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Im Rahmen dieser Arbeit wurden die elektronischen Eigenschaften von Graphen auf Metalloberflächen mittels Rastertunnelmikroskopie und Quasiteilcheninterferenz (englisch quasiparticle interference, QPI)-Messungen untersucht. Durch das Verwenden schwerer Substrate sollte die Spin-Bahn-Wechselwirkung des Graphen verstärkt werden und damit eine Bandlücke am K-Punkt der Bandstruktur mittels QPI beobachtet werden. Um das Messen von QPI auf Graphen zu testen, wurde auf der Oberfläche eines SiC(0001)-Kristalls durch Erhitzen Graphen erzeugt und mit dem Rastertunnelmikroskop untersucht. Dieses System wurde schon ausführlich 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 Qualität 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 für 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 zusätzlich eine Temperaturabhängigkeit nachgewiesen werden konnte. Beim Versuch, Gadolinium zu interkalieren, wurden zwei verschieden Oberflächenstrukturen beobachtet, die auf eine unterschiedlich Anordnung bzw. Menge des interkalierten Gadoliniums zurückzuführen sein könnten. 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 temperaturabhängige Austauschaufspaltung reproduziert werden. Darüber hinaus konnten sechs verschieden magnetische Domänen beobachtet werden. Zusätzlich sind auf der Oberfläche magnetische Streifen auszumachen, die möglicherweise auf einer Spinspirale basieren. Als Grundlage für die mögliche zukünftige Erzeugung Graphen-artiger Molekülgitter wurde das Wachstum von H-TBTQ und Me-TBTQ auf Ag(111) untersucht. Die Moleküle richten sich dabei nach der Oberflächenstruktur des Silber aus und bilden längliche Inseln, deren Kanten in drei Vorzugsrichtungen verlaufen. Auf H-TBTQ wurde zudem eine zweite, Windmühlen-artige Ausrichtung der Moleküle auf der Oberfläche beobachtet. Auf den mit den Molekülen bedeckten Stellen der Oberfläche wurde eine Verschiebung des Ag-Oberflächenzustands beobachtet, die mit einem Ladungstransfer vom Ag(111)-Substrat auf die TBTQ-Moleküle zu erklären sein könnte.
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.
Mechanistic Insights into the Inhibition of Cathepsin B and Rhodesain with Low-Molecular Inhibitors
(2019)
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.
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.
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.
Im Rahmen dieser Arbeit konnten nasschemische Synthesen für 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 Müssig zur Synthese von B2I4 gelang die Darstellung aller vier Dibortetrahalogenide mittels einfacher Schlenktechnik basierend auf der Synthese von B2Br4 durch Nöth 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 führte zunächst zur Ausbildung des Bisadduktes 53, allerdings konnte in Lösung eine Umlagerung beobachtet werden, deren Verlauf 11B-NMR-spektroskopisch verfolgt wurde, jedoch nicht final aufgeklärt werden konnte. Durch die Zugabe eines Unterschusses der Lewis-Basen IDipp bzw. PCy3 sollten zunächst Monoaddukte von B2Cl4 dargestellt werden, deren Umsetzung mit einer weiteren Lewis-Base die Synthese asymmetrischer Lewis-Basen-Addukte von B2Cl4 ermöglichen sollte. Die sp2-sp3-Diborane 56 und 57 konnten bei tiefen Temperaturen 11B-NMR-spektroskopisch nachgewiesen werden, allerdings führte eine Abfangreaktion mit diversen Lewis-Basen nicht zu den gewünschten asymmetrischen Addukten. Bei Raumtemperatur konnte eine Folgereaktion von 56 zur Chlorid-verbrückten 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 Reaktivität von B2Cl4 gegenüber ungesättigten 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 zunächst über 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 für 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 für eine weitere Reduktion zur B-B-Doppelbindung nötig wäre, 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) führte zu den chloridverbrückten Monoaddukten 74−76 und 79−81. Alle Verbindungen dieses Typs zeigten in NMR-spektroskopischen Untersuchungen ein sp2- und ein sp3-koordiniertes Borzentrum, welche für die CAAC-stabilisierten Verbindungen auch röntgenkristallografisch nachgewiesen werden konnten. Theoretische Untersuchungen bestätigten die Relevanz des verbrückenden Chloratoms zur Stabilisierung dieser Verbindungen. Für die Stammverbindung der Diborylalkene (59 (R = H)) konnte bei der Umsetzung mit MeCAAC eine unlösliche Verbindung erhalten werden, deren Struktur als Bisaddukt 82 mittels NMR-spektroskopischen Untersuchungen im Festkörper und durch Verbrennungsanalyse bestätigt werden konnte.
Die Reduktion der CAAC-stabilisierten Diborylalkene 79 und 80 in Gegenwart von MeCAAC führte zu den captodativ-stabilisierten Diborylradikalen 83 und 84, deren Strukturanalyse eine orthogonale Anordnung der C2-Brücke zur B(CAAC)-Einheit offenlegt. Ausführliche EPR-spektroskopische Untersuchungen bei variabler Temperatur und theoretische Berechnungen bestätigen 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 Molekülorbitale (SOMO) bestätigen eine Delokalisierung der Spindichte über die NCAAC-CCAAC-B-Einheit. Der Austausch der verbrückenden Einheit und die somit einhergehende Verringerung der Sterik führt zu einer Planarisierung des Moleküls im Festkörper (87). Theoretische Untersuchungen und die Auswertung der strukturellen Parameter ergeben eine Delokalisierung der Elektronendichte über 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 vollständige 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) durchgeführt, die in der Ausbildung der Diborylene 99−104 resultierten. Die Darstellung einer para-Phenylen-verbrückten Donor-Akzeptor-Verbindung (D: Borylen, A: BMes2) gelang nicht.
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.
Theoretical Investigations on the Interactions of Small Compounds with their Molecular Environments
(2015)
In the first part of this work, a combination of theoretical methods for the rational design of covalent inhibitor is presented. Starting from the crystal structure of the covalent complex of a lead compound, quantum mechanical and QM/MM calculations were used to derive the exact geometry of the preceeding non-covalent enzyme inhibitor complex. The geometry of the latter mainly determines the reactivity of the inhibitor against its target enzyme concerning the formation of the covalent bond towards an active site residue. Therefore, this geometry was used as starting point for the optimization of the substitution pattern of the inhibitor such as to increase its binding affinity without loosing its ability to covalently bind to the target protein. The optimization of the chemical structure was supported by using docking procedures, which are best suited to estimate binding affinities that arise from the introduced changes. A screening of the novel substitution patterns resulted in a first generation of model compounds which were further tested for their reactivity against the target. Dynamic simulations on the novel compounds revealed that the orientation that compounds adopt within the active site are such that a covalent interaction with the enzyme is no longer possible. Hence, the chemical structure was further modified, including not only changes in the substituents but also within the core of the molecule. Docking experiments have been conducted to assure sufficiently high binding affinities and to obtain the most favored binding poses. Those have then again been used for dynamic simulations which resulted in structures, for which the bond formation process appeared feasible. A final series of QM/MM calculations considering various protonation states was computed to estimate the reaction energies for the covalent attachment of the inhibitor to the enzyme. The theoretical results indicate a reasonable high inhibition potency of the novel compounds.
The second part concentrates on the environmental influences on the electron density of an inhibitor molecule. Therefore, a vinylsulfone-based model compound was selected for which an experimental crystal structure for the pure compound as well as a theoretically determined enzyme-inhibitor complex have been available. To provide reference data for the larger systems, the conformational space of the isolated molecule was screened for favorable geometries which were later compared to those within the crystal and protein surrounding. The geometry of the crystal structure could readily be taken from the experimental data whereas calculations on the protein complex revealed four potential non-covalent complexes exhibiting different arrangements of the molecule within the active site of the protein as well as two possible protonation states of the catalytic dyad. Hence, all four protein complexes have been compared to the crystal structure of the molecule as well as against the more favorable geometries of the isolated molecule being determined within vacuum or aqueous surrounding. Whereas the molecule itself was found to adopt comparable geometries within all investigated environments, the interactions pattern between the crystal surrounding and the protein differed largely from each other. The favorable formation of dimers within the crystal has a strong stabilizing effect and explains the extraordinarily good quality of the crystal. Within the protein however, repulsive forces have been found between the protein and the inhibitor. The origin of the repulsion could be traced back to effect of on of the substituents to the vinyl scaffold. The difference in the chemical structure in comparison to a well known inhibitor might also explain the experimentally found loss of activity for the model compound in comparison to K11777.
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.
Part 1 of this work describes the development of accurate physically grounded force fields for
intermolecular Cation-π interactions based on SAPT energy decomposition analysis.
The presented results demonstrate the benefits of the used DFT-SAPT method to describe non-bonding
interactions. First of all, this method is able to reproduce the high level CCSD(T) energy values
but using much less computational time. Second it provides the possibility to separate the total
intermolecular interaction energy into several physically meaningful contributions. The relative
contributions of the dimers investigated can be seen in Fig. 6.16. In Tab. 6.3 the percentage
contribution of the attractive energy parts to the stabilization energy is shown. The polarization
energy is important for the NH+...C6H6 interaction, whereas it becomes less crucial
considering other dimers. The dispersion energy contribution is large in the case of
the C6H6...H2O dimers, whereas it is relatively less important for the NH+...C6H6
interaction. The electrostatic energy contributes a large amount of stabilizing energy
in all considered dimer interactions. ...
As organic semiconductors gain more importance for application, research into their properties has become necessary. This work investigated the exciton and charge transport properties of organic semiconducting crystals. Based on a hopping approach, protocols have been developed for the calculation of Charge mobilities and singlet exciton diffusion coefficients. The protocols do not require any input from experimental data except for the x-ray crystal structure, since all needed quantities can be taken from high-level quantum chemical calculations. Hence, they allow to predict the transport properties of yet unknown compounds for given packings, which is important for a rational design of new materials. Different thermally activated hopping models based on time-dependent perturbation theory were studied for the charge and exciton transport; i. e. the spectral overlap approach, the Marcus theory, and the Levich-Jortner theory. Their derivations were presented coherently in order to emphasize the different levels of approximations and their respective prerequisites. A short reference was made to the empirical Miller-Abrahams hopping rate. Rate equation approaches to calculate the stationary charge carrier mobilities and exciton diffusion coefficients have been developed, which are based on the master equation. The rate equation approach is faster and more efficient than the frequently used Monte Carlo method and, therefore, provides the possibility to study the anisotropy of the transport parameters and their three-dimensional representation in the crystal. The Marcus theory, originally derived for outer sphere electron transfer in solvents, had already been well established for charge transport in organic solids. It was shown that this theory fits even better for excitons than for charges compared with the experiment. The Levich-Jortner theory strongly overestimates the charge carrier mobilities and the results deviate even stronger from the experiment than those obtained with the Marcus theory. The latter contains larger approximations by treating all vibrational modes classically. The spectral overlap approach in combination with the developed rate equations leads to even quantitatively very good results for exciton diffusion lengths compared to experiment. This approach and the appendant rate equations have also been adapted to charge transport. The Einstein relation, which relates the diffusion coefficient with the mobility, is important for the rate equations, which have been developed here for transport in organic crystals. It has been argued that this relation does not hold in disordered organic materials. This was analyzed within the Framework of the Gaussian disorder model and the Miller-Abrahams hopping rate.
Pulse-Sequence Approaches for Multidimensional Electronic Spectroscopy of Ultrafast Photochemistry
(2014)
Observing chemical reactions in real time with femtosecond laser pulses has evolved into a very popular field of research since it provides fascinating insights into the nature of photochemical transformations. Nevertheless, many photochemical reactions are still too complex for which reason the underlying mechanisms and all engaged species cannot be identified thoroughly. In these cases, conventional time-resolved spectroscopy techniques reach their technical limits and advanced approaches are required to follow the conversion of reactants to their products including all reaction intermediates.
The aim of this work was therefore the development of novel methods for ultrafast spectroscopy of photoreactive systems. Though the concept of coherent multidimensional spectroscopy has so far exclusively been used to explore photophysical phenomena, it also offers great potential for the study of photochemical processes due to its capability of extracting spectroscopic information along several frequency dimensions. This allows resolving the photochemical connectivity between various interconvertible molecular species with ultrafast temporal resolution on the basis of their absorption and emission properties as the spectral correlations are explicitly visualized in the detected spectra.
The ring-open merocyanine form of the photochromic compound 6-nitro BIPS was studied in Chap. 4 of this work. Merocyanines and their associated ring-closed spiropyrans are promising candidates for future applications as, for instance, molecular electronics or optical data storage due to their unique property of being switchable between two stable congurations via light illumination. Transient absorption with sub-50 fs temporal resolution and broadband probing was employed to characterize the photodynamics of this system with variable excitation wavelengths. Using global data analysis, it could be inferred that two different merocyanine isomers with differing excited-state lifetimes exist in solution. These isomers differ in the cis/trans conguration in the last bond of the methine bridge. The minority of isomers exist in the all-trans conguration (TTT) while the isomer with a cis conguration of the third dihedral angle (TTC) is dominant. A characteristic band, detected after long pump-probe delays, was attributed to the unidirectional cis->trans photoisomerization reaction of the TTC to the TTT form. The quantum yield of the reaction was estimated to be (18+-4) %. In addition, pronounced coherent vibrational wave-packet oscillations were observed and it was concluded that these signatures are related to the product formation.
Coherent two-dimensional electronic spectroscopy was successfully implemented using a partially collinear pump-probe beam geometry in combination with a femtosecond pulse shaper. The use of a whitelight probe continuum enabled us to probe contributions far-off the diagonal over the complete visible range. By properly adjusting the relative phase between the first two laser pulses with the pulse shaper, the principle of phase-cycling was explained and it was demonstrated that the measurement can be carried out in the so-called "rotating frame" in which the observed frequencies detected during the coherence time are shifted to lower values. It was shown that these concepts allow the extraction of the desired background-free photon echo while the amount of necessary data points is highly reduced.
In order to put our proposal of multidimensional spectroscopy of photoreactive systems into practice, third-order two- and three-dimensional spectroscopy was then employed for an in-depth analysis of a photoreactive process, in which the photoisomerization of 6-nitro BIPS served as a model system. The measured two-dimensional spectra revealed the cis->trans photoisomerization after long population times. By collecting a large data set of two-dimensional spectra for short population times and by applying a Fourier transform along the population time axis, the third-order three-dimensional spectrum was obtained. The novelty of this approach compared to coherent two-dimensional spectroscopy is the introduction of a third axis associated with the vibrational frequencies of the molecular system. In this way, the formation of the reaction product was evidenced and it was shown that the product is formed in its first excited singlet state within 200 fs after excitation. This method hence visualizes the photochemical connections between different reactive molecular species in an intuitive manner and further exposes the normal modes connecting reactant and product. Such conclusions cannot be drawn with conventional third-order techniques such as transient absorption since they are
not capable of capturing the full third-order response, but only a subset of it. The reaction mechanism and the role of the observed vibrational modes were uncovered by comparing the experimental data with the results of high-level quantum-chemical calculations performed by our collaborators in the group of Prof. B. Engels from the
theoretical chemistry department at the University of Würzburg. Specific calculated molecular normal modes could be assigned to the experimentally observed vibrational frequencies and potential energy surfaces of the electronic ground state and of the first excited state were computed. The technique implemented in this chapter is general and is applicable for the time-resolved analysis of a wide range of chemical reaction networks.
In the first part of Chap. 5, coherent two-dimensional spectroscopy was employed to track the reaction paths of the related 6,8-dinitro BIPS after S1 excitation. Several differences to the photochemical properties of 6-nitro BIPS were found. From the 2D spectra, the cis-trans isomerization between the two merocyanine isomers could be excluded as a major reaction path for this compound. To explore the dynamics after reexcitation to higher-lying electronic states, pump-repump-probe spectroscopy was implemented and the formation of a new species, a radical cation, was observed. To identify the precursor isomer, triggered-exchange two-dimensional spectroscopy, a fifth-order technique previously only available in the infrared regime for vibrational transitions, was implemented for the first time for electronic excitations in the visible. This approach combines the properties of the pump-repump-probe technique with the potential of coherent two-dimensional spectroscopy. It correlates the absorption frequency of a reactive molecular species with the emission signatures of the product formed from this species after an additional absorption of a photon. Using this method, it was unambiguously proven that only the TTC isomer reacts to the radical cation thus forming the precursor species of the reaction. Electronic triggered-exchange two-dimensional spectroscopy is hence another improved technology for time-resolved spectroscopy with applications in the study of multistep photoreactions and higher-lying electronic states. While in the two preceding chapters third- and fifth-order experiments were discussed that neglect the vectorial character of light-matter interactions, Chap. 6 focused on a novel theoretical formalism enabling the description of light fields optimized for polarization-sensitive higher-order nonlinearities. This formalism is based on the von Neumann time-frequency representation of shaped femtosecond laser pulses which permits the definition of multipulse sequences on a discrete time-frequency lattice. Hence, not only the temporal spacing between subpulses is adjustable, but also the center frequencies may be adapted such that they fit the experimental requirements. This method was generalized to the description of pulse sequences with time-varying polarization states. It was shown that by using this description, the polarization ellipticity, orientation angle, relative phase and intensity, and the time-frequency location of each subpulse is explicitly controllable. The accuracy of the transformations from Fourier space to von Neumann domain and vice versa was demonstrated. Moreover, a strict accordance between the von Neumann polarization parameters with the conventional parameters in time domain was found for well separated subpulses. A potential future application of this approach is polarization-sensitive multidimensional spectroscopy in which hidden cross peaks may be isolated by defining the pulses in the von Neumann picture with suitable polarization sequences. This method could also be used in quantum control experiments in which the polarization of the light field is used as a major control knob.
This thesis summarizes our efforts to open the field of femtochemistry to the concept of coherent multidimensional electronic spectroscopy. Making use of femtosecond pulse shaping, sub-50 fs temporal resolution, broadband spectral probing, higher-order nonlinearities, and new types of laser pulse descriptions, the presented methods might stimulate further future advancements in this research area.
Quantenchemische Untersuchungen von Umgebungseinflüssen bei offen- und geschlossenschaligen Systemen
(2022)
In dieser Dissertation werden die Umgebungseinflüsse auf die strukturellen und elektronischen Eigenschaften von verschiedenen offen- und geschlossenschaligen Systemen mittels quantenchemischer Methoden berechnet.
Ein Kernpunkt umfasst die Untersuchung von verdreht angeordneten, biradikalischen Diborylalkenen, welche eine ungesättigte C2R2-Brücke (R = Et, Me) besitzen und durch cyclische (Alkyl)(amino)carbene (CAACs) stabilisiert werden. Quantenchemische Berechnungen zeigen, dass hauptsächlich sterische Effekte für die Ausbildung einer verdrehten Molekülanordnung verantwortlich sind, während bei geringen sterischen Wechselwirkungen (R = H) die Delokalisationseffekte überwiegen, wodurch eine planare Struktur begünstigt wird. Die Bevorzugung einer offenschaligen Singulettkonfiguration anstelle eines Tripletts ist auf den großen Energieunterschied der beiden einfach besetzten Molekülorbitale zurückzuführen. Durch die Berechnung der Lösungsmitteleffekte mithilfe von polarisierbaren Kontinuumsmodellen kann gefolgert werden, dass mit zunehmender statischer Dielektrizitätskonstante eine planare und geschlossenschalige Struktur stärker stabilisiert wird als eine verdrehte Anordnung.
Ein weiteres Thema dieser Dissertation befasst sich mit der quantenchemischen Analyse eines makrozyklischen Perylenbisimid-Trimersystems, welches eingebettet in einer Polymethylmethacrylat-Matrix bei Temperaturen nahe dem absoluten Nullpunkt eine Lokalisierung der ersten drei angeregten Zustände zeigt. Quantenchemische Vakuumberechnungen ergeben, dass unabhängig von der gegenseitigen geometrischen Orientierung der drei Perylenbisimid-Chromophore der Übergang vom Grundzustand in den S1-Zustand verboten ist und dass die ersten drei angeregten Zustände delokalisiert vorliegen. Mithilfe von expliziten Lösungsmittelmodellen kann jedoch gezeigt werden, dass das Auftreten dieser Lokalisierungen auf eine inhomogene Polymethylmethacrylat-Umgebung zurückzuführen ist, die zu einem Symmetriebruch und somit zu einer Zunahme der Oszillatorstärke für S1 und der Lokalisierungsgrade für S1, S2 und S3 führt.
Darüber hinaus wird der Lösungsmitteleinfluss auf die angeregten Zustände des Azulens mittels impliziter und expliziter Lösungsmittelmodelle berechnet. Bei einer Erhöhung der dynamischen Dielektrizitätskonstante im impliziten Modell nehmen die Anregungsenergien der vertikalen Singulettzustände ab, wobei der Effekt mit steigender Oszillatorstärke zunimmt. Die Auswirkung der statischen Dielektrizitätskonstante auf die Anregungsenergien ist dagegen deutlich schwächer ausgeprägt. Im expliziten Modell bewirkt das Lösungsmittel ebenfalls eine Abnahme der Anregungsenergie des hellen Singulettzustands, wenn auch in geringerem Umfang als im impliziten Modell.
Als letztes Thema wird der Inhibitionsmechanismus der Cysteinprotease Rhodesain durch zwei modifizierte 1,4-Naphthoquinone untersucht. Während beide Naphthoquinone an der 2-Position eine Dipeptideinheit aufweisen, besitzen sie an der 3-Position entweder einen Nitril- oder Chloridsubstituenten. Zwar erfolgt bei beiden Derivaten die Inhibition über einen kovalent-reversiblen Mechanismus, jedoch verläuft die Hemmung im Falle des Nitrilderivats erheblich effektiver. Die quantenchemischen Berechnungen eines vereinfachten Modells zeigen, dass die Cysteineinheit (HS-R) bevorzugt in einer exothermen und reversiblen Additionsreaktion an die elektronenarme C-C-Doppelbindung der Naphthoquinone anlagert. Dabei werden kleinere Reaktionsenergien für die Reaktion des Chlorderivats als für die Reaktion des Nitrilderivats erhalten. Durch die Berücksichtigung von Wasser in einem impliziten Lösungsmittelmodell kommt es bei fast allen Reaktionsprodukten zu einer Energiezunahme, die bei der Reaktion des Nitrilderivats stärker ausfällt als bei der Reaktion des Chlorderivats.
In this thesis, several contributions to the understanding and modeling of chemical phenomena using computational approaches are presented. These investigations are characterized by the usage of non-standard computational modeling techniques, which is necessitated by the complex nature of the electronic structure or atomic fluctuations of the target molecules.
Multiple biradical-type molecules and their spectroscopic properties were modeled. In the course of the investigation, it is found that especially the impact of correct molecular geometries on the computationally predicted absorption properties may be critical. In order to find the correct minimum geometries, Multi-Reference methods may have to be invoked.
The impact of geometry relaxation on the excitonic properties of Perylene Bisimide dimers were investigated. Oftentimes, these geometry factors are neglected in Organic Semiconductor modeling as an approximation. This present investigation suggests that this approximation is not always valid, as certain regimes are identified where geometrical parameters have critical impact on the localization and energetic properties of excitons.
The mechanism of the Triazolinedione (TAD) tyrosine bioconjugation reaction is investigated using quantum-chemical methods. By comparison of different conceivable mechanisms and their energetic ordering, the TAD tyrosine bioconjugation is found to proceed by means of a base-mediated electrophilic aromatic substitution reaction.
The kth nearest neighbor entropy estimation protocol is investigated. This estimator promises accurate entropy estimates even for flexible molecules with multiple structural minima. Our granular investigation of formal and practical properties of the estimator suggests that the uneven variance of a molecule’s vibrational modes is the cause of the observed slow convergence of the estimator. A rescaling procedure to reestablish fast convergence is suggested and benchmarks are performed.
The introductory chapter reviews the current state of mechanistic understanding of the hexadehydro-Diels-Alder (HDDA) reaction. With the rapid development of the HDDA reaction from its first discovery in 1997, the question of whether a concerted or stepwise mechanism better describes the thermally activated formation of ortho-benzyne from a diyne and a diynophile has been debated. Mechanistic and kinetic investigations were able to show that this is not a black or white situation, as minor changes can tip the balance. In chapter 2 of this thesis, the catalytic process leading from 1,11-bis(p-tolyl)undeca-1,3,8,10-tetrayne to fully-substituted naphthalene and azulene derivatives, by two different platinum-catalyzed dimerization pathways, was investigated. In chapter 3, the cannibalistic self-trapping reaction of an ortho-benzyne derivative generated from 1,11-bis(p-tolyl)undeca-1,3,8,10-tetrayne in an HDDA reaction was investigated. Without adding any specific trapping agent, the highly reactive benzyne is trapped by another bisdiyne molecule in at least three different modes. In chapter 4 direct UV/VIS spectroscopic evidence for the existence of an o-benzyne in solution is reported, and the dynamics of its formation in a photo-induced reaction are established. For this purpose, 1,11-bis(p-tolyl)undeca-1,3,8,10-tetrayne was investigated, using femtosecond transient absorption spectroscopy in the ultraviolet/visible region. In chapter 5, following the isolation and characterization of the reaction products discussed in chapter 3, further species resulting from reactions of the highly reactive ortho-benzyne derivative were identified.
Within this work, an additive and a subtractive QM/MM interface were implemented into CAST. The interactions between QM and MM system are described via electrostatic embedding. Link atoms are used to saturate dangling bonds originating from the separation of QM and MM system. Available energy evaluation methods to be combined include force fields (OPLSAA and AMBER), semi-empirical programs (Mopac and DFTB+), and quantum-chemical methods (from Gaussian, Orca, and Psi4). Both the additive and the subtractive interface can deal with periodic boundary conditions. The subtractive scheme was extended to enable QM/QM, three-layer, and multi-center calculations. Another feature only available within the subtractive interface is the microiteration procedure for local optimizations.
The novel QM/MM methods were applied to the investigation of the reaction path for the complex formation between rhodesain and K11777. Benchmark calculations show a very good agreement with results from Gaussian-ONIOM. When comparing the relative energies obtained with different options to a computation where the whole system was treated with the “QM method” DFTB3, the electrostatic embedding scheme with option “delM3” gives the best results. “delM3” means that atoms with up to three bonds distance to the QM region are ignored when creating the external charges. This is done in order to avoid a double counting of Coulomb interactions between QM and MM system. The embedding scheme for the inner system in a three-layer calculation, however, does not have a significant influence on the energies. The same is true for the choice of the coupling scheme: Whether the additive or the subtractive QM/MM interface is applied does not alter the results significantly. The choice of the QM region, though, proved to be an important factor. As can be seen from the comparison of two QM systems of different size, bigger is not always better here. Instead, one has to make sure not to separate important (polar) interactions by the QM/MM border.
After this benchmark study with singlepoint calculations, the various possibilities of CAST were used to approximate the solution of a remaining problem: The predicted reaction energy for the formation of the rhodesain-K11777 complex differs significantly depending on the starting point of the reaction path.
The reason for this is assumed to be an inadequate adjustment of the environment during the scans, which leads to a better stabilization of the starting structure in comparison to the final structure. The first approach to improve this adjustment was performing the relaxed scan with a bigger QM region instead of the minimal QM system used before. While the paths starting from the covalent complex do not change significantly, those starting from the non-covalent complex become more exothermic, leading to a higher similarity of the two paths. Nevertheless, the difference of the reaction energy is still around 15 kcal/mol, which is far from a perfect agreement. For this reason, Umbrella Samplings were run. Here, the adjustment of the environment is not done by local optimizations like in the scans, but by MD simulations. This has the advantage that the system can cross barriers and reach different local minima. The relative free energies obtained by Umbrella Samplings with suitable QM regions are nearly identical, independently of the starting point of the calculation. Thus, \(\Delta A\) evaluated by these computations can be assumed to reproduce the real energy change best. An MD simulation that was started from the transition state in order to mimic a “real-time” reaction indicates a very fast adjustment of the environment during the formation of the complex. This confirms that Umbrella Sampling is probably better suitable to describe the reaction path than a scan, where the environment can never move strong enough to leave the current local minimum.
Reactive hydrocarbon species are important in a multitude of different scientific areas. In this thesis, the vibrational spectra of hydrocarbon radicals, biradicals and their reaction product have been studied in a gas-phase environment. The specific molecules investigated here, are of particular importance in the field of combustion and astrochemistry. They were produced from suitable precursors in a pyrolytically heated micro-reactor and subsequently seeded in an appropriate carrier gas. As methodology, IR/UV ion dip spectroscopy has been utilized, which delivers massselected gas-phase IR spectra of all ionizable species detectable in the molecular beam. These, with the help of DFT calculations, allow for determination of the fingerprint IR spectra, identification of mass carriers and formulation of potential reaction mechanisms. All studies have been conducted in collaboration with the group of Prof. Dr. Anouk M. Rjis and the necessary potent IR radiation has been provided by the free-electron laser FELIX. Thus, the IR/UV measurements have been executed at the FELIX Laboratory of the Radboud University in Nijmegen. The first study presented in this thesis is the investigation of ortho-benzyne in Chapter 3.1. This molecule is of particular interest due to its uncommon electronic structure and its role in high-temperature reactions. Although, the infrared spectrum of o-C6H4 was not accessible, a number of reaction products were identified via their fingerprint spectra. Masses in the range from 78 - 228 were assigned to their respective carrier. The identified species include typical PAHs like naphthalene, phenanthrene, up to triphenylene. The identified masses further suggest a PAH growth heavily influenced by diradical 1,4-cycloaddition followed by fragmentation, as well as by classical HACA- and PAC-like mechanisms. These results were augmented by threshold photoionization measurements from Engelbert Reusch, who identified lighter reaction products, which have insufficient IR absorption or unsuitable ionization characteristics to be identified in the IR/UV experiment. An interesting observation is the identification of m/z = 152. This carrier has been assigned differently by the IR and TPES experiments. Whereas the IR spectrum clearly identifies the species as 2-ethynylnaphthalene, the TPES evidently is in great agreement with biphenylene. This is a good example how different experimental methodologies can benefit from each other to gain a deeper insight into the actual science of a particular system. Probably, the prime example for an aromatically resonance stabilized radical is benzyl. This radical is of high importance for many combustion studies, as it represents the primary high-temperature decomposition product of toluene. The goal of the study was the identification of the benzyl self reaction products and the results are discussed in Section 3.2. The radical was pyrolytically produced by its respective nitrite precursor. The mass spectrum showed that the benzyl self reaction formed two products with C11 and three with C14 constitution. All mass peaks were evenly spaced by two mass units, respectively, which suggests a close relation in formation. Indeed, the C11 products were identified as diphenylmethane and fluorene, which are simply connected via cyclization. The heaviest product was identified as phenanthrene, which is formed via the cyclization of bibenzyl to 9,10-dihydrophenanthrene and subsequent elimination of hydrogen. This result was quiet interesting as the intermediate of this reaction was often assumed to be stilbene, which was not observed in the study. Hence, the reaction seems to undergo cyclization first before phenanthrene is finally formed via hydrogen elimination. Expanding the molecular frame of benzyl by an additional methyl group leads to the xylyl radicals and its decomposition product the xylylenes. Also important in combustion research, xylyl radicals represent the preferred decomposition products of xylene, a frequently used anti-knock agent in modern gasoline blends. After further hydrogen elimination the xylyl radicals can then form their respective xylylenes. The results of the xylyl experiments are discussed in Section 3.3. Here the gas-phase vibrational spectrum in the fingerprint region for all three isomers has been recorded for the first time in isolation. Although, all isomers have a very similar structure and symmetry, and consequently similar vibrational bands, the resolution of the experimental data was exceedingly sufficient for a clear assignment. Additionally, the dimerization products of meta- and para-xylyl could also be identified. A similar approach was taken to determine the fingerprint spectra for the xylylenes. Here, only para-xylylene could be unambiguously identified as the carrier of mass 104. For both ortho- and meta-xylylene precursors, only isomerization products were observed as the carriers of mass 104; benzocyclobutene and styrene, respectively. A possible explanation is elaborated upon in the troubleshooting Sec- tion 3.4.3.5. In the final experimental section a study on the decomposition of phthalide is presented. The objective of this experiment was mainly focused around the formation of C7 species, particularly the fulvenallenyl radical C7H5. In fact, the first experimental fingerprint spectrum of isolated C7H5 in the gas-phase was measured and is displayed in Fig. 3.45. Furthermore, the experiment demonstrates that the pyrolysis products of phthalide are excellent soot precursors, as many heavier reaction products have been identified. These include typical PAH species like naphthalene and phenanthrene as well as their methylated isomers. A large number of molecules with terminal ethynyl moieties indicate a strong influence of HACA growth in the experimental environment. However, many formation pathways of products have been discussed, which are formed involving experiment specific species, like C5H5 and C7H5, and often include expansion steps from 5- to 6-membered rings.
In this work, we elucidated recombination kinetics in organic and hybrid semiconductors by steady-state and time-resolved PL spectroscopy. Using these simple and very flexible experimental techniques, we probed the infrared emission from recombining free charge carriers in metal–halide perovskites, as well as the deep blue luminescence from intramolecular charge-transfer states in novel OLED emitters. We showed that similar state diagrams and kinetic models accurately describe the dynamics of excited species in these very different material systems.
In Chapters 4 and 5, we focused on lead iodide perovskites (MAPI and FAPI), whose comparatively developed deposition techniques suited the systematic material research. In MAPI, we harnessed the anomalous dependence of transient PL on the laser repetition rate in order to investigate the role of interfaces with the commonly used charge-selective layers: PC60BM, spiro-MeOTAD, and P3HT. The film was deposited on a large precut substrate and separated into several parts, which were then covered with the charge-selective layers. Thereby, the same bulk perovskite structure was maintained for all samples. Consequently, we were able to isolate interface-affected and bulk carrier recombination. The first one dominated the fast component of PL decay up to 300 ns, whereas the last was assigned to the remaining slow component. The laser repetition rate significantly prolonged PL decay in MAPI with additional interfaces while shortening the charge carrier lifetime in the pristine film. We qualitatively explained this effect by a kinetic model that included radiative electron–hole recombination and nonradiative trap-assisted recombination. All in all, we showed that the apparent PL lifetime in MAPI is to large extend defined by the laser repetition rate and by the adjacent interfaces.
Further, we studied photon recycling in MAPI and FAPI. We monitored how the microscopic PL transforms while propagating through the thin perovskite film. The emission was recorded within 5orders of magnitude in intensity up to 70μm away from the excitation spot. The Beer–Lambert law previously failed to describe the complex interplay of the intrinsic PL spectrum and the additional red-shifted peak. Therefore, we developed a general numerical model that accounts for self-absorption and diffusion of the secondary charge carriers. A simulation based on this model showed excellent agreement with the experimental spatially resolved PL maps. The proposed model can be applied to any perovskite film, because it uses easily measurable intrinsic PL spectrum and macroscopic absorption coefficient as seeding parameters.
In Chapter 6, we conducted an extensive photophysical study of a novel compact deep blue OLED emitter, SBABz4, containing spiro-biacridine and benzonitrile units. We also considered its single-donor monomer counterpart, DMABz4, in order to highlight the structure–property relationships. Both compounds exhibited thermally activated delayed fluorescence (TADF), which was independently proven by oxygen quenching and temperature-dependent transient PL measurements. The spiro-linkage in the double-donor core of SBABz4 rendered its luminescence pure blue compared to the blue-green emission from the single-donor DMABz4. Thus, the core-donor provided desirable color tuning in the deep blue region, as opposed to the common TADF molecular design with core-acceptor. Using PL lifetimes and efficiencies, we predicted EQEmax = 7.1% for SBABz4-based OLED, whereas a real test device showed EQEmax = 6.8%. Transient PL was recorded from the solutions and solid films in the unprecedentedly broad dynamic range covering up to 6orders of magnitude in time and 8orders of magnitude in intensity. The stretched exponent was shown to fit the transient PL in the films very well, whereas PL decay in dilute solution was found purely exponential. When the emitter was embedded in the host matrix that prevented aggregation, its TADF properties were superior in comparison with the pure SBABz4 film. Finally, using temperature-dependent transient PL data, we calculated the TADF activation energy of 70 meV.
To sum up, this Thesis contributes to the two fascinating topics of the last decade’s material research: perovskite absorbers for photovoltaics and TADF emitters for OLEDs. We were lucky to work with the emerging systems and tailor for them new models out of the well-known physical concepts. This was both exciting and challenging. In the end, science of novel materials is always a mess. We hope that we brought there a bit of clarity and light.
Diese Dissertation beschäftigt sich mit der Exzitonendynamik molekularer Aggregate, die nach Mehrphotonen-Anregung auf ultrakurzer Zeitskala stattfindet. Hierbei liegt der Fokus auf der Charakterisierung der Exziton-Exziton-Annihilierung (EEA) mithilfe von zweidimensionaler optischer Spektroskopie fünfter Ordnung. Dazu werden zwei verschiedene Modellsysteme implementiert: Das elektronische Homodimer und das elektronische Homotrimer-Modell, wobei Letzteres eine Erweiterung des Dimer-Modells darstellt. Die Kopplung des quantenmechanischen Systems an die Umgebung wird mithilfe des Quantum-Jump-Ansatzes umgesetzt. Besonderes Interesse kommt der Analyse des Signals fünfter Ordnung in Abhängigkeit der Populationszeit T zu.
Anhand des Dimer-Modells als kleinstmögliches Aggregat lassen sich bereits gute Vorhersagen auch über das Verhalten größerer molekularer Aggregate treffen. Der Zerfall des oszillierenden Signals für lange Populationszeiten korreliert mit der EEA. Dies zeigt, dass die zweidimensionale optische Spektroskopie genutzt werden kann, um den Annihilierungsprozess zu charakterisieren. Innerhalb des Modells des Dimers wird weiterhin der Einfluss der Intraband-Relaxation untersucht. Zunehmende Intraband-Relaxation verhindert den Austausch zwischen den lokalen Zuständen, der essentiell für den Annihilierungsprozess ist, und die EEA wird blockiert.
Das elektronische Trimer-Modell erweitert das Dimer-Modell um eine Monomereinheit. Somit befinden sich die Exzitonen im Anschluss an die Anregung nicht mehr unvermeidlich nebeneinander. Es gibt somit eine Konfiguration, bei der sich die Exzitonen zunächst zueinander bewegen müssen, bevor die Startbedingung des Annihilierungsprozesses gegeben ist. Dieser zusätzliche Schritt wird auch Exzitonendiffusion genannt. Die Ergebnisse dieser Arbeit legen nahe, dass das erwartete Verhalten nur zu sehr kurzen Zeiten im Femtosekundenbereich auftritt und somit die Zeitskala der Exzitonendiffusion im Falle des Trimers nicht sichtbar wird. Es bedarf demnach eines größeren Modellsystems, bei dem sich der Effekt der zeitverzögert eintretenden EEA deutlich in der Zerfallsdynamik manifestieren kann.