Two recently developed theories of electronic energy transfer/migration were for the first time applied to real protein systems for extracting molecular distances. The partial donor-donor energy migration (PDDEM) is an extension to the previously developed donor-donor energy migration (DDEM, F Bergström et al PNAS 96, 1999, 12477) which allows using chemically identical but photophysically different fluorophores in energy migration experiments. A method based on fluorescence quenching was investigated and applied to create an asymmetric energy migration between fluorophores which were covalently and specifically attached to plasminogen activator inhibitor type 2 (PAI-2). It was also shown experimentally that distance information can be obtained if the fluorescence relaxation for photophysically identical donors, exhibits multi-exponential relaxation. An extended Förster theory (EFT) that was previously derived (L. B.-Å. Johansson et al J. Chem. Phys., 1996, 105) ha been developed for analysis of donor-acceptor energy transfer systems as well as DDEM systems. Recently the EFT was also applied to determine intra molecular distances in the protein plasminogen activator inhibitor type 1 (PAI-1) which was labelled with a sulfhydryl specific derivative of BODIPY. The EFT explicitly accounts for the time-dependent reorientations which in a complex manner influence the rate of electronic energy transfer/migration. This difficulty is related to the “k2-problem”, which has been solved. It is also shown experimentally that the time-correlated single-photon counting (TCSPC) data is sensitive to the mutual configuration between the interacting fluorophores. To increase the accuracy in the extracted parameters it is furthermore suggested to collect the fluorescence data under various physico-chemical conditions. It was also shown that the Förster theory is only valid in the initial part of the fluorescence decay.

Glutathione transferases (GSTs) play a pivotal role in cellular defense, since they are main contributors to the inactivation of genotoxic compounds of exogenous and endogenous origins. Directed evolution was used to improve the catalytic activities of Theta class GST T1-1 toward different substrates. The library was constructed by recombination of cDNA coding for human GST T1-1 and rodent Theta class GSTs, resulting in the F2-F5 generations. The clones were heterologously expressed in Escherichia coli and screened for variants with enhanced alkyltransferase activity. A mutant, F2:1215, with a 70-fold increased catalytic efficiency with 4-nitrophenethyl bromide (NPB) compared to human GST T1-1, was isolated from the second generation. NPB was used as a surrogate substrate of the anticancer drug 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) in order to facilitate the screening process. The catalytic efficiency of the F2:1215 with BCNU had improved 170-fold compared to wild-type human GST T1-1, suggesting that NPB is a suitable model substrate for the anticancer drug BCNU. The sequence of the F2:1215 mutant differs from wild-type human GST T1-1 by three residues; one of these differences is Arg234, which corresponds to Trp in the human enzyme. Upon replacing the Trp234 in the human GST T1-1 with Arg, the resulting mutant (hTrp234Arg) showed enhanced alkyltransferase activity with a wide range of substrates (e.g. haloalkanes and other typical GSTs substrates). The three-dimensional structures of both wild-type human GST T1-1 and hTrp234Arg mutant help to explain the higher activity showed by of hTrp234Arg mutant compared to wild-type enzyme. The reciprocal mutation of the residue 234 in mouse GST T1-1 to that found in human, mArg234Trp, caused a dramatic decrease in the activity of the mouse enzyme to be similar to human GST T1-1. This indicates that residue 234 can be considered as a master switch of activities between human and rodent GST T1-1. Another important residue in the C-terminal helix of GST T1-1 is Met232. Although residue 232 points away from the H-site, it influences the catalytic activity and substrate selectivity of the mouse GST T1-1. A minor modification of Met232 induces major changes in the substrate-activity profile of the mouse GST T1-1 to favor novel substrates such as isothiocyanates and hydroperoxides and decreases the activity toward substrates that catalyzed by the wild-type enzyme.

Free radical cyclization methodology has been used extensively in synthesis for manipulation of complex molecules such as alkaloids, terpenes, carbohydrates, peptides and nucleic acids. The methodology has emerged as a result of work by physical organic chemists who determined rate constants for the most common radical reactions used in organic synthesis. A novel route to cyclic imines based on 5-exo radical cyclization was explored. The radical precursors were imines prepared from allylamine and readily available a-phenylselenenyl ketones. The synthesis of conformationally constrained bicyclic nucleosides is also reported using 5-exo and 6-exo cyclizations of hexenyl and heptenyl radicals in thymidine nucleosides. The nucleosides were incorporated in a 15mer antisense oligonucleotide via solid-phase oligonucleotide synthesis. The AONs with the modifications were tested for target affinity and stability and compared with the well known LNA modified AONs. The thesis discusses the unique qualities of these novel molecules and presents them as potential candidates for antisense therapeutic agents. Keeping up with the theme of intramolecular carbon-carbon bond formation, microwave induced carbodechalcogenation of chalcogenoanhydrides was explored. Poor generality in these reactions made us turn to transition metal catalysis for Sonogashira cross-coupling reactions using alkyl aryl and diaryl tellurides as coupling partners.

HTML clipboardIn this thesis, dynamic effects on electron transport in molecular electronic devices are presented. Special attention is paid to the dynamics of atomic motions of bridged molecules, thermal motions of surrounding solvents, and many-body electron correlations in molecular junctions. In the framework of single-body Green’s function, the effect of nuclear motions on electron transport in molecular junctions is introduced on the basis of Born-Oppenheimer approximation. Contributions to electron transport from electron-vibration coupling are investigated from the second derivative of current-voltage characteristics, in which each peak is corresponding to a normal mode of the vibration. The inelastic-tunneling spectrum is thus a useful tool in probing the molecular conformations in molecular junctions. By taking account of the many-body interaction between electrons in the scattering region, both time-independent and time-dependent many-body Green’s function formula based on timedependent density functional theory have been developed, in which the concept of state of the system is used to provide insight into the correlation effect on electron transport in molecular devices. An effective approach that combines molecular dynamics simulations and first principles calculations has also been developed to study the statistical behavior of electron transport in electro-chemically gated molecular junctions. The effect of thermal motions of polar water molecules on electron transport at different temperatures has been found to be closely related to the temperature-dependent dynamical hydrogen bond network. / QC20100630

Because of the generation of polaritons, which are quasiparticles possessing the characteristics of both photonics and electronics, active photonic materials offer a possible solution to transfer electromagnetic energy below the diffraction limit and further increase the density of photonic integrated circuits. A theoretical investigation of these exciting materials is, therefore, very important for practical applications. Four different kinds of polaritons have been studied in this thesis, (1) surface polaritons of negative-index-material cylindric rods, (2) exciton polaritons of semiconductor quantum dots, (3) localized plasmon polaritons of metallic nanoshells, and (4) surface plasmon polaritons of subwavelength hole arrays in thin metal films. All these types of polaritons were found to strongly affect the optical properties of the studied active photonic materials. More specifically, (1) for two-dimensional photonic crystals composed of negative-index-material cylindric rods, the coupling among surface polaritons localized in the rods results in dispersionless anti-crossing bands; (2) for three-dimensional diamond-lattice quantum-dot photonic crystals, the exciton polariton resonances lead to the formation of complete band gaps in the dispersion relationships; (3) for metallic nanoshells, the thickness of the metal shell strongly modifies the localized plasmon polaritons, and therefore influences the degree of localization of the electromagnetic field inside the metallic nanoshells; (4) for subwavelength hole arrays in thin metal films, high-order surface-polariton Bloch waves contribute significantly to the efficient transmission. To numerically simulate these active photonic materials, we introduced three approaches, (1) an extended plane-wave-based transfer-matrix approach for negative- index-material media, (2) a plane-wave method for semiconductor quantum-dot photonic crystals, and (3) an auxiliary-differential-equation finite-difference time- domain approach for semiconductor quantum-dot arrays. A brief perspective is also given at the end of this thesis. / QC 20100825

This thesis deals with the study of oxazoline-based ligands in metal-catalyzed asymmetric reactions. The first part describes the synthesis of six new bifunctinal pyridine-bis(oxazoline) ligands and their applications in asymmetric metal-catalysis. These ligands, in addition to a Lewis acid coordination site, are equipped with a Lewis basic part in the 4-position of the oxazoline rings. Dual activation by means of this system was probed in cyanide addition to aldehydes. The second part is concerned with the synthesis of two pyridine-bis(oxazoline) ligands bearing bulky triazole groups in the 4-position of the oxazoline rings and a macrocyclic ligand consisting of a pyridine-bis(oxazoline) moiety and a diaza-18-crown-6 ether. The synthesis of these compounds benefits from the use of “click chemistry”. The ligands thus obtained were tested in different asymmetric catalytic reactions. Complexation studies with different bifunctional molecules that could bind into the cavity of the macrocycle were carried out using NMR spectroscopy. A third chapter is devoted to the synthesis of a supported pyridine-bis(oxazoline) catalyst and its use in catalysis. The pyridine-bis(oxazoline) ligand was efficiently connected to a polystyrene resin via a robust triazole linker. This resin could be employed in different metal-catalyzed asymmetric reactions and good results were obtained in terms of yield and enantioselectivity. Moreover, this polymer-bound ligand could be easily and efficiently recycled. Finally, the last part deals with the use of a hydroxy-containing phosphinooxazoline ligand in the hydrosilylation of imines and in the asymmetric intermolecular Heck reaction. A cationic iridium complex of this ligand was studied by NMR spectroscopy. / QC 20100914

Single-particle cryo-electron microscopy (cryo-EM) is a method capable of obtaining information about the structural organization and dynamics of large macromolecular assemblies. In the late nineties, the method was suggested to have the potential of generating “atomic resolution” reconstructions of particles above a certain mass. However, visualization of secondary structure elements in cryo-EM reconstructions has so far been achieved mainly for highly symmetrical macromolecular assemblies or by using previously existing X-ray structures to solve the initial alignment problem. A factor that severely limits the resolution for low-symmetry (point group symmetry Cn) particles is the problem of ab initio three-dimensional alignment of cryo-EM projection images of proteins in vitreous ice. A more general problem in the field of molecular biology is the study of heterogeneous structural properties of particles in preparations of purified macromolecular complexes. If not resolved, structural heterogeneity limits the achievable resolution of a cryo-EM reconstruction and makes correct biological interpretation difficult. If resolved, the heterogeneity instead offers a tremendous biological insight into the dynamic behaviour of a structure, and statistical information about partitioning over subpopulations with distinct structural features within the ensemble of particles may be gained. This thesis adds to the existing body of methods in the field of single-particle cryo-EM by addressing the problem of ab initio rotational alignment and the problem of resolving structural heterogeneity without using a priori information about the structural variability within large populations of cryo-EM projections of unstained proteins. The thesis aims at making the single-particle cryo-EM method a generally applicable tool for generating subnanometer resolution reconstructions and perform heterogeneity analysis of biological macromolecules. / QC 20100719

In this thesis, quantum chemistry, in particular the B3LYP density functional method, is used to investigate a number of methyl transfer enzymes. Quantum chemical methodology is today a very important tool in the elucidation of properties and reaction mechanisms of enzyme active sites. The enzymes considered in this thesis are the S-adenosyl L-methionine-dependent enzymes - glycine N-methyltransferase, guanidinoacetate methyltransferase, phenylethanolamine N-methyltransferase, and histone lysine methyltransferase. In addition, the reaction mechanism of the DNA repairing enzyme O6-methylguanine methyltransferase is studied. Active site models of varying sizes were designed and stationary points along the reaction paths were optimized and characterized. Potential energy surfaces for the reactions were calculated and the feasibility of the suggested reaction mechanisms was able to be judged. By systematically increasing the size of the models, deeper insight into the details of the reactions was obtained, the roles of the various active site residues could be analyzed, and, very importantly, the adopted modeling strategy was evaluated. / QC 20100927

Syftet med mitt examensarbete var att ta reda på kemins roll i förskolan. Jag valde då att genomföra undersökningen med hjälp av intervjuer med pedagoger i olika förskolor. Hälften av de tillfrågade pedagogerna ansåg att de arbetade med kemi i förskolan. Elva av tolv pedagoger ansåg att kemi i förskolan gav fördelar. Det upptäckande arbetssättet som uppstår ger barnen lust att undersöka och de vågar sig på problemlösningar. Detta arbetssätt, det naturvetenskapliga, skapar en arena för lärande om de närvarande pedagogerna tar chansen att vara medupptäckare och att dessa genom diskussioner med barnen leder lärandet framåt.

Sammanfattning: Syftet med detta arbete är att skapa ett lättillgängligt material i fysik och kemi, och därigenom få fler pedagoger att arbeta med dessa ämnen i förskolan. Ett handledarhäfte med enkla experiment skapades och utvärderades på två förskolor. Pedagogerna arbetade med detta häfte i två veckor, för att sedan utvärdera det via en enkät. Resultatet visade sig positivt, de tyckte att det varit roligt att arbeta med fysik och kemi med barnen. Häftet var lättförståligt och man använde sig av material som normalt finns på en förskola. Barnen förde diskussioner utifrån de diskussionsfrågor som finns till varje experiment och de fick samtidigt en positiv upplevelse av fysik och kemi. Barnen kommer förhoppningsvis att ha med sig denna känsla för fysik och kemi när de fortsätter upp i skolan, där många elever upplever fysik och kemi som svåra och ointressanta ämnen.