In the present work, the plasma repair for damaged ultra-low-k (ULK) materials, newly developed at the Fraunhofer ENAS, is studied with density functional theory (DFT) and molecular dynamic (MD) methods to obtain new insights into this repair mechanism. The ULK materials owe their low dielectric constant (k-value) to the insertion of k-value lowering methyl groups. During the manufacturing process, the ULK materials are damaged and their k-values increase due to the adsorbtion of hydroxyl groups (OH-damage) and hydrogen atoms (H-damage) that replaced themethyl groups. The first investigation point is the creation of repair fragments. For this purpose the silylation molecules bis(dimethylamino)-dimethylsilane (DMADMS) and octamethylcyclotetrasiloxane (OMCTS) are fragmented. Here, only fragmentation reactions that lead to repair fragments that contain one silicon atom and at least one methyl group were considered. It is shown that the repair fragments that contain three methyl groups are preferred, especially in a methyl rich atmosphere. The effectivity of the obtained repair fragments to cure an OH- and H-damage are investigated with two model systems. The first system consists of an assortment of small ULK-fragments, which is used to scan through the wide array of possible repair reactions. The second system is a silicon oxide cluster that investigates whether the presence of a cluster influences the reaction energies. In both model systems, repair fragments that contain three methyl groups or two oxygen atoms are found to be most effective. Finally, the quantum chemical results are compared to experimental findings to get deeper insight into the repair process.

In the present work, the plasma repair for damaged ultra-low-k (ULK) materials, newly developed at the Fraunhofer ENAS, is studied with density functional theory (DFT) and molecular dynamic (MD) methods to obtain new insights into this repair mechanism. The ULK materials owe their low dielectric constant (k-value) to the insertion of k-value lowering methyl groups. During the manufacturing process, the ULK materials are damaged and their k-values increase due to the adsorbtion of hydroxyl groups (OH-damage) and hydrogen atoms (H-damage) that replaced themethyl groups. The first investigation point is the creation of repair fragments. For this purpose the silylation molecules bis(dimethylamino)-dimethylsilane (DMADMS) and octamethylcyclotetrasiloxane (OMCTS) are fragmented. Here, only fragmentation reactions that lead to repair fragments that contain one silicon atom and at least one methyl group were considered. It is shown that the repair fragments that contain three methyl groups are preferred, especially in a methyl rich atmosphere. The effectivity of the obtained repair fragments to cure an OH- and H-damage are investigated with two model systems. The first system consists of an assortment of small ULK-fragments, which is used to scan through the wide array of possible repair reactions. The second system is a silicon oxide cluster that investigates whether the presence of a cluster influences the reaction energies. In both model systems, repair fragments that contain three methyl groups or two oxygen atoms are found to be most effective. Finally, the quantum chemical results are compared to experimental findings to get deeper insight into the repair process.:1. Introduction 2. Theoretical Background 2.1. Ultra-low-k Materials 2.1.1. Definition, Usage and Challenges 2.1.2. k-Restore 2.2. Reaction Theory 2.2.1. Reaction Process 2.2.2. Thermal Influence 3. Computational Methods 3.1. Overview 3.2. Density Functional Theory 3.2.1. Theoretical Background 3.2.1.1. The Schrödinger Equation and the Variational Principle 3.2.1.2. From the Electron Density to the Kohn-Sham Approach 3.2.1.3. Exchange-Correlation Functionals and Basis Sets 3.2.2. Used Program Packages 3.3. ReaxFF 3.3.1. Theoretical Background 3.3.2. Used Program Packages 4. Model System 4.1. Damaged ULK Materials 4.1.1. ULK-Fragments 4.1.2. Silicon Oxide Cluster 4.2. Repair Fragments 4.2.1. Overview 4.2.2. Fragmentation of DMADMS 4.2.3. Fragmentation of OMCTS 4.2.4. Continuing Reactions 5. Results and Discussion 5.1. Reactions between Repair Fragments and ULK-Fragments 5.1.1. Repair of OH-damages 5.1.2. Repair of H-damages 5.1.3. Selected Repair Reactions with Gaussian 5.2. Reactions Between Repair Fragments and Silicon Oxide Cluster 5.2.1. Comparison Between ULK-Fragments and Silicon Oxide Cluster 5.2.2. Comparability of DFT and MD Results 5.3. Comparison with Experimental Results 6. Summary and Outlook A. Appendix A.1. Temperature Influence . A.1.1. Temperature Influence on the DMADMS Fragmentation in Dmol3 A.1.2. Temperature Influence on the OMCTS Fragmentation in Dmol3 . A.2. Tests A.2.1. DMADMS Fragmentation with Gaussian A.2.2. G2 Test Set A.2.3. Calculation Time of the Silicon Oxide Cluster in Dmol3 A.3. Error Analysis A.3.1. Basis Set Superposition Error in Dmol3 A.3.2. Dispersion Correction A.4. Illustration of Defects A.5. Bookmark

Wird DNA mit UV-Licht bestrahlt, kommt es zur Bildung von Photoschäden, die zu Zelltod oder Krebs führen können. In dieser Arbeit wird die primäre Elektronentransferreaktion des lichtaktivierten Reparaturprozesses des (6-4)-Schadens in Drosophila melanogaster charakterisiert. Der katalytische Reparaturzyklus wird durch das Flavoprotein (6-4)-Photolyase (PL) realisiert. Der Elektronentransfer (ET) vom Flavin-Adenin-Dinukleotid (FADH⁻) Kofaktor zum Schaden initiiert die molekularen Umlagerungen. Diese Arbeit charakterisiert die primäre ET Reaktion mithilfe von molekulardynamischen Langzeitsimulationen (µs) in Kombination mit Quantenmechanik/Molekularmechanik-Simulationen. Ab initio lokale Coupled-Cluster- und Dichtefunktionaltheorierechnungen wurden angewendet, um die relative Energetik von lokal angeregten und Ladungstransferzuständen des (6-4)-Reparaturkomplexes zu charakterisieren. Es zeigt sich, dass die Reduktion des (6-4)-Schadens durch einen Ladungstransferzustand ermöglicht wird an dem die Adeninstruktur des FADH⁻ -Kofaktors beteiligt ist. Über die Simulationen wird ein mikroskopisches Bild der Reaktionskoordinate der Elektronentransferreaktion im Marcusbild entwickelt. Diese ist nicht vollständig durch parabolische freie Energiekurven beschrieben sondern wird, durch Wechselwirkungen in der aktiven Tasche, ein Multiminima-Reaktionspfad ausgebildet. Hierbei hat die Rotation der Seitenkette der benachbarten, geladenen Aminosäure Lys246 dominanten Einfluss. Dies legt nahe, dass die primäre ET Reaktion der (6-4) Schadensreparatur, einen vom Adenin unterstützten ET Weg von der PL zur 5’ Seite des Schadens nimmt. Dieser Prozess wird durch benachbarte Aminosäuren und einer Stärkung der Wasserstoffbrücken mit Wassermolekülen stabilisiert. Die Ergebnisse dieser Arbeit zeigen, dass ET-Reaktionen in komplexen enzymatischen Systemen nicht im Kontinuumsbild von ET beschrieben werden können, da lokale Wechselwirkungen drastischen Einfluss auf die ET Reaktionen haben. / UV-light irradiation of DNA leads to the formation of photolesions that can cause cell death and cancer. This thesis aims at the characterization of the primary electron transfer (ET) reaction in the photoactivated repair process of the (6-4) lesion in Drosophila melanogaster. The catalytic repair cycle is realized by a flavoprotein called photolyase (PL). The ET from the fully reduced flavin-adenine-dinucleotide (FADH⁻) cofactor of the PL to the lesion initiates molecular rearrangements. In this thesis fluctuation properties of the enzyme environment on the excited states are considered by conducting long-time (µs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical simulations. Ab initio local coupled cluster simulations and density functional theory are applied to characterize the relative energetics of locally excited and charge transfer (CT) states in the (6-4) lesion repair complex. Reduction of the (6-4) lesion is found to be enabled by a CT state involving the adenine moiety of the FADH⁻ cofactor. Microscopic characterization of a Marcus-type free energy reaction coordinate reveals that it cannot be fully described by parabolic free energy curves. Specifically, rotation of the side chain of nearby charged amino acid Lys246 imposes a double-well character on the potential energy surface along the reaction coordinate of the ET. For the ET reaction triggering the catalytic (6-4) lesion repair, the findings of this thesis suggest an ET pathway to the 5’ side of the (6-4) lesion mediated by the adenine moiety. The process is stabilized by neighboring amino acids and a strengthening of hydrogen bonds with water molecules. The presented results demonstrate that ET reactions in complex enzymatic systems cannot be described within the continuum ET picture, as local interactions drastically tune the ET reaction.