@phdthesis{Vogt2020, author = {Vogt, Matthias Guido}, title = {Elektronische Eigenschaften von Wabengittern mit starker Spin-Bahn-Kopplung}, doi = {10.25972/OPUS-20750}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-207506}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2020}, abstract = {Im Rahmen dieser Arbeit wurden die elektronischen Eigenschaften von Graphen auf Metalloberfl{\"a}chen mittels Rastertunnelmikroskopie und Quasiteilcheninterferenz (englisch quasiparticle interference, QPI)-Messungen untersucht. Durch das Verwenden schwerer Substrate sollte die Spin-Bahn-Wechselwirkung des Graphen verst{\"a}rkt werden und damit eine Bandl{\"u}cke am K-Punkt der Bandstruktur mittels QPI beobachtet werden. Um das Messen von QPI auf Graphen zu testen, wurde auf der Oberfl{\"a}che eines SiC(0001)-Kristalls durch Erhitzen Graphen erzeugt und mit dem Rastertunnelmikroskop untersucht. Dieses System wurde schon ausf{\"u}hrlich in der Literatur beschrieben und bereits bekannte QPI-Messungen von Streuringen, die auf den Dirac-Kegeln des Graphen am K-Punkt basieren, konnte ich auf gr/SiC(0001) in guter Qualit{\"a}t erfolgreich reproduzieren. Anschließend wurde Graphen nach einem wohlbekannten Verfahren durch Aufbringen von Ethylen auf ein erhitztes Ir(111)-Substrat erzeugt. Dieses gr/Ir(111)-System diente auch als Grundlage f{\"u}r Interkalationsversuche von Bismut (gr/Bi/Ir(111)) und Gadolinium (gr/Gd/Ir(111)) zwischen das Graphen und das Substrat. Auf gr/Bi/Ir(111) wurde ein schon aus der Literatur bekanntes Netzwerk aus Versetzungslinien beobachtet, dem zus{\"a}tzlich eine Temperaturabh{\"a}ngigkeit nachgewiesen werden konnte. Beim Versuch, Gadolinium zu interkalieren, wurden zwei verschieden Oberfl{\"a}chenstrukturen beobachtet, die auf eine unterschiedlich Anordnung bzw. Menge des interkalierten Gadoliniums zur{\"u}ckzuf{\"u}hren sein k{\"o}nnten. Auf keinem dieser drei Systeme konnten allerdings Streuringe mittels QPI beobachtet werden. Als Vorbereitung der Interkalation von Gadolinium wurden dessen Wachstum und magnetische Eigenschaften auf einem W(110)-Kristall untersucht. Dabei konnte eine aus der Literatur bekannte temperaturabh{\"a}ngige Austauschaufspaltung reproduziert werden. Dar{\"u}ber hinaus konnten sechs verschieden magnetische Dom{\"a}nen beobachtet werden. Zus{\"a}tzlich sind auf der Oberfl{\"a}che magnetische Streifen auszumachen, die m{\"o}glicherweise auf einer Spinspirale basieren. Als Grundlage f{\"u}r die m{\"o}gliche zuk{\"u}nftige Erzeugung Graphen-artiger Molek{\"u}lgitter wurde das Wachstum von H-TBTQ und Me-TBTQ auf Ag(111) untersucht. Die Molek{\"u}le richten sich dabei nach der Oberfl{\"a}chenstruktur des Silber aus und bilden l{\"a}ngliche Inseln, deren Kanten in drei Vorzugsrichtungen verlaufen. Auf H-TBTQ wurde zudem eine zweite, Windm{\"u}hlen-artige Ausrichtung der Molek{\"u}le auf der Oberfl{\"a}che beobachtet. Auf den mit den Molek{\"u}len bedeckten Stellen der Oberfl{\"a}che wurde eine Verschiebung des Ag-Oberfl{\"a}chenzustands beobachtet, die mit einem Ladungstransfer vom Ag(111)-Substrat auf die TBTQ-Molek{\"u}le zu erkl{\"a}ren sein k{\"o}nnte.}, subject = {Spin-Bahn-Wechselwirkung}, language = {de} } @phdthesis{Brueckner2017, author = {Br{\"u}ckner, Charlotte}, title = {The Electronic Structure and Optoelectronic Processes at the Interfaces in Organic Solar Cells Composed of Small Organic Molecules - A Computational Analysis of Molecular, Intermolecular, and Aggregate Aspects}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-141652}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Describing the light-to-energy conversion in OSCs requires a multiscale understanding of the involved optoelectronic processes, i.e., an understanding from the molecular, intermolecular, and aggregate perspective. This thesis presents such a multiscale description to provide insight into the processes in the vicinity of the organic::organic interface, which are crucial for the overall performance of OSCs. Light absorption, exciton diffusion, photoinduced charge transfer at the donor-acceptor interface, and charge separation are included. In order to establish structure-property relationships, a variety of different molecular p-type semiconductors are combined at the organic donor-acceptor heterojunction with fullerene C60, one of the most common acceptors in OSCs. Starting with a comprehensive analysis of the accuracy of diverse ab initio, DFT, and semiempiric methods for the properties of the individual molecules, the intermolecular, and aggregate/device stage are subsequently addressed. At all stages, both methodological concepts and physical aspects in OSCs are discussed to extend the microscopic understanding of the charge generation processes.}, subject = {Benchmark}, language = {en} } @phdthesis{Heilos2019, author = {Heilos, Anna}, title = {Mechanistic Insights into the Inhibition of Cathepsin B and Rhodesain with Low-Molecular Inhibitors}, doi = {10.25972/OPUS-17822}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178228}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2019}, abstract = {Cysteine proteases play a crucial role in medical chemistry concerning various fields reaching from more common ailments like cancer and hepatitis to less noted tropical diseases, namely the so-called African Sleeping Sickness (Human Arfican Trypanosomiasis). Detailed knowledge about the catalytic function of these systems is highly desirable for drug research in the respective areas. In this work, the inhibition mechanisms of the two cysteine proteases cathepsin B and rhodesain with respectively one low-molecular inhibitor class were investigated in detail, using computational methods. In order to sufficiently describe macromolecular systems, molecular mechanics based methods (MM) and quantum mechanical based method (QM), as well as hybrid methods (QM/MM) combining those two approaches, were applied. For Cathespin B, carbamate-based molecules were investigated as potential inhibitors for the cysteine protease. The results indicate, that water-bridged proton-transfer reactions play a crucial role for the inhibition. The energetically most favoured pathway (according to the calculations) includes an elimination reaction following an E1cB mechanism with a subsequent carbamylation of the active site amino acid cysteine. Nitroalkene derivatives were investigated as inhibitors for rhodesain. The investigation of structurally similar inhibitors showed, that even small steric differences can crucially influence the inhibition potential of the components. Furthermore, the impact of a fluorination of the nitroalkene inhibitors on the inhibition mechanism was investigated. According to experimental data measured from the working group of professor Schirmeister in Mainz, fluorinated nitroalkenes show - in contrast to the unfluorinated compounds - a time dependent inhibition efficiency. The calculations of the systems indicate, that the fluorination impacts the non-covalent interactions of the inhibitors with the enzymatic environment of the enzyme which results in a different inhibition behaviour.}, subject = {Cysteinproteasen}, language = {en} } @phdthesis{Bellinger2016, author = {Bellinger, Daniel}, title = {Implementation of new reaction pathway determining methods and study of solvent effects on the excited state nature of perylene based dyes}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144435}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Two thematic complexes were addressed within this work. One part is related to improvements and new implementations into the CAST program package. Thereby the main focus laid on the delivery of a tool which can be used to characterize complex reactions and their mechanisms. But also within the new force field (FF) method (SAPT-FF) within the CAST program, several improvements were made. The second topic is related to the description of dye molecules and their spectral properties. The main focus within these studies was set on the influence of the environment on these properties. In the first topic improvements of the local acting NEB (nudged elastic band) methods were included and the number of available methods was extended. The initial pathway generation was improved by implementing the IDPP (image dependent pair potential) method and a new method was implemented for describing temperature dependent pathways. Additionally, improvements have been made to the optimization routines (global NEB). As a second part the Pathopt (PO) method was considerably improved. In the beginning of the work the original PO idea was used. In this approach one starts with a global optimization on one n-1 dimensional hyperplane which divides the reaction into two sub-areas for obtaining guesses of TSs (transition states). These found TS guesses were used to optimize to the "true" TS. Starting from the optimized ones a relaxation to the next connected minima is done. This idea has been automatically implemented and extended to several number of hyperplanes. In this manner a group of pathsegments is obtained which needs to be connected, but within this work it was realized that such a procedure might be not very efficient. Therefore, a new strategy was implemented which is founded on the same constrained global optimization scheme (MCM) for which the user defines the number of hyperplanes generated. The number of such generated hyperplanes should be large enough 134 to describe the space between the concerning reactants in a sufficient way. The found minima are directly used to built up the reaction pathway. For this purpose a RMSD (root mean square deviation) criterion is used to walk along ways of minimal change from one to another hyperplane. To prove the implementations various test calculations were carried out and extensions included to prove the capabilities of the new strategy. Related to these tests a new strategy for applying the move steps in MCM (Monte Carlo with minimization) was realized which is also related to the question of the coordinates representation. We were able to show that the hopping steps in MCM can be improved by applying Cartesian steps in combination of random dihedral moves with respect to the constraint. In this way it was possible to show that a large variety of systems can be treated. An additional chapter shows the improvements of the SAPT-FF implementation and related test cases. It was possible to treat benzene dimer and cluster systems of different sizes consistently also in accordance with high level ab initio based approaches. Furthermore, we showed that the SAPT-FF with the right parameters outperforms the standard AMOEBA implementation which is the basis of the SAPT-FF implementation. In the last three chapters deal with the description of perlyene-based dyes. In the first smaller chapter ground state chemistry description of macro cycles of PBI (perylene bisimide) derivatives were investigated. Therefore, AFM (atomic force microscopy) based pictures were explained within our study. The methods to explain aggregation behavior in dependency of the ring size were MD simulations and configuration studies. The last two chapters deal with opto-electronic or photo-physical properties of PBI and PTCDA (perylene-3,4,9,10-tetracarboxylic dianhydride). In detail, we investigated the role of the environment and the aggregate or crystal surrounding by applying different models. In that way implicit and explicit solvation models, the size of aggregates and vibration motions were used. In the case of PBI the recent work is found on preliminary studies related to my bachelor thesis and extends it. It was shown that the direct influence of a polarizable surrounding, as well as explicit inclusion of solvent molecules on the overall description of the excitations and nature of the excited states is weaker as one might expect. However the inclusion of intra-molecular degrees of freedom showed a stronger influence on the state characteristics and can induce a change of the order of states within the dimer picture. For the PTCDA molecule the main focus was set on the description of the absorption spectrum of crystalline thin films. Related to this older works exist which already gave a description and assignment of the absorption band, but are based on different approaches compared to the one used in this work. We used the supermolecule ansatz, whereas the environment and different aggregate sizes were investigated. Within the dimer based approach we were able to show that using continuum solvation (IEFPCM/COSMO) based description for the environment the relative order of states remains unchanged. Similar to the PBI calculations the influence of the vibrational motions /distortions is larger. The simulation of the crystal environment by using QM/MM (quantum mechanics/molecular mechanics) approaches delivered that an asymmetric charge distribution might induce a localization of the excitation and a stronger mixing of states. For obtaining further insights we go beyond the dimer picture and aggregates of different sizes were used, whereas the simulations up to the octadecamer mono- and even dual-layer stack were carried out. Within these calculations it was shown that the H-coupling is dominating over a weaker J-coupling between different stacks. Additionally the calculations based on DFT (density functional theory) and semi-empirics showed that the lowest state in terms of energy are mostly of Frenkel type, whereas the higher lying states are CT ones which mix with embedded Frenkel type states. The first band of the absorption spectrum was explained by inclusion of vibrational motions within the stacks which induce an intensity gain of the first excited state. This intensity was not explainable by using the undistorted stacks. Also relaxations at the crystal surface might play a role, but are experimentally not explainable.}, subject = {Globale Optimierung}, language = {en} } @phdthesis{Le2020, author = {Le, Thien Anh}, title = {Theoretical investigations of proton transfer and interactions or reactions of covalent and non-covalent inhibitors in different proteins}, doi = {10.25972/OPUS-17051}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170511}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2020}, abstract = {Nowadays, computational-aided investigations become an essential part in the chemical, biochemical or pharmaceutical research. With increasing computing power, the calculation of larger biological systems becomes feasible. In this work molecular mechanical (MM) and quantum mechanical approaches (QM) and the combination of both (QM/MM) have been applied to study several questions which arose from different working groups. Thus, this work comprises eight different subjects which deals with chemical reactions or proton transfer in enzymes, conformational changes of ligands or proteins and verification of experimental data. This work firstly deals with reaction mechanisms of aromatic inhibitors of cysteine proteases which can be found in many organisms. These enzymes are responsible for various cancer or diseases as for example Human African Trypanosomiasis (HAT) or the Chagas disease. Aromatic SNAr-type electrophiles might offer a new possibility to covalently modify these proteases. Quantum mechanical calculations have been performed to gain insights into the energetics and possible mechanisms. The next chapter also deals with Trypanosomiasis but the focus was set on a different enzyme. The particularity of Trypanosomiasis is the thiol metabolism which can also be modified by covalent inhibitors. In this context, the wild type and point mutations of the enzyme tryparedoxin have been investigated via molecular dynamic (MD) simulations to examine the influence of specific amino acids in regard to the inhibitor. Experimental data showed that a dimerization of the enzyme occurs if the inhibitor is present. Simulations revealed that the stability of the dimer decreases in absence of the inhibitor and thus confirms these experiments. Further investigations concerning cysteine proteases such as cruzain and rhodesain have been conducted with respect to experimental kinetic data of covalent vinylsulfone inhibitors. Several approaches such as QM or QM/MM calculations and docking, MD or MMPBSA/MMGBSA simulations have been applied to reproduce these data. The utilization of force field approaches resulted in a qualitatively accurate prediction. The kinase AKT is involved in a range of diseases and plays an important role in the formation of cancer. Novel covalent-allosteric inhibitors have been developed and crystallized in complex with AKT. It was shown that depending on the inhibitor a different cysteine residue is modified. To investigate these differences in covalent modification computational simulations have been applied. Enoyl-(acyl carrier) (ENR) proteins are essential in the last step of the fatty acid biosynthesis II (FAS) and represent a good target for inhibition. The diphenylether inhibitor SKTS1 which was originally designed to target the ENR's of Staphylococcus aureus was also crystallized in InhA, the ENR of Mycobacterium tuberculosis (TB). Crystal structures indicate a change of the inhibitor's tautomeric form. This subject was investigated via MD simulations. Results of these simulations confirmed the tautomerization of the inhibitor. This work also deals with the development of a covalent inhibitor originating from a non-covalent ligand. The target FadA5 is an essential enzyme for the degradation of steroids in TB and is responsible for chronic tuberculosis. This enzyme was crystallized in complex with a non-covalent ligand which served as starting point for this study. Computations on QM or QM/MM level and docking and MD simulations have been applied to evaluate potential candidates. The next chapter focuses on the modification of the product spectrum of Bacillus megaterium levansucrase, a polymerase which catalyzes the biosynthesis of fructans. The covalent modification of the wild type or mutants of the enzyme lead to an accumulation of oligosaccharides but also to polymers with higher polymerization degree. To understand these changes in product spectra MD simulations have been performed. Finally, the proton transfer in catalytic cysteine histidine dyads was investigated. The focus was set on the influence of the relaxation of the protein environment to the reaction. Calculations of the enzymes FadA5 and rhodesain revealed that the preferred protonation state of the dyade depends on the protein environment and has an impact on the reaction barrier. Furthermore, the adaptation of the environment to a fixed protonation state was analyzed via MD simulations.}, subject = {Computational chemistry}, language = {en} } @phdthesis{Welz2020, author = {Welz, Eileen}, title = {Theoretical Investigations on Inorganic, Boron-containing Biradicals with a unique Structure}, doi = {10.25972/OPUS-20259}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-202598}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2020}, abstract = {In this work, biradical boron containing systems with various structures are investigated to reveal the dependency of the biradical character on the ligated carbene (NHC, CAAC) and the related steric demands of the substituents.}, subject = {Biradical}, language = {en} } @phdthesis{Deissenberger2020, author = {Deißenberger, Andrea}, title = {Dibortetrahalogenide f{\"u}r die Darstellung neuer borhaltiger Verbindungen in niedrigen Oxidationsstufen}, doi = {10.25972/OPUS-18775}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-187758}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2020}, abstract = {Im Rahmen dieser Arbeit konnten nasschemische Synthesen f{\"u}r Dibortetrafluorid und chlorid ausgehend von Dibortetrabromid entwickelt werden, die durch einfachen Halogenaustausch mit SbF3 bzw. GaCl3 realisiert wurden. In Verbindung mit Arbeiten von Dr. Jonas M{\"u}ssig zur Synthese von B2I4 gelang die Darstellung aller vier Dibortetrahalogenide mittels einfacher Schlenktechnik basierend auf der Synthese von B2Br4 durch N{\"o}th und Pommerening im Jahr 1981. Dibortetrachlorid konnte mit Phosphanen (PMe3, PCy3 und PPh3) und Singulett-Carbenen (IDipp und MeCAAC) zu den klassischen Bisaddukten 44-46 bzw. 54 und 55 umgesetzt werden. Die Addition eines Isonitrils (CNtBu) an B2Cl4 f{\"u}hrte zun{\"a}chst zur Ausbildung des Bisadduktes 53, allerdings konnte in L{\"o}sung eine Umlagerung beobachtet werden, deren Verlauf 11B-NMR-spektroskopisch verfolgt wurde, jedoch nicht final aufgekl{\"a}rt werden konnte. Durch die Zugabe eines Unterschusses der Lewis-Basen IDipp bzw. PCy3 sollten zun{\"a}chst Monoaddukte von B2Cl4 dargestellt werden, deren Umsetzung mit einer weiteren Lewis-Base die Synthese asymmetrischer Lewis-Basen-Addukte von B2Cl4 erm{\"o}glichen sollte. Die sp2-sp3-Diborane 56 und 57 konnten bei tiefen Temperaturen 11B-NMR-spektroskopisch nachgewiesen werden, allerdings f{\"u}hrte eine Abfangreaktion mit diversen Lewis-Basen nicht zu den gew{\"u}nschten asymmetrischen Addukten. Bei Raumtemperatur konnte eine Folgereaktion von 56 zur Chlorid-verbr{\"u}ckten kationischen Spezies 58 mit einem Tetrachloroborat-Anion beobachtet werden. Im Fall von Dibortetrafluorid konnten keine Lewis-Basen-Addukte (LB = PMe3 und MeCAAC) isoliert werden. Die Reaktivit{\"a}t von B2Cl4 gegen{\"u}ber unges{\"a}ttigten Substraten wurde anhand mehrerer literaturbekannter Beispiele (Acetylen, 2-Butin, 3-Hexin, Diphenylacetylen und Bis(trimethylsilyl)acetylen) nachvollzogen und um die terminalen Alkine Propin und 1 Hexin erweitert. Eine selektive Addition von B2Br4 an Dreifachbindungen gelang nicht. Die so erhaltenen Diborylalkene sollten zur Darstellung von 1,2-Diboreten genutzt werden, wobei zun{\"a}chst {\"u}ber eine von Siebert et al. entwickelte Route die Bis(N,N-dialkylaminochlorboryl)alkene 67g, h, j und k dargestellt wurden. Ein nachfolgender Ringschluss unter reduktiven Bedingungen verlief nur f{\"u}r die Diisopropyl¬amino-substituierten Diborylalkene 67g und j selektiv und lieferte das 1,2-Dihydro-1,2-diboret 71g und das umgelagerte 1,3-Dihydro-1,3-diboret 68j. Der Austausch der Aminosubstituenten gegen Halogenide, der f{\"u}r eine weitere Reduktion zur B-B-Doppelbindung n{\"o}tig w{\"a}re, gelang nicht. Die Umsetzung der Diborylalkene 61 (R = Me), 62 (R = Et) und 65 (R = Ph) mit Singulett-Carbenen (LB = IMe, IiPr, IDipp und MeCAAC) f{\"u}hrte zu den chloridverbr{\"u}ckten Monoaddukten 74-76 und 79-81. Alle Verbindungen dieses Typs zeigten in NMR-spektroskopischen Untersuchungen ein sp2- und ein sp3-koordiniertes Borzentrum, welche f{\"u}r die CAAC-stabilisierten Verbindungen auch r{\"o}ntgenkristallografisch nachgewiesen werden konnten. Theoretische Untersuchungen best{\"a}tigten die Relevanz des verbr{\"u}ckenden Chloratoms zur Stabilisierung dieser Verbindungen. F{\"u}r die Stammverbindung der Diborylalkene (59 (R = H)) konnte bei der Umsetzung mit MeCAAC eine unl{\"o}sliche Verbindung erhalten werden, deren Struktur als Bisaddukt 82 mittels NMR-spektroskopischen Untersuchungen im Festk{\"o}rper und durch Verbrennungsanalyse best{\"a}tigt werden konnte. Die Reduktion der CAAC-stabilisierten Diborylalkene 79 und 80 in Gegenwart von MeCAAC f{\"u}hrte zu den captodativ-stabilisierten Diborylradikalen 83 und 84, deren Strukturanalyse eine orthogonale Anordnung der C2-Br{\"u}cke zur B(CAAC)-Einheit offenlegt. Ausf{\"u}hrliche EPR-spektroskopische Untersuchungen bei variabler Temperatur und theoretische Berechnungen best{\"a}tigen eine schwache Wechselwirkung der beiden Radikalzentren und einen offenschaligen Singulett-Grundzustand mit einem energetisch tiefliegenden Triplett-Zustand (ΔES T = 0.017 kcal mol-1). Der experimentell bestimmte Spin-Spin-Abstand und die Analyse der einfach besetzten Molek{\"u}lorbitale (SOMO) best{\"a}tigen eine Delokalisierung der Spindichte {\"u}ber die NCAAC-CCAAC-B-Einheit. Der Austausch der verbr{\"u}ckenden Einheit und die somit einhergehende Verringerung der Sterik f{\"u}hrt zu einer Planarisierung des Molek{\"u}ls im Festk{\"o}rper (87). Theoretische Untersuchungen und die Auswertung der strukturellen Parameter ergeben eine Delokalisierung der Elektronendichte {\"u}ber das gesamte planare System. EPR- und NMR-spektroskopische Untersuchungen ergaben dennoch Hinweise auf das Vorliegen einer paramagnetischen Verbindung. Untersuchungen zum Reduktionsverhalten von zweifach CAAC-stabilisiertem 1,4-Bis-(dibromboryl)benzol (97) ergaben die vollst{\"a}ndige Enthalogenierung der Borzentren. Im Zuge dessen entstand ein hochreaktives, lineares Borylen, welches eine CH-Aktivierung mit dem Isopropylsubstituenten des CAAC-Liganden eingeht (98). Zur Stabilisierung des Borylens wurde die Reduktion in Gegenwart weiterer Lewis-Basen (Pyridin (Pyr), IiPr, IMeMe, PMe3, CNtBu und CO) durchgef{\"u}hrt, die in der Ausbildung der Diborylene 99-104 resultierten. Die Darstellung einer para-Phenylen-verbr{\"u}ckten Donor-Akzeptor-Verbindung (D: Borylen, A: BMes2) gelang nicht.}, subject = {Dibortetrahalogenide}, language = {de} } @phdthesis{Walter2015, author = {Walter, Christof}, title = {Excitonic States and Optoelectronic Properties of Organic Semiconductors - A Quantum-Chemical Study Focusing on Merocyanines and Perylene-Based Dyes Including the Influence of the Environment}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123494}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {The scope of computational chemistry can be broadened by developing new methods and more efficient algorithms. However, the evaluation of the applicability of the methods for the different fields of chemistry is equally important. In this thesis systems with an unusual and complex electronic structure, such as excitonic states in organic semiconductors, a boron-containing bipolaron and the excited states of pyracene were studied and the applicability of the toolkit of computational chemistry was investigated. Concerning the organic semiconductors the focus was laid on organic solar cells, which are one of the most promising technologies with regard to satisfying the world's need for cheap and environmentally sustainable energy. This is due to the low production and material costs and the possibility of using flexible and transparent devices. However, their efficiency does still not live up to the expectations. Especially the exciton diffusion lengths seem to be significantly too short. In order to arrive at improved modules, a fundamental understanding of the elementary processes occurring in the cell on the molecular and supramolecular level is needed. Computational chemistry can provide insight by separating the different effects and providing models for predictions and prescreenings. In this thesis, the focus was laid on the description of excitonic states in merocyanines and perylene-based dyes taking the influence of the environment into account. At first, the photochemical isomerization between two configurations of 6-nitro BIPS observed experimentally was studied by first benchmarking several functionals against SCS-ADC(2) in the gas phase and subsequently calculating the excited-state potential energy surface. The geometries obtained from a relaxed scan in the ground state as well as from a scan in the excited state were used. The environment was included using different polarizable continuum models. It was shown that the choice of the model and especially the question of the state specificity of the approach is of vital importance. Using the results of the calculations, a two-dimensional potential energy surface could be constructed that could be used to explain the experimental findings. Furthermore, the importance of the excited-state isomerization as a potential deactivation channel in the exciton transport was pointed out. Then the assessment of the suitability of different merocyanines for optoelectronic applications with quantum-chemical methods was discussed. At first, the effect of the environment on the geometry, especially on the bond length alternation pattern, was investigated. It was shown that the environment changes the character of the ground-state wave function of several merocyanines qualitatively, which means that the results of gas-phase calculations are meaningless - at least when a comparison with solution or device data is desired. It was demonstrated that using a polarizable continuum model with an effective epsilon, a qualitative agreement between the calculated geometry and the geometry in the crystal structure can be obtained. Therefore, by comparing the bond length alternation in solution and in the crystal, a rough estimate of the effect of the crystal environment can be made. It was further shown that the connection between the HOMO energy and the open-circuit voltage is not as simple as it is often implied in the literature. It was discussed that it is not clear whether the HOMO of a single molecule or a \$\pi\$-stack containing several monomers should be used and if the environmental charges of the bulk phase or the interface should be included. Investigating the dependence of the HOMO energy on the stack size yielded no definitive trend. Furthermore, it was discussed that the effect due the optimization of the modules (solvent, bulk heterojunction) during the production masks any potential correlation between the HOMO energy and measured open-circuit values. Therefore, a trend can only be expected for unoptimized bilayer cells. It was concluded that ultimately, the importance of the HOMO energy should not be overestimated. The correlation between the exciton reorganization energy and the so-called cyanine limit, which is predicted by a simple two-state model, was also discussed. By referring to the results of VB calculations, it was discussed that the correlation indeed exists and is non-negligible, although the effect is not as strong as one might have expected. In this context, a potential application of a VB/MM approach was covered briefly. The importance of the molecular reorganization energy and the device morphology was also discussed. It was concluded that the optimization of merocyanines for organic optoelectronic devices is inherently a multiparameter problem and one cannot expect to find one particular parameter, which solely controls the efficiency. The perylene-based dyes were studied with a focus on the description of a potential trapping mechanism involving an intermolecular motion in a dimer. The aim was to find methods which can be applied to larger model systems than a dimer and take the effect of the environment into account. As a test coordinate the longitudinal shift of two monomers against each other was used. At first, it was demonstrated how the character of an excited state in a dimer can be defined and how it can be extracted from a standard quantum-chemical calculation. Then several functionals were benchmarked and their applicability or failure was rationalized using the character analysis. Two recipes could be proposed, which were applied to a constraint optimization (only intermolecular degrees of freedom) in the excited states of the PBI dimer and to the description of the potential energy surfaces of ground and excited states along a longitudinal displacement in the perylene tetramer, respectively. It was further demonstrated that the semi-empirical OMx methods fail to give an accurate description of the excited-state potential energy surfaces as well as the ground-state surface along the test coordinate. This failure could be attributed to an underestimation of overlap-dependent terms. Consequently, it could be shown that the methods are applicable to large intermolecular distances, where the overlap is negligible. The results of DFT calculations with differently composed basis sets suggested that adding an additional single p-function for each atom should significantly improve the performance. QM/MM methods are ideally suited to take the effect of the environment on a a dimer model system into account. However, it was shown that standard force fields also give an incorrect description of the interaction between the monomers along the intermolecular coordinate. This failure was attributed to the isotropic atom-atom interaction in the repulsion term of the Lennard-Jones potential. This was corroborated using two simple proof-of-principle anisotropy models. Therefore, a novel force field called OPLS-AA_O was presented that is based on OPLS-AA, but uses an anisotropic model for the repulsion. The model involves the overlap integral between the molecular densities, which are modeled as a sum of atom-centered p-type Gaussian functions. It was shown that using this force field an excellent agreement with the DFT results can be obtained when the correct parameters are used. These parameters, however, are not very generalizable, which was attributed to the simplicity of the model in its current state (using the same exponential parameter for all atoms). As a short excursion, the applicability of an MO-based overlap model was discussed. It was demonstrated that the repulsion term based on the density overlap can be used to correct the failure of the OMx methods for the ground states. This is in accord with the assumption that an underestimation of the overlap terms is responsible for the failure. It was shown that OPLS-AA_O also gives an excellent description of the longitudinal shift in a PBI tetramer. Using the tetramer as a test system and applying the recipe obtained in the TDDFT benchmark for the QM-part and OPLS-AA_O for the MM-part in conjunction with an electrostatic embedding scheme, a QM/MM description of the excited states of the PBI dimer including the effect of the environment could be obtained. In the last chapter the theoretical description of the Bis(borolyl)thiophene dianion and the excited states of pyracene were discussed. The electronic structure of the Bis(borolyl)thiophene dianion - a negative bipolaron - was elucidated using DFT and CASPT2 methods. Furthermore, an estimation of the extent of triplet admixture to the ground state due to spin-orbit coupling was given. In the second project the S1 and S2 states of pyracene were computed using SCS-CC2 and SCS-ADC(2) and an estimation for the balance between aromaticity and ring strain was given. This also involved computing the vibrational frequencies in the excited states. In both studies the results of the computations were able to rationalize and complete experimental results.}, subject = {Exziton}, language = {en} } @phdthesis{Schmidt2015, author = {Schmidt, Thomas Christian}, title = {Theoretical Investigations on the Interactions of Small Compounds with their Molecular Environments}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127860}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {Im ersten Teil dieser Arbeit wird eine Kombination theoretischer Methoden f{\"u}r die strukturbasierte Entwicklung neuer Wirkstoffe pr{\"a}sentiert. Ausgehend von der Kristallstruktur eines kovalenten Komplexes einer Modellverbindung mit dem Zielprotein wurde mit Hilfe von quantenmechanischen und QM/MM Rechnungen die genaue Geometrie des vorausgehenden nicht-kovalenten Komplexes betimmt. Letztere ist der bestimmende Faktor f{\"u}r die Reaktivit{\"a}t des Inhibitors gegen{\"u}ber der katalytisch aktiven Aminos{\"a}ure und damit f{\"u}r die Ausbildung einer kovalenten Bindung. Aus diesem Grund wurde diese Geometrie auch f{\"u}r die Optimierung der Substitutionsmusters des Ihnibitors verwendet, um dessen Affinit{\"a}t zum Zielenzyme zu verbessern ohne dass dieser seine F{\"a}higkeit kovalent an das aktive Zentrum zu binden verliert. Die Optimierung des Substitutionsmuster wurde doch Methode des Molekularen Dockings unterst{\"u}tzt, das diese optimal dazu geeignet sind, Bindungsaffinit{\"a}ten vorherzusagen, die durch eine Modifikation der chemischen Struktur entstehen. Eine Auswahl der besten Strukturen wurde anschließend verwendet, um zu {\"u}berpr{\"u}fen, ob die ver{\"a}nderten Molek{\"u}le noch gen{\"u}gen Reaktivit{\"a}t gegen{\"u}ber dem Zielprotein aufweisen. Molek{\"u}ldynamik Simulationen der neuen Verbindungen haben jedoch gezeigt, dass die ver{\"a}nderten Verbindungen nur so and das Protein binden, dass die Bilung eine kovalenten Bindung zum Enzym nicht mehr m{\"o}glich ist. Daher wurden in einem weiteren Schritt die Modellverbindungen weiter modifiziert. Neben {\"A}nderungen im Substitutionsmuster wurde auch die chemische Struktur im Kern ver{\"a}ndert. Die Bindungsaffinit{\"a}ten wurde wieder mittels Docking {\"u}berpr{\"u}ft. F{\"u}r die besten Bindungsposen wurden wieder Simulationen zur Molek{\"u}ldynamik durchgef{\"u}hrt, wobei diesmal die Ausbildung einer kovalenten Bindung zum Enzyme m{\"o}glich erscheint. In einer abschließenden Serie von QM/MM Rechnungen unter Ber{\"u}cksichtigung verschiedener Protonierungszust{\"a}nde des Inhibitors und des Proteins konnten Reaktionspfade und zugeh{\"o}rige Reaktionsenergien bestimmt werden. Die Ergebnisse lassen darauf schließen, dass eines der neu entwickelten Molek{\"u}le sowohl eine stark verbesserte Bindungsaffinit{\"a}t wie auch die M{\"o}glichkeit der kovalenten Bindung an Enzyme aufweist. Der zweite Teil der Arbeit konzentriert sich auf die Umgebungseinfl{\"u}sse auf die Elektronenverteilung eines Inhibitormodells. Als Grundlage dient ein vinylsulfon-basiertes Moek{\"u}l, f{\"u}r das eine experimentell bestimmte Kristallstruktur sowie ein theoretisch berechneter Protein Komplex verf{\"u}gbar sind. Ein Referendatensatz f{\"u}r diese Systeme wurde erstellt, indem der Konformationsraum des Inhibitors nach m{\"o}glichen Minimumsstrukturen abgesucht wurde, welche sp{\"a}ter mit den Geometrien des Molek{\"u}ls im Kristall und im Protein verglichen werden konnten. The Geometrie in der Kristallumgebung konnte direkt aus den experimentellen Daten {\"u}bernommen werden. Rechnungen zum nicht-kovalenten Protein Komplex hingegen haben gezeigt, dass f{\"u}r das Modellsystem mehrere Geometrien des Inhibiors sowie zwei Protonierungszust{\"a}nde f{\"u}r die katalytisch aktiven Aminos{\"a}uren m{\"o}glich sind. F{\"u}r die Analyse wurden daher alle m{\"o}glichen Proteinkomplexe mit der Kristallstruktur verglichen. Ebenso wurden Vergleiche mit der Geometrie des isolierten Molek{\"u}ls im Vakuum sowie der Geometrie in w{\"a}ssriger L{\"o}sung angestellt. F{\"u}r die Geometrie des Molek{\"u}ls an sich ergab sich eine gute {\"U}bereinstimmung f{\"u}r alle Modellsysteme, f{\"u}r die Wechselwirkungen mit der Umgebung jedoch nicht. Die Ausbildung von Dimeren in der Kristallumgebung hat einen stark stablisierenden Effekt und ist einer der Gr{\"u}nde, warum dieser Kristall so gut wie keine Fehlordungen aufweist. In den Proteinkomplexen hingegen ergibt sich eine Abstoßung zwischen dem Inhibitor und einer der katalytisch aktiven Aminos{\"a}uren. Als Ursache f{\"u}r diese Abstoßung konnte die Einf{\"u}hrung der Methylaminfunktion ausgemacht werden. Vermutlicherweise f{\"u}hrt diese strukturelle {\"A}nderung auch dazu, dass der Modellinhibitor nicht in der Lage ist, so wie die Leitstruktur K11777 an das aktive Zentrum des Enzyms zu binden.}, subject = {Theoretische Chemie}, language = {en} } @phdthesis{Becker2015, author = {Becker, Johannes}, title = {Development and implementation of new simulation possibilities in the CAST program package}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-132032}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {The aim of the present work is the development and implementation of new simulation possibilities for the CAST program package. Development included, among other things, the partial parallelization of the already existing force fields, extension of the treatment of electrostatic interactions and implementation of molecular dynamics and free energy algorithms. The most time consuming part of force field calculations is the evaluation of the nonbonded interactions. The calculation of these interactions has been parallelized and it could be shown to yield a significant speed up for multi-core calculations compared to the serial execution on only one CPU. For both, simple energy/gradient as well as molecular dynamics simulations the computational time could be significantly reduced. To further increase the performance of calculations employing a cutoff radius, a linkedcell algorithm was implemented which is able to build up the non-bonded interaction list up to 7 times faster than the original algorithm. To provide access to dynamic properties based on the natural time evolution of a system, a molecular dynamics code has been implemented. The MD implementation features two integration schemes for the equations of motion which are able to generate stable trajectories. The basic MD algorithm as described in Section 1.2 leads to the sampling in the microcanonical (NVE) ensemble. The practical use of NVE simulations is limited though because it does not correspond to any experimentally realistic situation. More realistic simulation conditions are found in the isothermal (NVT) and isothermalisobaric (NPT) ensembles. To generate those ensembles, temperature and pressure control has been implemented. The temperature can be controlled in two ways: by direct velocity scaling and by a Nose-Hoover thermostat which produces a real canonical ensemble. The pressure coupling is realized by implementation of a Berendsen barostat. The pressure coupling can be used for isotropic or anisotropic box dimensions with the restriction that the angles of the box need to be 90� . A crucial simulation parameter in MD simulations is the length of the timestep. The timestep is usually in the rang of 1fs. Increasing the timestep beyond 1fs can lead to unstable trajectories since the fastest motion in the system, usually the H-X stretch vibration can not be sampled anymore. A way to allow for bigger timesteps is the use of a constraint algorithm which constrains the H-X bonds to the equilibrium distance. For this the RATTLE algorithm has been implemented in the CAST program. The velocity Verlet algorithm in combination with the RATTLE algorithm has been shown to yield stable trajectories for an arbitrary length of simulation time. In a first application the MD implementation is used in conjunction with the MOPAC interface for the investigation of PBI sidechains and their rigidity. The theoretical investigations show a nice agreement with experimentally obtained results. Based on the MD techniques two algorithms for the determination of free energy differences have been implemented. The umbrella sampling algorithm can be used to determine the free energy change along a reaction coordinate based on distances or dihedral angles. The implementation was tested on the stretching of a deca-L-alanine and the rotation barrier of butane in vacuum. The results are in nearly perfect agreement with literature values. For the FEP implementation calculations were performed for a zero-sum transformation of ethane in explicit solvent, the charging of a sodium ion in explicit solvent and the transformations of a tripeptide in explicit solvent. All results are in agreement with benchmark calculations of the NAMD program as well as literature values. The FEP formalism was then applied to determine the relative binding free energies between two inhibitors in an inhibitor-protein complex. Next to force fields, ab-initio methods can be used for simulations and global optimizations. Since the performance of such methods is usually significantly poorer than force field applications, the use for global optimizations is limited. Nevertheless significant progress has been made by porting these codes to GPUs. In order to make use of these developments a MPI interface has been implemented into CAST for communication with the DFT code TeraChem. The CAST/TeraChem combination has been tested on the \$H_2 O_{10}\$ cluster as well as the polypeptide met-Enkephalin. The pure ab-initio calculations showed a superior behavior compared to the standard procedure where the force field results are usually refined using quantum chemical methods.}, subject = {Molekulardynamik}, language = {en} }