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  • 1.
    Abdellah, Mohamed
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. South Valley Univ, Qena Fac Sci, Dept Chem, Qena 83523, Egypt..
    El-Zohry, Ahmed M.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Antila, Liisa J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Windle, Christopher D.
    Univ Cambridge, Dept Chem, Christian Doppler Lab Sustainable SynGas Chem, Lensfield Rd, Cambridge CB2 1EW, England..
    Reisner, Erwin
    Univ Cambridge, Dept Chem, Christian Doppler Lab Sustainable SynGas Chem, Lensfield Rd, Cambridge CB2 1EW, England..
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Time-Resolved IR Spectroscopy Reveals a. Mechanism with TiO2 as a Reversible Electron Acceptor in a TiO2-Re Catalyst System for CO2 Photoreduction2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 3, p. 1226-1232Article in journal (Refereed)
    Abstract [en]

    Attaching the phosphonated molecular catalyst [(ReBr)-Br-I(bpy)-(CO)(3)](0) to the wide-bandgap semiconductor TiO2 strongly enhances the rate of visible-light-driven reduction of CO2 to CO in dimethylformamide with triethanolamine (TEOA) as sacrificial electron donor. Herein, we show by transient mid-IR spectroscopy that the mechanism of catalyst photoreduction is initiated by ultrafast electron injection into TiO2, followed by rapid (ps-ns) and sequential two-electron oxidation of TEOA that is coordinated to the Re center. The injected electrons can be stored in the conduction band of TiO2 on an ms-s time scale, and we propose that they lead to further reduction of the Re catalyst and completion of the catalytic cycle. Thus, the excited Re catalyst gives away one electron and would eventually get three electrons back. The function of an electron reservoir would represent a role for TiO2 in photocatalytic CO2 reduction that has previously not been considered. We propose that the increase in photocatalytic activity upon heterogenization of the catalyst to TiO2 is due to the slow charge recombination and the high oxidative power of the Re-II species after electron injection as compared to the excited MLCT state of the unbound Re catalyst or when immobilized on ZrO2, which results in a more efficient reaction with TEOA.

  • 2.
    Abrahamsson, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, För teknisk-naturvetenskapliga fakulteten gemensamma enheter, Accelerator mass spectrometry group. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Jäger, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Kumar, Rohan J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Österman, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Persson, Petter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Becker, Hans-Christian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Johansson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Bistridentate Ruthenium(II)polypyridyl-Type Complexes with Microsecond 3MLCT State Lifetimes: Sensitizers for Rod-Like Molecular Arrays2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 46, p. 15533-15542Article in journal (Refereed)
    Abstract [en]

    A series of bistridentate ruthenium(II) polypyridyl-type complexes based on the novel 2,6-di(quinolin-8-yl)pyridine (dqp) ligand have been synthesized and their photophysical properties have been studied. The complexes are amenable to substitution in the 4-position of the central pyridine with conserved quasi-C2v symmetry, which allows for extension to isomer-free, rod-like molecular arrays for vectorial control of electron and energy transfer. DFT calculations performed on the parent [Ru(dqp) 2](2+) complex (1) predicted a more octahedral structure than in the typical bistridentate complex [Ru(tpy)2](2+) (tpy is 2,2':6',2"-terpyridine) thanks to the larger ligand bite angle, which was confirmed by X-ray crystallography. A strong visible absorption band, with a maximum at 491 nm was assigned to a metal-to-ligand charge transfer (MLCT) transition, based on time-dependent DFT calculations. 1 shows room temperature emission (Phi = 0.02) from its lowest excited ((3)MLCT) state that has a very long lifetime (tau = 3 micros). The long lifetime is due to a stronger ligand field, because of the more octahedral structure, which makes the often dominant activated decay via short-lived metal-centered states insignificant also at elevated temperatures. A series of complexes based on dqp with electron donating and/or accepting substituents in the 4-position of the pyridine was prepared and the properties were compared to those of 1. An unprecedented (3)MLCT state lifetime of 5.5 micros was demonstrated for the homoleptic complex based on dqpCO2Et. The favorable photosensitizer properties of 1, such as a high extinction coefficient, high excited-state energy and long lifetime, and tunable redox potentials, are maintained upon substitution. In addition, the parent complex 1 is shown to be remarkably photostable and displays a high reactivity in light-induced electron and energy transfer reactions with typical energy and electron acceptors and donors: methylviologen, tetrathiofulvalene, and 9,10-diphenylanthracene. This new class of complexes constitutes a promising starting point for the construction of linear, rod-like molecular arrays for photosensitized reactions and applications in artificial photosynthesis and molecular electronics.

  • 3.
    Abrahamsson, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, För teknisk-naturvetenskapliga fakulteten gemensamma enheter, Accelerator mass spectrometry group. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Jäger, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Österman, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Eriksson, Lars
    Persson, Petter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Becker, Hans-Christian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Johansson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    A 3.0 mu s room temperature excited state lifetime of a bistridentate Ru-II-polypyridine complex for rod-like molecular arrays2006In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 128, no 39, p. 12616-12617Article in journal (Refereed)
    Abstract [en]

    A bistridentate RuII-polypyridine complex [Ru(bqp)2]2+ (bqp = 2,6-bis(8'-quinolinyl)pyridine) has been prepared, which has a coordination geometry much closer to a perfect octahedron than the typical Ru(terpyridine)2-type complex. Thus, the complex displays a 3.0 mus lifetime of the lowest excited metal-to-ligand charge transfer (3MLCT) state at room temperature. This is, to the best of our knowledge, the longest MLCT state lifetime reported for a RuII-polypyridyl complex at room temperature. The structure allows for the future construction of rod-like, isomer-free molecular arrays by substitution of donor and acceptor moieties on the central pyridine units. This makes it a promising photosensitizer for applications in molecular devices for artificial photosynthesis and molecular electronics.

  • 4.
    Acharya, P
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cheruku, P
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chatterjee, Sunanda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Karthick Babu, S
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, S
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes2004In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, no 9, p. 2862-2869Article in journal (Refereed)
    Abstract [en]

    To understand why the RNA-RNA duplexes in general has a higher thermodynamic stability over the corresponding DNA-DNA duplexes, we have measured the pK(a) values of both nucleoside 3',5'-bis-ethyl phosphates [Etp(d/rN)pEt] and nucleoside 3'-ethyl phosphates [(d/rN)pEt] (N = A, G, C, or T/U), modeling as donors and acceptors of base pairs in duplexes. While the 3',5'-bis-phosphates, Etp(d/rN)pEt, mimic the internucleotidic monomeric units of DNA and RNA, in which the stacking contribution is completely absent, the 3'-ethyl phosphates, (d/rN)pEt, mimic the nucleotide at the 5'-end. The pK(a) values of the nucleobase in each of these model nucleoside phosphates have been determined with low pK(a) error (sigma = +/-0.01 to 0.02) by (1)H NMR (at 500 MHz) with 20-33 different pH measurements for each compound. This study has led us to show the following: (1) All monomeric DNA nucleobases are more basic than the corresponding RNA nucleobases in their respective Etp(d/rN)pEt and (d/rN)pEt. (2) The pK(a) values of the monomeric nucleotide blocks as well as Delta pK(a) values between the donor and acceptor can be used to understand the relative base-pairing strength in the oligomeric duplexes in the RNA and DNA series. (3) The Delta G*(pKa) of the donor and acceptor of the base pair in duplexes enables a qualitative dissection of the relative strength of the base-pairing and stacking in the RNA-RNA over the DNA-DNA duplexes. (4) It is also found that the relative contribution of base-pairing strength and nucleobase stacking in RNA-RNA over DNA-DNA is mutually compensating as the % A-T/U content increases or decreases. This interdependency of stacking and hydrogen bonding can be potentially important in the molecular design of the base-pair mimics to expand the alphabet of the genetic code.

  • 5.
    Acharya, Parag
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, Sandipta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cheruku, P
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Amirkhanov, N. V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Földesi, A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions2003In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, no 33, p. 9948-9961Article in journal (Refereed)
    Abstract [en]

    The pH titration studies (pH 6.7-12.1) in a series of dimeric, trimeric, tetrameric, pentameric, and hexameric oligo-RNA molecules [GpA (2a), GpC (3a), GpApC (5), GpA(1)pA(2)pC (6), GpA(1)pA(2)pA(3)pC (7), GpA(1)pA(2)pA(3)pA(4)pC (8)] have shown that the pK(a) of N(1)-H of 9-guaninyl could be measured not only from its own deltaH8G, but also from the aromatic marker protons of other constituent nucleobases. The relative chemical shift differences [Deltadelta((N)(-)(D))] between the protons in various nucleotide residues in the oligo-RNAs at the neutral (N) and deprotonated (D) states of the guanine moiety show that the generation of the 5'-(9-guanylate ion) in oligo-RNAs 2-8 reduces the stability of the stacked helical RNA conformation owing to the destabilizing anion(G(-))-pi/dipole(Im(delta)(-)) interaction. This destabilizing effect in the deprotonated RNA is, however, opposed by the electrostatically attractive atom-pisigma (major) as well as the anion(G(-))-pi/dipole(Py(delta)(+)) (minor) interactions. Our studies have demonstrated that the electrostatically repulsive anion(G(-))-pi/dipole(Im(delta)(-)) interaction propagates from the first to the third nucleobase quite strongly in the oligo-RNAs 6-8, causing destacking of the helix, and then its effect is gradually reduced, although it is clearly NMR detectable along the RNA chain. Thus, such specific generation of a charge at a single nucleobase moiety allows us to explore the relative strength of stacking within a single-stranded helix. The pK(a) of 5'-Gp residue from its own deltaH8G in the hexameric RNA 8 is found to be 9.76 +/- 0.01; it, however, varies from 9.65 +/- 0.01 to 10.5 +/- 0.07 along the RNA chain as measured from the other marker protons (H2, H8, H5, and H6) of 9-adeninyl and 1-cytosinyl residues. This nucleobase-dependent modulation of pK(a)s (DeltapK(a) +/- 0.9) of 9-guaninyl obtained from other nucleobases in the hexameric RNA 8 represents a difference of ca. 5.1 kJ mol(-)(1), which has been attributed to the variable strength of electrostatic interactions between the electron densities of the involved atoms in the offset stacked nucleobases as well as with that of the phosphates. The chemical implication of this variable pK(a) for guanin-9-yl deprotonation as obtained from all other marker protons of each nucleotide residue within a ssRNA molecule is that it enables us to experimentally understand the variation of the electronic microenvironment around each constituent nucleobase along the RNA chain in a stepwise manner with very high accuracy without having to make any assumption. This means that the pseudoaromaticity of neighboring 9-adeninyl and next-neighbor nucleobases within a polyanionic sugar-phosphate backbone of a ssRNA can vary from one case to another due to cross-modulation of an electronically coupled pi system by a neighboring nucleobase. This modulation may depend on the sequence context, spatial proximity of the negatively charged phosphates, as well as whether the offset stacking is ON or OFF. The net outcome of this electrostatic interaction between the neighbors is creation of new sequence-dependent hybrid nucleobases in an oligo- or polynucleotide whose properties are unlike the monomeric counterpart, which may have considerable biological implications.

  • 6.
    Acharya, Sandipta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Barman, Jharna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cheruku, Pradeep
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chatterjee, Subhrangsu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, Parag
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Isaksson, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, Jyoti
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA2004In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, no 28, p. 8674-8681Article in journal (Refereed)
  • 7. Aili, Daniel
    et al.
    Enander, Karin
    Rydberg, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry II.
    Nesterenko, Irina
    Björefors, Fredrik
    Baltzer, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry II.
    Liedberg, Bo
    Folding Induced Assembly of Polypeptide Decorated Gold Nanoparticles2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 17, p. 5780-5788Article in journal (Refereed)
    Abstract [en]

    Reversible assembly of gold nanoparticles controlled by the homodimerization and folding of an immobilized de novo designed synthetic polypeptide is described. In solution at neutral pH, the polypeptide folds into a helix-loop-helix four-helix bundle in the presence of zinc ions. When immobilized on gold nanoparticles, the addition of zinc ions induces dimerization and folding between peptide monomers located on separate particles, resulting in rapid particle aggregation. The particles can be completely redispersed by removal of the zinc ions from the peptide upon addition of EDTA. Calcium ions, which do not induce folding in solution, have no effect on the stability of the peptide decorated particles. The contribution from folding on particle assembly was further determined utilizing a reference peptide with the same primary sequence but containing both D and L amino acids. Particles functionalized with the reference peptide do not aggregate, as the peptides are unable to fold. The two peptides, linked to the nanoparticle surface via a cysteine residue located in the loop region, form submonolayers on planar gold with comparable properties regarding surface density, orientation, and ability to interact with zinc ions. These results demonstrate that nanoparticle assembly can be induced, controlled, and to some extent tuned, by exploiting specific molecular interactions involved in polypeptide folding.

  • 8.
    Alonso, Diego A
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry, Organic Chemistry.
    Brandt, P
    Nordin, Sofia J M
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry, Organic Chemistry.
    Andersson, Pher G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry, Organic Chemistry.
    Ru(arene)(amino alcohol)-Catalyzed Transfer Hydrogenation of Ketones: Mechanism and Origin of Enantioselectivity1999In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 121, no 41, p. 9580-9588Article in journal (Refereed)
    Abstract [en]

    The mechanism of the Ru(arene)(amino alcohol)-catalyzed transfer hydrogenation of ketones using isopropyl alcohol as the hydrogen source has been studied by means of hybrid density functional methods (B3PW91). Three mechanistic alternatives were evaluated, and it was shown that the reaction takes place via a six-membered transition state, where a metal-bound hydride and a proton of a coordinated amine are transferred simultaneously to the ketone. Further calculations provided a general rationale for the rate of the reaction by comparison of steric effects in the ground and transition states of the ruthenium hydride complex. It was found that the TS has a strong preference for planarity, and this in turn is dependent on the conformational behavior of the O,N-linkage of the amino alcohol ligand. Finally, a general model, rationalizing the enantioselectivity of the reaction, was developed. Experimental studies of both rate and enantioselectivity were used in order to support the computational results.

  • 9.
    Amft, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Edvinsson, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Inorganic Chemistry.
    Skorodumova, Natalia V.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Thermally Excited Vibrations in Copper, Silver, and Gold Trimers and Enhanced Binding of CO2010In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126Article in journal (Other academic)
  • 10. Andersen, Thomas L.
    et al.
    Friis, Stig D.
    Audrain, Helene
    Nordeman, Patrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preclinical PET Platform.
    Antoni, Gunnar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preclinical PET Platform.
    Skrydstrup, Troels
    Efficient C-11-Carbonylation of Isolated Aryl Palladium Complexes for PET: Application to Challenging Radiopharmaceutical Synthesis2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 4, p. 1548-1555Article in journal (Refereed)
    Abstract [en]

    We describe the successful implementation of palladium-aryl oxidative addition complexes as stoichiometric reagents in carbonylation reactions with (CO)-C-11 to produce structurally challenging, pharmaceutically relevant compounds. This method enables the first C-11-carbonyl labeling of an approved PET tracer, [C-11]raclopride, for the dopamine D2/D3 receptor by carbonylation with excellent radiochemical purity and yield. Two other molecules, [C-11]olaparib and [C-11]JNJ 31020028, were efficiently labeled in this manner. The technique distinguishes itself from existing methods by the markedly improved purity profiles of the tracer molecules produced and provides access to complex structures in synthetically useful yields, hereby offering a viable alternative to other C-11-labeling strategies.

  • 11.
    Atluri, Rambabu
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Garcia-Bennett, Alfonso
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Hedin, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Nonsurfactant Supramolecular Synthesis of Ordered Mesoporous Silica2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 9, p. 3189-3191Article in journal (Refereed)
    Abstract [en]

    Hoogsteen-bonded tetrads and pentamers are formed by a large variety of organic molecules through H-donor and acceptor groups capable of inducing self-organization to form columnar and hexagonal mesophases. The biological importance of such macromolecular structures is exemplified by the assembly of guanosine-rich groups of telomere units and their implication in chromosomal replication. Folic acid is composed of a pterin group, chemically and structurally similar to guanine, conjugated to an l-glutamate moiety via a p-amino benzoic acid. Our aim has been to develop a delivery vehicle for folic acid and at the same time provide a novel synthetic route for ordered mesoporous materials without the use of amphiphilic surfactants. We present a new nonsurfactant route for the synthesis of highly ordered mesoporous materials, based on the supramolecular templating of stacked arrays of the tetramer-forming pterin groups of folic acid under a variety of synthetic conditions. This method leads to hexagonally ordered mesoporous structures with gyroid, spherical, and chiral morphologies with pores on the order of 25−30 Å in diameter and surface areas above 1000 m2/g. More importantly circular dichroism studies reveal that the folate template possesses a chiral signature within the pores in the as-synthesized solid and that chirality is transferred from the folate template to the pore surface via the aminopropyl triethoxysilane costructure directing agent used in the supramolecular assembly. This novel templating approach for ordered mesoporous materials breaks the hegemony of surfactant micellar systems for the preparation of these exciting high surface area solids and opens new opportunities for structural control, design of pore geometry, and novel applications.

  • 12.
    Barrozo, Alexandre
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Duarte, Fernanda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bauer, Paul
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Carvalho, Alexandra T. P.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 28, p. 9061-9076Article in journal (Refereed)
    Abstract [en]

    It is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. In this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. In the present work, we model the selectivity of two multiply promiscuous members of this superfamily, namely the phosphonate monoester hydrolases from Burkholderia caryophylli and Rhizobium leguminosarum. We have performed extensive simulations of the enzymatic reaction of both wild-type enzymes and several experimentally characterized mutants. Our computational models are in agreement with key experimental observables, such as the observed activities of the wild-type enzymes, qualitative interpretations of experimental pH-rate profiles, and activity trends among several active site mutants. In all cases the substrates of interest bind to the enzyme in similar conformations, with largely unperturbed transition states from their corresponding analogues in aqueous solution. Examination of transition-state geometries and the contribution of individual residues to the calculated activation barriers suggest that the broad promiscuity of these enzymes arises from cooperative electrostatic interactions in the active site, allowing each enzyme to adapt to the electrostatic needs of different substrates. By comparing the structural and electrostatic features of several alkaline phosphatases, we suggest that this phenomenon is a generalized feature driving selectivity and promiscuity within this superfamily and can be in turn used for artificial enzyme design.

  • 13.
    Barz, Bogdan
    et al.
    Forschungszentrum Jülich GmbH, Institute of Complex Systems: Structural Biochemistry (ICS-6), Jülich; Heinrich Heine University Düsseldorf, Institute of Theoretical and Computational Chemistry, Düsseldorf.
    Liao, Qinghua
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Biology. Forschungszentrum Jülich GmbH, Institute of Complex Systems: Structural Biochemistry (ICS-6), Jülich.
    Strodel, Birgit
    Forschungszentrum Jülich GmbH, Institute of Complex Systems: Structural Biochemistry (ICS-6), Jülich; Heinrich Heine University Düsseldorf, Institute of Theoretical and Computational Chemistry, Düsseldorf.
    Pathways of Amyloid-β Aggregation Depend on Oligomer Shape2018In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, no 1, p. 319-327Article in journal (Refereed)
    Abstract [en]

    One of the main research topics related to Alzheimer’s disease is the aggregation of the amyloid-β peptide, which was shown to follow different pathways for the two major alloforms of the peptide, Aβ40 and the more toxic Aβ42. Experimental studies emphasized that oligomers of specific sizes appear in the early aggregation process in different quantities and might be the key toxic agents for each of the two alloforms. We use transition networks derived from all-atom molecular dynamics simulations to show that the oligomers leading to the type of oligomer distributions observed in experiments originate from compact conformations. Extended oligomers, on the other hand, contribute more to the production of larger aggregates thus driving the aggregation process. We further demonstrate that differences in the aggregation pathways of the two Aβ alloforms occur as early as during the dimer stage. The higher solvent-exposure of hydrophobic residues in Aβ42 oligomers contributes to the different aggregation pathways of both alloforms and also to the increased cytotoxicity of Aβ42.

  • 14. Bertelsen, Søren
    et al.
    Dinér, Peter
    Center for Catalysis, Department of Chemistry, Aarhus University.
    Johansen, Rasmus Lyng
    Jørgensen, Karl Anker
    Asymmetric organocatalytic beta-hydroxylation of alpha, beta-unsaturated aldehydes2007In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 129, no 6, p. 1536-1537Article in journal (Refereed)
    Abstract [en]

    The first catalytic enantioselective beta-hydroxylation of alpha,beta-unsaturated aldehydes is presented. Using commercially available (E)-benzaldehyde oxime in the presence of 2-[bis(3,5-bis-trifluoromethyl-phenyl)trimethyl-silanyloxymethyl]pyrrolidine as organocatalyst, the corresponding chiral carbonyl beta-oxime ethers are obtained in high yields and with excellent enantioselectivities. These optically active carbonyl and hydroxy beta-oxime ethers are highly interesting biological compounds in, e.g., sex pheromone analogues, highly potent antiinflammatory agents, and penicillin and cephalosporin analogues. The chiral carbonyl beta-oxime ethers can be reduced to the corresponding 1,3-diols in high yields. Furthermore, the organocatalytic enantioselective beta-hydroxylation of alpha,beta-unsaturated aldehydes could be performed on gram scale without loss of enantioselectivity.

  • 15. Bertelsen, Søren
    et al.
    Marigo, Mauro
    Brandes, Sebastian
    Dinér, Peter
    Center for Catalysis, Department of Chemistry, Aarhus University.
    Jørgensen, Karl Anker
    Dienamine catalysis: organocatalytic asymmetric gamma-amination of alpha,beta-unsaturated aldehydes2006In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 128, no 39, p. 12973-12980Article in journal (Refereed)
    Abstract [en]

    A new concept in organocatalysis is presented, the direct asymmetric gamma-functionalization of alpha,beta-unsaturated aldehydes. We disclose that secondary amines can invert the usual reactivity of alpha,beta-unsaturated aldehydes, enabling a direct gamma-amination of the carbonyl compound using azodicarboxylates as the electrophilic nitrogen-source. The scope of the reaction is demonstrated for the enantioselective gamma-amination of different alpha,beta-unsaturated aldehydes, giving the products in moderate to good yields and with high enantioselectivities up to 93% ee. Experimental investigations and DFT calculations indicate that the reaction might proceed as a hetero-Diels-Alder cycloaddition reaction. Such a mechanism can explain the "unexpected" stereochemical outcome of the reaction.

  • 16.
    Blaha-Nelson, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Krüger, Dennis M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Szeler, Klaudia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ben-David, Moshe
    Weizmann Inst Sci, Dept Biol Chem, IL-76100 Rehovot, Israel.;Univ Toronto, Banting & Best Dept Med Res, Donnelly Ctr Cellular & Biomol Res, 160 Coll St, Toronto, ON M5S 3E1, Canada..
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 12017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 3, p. 1155-1167Article in journal (Refereed)
    Abstract [en]

    Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed beta-propeller with a flexible loop (residues 70-81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1's lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1's lactonase activity is minimal, whereas the k(cat) for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1's active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar "gating loop" or a highly buried solvent excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates.

  • 17. Borgström, Magnus
    et al.
    Shaikh, Nizamuddin
    Johansson, Olof
    Anderlund, Magnus F
    Styring, Stenbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Åkermark, Björn
    Magnuson, Ann
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Light-Induced Manganese Oxidation and Long-Lived Charge Separation in a Mn2II,II─RuII─Acceptor Triad.2005In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 127, p. 17504-17515Article in journal (Refereed)
  • 18.
    Borgström, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Shaikh, Nizamuddin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Molecular Biomimetics.
    Johansson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Anderlund, Magnus
    Styring, Stenbjörn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Molecular Biomimetics.
    Åkerman, Björn
    Magnusson, Ann
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Molecular Biomimetics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Light induced manganese oxidation and long-lived charge separation in a Mn2II,II-RuII(bpy)3-acceptor triad2005In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 127, no 49, p. 17504-17515Article in journal (Refereed)
    Abstract [en]

    The photoinduced electron-transfer reactions in a Mn2II,II-RuII-NDI triad (1) ([Mn2(bpmp)(OAc)2]+, bpmp = 2,6-bis[bis(2-pyridylmethyl)aminomethyl]-4-methylphenolate and OAc = acetate, RuII = tris-bipyridine ruthenium(II), and NDI = naphthalenediimide) have been studied by time-resolved optical and EPR spectroscopy. Complex 1 is the first synthetically linked electron donor-sensitizer-acceptor triad in which a manganese complex plays the role of the donor. EPR spectroscopy was used to directly demonstrate the light induced formation of both products: the oxidized manganese dimer complex (Mn2II,III) and the reduced naphthalenediimide (NDI*-) acceptor moieties, while optical spectroscopy was used to follow the kinetic evolution of the [Ru(bpy)3]2+ intermediate states and the NDI*- radical in a wide temperature range. The average lifetime of the NDI*- radical is ca. 600 micros at room temperature, which is at least 2 orders of magnitude longer than that for previously reported triads based on a [Ru(bpy)3]2+ photosensitizer. At 140 K, this intramolecular recombination was dramatically slowed, displaying a lifetime of 0.1-1 s, which is comparable to many of the naturally occurring charge-separated states in photosynthetic reaction centra. It was found that the long recombination lifetime could be explained by an unusually large reorganization energy (lambda approximately 2.0 eV), due to a large inner reorganization of the manganese complex. This makes the recombination reaction strongly activated despite the large driving force (Delta-G degrees = 1.07 eV). Thus, the intrinsic properties of the manganese complex are favorable for creating a long-lived charge separation in the "Marcus normal region" also when the charge separated state energy is high.

  • 19.
    Bowring, Miriam A.
    et al.
    Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA;Univ Washington, Dept Chem, Seattle, WA 98195 USA;Reed Coll, Dept Chem, Portland, OR 97202 USA.
    Bradshaw, Liam R.
    Univ Washington, Dept Chem, Seattle, WA 98195 USA.
    Parada, Giovanny A.
    Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA.
    Pollock, Timothy P.
    Univ Washington, Dept Chem, Seattle, WA 98195 USA.
    Fernandez-Teran, Ricardo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Kolmar, Scott S.
    Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA.
    Mercado, Brandon Q.
    Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA.
    Schlenker, Cody W.
    Univ Washington, Dept Chem, Seattle, WA 98195 USA.
    Gamelin, Daniel R.
    Univ Washington, Dept Chem, Seattle, WA 98195 USA.
    Mayer, James M.
    Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA;Univ Washington, Dept Chem, Seattle, WA 98195 USA.
    Activationless Multiple-Site Concerted Proton-Electron Tunneling2018In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, no 24, p. 7449-7452Article in journal (Refereed)
    Abstract [en]

    The transfer of protons and electrons is key to energy conversion and storage, from photosynthesis to fuel cells. Increased understanding and control of these processes are needed. A new anthracene-phenol-pyridine molecular triad was designed to undergo fast photo-induced multiple-site concerted proton-electron transfer (MS-CPET), with the phenol moiety transferring an electron to the photoexcited anthracene and a proton to the pyridine. Fluorescence quenching and transient absorption experiments in solutions and glasses show rapid MS-CPET (3.2 X 10(10) s(-1) at 298 K). From 5.5 to 90 K, the reaction rate and kinetic isotope effect (KIE) are independent of temperature, with zero Arrhenius activation energy. From 145 to 350 K, there are only slight changes with temperature. This MS-CPET reaction thus occurs by tunneling of both the proton and electron, in different directions. Since the reaction proceeds without significant thermal activation energy, the rate constant indicates the magnitude of the electron/proton double tunneling probability.

  • 20. Brath, Ulrika
    et al.
    Swamy, Shashikala I
    Veiga, Alberte X
    Tung, Ching-Chieh
    Van Petegem, Filip
    Erdelyi, Mate
    Paramagnetic Ligand Tagging To Identify Protein Binding Sites.2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 35, p. 11391-11398Article in journal (Refereed)
    Abstract [en]

    Transient biomolecular interactions are the cornerstones of the cellular machinery. The identification of the binding sites for low affinity molecular encounters is essential for the development of high affinity pharmaceuticals from weakly binding leads but is hindered by the lack of robust methodologies for characterization of weakly binding complexes. We introduce a paramagnetic ligand tagging approach that enables localization of low affinity protein-ligand binding clefts by detection and analysis of intermolecular protein NMR pseudocontact shifts, which are invoked by the covalent attachment of a paramagnetic lanthanoid chelating tag to the ligand of interest. The methodology is corroborated by identification of the low millimolar volatile anesthetic interaction site of the calcium sensor protein calmodulin. It presents an efficient route to binding site localization for low affinity complexes and is applicable to rapid screening of protein-ligand systems with varying binding affinity.

  • 21.
    Brena, Barbara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Siegbahn, P. E. M.
    Ågren, H.
    Modeling near-edge fine structure x-ray spectra of the manganese catalytic site for water oxidation in photosystem II2012In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, no 41, p. 17157-17167Article in journal (Refereed)
    Abstract [en]

    The Mn 1s near-edge absorption fine structure (NEXAFS) has been computed by means of transition-state gradient-corrected density functional theory (DFT) on four Mn 4Ca clusters modeling the successive S 0 to S 3 steps of the oxygen-evolving complex (OEC) in photosystem II (PSII). The model clusters were obtained from a previous theoretical study where they were determined by energy minimization. They are composed of Mn(III) and Mn(IV) atoms, progressing from Mn(III) 3Mn(IV) for S 0 to Mn(III) 2Mn(IV) 2 for S 1 to Mn(III)Mn(IV) 3 for S 2 to Mn(IV) 4 for S 3, implying an Mn-centered oxidation during each step of the photosynthetic oxygen evolution. The DFT simulations of the Mn 1s absorption edge reproduce the experimentally measured curves quite well. By the half-height method, the theoretical IPEs are shifted by 0.93 eV for the S 0 → S 1 transition, by 1.43 eV for the S 1 → S 2 transition, and by 0.63 eV for the S 2 → S 3 transition. The inflection point energy (IPE) shifts depend strongly on the method used to determine them, and the most interesting result is that the present clusters reproduce the shift in the S 2 → S 3 transition obtained by both the half-height and second-derivative methods, thus giving strong support to the previously suggested structures and assignments.

  • 22.
    Brown, Allison
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Antila, Liisa
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Mirmohades, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Pullen, Sonja
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Ott, Sascha
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Ultrafast Electron Transfer between Dye and Catalyst on a Mesoporous NiO Surface2016In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 26, p. 8060-8063Article in journal (Other academic)
    Abstract [en]

    The combination of molecular dyes and catalysts with semiconductors into dye-sensitized solar fuel devices (DSSFDs) requires control of efficient interfacial and surface charge transfer between the components. The present study reports on the light-induced electron transfer processes of p-type NiO films cosensitized with coumarin C343 and a bioinspired proton reduction catalyst, [FeFe](mcbdt)(CO)(6) (mcbdt = 3-carboxybenzene-1,2-dithiolate). By transient optical spectroscopy we find that ultrafast interfacial electron transfer (tau approximate to 200 fs) from NiO to the excited C343 ("hole injection") is followed by rapid (t(1/2) approximate to 10 ps) and efficient surface electron transfer from C343 to the coadsorbed [FeFe] (mcbdt)(CO)(6). The reduced catalyst has a clear spectroscopic signature that persists for several tens of microseconds, before charge recombination with NiO holes occurs. The demonstration of rapid surface electron transfer from dye to catalyst on NiO, and the relatively long lifetime of the resulting charge separated state, suggests the possibility to use these systems for photocathodes on. DSSFDs.

  • 23.
    Bunrit, Anon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Dahlstrand, Christian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Olsson, Sandra K.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Srifa, Pemikar
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Huang, Genping
    Orthaber, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Sjöberg, Per J. R.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Biswas, Srijit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Himo, Fahmi
    Samec, Joseph S. M.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Bronsted Acid-Catalyzed Intramolecular Nucleophilic Substitution of the Hydroxyl Group in Stereogenic Alcohols with Chirality Transfer2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 14, p. 4646-4649Article in journal (Refereed)
    Abstract [en]

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

  • 24.
    Calixto, Ana R.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Moreira, Catia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Pabis, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kötting, Carsten
    Ruhr Univ Bochum, Dept Biophys, D-44801 Bochum, Germany.
    Gerwert, Klaus
    Ruhr Univ Bochum, Dept Biophys, D-44801 Bochum, Germany.
    Rudack, Till
    Ruhr Univ Bochum, Dept Biophys, D-44801 Bochum, Germany.
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases2019In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 27, p. 10684-10701Article in journal (Refereed)
    Abstract [en]

    GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the G(alpha i), subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.

  • 25.
    Cappel, Ute B.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Feldt, Sandra M.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Schoeneboom, Jan
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Boschloo, Gerrit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    The influence of local electric fields on photoinduced absorption in dye-sensitized solar cells.2010In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 132, no 26, p. 9096-9101Article in journal (Refereed)
    Abstract [en]

    The dye-sensitized solar cell (DSC) challenges conventional photovoltaics with its potential for low-cost production and its flexibility in terms of color and design Transient absorption spectroscopy is widely used to unravel the working mechanism of DSCs A surprising, unexplained feature observed in these studies is an apparent bleach of the ground-state absorption of the dye, under conditions where the dye is in the ground state. Here, we demonstrate that this feature can be attributed to a change of the local electric field affecting the absorption spectrum of the dye, an effect related to the Stark effect first reported in 1913 We present a method for measuring the effect of an externally applied electric field on the absorption of dye monolayers adsorbed on flat TiO2 substrates. The measured signal has the shape of the first derivative of the absorption spectra of the dyes and reverses sign along with the reversion of the direction of the change in dipole moment upon excitation relative to the TiO2 surface A very similar signal is observed in photoinduced absorption spectra of dye-sensitized TiO2 electrodes under solar cell conditions, demonstrating that the electric field across the dye molecules changes upon illumination This result has important implications for the analysis of transient absorption spectra of DSCs and other molecular optoelectronic devices and challenges the interpretation of many previously published results.

  • 26.
    Carlsson, Anna-Carin C
    et al.
    Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
    Grafenstein, Jurgen
    Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
    Budnjo, Adnan
    Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
    Laurila, Jesse L
    Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Karim, Alavi
    Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
    Kleinmaier, Roland
    Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
    Brath, Ulrika
    Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
    Erdelyi, Mate
    Department of Chemistry and Molecular Biology, University of Gothenburg and The Swedish NMR Centre, Gothenburg, Sweden.
    Symmetric halogen bonding is preferred in solution2012In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, no 12, p. 5706-5715Article in journal (Refereed)
    Abstract [en]

    Halogen bonding is a recently rediscovered secondary interaction that shows potential to become a complementary molecular tool to hydrogen bonding in rational drug design and in material sciences. Whereas hydrogen bond symmetry has been the subject of systematic studies for decades, the understanding of the analogous three-center halogen bonds is yet in its infancy. The isotopic perturbation of equilibrium (IPE) technique with 13C NMR detection was applied to regioselectively-deuterated pyridine complexes to investigate the symmetry of [N–I–N]+ and [N–Br–N]+ halogen bonding in solution. Preference for a symmetric arrangement was observed for both a freely adjustable and for a conformationally restricted [N–X–N]+ model system, as also confirmed by computation on the DFT level. A closely attached counter ion is shown to be compatible with the preferred symmetric arrangement. The experimental observations and computational predictions reveal a high energetic gain upon formation of symmetric, three-center four-electron halogen bonding. Whereas hydrogen bonds are generally asymmetric in solution and symmetric in the crystalline state, the analogous bromine and iodine centered halogen bonds prefer symmetric arrangement in solution.

  • 27.
    Carlsson, Anna-Carin C.
    et al.
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden.;Colorado State Univ, Dept Biochem & Mol Biol, Ft Collins, CO 80523 USA..
    Mehmeti, Krenare
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Uhrbom, Martin
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden.;AstraZeneca, CVMD iMED, Pepparedsleden 1, S-43183 Molndal, Sweden..
    Karim, Alavi
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Bedin, Michele
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Puttreddy, Rakesh
    Univ Jyvaskyla, Dept Chem, Nanosci Ctr, POB 35, FI-40014 Jyvaskyla, Finland..
    Kleinmaier, Roland
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden.;Chemtura Organometall GmbH, D-59192 Bergkamen, Germany..
    Neverov, Alexei A.
    Queens Univ, Dept Chem, Kingston, ON K7L 3N6, Canada.;Afton Chem, Richmond, VA 23219 USA..
    Nekoueishahraki, Bijan
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Grafenstein, Jurgen
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Rissanen, Kari
    Univ Jyvaskyla, Dept Chem, Nanosci Ctr, POB 35, FI-40014 Jyvaskyla, Finland..
    Erdelyi, Mate
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden.;Swedish NMR Ctr, Medicinaregatan 5, SE-41390 Gothenburg, Sweden..
    Substituent Effects on the [N-I-N](+) Halogen Bond2016In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 138, no 31, p. 9853-9863Article in journal (Refereed)
    Abstract [en]

    We have investigated the influence of electron density on the three-center [N-I-N](+) halogen bond. A series of [bis(pyri din e) io dine](+) and [1,2-bis ( (pyridin e-2-71 ethynyl)b e nze n e)io dine](+) BF4- complexes substituted with electron withdrawing and donating functionalities in the para-position of their pyridine nitrogen were synthesized and studied by spectroscopic and computational methods. The systematic change of electron density of the pyridine nitrogens upon alteration of the para-substituent (NO2, CF3, H, F, Me, OMe, NMe2) was confirmed by N-15 NMR and by computation of the natural atomic population and the pi electron population of the nitrogen atoms. Formation of the [N-I-N](+) halogen bond resulted in >100 ppm N-15 NMR coordination shifts. Substituent effects on the N-15 NMR chemical shift are governed by the pi population rather than the total electron population at the nitrogens. Isotopic perturbation of equilibrium NMR studies along with computation on the DFT level indicate that all studied systems possess static, symmetric [N-I-N](+) halogen bonds, independent of their electron density. This was further confirmed by single crystal X-ray diffraction data of 4-substituted [bis(pyridine)iodine](+) complexes. An increased electron density of the halogen bond acceptor stabilizes the [N center dot center dot center dot I center dot center dot center dot N](+) bond, whereas electron deficiency reduces the stability of the complexes, as demonstrated by UV-kinetics and computation. In contrast, the N-I bond length is virtually unaffected by changes of the electron density. The understanding of electronic effects on the [N-X-N](+) halogen bond is expected to provide a useful handle for the modulation of the reactivity of [bis(pyridine)halogen](+)-type synthetic reagents.

  • 28. Chavillon, Benoit
    et al.
    Cario, Laurent
    Renaud, Adele
    Tessier, Franck
    Chevire, Francois
    Boujtita, Mohammed
    Pellegrin, Yann
    Blart, Errol
    Smeigh, Amanda
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Hammarstrom, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Odobel, Fabrice
    Jobic, Stephane
    P-Type Nitrogen-Doped ZnO Nanoparticles Stable under Ambient Conditions2012In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, no 1, p. 464-470Article in journal (Refereed)
    Abstract [en]

    Zinc oxide is considered as a very promising material for optoelectronics. However, to date, the difficulty in producing stable p-type ZnO is a bottleneck, which hinders the advent of ZnO-based devices. In that context, nitrogen-doped zinc oxide receives much attention. However, numerous reviews report the controversial character of p-type conductivity in N-doped ZnO, and recent theoretical contributions explain that N-doping alone cannot lead, to p-typeness in Zn-rich ZnO. We report here that the ammonolysis at low temperature or ZnO2 yields pure wurtzite-type N-doped ZnO nanoparticles with an extraordinarily large amount of Zn vacancies (up to 20%). Electrochemical and transient spectroscopy studies demonstrate that these Zn-poor nanoparticles exhibit a p-type conductivity that is stable over more than 2 years under ambient conditions.

  • 29.
    Cheruku, Pradeep
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    Diesen, Jarle
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    Andersson, Pher
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    Asymmetric Hydrogenation of Di and Trisubstituted Enol Phosphinates with N,P-Ligated Iridium Complexes2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 16, p. 5595-5599Article in journal (Refereed)
    Abstract [en]

    The iridium-catalyzed asymmetric hydrogenation of various di- and trisubstituted enol phosphinates has been studied. Excellent enantioselectivities (up to >99% ee) and full conversion were observed for a range of substrates with both aromatic and aliphatic side chains. Enol phosphinates are structural analogues of enol acetates, and the hydrogenated alkyl phosphinate products can easily be transformed into the corresponding alcohols with conservation of stereochemistry. We have also hydrogenated, in excellent ee, several purely alkyl-substituted enol phosphinates, producing chiral alcohols that are difficult to obtain highly enantioselectively from ketone hydrogenations.

  • 30.
    Cheruku, Pradeep
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Paptchikhine, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Church, Tamara L
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Andersson, Pher G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Iridium-N,P-ligand-catalyzed enantioselective hydrogenation of diphenylvinylphosphine oxides and vinylphosphonates2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 23, p. 8285-8289Article in journal (Refereed)
    Abstract [en]

    Diphenylvinylphosphine oxides and di- and trisubstituted vinylphosphonates have been employed as substrates in iridium-catalyzed asymmetric hydrogenations. Complete conversions and excellent enantioselectivities (up to and above 99% ee) were observed for a range of substrates with both aromatic and aliphatic groups at the prochiral carbon. We have also hydrogenated electron-deficient carboxyethylvinylphosphonates with excellent stereoselectivity (up to and above 99% ee). The hydrogenated products of both classes of substrates are synthetically useful intermediates.

  • 31. Chung, L. W.
    et al.
    Hayashi, S.
    Lundberg, Marcus
    Kyoto University.
    Nakatsu, T.
    Kato, H.
    Morokuma, K.
    Mechanism of efficient firefly bioluminescence via adiabatic transition state and seam of sloped conical intersection.2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 39, p. 12880-12881Article in journal (Refereed)
    Abstract [en]

    Firefly emission is a well-known efficient bioluminescence. However, the mystery of the efficient thermal generation of electronic excited states in firefly still remains unsolved, particularly at the atomic and molecular levels. We performed SA-CASSCF(12,12)/6-31G* and CASPT2(12,12)/6-31G*//SA-CASSCF(12,12)/6-31G* calculations to elucidate the reaction mechanism of bioluminescence from the firefly dioxetanone in the gas phase. Adiabatic transition state (TS) for the O-O bond cleavage and the minimum energy conical intersection (MECI) were located and characterized. The unique topology of MECI featuring a seam of a sloped conical intersection for the firefly dioxetanone, which was uncovered for the first time, emerges along the reaction pathway to provide a widely extended channel to diabatically access the excited-state from the ground state.

  • 32.
    Church, Tamara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Byrne, Christopher M.
    Lobkovsky, Emil B.
    Coates, Geoffrey W.
    A New Multicomponent Reaction Catalyzed by a [Lewis Acid]+[Co(CO)4]- Catalyst:  Stereospecific Synthesis of 1,3-Oxazinane-2,4-diones from Epoxides, Isocyanates, and CO2007In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 129, no 26, p. 8156-8162Article in journal (Refereed)
    Abstract [en]

    The use of mechanistic information to develop a new, catalytic multicomponent reaction is described. The complex [(salph)Al(THF)2+[co(CO)4]-(1, salph = N,N-o-phenylenebis(3,5-di-tert-butylsalicylideneimine), THF = tetrahydrofuran), wich is known to carbonylate epoxides, aziridines, and B-lactones, was used to catalyze the synthesis of 1,3-oxazinane-2,4-diones from epoxides, isocyanates, and CO. Under optimized conditions, the reaction was both selective and high-yielding. 1,3-Oxazinane-2,4-diones were synthesized from a variety of epoxides and isocyanates, including some epoxides that do not undergo simple ring-expansion carbonylation. The best results were obtained using highly electrophilic isocyanates. The mechanism of the multicomponent reaction was investigated using labeling and stereochemsitry, and the data obtained were consistent with the 1-catalyzed formation of B-lactone and 1,3-oxazinane-2,4-dione from a common intermediate.

  • 33. Diéguez, Montserrat
    et al.
    Mazuela, Javier
    Pàmies, Oscar
    Verendel, J Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Andersson, Pher G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    Chiral pyranoside phosphite-oxazolines: a new class of ligand for asymmetric catalytic hydrogenation of alkenes2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 23, p. 7208-7209Article in journal (Refereed)
    Abstract [en]

    We have described the first successful application of a phosphite-oxazoline ligand library in the asymmetric Ir-catalyzed hydrogenation of several unfunctionalized olefins. The introduction of a bulky biaryl phosphite moiety in the ligand design is highly adventitious in the product outcome. By carefully selecting the ligand components, we obtained high activities (TOFs up to >1500 mol x (mol x h)(-1) at 1 bar of H2) and enantioselectivities (ee values up to >99%) and, at the same time, show a broad scope for different substrate types. So, this is an exceptional ligand class that competes favorably with a few other ligand series that also provide high ee values for tri- and disubstituted substrate types.

  • 34.
    Dongare, Prateek
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Maji, Somnath
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Direct Evidence of a Tryptophan Analogue Radical Formed in a Concerted Electron-Proton Transfer Reaction in Water2016In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 138, no 7, p. 2194-2199Article in journal (Refereed)
    Abstract [en]

    Proton-coupled electron transfer (PCET) is a fundamental reaction step of many chemical and biological processes. Well-defined biomimetic systems are promising tools for investigating the PCET mechanisms relevant to natural proteins. Of particular interest is the possibility to distinguish between stepwise and concerted transfer of the electron and proton, and how PCET is controlled by a proton acceptor such as water. Thus, many tyrosine and phenolic derivatives have been shown to undergo either stepwise or concerted PCET, where the latter process is defined by simultaneous tunneling of the electron and proton from the same transition state. For tryptophan instead, it is theoretically predicted that a concerted pathway can never compete with the stepwise electron-first mechanism (ETPT) when neat water is the primary proton acceptor. The argument is based on the radical pK(a)(similar to 4.5) that is much higher than that for water (pK(a)(H3O+) = 0), which thermodynamically disfavors a concerted proton transfer to H2O. This is in contrast to the very acidic radical cation of tyrosine (pK(a) similar to -2). However, in this study we show, by direct time-resolved absorption spectroscopy on two [Ru(bpy)(3)](2+) tryptophan (bpy = 2,2'-bipyridine) analogue complexes, that also tryptophan oxidation with water as a proton acceptor can occur via a concerted pathway, provided that the oxidant has weak enough driving force. This rivals the theoretical predictions and suggests that our current understanding of PCET reactions in water is incomplete.

  • 35.
    Duarte, Fernanda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Oxford, Chem Res Lab, 12 Mansfield Rd, Oxford OX1 3TA, England.;Univ Oxford, Phys & Theoret Chem Lab, S Parks Rd, Oxford OX1 3QZ, England..
    Barrozo, Alexandre
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Williams, Nicholas H.
    Univ Sheffield, Dept Chem, Sheffield S3 7HF, S Yorkshire, England..
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis2016In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 138, no 33, p. 10664-10673Article in journal (Refereed)
    Abstract [en]

    Despite the numerous experimental and theoretical studies on phosphate monoester hydrolysis, significant questions remain concerning the mechanistic details of these biologically critical reactions. In the present work we construct a linear free energy relationship for phosphate monoester hydrolysis to explore the effect of modulating leaving group plc on the competition between solvent- and substrate-assisted pathways for the hydrolysis of these compounds. Through detailed comparative electronic-structure studies of methyl phosphate and a series of substituted aryl phosphate monoesters, we demonstrate that the preferred mechanism is dependent on the nature of the leaving group. For good leaving groups, a strong preference is observed for a more dissociative solvent-assisted pathway. However, the energy difference between the two pathways gradually reduces as the leaving group pK(a) increases and creates mechanistic ambiguity for reactions involving relatively poor alkoxy leaving groups. Our calculations show that the transition-state structures vary smoothly across the range of pK(a)s studied and that the pathways remain discrete mechanistic alternatives. Therefore, while not impossible, a biological catalyst would have to surmount a significantly higher activation barrier to facilitate a substrate-assisted pathway than for the solvent-assisted pathway when phosphate is bonded to good leaving groups. For poor leaving groups, this intrinsic preference disappears.

  • 36.
    Duarte, Fernanda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Williams, Nicholas H
    Kamerlin, Shina C Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis.2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 3, p. 1081-93Article in journal (Refereed)
    Abstract [en]

    Understanding phosphoryl and sulfuryl transfer is central to many biochemical processes. However, despite decades of experimental and computational studies, a consensus concerning the precise mechanistic details of these reactions has yet to be reached. In this work we perform a detailed comparative theoretical study of the hydrolysis of p-nitrophenyl phosphate, methyl phosphate and p-nitrophenyl sulfate, all of which have served as key model systems for understanding phosphoryl and sulfuryl transfer reactions, respectively. We demonstrate the existence of energetically similar but mechanistically distinct possibilities for phosphate monoester hydrolysis. The calculated kinetic isotope effects for p-nitrophenyl phosphate provide a means to discriminate between substrate- and solvent-assisted pathways of phosphate monoester hydrolysis, and show that the solvent-assisted pathway dominates in solution. This preferred mechanism for p-nitrophenyl phosphate hydrolysis is difficult to find computationally due to the limitations of compressing multiple bonding changes onto a 2-dimensional energy surface. This problem is compounded by the need to include implicit solvation to at least microsolvate the system and stabilize the highly charged species. In contrast, methyl phosphate hydrolysis shows a preference for a substrate-assisted mechanism. For p-nitrophenyl sulfate hydrolysis there is only one viable reaction pathway, which is similar to the solvent-assisted pathway for phosphate hydrolysis, and the substrate-assisted pathway is not accessible. Overall, our results provide a unifying mechanistic framework that is consistent with the experimentally measured kinetic isotope effects and reconciles the discrepancies between theoretical and experimental models for these biochemically ubiquitous classes of reaction.

  • 37.
    Eildal, Jonas N. N.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hultqvist, Greta
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Balle, Thomas
    Stuhr-Hansen, Nicolai
    Padrah, Shahrokh
    Gianni, Stefano
    Stromgaard, Kristian
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Probing the Role of Backbone Hydrogen Bonds in Protein-Peptide Interactions by Amide-to-Ester Mutations2013In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, no 35, p. 12998-13007Article in journal (Refereed)
    Abstract [en]

    One of the most frequent protein-protein interaction modules in mammalian cells is the postsynaptic density 95/discs large/zonula occludens 1 (PDZ) domain, involved in scaffolding and signaling and emerging as an important drug target for several diseases. Like many other protein-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as beta-strands to form an extended antiparallel beta-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the, amino acid side chains of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, Delta Delta G = 1.3 to >3.8 kcal mol(-1)). This decrease in affinity was mainly due to an increase in the dissociation rate constant, but a significant decrease in the association rate constant was found for some amide-to-ester mutations Suggesting that native hydrogen bonds have begun to form in the transition state of the binding reaction. This study provides a general framework for studying the role of backbone hydrogen bonds in protein-peptide interactions and for the first time specifically addresses these for PDZ domain-peptide interactions.

  • 38.
    Emanuelsson, Rikard
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Sterby, Mia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Strømme, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Sjödin, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    An All-Organic Proton Battery2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 13, p. 4828-4834Article in journal (Refereed)
    Abstract [en]

    Rechargeable batteries that use organic matter as. the capacity-carrying material have previously been considered a technology for the future. Earlier batteries in which both the anode and cathode consisted of organic material required significant amounts of conductive additives and were often based on metal-ion electrolytes containing Li+ or Na+. However, we have used conducting poly(3,4-ethylenedioxythiophene) (PEDOT), functionalized with anthraquinone (PEDQT-AQ) or, benzonquinone (PEDOT-BQ) pendant groups as the negative and positive electrode materials, respectively, to make an all-organic proton battery devoid of metals. The electrolyte consists of a proton donor and acceptor slurry containing substituted pyridinium triflates and the corresponding pyridine base. This slurry allows the 2e(-)/2H(+) quinone/hydroquinone redox reactions while suppressing proton reduction in the battery cell. By using strong (acidic) proton donors, the formal potential of the quinone redox reactions is tuned into the potential region in which the PEDOT backbone is conductive, thus eliminating the need for conducting additives. In this all-organic proton battery cell, PEDOT-AQ and PEDOT-BQ deliver 103 and 120 mAh g(-1), which correspond to 78% and 75%, respectively, of the theoretical specific capacity of the materials at an average cell potential of 0.5 V. We show that PEDOT-BQ determines the cycling stability of the device while PEDOT-AQ provides excellent reversibility for at least 1000 cycles. This proof-of-concept shows the feasibility of assembling all organic proton batteries which require no conductive additives and also reveals where the challenges and opportunities lie on the path to producing plastic batteries.

  • 39.
    Engman, Mattias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Diesen, Jarle S.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Paptchikhine, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Andersson, Pher G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Iridium-Catalyzed Asymmetric Hydrogenation of Fluorinated Olefins Using N,P-Ligands: A struggle with hydrogenolysis and selectivity2007In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 129, no 15, p. 4536-4537Article in journal (Refereed)
    Abstract [en]

    To broaden the substrate scope of asymmetric iridium-catalyzed hydrogenation, fluorine-functionalized olefins were synthesized and hydrogenated with iridium complexes. Preliminary results showed high levels of fluorine elimination together with low selectivity. The loss of vinylic fluorine at first seemed difficult to handle, but further studies revealed that a catalyst with an azanorbornyl scaffold in the ligand gave more promising results. With this in mind, a new ligand was developed. This gave among the best results published to date for fluorine asymmetric hydrogenation, yielding high conversion and very high ee's with very little fluorine elimination. Further increasing the selectivity, the trials also revealed that tetrasubstituted fluorine-containing olefins can be hydrogenated with high ee's, despite that this class of compounds has usually shown low reactivity in this reaction type.

  • 40.
    Esfandiarfard, Keyhan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Mai, Juri
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Ott, Sascha
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Unsymmetrical E-Alkenes from the Stereoselective Reductive Coupling of Two Aldehydes2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 8, p. 2940-2943Article in journal (Refereed)
    Abstract [en]

    The unprecedented formation of unsymmetrical alkenes from the intermolecular reductive coupling of two different aldehydes is described. In contrast to the McMurry reaction which affords statistical product mixtures, selectivity in the reported procedure is achieved by a sequential ionic mechanism in which a first aldehyde is reacted with a phosphanylphosphonate to afford a phosphaalkene intermediate which, upon activation by hydroxide, reacts with a second aldehyde to the unsymmetrical E-alkenes. The described reaction is free of transition metals and proceeds under ambient temperature within minutes in good to excellent overall yields. It is a new methodology to use feedstock aldehydes for the direct production of C=C double bond-containing products and may impact how chemists think of multistep synthetic sequences in the future.

  • 41.
    Favereau, Ludovic
    et al.
    Univ Nantes, CNRS, UMR CNRS 6230, CEISAM Chim & Interdisciplinarite Synth Anal Mode, 2 Rue Houssiniere,BP 92208, F-44322 Nantes 3, France..
    Makhal, Abhinandan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Pellegrin, Yann
    Univ Nantes, CNRS, UMR CNRS 6230, CEISAM Chim & Interdisciplinarite Synth Anal Mode, 2 Rue Houssiniere,BP 92208, F-44322 Nantes 3, France..
    Blart, Errol
    Univ Nantes, CNRS, UMR CNRS 6230, CEISAM Chim & Interdisciplinarite Synth Anal Mode, 2 Rue Houssiniere,BP 92208, F-44322 Nantes 3, France..
    Petersson, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Göransson, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Hammarstrom, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Odobel, Fabrice
    Univ Nantes, CNRS, UMR CNRS 6230, CEISAM Chim & Interdisciplinarite Synth Anal Mode, 2 Rue Houssiniere,BP 92208, F-44322 Nantes 3, France..
    A Molecular Tetrad That Generates a High-Energy Charge-Separated State by Mimicking the Photosynthetic Z-Scheme2016In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 138, no 11, p. 3752-3760Article in journal (Refereed)
    Abstract [en]

    The oxygenic photosynthesis of green plants, green algae, and cyanobacteria is the major provider of energy rich compounds in the biosphere. The so-called "Z-scheme" is at the heart of this "engine of life". Two photosystems (photo system I and II) work in series to build up a higher redox ability than each photosystem alone can provide, which is necessary to drive water oxidation into oxygen and NADP(+) reduction into NADPH with visible light. Here we show a mimic of the Z-scheme with a molecular tetrad. The "tetrad Bodipy-NDI-TAPD-Ru is composed of two different dyes-4,4-difluoro-1,3,5,7-tetramethyl-2,6-diethy1-4-bora-3a,4a-diaza-s-indacene (Bodipy) and a Ru-II(bipyridine), (Ru) derivative-which are connected to a naphthalene diimide (NDI) electron acceptor and tetraalkylphenyldiamine (TAPD) playing the role of electron donor. A strong laser pulse excitation of visible light where the two dye molecules (Ru and Bodipy) absorb with equal probability leads to the cooperative formation of a highly energetic charge-separated state composed of an oxidized Bodipy and a reduced Ru. The latter state cannot be reached by one single photon absorption. The energy of the final charge-separated state (oxidized Bodipy/reduced Ru) in the tetrad lies higher than that in the reference dyads (Bodipy-NDI and TAPD-Ru), leading to the energy efficiency of the tetrad being 47% of the sum of the photon threshold energies. Its lifetime was increased by several orders of magnitude compared to that in the reference dyads Bodipy-NDI and TAPD-Ru, as it passes from about 3 ns in each dyad to 850 ns in the tetrad. The overall quantum yield formation of this extended charge-separated state is estimated to be 24%. Our proof-of-concept result demonstrates the capability to translate a crucial photosynthetic energy conversion principle into man-made molecular systems for solar fuel formation, to obtain products of higher energy content than those produced by a single photon absorption.

  • 42.
    Feldt, Sandra M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Gibson, Elizabeth A.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Gabrielsson, Erik
    KTH, Organisk kemi.
    Sun, Licheng
    KTH, Organisk kemi.
    Boschloo, Gerrit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Hagfeldt, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Design of organic dyes and cobalt polypyridine redox mediators for high-efficiency dye-sensitized solar cells2010In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 132, no 46, p. 16714-16724Article in journal (Refereed)
    Abstract [en]

    Dye-sensitized solar cells (DSCs) with cobalt-based mediators with efficiencies surpassing the record for DSCs with iodide-free electrolytes were developed by selecting a suitable combination of a cobalt polypyridine complex and an organic sensitizer. The effect of the steric properties of two triphenylamine-based organic sensitizers and a series of cobalt polypyridine redox mediators on the overall device performance in DSCs as well as on transport and recombination processes in these devices was compared. The recombination and mass-transport limitations that, previously, have been found to limit the performance of these mediators were avoided by matching the properties of the dye and the cobalt redox mediator. Organic dyes with higher extinction coefficients than the standard ruthenium sensitizers were employed in DSCs in combination with outer-sphere redox mediators, enabling thinner TiO2 films to be used. Recombination was reduced further by introducing insulating butoxyl chains on the dye rather than on the cobalt redox mediator, enabling redox couples with higher diffusion coefficients and more suitable redox potential to be used, simultaneously improving the photocurrent and photovoltage of the device. Optimization of DSCs sensitized with a triphenylamine-based organic dye in combination with tris(2,2'-bipyridyl)cobalt(II/III) yielded solar cells with overall conversion efficiencies of 6.7% and open-circuit potentials of more than 0.9 V under 1000 W m(-2) AM1.5 G illumination. Excellent performance was also found under low light intensity indoor conditions.

  • 43.
    Friemann, Rosmarie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Wang, Yaofeng
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in Vacuo2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 46, p. 16606-16607Article in journal (Refereed)
    Abstract [en]

    We report the first molecular dynamics simulations of an integral membrane protein in a detergent micelle under vacuum conditions. To mimic the dehydration process in electrospray ionization, the N-terminal outer membrane protein A transmembrane domain (OmpA171) from Escherichia coli embedded in a dodecylphosphocholine (DPC) detergent micelle has been simulated with water shells of varying thickness. Removal of the water molecules leaves the membrane protein relatively unaffected by the vacuum conditions. The major structural change occurs in the surrounding micelle, where the DPC molecules structurally rearrange from a normal-phase micelle with DPC detergents radiating spherically from OmpA171 to a structure where the DPC molecules form a layered onion structure in which the head groups, which strive to interact with each other, form an intermediate layer between the inner layer of tail groups that are expelled to the surface, protruding into the void.

  • 44. Gardner, James M.
    et al.
    Beyler, Maryline
    Karnahl, Michael
    Tschierlei, Stefanie
    Ott, Sascha
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Light-driven electron transfer between a photosensitizer and a proton-reducing catalyst Co-adsorbed to NiO2012In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, no 47, p. 19322-19325Article in journal (Refereed)
    Abstract [en]

    While intermolecular hole-hopping along the surface of semiconductors is known, there are no previous examples of electron-hopping between molecules on a surface. Herein, we present the first evidence of electron transfer from the photoreduced sensitizer Coumarin-343 (C343) to complex 1, both bound on the surface of NiO. In solution, 1 has been shown to be a mononuclear Fe-based proton-reducing catalyst. The reduction of 1 is reversible and occurs within 50 ns after excitation of C343. Interfacial recombination between the reduced 1 (-) and NiO hole occurs on a 100 μs time scale by non-exponential kinetics. The observed process is the first essential step in the photosensitized generation of H 2 from a molecular catalyst in the absence of a sacrificial donor reagent.

  • 45.
    Glover, Starla D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Jorge, Christine
    Liang, Li
    Valentine, Kathleen G.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Tommos, Cecilia
    Photochemical Tyrosine Oxidation in the Structurally Well-Defined alpha Y-3 Protein: Proton-Coupled Electron Transfer and a Long-Lived Tyrosine Radical2014In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 136, no 40, p. 14039-14051Article in journal (Refereed)
    Abstract [en]

    Tyrosine oxidation-reduction involves proton-coupled electron transfer (PCET) and a reactive radical state. These properties are effectively controlled in enzymes that use tyrosine as a high-potential, one-electron redox cofactor. The alpha Y-3 model protein contains Y32, which can be reversibly oxidized and reduced in voltammetry measurements. Structural and kinetic properties of alpha Y-3 are presented. A solution NMR structural analysis reveals that Y32 is the most deeply buried residue in alpha Y-3. Time-resolved spectroscopy using a soluble flash-quench generated [Ru(2,2'-bipyridine)(3)](3+) oxidant provides high-quality Y32-O center dot absorption spectra. The rate constant of Y32 oxidation (k(pCET)) is pH dependent: 1.4 x 10(4) M-1 s(-1) (pH 5.5), 1.8 x 10(5) M-1 s(-1) (pH 8.5), 5.4 x 10(3) M-1 s(-1) (pD 5.5), and 4.0 x 10(4) M-1 s(-1) (pD 8.5). k(H)/k(D) of Y32 oxidation is 2.5 +/- 0.5 and 4.5 +/- 0.9 at pH(D) 5.5 and 8.5, respectively. These pH and isotope characteristics suggest a concerted or stepwise, proton-first Y32 oxidation mechanism. The photochemical yield of Y32-O center dot is 28-58% versus the concentration of [Ru(2,2'-bipyridine)(3)](3+). Y32-O center dot decays slowly, t(1/2) in the range of 2-10 s, at both pH 5.5 and 8.5, via radical-radical dimerization as shown by second-order kinetics and fluorescence data. The high stability of Y32-O center dot is discussed relative to the structural properties of the Y32 site. Finally, the static alpha Y-3 NMR structure cannot explain (i) how the phenolic proton released upon oxidation is removed or (ii) how two Y32-O center dot come together to form dityrosine. These observations suggest that the dynamic properties of the protein ensemble may play an essential role in controlling the PCET and radical decay characteristics of alpha Y-3.

  • 46.
    Glover, Starla D.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Parada, Giovanny A.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Yale Univ, Dept Chem, POB 208107,225 Prospect St, New Haven, CT 06520 USA..
    Markle, Todd F.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Yale Univ, Dept Chem, POB 208107,225 Prospect St, New Haven, CT 06520 USA..
    Ott, Sascha
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Isolating the Effects of the Proton Tunneling Distance on Proton-Coupled Electron Transfer in a Series of Homologous Tyrosine-Base Model Compounds2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 5, p. 2090-2101Article in journal (Refereed)
    Abstract [en]

    The distance dependence of concerted proton-coupled electron transfer (PCET) reactions was probed in a series of three new compounds, where a phenol is covalently bridged by a 5, 6, or 7 membered carbocycle to the quinoline. The carbocycle bridge enforces the change in distance between the phenol oxygen (proton donor) and quinoline nitrogen (proton acceptor), d(O center dot center dot center dot N), giving rise to values ranging from 2.567 to 2.8487 angstrom, and resulting in calculated proton tunneling distances, r(0), that span 0.719 to 1.244 angstrom. Not only does this series significantly extend the range of distances that has been previously accessible for experimental distance dependent PCET studies of synthetic model compounds, but it also greatly improves the isolation of d(O center dot center dot center dot N) as a variable compared to earlier reports. Rates of PCET were determined by time-resolved optical spectroscopy with flash-quench generated [Ru(bpy)(3)](3+) and [Ru(dce)(3)](3+), where bpy = 2,2'-bipyridyl and dce = 4,4'-dicarboxyethylester-2,2'-bipyridyl. The rates increased as d(O center dot center dot center dot N) decreased, as can be expected from a static proton tunneling model. An exponential attenuation of the PCET rate constant was found: k(PCET)(d) = k(PCET)(0)exp[-beta(d-d(0))], with beta similar to 10 angstrom(-1). The observed kinetic isotope effect (KIE = k(H)/k(D)) ranged from 1.2 to 1.4, where the KIE was observed to decrease slightly with increasing d(O center dot center dot center dot N). Both beta and KIE values are significantly smaller than what is predicted by a static proton tunneling model. We conclude that vibrational compression of the tunneling distances, as well as higher vibronic transitions, that contribute to concerted proton coupled electron transfer must also be considered.

  • 47.
    Glover, Starla
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Univ Penn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia.
    Tyburski, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Liang, Li
    Univ Penn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia.
    Tommos, Cecilia
    Univ Penn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Pourbaix Diagram, Proton-Coupled Electron Transfer, and Decay Kinetics of a Protein Tryptophan Radical: Comparing the Redox Properties of W32 and Y32 Generated Inside the Structurally Characterized α3W and α3Y Proteins2018In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, no 1, p. 185-192Article in journal (Refereed)
    Abstract [en]

    Protein-based “hole” hopping typically involves spatially arranged redox-active tryptophan or tyrosine residues. Thermodynamic information is scarce for this type of process. The well-structured α3W model protein was studied by protein film square wave voltammetry and transient absorption spectroscopy to obtain a comprehensive thermodynamic and kinetic description of a buried tryptophan residue. A Pourbaix diagram, correlating thermodynamic potentials (E°′) with pH, is reported for W32 in α3W and compared to equivalent data recently presented for Y32 in α3Y (Ravichandran, K. R.; Zong, A. B.; Taguchi, A. T.; Nocera, D. G.; Stubbe, J.; Tommos, C. J. Am. Chem. Soc. 2017, 139, 2994−3004). The α3W Pourbaix diagram displays a pKOX of 3.4, a E°′(W32(N•+/NH)) of 1293 mV, and a E°′(W32(N/NH); pH 7.0) of 1095 ± 4 mV versus the normal hydrogen electrode. W32(N/NH) is 109 ± 4 mV more oxidizing than Y32(O/OH) at pH 5.4–10. In the voltammetry measurements, W32 oxidation–reduction occurs on a time scale of about 4 ms and is coupled to the release and subsequent uptake of one full proton to and from bulk. Kinetic analysis further shows that W32 oxidation likely involves pre-equilibrium electron transfer followed by proton transfer to a water or small water cluster as the primary acceptor. A well-resolved absorption spectrum of W32 is presented, and analysis of decay kinetics show that W32 persists ∼104 times longer than aqueous W due to significant stabilization by the protein. The redox characteristics of W32 and Y32 are discussed relative to global and local protein properties.

  • 48.
    Gogoll, Adolf
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry.
    Örnebro, Jörgen
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry.
    Grennberg, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry.
    Bäckvall, Jan-Erling
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry.
    Mechanism of Apparent π-Allyl Rotation in (π-Allyl)Palladium Complexes with Bidentate Nitrogen Ligands1994In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 116, no 8, p. 3631-3632Article in journal (Refereed)
  • 49. Goguet, Alexandre
    et al.
    Hardacre, Christopher
    Harvey, Ian
    Narasimharao, Katabathini
    Saih, Youssef
    Sa, Jacinto
    Increased dispersion of supported gold during methanol carbonylation conditions.2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 20, p. 6973-5Article in journal (Refereed)
    Abstract [en]

    The active site in supported gold catalysts for the carbonylation of methanol has been identified as dimers/trimers of gold which are formed from large gold particles >10 nm in diameter. Methyl iodide was found to be critical for this dispersion process and to maintain the catalyst in the active form. This study also shows that it may be possible to redisperse gold catalysts, in general, after reaction.

  • 50. Grigalunas, Michael
    et al.
    Ankner, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Norrby, Per-Ola
    Wiest, Olaf
    Helquist, Paul
    Ni-Catalyzed Alkenylation of Ketone Enolates under Mild Conditions: Catalyst Identification and Optimization2015In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 22, p. 7019-7022Article in journal (Refereed)
    Abstract [en]

    A procedure for Ni-catalyzed cross-coupling of ketone enolates with alkenyl halides has been developed. Intermolecular coupling of aromatic and aliphatic ketone lithium enolates with a variety of alkenyl halides is achieved in the presence of Ni(cod)(2) catalyst (5 mol %), an N-heterocyclic carbene (NHC) ligand, and LiI (10 mol %) at 6-22 degrees C for 0.5-12 h with yields of up to 90%. During the initial development of this reaction, a misleading result with respect to the actual active catalyst was obtained using commercially available Q:Phos ligand, which was found to contain a trace of Pd metal contaminant sufficient to catalyze the reaction. However, under the final conditions optimized for Ni(cod)(2) in the presence of an NHC ligand, Pd was incompetent as a catalyst.

1234 1 - 50 of 164
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