This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial charges and the inter-atomic interactions are modeled by approximate potential functions that produce satisfactory results at an economical computational cost. The three-dimensional trajectory of a many-body system is generated by integrating Newton’s equations of motion, and subsequent statistical analysis on the trajectories provides microscopic insight into the physical properties of the system. The applications in this thesis of molecular dynamics simulations in solution chemistry comprise four aspects: the 113Cd nuclear magnetic resonance shielding constant of aqua Cd(II) ions, paramagnetic 19F nuclear magnetic resonance shift in fluorinated cysteine, solvation free energies and structures of metal ions, and protein adsorption onto TiO2. In the studies of nuclear magnetic resonance parameters, the relativistic effect of the 113Cd nucleus and the paramagnetic shift of 19F induced by triplet O2 are well reproduced by a combined molecular dynamics and density functional theory approach. The simulation of the aqua Cd(II) ion is also extended to several other monovalent, divalent and trivalent metal ions, where careful parameterization of the metal ions ensures the reproduction of experimental solvation structures and free energies. Molecular dynamics simulations also provided insight into the mechanism of protein adsorption onto the TiO2 surface by suggesting that the interfacial water molecules play an important role of mediating the adsorption and that the hydroxylated TiO2 surface has a large affinity to the proteins. The applications of molecular dynamics simulations in atmospheric chemistry are mainly focused on two types of organic components in aerosol droplets: humic-like compounds and amino acids. The humic-like substances, including cis-pinonic acid, pinic acid and pinonaldehyde, are surface-active organic compounds that are able to depress the surface tension of water droplets, as revealed by both experimental measurements and theoretical computations. These compounds either concentrate on the droplet surface or aggregate inside the droplet. Their effects on the surface tension can be modeled by the Langmuir-Szyszkowski equation. The amino acids are not strong surfactants and their influence on the surface tension is much smaller. Simulations show that the zwitterionic forms of serine, glycine and alanine have hydrophilic characteristics, while those of valine, methionine and phenylalanine are hydrophobic. The curvature dependence of the surface tension is also analyzed, and a slight improvement in the Köhler equation is obtained by introducing surface tension corrections for droplets containing glycine and serine. Through several examples it is shown that molecular dynamics simulations serve as a promising tool in the study of aqueous systems. Both solute-solvent interactions and interfaces can be treated properly by choosing suitable potential functions and parameters. Specifically, molecular dynamics simulations provide a microscopic picture that evolves with time, making it possible to follow the dynamic processes such as protein adsorption or atmospheric droplet formation. Moreover, molecular dynamics simulations treat a large number of molecules and give a statistical description of the system; therefore it is convenient to compare the simulated results with experimentally measured data. The simulations can provide hints for better design of experiments, while experimental data can be fed into the refinement of the simulation model. As an important complementary to experiments, molecular dynamics simulations will continue to play significant roles in the research fields of physics, chemistry, materials science, biology and medicine. / QC 20110511

The major part of this thesis describes the synthesis of enantiopure alcohols and diols by combining ruthenium-catalyzed racemization or epimerization and lipase-catalyzed asymmetric transformations. A minor part of this thesis is focused on ruthenium-catalyzed redox reactions for transfer hydrogenation of 1,3-cycloalkanediketones. Kinetic resolution of racemic γ-hydroxy acid derivatives was performed via Pseudomonas cepacia lipase (PS-C)-catalyzed transesterification. γ-Hydroxy esters and γ-hydroxy amides were studied showing in higher selec-tivity and yields for the γ-hydroxy amides. The enzyme PS-C tolerates both variation in the chain length and different functionalities giving good to high enantioselectivity. Combining enzymatic kinetic resolution with a ruthenium-catalyzed racemization led to a dynamic kinetic resolution (DKR). The use of 2,4-dimethyl-3-pentanol as a hydrogen source to suppress ketone formation in the dynamic kinetic resolution increased the yields of the acetate product. The synthetic utility of this procedure was illustrated by the practical synthesis of the γ-lactone (R)-5-methyltetrahydrofuran-2-one. A distereoselective transformation of cis/trans-1,3-cyclohexandiol using Candida antarctica lipase B (CALB)-catalyzed transesterification was of interest. Desymmetrization of cis-1,3-cyclohexanediol to the (R-monoacetate was successfully accomplished. Enantiopure (R,R)-diacetate was obtained from the (R)-monoacetate in a DYKAT process at room tem-perature. Metal- and enzyme-catalyzed transformation of cis/trans-1,3-cyclohexanediol using PS-C, gives a high diastereoselectivity for cis-diacetate. The (S)-mono-acetate was obtained from cis-diacetate by CALB-catalyzed hydrolysis. In addition, it was shown, by the use of deuterium-labeling that intramolecular acyl migration does not occur in the transformation of cis-monoacetate to the cis-diacetate. Ruthenium-catalyzed transfer hydrogenation of 1,3-cyclohexanedione under microwave heating was developed as an efficient and fast method for the preparation of 1,3-cycloalkandiols.

The positron emitting 68Ga radionuclide (T1/2 = 68 min) has the potential of practical interest for clinical PET. The metallic cation, 68Ga3+, is suitable for complexation reactions with chelators either naked or conjugated with macromolecules such as peptides and oligonucleotides. Such labeling procedures require pure and concentrated radiometal preparations, which cannot be sufficiently fulfilled by the presently available 68Ge/68Ga generator eluate. This thesis presents a method to increase the concentration and purity of 68Ga obtained from a commercial 68Ge/68Ga generator. DOTATOC (DOTA = 1,4,7,10-tetraazacyclo-dodecane-1,4,7,10-tetraacetic acid, TOC = D-Phe1-Tyr3–Octreotide) was used as a test molecule for comparing the labeling properties of different 68Ga preparations. In addition, DOTA-RDG (RGD = Cys2-6; c[CH2CO-Lys(DOTA)-Cys-Arg-Gly-Asp-Cys-Phe-Cys]-CCX6-NH2) and NODAGATATE (NODAGA = 1,4,7-triazacyclononane-1,4,7-triacetic, TATE = Tyr3 - Octreotate) were used to prove the concept. The use of the concentrated and purified 68Ga eluate along with microwave activation allowed quantitative 68Ga-labelling of peptide conjugates of ≤1 nanomolar quantities within 10 min. The specific radioactivity of the radiolabelled peptides was improved by a factor of >100 compared to previously applied techniques using non-treated generator eluate and conventional heating. A commercial 68Ge/68Ga generator in combination with this method for purification, concentration and microwave activated labeling resulted in a kit technology for 68Ga-tracer production.Four 17-mer oligonucleotides modified and functionalised with an hexylamine group in the 3'- or 5'- position were conjugated with DOTA and labelled with 68Ga using microwave activation. Chemical modification of the oligonucleotide backbone or sugar moiety did not influence the labelling nor the hybridisation ability of the oligonucleotides. However, the radioactivity organ biodistribution in rats differed dependent on the oligonucleotide structure. This indicated that metabolism and non-specific binding were affected by the backbone and sugar moiety structure.

Carbohydrates are a complex group of biomolecules with a high structural diversity. Their almost omnipresent occurrence has generated a broad field of research in both biology and chemistry. This thesis focuses on three different aspects of carbohydrate chemistry, synthesis, structure elucidation and the conformational analysis of carbohydrates. The first paper describes the synthesis of a penta- and a tetrasaccharide related to the highly branched capsular polysaccharide from Streptococcus pneumoniae type 37. In the second paper, the structure of the O-antigenic repeating unit from the lipopolysaccharide of E. coli 396/C1 was determined along with indications of the structure of the biological repeating unit. In addition, its structural and immunological relationship with E. coli O126 is discussed. In the third paper, partially protected galactopyranosides were examined to clarify the origin of an intriguing 4JHO,H coupling, where a W-mediated coupling pathway was found to operate. In the fourth paper, the conformation of methyl a-cellobioside is studied with a combination of molecular dynamics simulations and NMR spectroscopy. In addition to the expected syn-conformation, detection and quantification of anti-ø and anti-ψ conformers was also possible.

This thesis deals with ruthenium-catalyzed hydrogen transfer involving amines and imines and is divided into two parts. In Part 1 a mechanistic study has been performed. The complexation of the imine to the catalyst and the decomplexation patterns of the formed ruthenium-amine complexes, isotope studies, and exchange studies show that the mechanism of the hydrogen transfer involving amines and imines is different from the hydrogen transfer involving alcohols and carbonyls. In Part 2 synthetic applications of the hydrogen transfer is presented. First the rutheniumcatalyzed transfer hydrogenation of imines by 2-propanol in an unpolar solvent was investigated. The corresponding amines were isolated in good to excellent yields. Even imines bearing labile functional groups were smoothly transferred to amines with very low catalyst loadings and short reaction times employing microwave heating. Then the reverse reaction, transfer dehydrogenation of amines to imines, was investigated using either MnO2 or oxygen as terminal oxidant. Important products such as aldimines, ketimines, and non benzylic anilines were prepared in the aerobic oxidation. We also demonstrated that the aerobic oxidation is compatible with proline-mediated organocatalysis, yielding amines in high yields and ee:s. Finally the racemization of chiral amines was investigated. A cumbersome side product formation was investigated and hampered by the use of a mild hydrogen donor, giving a mild and efficient racemization process for both primary and secondary amines.

In this thesis, the syntheses of oligosaccharides for interaction studies with various lectins are described. The first section reports the syntheses of tetra, tri- and disaccharides corresponding to truncated versions of the glucosylated arm of Glc1Man9(GlcNAc)2, found in the biosynthesis of N-glycans. The thermodynamic parameters of their interaction with calreticulin, a lectin assisting and promoting the correct folding of newly synthesised glycoproteins, were established by isothermal titration calorimetry. In the second section, a new synthetic pathway leading to the same tetra- and trisaccharides is discussed. Adoption of a convergent strategy and of a different protecting group pattern resulted in significantly increased yields of the target structures. The third section describes the syntheses of a number of monodeoxy-trisaccharides related to the above trisaccharide Glc-α-(1→3)-Man-α-(1→2)-Man-α-OMe. Differentsynthetic approaches were explored and the choice of early introduction of the deoxy functionality proved the most beneficial. In the last section, the synthesis of spacer-linked LacNAc dimers as substrates for the lectins galectin-1 and -3 is presented. This synthesis was realized by glycosidation of a number diols with peracetylated LacNAc-oxazoline. Pyridinium triflate was tested as a new promoter, affording the target dimers in high yields. This promoter in combination with microwave irradiation gave even higher yields and also shortened the reaction times.

In order to find suitable stable vaccine candidates against Neisseria meningitidis group A, several structures related to the capsular polysaccharide have been synthesised. The first part of the thesis describes the synthesis of C-phosphonate analogues starting from glucose. The key step is a Mitsunobu coupling of a methyl C-phosphonate monomer to the 6-hydroxyl group of a 2-acetamido mannose derivative. Contained within this work is a description of an improved synthesis of 2-azido-2-deoxy-D-mannopyranose. The second part outlines the synthesis of structural elements present in the native capsular polysaccharide of Neisseria meningitidis serotype A including different acetylation and phosphorylation patterns. The final chapter describes an improved synthesis of the Lewis b hexasaccharide needed for purification of and interaction studies with the Helicobacter pylori adhesin BabA.

This thesis reports an investigation of how acid-base models are taught and understood in Swedish upper secondary school. The definition of the concepts of acids and bases has evolved from a phenomenological level to an abstract (particle) level. Several models of acids and bases are introduced in Swedish secondary school. Among them an ancient model, the Arrhenius model and the Brønsted model. The aim of this study was to determine how teachers handle these models in their teaching. Further, to investigate Swedish upper secondary students’ ideas about the role of chemistry models, in general, and more specific, of models of acids and bases. The study consisted of two parts. First, a study was performed to get an overview of how acids and bases are taught and understood in Swedish upper secondary schools. It consisted of three steps: (i) the most widely used chemistry textbooks for upper secondary school in Sweden were analysed, (ii) six chemistry teachers were interviewed, and, (iii) finally also seven upper secondary school students were interviewed. The results from this study were used in the second part which consisted of two steps: (i) nine chemistry teachers were interviewed regarding their pedagogical content knowledge (PCK) of teaching acids and bases, and (ii) a questionnaire was administered among chemistry teachers of 441 upper secondary schools in Sweden. The results from the interviews show that only a few teachers chose to emphasise the different models of acids and bases. Most of the teachers thought it was sufficient to distinguish clearly between the phenomenological level and the particle level. In the analysis of the questionnaire three subgroups of teachers were identified. Swedish upper secondary chemistry teachers, on the whole, had a strong belief in the Brønsted model of acids and bases. However, in subgroup one (47 %) teachers’ knowledge of how the Brønsted model differs from older models was limited and diverse. Teachers in subgroup two (38 %) and three (15 %) seemed to understand the differences between the Brønsted model and older models, but teachers in subgroup 2 did not explain the history of the development of acids and bases in their teaching. Instead they (as teachers in subgroup one) relied more on the content in the textbooks than teachers in the third subgroup. Implications for textbook writers, teaching, and further research are discussed.

When making paper, fibers and additives are suspended in water to a fiber suspension. The sheet is formed by draining a specific amount of suspension through a wire-cloth. The procedure is well known, but the underlying mechanisms are not fully understood. To understand how the different particles such as fines, fibers, retention aids and other additives interact with each other, further research is needed. This knowledge is important because in the production of paper, the retention and the distribution of fines and additives within a paper structure are vital parameters for the properties and also for the profitability of the final product. In this study fluorescence microscopy was used to study fines from bleached kraft pulp which were labeled with fluorophores. When the fines exhibit fluorescence we can study their individual trajectories and understand more about the interactions between fibers, fines and additives in different chemical environments. Fines from bleached kraft pulp have no fluorescent properties and therefore it is necessary to bind a fluorophore to the material. It was difficult to find a suitable fluorophore which binds covalently to the cellulose, the dominating part of fines. The result from this study was that the labeled fines did exhibited fluorescence. As the fines were aggregated no individual trajectories could be analyzed with fluorescence microscopy. Further development of the technique for labeling fines must be carried out to avoid aggregation of fines. / Vid tillverkning av papper, blandas fibrer och tillsatser i vatten till en fibersuspension. Arket bildas genom att avvattna suspensionen genom en vira. Förfarandet är välkänt men för att förstå mekanismerna måste vi förstå hur olika partiklar som fines, fibrer, retentionsmedel och andra tillsatser interagerar med varandra. Denna kunskap är viktigt eftersom i produktionen av papper är retention och distribution av fines och tillsatser i en pappersstruktur avgörande parametrar för de egenskaper, och även för lönsamheten, som erhålls i den slutliga produkten. I denna studie används fluorescensmikroskopi för att kunna studera fines av blekt sulfatmassa som blivit märkta med fluoroforer. När materialet uppvisar fluorescens kan deras individuella rörelsemönster studeras och därmed kan interaktionen som sker mellan fibrer, fines och tillsatser i olika kemiska miljöer förstås. Fines av blekt sulfatmassa har inga fluorescerande egenskaper och därför är det nödvändigt att binda en fluorfor till materialet. Det var svårt att hitta en lämplig fluorofor som binder kovalent till cellulosa, den dominerande delen av fines. Resultatet från denna studie visar att lösningarna med fluorescentmärkta fines uppvisade fluorescens. Eftersom det skedde en aggregering av fines kunde inte deras individuella rörelsemönster analyseras med fluorescensmikroskopi. Modifiering av märkningen måste göras för att kunna undvika aggregeringen av fines.

In this thesis, synthesis of structures related to antifreeze glycoproteins (AFGPs) are presented. Synthetic routes to a protected carbohydrate derivative, 2,3,4,6-tetra-O-benzyl-β-galactopyranosyl-(1→3)-2-deoxy-2-azido-4,6-di-O-benzyl-β-D-thio-1-galactopyranoside, and a tBu-Ala-Thr-Ala-Fmoc tripeptide, are described. These compounds are meant to be used in the assembly of AFGPs and analogues thereof. A Gal-GlcN disaccharide was synthesized via glycosylation between the donor, bromo-2-O-benzoyl-3,4,6-tri-O-benzyl-α-Dgalactopyranoside, and acceptor, ethyl 4,6-O-benzylidene-2-deoxy-2-N-phthalimido-β-D-1-thio-glucopyranoside, using silver triflate activation. Subsequent epimerization to a Gal-GalN disaccharide was achieved using Moffatt oxidation followed by L-selectride® reduction. The tripeptide was synthesized in a short and convenient manner using solid phase peptide synthesis with immobilized Fmoc-Ala on Wang® resins as starting point.