Atomistic simulations of cosolvent/water mixtures

In this thesis, atomistic simulations are performed to investigate hydrophobic solvation and hydrophobic interactions in cosolvent/water binary mixtures. Many cosolvent/water binary mixtures exhibit non-ideal behavior caused by aggregation at the molecular scale level although they are stable and homogenous at the macroscopic scale. Force-field based atomistic simulations provide routes to relate atomistic-scale structure and interactions to thermodynamic solution properties. The predicted solution properties are however sensitive to the parameters used to describe the molecular interactions. In this thesis, a force field for tertiary butanol (TBA) and water mixtures is parameterized by making use of the Kirkwood-Buff theory of solution. The new force field is capable of describing the alcohol-alcohol, water-water and alcohol-water clustering in the solution as well as the solution components’ chemical potential derivatives in agreement with experimental data. With the new force field, the preferential solvation and the solvation thermodynamics of a hydrophobic solute in TBA/water mixtures have been studied. First, methane solvation at various TBA/water concentrations is discussed in terms of solvation free energy-, enthalpy- and entropy- changes, which have been compared to experimental data. We observed that the methane solvation free energy varies smoothly with the alcohol/water composition while the solvation enthalpies and entropies vary nonmonotonically. The latter occurs due to structural solvent reorganization contributions which are not present in the free energy change due to exact enthalpy-entropy compensation. It is therefore concluded that the enthalpy and entropy of solvation provide more detailed information on the reorganization of solvent molecules around the inserted solute. Hydrophobic interactions in binary urea/water mixtures are next discussed. This system is particularly relevant in biology (protein folding/unfolding), however, changes in the hydrophobic interaction induced by urea molecules are not well understood. In this thesis, this interaction has been studied by calculating the free energy (potential of mean force), enthalpy and entropy changes as a function of the solute-solute distance in water and in aqueous urea (6.9 M) solution. In chapter 5, the potential of mean force in both solution systems is analyzed in terms of its enthalpic and entropic contributions. In particular, contributions of solvent reorganization in the enthalpy and entropy changes are studied separately to better understand what are the changes in interactions in the system that contribute to the free energy of association of the nonpolar solutes. We observe that in aqueous urea the association between nonpolar solutes remains thermodynamically favorable (i.e., as it is the case in pure water). This observation contrasts a long-standing belief that clusters of nonpolar molecules dissolve completely in the presence of urea molecules. The consequences of our observations for the stability of proteins in concentrated urea solutions are discussed in the chapter 6 of the thesis.

Untersuchungen zur Reparatur und Mutagenität oxidativer DNA-Schäden in vivo und deren Bedeutung für die Kanzerogenese

Gegenstand dieser Arbeit war die Untersuchung, welche Rolle endogen gebildete oxidative DNA-Modifikationen bei der Kanzerogenese spielen. Dazu wurden Cockayne Syndrom B-knockout-Mäuse (Csb-/-), 8-Hydroxyguanin-DNA-Glykosylase-knockout-Mäuse (Ogg1-/-) und Csb-/-/Ogg1-/- Mäuse generiert, die das bakterielle lacI-Gen (Big Blue®) tragen und somit für in vivo Mutationstests eingesetzt werden können. Die Ergebnisse zeigen, dass es in den Lebern der Ogg1-/- Mäuse zu einem 2,1-fachen und in Csb-/-/Ogg1-/- Mäusen zu einem statistisch signifikanten 3,3-fachen Anstieg der Mutationsfrequenz kommt. Die gefundene Erhöhung der Mutationsfrequenz war vor allem auf eine Erhöhung der G:C zu T:A Transversionen zurückzuführen, die typischerweise aus nicht repariertem 8 Hydroxyguanin (8-oxoG) entstehen. Aus mechanistischer Sicht verdeutlichen die Ergebnisse, dass OGG1 das primäre Abwehrsystem gegen oxidative DNA-Modifikationen darstellt und dass das CSB-Protein einen Ausfall von OGG1, selbst in nicht transkribierter DNA, teilweise kompensieren kann. Aus der Korrelation der gefundenen oxidativen DNA-Schäden - bestimmt mittels Alkalischer Elution und der bakteriellen Formamidopyrimidin-DNA-Glykosylase (Fpg-Protein) - mit der Mutationsfrequenz konnte abgeleitet werden, dass bereits weniger als 0,2 Fpg-sensitive DNA-Modifikationen pro 1 Million Basenpaare ausreichen, die spontane Mutationsfrequenz in vivo zu verdoppeln. Zur Untersuchung, welche Rolle die erhöhte Mutationsfrequenz bei der Krebsentstehung spielt, wurden Csb-/-/Ogg1-/- und Wildtyp-Mäuse mit dem Peroxisomenproliferator und spezifischem Leberpromotor WY-14,643 behandelt um spontan initiierte Hepatozyten zur Proliferation anzuregen. Als Endpunkt einer malignen Entartung wurde das Auftreten von Glucose-6-Phosphatase positiven und negativen Läsionen beobachtet. Es zeigte sich, dass Csb-/-/Ogg1-/- Mäuse signifikant mehr enzymveränderte Läsionen in ihren Lebern aufwiesen, als die Wildtyp-Kontrollen. Die Ergebnisse verdeutlichen, dass endogen gebildete oxidative DNA-Modifikationen und daraus resultierende Mutationen grundsätzlich einen erheblichen Anteil zur hohen spontanen Krebsinzidenz in der Bevölkerung leisten könnten.

From polymer precursors to metal oxides

We report on a strategy to prepare metal oxides including binary oxide and mixed metal oxide (MMO) in form of nanometer-sized particles using polymer as precursor. Zinc oxide nanoparticles are prepared as an example. The obtained zinc polyacrylate precursor is amorphous as confirmed by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The conversion from polymer precursor to ZnO nanocrystals by thermal pyrolysis was investigated by means of XRD, thermogravimetric analysis (TGA) and electron microscopy. The as-synthesized ZnO consists of many individual particles with a diameter around 40 nm as shown by scanning electron microscopy (SEM). The photoluminescence (PL) and electron paramagnetic (EPR) properties of the material are investigated, too. Employing this method, ZnO nanocrystalline films are fabricated via pyrolysis of a zinc polyacrylate precursor film on solid substrate like silicon and quartz glass. The results of XRD, absorption spectra as well as TEM prove that both the ZnO nanopowder and film undergo same evolution process. Comparing the PL properties of films fabricated in different gas atmosphere, it is assigned that the blue emission of the ZnO films is due to crystal defect of zinc vacancy and green emission from oxygen vacancy. Two kinds of ZnO-based mixed metal oxide (Zn1-xMgxO and Zn1-xCoxO) particles with very precise stoichiometry are prepared by controlled pyrolysis of the corresponding polymer precursor at 550 oC. The MMO crystal particles are typically 20-50 nm in diameter. Doping of Mg in ZnO lattice causes shrinkage of lattice parameter c, while it remains unchanged with Co incorporation. Effects of bandgap engineering are seen in the Mg:ZnO system. The photoluminescence in the visible is enhanced by incorporation of magnesium on zinc lattice sites, while the emission is suppressed in the Co:ZnO system. Magnetic property of cobalt doped-ZnO is checked too and ferromagnetic ordering was not found in our samples. An alternative way to prepare zinc oxide nanoparticles is presented upon calcination of zinc-loaded polymer precursors, which is synthesized via inverse miniemulsion polymerization of the mixture of the acrylic acid and zinc nitrate. The as-prepared ZnO product is compared with that obtained from polymer-salt complex method. The obtained ZnO nanoparticles undergo surface modification via a phosphate modifier applying ultrasonication. The morphology of the modified particles is checked by SEM. And stability of the ZnO nanoparticles in aqueous dispersion is enhanced as indicated by the zeta-potential results.