@phdthesis{WagenhaeusergebVonhausen2024, author = {Wagenh{\"a}user [geb. Vonhausen], Yvonne}, title = {Thermodynamic Investigations on the Dimerization and Anti-Cooperative Self-Assembly of Dipolar Merocyanines}, doi = {10.25972/OPUS-35211}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-352111}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {Dipolar merocyanines are very attractive supramolecular building blocks, as they combine interesting functional properties with strong, directional intermolecular interactions. The pyridine dioxocyano-pyridine (PYOP) chromophore (Chapter 2.2), used in this thesis, stands out because of its exceptionally high ground state dipole moment (g ~ 17 D), in combination with the option to retain good solubility also in unpolar solvents, by decoration with solubilizing groups. The reliable binding motif of anti-parallel -stacking due to dipole-dipole interactions has allowed the design of molecular building blocks that form assemblies of predictable geometry. The intense unstructured charge transfer UV/Vis absorption band (eg ~ 10.7 D) is a result of the dominant contribution of the zwitterionic resonance structure which brings the PYOP chromophore just beyond the cyanine limit in solvents of low polarity (c2 = 0.60, 1,4 dioxane). The high sensitivity of the S0 - S1 UV/Vis absorption band to the environment manifests itself in a pronounced negative solvatochromism and strong H-type exciton coupling within -stacked PYOP assemblies. In accordance with the classical molecular exciton theory, an increasing hypsochromic shift of the dominant absorption band of these H aggregates can be observed as the stack size increases up to about six chromophores, where it levels out at about max ~ 440 nm (CHCl3). This allows a uniquely simple estimation of the number of interacting chromophores within the self-assembled structure from a single UV/Vis absorption spectrum of an aggregate. The defined and well investigated PYOP dimer formation was employed in this thesis to probe the applicability and limitations of concentration-, temperature-, and solvent-dependent self-assembly studies (Chapter 3). Straightforward theoretical models to evaluate datasets of concentration-, temperature-, and solvent-dependent UV/Vis absorption by nonlinear regression analysis were derived for the case of dimer formation (Chapter 2.1). Although the dimer model is well known and widely applied in literature, this detailed derivation is helpful to understand assumptions and potential problems of the different approaches for the determination of thermodynamic parameters. This helps to decide on the most appropriate method to analyse a system of interest. In this regard it should be noted that covering a large portion of the self-assembly process with the experimental data is a prerequisite for the accuracy of the analysis. Additionally, many of the insights can also be transferred to other self-assembly systems like supramolecular polymerization or host-guest interactions. The concentration-dependent analysis is the most straightforward method to investigate self-assembly equilibria. No additional assumptions, besides mass balance and mass action law, are required. Since it includes the least number of parameters (only K, if M/D are known), it is the most, or even only, reliable method, to elucidate the self-assembly mechanism of an unknown system by model comparison. To cover a large concentration range, however, the compound must be soluble enough and generally sample amounts at least in the low mg scale must be available. The temperature-dependent analysis has the advantage that all thermodynamic parameters G0, H0 and S0 can be obtained from a single sample in one automated measurement. However, the accessible temperature-range is experimentally often quite limited and dependent on the solvent. For systems which do not show the transition from monomer to aggregate in a narrow temperature range, as given for, e.g., cooperative aggregation or processes with a high entropy contribution, often not the entire self-assembly process can be monitored. Furthermore, the assumptions of temperature-independent extinction coefficients of the individual species as well as temperature-independent H0 and S0 must be met. Monte Carlo simulations of data sets demonstrated that even minor changes in experimental data can significantly impact the optimized values for H0 and S0. This is due to the redundancy of these two parameters within the model framework and even small thermochromic effects can significantly influence the results. The G0 value, calculated from H0 and S0, is, however, still rather reliable. Solvent-dependent studies can often cover the entire self-assembly process from monomeric (agg = 0) to the fully aggregated state (agg = 1). However, for dyes with strong solvatochromic effects, such as the dipolar merocyanines investigated in this thesis, the results are affected. Also, the assumption of a linear relation of the binding energy G0 and the fraction of denaturating solvent f, which is based on linear free energy relationships between G0 and the solvent polarity, can lead to errors. Especially when specific solvent effects are involved. For the evaluation of experimental data by nonlinear regression, general data analysis software can be used, where user-defined fit models and known parameters can be implemented as desired. Alternatively, multiple specialized programs for analysing self-assembly data are available online. While the latter programs are usually more user-friendly, they have the disadvantage of being a "black box" where only pre-implemented models can be used without the option for the user to adapt models or parameters for a specific system. In Chapter 3 comprehensive UV/Vis absorption datasets are presented for the dimerization of merocyanine derivative 1 in 1,4-dioxane, which allowed for the first time a direct comparison of the results derived from concentration-, temperature-, and solvent-dependent self-assembly studies. The results for the binding constant K and corresponding G0 from the concentration- and temperature-dependent analysis were in very good agreement, also in comparison to the results from ITC. For the temperature-dependent analysis, though, multiple datasets of samples with different concentration had to be evaluated simultaneously to cover a meaningful part of the self-assembly process. Furthermore, a significant dependence of the optimized parameters H0 and S0 on the wavelength chosen for the analysis was observed. This can be rationalized by the small thermochromic shifts of both the monomer and the dimer UV/Vis absorption band. The results from the solvent-dependent evaluation showed the largest deviation, as expected for the highly solvatochromic merocyanine dye. However, even here by evaluation at 491 and 549 nm the deviation for G0 was only 2.5 kJ mol1 (9\%) with respect to the results from the concentration-dependent analysis (G0 = 29.1 kJ mol1). Thus, despite the strong solvatochromism of the dipolar chromophore, it can still be considered a reliable method for estimating the binding strength. Furthermore, multiple repetitions of the concentration-, temperature-, and solvent-dependent studies provided insight into the reproducibility of the results and possible sources of experimental errors. In all cases, the deviations of the results were small (G0 < 0.4 kJ mol1) and within the same range as the fit error from the nonlinear regression analysis. The insights from these studies were an important basis for the in-depth investigation of a more complex supramolecular system in Chapter 4, as a single method is often not enough to capture the full picture of a more complicated self-assembly process. To elucidate the anti-cooperative self-assembly of the chiral merocyanine 2, a combination of multiple techniques had to be applied. Solvent-dependent UV/Vis absorption studies in CH2Cl2/MCH mixtures showed the step-wise assembly of the merocyanine monomer (max(M) = 549 nm, CH2Cl2) to first a dimer (max(D) = 498 nm, CH2Cl2/MCH 15:85) by dipole-dipole interactions, and then a -stacked higher aggregate (max(H) = 477 nm, MCH), with pronounced H-type coupling. The thermodynamic evaluation of this data, however, suffered from the severe solvatochromism, especially of the monomeric species (max(M, CH2Cl2) = 549 nm, max(M, MCH) = 596 nm). Therefore, concentration-dependent studies were performed at three different temperatures (298, 323, 353 K) to elucidate the self-assembly mechanism and determine reliable thermodynamic parameters. The studies at elevated temperatures were hereby necessary, to obtain experimental data over a larger agg--range. Due to the pronounced difference in the thermodynamic driving force for dimerization and higher aggregate formation (KD/K5 = 6500) a concentration range exists in MCH where almost exclusively the dimer species of 2 is present, before further self-assembly by dispersion interactions occurs. Therefore, the data could be evaluated independently for the two self-assembly steps. The self-assembly of dimers into the higher aggregate could not be described by the isodesmic model but was fitted satisfactorily to a pentamer model. This rather small size of about ten -stacked PYOP chromophores was, furthermore, consistently indicated by AFM, VPO and DOSY NMR measurements. Based on 1D and 2D NMR data as well as the strong bisignate CD signal of the higher aggregate in combination with TD-DFT calculations, a P-helical stack is proposed as its structure. The small size can be rationalized by the anti-cooperative self-assembly mechanism and the sterical demand of the solubilizing trialkoxyphenyl and the chiral tetralin substituents. Additionally, the aliphatic shell formed by the solubilizing chains around the polar chromophore stack, can account for the exceptionally high solubility of 2 in MCH (> 15 mg mL1). These combined studies of the self-assembly process enabled the identification of suitable conditions for the investigation of fluorescence properties of the individual aggregate species. Aggregation-induced emission enhancement was observed for the almost non-emissive monomer (Fl(M) = 0.23\%), which can be rationalized by the increasing rigidification within the dimer (Fl(D) = 2.3\%) and the higher aggregate (Fl(H) = 4.5\%). The helical chirality of the PYOP decamer stack, furthermore, gave rise to a strong CPL signal with a large glum value of 0.011. The important conclusion of this thesis is that the temperature- and solvent-dependent analyses are valid alternatives to the classical concentration-dependent analysis to determine thermodynamic parameters of self-assembly equilibria. Although, for a specific supramolecular system, one approach might be favourable over the others for a variety of reasons. The experimental limitations often demand a combination of techniques to fully elucidate a self-assembly process and to gain insights in the aggregate structure. The anti-cooperative merocyanine self-assembly, which was described here for the first time for the PYOP merocyanine 2, is no exception. Besides the interest in the merocyanine assemblies from a structural and functional point of view, the insights gained from the presented studies can also be transferred to other self-assembly systems and be a guide to find the most appropriate analysis technique.}, subject = {Merocyanine}, language = {en} } @unpublished{SeitzJungnickelKleiberetal.2024, author = {Seitz, Florian and Jungnickel, Tina and Kleiber, Nicole and Kretschmer, Jens and Dietzsch, Julia and Adelmann, Juliane and Bohnsack, Katherine E. and Bohnsack, Markus T. and H{\"o}bartner, Claudia}, title = {Atomic mutagenesis of N\(^6\)-methyladenosine reveals distinct recognition modes by human m\(^6\)A reader and eraser proteins}, series = {Journal of the American Chemical Society}, journal = {Journal of the American Chemical Society}, doi = {10.1021/jacs.4c00626}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-352376}, year = {2024}, abstract = {N\(^6\)-methyladenosine (m\(^6\)A) is an important modified nucleoside in cellular RNA associated with multiple cellular processes and is implicated in diseases. The enzymes associated with the dynamic installation and removal of m\(^6\)A are heavily investigated targets for drug research, which requires detailed knowledge of the recognition modes of m\(^6\)A by proteins. Here, we use atomic mutagenesis of m\(^6\)A to systematically investigate the mechanisms of the two human m\(^6\)A demethylase enzymes FTO and ALKBH5 and the binding modes of YTH reader proteins YTHDF2/DC1/DC2. Atomic mutagenesis refers to atom-specific changes that are introduced by chemical synthesis, such as the replacement of nitrogen by carbon atoms. Synthetic RNA oligonucleotides containing site-specifically incorporated 1-deaza-, 3-deaza-, and 7-deaza-m\(^6\)A nucleosides were prepared by solid-phase synthesis and their RNA binding and demethylation by recombinant proteins were evaluated. We found distinct differences in substrate recognition and transformation and revealed structural preferences for the enzymatic activity. The deaza m\(^6\)A analogues introduced in this work will be useful probes for other proteins in m\(^6\)A research.}, language = {en} } @phdthesis{Neitz2024, author = {Neitz, Hermann}, title = {Hydrophobic recognition motifs in functionalized DNA}, doi = {10.25972/OPUS-34838}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348382}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {In w{\"a}ssriger Umgebung spielen hydrophobe Wechselwirkungen eine wichtige Rolle f{\"u}r die DNA. Die Einf{\"u}hrung von Modifikationen, die auf hydrophoben aromatischen Einheiten basieren, kann die Erkennung und Reaktivit{\"a}t von funktionellen Gruppen in der DNA steuern. Modifikationen k{\"o}nnen durch ein k{\"u}nstliches R{\"u}ckgrat oder in Form einer Erweiterung der Nukleobasen eingebracht werden und so zu zus{\"a}tzlichen Eigenschaften der DNA f{\"u}hren. Diese Dissertation befasst sich mit der Verwendung von hydrophoben Einheiten zur Funktionalisierung von DNA. Im ersten Teil der Arbeit wurde das Tolanmotiv (Diphenylacetylen) in Kombination mit dem acyclischen R{\"u}ckgrat von GNA und BuNA verwendet, um Erkennungseinheiten im DNA-Kontext zu erzeugen. Die gezielte Fluorierung der aromatischen Ringe des Tolan-Bausteins bildete die Grundlage f{\"u}r eine supramolekulare Sprache, die auf Aren-Fluoroaren-Wechselwirkungen basiert. Die spezifische Erkennung wurde mittels thermodynamischer, kinetischer und NMR-spektroskopischer Methoden untersucht. Im zweiten Teil der Arbeit wurden Desoxyuridin-Derivate mit einer hydrophoben aromatischen Modifikation hergestellt und in die DNA-Doppelhelix eingebaut. Die Bestrahlung mit UV-Licht f{\"u}hrte zu einer [2+2]-Cycloaddition zwischen zwei modifizierten Nukleosiden in der DNA. Das Reaktionsprodukt wurde strukturell charakterisiert und die Reaktion in verschiedenen biochemischen und nanotechnologischen DNA-Anwendungen eingesetzt.}, subject = {Supramolekulare Chemie}, language = {en} } @phdthesis{Bauer2023, author = {Bauer, Christian}, title = {Towards ecological and efficient electrochemical energy storage in supercapacitors and sodium ion batteries using onion-like carbon}, doi = {10.25972/OPUS-31795}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-317956}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {In this thesis, the usage of onion-like carbon (OLC) for energy storage applications was researched regarding sustainability, performance and processability. This work targets to increase the scientific understanding regarding the role of OLC in electrodes and to facilitate a large-scale production, which is the foundation for commercial application. Research was devoted to increase the knowledge in the particular field, to yield synergistic approaches and a shared value regarding sustainability and performance.}, subject = {Elektrochemie}, language = {en} } @phdthesis{Mahlmeister2023, author = {Mahlmeister, Bernhard}, title = {Twisted Rylene Bisimides for Organic Solar Cells and Strong Chiroptical Response in the Near Infrared}, doi = {10.25972/OPUS-34610}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346106}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {The chirality of the interlocked bay-arylated perylene motif is investigated upon its material prospect and the enhancement of its chiroptical response to the NIR spectral region. A considerable molecular library of inherently chiral perylene bisimides (PBIs) was utilized as acceptors in organic solar cells to provide decent device performances and insights into the structure-property relationship of PBI materials within a polymer blend. For the first time in the family of core-twisted PBIs, the effects of enantiopurity on the device performance was thoroughly investigated. The extraordinary structural sensitivity of CD spectroscopy served as crucial analytical tool to bridge the highly challenging gap between molecular properties and device analytics by proving the excitonic chirality of a helical PBI dimer. The chirality of this perylene motif could be further enhanced on a molecular level by both the expansion and the enhanced twisting of the π-scaffold to achieve a desirable strong chiroptical NIR response introducing a new family of twisted QBI-based nanoribbons. These achievements could be substantially further developed by expanding this molecular concept to a supramolecular level. The geometrically demanding supramolecular arrangement necessary for the efficient excitonic coupling was carefully encoded into the molecular design. Accordingly, the QBIs could form the first J-type aggregate constituting a fourfold-stranded superhelix of a rylene bisimide with strong excitonic chirality. Therefore, this thesis has highlighted the mutual corroboration of experimental and theoretical data from the molecular to the supramolecular level. It has demonstrated that for rylene bisimide dyes, the excitonic contribution to the overall chiroptical response can be designed and rationalized. This can help to pave the way for new organic functional materials to be used for chiral sensing or chiral organic light-emitting devices.}, subject = {Molek{\"u}l}, language = {en} } @article{BrennerGeigerSchlegeletal.2023, author = {Brenner, Daniela and Geiger, Nina and Schlegel, Jan and Diesendorf, Viktoria and Kersting, Louise and Fink, Julian and Stelz, Linda and Schneider-Schaulies, Sibylle and Sauer, Markus and Bodem, Jochen and Seibel, J{\"u}rgen}, title = {Azido-ceramides, a tool to analyse SARS-CoV-2 replication and inhibition — SARS-CoV-2 is inhibited by ceramides}, series = {International Journal of Molecular Sciences}, volume = {24}, journal = {International Journal of Molecular Sciences}, number = {8}, issn = {1422-0067}, doi = {10.3390/ijms24087281}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-313581}, year = {2023}, abstract = {Recently, we have shown that C6-ceramides efficiently suppress viral replication by trapping the virus in lysosomes. Here, we use antiviral assays to evaluate a synthetic ceramide derivative α-NH2-ω-N3-C6-ceramide (AKS461) and to confirm the biological activity of C6-ceramides inhibiting SARS-CoV-2. Click-labeling with a fluorophore demonstrated that AKS461 accumulates in lysosomes. Previously, it has been shown that suppression of SARS-CoV-2 replication can be cell-type specific. Thus, AKS461 inhibited SARS-CoV-2 replication in Huh-7, Vero, and Calu-3 cells up to 2.5 orders of magnitude. The results were confirmed by CoronaFISH, indicating that AKS461 acts comparable to the unmodified C6-ceramide. Thus, AKS461 serves as a tool to study ceramide-associated cellular and viral pathways, such as SARS-CoV-2 infections, and it helped to identify lysosomes as the central organelle of C6-ceramides to inhibit viral replication.}, language = {en} } @unpublished{SaalSwainSchmiedeletal.2023, author = {Saal, Fridolin and Swain, Asim and Schmiedel, Alexander and Holzapfel, Marco and Lambert, Christoph and Ravat, Prince}, title = {Push-Pull [7]Helicene Diimide: Excited-State Charge Transfer and Solvatochromic Circularly Polarised Luminescence}, edition = {submitted version}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345207}, year = {2023}, abstract = {In this communication we describe a helically chiral push-pull molecule named 9,10-dimethoxy-[7]helicene diimide, displaying fluorescence (FL) and circularly polarised luminescence (CPL) over nearly the entire visible spectrum dependent on solvent polarity. The synthesised molecule exhibits an unusual solvent polarity dependence of FL quantum yield and nonradiative rate constant, as well as remarkable gabs and glum values along with high configurational stability.}, language = {en} } @phdthesis{Scheitl2023, author = {Scheitl, Carolin P. M.}, title = {In vitro selected ribozymes for RNA methylation and labeling}, doi = {10.25972/OPUS-33004}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-330049}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {The focus of this work was the development and application of highly efficient RNA catalysts for the site-specific modification of RNA with special focus on methylation. In the course of this thesis, the first methyltransferase ribozyme (MTR1), which uses m6G as the methyl group donor was developed and further characterized. The RNA product was identified as the natural modification m1A. X-Ray crystallography was used to solve the 3D structure of the ribozyme, which directly suggested a plausible reaction meachnism. The MTR1 ribozyme was also successfully repurposed for a nucleobase transformation reaction of a purine nucleoside. This resulted in a formyl-imidazole moiety directly on the intact RNA, which was directly used for further bioconjugation reactions. Finally, additional selections and reselections led to the identification of highly active alkyltransferase ribozymes that can be used for the labeling of various RNA targets}, subject = {Methylierung}, language = {en} } @article{OkudaLenzSeitzetal.2023, author = {Okuda, Takumi and Lenz, Ann-Kathrin and Seitz, Florian and Vogel, J{\"o}rg and H{\"o}bartner, Claudia}, title = {A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells}, series = {Nature Chemistry}, journal = {Nature Chemistry}, doi = {10.1038/s41557-023-01320-z}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328762}, year = {2023}, abstract = {Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.}, language = {en} } @unpublished{NeitzHoebartner2023, author = {Neitz, Hermann and H{\"o}bartner, Claudia}, title = {A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker}, series = {Chemical Communications}, journal = {Chemical Communications}, edition = {submitted version}, doi = {10.1039/D3CC03796G}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328255}, year = {2023}, abstract = {We report the fluorescent nucleoside ToldU and its application as a photoresponsive crosslinker in three different DNA architectures with enhanced fluorescence emission of the crosslinked products. The fluorogenic ToldU crosslinking reaction enables the assembly of DNA polymers in a hybridization chain reaction for the concentration-dependent detectio of a specific DNA sequence.}, language = {en} } @unpublished{DietzschJayachandranMuelleretal.2023, author = {Dietzsch, Julia and Jayachandran, Ajay and Mueller, Stefan and H{\"o}bartner, Claudia and Brixner, Tobias}, title = {Excitonic coupling of RNA-templated merocyanine dimer studied by higher-order transient absorption spectroscopy}, series = {Chemical Communications}, journal = {Chemical Communications}, edition = {submitted version}, doi = {10.1039/D3CC02024J}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-327772}, year = {2023}, abstract = {We report the synthesis and spectroscopic analysis of RNA containing the barbituric acid merocyanine rBAM2 as a nucleobase surrogate. Incorporation into RNA strands by solid-phase synthesis leads to fluorescence enhancement compared to the free chromophore. In addition, linear absorption studies show the formation of an excitonically coupled H-type dimer in the hybridized duplex. Ultrafast third- and fifth-order transient absorption spectroscopy of this non-fluorescent dimer suggests immediate (sub-200 fs) exciton transfer and annihilation due to the proximity of the rBAM2 units.}, language = {en} } @phdthesis{SanchezNaya2023, author = {S{\´a}nchez Naya, Roberto}, title = {Synthesis and Characterization of Dye-Containing Covalent Organic Frameworks}, doi = {10.25972/OPUS-28899}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-288996}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {The present thesis adress the synthesis and characterization of novel COFs that contain dye molecules as integral components of the organic backbone. These chromophore-containing frameworks open new research lines in the field and call for the exploration of applications such as catalysis, sensing, or in optoelectronic devices. Initially, the fabrication of organic-inorganic composites by the growth of DPP TAPP COF around functionalized iron oxide nanoparticles is reported. By varying the ratio between inorganic nanoparticles and organic COFs, optoelectronic properties of the materials are adjusted. The document also reports the synthesis of a novel boron dipyrromethene-containing (BODIPY) COF. Synthesis, full characterization and the scope of potential applications with a focus on environmental remediation are discussed in detail. Last, a novel diketopyrrolopyrrole-containing (DPP) DPP-Py-COF based on the combination of DDP and pyrene building blocks is presented. The very low bandgap of these materials and initial investigations on the photosensitizing properties are discussed.}, subject = {Organische Chemie}, language = {en} } @phdthesis{Menekşe2023, author = {Menek{\c{s}}e, Kaan}, title = {Fabrication of Organic Solar Cells, Screening of Non-Fullerene Acceptors and the Investigation of their Intermolecular Interactions}, doi = {10.25972/OPUS-29112}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-291124}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {In this thesis, intermolecular acceptor-acceptor interactions in organic solar cells based on new non-fullerene acceptors are addressed. For this purpose, first the reproducibility of organic electronic devices was tested on a new facility for their fabrication. This was followed by the screening for new acceptor materials. Based on this, three molecular systems were investigated with regard to their acceptor-acceptor interactions and their influence on solar cell efficiency.}, subject = {Organische Solarzelle}, language = {en} } @article{ScheitlOkudaAdelmannetal.2023, author = {Scheitl, Carolin P. M. and Okuda, Takumi and Adelmann, Juliane and H{\"o}bartner, Claudia}, title = {Ribozyme-catalyzed late-stage functionalization and fluorogenic labeling of RNA}, series = {Angewandte Chemie International Edition}, volume = {62}, journal = {Angewandte Chemie International Edition}, doi = {10.1002/anie.202305463}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-327543}, year = {2023}, abstract = {Site-specific introduction of biorthogonal handles into RNAs is in high demand for decorating RNAs with fluorophores, affinity labels or other modifications. Aldehydes represent attractive functional groups for post-synthetic bioconjugation reactions. Here, we report a ribozyme-based method for the synthesis of aldehyde-functionalized RNA by directly converting a purine nucleobase. Using the methyltransferase ribozyme MTR1 as an alkyltransferase, the reaction is initiated by site-specific N1 benzylation of purine, followed by nucleophilic ring opening and spontaneous hydrolysis under mild conditions to yield a 5-amino-4-formylimidazole residue in good yields. The modified nucleotide is accessible to aldehyde-reactive probes, as demonstrated by the conjugation of biotin or fluorescent dyes to short synthetic RNAs and tRNA transcripts. Upon fluorogenic condensation with a 2,3,3-trimethylindole, a novel hemicyanine chromophore was generated directly on the RNA. This work expands the MTR1 ribozyme's area of application from a methyltransferase to a tool for site-specific late-stage functionalization of RNA.}, language = {en} } @phdthesis{Fink2023, author = {Fink, Julian}, title = {Synthese von molekularen Werkzeugen zur Visualisierung und Untersuchung des Sphingolipidmetabolismus und weiterer biologischer Prozesse}, doi = {10.25972/OPUS-28699}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-286992}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {Die Zelle stellt die kleinste Einheit des Lebens dar und zeichnet sich durch die hoch koordinierte Anordnung von mehreren Millionen (Bio-)Molek{\"u}len zu einem mikrometergroßen Objekt aus. Als struktureller Bestandteil der Lipiddoppelschicht eukaryotischer Zellen spielt neben Sterolen und Glycerolipiden die Verbindungsklasse der Sphingolipide eine zentrale Rolle bei der Aufrechterhaltung der Membranintegrit{\"a}t.[472] Dar{\"u}ber hinaus sind bioaktive Sphingolipide bei vielen grundlegenden zellul{\"a}ren Prozessen wie Apoptose, Wachstum, Differenzierung, Migration und Adh{\"a}sion entscheidend beteiligt.[87,120] Ein gest{\"o}rtes Gleichgewicht des Sphingolipidmetabolismus und Defekte der entsprechenden Stoffwechselwege stehen im Zusammenhang mit vielen Krankheiten wie Krebs, Diabetes, Adipositas, Arteriosklerose, chronischen Entz{\"u}ndungen und Autoimmunerkrankungen sowie viraler und bakterieller Pathogenese.[22,143,473,474] Die Entwicklung und Anwendung von Sphingolipidanaloga als potenzielle Wirkstoffe r{\"u}ckten in den letzten Jahren immer weiter in den Fokus der interdisziplin{\"a}ren Forschung von Biologen, Chemikern und Medizinern. Als bekanntestes Beispiel ist Fingolimod (FTY720) zu nennen, das als Sphingosin-1-phosphat-Mimetikum heute unter dem Markennamen Gilenya® erfolgreich als Arzneistoff zur Behandlung von Multipler Sklerose eingesetzt wird.[475] Es besteht jedoch die Gefahr, dass Fingolimod zur Sch{\"a}digung anderer Zellfunktionen und zu gravierenden Nebeneffekten wie Bradykardie f{\"u}hren kann.[476] Da Sphingolipide ebenfalls in der Kontrolle von bakteriellen und viralen Infektionen essentiell beteiligt sind, spielen Sphingolipide und deren synthetisch dargestellte Derivate vermehrt eine Rolle in der Wirkstoffentwicklung im Kampf gegen pathogene Krankheitserreger.[175,477-479] Die Wirkweise von antimikrobiellen Sphingolipiden ist bisher nicht vollst{\"a}ndig aufgekl{\"a}rt. F{\"u}r eine Weiterentwicklung von bekannten Medikamenten gegen verschiedene Krankheiten oder f{\"u}r die Entwicklung neuartiger Wirkstoffe gegen Erreger ist eine umfassende Untersuchung der zugrundeliegenden zellul{\"a}ren Mechanismen auf molekularer Ebene entscheidend. Hierf{\"u}r finden aufgrund der relativ einfachen Detektion mittels Fluoreszenzmikroskopie h{\"a}ufig fluoreszenzmarkierte Sphingolipidderivate breite Anwendung.[480] Die kovalent gebundene Farbstoffeinheit bringt jedoch wesentliche Nachteile mit sich, da sich die Biomolek{\"u}le durch die ver{\"a}nderte Struktur und Polarit{\"a}t in ihren biologischen Eigenschaften von den nat{\"u}rlichen Substraten unterscheiden k{\"o}nnen. Die Verwendung von bioorthogonal funktionalisierten Biomolek{\"u}len umgeht dieses Problem, da die strukturellen {\"A}nderungen minimal gehalten werden. Nach dem zellul{\"a}ren Einbau dieser Derivate ist eine schnelle und spezifische Konjugation mit einem komplement{\"a}ren Fluorophor zu einem gew{\"u}nschten Zeitpunkt durch sogenannte Click-Reaktionen wie CuAAC oder SPAAC m{\"o}glich.[12,46] Das Prinzip der Click-Chemie wurde bereits auf eine Vielzahl an Biomolek{\"u}len wie Sphingolipide, Fetts{\"a}uren, Aminos{\"a}uren, Proteine, Kohlenhydrate, Nukleoside oder Nukleins{\"a}uren (DNA und RNA) {\"u}bertragen.[47,280] Jedoch bedarf es weiterer spezifisch modifizierter Verbindungen, die vielf{\"a}ltige bioorthogonale Reaktionen f{\"u}r die Untersuchung von Zellprozessen zulassen ‒ sowohl in vitro als auch in vivo. Um neue Therapieans{\"a}tze gegen verschiedene Krankheiten zu entwickeln und schwerwiegende Nebenwirkungen zu vermeiden, ist die detaillierte Erforschung hochkomplexer Zellvorg{\"a}nge auf molekularer Ebene von entscheidender Bedeutung. Das Ziel dieser Arbeit war daher die Synthese und Charakterisierung von molekularen Werkzeugen, die in Kombination mit verschiedenen aktuellen Mikroskopie- und Massenspektrometriemethoden die Visualisierung und Untersuchung des Sphingolipidmetabolismus und weiterer biologischer Prozesse erm{\"o}glichen. Zusammenfassend wurde in dieser Arbeit eine Vielzahl an Sphingolipiden und deren bioorthogonal funktionalisierte Analoga ausgehend von der Aminos{\"a}ure L-Serin erfolgreich synthetisiert. Die vorgestellten Verbindungen eignen sich in Kombination mit Massenspektrometrie und Fluoreszenz- oder Elektronenmikroskopie als molekulare Werkzeuge zur Untersuchung des komplexen Sphingolipidmetabolismus sowie des Einbaus und der Dynamik von Sphingolipiden in Modell- und Zellmembranen. Sowohl in humanen und tierischen Zellen als auch in Bakterien wurden die azidmodifizierten Sphingolipide durch Click-Reaktionen visualisiert, um ein verbessertes Verst{\"a}ndnis von bakteriellen und viralen Infektionsprozessen zu erhalten. Der modulare Ansatz der Click-Chemie erm{\"o}glicht die Verwendung verschiedener komplement{\"a}r funktionalisierter Farbstoffe, die unterschiedliche Eigenschaften bez{\"u}glich der Membrandurchg{\"a}ngigkeit oder Absorptions- und Emissionswellenl{\"a}ngen besitzen und somit je nach biologischer Fragestellung gezielt eingesetzt werden k{\"o}nnen. Alles in allem tragen die in dieser Arbeit synthetisierten Verbindungen dazu bei, die Rolle von Sphingolipiden bei Infektionsprozessen und Krankheitsverl{\"a}ufen auf subzellul{\"a}rer Ebene aufzukl{\"a}ren. Dadurch wird ein entscheidender Beitrag f{\"u}r die Entwicklung neuartiger Wirkstoffe gegen bakterielle oder virale Erreger sowie innovativer Therapien gegen verschiedene humane Krankheiten geliefert.}, subject = {Chemische Synthese}, language = {de} } @article{WildervanckHechtNowakKrol2022, author = {Wildervanck, Martijn J. and Hecht, Reinhard and Nowak-Kr{\´o}l, Agnieszka}, title = {Synthesis and strong solvatochromism of push-pull thienylthiazole boron complexes}, series = {Molecules}, volume = {27}, journal = {Molecules}, number = {17}, issn = {1420-3049}, doi = {10.3390/molecules27175510}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-286186}, year = {2022}, abstract = {The solvatochromic behavior of two donor-π bridge-acceptor (D-π-A) compounds based on the 2-(3-boryl-2-thienyl)thiazole π-linker and indandione acceptor moiety are investigated. DFT/TD-DFT calculations were performed in combination with steady-state absorption and emission measurements, along with electrochemical studies, to elucidate the effect of two different strongly electron-donating hydrazonyl units on the solvatochromic and fluorescence behavior of these compounds. The Lippert-Mataga equation was used to estimate the change in dipole moments (Δµ) between ground and excited states based on the measured spectroscopic properties in solvents of varying polarity with the data being supported by theoretical studies. The two asymmetrical D-π-A molecules feature strong solvatochromic shifts in fluorescence of up to ~4300 cm\(^{-1}\) and a concomitant change of the emission color from yellow to red. These changes were accompanied by an increase in Stokes shift to reach values as large as ~5700-5800 cm\(^{-1}\). Quantum yields of ca. 0.75 could be observed for the N,N-dimethylhydrazonyl derivative in nonpolar solvents, which gradually decreased along with increasing solvent polarity, as opposed to the consistently reduced values obtained for the N,N-diphenylhydrazonyl derivative of up to ca. 0.20 in nonpolar solvents. These two push-pull molecules are contrasted with a structurally similar acceptor-π bridge-acceptor (A-π-A) compound.}, language = {en} } @article{EderHollmannMandasarietal.2022, author = {Eder, Sascha and Hollmann, Claudia and Mandasari, Putri and Wittmann, Pia and Schumacher, Fabian and Kleuser, Burkhard and Fink, Julian and Seibel, J{\"u}rgen and Schneider-Schaulies, J{\"u}rgen and Stigloher, Christian and Beyersdorf, Niklas and Dembski, Sofia}, title = {Synthesis and characterization of ceramide-containing liposomes as membrane models for different T cell subpopulations}, series = {Journal of Functional Biomaterials}, volume = {13}, journal = {Journal of Functional Biomaterials}, number = {3}, issn = {2079-4983}, doi = {10.3390/jfb13030111}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-286130}, year = {2022}, abstract = {A fine balance of regulatory (T\(_{reg}\)) and conventional CD4\(^+\) T cells (T\(_{conv}\)) is required to prevent harmful immune responses, while at the same time ensuring the development of protective immunity against pathogens. As for many cellular processes, sphingolipid metabolism also crucially modulates the T\(_{reg}\)/T\(_{conv}\) balance. However, our understanding of how sphingolipid metabolism is involved in T cell biology is still evolving and a better characterization of the tools at hand is required to advance the field. Therefore, we established a reductionist liposomal membrane model system to imitate the plasma membrane of mouse T\(_{reg}\) and T\(_{conv}\) with regards to their ceramide content. We found that the capacity of membranes to incorporate externally added azide-functionalized ceramide positively correlated with the ceramide content of the liposomes. Moreover, we studied the impact of the different liposomal preparations on primary mouse splenocytes in vitro. The addition of liposomes to resting, but not activated, splenocytes maintained viability with liposomes containing high amounts of C\(_{16}\)-ceramide being most efficient. Our data thus suggest that differences in ceramide post-incorporation into T\(_{reg}\) and T\(_{conv}\) reflect differences in the ceramide content of cellular membranes.}, language = {en} } @article{OuyangRueheZhangetal.2022, author = {Ouyang, Guanghui and R{\"u}he, Jessica and Zhang, Yang and Lin, Mei-Jin and Liu, Minghua and W{\"u}rthner, Frank}, title = {Intramolecular Energy and Solvent-Dependent Chirality Transfer within a BINOL-Perylene Hetero-Cyclophane}, series = {Angewandte Chemie International Edition}, volume = {61}, journal = {Angewandte Chemie International Edition}, number = {31}, doi = {10.1002/anie.202206706}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-318818}, year = {2022}, abstract = {Multichromophoric macrocycles and cyclophanes are important supramolecular architectures for the elucidation of interchromophoric interactions originating from precise spatial organization. Herein, by combining an axially chiral binaphthol bisimide (BBI) and a bay-substituted conformationally labile twisted perylene bisimide (PBI) within a cyclophane of well-defined geometry, we report a chiral PBI hetero-cyclophane (BBI-PBI) that shows intramolecular energy and solvent-regulated chirality transfer from the BBI to the PBI subunit. Excellent spectral overlap and spatial arrangement of BBI and PBI lead to efficient excitation energy transfer and subsequent PBI emission with high quantum yield (80-98 \%) in various solvents. In contrast, chirality transfer is strongly dependent on the respective solvent as revealed by circular dichroism (CD) spectroscopy. The combination of energy and chirality transfer affords a bright red circularly polarized luminescence (CPL) from the PBI chromophore by excitation of BBI.}, language = {en} } @article{ScheidelOestreicherMarketal.2022, author = {Scheidel, Sebastian and {\"O}streicher, Laurina and Mark, Isabelle and P{\"o}ppler, Ann-Christin}, title = {You cannot fight the pressure: Structural rearrangements of active pharmaceutical ingredients under magic angle spinning}, series = {Magnetic Resonance in Chemistry}, volume = {60}, journal = {Magnetic Resonance in Chemistry}, number = {6}, doi = {10.1002/mrc.5267}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-318838}, pages = {572 -- 582}, year = {2022}, abstract = {Although solid-state nuclear magnetic resonance (NMR) is a versatile analytical tool to study polymorphs and phase transitions of pharmaceutical molecules and products, this work summarizes examples of spontaneous and unexpected (and unwanted) structural rearrangements and phase transitions (amorphous-to-crystalline and crystalline-to-crystalline) under magic angle spinning (MAS) conditions, some of them clearly being due to the pressure experienced by the samples. It is widely known that such changes can often be detected by X-ray powder diffraction (XRPD); here, the capability of solid-state NMR experiments with a special focus on \(^{1}\)H-\(^{13}\)C frequency-switched Lee-Goldburg heteronuclear correlation (FSLG HETCOR)/MAS NMR experiments to detect even subtle changes on a molecular level not observable by conventional 1D NMR experiments or XRPD is presented. Furthermore, it is shown that a polymorphic impurity combined with MAS can induce a crystalline-to-crystalline phase transition. This showcases that solid-state NMR is not always noninvasive and such changes upon MAS should be considered in particular when compounds are studied over longer time spans.}, language = {en} } @article{LiuVonhausenSchulzetal.2022, author = {Liu, Bin and Vonhausen, Yvonne and Schulz, Alexander and H{\"o}bartner, Claudia and W{\"u}rthner, Frank}, title = {Peptide Backbone Directed Self-Assembly of Merocyanine Oligomers into Duplex Structures}, series = {Angewandte Chemie International Edition}, volume = {61}, journal = {Angewandte Chemie International Edition}, number = {21}, doi = {10.1002/anie.202200120}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-318797}, year = {2022}, abstract = {The pseudopeptide backbone provided by N-(2-aminoethyl)-glycine oligomers with attached nucleobases has been widely utilized in peptide nucleic acids (PNAs) as DNA mimics. Here we demonstrate the suitability of this backbone for the formation of structurally defined dye stacks. Toward this goal a series of peptide merocyanine (PMC) dye oligomers connected to a N-(2-aminoethyl)-glycine backbone were prepared through peptide synthesis. Our concentration-, temperature- and solvent-dependent UV/Vis absorption studies show that under the control of dipole-dipole interactions, smaller-sized oligomers consisting of one, two or three dyes self-assemble into defined duplex structures containing two up to six chromophores. In contrast, upon further extension of the oligomer, the chosen peptide backbone cannot direct the formation of a defined duplex architecture anymore due to intramolecular aggregation between the dyes. For all aggregate species a moderate aggregation-induced emission enhancement is observed.}, language = {en} }