituents is also rationalized.

  • 28.
    Lind, Maria E. S.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical Study of Reaction Mechanism and Stereoselectivity of Arylmalonate Decarboxylase2014In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 4, no 11, p. 4153-4160Article in journal (Refereed)
    Abstract [en]

    The reaction mechanism of arylmalonate decarboxylase is investigated using density functional theory calculations. This enzyme catalyzes the asymmetric decarboxylation of prochiral disubstituted malonic acids to yield the corresponding enantiopure carboxylic acids. The quantum chemical cluster approach is employed, and two different models of the active site are designed: a small one to study the mechanism and characterize the stationary points and a large one to study the enantioselectivity. The reactions of both α-methyl-α-phenylmalonate and α-methyl-α-vinylmalonate are considered, and different substrate binding modes are assessed. The calculations overall give strong support to the suggested mechanism in which decarboxylation of the substrate first takes place, followed by a stereoselective protonation by a cysteine residue. The enediolate intermediate and the transition states are stabilized by a number of hydrogen bonds that make up the dioxyanion hole, resulting in feasible energy barriers. It is further demonstrated that the enantioselectivity in the case of α-methyl-α-phenylmalonate substrate is dictated already in the substrate binding, because only one binding mode is energetically accessible, whereas in the case of the smaller α-methyl-α-vinylmalonate substrate, both the binding and the following transition states contribute to the enantioselectivity.

  • 29.
    Liu, Jianguo
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Asymmetric hydrogenation of allylic alcoholsusing iridium catalysts2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The first part of this thesis is focussed on the enantioselective iridium catalyzeda symmetric hydrogenation of allylic alcohols. The study involved the preparation of a range of allylic alcohols. These allylic alcohols were then hydrogenated, using iridium catalysts that have been previously prepared, to produce chiral alcohols with high yields and excellent enantioselectivity. The selectivity model of the reaction was used to accurately predict the absolute configuration of the hydrogenated products.

    The second part of the thesis was directed on the application of iridium catalyzed asymmetric hydrogenation of allylic alcohols in the synthesis of a late-stage intermediate of Aliskiren. A total of three synthetic routes were evaluated. The best synthesis relies on asymmetric hydrogenation of an allylic ester and an allylic alcohol as key-steps. Full conversion and 94% ee for the allylic alcohol were achieved. The late-stage intermediate of Aliskiren was successfully synthesized in eight steps.

  • 30.
    Maliniak, Arnold
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structural Analysis of Carbohydrates by Nuclear Magnetic Resonance Spectroscopy and Molecular Simulations: Application to Human Milk Oligosaccharides2014In: FOOD OLIGOSACCHARIDES: PRODUCTION, ANALYSIS AND BIOACTIVITY, OXFORD: BLACKWELL SCIENCE PUBL , 2014, p. 320-349Chapter in book (Refereed)
  • 31. Malkov, Andrei V.
    et al.
    Derrien, Nolwenn
    Barlog, Maciej
    Kocovsky, Pavel
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-Catalyzed Alkoxycarbonylation of Terminal Alkenes To Produce alpha, beta-Unsaturated Esters: The Key Role of Acetonitrile as a Ligand2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 16, p. 4542-4547Article in journal (Refereed)
    Abstract [en]

    A mild protocol has been developed for the Pd-II-catalyzed alkoxycarbonylation of terminal olefins to produce ,-unsaturated esters with a wide range of substrates. Key features are the use of MeCN as solvent (and/or ligand) to control the reactivity of the intermediate Pd complexes and the combination of CO with O-2, which facilitates the Cu-II-mediated reoxidation of the Pd-0 complex to Pd-II and prevents double carbonylation.

  • 32. Malkov, Andrei V.
    et al.
    Lee, Darren S.
    Barlog, Maciej
    Elsegood, Mark R. J.
    Kocovsky, Pavel
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Palladium-Catalyzed Stereoselective Intramolecular Oxidative Amidation of Alkenes in the Synthesis of 1,3-and 1,4-Amino Alcohols and 1,3-Diamines2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 17, p. 4901-4905Article in journal (Refereed)
    Abstract [en]

    An efficient and practical Pd-catalyzed intramolecular oxidative allylic amidation provides facile access to derivatives of 1,3- and 1,4-amino alcohols and 1,3-diamines. The method operates under mild reaction conditions (RT) with molecular oxygen (1atm) as the sole reoxidant of Pd. Excellent diastereoselectivities were attained with substrates bearing a secondary stereogenic center

  • 33.
    Manta, Bianca
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Studies of Enzymatic Reaction Mechanisms: Investigations of Cytosine Deaminase and ω-Transaminase2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, density functional theory is used to study the reaction mechanisms of two dierent enzymes. Quantum chemical cluster models of the active sites were designed using available crystal structures. In this approach only the active site residues are considered and the effects of the surroundings are accounted for by a coordinate-locking scheme and a polarizable continuum model.

    The enzymes studied are cytosine deaminase (CDA) from Escherichia coli and ω-transaminase from Chromobacterium violaceum (Cv-ωTA). CDA is a zinc-dependentenzyme that catalyzes the hydrolytic deamination of cytosine into uracil and ammonia. Cv-ωTA carries out the interchange of amino and keto groups by utilizing the cofactor pyridoxal-5’-phosphate (PLP). The calculations provide optimized geometries and energies of transition states and intermediates, which are analyzed and used to construct a potential energy prole for the reaction and to identify the rate-limiting step. Each theoretical investigation provides a detailed description of the catalytic mechanism and establishes the roleof important active site residues.

    In the rst study (Paper I), it was found that a glutamate and an aspartate residue assist in the proton transfer events throughout the reaction. In the second study (Paper II), it was found that the lysine residue, which in the holo enzyme binds the cofactor PLP, assists in several proton transfer events once it has been replaced by the amino substrate. It was also found that the water substrate can be utilized as a proton shuttle before it is consumed at a later stage in the reaction mechanism.

    Apart from the detailed chemical insight, the results in this thesis confirmthat density functional theory together with cluster models of active sites is a very useful approach for studying diverse enzymatic reaction mechanisms.

  • 34.
    Manta, Bianca
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Raushel, Frank M.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Reaction Mechanism of Zinc-Dependent Cytosine Deaminase from Escherichia coli: A Quantum-Chemical Study2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 21, p. 5644-5652Article in journal (Refereed)
    Abstract [en]

    The reaction mechanism of cytosine deaminase from Escherichia coli is studied using density functional theory. This zinc-dependent enzyme catalyzes the deamination of cytosine to form uracil and ammonia. The calculations give a detailed description of the catalytic mechanism and establish the role of important active-site residues. It is shown that Glu217 is essential for the initial deprotonation of the metal-bound water nucleophile and the subsequent protonation of the substrate. It is also demonstrated that His246 is unlikely to function as a proton shuttle in the nucleophile activation step, as previously proposed. The steps that follow are nucleophilic attack by the metal-bound hydroxide, protonation of the leaving group assisted by Asp313, and C-N bond cleavage. The calculated overall barrier is in good agreement with the experimental findings. Finally, the calculations reproduce the experimentally determined inverse solvent deuterium isotope effect, which further corroborates the suggested reaction mechanism.

  • 35.
    Martín-Matute, Belén
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Szabó, Kálmán J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mitchell, Terence N.
    6. Organotin Reagents in Cross-Coupling Reactions2014In: Metal-Catalyzed Cross-Coupling Reactions and More / [ed] Armin de Meijere, Stefan Bräse, Martin Oestreich, Weinheim: Wiley-VCH Verlagsgesellschaft, 2014, 1, p. 423-474Chapter in book (Refereed)
  • 36.
    Nordin, Mikael
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Computational Studies of Transition Metal-Catalyzed Asymmetric Transfer Hydrogenation Reactions2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on two studies dealing with the computational investigation of asymmetric transfer hydrogenation reactions, in which hydrogen is transferred from a donor molecule (e.g. alcohol) to a substrate (ketone), via mediation of a metal-ligand catalyst complex. The catalysts, employing either rhodium or ruthenium in combination with pseudo-dipeptideligands, enantioselectively reduce acetophenone into the secondary alcohol. Stereochemically pure secondary alcohols are important intermediates in the synthesis of many pharmaceutical, agricultural and fine chemistry products. The demand for developing effective, mild and reproducible methods for making these alcohols is high.

    The present studies were made using density functional theory calculations, aiming at explaining the sources of enantioselectivity in the reactions. The calculations reproduce the trends in enantioselectivity quite satisfactorily. In the analysis of the obtained free energy graphs and the optimized geometries several factors that contribute to the enantioselectivity are identified

  • 37.
    Pace, Vittorio
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. University of Vienna, Austria.
    Holzer, Wolfgang
    Olofsson, Berit
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Increasing the Reactivity of Amides towards Organometallic Reagents: An Overview2014In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 356, no 18, p. 3697-3736Article, review/survey (Refereed)
    Abstract [en]

    The nucleophilic addition of carbon nucleophiles to amides has traditionally been a difficult task, both due to reactivity and selectivity problems. When successful, these processes would represent straightforward routes towards carbonyl-type or amine compounds, depending on the fate of the generated tetrahedral intermediate. The direct addition of nucleophiles to amides for the preparation of ketones has been studied and applied to the syntheses of several natural products. On the other hand, the addition of nucleophiles to amides to obtain substituted amines represented a major challenge, and only scattered applications on particular substrates have appeared. Initial improvements were based on the activation of amides by introduction of particular substituents, such as in N-methoxy amides (Weinreb amides) or electron-withdrawing groups able to increase the carbon nucleophilicity. Although these strategies facilitate the introduction of nucleophiles, chemoselectivity issues arise when additional electrophilic moieties (i.e., carbonyls) are present, thus decreasing the versatility of the methods. In recent years, important advancements towards fully chemoselective methods have been realized. The capture of tetrahedral intermediates with acids generates highly electrophilic iminium species able to undergo chemoselective additions of various nucleophiles, thus accessing substituted amines. Alternatively, the in situ generation of an iminium triflate ion allows highly chemoselective additions of nucleophiles, yielding amines, ketones or ketimines. Also thioamides can be used as precursors of ketones or alpha-substituted amines. The success of the above methodologies is further showcased by the application in various syntheses of natural products or biologically active molecules.

  • 38.
    Pascanu, Vlad
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Supported Palladium Nanoparticles for Sustainable Cross-Coupling and Oxidation Reactions2014Licentiate thesis, monograph (Other academic)
    Abstract [en]

    The work presented in this thesis aims to combine the rich chemistry ofpalladium and the benefits of heterogeneous catalysis with metal-organic frameworks(MOFs) in developing robust materials that are recyclable and adaptable to operationunder a continuous flow regime.

    Two new catalysts were created based on palladium nanoparticles in themesoporous MOFs MIL-101 and MIL-88B. They were synthesized and rigorouslycharacterized. All the parameters that can influence the outcome of the desiredchemical transformations were investigated, leading to the development of veryefficient methodologies.

    Pd@MIL-101-NH2 was employed in the Suzuki-Miyaura cross-couplingreaction and it displayed a remarkable efficiency in some of the mildest conditionsreported to date. Moreover, it displays a very good tolerance to highly functionalizedsubstrates, obtaining biaryl motifs that are of potential interest for the pharmaceuticalindustry. Also, a small library of 11 compounds could be synthesized in a singlecontinuous flow experiment proving that the catalyst is amenable to a packed-bedmicro-flow reactor.

    An innovative double support was also used for encapsulating palladiumnanoparticles in a mixed MOF-silica matrix. The resulting material was denotedPd@MIL-88B-NH2@SiO2 and it was employed in a greener approach towards theaerobic oxidation of alcohols. The increased protection of the support allows thecatalyst to maintain a very good performance profile over 7 days of continuousoperation under high mechanical and chemical stress, with no sign of deactivation.

  • 39.
    Peters, Byron K.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhou, Taigang
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rujirawanich, Janjira
    Cadu, Alban
    Singh, Thishana
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Uppsala University, Sweden.
    Rabten, Wangchuk
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kerdphon, Sutthichat
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Andersson, Pher G.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    An Enantioselective Approach to the Preparation of Chiral Sulfones by Ir-Catalyzed Asymmetric Hydrogenation2014In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 136, no 47, p. 16557-16562Article in journal (Refereed)
    Abstract [en]

    Several chiral sulfonyl compounds were prepared using the iridium catalyzed asymmetric hydrogenation reaction. Vinylic, allylic and homoallylic sulfone substitutions were investigated, and high enantioselectivity is maintained regardless of the location of the olefin with respect to the sulfone. Impressive stereoselectivity was obtained for dialkyl substitutions, which typically are challenging substrates in the hydrogenation. As expected, the more bulky Z-substrates were hydrogenated slower than the corresponding E isomers, and in slightly lower enantioselectivity.

  • 40.
    Pu, Maoping
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dynamical Analysis of Chemical Activity of Sterically Encumbered Lewis acid/base Pairs2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This licentiate thesis is about the dynamics analysis of chemical reactions involving a stoichiometric mixture of sterically hindered Lewis base (LB) and Lewis acid (LA) – the so-called frustrated Lewis pairs (FLPs). The tool for dynamical description of chemical reactions is the ab initio molecular dynamics (AIMD) simulations together with the calculation of minimum energy paths (MEPs) on the potential energy surfaces (PESs). The aim is to take into account both the interatomic forces, computed with the dispersion-corrected density functional theory, and the motion of the atoms at finite (non-zero) temperature. With extensive AIMD/PES simulations, we have exposed and explained transition state theory (TST)/MEP paradigm failures for such important chemical reactions as binding (sequestration) of CO2 and the heterolytic cleavage of H2 by a Lewis base, tBu3P, and a Lewis acid, B(C6F5)3. The insight into dynamical aspects of FLP activity, obtained from a synergistic combination of AIMD and PES calculations, is the basis for qualitative and quantitative predictions which could be useful for future experiments

  • 41.
    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 Study of Hydrogen Cleavage by a Lewis Base [tBu(3)P] and a Lewis Acid [B(C6F5)(3)] at the Mesoscopic Level-Dynamics in the Solute-Solvent Molecular Clusters2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 17, p. 3714-3719Article in journal (Refereed)
    Abstract [en]

    With the help of state-of-the-art ab initio molecular dynamics methods, we investigated the reaction pathway of the {tBu(3)P + H-2 + B(C6F5)(3)} system at the mesoscopic level. It is shown that: i) the onset of H-2 activation is at much larger boronphosphorus distances than previously thought; ii) the system evolves to the product in a roaming-like fashion because of quasi-periodic nuclear motion along the asymmetric normal mode of PHHB fragment; iii) transient configurations of a certain type are present despite structural interference from the solvent; iv) transient-state configurations with sub-picosecond lifetime have potentially interesting infrared activity in the organic solvent (toluene) as well as in the gas phase. The presented results should be helpful for future experimental and theoretical studies of frustrated Lewis pair (FLP) activity.

  • 42.
    Pu, Maoping
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    How Frustrated Lewis Acid/Base Systems Pass through Transition-State Regions: H-2 Cleavage by [tBu(3)P/B(C6F5)(3)]2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 14, p. 2936-2944Article in journal (Refereed)
    Abstract [en]

    We investigate the transition-state (TS) region of the potential energy surface (PES) of the reaction tBu(3)P+H-2 +B(C6F5)(3)-> tBu(3)P-H(+)+H(-)-B(C6F5)(3) and the dynamics of the TS passage at room temperature. Owing to the conformational inertia of the phosphane center dot center dot center dot borane pocket involving heavy tBu(3)P and B(C6F5)(3) species and features of the PES E(P center dot center dot center dot H, B center dot center dot center dot H vertical bar B center dot center dot center dot P) as a function of P center dot center dot center dot H, B center dot center dot center dot H, and B center dot center dot center dot P distances, a typical reactive scenario for this reaction is a trajectory that is trapped in the TS region for a period of time (about 350 fs on average across all calculated trajectories) in a quasi-bound state (scattering resonance). The relationship between the timescale of the TS passage and the effective conformational inertia of the phosphane center dot center dot center dot borane pocket leads to a prediction that isotopically heavier Lewis base/Lewis acid pairs and normal counterparts could give measurably different reaction rates. Herein, the predicted quasi-bound state could be verified in molecular collision experiments involving femtosecond spectroscopy.

  • 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.
    Multiple-Pathways of Carbon Dioxide Binding by a Lewis Acid [B(C6F5)(3)] and a Lewis Base [P(tBu)(3)]: The Energy Landscape Perspective2014In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 114, no 4, p. 289-294Article in journal (Refereed)
    Abstract [en]

    Using the reaction-relevant two-dimensional potential energy surface, an accurate reaction-pathway mapping and ab inito molecular dynamics, it is shown that CO2 capture by P(tBu)(3) and B(C6F5)(3) species has many nearly degenerate reaction-routes to take. The explanation of that is in the topography of the transition state (saddle) area. An ensemble of asynchronous reaction-routes of CO2 binding is described in fine detail.

  • 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.
    Uncovering the Role of Intra- and Intermolecular Motion in Frustrated Lewis Acid/Base Chemistry: Ab Initio Molecular Dynamics Study of CO2 Binding by Phosphorus/Boron Frustrated Lewis Pair [tBu(3)P/B(C6F5)(3)]2014In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 53, no 9, p. 4598-4609Article in journal (Refereed)
    Abstract [en]

    The role of the intra- and intermolecular motion, i.e., molecular vibrations and the relative motion of reactants, remains largely unexplored in the frustrated Lewis acid/base chemistry. Here, we address the issue with the ab initio molecular dynamics (AIMD) study of CO2 binding by a Lewis acid (LA) and a Lewis base (LB), i.e., tBu(3)P + CO2 + B(C6F5)(3) -> tBu(3)P-C(O)O-B(C6F5)(3) ([1]). Reasonably large ensemble of AIMD trajectories propagated at 300 K from structures in the saddle region as well as trajectories propagated directly from the reactants region revealed an effect arising from significant recrossing of the saddle area. The effect is that transient complexes composed of weakly interacting reactants nearly cease to progress along the segment of the minimum energy pathway (MEP) at the saddle region for a (subpicosecond) period of time during which the dominant factor is the light-to-heavy type of relative motion of the vibrating reactants, i.e., the bouncing-like movement of CO2 with respect to much heavier phosphine and borane as main contributor to the mode that is perpendicular to the MEP-direction. In terms of how P...C and B...O distances change with time, the roaming-like patterns of typical AIMD trajectories, reactive and nonreactive alike, extend far beyond the saddle region. In addition to the dynamical portrayal of [1], we provide the energy-landscape perspective that takes into account the hierarchy of time scales. The verifiable implication of the effect found here is that the isotopically substituted (heavier) LB/LA pair should be less reactive that the normal and thus lighter counterpart.

  • 45.
    Rabbani, Faiz
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Svengren, Henrik
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zimmermann, Iwan
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hu, Shichao
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laine, Tanja
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Hao, Wenming
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johnsson, Mats
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Cobalt selenium oxohalides: catalysts for water oxidation2014In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 43, no 10, p. 3984-33989Article in journal (Refereed)
    Abstract [en]

    Two new oxohalides Co4Se3O9Cl2 and Co3Se4O10Cl2 have been synthesized by solid state reactions. They crystallize in the orthorhombic space group Pnma and the monoclinic space group C2/m respectively. The crystal structure of the two compounds are made up of similar building blocks; Co4Se3O9Cl2 is made up of [CoO4Cl2], [CoO5Cl] and [SeO3] polyhedra and Co3Se4O10Cl2 is made up of [CoO4Cl2] and [SeO3] polyhedra. As several Co-containing compounds have proved to be good catalysts for water oxidation, the activities of the two new compounds were compared with the previously found oxohalide Co5Se4O12Cl2 in reference to CoO and CoCl2. The one electron oxidant Ru(bpy)33+ was used as oxidizing species in a phosphate buffer and it was found that the activities of the oxohalide species were in between CoO and CoCl2. The roles of Cl and PO43− ions are discussed.

  • 46.
    Santoro, Stefano
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Azeredo, Juliano B.
    Nascimento, Vanessa
    Sancineto, Luca
    Braga, Antonio L.
    Santi, Claudio
    The green side of the moon: ecofriendly aspects of organoselenium chemistry2014In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 4, no 60, p. 31521-31535Article in journal (Refereed)
    Abstract [en]

    Organoselenium chemistry has proven to be a powerful tool for organic synthesis over several decades. Nevertheless, the use of selenating reagents has often been limited by a generally bad reputation surrounding selenium toxicity and its potential impact on the environment. In this review we would like to stress some aspects that will encourage the reader to discover an unexpected green side to this element and the chemistry connected with its organic derivatives.

  • 47.
    Santoro, Stefano
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Deiana, Luca
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhao, Gui-Ling
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lin, Shuangzheng
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Cordova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Mid Sweden University, Sweden.
    Mechanism of Palladium/Amine Cocatalyzed Carbocyclization of Aldehydes with Alkynes and Its Merging with Pd Oxidase Catalysis2014In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 4, no 12, p. 4474-4484Article in journal (Refereed)
    Abstract [en]

    The reaction mechanism for the palladium and amine cocatalyzed carbocyclization of aldehydes with alkynes has been investigated by means of density functional theory calculations and experiments. The Pd/amine cocatalyzed transformation is a carbocyclization of in situ generated enaminynes where the C-C bond-forming step is most likely promoted by a Pd(II) species. Notably, the latent Pd(O)/Pd(Ip catalytic redox cycle of this metal/organo cooperative catalytic reaction can be merged with catalytic direct aerobic alcohol oxidation (Pd oxidase catalysis).

  • 48.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Water oxidation energy diagrams for photosystem II for different protonation states, and the effect of removing calcium2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 24, p. 11893-11900Article in journal (Refereed)
    Abstract [en]

    The main parts of the water oxidation mechanism in photosystem II have now been established both from theory and experiments. Still, there are minor questions remaining. One of them concerns the charge and the protonation state of the oxygen evolving complex (OEC). Previously, theory and experiments have agreed that the two water derived ligands on the outer manganese should be one hydroxide and one water. In the present study it is investigated whether both of them could be water. This question is addressed by a detailed study of energy diagrams, but in this context it is more conclusive to compare the redox potential of the OEC to the one of Tyr(Z). Both procedures lead to the conclusion that one of the ligands is a hydroxide. Another question concerns the protonation of the second shell His337, where the results are more ambiguous. The final part of the present study describes results when calcium is removed from the OEC. Even though protons enter to compensate the charge of the missing Ca2+, the redox potential and the pK(a) value of the OEC change dramatically and prevent the progress after S-2.

  • 49.
    Siegbahn, Per E. M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Energy Diagrams for Water Oxidation in Photosystem II Using Different Density Functionals2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 1, p. 268-272Article in journal (Refereed)
    Abstract [en]

    The full sequence of intermediates in the water oxidation process in photosystem II has recently been characterized by model calculations, in good agreement with experiments. In the present paper, the energy diagram obtained is used as a benchmark test for several density functionals. Only the results using B3LYP with 15% or 20% show good agreement with experiments. The other functionals tried show errors for some energy levels as large as 20-30 kcal/mol. The reason for these large errors is that the error for three consecutive oxidations of Mn(III) to Mn(IV) accumulates as the cluster is oxidized.

  • 50.
    Siegbahn, Per E. M.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mutations in the D-channel of cytochrome c oxidase causes leakage of the proton pump2014In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 588, no 4, p. 545-548Article in journal (Refereed)
    Abstract [en]

    It has experimentally been found that certain mutations close to the entry point of the proton transfer channel in cytochrome c oxidase stop proton translocation but not the oxygen reduction chemistry. This effect is termed uncoupling. Since the mutations are 20 angstrom away from the catalytic center, this is very surprising. A new explanation for this phenomenon is suggested here, involving a local effect at the entry point of the proton channel, rather than the long range effects suggested earlier. (C) 2013 Federation of European Biochemical Societies.

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