<p>The electronic structures of the nucleobases, 5-fluorouracil compounds, DNA, metallic DNA, and samples of boron nitride are investigated. Soft X-ray absorption (XAS) and emission (XES) spectroscopy using synchrotron radiation are used to probe the unoccupied and occupied partial densities of electronic states, respectively. Hartree-Fock and density functional theory calculations have been included to compare with experimental results.</p> <p>A systematic approach to understanding the complicated electronic structure of DNA and metallic DNA systems is to initially examine smaller components. Detailed experiment and theory for both absorption and emission spectroscopy was. performed for the nucleobases and 5-fluorouracil compounds. Main transitions in the XAS and XES spectra are identified. X-ray spectroscopy has proven to be extremely sensitive to changes in the environment of various DNA samples. The local chemical environment plays an important role in determining the electronic structure of DNA. In agreement with previous results indicating metallic DNA is more efficient at the transfer of electrons than DNA, XES measurements reveal that there are a higher number of charge carriers in the metallic system. Both liquid and powder samples of (Ni)·M-DNA are found to have a high spin Ni(II) configuration. The drying process significantly alters the electronic structure of the metallic DNA sample. A comparison of high quality single crystals and thin films of boron nitride found that differences between the electronic structures of the nanocrystalline films and the single crystal samples exist, and the surface roughness of the substrate plays an important role in determining the structure of the resulting deposited film.</p>

This Master's thesis deals with determination of nucleobases in formamide samples (pure or catalyzed form) after their initiation by high-power density energy events. The theoretical part states the reader to the problems of prebiotic chemistry and acquaints him with the various theories of the origin of the nucleobases. The experimental part deals with the analysis of the samples initiated by Laser System PALS, which was used for the simulation high-power density energy events. For the identification and determination of the final products of laser plasma initiated chemical reactions in the gaseous phase of the samples was used the Fourier Transform Infrared Spectroscopy. The liquid part of the samples and the nucleobases in this part were analyzed by the gas chromatography with the mass detection.

Diese Arbeit zeigt die Verwendung ueberkritischer Fluide als analytisches Werkzeug fuer den Transport einer Gruppe nichtfluechtiger Molekuele, naemlich Nucleobasen, in die Gasphase. Das am haeufigsten verwendete ueberkritische Fluid ist Kohlendioxid, welches sich jedoch als zu ineffizient bei der Aufloesung von Nucleobasen herausstellte. Deshalb wurde ein Gemisch aus Ethylen mit Ethanol als Cosolvens als ueberkritisches Loesungsmittel verwendet. Für die Erkennung des kritischen Punktes reiner Fluide oder verduennter Fluidmischungen wurde eine neue Methode entwickelt. Die Verschiebung des kritischen Punktes von Ethylen durch Zugabe von Ethanol wurde experimentell ermittelt und mit der Zustandsgleichung von Soave Redlich Kwong in Beziehung gesetzt. Fuer einen Molenbruch des Cosolvens Ethanol von 0.054 erhoeht sich die kritische Temperatur nur um 5,5 C, wohingegen die Theorie eine Erhoehung um 10 C vorhersagt. Fuenf biologisch relevante Nucleobasen wurden mit Hilfe von 3% Ethanol als Cosolvens in ueberkritischem Ethylen geloest. Die Zusammensetzung des Ueberschall-Molekularstrahles der expandierten Loesung wurde mit einem Quadrupol-Massenspektrometer quantitativ analysiert. Das Signalverhaeltnis der Nucleobasen zu Ethylen lag in der Groessenordnung von 10^-4 bis 10^-5. Diese Nucleobasen wurden auch auf Oberflaechen abgeschieden, sowohl durch Hochdruckexpansion der ueberkritischen Loesungen, als auch durch Verdampfung von alkoholischen Loesungen (nach der ’Drop Casting’ Methode). Die dabei entstehenden Morphologien wurden ex-situ mittels Rasterkraftmikroskopie untersucht. Die Ursachen dieser Unterschiede werden anhand der relevanten Nukleationsmechanismen diskutiert. / This work highlights the use of supercritical fluids (SCF) as an analytical tool for the transfer of a group of non-volatile molecules, namely nucleobases, into the gas phase. The most commonly used SCF carbon dioxide was found inefficient in dissolving the nucleobases. Therefore, a mixture of ethylene (p_c = 50.6 bar and T_c = 9.35 C) with a cosolvent was used as the SC solvent. A new bracketing method was developed for detecting the critical point (CP) of pure fluids and diluted mixtures of fluids. The shift in CP of ethylene on addition of ethanol was determined and related to theoretical calculations by using the Soave Redlich Kwong equation of state. Comparing the experimental results to theoretical methods for calculating the CP showed large deviations. The critical temperature shifted by only 5.5 C when the mole fraction of the cosolvent i.e. ethanol was 0.054. Five biologically relevant were dissolved in SC ethylene using 3% of ethanol as cosolvent. The supersonic molecular beam composition of the expanded solution was analyzed quantitatively using a quadrupole mass spectrometer and the ratio of the nucleobases to ethylene in the beam was found to be of the order of 10^-4 to 10^-5. Surface deposition of the nucleobases through SCF solutions was carried out and the morphology was recorded using Atomic Force Microscopy. Remarkable differences were observed while comparing the morphology obtained after deposition using rapid expansion of supercritical solutions (RESS) and drop casting method. These differences are discussed in terms of diffusion, rate of evaporation of the solvent, degree of supersaturation, and the nucleation process.

This thesis presents experimental and related theoretical studies of single layer graphene, bilayer graphene and single walled carbon nanotubes. The thesis is divided into three parts; the first part describes the phonon renormalization due to doping in two dimensional graphene and one dimensional carbon nanotubes. In the recent years, there is a tremendous interest both experimentally and theoretically, in the issues related to electron-phonon coupling in nanotubes and graphene. Theoretically, it is expected that the presence of Kohn anomalies in graphene and metallic nanotubes will result in significant changes in the self energy of phonons due to doping. In particular, with Fermi energy shift how the blockage of phonon decay (due to Pauli Exclusion Principle) into electron-hole excitations changes the phonon frequencies as well as its life time have been studied in details in the first part of the thesis. Since in graphene and metallic nanotubes, the momentum relaxation time of electrons is comparable to the phonon pulsation time, the phonon cannot be treated as a static perturbation and hence non-adiabatic effects are taken into account using time dependent perturbation theory. Electron-phonon coupling constant is also a key parameter to understand the mobility of carrier due to electron scattering by optical phonons at room temperature and limitation of the maximum current carrying capacity of graphene and nanotubes. All these parameters are determined in the first part of the thesis by performing in-situ transport and Raman measurements on graphene and nanotubes based field effect transistors. The second part of the thesis deals with the interaction of bio-molecules (nucleobases) with the nanotubes and graphene. The binding energies of various nucleobases with nanotubes and graphene have been calculated theoretically using quantum chemical and classical force field calculations, and experimentally from isothermal titration (micro) calorimetry. In this part we also present an experimental study on the dynamics of water confined inside the carbon nanotubes. Proton nuclear magnetic resonance studies have been used to probe the freezing and dynamics of the confined water inside 1.4 nm diameter single walled carbon nanotubes. We have observed that the confined water does not freeze up to 223K. The dynamics of confined water has been studied using pulsed field gradient technique. The decay of spin echo intensity as a function of gradient field shows characteristic features of water confined in unidimensional channels. From the decay profiles the mean squared displacement of water molecules is obtained for different diffusive times, showing an unambiguous evidence of single file diffusion of water molecules inside the nanotubes i.e mean squared displacement varying as square root of time. In the last part, we have developed carbon nanotube based vibration sensor and accelerometer to detect the vibrations of liquid and solid, respectively, using the property of voltage generation in nanotubes due to liquid flow.

This PhD thesis is focused on the synthesis of DNA modified with photocleavable 2- nitrobenzyl protecting groups in major groove and its applications in the regulation of gene expression in the level of transcription. In the first part of my thesis, the synthesis of photocaged 2'-deoxyribonucleosides triphosphates and their photolysis to unprotected 5-hydroxymethylated nucleotides is described. All prepared nucleoside triphosphates were good substrates for their enzymatic incorporation into DNA. Synthesized 5-(2-nitrobenzyloxy)methyl-2'-deoxyuridine-5'- monophosphate (dUNBMP) and DNA with one 5-(2-nitrobenzyloxy)methyl- modification in the sequence were used for the detailed kinetic studies of photocleavage reactions. In the second part of the thesis, the series of modified DNAs with specific sequences were prepared by primer extension (PEX) and/or polymerase chain reaction (PCR). A cleavage of prepared modified DNAs was studied by selected restriction endonucleases (REs). In all cases, the nitrobenzylated DNA fully resist the cleavage by REs. The deprotection/ photocleavage conditions for nitrobenzylated DNA were studied in the case of DNAs with positive restriction endonuclease digestion of hydroxymethylated DNA. The resulting photocleaved DNA was fully digested by REs, therefore 2-nitrobenzyl...

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