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  • 1.
    Abbrent, Sabina
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Chemistry.
    Lithium ion interactions in polymer gel electrolytes: Effect on structure, dynamics and morphology2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Polymer electrolytes are an essential part of the modern all-solid lithium battery. Several properties, such as mechanical and thermal stability, good ionic conductivity and compatibility with other materials used in the battery are necessary for a successful material.

    This thesis is focused on the ionic interactions in two electrolyte systems, based on a cross-linked polyethylene oxide (nona(ethylene oxide)dimethacrylate) or a fluorinated copolymer (polyvinylidene fluoride-hexafluoropropylene). Changes of thermal properties and morphology of and coordination in the electrolyte on addition of a lithium salt (LiTFSI) and different types and concentrations of solvents are studied. These properties are shown to control the ionic conductivity of the resulting material, influencing the conductivity mechanism.

    The presumably inert polyvinylidene fluoride is shown to undergo large structural changes, where polar conformations of the polymer backbone appear on salt addition, inducing a different crystalline phase. The lithium cation in the polyethylene oxide based electrolyte can coordinate either to the polymer chain or to the solvent. In for example systems containing propylene carbonate, the lithium ion binds more strongly to the polymer than to the solvent. This is in contrast to the systems with dimethyl sulphoxide where the ion prefers the solvent. This variation in coordination also strongly affects the mobility of the cation, reflected both in diffusion constants and in conductivity data.

    A combination of techniques was necessary to use for a deeper understanding of these complex materials. Coordination has been studied by FTIR and high resolution NMR, dynamics by NMR diffusion measurements and impedance spectroscopy, and morphology by diffraction techniques and DSC.

  • 2.
    Abdu, Yassir Ahmed Mohamed
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Earth Sciences, Department of Earth Sciences.
    Mössbauer Spectroscopy of Meteoritic and Synthetic Fe-Ni Alloys2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis reports on the results of investigating Fe-containing minerals in meteorites, with focus on Fe-Ni minerals and their magnetic properties, along with some synthetic Fe-Ni analogues. The New Halfa meteorite, which fell in Sudan 1994, has been studied using Mössbauer spectroscopy, X-ray diffraction, and electron microprobe analysis techniques, and classified as an ordinary L-type chondrite of petrologic type 4. Mössbauer spectra of taenite-enriched samples from the metal particles of the New Halfa (L4) and Al Kidirate (H6) meteorites identify the following γ (fcc) Fe-Ni phases: the ferromagnetic atomically ordered taenite (tetrataenite) with ~ 50 at % Ni, the ferromagnetic disordered taenite with ~ 50 at % Ni, the low-Ni (~ 25 at %) paramagnetic taenite (antitaenite). The presence of the superstructure of tetrataenite is confirmed by synchrotron X-ray diffraction.

    Fe-rich γ (fcc) Fe-Ni alloys with compositions Fe79Ni21, Fe76Ni24, and Fe73Ni27, which serve as synthetic analogues of antitaenite, are prepared by mechanical alloying and subsequent annealing at 650 °C. The Mössbauer results indicate that these alloys are inhomogeneous and contain a high moment (HM) ferromagnetic Ni-rich phase (> 30 at % Ni) and a low moment (LM) paramagnetic Fe-rich phase, which orders antiferromagnetically at low temperature. The coexistence of these phases is attributed to phase segregation occurring on short range, probably nanometer scale, consistent with the Fe-Ni phase diagram below 400 °C where there is a miscibility gap associated with a spinodal decomposition in alloys with < 50 at % Ni.

    The combined high field Mössbauer spectroscopy and SQUID magnetometry results on these alloys at room temperature indicate large induced local magnetic moments in the paramagnetic part of the sample, which increases with increasing the Ni content. The results, when compared with the high field Mössbauer results on antitaenite from the metal particle of Al Kidirate and New Halfa meteorites may be used to estimate the Ni content of antitaenite in meteorites.

    High pressure 57Fe Mössbauer spectroscopy measurements up to ~ 41 GPa have been carried out at room temperature using the diamond anvil cell (DAC) technique in order to investigate the magnetic properties of γ (fcc) 57Fe53Ni47 alloy. The results indicate a pressure induced Invar effect at ~ 7 GPa and a non-magnetic or paramagnetic state above 20 GPa, demonstrating the volume dependence of the magnetic moment of γ (fcc) Fe-Ni alloys.

    List of papers
    1. Mössbauer spectroscopy, X-ray diffraction and electron microprobe analysis of the New Halfa meteorite
    Open this publication in new window or tab >>Mössbauer spectroscopy, X-ray diffraction and electron microprobe analysis of the New Halfa meteorite
    1997 In: Meteoritics and Planetary Science, Vol. 32, p. 373-375Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91276 (URN)
    Available from: 2004-01-15 Created: 2004-01-15Bibliographically approved
    2. Mössbauer studies on the metallic phases of Al Kidirate and New Halfa Meteorites
    Open this publication in new window or tab >>Mössbauer studies on the metallic phases of Al Kidirate and New Halfa Meteorites
    Show others...
    2002 In: Hyperfine Interactions C, Vol. 5, p. 375-378Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91277 (URN)
    Available from: 2004-01-15 Created: 2004-01-15Bibliographically approved
    3. Coexisting antiferromagnetism and ferromagnetism in mechanically alloyed Fe-rich Fe-Ni alloys: Implications regarding the Fe-Ni phase diagram below 400 °C
    Open this publication in new window or tab >>Coexisting antiferromagnetism and ferromagnetism in mechanically alloyed Fe-rich Fe-Ni alloys: Implications regarding the Fe-Ni phase diagram below 400 °C
    2004 (English)In: Journal of Magnetism and Magnetic Materials, ISSN 0304-8853, E-ISSN 1873-4766, Vol. 280, no 2-3, p. 395-403Article in journal (Refereed) Published
    Abstract [en]

    Fe–Ni alloys below the Invar region with compositions Fe100−xNix (x=21, 24, and 27 at%) were prepared by high-energy ball milling technique (mechanical alloying). The as-milled samples, characterized by X-ray diffraction and Mössbauer spectroscopy, contain a mixture of α (BCC) and γ (FCC) phases, whereas the samples annealed at 650°C for 0.5 h show a single γ (FCC) phase displaying a single line Mössbauer spectrum at room temperature (RT). At low temperature, the Mössbauer spectra of annealed Fe76Ni24 and Fe73Ni27 alloys show the existence of a magnetically split pattern together with a broad singlet, which are ascribed to a high-moment ferromagnetic Ni-rich phase and a low-moment Fe-rich phase, respectively. The Fe-rich phase in annealed Fe76Ni24 alloy, which is paramagnetic at RT, undergoes antiferromagnetic ordering at ∼40 K, estimated from the dramatic line broadening of its spectrum, giving rise to a small hyperfine field (e.g. ∼2 T at 6 K). The coexistence of these phases is attributed to phase segregation occurring in these alloys as a result of enhanced atomic diffusion. The stability of these alloys towards martensitic (FCC→BCC) transformation at low temperatures is discussed in connection with the Fe–Ni phase diagram below 400°C.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91278 (URN)10.1016/j.jmmm.2004.03.036 (DOI)
    Available from: 2004-01-15 Created: 2004-01-15 Last updated: 2017-12-14Bibliographically approved
    4. Field induced local magnetic moments in gamma-fcc Fe-Ni anti-Invar alloys
    Open this publication in new window or tab >>Field induced local magnetic moments in gamma-fcc Fe-Ni anti-Invar alloys
    2004 (English)In: Journal of Magnetism and Magnetic Materials, ISSN 0304-8853, E-ISSN 1873-4766, Vol. 280, p. 243-250Article in journal (Refereed) Published
    Abstract [en]

    Mössbauer spectroscopy in longitudinal external fields (up to 7 T) and SQUID magnetometry (up to 5 T)measurements have been carried out on mechanically alloyed (MA) g (FCC) Fe100xNix (x ¼ 21; 24, and 27 at%) alloysat room temperature. The zero-field M.ossbauer spectra of these alloys show only singlets. The high field M.ossbauerresults indicate that large amounts of the material is in the paramagnetic state, giving rise to two spectral componentswith their effective fields almost linearly depend on the external field, but with slopes that are smaller than unity. The infieldM.ossbauer spectra of the x ¼ 27 at% alloy show an additional component with a hyperfine field of E21 T, whichis attributed to Ni-rich (>30 at% Ni) clusters (domains) of ferromagnetically ordered HM phase that behavessuperparamagnetically at room temperature and shows a non-linear character in the magnetization (M–H) curves atlow fields. This HM phase is also present in the x ¼ 21 and 24 at% samples but with smaller amounts. The resultssuggest induced hyperfine fields and hence induced moments in the paramagnetic components, which increases withincreasing Ni contents. Taenite-enriched samples from the metal particles of two stony meteorites, Al Kidirate (H6)and New Halfa (L4), are also studied by high field M.ossbauer spectroscopy and the results are compared to that ofMA samples.

    Keywords
    Mössbauer spectroscopy; External field; Magnetization; Fe–Ni alloys; Antitaenite
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91279 (URN)
    Available from: 2004-01-15 Created: 2004-01-15 Last updated: 2017-12-14Bibliographically approved
    5. Non-magnetic stainless steels reinvestigated: A small effective field component in external magnetic fields
    Open this publication in new window or tab >>Non-magnetic stainless steels reinvestigated: A small effective field component in external magnetic fields
    2004 (English)In: Hyperfine Interactions, ISSN 0304-3843, E-ISSN 1572-9540, Vol. 156/157, p. 151-155Article in journal (Refereed) Published
    Abstract [en]

    Three standard non-magnetic stainl ess steels of composition (wt%) Fe 70 Cr 19 Ni 11 , Fe 70 Cr 17 Ni 13 and Fe 69 Cr 18 . 5 Ni 10 . 3 Mn 1 . 8 Ti 0 . 4 have been investigated by Mössbauer spectroscopy (5–295 K and in external fields 7 T at room temperature) and ma gnetization measurements (10– 300 K) using a SQUID magnetometer. There are indications of a field induced ferromagnetic inter- action in the samples at room temperature

    Keywords
    stainless steel, external field, field induced ferromagnetism
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91280 (URN)
    Available from: 2004-01-15 Created: 2004-01-15 Last updated: 2017-12-14Bibliographically approved
    6. High pressure Mössbauer studies on fcc Fe53Ni47 alloy
    Open this publication in new window or tab >>High pressure Mössbauer studies on fcc Fe53Ni47 alloy
    2004 (English)In: Hyperfine Interactions, ISSN 0304-3843, E-ISSN 1572-9540, Vol. 156, p. 394-, article id 389Article in journal (Refereed) Published
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91281 (URN)10.1007/978-1-4020-2852-6_59 (DOI)
    Available from: 2004-01-15 Created: 2004-01-15 Last updated: 2017-12-14Bibliographically approved
  • 3.
    Abdulkarim, Farhad
    Uppsala University, Disciplinary Domain of Science and Technology.
    Genetic analysis of elongation factor Tu and the tuf genes 1995Doctoral thesis, comprehensive summary (Other academic)
  • 4.
    Abrahamsson, Malin L. A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical Chemistry.
    Electron Transfer in Ruthenium-Manganese Complexes for Artificial Photosynthesis: Studies in Solution and on Electrode Surfaces2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In today’s society there is an increasing need for energy, an increase which for the most part is supplied by the use of fossil fuels. Fossil fuel resources are limited and their use has harmful effects on the environment, therefore the development of technologies that produce clean energy sources is very appealing. Natural photosynthesis is capable of converting solar energy into chemical energy through a series of efficient energy and electron transfer reactions with water as the only electron source. Thus, constructing an artificial system that uses the same principles to convert sunlight into electricity or storable fuels like hydrogen is one of the major forces driving artificial photosynthesis research.

    This thesis describes supramolecular complexes with the intention of mimicking the electron transfer reactions of the donor side in Photosystem II, where a manganese cluster together with a tyrosine catalyses the oxidation of water. All complexes are based on Ru(II)-trisbipyridine as a photosensitizer that is covalently linked to electron donors like tyrosine or manganese. Photochemical reactions are studied with time-resolved transient absorption and emission measurements. Electrochemical techniques are used to study the electrochemical behavior, and different photoelectrochemical techniques are used to investigate the complexes adsorbed onto titanium dioxide surfaces. In all complexes, intramolecular electron transfer occurs from the linked donor to photo-oxidized Ru(III). It is also observed that coordinated Mn(II) quenches the excited state of Ru(II), a reaction that is found to be distance dependent. However, by modifying one of the complexes, its excited state properties can be tuned in a way that decreases the quenching and keeps the electron transfer properties. The obtained results are of significance for the development of multinuclear Ru-Mn complexes that are capable of multi-electron transfer.

    List of papers
    1. Ruthenium-Manganese Complexes for Artificial Photosynthesis: Factors Controlling Intramolecular Electron Transfer and Excited State Quenching Reactions
    Open this publication in new window or tab >>Ruthenium-Manganese Complexes for Artificial Photosynthesis: Factors Controlling Intramolecular Electron Transfer and Excited State Quenching Reactions
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    2002 (English)In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 41, no 6, p. 1534-1544Article in journal (Refereed) Published
    Abstract [en]

    Continuing our work toward a system mimicking the electron-transfer steps from manganese to P(680)(+) in photosystem II (PS II), we report a series of ruthenium(II)-manganese(II) complexes that display intramolecular electron transfer from manganese(II) to photooxidized ruthenium(III). The electron-transfer rate constant (k(ET)) values span a large range, 1 x 10(5)-2 x 10(7) s(-1), and we have investigated different factors that are responsible for the variation. The reorganization energies determined experimentally (lambda = 1.5-2.0 eV) are larger than expected for solvent reorganization in complexes of similar size in polar solvents (typically lambda approximately 1.0 eV). This result indicates that the inner reorganization energy is relatively large and, consequently, that at moderate driving force values manganese complexes are not fast donors. Both the type of manganese ligand and the link between the two metals are shown to be of great importance to the electron-transfer rate. In contrast, we show that the quenching of the excited state of the ruthenium(II) moiety by manganese(II) in this series of complexes mainly depends on the distance between the metals. However, by synthetically modifying the sensitizer so that the lowest metal-to-ligand charge transfer state was localized on the nonbridging ruthenium(II) ligands, we could reduce the quenching rate constant in one complex by a factor of 700 without changing the bridging ligand. Still, the manganese(II)-ruthenium(III) electron-transfer rate constant was not reduced. Consequently, the modification resulted in a complex with very favorable properties.

    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-89491 (URN)10.1021/ic0107227 (DOI)11896722 (PubMedID)
    Available from: 2001-10-19 Created: 2001-10-19 Last updated: 2017-12-14Bibliographically approved
    2. A Biomimetic Model System for the Water Oxidizing Triad in Photosystem II
    Open this publication in new window or tab >>A Biomimetic Model System for the Water Oxidizing Triad in Photosystem II
    Show others...
    1999 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 121, no 1, p. 89-96Article in journal (Refereed) Published
    Abstract [en]

    In plants, solar energy is used to extract electrons from water, producing atmospheric oxygen. This is conducted by Photosystem II, where a redox ”triad” consisting of chlorophyll, a tyrosine, and a manganese cluster, governs an essential part of the process. Photooxidation of the chlorophylls produces electron transfer from the tyrosine, which forms a radical. The radical and the manganese cluster together extract electrons from water, providing the biosphere with an unlimited electron source. As a partial model for this system we constructed a ruthenium(II) complex with a covalently attached tyrosine, where the photooxidized ruthenium was rereduced by the tyrosine. In this study we show that the tyrosyl radical, which gives a transient EPR signal under illumination, can oxidize a manganese complex. The dinuclear manganese complex, which initially is in the Mn(III)/(III) state, is oxidized by the photogenerated tyrosyl radical to the Mn(III)/(IV) state. The redox potentials in our system are comparable to those in Photosystem II. Thus, our synthetic redox “triad” mimics important elements in the electron donor ”triad” in Photosystem II, significantly advancing the development of systems for artificial photosynthesis based on ruthenium−manganese complexes.

    Keywords
    Electron-Transfer, Y-Z, Photosynthesis, Mechanism, Complexes, Tyrosine, Oxygen, Light
    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-89492 (URN)10.1021/ja981494r (DOI)
    Available from: 2001-10-19 Created: 2001-10-19 Last updated: 2017-12-14
    3. Hydrogen-Bond Promoted Intramolecular Electron Transfer to Photogenerated Ru(III): A Functional Mimic of TyrosineZ and Histidine 190 in Photosystem II
    Open this publication in new window or tab >>Hydrogen-Bond Promoted Intramolecular Electron Transfer to Photogenerated Ru(III): A Functional Mimic of TyrosineZ and Histidine 190 in Photosystem II
    Show others...
    1999 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 121, no 29, p. 6834-6842Article in journal (Refereed) Published
    Abstract [en]

    As a model for redox components on the donor side of photosystem II (PS II) in green plants, a supramolecular complex 4 has been prepared. In this, a ruthenium(II) tris-bipyridyl complex which mimics the function of P680 in PS II, has been covalently linked to a tyrosine unit which bears two hydrogen-bonding substituents, dipicolylamine (dpa) ligands. Our aim is to mimic the interaction between tyrosineZ and a basic histidine residue, namely His190 in PSII, and also to use the dpa ligands for coordination of manganese. Two different routes for the synthesis of the compound 4 are presented. Its structure was fully characterized by 1H NMR, COSY, NOESY, 13C NMR, IR, and mass spectrometry. 1H NMR and NOESY gave evidence for the existence of intramolecular hydrogen bonding in 4. The interaction between the ruthenium and the substituted tyrosine unit was probed by steady-state and time-resolved emission measurements as well as by chemical oxidation. Flash photolysis and EPR measurements on 4 in the presence of an electron acceptor (methylviologen, MV2+, or cobalt pentaminechloride, Co3+) showed that an intermolecular electron transfer from the excited state of Ru(II) in 4 to the electron acceptor took place, forming Ru(III) and the methylviologen radical MV+ or Co2+. This was followed by intramolecular electron transfer from the substituted tyrosine moiety to the photogenerated Ru(III), regenerating Ru(II) and forming a tyrosyl radical. In water, the radical has a g value of 2.0044, indicative of a deprotonated tyrosyl radical. In acetonitrile, a radical with a g value of 2.0029 was formed, which can be assigned to the tyrosine radical cation. In both solvents the electron transfer is intramolecular with a rate constant kET > 1 × 107 s-1. This is 2 orders of magnitude greater than the one for a similar compound 3, in which no dpa arm is attached to the tyrosine unit. Therefore the hydrogen bonding between the substituted tyrosine and the dpa arms in 4 is proposed to be responsible for the fast electron transfer. This interaction mimics the proposed His190 and tyrosineZ interaction in the donor side of PS II.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-89493 (URN)10.1021/ja984048c (DOI)
    Available from: 2001-10-19 Created: 2001-10-19 Last updated: 2017-12-14
    4. Towards an artificial model for Photosystem II: A manganese(II,II) dimer covalently linked to ruthenium(II) tris-bipyridine via a tyrosine derivative
    Open this publication in new window or tab >>Towards an artificial model for Photosystem II: A manganese(II,II) dimer covalently linked to ruthenium(II) tris-bipyridine via a tyrosine derivative
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    2000 (English)In: Journal of Inorganic Biochemistry, ISSN 0162-0134, E-ISSN 1873-3344, Vol. 78, no 1, p. 15-22Article in journal (Refereed) Published
    Abstract [en]

    In order to model the individual electron transfer steps from the manganese cluster to the photooxidized sensitizer P680+ in Photosystem II (PS II) in green plants, the supramolecular complex 4 has been synthesized. In this complex, a ruthenium(II) tris-bipyridine type photosensitizer has been linked to a manganese(II) dimer via a substituted L-tyrosine, which bridges the manganese ions. The trinuclear complex 4 was characterized by electron paramagnetic resonance (EPR) and electrospray ionization mass spectrometry (ESI-MS). The excited state lifetime of the ruthenium tris-bipyridine moiety in 4 was found to be about 110 ns in acetonitrile. Using flash photolysis in the presence of an electron acceptor (methylviologen), it was demonstrated that in the supramolecular complex 4 an electron was transferred from the excited state of the ruthenium tris-bipyridine moiety to methylviologen, forming a methylviologen radical and a ruthenium(III) tris-bipyridine moiety. Next, the Ru(III) species retrieved the electron from the manganese(II/II) dimer in an intramolecular electron transfer reaction with a rate constant kET > 1.0 x 10(7) s(-1), generating a manganese(II/III) oxidation state and regenerating the ruthenium(II) photosensitizer. This is the first example of intramolecular electron transfer in a supramolecular complex, in which a manganese dimer is covalently linked to a photosensitizer via a tyrosine unit, in a process which mimics the electron transfer on the donor side of PS II.

    Keywords
    ruthenium complexes, manganese dimer complexes, artificial photosynthesis, electron transfer, photosystem II, ELECTRON-TRANSFER, MNIIMNIII COMPLEXES, PHOTOSYNTHESIS, PROTEINS, CATALASE, SPECTRA, ENZYMES, SYSTEMS, REDOX
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-89494 (URN)10.1016/S0162-0134(99)00200-7 (DOI)10714701 (PubMedID)
    Available from: 2001-10-19 Created: 2001-10-19 Last updated: 2017-12-14
    5. Ruthenium Trisbipyridyl Complexes Covalently Linked to Phenolate Ligands that Coordinates Manganese
    Open this publication in new window or tab >>Ruthenium Trisbipyridyl Complexes Covalently Linked to Phenolate Ligands that Coordinates Manganese
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    Article in journal (Refereed) In press
    Identifiers
    urn:nbn:se:uu:diva-89495 (URN)
    Available from: 2001-10-19 Created: 2001-10-19 Last updated: 2010-01-14Bibliographically approved
    6. Electron Transfer Kinetics for Ruthenium-Manganese Complexes Adsorbed onto Nanocrystalline TiO2 Films
    Open this publication in new window or tab >>Electron Transfer Kinetics for Ruthenium-Manganese Complexes Adsorbed onto Nanocrystalline TiO2 Films
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    2001 (English)Article in journal (Refereed) In press
    Identifiers
    urn:nbn:se:uu:diva-89496 (URN)
    Available from: 2001-10-19 Created: 2001-10-19 Last updated: 2014-01-24Bibliographically approved
  • 5.
    Abramson, Jeff
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Biochemistry.
    Structural studies on the integral membrane protein, ubiquinol oxidase from Escherichia coli2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Heme-copper oxidases are redox-driven proton pumps that couple the reduction of molecular oxygen to water with the vectorial translocation of protons across the membrane. The proton gradient generated by heme-copper oxidases and the other members of the aerobic respiratory chain is ultimately used to drive the synthesis of ATP. There are two main branches of the heme-copper oxidases that are characterized by the electron donating substrate; the cytochrome c oxidases, which use cytochrome c as the electron donor, and the ubiquinol oxidases, which use a lipid-soluble molecule, ubiquinol, as their electron donor. These enzymes share important structural and functional features.

    This thesis presents the procedures that have led to the first crystal structure of a ubiquinol oxidase, cytochrome bo, oxidase from Escherichia coli, at a resolution of 3.5 Å. The overall structure of the enzyme is similar to those of cytochrome c oxidases; however the membrane spanning region of subunit I contains a cluster of polar residues exposed to the interior of the lipid bilayer. No such structural feature is present in cytochrome c oxidases. Mutagenesis studies on residues in this region strongly suggest that this area forms a ubiquinone binding site. A comparison of this region with known ubiquinone binding sites shows remarkable similarities. In light of these findings specific roles for these polar residues is proposed in electron and proton transfer in ubiquinol oxidase.

    A fusion protein of cytochrome bo3-Protein Z was generated in an attempt to increase the hydrophilic surface of the protein, thus extending protein-protein contacts within the crystal lattice structure. Such an approach can be used to facilitate crystallization.

  • 6.
    Abramsson Zetterberg, Lilianne
    Uppsala University, Disciplinary Domain of Science and Technology.
    Chromosome aberrations detected by the flow cytometer based micronucleus assay: studies of rodent erythrocytes after exposure to very low doses of ionizing radiation or to chemicals 1997Doctoral thesis, comprehensive summary (Other academic)
  • 7.
    Acharya, Parag
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Studies on the Non-covalent Interactions (Stereoelectronics, Stacking and Hydrogen Bonding) in the Self-assembly of DNA and RNA2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3'-anthraniloyl adenosine (a mimic of 3'-teminal CCAOH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2'-anthraniloyl adenosine, thereby showing (Paper III) that the 2’-endo sugar conformation is a more suitable mimic of the transition state geometry than the 3’-endo conformation in discriminating between correctly and incorrectly charged aminoacyl-tRNAPhe by EF-Tu during protein synthesis. The presence of 2'-OH in RNA distinguishes it from DNA both functionally as well as structurally. This work (Paper IV) provides straightforward NMR evidence to show that the 2'-OH is intramolecularly hydrogen bonded with the vicinal 3'-oxygen, and the exposure of the 3'-phosphate of the ribonucleotides to the bulk water determines the availability of the bound water around the vicinal 2'-OH, which then can play various functional role through inter- or intramolecular interactions. The pH-dependent 1H NMR study with nicotinamide derivatives demonstrates (Paper V) that the cascade of intramolecular cation (pyridinium)-π(phenyl)-CH(methyl) interaction in edge-to-face geometry is responsible for perturbing the pKa of the pyridine-nitrogen as well as for the modulation of the aromatic character of the neighboring phenyl moiety, which is also supported by the T1 relaxation studies and ab initio calculations. It has been found (Papers VI-IX) that the variable intramolecular electrostatic interaction between electronically coupled nearest neighbor nucleobases (steered by their respective microenvironments) can modulate their respective pseudoaromatic characters. The net result of this pseudoaromatic cross-modulation is the creation of a unique set of aglycones in an oligo or polynucleotide, whose physico-chemical properties are completely dependent upon the propensity and geometry of the nearest neighbor interactions (extended genetic code). The propagation of the interplay of these electrostatic interactions across the hexameric ssDNA chain is considerably less favoured (effectively up to the fourth nucleobase) compared to that of the isosequential ssRNA (up to the sixth nucleobase). The dissection of the relative strength of basepairing and stacking in a duplex shows that stability of DNA-DNA duplex weakens over the corresponding RNA-RNA duplexes with the increasing content of A-T/U base pairs, while the strength of stacking of A-T rich DNA-DNA duplex increases in comparison with A-U rich sequence in RNA-RNA duplexes (Paper X).

    List of papers
    1. The Transmission of the Electronic Character of Guanin-9-yl Drives the Sugar-phosphate Backbone Torsions in Guanosine 3',5'-bisphosphate.
    Open this publication in new window or tab >>The Transmission of the Electronic Character of Guanin-9-yl Drives the Sugar-phosphate Backbone Torsions in Guanosine 3',5'-bisphosphate.
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    1999 In: Angew. Chem. Int. Ed., Vol. 38, no 24, p. 3645-3650Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91143 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    2. The RNA Molecular Wire: The pH-Dependent Change in Electronic Character of Adenine-9-yl is Transmitted to Drive the Sugar-Phosphate Backbone Torsions in Adenosine 3', 5'-bisphosphate
    Open this publication in new window or tab >>The RNA Molecular Wire: The pH-Dependent Change in Electronic Character of Adenine-9-yl is Transmitted to Drive the Sugar-Phosphate Backbone Torsions in Adenosine 3', 5'-bisphosphate
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    2000 In: J. Phys. Org. Chem., Vol. 13, p. 300-305Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91144 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    3. The Strength of the 3'-gauche effect Dictates the Structure of 3'-anthraniloyladenosine and its 5'-phosphate, Two Analogues of the 3'-end of Aminoacyl tRNA
    Open this publication in new window or tab >>The Strength of the 3'-gauche effect Dictates the Structure of 3'-anthraniloyladenosine and its 5'-phosphate, Two Analogues of the 3'-end of Aminoacyl tRNA
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    1999 In: J. Chem. Soc. Perkin 2, p. 1531-1536Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91145 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    4. The Hydrogen Bonding and Hydration of 2'-OH in Adenosine and Adenosine 3'-ethylphosphate
    Open this publication in new window or tab >>The Hydrogen Bonding and Hydration of 2'-OH in Adenosine and Adenosine 3'-ethylphosphate
    2002 In: J. Org. Chem., Vol. 67, no 6, p. 1852-1865Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91146 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    5. A Repertoire of Pyridinium-Phenyl-Methyl Cross-Talk through a Cascade of Intramolecular Electrostatic Interactions
    Open this publication in new window or tab >>A Repertoire of Pyridinium-Phenyl-Methyl Cross-Talk through a Cascade of Intramolecular Electrostatic Interactions
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    2003 In: J. Org. Chem., Vol. 68, no 4, p. 1529-1538Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91147 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    6. Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') monophosphates by the Nearest Neighbor Interaction in the Stacked State
    Open this publication in new window or tab >>Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') monophosphates by the Nearest Neighbor Interaction in the Stacked State
    2002 In: J. Am. Chem. Soc., Vol. 124, no 46, p. 13722-13730Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91148 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    7. Tandem Electrostatic Effect From the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-neighbor Stacking
    Open this publication in new window or tab >>Tandem Electrostatic Effect From the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-neighbor Stacking
    2003 In: J. Am. Chem. Soc., Vol. 125, no 8, p. 2094-2100Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91149 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    8. Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
    Open this publication in new window or tab >>Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
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    2003 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, no 33, p. 9948-9961Article in journal (Refereed) Published
    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.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91150 (URN)10.1021/ja034651h (DOI)12914458 (PubMedID)
    Available from: 2003-11-26 Created: 2003-11-26 Last updated: 2017-12-14Bibliographically approved
    9. The Nucleobases in Single-stranded DNA are Better Stacked and Yet Their Pseudoaromatic Characters are More Poorly Cross-modulated Than in the RNA Counterparts Due to Variable Tandem Nearest-neighbour Electrostatic Interactions
    Open this publication in new window or tab >>The Nucleobases in Single-stranded DNA are Better Stacked and Yet Their Pseudoaromatic Characters are More Poorly Cross-modulated Than in the RNA Counterparts Due to Variable Tandem Nearest-neighbour Electrostatic Interactions
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    In: J. Am. Chem. Soc.Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-91151 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    10. Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
    Open this publication in new window or tab >>Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
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    2004 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, no 9, p. 2862-2869Article in journal (Refereed) Published
    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.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91152 (URN)10.1021/ja0386546 (DOI)14995203 (PubMedID)
    Available from: 2003-11-26 Created: 2003-11-26 Last updated: 2017-12-14Bibliographically approved
  • 8.
    Adam, Gail I. R.
    Uppsala University, Disciplinary Domain of Science and Technology.
    Non-classical regulation of gene transcription: a study of the human PDGF-B, H19 and IGF2 genes 1996Doctoral thesis, comprehensive summary (Other academic)
  • 9.
    Adawi, Tom W.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics, Physics Didactics.
    From Branes to Brains: On M-theory and Understanding Thermodynamics2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is concerned with research in both physics and physics education, and is divided into two parts.

    Part I

    String theory has been the leading candidate over the past few years for a theory that unifies all the fundamental forces of nature. The fundamental objects are one-dimensional strings whose vibrational modes should correspond to the usual elementary particles. However, the recent discovery of the profound role played by extended solitonic objects in string theory, referred to as p-branes, has questioned the foundational position of the string itself. A key ingredient in these developments is the notion of duality, a symmetry which provides a handle on non-perturbative physics. As a result, all five string theories, as well as eleven-dimensional supergravity, are but special limits of a conjectural theory, referred to as M-theory. In this part of the thesis, various aspects of p-branes with relevance for M-theory are investigated. Special emphasis is given to the interpretation of p-branes as solitons. Furthermore, some of the features of the superembedding approach to describe p-brane dynamics are examined.

    Part II

    There is now a consensus among educational researchers that it is essential to gain a better understanding of how people understand key concepts in physics in order to improve teaching and learning in physics. This part of the thesis reports on a phenomenographic study investigating the qualitatively different ways in which lay adults, taking an introductory overview course in physics, understand the concepts of heat and temperature. Implications for teaching the topics in higher education forms an essential component of the analysis. This is followed by a theoretical component that draws on the empirical analysis as a contribution to the development of the notion of context in phenomenographic research.

  • 10.
    Adsten, Monika
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Materials Science.
    Solar Thermal Collectors at High Latitudes: Design and performance of non-tracking concentrators2002Doctoral thesis, comprehensive summary (Other academic)