@phdthesis{Stepanenko2008,
  author    = {Stepanenko, Vladimir},
  title     = {Self-Assembly of Bay-Substituted Perylene Bisimide by Ligand-Metal Ion Coordination},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-32063},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {The subject of this thesis is the synthesis and characterization of PBI-based fluorescent metallosupramolecular polymers and cyclic arrays. Terpyridine receptor functionalized PBIs of predesigned geometry have been used as building blocks to construct desired macromolecular structures through metal-ion-directed self-assembly. These metallosupramolecular architectures have been investigated by NMR, UV/Vis and fluorescence spectroscopy, mass spectrometry, and atomic force microscopy.},
  subject      = {Supramolekulare Chemie},
  language  = {en}
}
@phdthesis{Stepanenko2008,
  author    = {Stepanenko, Svetlana},
  title     = {Global Optimization Methods based on Tabu Search},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-30605},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {This work encompasses three parts. The first part provides a concise review of the most prominent metaheuristic concepts currently available and gives essential preliminaries together with definition of the combinatorial optimization problems. It substantiates the choice of the investigation direction and basis idea of the developed methods. In the second part the new nonlinear global optimization routines based on the TS strategy are described. The new approaches are the Gradient Tabu Search (GTS), the Gradient Only Tabu Search (GOTS), and the Tabu Search with Powell's Algorithm (TSPA). In the last part of the work the GOTS is applied for such chemical optimization problems. The chapter provides a systematic approach how the variables are chosen and the adjustable parameters are set. As test cases the global minimum energy conformation of some amino acids, of two angiotensin converting enzyme (ACE) inhibitors, of 2-acetoxy-N,N,N-trimethylethanaminium, and of a HIV-1 protease inhibitor is determined.},
  subject      = {Tabusuche},
  language  = {en}
}
@phdthesis{Schmidt2008,
  author    = {Schmidt, R{\"u}diger},
  title     = {Perylene Bisimide and Acene Derivatives as Organic Semiconductors in OTFTs},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29314},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {This thesis deals with the synthesis of improved organic semiconductors, the detailed investigation of the molecular properties and the solid state arrangements revealed by single crystal X-ray diffraction and finally the development of structureperformance dependencies by measuring of the charge carrier mobilities of the derivatives in thin film transistors. The two main-goals of this thesis were achieved. Well soluble acene derivatives for spin-coated TFTs were obtained, showing charge carrier mobilities in the range of polymer p-type materials. Novel core-fluorinated perylene bisimide dyes were synthesized particularly and the use of electron deficient substituents lead to PBIs with outstanding air-stable mobilities in thin film transistors prepared by vacuum deposition techniques. The relationship between performance, air stability and solid state packing was elucidated in detail by single crystal X-ray diffraction analysis.},
  subject      = {D{\"u}nnschichttransistor},
  language  = {en}
}
@phdthesis{Rehm2008,
  author    = {Rehm, Thomas Helge},
  title     = {A Guide to Supramolecular Assemblies in Polar Solutions - From Nanometre-Sized Cyclic Dimers to Large Vesicular Structures},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-28359},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {This PhD thesis introduced several concepts for the construction of new supramolecular assem-blies in polar solvents. Although the building blocks differ in their binding mode and association strength they follow the same principle: one main driving force for the self-assembly in polar solutions in combination with one texturing force. The main self-assembly process is based on the mutual interaction of hydrogen-bond enforced ion pairs which deliver the association energy needed for stable, supramolecular structures even in polar solvents. The texturing force itself is represented by the linkers between the zwitterionic building blocks or parts of them. The different length and functionalization of the linkers have a tremendous influence on the mode of self-assembly leading to cyclic dimers, vesicles, layers or solid spheres. Hence, this principle is suitable for the construction of programmable monomers. Since the derivatisation of the main binding motive is rather simple it offers a great number of new and undoubtedly fascinating structures with potential applications in material and biomimetic science.},
  subject      = {Supramolekulare Chemie},
  language  = {en}
}
@phdthesis{Mladenovic2008,
  author    = {Mladenovic, Milena},
  title     = {Theoretical Investigation into the Inhibition of Cystein Proteases},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-25763},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {Although known about and investigated since the late 1970's, the picture of the basic principles governing inhibitor strengths and the structure-activity relationships of the cysteine protease inhibition mechanism is still very incomplete. Computational approaches can be a very useful tool for investigating such questions, as they allow the inspection of single, specific effects in isolation from all others, in a manner very difficult to achieve experimentally. The ab initio treatments of such large systems like proteins are still not feasible. However, there is a vast number of computational approaches capable of dealing with protein structures with reasonable accuracy. This work presents a summary of theoretical investigations into cysteine protease cathepsin B using a range of methods. We have concentrated on the investigation of cysteine protease inhibition by epoxide- and aziridine-based inhibitors in order to obtain better insight into these important topics. Various model systems are simulated by means of pure quantum mechanical methods and by hybrid (QM/MM) methods. Both approaches provide a static picture. Dynamical effects are then accounted for by additional molecular dynamics (MD) simulations, using both classical and QM/MM MD approaches. The quantum mechanical approach was used to study very small model systems consisting only of the electrophilic warhead of the inhibitor (both substitituted and not) and molecular moieties simulating a very simplified protein active site (methylthiolate instead of Cys29 and methylimidazolium instead of His199 residue) and solvent surroundings (two waters or two ammonium ions, in combination with a continuum solvent model). Although simple, such a system provides a good description of the most important interactions involved in the inhibition reaction. It also allows investigation of the influence of the properties of the electrophilic warhead on the reaction rate. Beside the properties of the electrophilic warhead, the protein and solvent environment is also an important factor in the irreversible deactivation of the enzyme active site by the inhibitor. The non-covalent interactions of the inhibitor with the oxyanion hole and other subsites of the enzyme, as well as its interaction with the solvent molecules, need to be explicitly taken into account in the calculations, because of their possible impact on the reaction profile. As molecular modeling methods allow the treatment of such large systems, but lack the possibility of describing covalent interactions, our method of choice was the combined quantum mechanics/molecular modeling approach. By splitting the system into a smaller part that undergoes the bond cleavage/formation process and must be treated quantum mechanically, and a larger part, comprised of the rest of the protein, which could be treated using force fields, we managed to simulate the system at the desired precision. Our investigations concentrated on the role of His199 in the inhibition mechanism as well as on the structure-reactivity relationships between cysteine protease and various inhibitors, yielding new insight into the kinetics, regio- and stereospecificity of the inhibition. In particular, our calculations provide the following insights: i.) an explanation for the regioselectivity of the reaction, and original insight into which interactions affect the stereoselectivity; ii.) a clear model which explains the known structure-activity relationships and connects these effects with the pH-dependency of the inhibition; iii.) our computations question the generally accepted two-step model by showing that substituent effects accelerate the irreversible step to such an extent that the achievement of an equilibrium in the first step is doubtful; iv.) by way of theoretical characterizations of aziridine models, the reasons for similarities and differences in the mode of action of epoxide- and aziridine-based inhibitors are elucidated; and finally, v.) combining our results with experimental knowledge will allow rational design of new inhibitors. To account for dynamical effects as well, molecular dynamics (MD) computations were also performed. In these calculations the potential energy was computed at the force field level. The results not only supported and clarified the QM/MM results, but comparison with previous X-ray structures helped correct existing errors in the available geometrical models and resolved inconsistencies in the weighting of various factors governing the inhibition. In the work the first QM/MM MD calculations on the active site of the cysteine proteases are presented. In contrast to the MD simulations, these calculations used potential energies computed at the QM/MM-level. With the help of these computations we sought to address strongly disputed questions about the reasons for the existence of the active site ion pair and its role in the high activity of the enzyme.},
  subject      = {Quantenchemie},
  language  = {en}
}
@phdthesis{Lohr2008,
  author    = {Lohr, Andreas},
  title     = {Self-Assembly of Merocyanines : Thermodynamic and Kinetic Insights into the Formation of Well-Defined Dye Aggregates},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-28964},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {The present thesis demonstrates the potential of dipolar aggregation of merocyanine dyes as novel directional and specific supramolecular binding motif for the creation of more elaborate supramolecular architectures beyond simple dimers. Furthermore, the self-assembly studies into bis(merocyanine) nanorods gave new insights into the kinetics of morphogenesis in supramolecular aggregates.},
  subject      = {Supramolekulare Chemie},
  language  = {en}
}