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Bioactivity-guided isolation supported by LC-HRESIMS metabolic profiling led to the isolation of two new compounds, a ceramide, stylissamide A (1), and a cerebroside, stylissoside A (2), from the methanol extract of the Red Sea sponge Stylissa carteri. Structure elucidation was achieved using spectroscopic techniques, including 1D and 2D NMR and HRMS. The bioactive extract’s metabolomic profiling showed the existence of various secondary metabolites, mainly oleanane-type saponins, phenolic diterpenes, and lupane triterpenes. The in vitro cytotoxic activity of the isolated compounds was tested against two human cancer cell lines, MCF-7 and HepG2. Both compounds, 1 and 2, displayed strong cytotoxicity against the MCF-7 cell line, with IC\(_{50}\) values at 21.1 ± 0.17 µM and 27.5 ± 0.18 µM, respectively. They likewise showed a promising activity against HepG2 with IC\(_{50}\) at 36.8 ± 0.16 µM for 1 and IC\(_{50}\) 30.5 ± 0.23 µM for 2 compared to the standard drug cisplatin. Molecular docking experiments showed that 1 and 2 displayed high affinity to the SET protein and to inhibitor 2 of protein phosphatase 2A (I2PP2A), which could be a possible mechanism for their cytotoxic activity. This paper spreads light on the role of these metabolites in holding fouling organisms away from the outer surface of the sponge, and the potential use of these defensive molecules in the production of novel anticancer agents.
Fluorogenic Aptamers and Fluorescent Nucleoside Analogs as Probes for RNA Structure and Function
(2020)
RNA plays a key role in numerous cellular processes beyond the central dogma of molecular biology. Observing and understanding this wealth of functions, discovering new ones and engineering them into purpose-built tools requires a sensitive means of observation. Over the past decade, fluorogenic aptamers have emerged to fill this niche. These short oligonucleotides are generated by in vitro selection to specifically interact with small organic fluorophores and can be utilized as genetically encoded tags for RNAs of interest.
The most versatile class of fluorogenic aptamers is based on derivatives of hydroxybenzylidene imidazolone (HBI), a conditional fluorophore mimicking the chromophore structure found in green and red fluorescent proteins. The respective aptamers are well-known by the “vegetable” nomenclature, including Spinach, Broccoli and Corn, and have found numerous applications for studying RNA function in vitro and in cells.
Their success, however, is somewhat overshadowed by individual shortcomings such as a propensity for misfolding, dependence on unphysiologically high concentrations of magnesium ions or, in the case of Corn, dimerization that might affect the function of the tagged RNA. Moreover, most fluorogenic aptamers exhibit limited ligand promiscuity by design, thereby restricting their potential for spectral tuning to a narrow window of wavelengths.
This thesis details the characterization of a new fluorogenic aptamer system nicknamed Chili. Chili is derived from an aptamer that was originally selected to bind 4-hydroxy-3,5-dimethoxy¬hydroxy-benzylidene imidazolone (DMHBI), resulting in a green fluorescent complex. Unlike other aptamers of its kind, Chili engages in a proton transfer cycle with the bound ligand, resulting in a remarkably large Stokes shift of more than 130 nm.
By means of an empirical ligand optimization approach, several new DMHBI derivatives were found that bind to Chili with high affinity, furnishing complexes up to 7.5 times brighter compared to the parent ligand. In addition, Chili binds to π-extended DMHBI derivatives that confer fluorescence in the yellow–red region of the visible spectrum. The highest affinity and degree of fluorescence turn-on for both green and red fluorogenic ligands were achieved by the incorporation of a unique, positively charged substituent into the HBI scaffold.
Supplemented by NMR spectroscopy, kinetic and thermodynamic studies showed that the binding site of Chili is loosely preorganized in the absence of ligand and likely forms a G-quadruplex upon ligand binding.
To showcase future applications, Chili was incorporated into a FRET sensor for monitoring the cleavage of an RNA substrate by a 10-23 DNAzyme.
Besides aptamers as macromolecular fluorescent complexes, fluorescent nucleobase analogs are powerful small isomorphic components of RNA suitable for studying structure and folding. Here, the highly emissive nucleobase analog 4-cyanoindole (4CI) was developed into a ribonucleoside (r4CI) for this purpose. A new phosphoramidite building block was synthesized to enable site-specific incorporation of 4CI into RNA.
Thermal denaturation experiments confirmed that 4CI behaves as a universal nucleobase, i.e. without bias towards any particular hybridization partner. Photophysical characterization established r4CI as a generally useful fluorescent ribonucleoside analog. In this work, it was employed to gain further insight into the structure of the Chili aptamer. Using several 4CI-modified Chili–HBI complexes, a novel base–ligand FRET assay was established to obtain a set of combined distance and orientation restraints for the tertiary structure of the aptamer.
In addition to their utility for interrogating structure and binding, supramolecular FRET pairs comprising a fluorescent nucleobase analog donor and an innately fluorogenic acceptor hold great promise for the construction of color-switchable RNA aptamer sensor devices.
We synthesized a series of new mono‐, di‐, tri‐ and tetra‐substituted perylene derivatives with strong bis(para‐methoxyphenyl)amine (DPA) donors at the uncommon 2,5,8,11‐positions. The properties of our new donor‐substituted perylenes were studied in detail to establish a structure‐property relationship. Interesting trends and unusual properties are observed for this series of new perylene derivatives, such as a decreasing charge transfer (CT) character with increasing number of DPA moieties and individual reversible oxidations for each DPA moiety. Thus, (DPA)‐Per possesses one reversible oxidation while (DPA)\(_{4}\)‐Per has four. The mono‐ and di‐substituted derivatives display unusually large Stokes shifts not previously reported for perylenes. Furthermore, transient absorption measurements of the new derivatives reveal an excited state with lifetimes of several hundred microseconds, which sensitizes singlet oxygen with quantum yields of up to 0.83.
Marine organisms and their associated microbes are rich in diverse chemical leads. With the development of marine biotechnology, a considerable number of research activities are focused on marine bacteria and fungi-derived bioactive compounds. Marine bacteria and fungi are ranked on the top of the hierarchy of all organisms, as they are responsible for producing a wide range of bioactive secondary metabolites with possible pharmaceutical applications. Thus, they have the potential to provide future drugs against challenging diseases, such as cancer, a range of viral diseases, malaria, and inflammation. This review aims at describing the literature on secondary metabolites that have been obtained from Scleractinian-associated organisms including bacteria, fungi, and zooxanthellae, with full coverage of the period from 1982 to 2020, as well as illustrating their biological activities and structure activity relationship (SAR). Moreover, all these compounds were filtered based on ADME analysis to determine their physicochemical properties, and 15 compounds were selected. The selected compounds were virtually investigated for potential inhibition for SARS-CoV-2 targets using molecular docking studies. Promising potential results against SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and methyltransferase (nsp16) are presented.
Obligate human pathogenic Neisseria gonorrhoeae are the second most frequent bacterial cause of sexually transmitted diseases. These bacteria invade different mucosal tissues and occasionally disseminate into the bloodstream. Invasion into epithelial cells requires the activation of host cell receptors by the formation of ceramide-rich platforms. Here, we investigated the role of sphingosine in the invasion and intracellular survival of gonococci. Sphingosine exhibited an anti-gonococcal activity in vitro. We used specific sphingosine analogs and click chemistry to visualize sphingosine in infected cells. Sphingosine localized to the membrane of intracellular gonococci. Inhibitor studies and the application of a sphingosine derivative indicated that increased sphingosine levels reduced the intracellular survival of gonococci. We demonstrate here, that sphingosine can target intracellular bacteria and may therefore exert a direct bactericidal effect inside cells.
Enzym-Modifikationen finden in der Natur in Form von posttranslationalen Protein-Modifikationen statt und sind ein faszinierender Mechanismus, um die biologische Vielfalt und Funktion von Proteinen um ein Vielfaches zu erhöhen. Daher ist es für ein ganzheitliches Verständnis bestimmter biologischer Prozesse oder enzymatischer Struktur-Funktions-Beziehungen unerlässlich, chemische Methoden zu entwickeln, die in der Lage sind, diese natürliche Diversität nachzuahmen.[61] Die wohl größte Herausforderung der chemischen Protein-Konjugation ist die chemo- und regioselektive Modifikation einer gezielten Aminosäure bei gleichzeitig milden und physiologischen Reaktionsbedingungen. Trotz zahlreich beschriebener Ansätze zur selektiven Protein-Modifikation, bedarf es weiterhin neuer Methoden, da viele bestehende Herangehens¬weisen auf ein spezielles System zugeschnitten sind.[9, 63]
Aus diesem Grund sollte im Rahmen dieser Arbeit eine breit anwendbare Methode zur selektiven chemischen Tyrosin-Modifikation am Modell der Levansucrase aus Bacillus megaterium entwickelt werden. Durch eine zweistufige Protein-Modifikation, bestehend aus einer En-Reaktion im ersten Schritt und einer Click-Reaktion im zweiten Konjugationsschritt, gelang es die Produktspezifität der Bm Levansucrase rational zu beeinflussen. Zunächst wurde die Tyrosin-spezifische En-Reaktion mit der Luminol-Verbindung 1 an natürlich vorkommenden Tyrosin-Seitenketten der Levansucrase erprobt und analysiert. Hierbei zeigte sich durch massenspektrometrische Untersuchungen, dass hauptsächlich zwei der 25 vorhandenen Tyrosin-Reste mit dem Luminol-Tag 1 modifiziert wurden, zu denen die Seitenketten Y247 und Y196 gehörten. Um die Auswirkungen der Tyrosin-Modifikation leichter interpretieren zu können und eine gegenseitige Beeinflussung auszuschließen, wurde vorerst mit der Einzelmutante Y247F gearbeitet. Da nach der ersten Modifikation der Variante Y247F geringe Veränderungen im Produkt¬spektrum beobachtet wurden, insbesondere im hoch-molekularen Bereich, wurde die Click-Reaktion im zweiten Schritt mit der Intention durchgeführt, diesen Effekt zu verstärken. Schließlich bewirkte die Click-Reaktion mit Azidoglucose (AzGlc) bei Variante Y247F-1-AzGlc eine erhebliche Verschiebung der Produktverteilung von kleinen Fructooligosacchariden (ca. 1100 Da) hin zu hoch-molekularem Levan (ca. 2,1∙106 Da).
Drei weitere Positionen, die in der dritten Zone des Enzyms liegen, wurden für die gentechnische Substitution gegen nicht-native Tyrosin-Reste ausgewählt. Dadurch wurden die Varianten E314Y, D248Y sowie F445Y erhalten und anschließend wie zuvor in zwei Schritten chemisch modifiziert. Die Modifikation dieser Varianten führte hinsichtlich der Veränderung des Produktprofils zu ähnlichen Ergebnissen, wie sie mit dem Enzym Y247F erhalten wurden (Übersicht 1, A). Um den Einfluss verschiedener Seitenketten zu analysieren, wurden neben der Azidoglucose vier weitere Azido-Verbindungen in der Click-Reaktion getestet.
Die Resultate aus den genannten Untersuchungen und die Einbeziehung molekular¬-dynamischer Simulationen ließen erste Rückschlüsse auf die mechanistischen Prozesse der Bm Levansucrase und deren gezielte Manipulation zu: Die Größe der eingeführten Seitenkette sowie die Fähigkeit des Tags polare Wechselwirkungen auszubilden, spielen eine entscheidende Rolle zur rationalen Modulation der Produkt¬spezifität. Insbesondere die räumliche Orientierung und Bewegung der Seitenkette 1 AzGlc und die damit einhergehende sterische Hinderung trugen dazu bei, eine vorzeitige Dissoziation der wachsenden Fructane zu verhindern und ermöglichten dadurch die prozessive Polymersynthese.
Weitere Erkenntnisse über den Levan-Elongationsmechanismus wurden durch die Modifikation der Varianten N126Y und S125Y erhalten. Diese lagen im Gegensatz zu den zuvor untersuchten Tyrosin-Resten nicht im Wachstumsverlauf des Substrats und besaßen zudem eine kürzere Distanz zum aktiven Zentrum. In beiden Fällen führte bereits die erste Modifikation mit Luminol-Derivat 1 zu völlig unter¬schiedlichen Produktprofilen im Vergleich zu den zuvor untersuchten Enzym-Varianten. Während mit der Variante N126Y-1 eine signifikante Akkumulation (bis zu 800 % Zunahme) verschiedener Oligosaccharide erzielt wurde, synthetisierte die Variante S125Y-1 schon nach dem ersten Modifikationsschritt Levan-Polymer (Übersicht 1, B/C). Die zugrunde-liegenden Interaktionen und Trajektorien der eingeführten Seitenkette wurden ebenfalls mit Hilfe von MD Simulationen analysiert und bestätigten die zuvor getroffenen Annahmen. Durch die räumliche Nähe zur Substrat-Bindungstasche reichte bei Variante S125Y 1 bereits die Luminol-Verbindung aus, um die Substrat-Dissoziation zu verhindern und damit die Polymer¬synthese zu induzieren. Hingegen dazu ergaben die Simulationen eine sehr dynamische und fluktuierende Seitenkette für N126Y-1, was vermutlich zur Destabilisierung initialer Wechselwirkungen zwischen Substrat und der Protein¬oberfläche führte und dadurch die Freisetzung und Akkumulation kurzer Oligo-saccharide begünstigte.
Durch die bioorthogonale chemische Einführung einer artifiziellen Seitenkette war es schließlich möglich, das Produktspektrum der Bm Levansucrase sowohl in Richtung Polymersynthese als auch in Richtung kurzer Oligosaccharide zu lenken. Unter Verwendung der Tyrosin-spezifischen En-Reaktion wurden dafür gezielt native und nicht-native Tyrosin-Reste selektiv modifiziert und in einer Folge¬reaktion mittels Click-Chemie zusätzlich derivatisiert. Die Auswirkungen der Modifikations-Reaktionen auf den Elongationsmechanismus des Substrats konnten durch MD-Simulationen aufgeklärt werden. Das Ziel, die Produktspezifität der Levansucrase rational zu beeinflussen und in eine gezielte Richtung zu steuern, wurde damit erfolgreich umgesetzt.
Ein weiterer Fokus dieser Arbeit lag darin, eine effiziente und einfache Methode zur Reinigung eines Fructan-Gemisches zu entwickeln, um damit den Zugang zu Oligo-sacchariden definierter Größen zu vereinfachen. Die Verfügbarkeit bestimmter Oligosaccharide in ausreichender Menge und Reinheit würde die Untersuchung von Fructanen auf ihre präbiotischen Eigenschaften erleichtern und zum Verständnis der Korrelation zwischen dem Darmmikrobiom und verschiedenen Krankheits¬bildern beitragen.[125] Mit Hilfe der Levansucrase-Variante K373L wurde ein Fructan-Gemisch synthetisiert, das im Vergleich zum Produkt¬profil des Wildtyps einen höheren Anteil kurzkettiger Oligosaccharide aufwies. In einem dreistufigen Reinigungsprozess wurde das Produktgemisch im ersten Schritt von den Monosacchariden Glucose und Fructose sowohl fermentativ durch den Hefe¬stamm H. polymorpha als auch chromatographisch per Silicagel separiert. Anschließend erfolgte eine grobe Trennung der Oligosaccharide nach dem Größen¬ausschlussprinzip mit einer Bio-Gel®P2-Säule. Im letzten Schritt wurde die Oligosaccharidfraktion, die hauptsächlich Tri- und Tetrasaccharide enthielt, schließlich mittels Umkehrphasen-Säulenchromatographie (RP18-HPLC) in die gewünschten Produkte aufgetrennt. Auf diese Weise gelang es, die Oligosaccharide 1 Kestose (28 %), 6 Kestose (56 %) und 6 Nystose (20 %) in hoher Reinheit (> 95 %) und moderaten Ausbeuten zu isolieren (Übersicht 2).
Der letzte Teil dieser Arbeit sollte die verschiedenen Disziplinen der Biokatalyse, chemischen Protein-Modifikation und Click-Reaktion mit einer neuen Kompontente, der Photokatalyse, verbinden und in einem innovativen Konzept die Grundlage für die Kombination dieser Forschungsbereiche schaffen. In diesem Kontext wurde einerseits eine lineare photo-biokatalysierte Kaskaden-Reaktion entworfen und vorbereitet, während andererseits die Synthese eines clickbaren Photokatalysators durchgeführt wurde (Übersicht 3). Für den enzymatischen Teil der Kaskaden-Reaktion wurden die Halogenasen RebH und RadH mit den zugehörigen Regenerationssystemen Fre und GDH erfolgreich in E. coli exprimiert, gereinigt und deren Aktivität nachgewiesen. Darüber hinaus wurde ein aktiver Alkin-funktionalisierter Photokatalysator synthetisiert, dessen Aktivität auch nach der Click-Reaktion mit einer Aminosäure und einem Peptid erhalten blieb. Damit wurden die Grundlagen geschaffen, um z. B. photoaktive Bausteine in ein Enzym einzubringen und somit neue lichtabhängige Reaktionszentren oder sogenannte Designer-Enzyme zu erzeugen.
Chemical processes mostly happen in fluid environments where reaction partners encounter via diffusion. The bimolecular encounters take place at a nanosecond time scale. The chemical environment (e.g., solvent molecules, (counter)ions) has a decisive influence on the reactivity as it determines the contact time between two molecules and affects the energetics. For understanding reactivity at an atomic level and at the appropriate dynamic time scale, it is crucial to combine matching experimental and theoretical data. Here, we have utilized all-atom molecular-dynamics simulations for accessing the key time scale (nanoseconds) using a QM/MM-Hamiltonian. Ion pairs consisting of a radical ion and its counterion are ideal systems to assess the theoretical predictions because they reflect dynamics at an appropriate time scale when studied by temperature-dependent EPR spectroscopy. We have investigated a diketone radical anion with its tetra-ethylammonium counterion. We have established a funnel-like transition path connecting two (equivalent) complexation sites. The agreement between the molecular-dynamics simulation and the experimental data presents a new paradigm for ion–ion interactions. This study exemplarily demonstrates the impact of the molecular environment on the topological states of reaction intermediates and how these states can be consistently elucidated through the combination of theory and experiment. We anticipate that our findings will contribute to the prediction of bimolecular transformations in the condensed phase with relevance to chemical synthesis, polymers, and biological activity.
Bowl-shaped naphthalimide-annulated corannulene as nonfullerene acceptor in organic solar cells
(2020)
An electron-poor bowl-shaped naphthalimide-annulated corannulene with branched alkyl residues in the imide position was synthesized by a palladium-catalyzed cross-coupling annulation sequence. This dipolar compound exhibits strong absorption in the visible range along with a low-lying LUMO level at –3.85 eV, enabling n-type charge transport in organic thin-film transistors. Furthermore, we processed inverted bulk-heterojunction solar cells in combination with the two donor polymers PCE–10 and PM6 to achieve open-circuit voltages up to 1.04 V. By using a blend of the self-assembled naphthalimide-annulated corannulene and PCE–10, we were able to obtain a power conversion efficiency of up to 2.1%, which is to the best of our knowledge the highest reported value for a corannulene-based organic solar cell to date.
Alzheimer′s disease (AD) is a neurological disorder with still no preventive or curative treatment. Flavonoids are phytochemicals with potential therapeutic value. Previous studies described the flavanone sterubin isolated from the Californian plant Eriodictyon californicum as a potent neuroprotectant in several in vitro assays. Herein, the resolution of synthetic racemic sterubin (1) into its two enantiomers, (R)‐1 and (S)‐1, is described, which has been performed on a chiral chromatographic phase, and their stereochemical assignment online by HPLC‐ECD coupling. (R)‐1 and (S)‐1 showed comparable neuroprotection in vitro with no significant differences. While the pure stereoisomers were configurationally stable in methanol, fast racemization was observed in the presence of culture medium. We also established the occurrence of extracted sterubin as its pure (S)‐enantiomer. Moreover, the activity of sterubin (1) was investigated for the first time in vivo, in an AD mouse model. Sterubin (1) showed a significant positive impact on short‐ and long‐term memory at low dosages.
Liquid crystal (LC) shape‐amphiphiles with a disc tethered to a fullerene have been intensely studied for the application in photovoltaics, and helical nanosegregation of C\(_{60}\) has been claimed around the π‐stacking disks based on X‐ray results. The most promising materials reported to date have been resynthesized and studied comprehensively by XRS, density measurements, modelling, and electron density reconstruction. In contrast to previous reports, the results indicate that metal phthalocyanine−fullerene mesogens pack in lamellar columnar phases with p2gm symmetry. Fullerenes assemble in layers and are flanked by phthalocyanine columns, thus explaining the balanced charge carrier mobility of electrons and holes. Such variable donor−acceptor structures are promising for organic electronic applications.
We present the rapid biophysical characterization of six previously reported putative G‐quadruplex‐forming RNAs from the 5′‐untranslated region (5′‐UTR) of silvestrol‐sensitive transcripts for investigation of their secondary structures. By NMR and CD spectroscopic analysis, we found that only a single sequence—[AGG]\(_{2}\)[CGG]\(_{2}\)C—folds into a single well‐defined G‐quadruplex structure. Sequences with longer poly‐G strands form unspecific aggregates, whereas CGG‐repeat‐containing sequences exhibit a temperature‐dependent equilibrium between a hairpin and a G‐quadruplex structure. The applied experimental strategy is fast and provides robust readout for G‐quadruplex‐forming capacities of RNA oligomers.
We report the direct imidization of naphthalene and perylene dicarboxylic anhydrides/esters with bulky ortho,ortho‐diaryl‐ and ortho,ortho‐dialkynylaniline derivatives. This imidization method uses n‐butyllithium as a strong base to increase the reactivity of bulky amine derivatives, proceeds under mild reaction conditions, requires only stoichiometric amounts of reactants and gives straightforward access to new sterically crowded rylene dicarboximides. Mechanistic investigations suggest an isoimide as intermediary product, which was converted to the corresponding imide upon addition of an aqueous base. Single‐crystal X‐ray diffraction analyses reveal dimeric packing motifs for monoimides, while two‐side shielded bisimides crystallize in isolated molecules without close π–π‐interactions. Spectroscopic investigations disclose the influence of the bulky substituents on the optical properties in the solid state.
Bioactivity-guided fractionation of a methanolic extract of the Red Sea cucumber Holothuria spinifera and LC-HRESIMS-assisted dereplication resulted in the isolation of four compounds, three new cerebrosides, spiniferosides A (1), B (2), and C (3), and cholesterol sulfate (4). The chemical structures of the isolated compounds were established on the basis of their 1D NMR and HRMS spectral data. Metabolic profiling of the H. spinifera extract indicated the presence of diverse secondary metabolites, mostly hydroxy fatty acids, diterpenes, triterpenes, and cerebrosides. The isolated compounds were tested for their in vitro cytotoxicities against the breast adenocarcinoma MCF-7 cell line. Compounds 1, 2, 3, and 4 displayed promising cytotoxic activities against MCF-7 cells, with IC\(_{50}\) values of 13.83, 8.13, 8.27, and 35.56 µM, respectively, compared to that of the standard drug doxorubicin (IC\(_{50}\) 8.64 µM). Additionally, docking studies were performed for compounds 1, 2, 3, and 4 to elucidate their binding interactions with the active site of the SET protein, an inhibitor of protein phosphatase 2A (PP2A), which could explain their cytotoxic activity. This study highlights the important role of these metabolites in the defense mechanism of the sea cucumber against fouling organisms and the potential uses of these active molecules in the design of new anticancer agents.
Deoxyribozymes (DNAzymes) are small, synthetic, single-stranded DNAs capable of catalysing chemical reactions, including RNA ligation. Herein, we report a novel class of RNA ligase deoxyribozymes that utilize 5’-adenylated RNA (5’-AppRNA) as the donor substrate, mimicking the activated intermediates of protein-catalyzed RNA ligation. Four new DNAzymes were identified by in vitro selection from an N40 random DNA library and were shown to catalyze the intermolecular linear RNA-RNA ligation via the formation of a native 3’-5’-phosphodiester linkage. The catalytic activity is distinct from previously described RNA-ligating deoxyribozymes. Kinetic analyses revealed the optimal incubation conditions for high ligation yields and demonstrated a broad RNA substrate scope. Together with the smooth synthetic accessibility of 5’-adenylated RNAs, the new DNA enzymes are promising tools for the protein-free synthesis of long RNAs, for example containing precious modified nucleotides or fluorescent labels for biochemical and biophysical investigations.
The self-assembly of a bowl-shaped naphthalimide-annulated corannulene of high solubility has been studied in a variety of solvents by NMR and UV/Vis spectroscopy. Evaluation by the anti-cooperative K\(_2\)-K model revealed the formation of supramolecular dimers of outstanding thermodynamic stability. Further structural proof for the almost exclusive formation of dimers over extended aggregates is demonstrated by atomic force microscopy (AFM) and diffusion ordered spectroscopy (DOSY) measurements as well as by theoretical calculations. Thus, herein we present the first report of a supramolecular dimer of an annulated corannulene derivative in solution and discuss its extraordinarily high thermodynamic stability with association constants up to > 10\(^6\)M\(^-\) \(^1\) in methylcyclohexane, which is comparable to the association constants given for planar phthalocyanine and perylene bisimide dyes.
In vitro selected ribozymes are promising tools for site-specific labeling of RNA. Previously known nucleic acid catalysts attached fluorescently labeled adenosine or guanosine derivatives through 2’,5’-branched phosphodiester bonds to the RNA of interest. Herein, we report new ribozymes that use orthogonal substrates, derived from the antiviral drug tenofovir, and attach bioorthogonal functional groups, as well as affinity handles and fluorescent reporter units through a hydrolytically more stable phosphonate ester linkage. The tenofovir transferase ribozymes were identified by in vitro selection and are orthogonal to nucleotide transferase ribozymes. As genetically encodable functional RNAs, these ribozymes may be developed for potential cellular applications. The orthogonal ribozymes addressed desired target sites in large RNAs in vitro, as shown by fluorescent labeling of E. coli 16S and 23S RNAs in total cellular RNA.
It is demonstrated that the di‐\(\pi\)‐methane (DPM) rearrangement of carbonyl‐substituted dibenzobarrelene (9,10‐dihydro‐9,10‐ethenoanthracene) derivatives is induced by visible‐light‐induced triplet photosensitization with Ir(ppy)\(_{3}\), Ir(dFppy)\(_{3}\) or 1‐butyl‐7,8‐dimethoxy‐3‐methylalloxazine as catalysts, whereas derivatives that lack carbonyl substituents are photoinert under these conditions. Notably, the products are formed almost quantitatively.
Catalytic water splitting is a viable process for the generation of renewable fuels. Here it is reported for the first time that a trinuclear supramolecular Ru(bda) (bda: 2,2′‐bipyridine‐6,6′‐dicarboxylate) catalyst, anchored on multi‐walled carbon nanotubes and subsequently immobilized on glassy carbon electrodes, shows outstanding performance in heterogeneous water oxidation. Activation of the catalyst on anodes by repetitive cyclic voltammetry (CV) scans results in a catalytic current density of 186 mA cm\(^{−2}\) at a potential of 1.45 V versus NHE. The activated catalyst performs water oxidation at an onset overpotential of 330 mV. The remarkably high stability of the hybrid anode is demonstrated by X‐ray absorption spectroscopy and electrochemically, revealing the absence of any degradation after 1.8 million turnovers. Foot of the wave analysis of CV data of activated electrodes with different concentrations of catalyst indicates a monomolecular water nucleophilic attack mechanism with an apparent rate constant of TOFmax (turnover frequency) of 3200 s\(^{−1}\).
N\(^6\)-Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes
(2020)
RNA-cleaving deoxyribozymes can serve as selective sensors and catalysts to examine the modification state of RNA. However, site-specific endonuclease deoxyribozymes that selectively cleave posttranscriptionally modified RNA are extremely rare and their specificity over unmodified RNA is low. In this study, we report that the native tRNA modification N\(^6\)-isopentenyladenosine (i\(^6\)A) strongly enhances the specificity and has the power to reconfigure the active site of an RNA-cleaving deoxyribozyme. Using in vitro selection, we identified a DNA enzyme that cleaves i\(^6\)A-modified RNA at least 2500-fold faster than unmodified RNA. Another deoxyribozyme shows unique and unprecedented behaviour by shifting its cleavage site in the presence of the i\(^6\)A RNA modification. Together with deoxyribozymes that are strongly inhibited by i\(^6\)A, these results highlight intricate ways of modulating the catalytic activity of DNA by posttranscriptional RNA modifications.
Single crystals of three at bay area tetraphenoxy‐substituted perylene bisimide dyes are grown by vacuum sublimation. X‐ray analysis reveals the self‐assembly of these highly twisted perylene bisimides (PBIs) in the solid state via imide–imide hydrogen bonding into hydrogen‐bonded PBI chains. The crystallographic insights disclose that the conformation and sterical congestion imparted by the phenoxy substituents can be controlled by ortho‐substituents. Accordingly, whilst sterically less demanding methyl and isopropyl substituents afford double‐stranded PBI chains of complementary P and M atropo‐enantiomers, single hydrogen‐bonded chains of homochiral PBIs are observed for the sterically more demanding ortho‐phenyl substituents. Investigation of the absorption and fluorescence properties of microcrystals and thin films of these PBIs allow for an unambiguous interpretation of these exciton systems. Thus, the J‐aggregates of the double‐stranded crystals exhibit a much larger (negative) exciton coupling than the single‐stranded one, which in contrast has the higher solid‐state fluorescence quantum yield.
Columnar Liquid Crystals from Star‐Shaped Conjugated Mesogens as Nano‐Reservoirs for Small Acceptors
(2020)
Shape‐persistent conjugated mesogens with oligothiophene arms of different lengths have been synthesized. Such mesogens possess free intrinsic space between their conjugated arms. They form columnar liquid‐crystalline phases, in which the void is filled by dense helical packing in the neat phase similar to an oligo(phenylene vinylene) derivative of equal size. The void can also be compensated by the inclusion of the small acceptor molecule 2,4,7‐trinitrofluorenone. In solution, the acceptor interacts with the core as the largest π‐surface, while in the solid material, it is incorporated between the arms and sandwiched by the star‐shaped neighbours along the columnar assemblies. The TNF acceptors are not nanosegregated from the star‐shaped donors, thus the liquid crystal structure converts to a nano‐reservoir for TNF (endo‐receptor). These host–guest arrangements are confirmed by comprehensive X‐ray scattering experiments and solid‐state NMR spectroscopy. This results in ordered columnar hexagonal phases at high temperatures, which change to helical columnar mesophases or to columnar soft crystals at room temperature.
Herein described is the discovery of three novel types of dimeric naphthylisoquinoline alkaloids, named mbandakamines, cyclombandakamines, and spirombandakamines. They were found in the leaves of a botanically as yet unidentified, potentially new Ancistrocladus species, collected in the rainforest of the Democratic Republic of the Congo (DRC). Mbandakamines showed an exceptional 6′,1′′-coupling, in the peri-position neighboring one of the outer axes, leading to an extremely high steric hindrance at the central axis, and to U-turn-like molecular shape, which – different from all other dimeric NIQs, whose basic structures are all quite linear – brings three of the four bicyclic ring systems in close proximity to each other. This created an unprecedented follow-up chemistry, involving ring closure reactions, leading to two further, structurally even more intriguing subclasses, the cyclo- and the spirombandakamines, displaying eight stereogenic elements (the highest total number ever found in naphthylisoquinoline alkaloids). The metabolites exhibited pronounced antiplasmodial and antitrypanosomal activities. Likewise reported in this doctoral thesis are the isolation and structural elucidation of naphthylisoquinoline alkaloids from two further potentially new Ancistrocladus species from DRC. Some of these metabolites have shown pronounced antiausterity activities against human pancreatic cancer PANC-1 cells.
In light of the rapidly increasing global demand of energy and the negative effects of climate change, innovative solutions that allow an efficient transition to a carbon-neutral economy are urgently needed. In this context, artificial photosynthesis is emerging as a promising technology to enable the storage of the fluctuating energy of sunlight in chemical bonds of transportable “solar fuels”. Thus, in recent years much efforts have been devoted to the development of robust water oxidation catalysts (WOCs) leading to the discovery of the highly reactive Ru(bda) (bda: 2,2’-bipyridine-6,6’-dicarboxylic acid) catalyst family. The aim of this thesis was the study of chemical and photocatalytic water oxidation with functionalized Ruthenium macrocycles to explore the impact of substituents on molecular properties and catalytic activities of trinuclear macrocyclic Ru(bda) catalysts. A further objective of this thesis comprises the elucidation of factors that influence the light-driven water oxidation process with this novel class of supramolecular WOCs.
The present thesis demonstrates how different thermodynamic aspects of self-assembly and stimuli-responsive properties in water can be encoded on the structure of π-amphiphiles, consisting of perylene or naphthalene bisimide cores. Initially, quantitative thermodynamic insights into the entropically-driven self-assembly was studied for a series of naphthalene bisimides with UV/Vis and ITC measurements, which demonstrated that their thermodynamic profile of aggregation is heavily influenced by the OEG side chains. Subsequently, a control over the bifurcated thermal response of entropically driven and commonly observed enthalpically driven self-assembly was achieved by the modulation of glycol chain orientation. Finally, Lower Critical Solution Temperature (LCST) phenomenon observed for these dyes was investigated as a precise control of this behavior is quintessential for self-assembly studies as well as to generate ‘smart’ materials. It could be shown that the onset of phase separation for these molecules can be encoded in their imide substituents, and they are primarily determined by the supramolecular packing, rather than the hydrophobicity of individual monomers.
The aim of the first part of this thesis was to investigate (R,R)-PBI as a model system for polymorphism at its origin by a supramolecular approach. The pathway complexity of (R,R)-PBI was fine-tuned by experimental parameters such as solvent, temperature and concentration to make several supramolecular polymorphs accessible. Mechanistic and quantum chemical studies on the kinetics and thermodynamics of the supramolecular polymerization of (R,R)-PBI were conducted to shed light on the initial stages of polymorphism. The second part of this work deals with mechanistic investigations on the supramolecular polymerization of the racemic mixture of (R,R)- and (S,S)-PBI with regard to homochiral and heterochiral aggregation leading to conglomerates and a racemic supramolecular polymer, respectively.
The research presented in this thesis illustrates that self-assembly of organic molecules guided by intermolecular forces is a versatile bottom-up approach towards functional materials. Through the specific design of the monomers, supramolecular architectures with distinct spatial arrangement of the individual building blocks can be realized. Particularly intriguing materials can be achieved when applying the supramolecular approach to molecules forming liquid-crystalline phases as these arrange in ordered, yet mobile structures. Therefore, they exhibit anisotropic properties on a macroscopic level. It is pivotal to precisely control the interchromophoric arrangement as functions originate in the complex structures that are formed upon self-assembly. Consequently, the aim of this thesis was the synthesis and characterization of liquid-crystalline phases with defined supramolecular arrangements as well as the investigation of the structure-property relationship. For this purpose, perylene bisimide and diketopyrrolopyrrole chromophores were used as they constitute ideal building blocks towards functional supramolecular materials due to their thermal stability, lightfastness, as well as excellent optical and electronic features desirable for the application in, e.g., organic electronics.
Squaraine dyes have attracted more attention in the past decade due to their strong and narrow absorption and fluorescence along with the easily functionalized molecular structure. One successful approach of core functionalization is to replace one oxygen of the squaric carbonyl group with a dicyanomethylene group, which shifts the absorption and emission into the near infrared (NIR) region and at the same time leads to a rigid, planar structure with C2v symmetry. However, such squaraines tend to aggregate cofacially in solution due to dispersion forces and dipole-dipole interactions, usually leading to H-type exciton coupling with undesired blue-shifted spectrum and quenched fluorescence. Therefore, the goal of my research was the design of dicyanomethylene-substituted squaraine dyes that self-assemble into extended aggregates in solution with J-type coupling, in order to retain or even enhance their outstanding optical properties. Toward this goal, bis(squaraine) dyes were envisioned with two squaraine units covalently linked to trigger a slip-stacked packing motif within the aggregates to enable J-type coupling.
In my first project, bis(squaraine) dye BisSQ1 was synthesized, in which two dicyanomethylene squaraine chromophores are covalently linked. Concentration and temperature-dependent UV/Vis/NIR spectroscopy experiments reveal that BisSQ1 undergoes cooperative self-assembly resulting in J-type aggregates in a solvent mixture of toluene/1,1,2,2-tetrachloroethane (TCE) (98:2, v/v). The J type exciton coupling is evident from the significantly red shifted absorption maximum at 886 nm and the fluorescence peak at 904 nm. In conclusion, this was a first example to direct squaraine dye aggregation in solution to the more desired slip-stacked packing leading to J-type exciton coupling by simply connecting two dyes in a head-to-tail bis chromophore structure.
Connecting two squaraine dyes with an additional phenylene spacer (BisSQ2) leads to two different polymorphs with very distinct absorption spectra upon cooling down a solution of BisSQ2 in a solvent mixture of toluene/TCE (98:2, v/v) with different rates. Accordingly, rapid cooling resulted in rigid helical nanorods with an absorption spectrum showing a panchromatic feature, while slow cooling led to a sheet-like structure with a significant bathochromic shift in the absorption spectrum.
It was discovered that the conventional molecular exciton model failed to explain the panchromatic absorption features of the nanorods for the given packing arrangement, therefore more profound theoretical investigations based on the Essential States Model (ESM) were applied to unveil the importance of intermolecular charge transfer (ICT) to adequately describe the panchromatic absorption spectrum. Moreover, the red-shift observed in the spectrum for the sheet-like structure can be assigned to the interplay of Coulomb coupling and ICT-mediated coupling.
Furthermore, the same bis-chromophore strategy was adopted for constructing an NIR-II emitter with a bathochromically-shifted spectrum. In chloroform, BisSQ3 exhibits an absorption maximum at 961 nm with a significant bathochromic shift (1020 cm−1) compared to the reference mono-squaraine SQ, indicating intramolecular J-type coupling via head-to-tail arrangement of two squaraine dyes. Moreover, BisSQ3 shows a fluorescence peak at 971 nm with a decent quantum yield of 0.33%. In less polar toluene, BisSQ3 self-assembles into nanofibers with additional intermolecular J-type coupling, causing a pronounced bathochromic shift with absorption maximum at 1095 nm and a fluorescence peak at 1116 nm. Thus, connecting two quinoline-based squaraines in a head-to-tail fashion leads to not only intra-, but also intermolecular J-type exciton coupling, which serves as a promising strategy to shift the absorption and emission of organic fluorophores into the NIR-II window while retaining decent quantum yields.
In conclusion, my research illustrates based on squaraine dyes how a simple modification of the molecular structure can significantly affect the aggregation behavior and further alter the optical properties of dye aggregates. Elongated supramolecular structures based on dicyanomethylene substituted squaraine dyes were successfully established by covalently linking two squaraine units to form a bis-chromophore structure. Then, a simple but efficient general approach was established to direct squaraine dye aggregation in solution to the more desired slip-stacked packing leading to J-type exciton coupling by directly connecting two squaraine dyes in a head-to-tail fashion without spacer units. Moreover, the additional spacer between the squaraine dyes in BisSQ2 allowed different molecular conformations, which leads to two different morphologies depending on the cooling rates for a hot solution. Hence, this is a promising strategy to realize supramolecular polymorphism.
In general, it is expected that the concept of constructing J-aggregates by the bis-chromophore approach can be extended to entirely different classes of dyes since J-aggregates possess a variety of features such as spectral shifts into the NIR window, fluorescence enhancement, and light harvesting, which are commonly observed and utilized for numerous fundamental studies and applications. Moreover, the insights on short-range charge transfer coupling for squaraine dyes is considered of relevance for all materials based on alternating donor-acceptor π-systems. The panchromatic spectral feature is in particular crucial for acceptor-donor-acceptor (ADA) dyes, which are currently considered as very promising materials for the development of bulk heterojunction solar cells.
Within this thesis the interactions between novel corannulene derivatives in solution as well as in the solid state by changing the imide residue of a literature known extended corannulene dicarboximide were investigated, in order to obtain a better understanding of the packing and possible charge transport in potential applications. Accordingly, the goal of the work was to synthesize and investigate an electron-poor corannulene bis(dicarboximide) based on previously published work but with higher solubility and less steric encumbrance in imide position to enable self-assembly in solution.
To obtain further insights into the conformational stability, structure and chiroptical properties of heavily twisted PBIs another aim of this thesis was the design, synthesis, and optoelectronic investigation of various fourfold directly arylated PBIs by substitution in bay position with smaller hydrocarbons with different steric demand, i.e., benzene, naphthalene and pyrene, which should be separable by chiral high performance liquid chromatography (HPLC).
As of yet, no concise study concerning the optical and electronic properties of differently core-substituted PBIs in the neutral as well as the mono- and dianionic state in solution is available, which also elucidates the origin of the different optical transitions observed in the absorption and emission spectra. Thus, in this thesis, the investigation of five PBI derivatives with different frontier energetic levels to produce a reference work of reduced PBIs was tackled.
The ongoing transition from fossil to renewable feedstocks demands new efficient processes for an economically viable production of biomass‐derived commodities and fine chemicals. Novel energy‐ and material‐efficient product purification and separation will play a crucial role due to altered product and feed composition. The present study comprises the synthesis and tests of cross‐linked p‐vinylphenylboronate polymers for the separation of 18 diols, sugar alcohols, and saccharides, which can be obtained during biomass processing. The separation was based on molecular recognition, that is, esterification of the phenylboronate with vicinal diols. A correlation of the molecular complexation constant, the polymer swelling, and the maximum adsorption capacity was found. The adsorption curves over time were recorded. Preliminary results on competitive adsorption of binary mixtures showed a high potential for the separation of substrates with significantly different complexation constants. Desorption tests implied easier desorption of substrates that only adsorb on the outer polymer shell.
Detection of metals in different environments with high selectivity and specificity is one of the prerequisites of the fight against environmental pollution with these elements. Pyrenes are well suited for the fluorescence sensing in different media. The applied sensing principle typically relies on the formation of intra- and intermolecular excimers, which is however limiting the sensitivity range due to masking of e. g. quenching effects by the excimer emission. Herein we report a highly selective, structurally rigid chemical sensor based on the monomer fluorescence of pyrene moieties bearing triazole groups. This sensor can quantitatively detect Cu\(^{2+}\), Pb\(^{2+}\) and Hg\(^{2+}\) in organic solvents over a broad concentrations range, even in the presence of ubiquitous ions such as Na\(^{+}\), K\(^{+}\), Ca\(^{2+}\) and Mg\(^{2+}\). The strongly emissive sensor's fluorescence with a long lifetime of 165 ns is quenched by a 1 : 1 complex formation upon addition of metal ions in acetonitrile. Upon addition of a tenfold excess of the metal ion to the sensor, agglomerates with a diameter of about 3 nm are formed. Due to complex interactions in the system, conventional linear correlations are not observed for all concentrations. Therefore, a critical comparison between the conventional Job plot interpretation, the method of Benesi-Hildebrand, and a non-linear fit is presented. The reported system enables the specific and robust sensing of medically and environmentally relevant ions in the health-relevant nM range and could be used e. g. for the monitoring of the respective ions in waste streams.
Within this PhD thesis, chromophore-bridged biradicals were synthesised and their properties characterised. Therefore, it was necessary to develop novel synthetic procedures and implement several experimental characterisation methods. In summary, within this thesis the scope of pigment chromophore phenoxyl radical decoration was further explored and expanded to IIn as well as DPP colourants. HOMA analysis highlighted the importance of aromaticity in order to understand the spin crossover from heteroaromatic quinoidal to aromatic open shell DPPs. Finally, PBI, IIn and DPP biradicals were advanced towards stable materials by introduction of nitronyl nitroxide radical centres.
Our research group focusses on the isolation, structural elucidation, and synthesis of bioactive natural products, among others, the naphthylisoquinoline alkaloids from tropical lianas. This intriguing class of compounds comprises representatives with activities against, e.g. P. falciparum, the cause of Malaria tropica, against the neglected disease leishmaniasis, and, as discovered more recently, against different types of cancer cells. Based on the high potency of theses extraordinary secondary metabolites, this thesis was devoted to the total synthesis of bioactive natural products and closely related analogs.
Deoxyribozymes are emerging as modification-specific endonucleases for the analysis of epigenetic RNA modifications. Here, we report RNA-cleaving deoxyribozymes that differentially respond to the presence of natural methylated cytidines, 3-methylcytidine (m\(^3\)C), N\(^4\)-methylcytidine (m\(^4\)C), and 5-methylcytidine (m\(^5\)C), respectively. Using in vitro selection, we found several DNA catalysts, which are selectively activated by only one of the three cytidine isomers, and display 10- to 30-fold accelerated cleavage of their target m\(^3\)C-, m\(^4\)C- or m\(^5\)C-modified RNA. An additional deoxyribozyme is strongly inhibited by any of the three methylcytidines, but effectively cleaves unmodified RNA. The mXC-detecting deoxyribozymes are programmable for the interrogation of natural RNAs of interest, as demonstrated for human mitochondrial tRNAs containing known m\(^3\)C and m\(^5\)C sites. The results underline the potential of synthetic functional DNA to shape highly selective active sites.
Deoxyribozymes are emerging as modification-specific endonucleases for the analysis of epigenetic RNA modifications. Here, we report RNA-cleaving deoxyribozymes that differentially respond to the presence of natural methylated cytidines, 3-methylcytidine (m\(^3\)C), N\(^4\)-methylcytidine (m\(^4\)C), and 5-methylcytidine (m\(^5\)C), respectively. Using in vitro selection, we found several DNA catalysts, which are selectively activated by only one of the three cytidine isomers, and display 10- to 30-fold accelerated cleavage of their target m\(^3\)C-, m\(^4\)C- or m\(^5\)C-modified RNA. An additional deoxyribozyme is strongly inhibited by any of the three methylcytidines, but effectively cleaves unmodified RNA. The m\(^X\)C-detecting deoxyribozymes are programmable for the interrogation of natural RNAs of interest, as demonstrated for human mitochondrial tRNAs containing known m\(^3\)C and m\(^5\)C sites. The results underline the potential of synthetic functional DNA to shape highly selective active sites.
Two series of organic–inorganic composite materials were synthesized through solvothermal imine condensation between diketopyrrolopyrrole dialdehyde DPP-1 and 5,10,15,20-tetrakis(4-aminophenyl)porphyrin (TAPP) in the presence of varying amounts of either amino- or carboxy-functionalized superparamagnetic iron oxide nanoparticles (FeO). Whereas high FeO loading induced cross-linking of the inorganic nanoparticles by amorphous imine polymers, a lower FeO content resulted in the formation of crystalline covalent organic framework domains. All hybrid materials were analyzed by magnetization measurements, powder X-ray diffraction, electron microscopy, IR, and UV/Vis absorption spectroscopy. Crystallinity, chromophore stacking, and visible absorption features are directly correlated to the mass fraction of the components, thus allowing for a fine-tuning of materials properties.
Chemical investigation of the methanolic extract of the Red Sea cucumber Holothuria spinifera led to the isolation of a new cerebroside, holospiniferoside (1), together with thymidine (2), methyl-α-d-glucopyranoside (3), a new triacylglycerol (4), and cholesterol (5). Their chemical structures were established by NMR and mass spectrometric analysis, including gas chromatography–mass spectrometry (GC–MS) and high-resolution mass spectrometry (HRMS). All the isolated compounds are reported in this species for the first time. Moreover, compound 1 exhibited promising in vitro antiproliferative effect on the human breast cancer cell line (MCF-7) with IC\(_{50}\) of 20.6 µM compared to the IC50 of 15.3 µM for the drug cisplatin. To predict the possible mechanism underlying the cytotoxicity of compound 1, a docking study was performed to elucidate its binding interactions with the active site of the protein Mdm2–p53. Compound 1 displayed an apoptotic activity via strong interaction with the active site of the target protein. This study highlights the importance of marine natural products in the design of new anticancer agents.
Metabolic glycoengineering enables a directed modification of cell surfaces by introducing target molecules to surface proteins displaying new features. Biochemical pathways involving glycans differ in dependence on the cell type; therefore, this technique should be tailored for the best results. We characterized metabolic glycoengineering in telomerase-immortalized human mesenchymal stromal cells (hMSC-TERT) as a model for primary hMSC, to investigate its applicability in TERT-modified cell lines. The metabolic incorporation of N-azidoacetylmannosamine (Ac\(_4\)ManNAz) and N-alkyneacetylmannosamine (Ac\(_4\)ManNAl) into the glycocalyx as a first step in the glycoengineering process revealed no adverse effects on cell viability or gene expression, and the in vitro multipotency (osteogenic and adipogenic differentiation potential) was maintained under these adapted culture conditions. In the second step, glycoengineered cells were modified with fluorescent dyes using Cu-mediated click chemistry. In these analyses, the two mannose derivatives showed superior incorporation efficiencies compared to glucose and galactose isomers. In time-dependent experiments, the incorporation of Ac\(_4\)ManNAz was detectable for up to six days while Ac\(_4\)ManNAl-derived metabolites were absent after two days. Taken together, these findings demonstrate the successful metabolic glycoengineering of immortalized hMSC resulting in transient cell surface modifications, and thus present a useful model to address different scientific questions regarding glycosylation processes in skeletal precursors.
Genetic deficiency for acid sphingomyelinase or its pharmacological inhibition has been shown to increase Foxp3\(^+\) regulatory T-cell frequencies among CD4\(^+\) T cells in mice. We now investigated whether pharmacological targeting of the acid sphingomyelinase, which catalyzes the cleavage of sphingomyelin to ceramide and phosphorylcholine, also allows to manipulate relative CD4\(^+\) Foxp3\(^+\) regulatory T-cell frequencies in humans. Pharmacological acid sphingomyelinase inhibition with antidepressants like sertraline, but not those without an inhibitory effect on acid sphingomyelinase activity like citalopram, increased the frequency of Foxp3\(^+\) regulatory T cell among human CD4\(^+\) T cells in vitro. In an observational prospective clinical study with patients suffering from major depression, we observed that acid sphingomyelinase-inhibiting antidepressants induced a stronger relative increase in the frequency of CD4\(^+\) Foxp3\(^+\) regulatory T cells in peripheral blood than acid sphingomyelinase-non- or weakly inhibiting antidepressants. This was particularly true for CD45RA\(^-\) CD25\(^{high}\) effector CD4\(^+\) Foxp3\(^+\) regulatory T cells. Mechanistically, our data indicate that the positive effect of acid sphingomyelinase inhibition on CD4\(^+\) Foxp3\(^+\) regulatory T cells required CD28 co-stimulation, suggesting that enhanced CD28 co-stimulation was the driver of the observed increase in the frequency of Foxp3+ regulatory T cells among human CD4\(^+\) T cells. In summary, the widely induced pharmacological inhibition of acid sphingomyelinase activity in patients leads to an increase in Foxp3+ regulatory T-cell frequencies among CD4\(^+\) T cells in humans both in vivo and in vitro.
Poorly water-soluble drugs frequently solubilize into bile colloids and this natural mechanism is key for efficient bioavailability. We tested the impact of pharmaceutical polymers on this solubilization interplay using proton nuclear magnetic resonance spectroscopy, dynamic light scattering, and by assessing the flux across model membranes. Eudragit E, Soluplus, and a therapeutically used model polymer, Colesevelam, impacted the bile-colloidal geometry and molecular interaction. These polymer-induced changes reduced the flux of poorly water-soluble and bile interacting drugs (Perphenazine, Imatinib) but did not impact the flux of bile non-interacting Metoprolol. Non-bile interacting polymers (Kollidon VA 64, HPMC-AS) neither impacted the flux of colloid-interacting nor colloid-non-interacting drugs. These insights into the drug substance/polymer/bile colloid interplay potentially point towards a practical optimization parameter steering formulations to efficient bile-solubilization by rational polymer selection.
Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryoelectron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3ʹ-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3ʹ-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3ʹ-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.
Two di- and tetranuclear Ru(bda) (bda: 2,2′-bipyridine-6,6′-dicarboxylate) macrocyclic complexes were synthesized and their catalytic activities in chemical and photochemical water oxidation investigated in a comparative manner to our previously reported trinuclear congener. Our studies have shown that the catalytic activities of this homologous series of multinuclear Ru(bda) macrocycles in homogeneous water oxidation are dependent on their size, exhibiting highest efficiencies for the largest tetranuclear catalyst. The turnover frequencies (TOFs) have increased from di- to tetranuclear macrocycles not only per catalyst molecule but more importantly also per Ru unit with TOF of 6 \(^{-1}\) to 8.7 \(^{-1}\) and 10.5 s\(^{-1}\) in chemical and 0.6 s\(^{-1}\) to 3.3 \(^{-1}\) and 5.8 \(^{-1}\) in photochemical water oxidation per Ru unit, respectively. Thus, for the first time, a clear structure–activity relationship could be established for this novel class of macrocyclic water oxidation catalysts.
Parallel polar dimers in the columnar self‐assembly of umbrella‐shaped subphthalocyanine mesogens
(2021)
The self-assembly of umbrella-shaped mesogens is explored with subphthalocyanine cores and oligo(thienyl) arms with different lengths in the light of their application as light-harvesting and photoconducting materials. While the shortest arm derivatives self-assemble in a conventional columnar phase with a single mesogen as a repeating unit, the more extended derivatives generate dimers that pile up into liquid crystalline columns.
In contrast to the antiparallel arrangement known from single crystals, the present mesogens align as parallel dimers in polar columnar phases as confirmed by X-ray scattering, experimental densities, dielectric spectroscopy, second harmonic generation, alignment, and conductivity studies.
UV–vis and fluorescence spectroscopies reveal a broad absorption in the visible range and only weak emission of the Q-band. Thus, these light-collecting molecules forming strongly polar columnar mesophases are attractive for application in the area of photoconductive materials.
Inspired by the fact that sufficient solubility in aqueous media can be achieved by functional substitution of perylene bisimides (PBIs) with polar groups, one of the essential aims of this thesis was the design and successful synthesis of the new water-soluble PBI cyclophanes [2PBI]-1m and [2PBI]-1p, which are appended with branched, hydrophilic oligoethylene glycol (OEG) chains. Subsequently, the focus was set on the elucidation of properties of PBI cyclophane hosts which are also of relevance for recognition processes in biological systems. The performance of the new amphiphilic PBI cyclophane [2PBI]-1p as synthetic receptors for various natural aromatic alkaloids in aqueous media was thoroughly investigated. Alkaloids represent a prominent class of ubiquitous nitrogen containing natural compounds with a great structural variety and diverse biological activity. As of yet, no chromophore host acting as a molecular probe for a range of alkaloids such as harmine or harmaline is known. In addition, the self-association behavior of cyclophane host [2PBI]-1m and its reference monomer in water was studied in order to gain insights into the thermodynamic driving forces affecting the self-assembly process of these two PBI systems in aqueous environment. Moreover, the chirality transfer upon guest binding previously observed for a PBI cyclophane was investigated further. The assignment of the underlying mechanism of guest recognition to either the induced fit or conformational selection model was of particular interest.
Main objectives of the present dissertation can be divided in two parts. The first part deals with setting up a spectroscopic technique for reliable and accurate measurements of the two-photon absorption (2PA) cross section spectra. In the second part, this firmly established experimental technique together with conventional spectroscopic characterization, quantum-chemical computations and theoretical modelling calculations was combined and therefore used as a tool to gain information for the so-called structure-property relationship through several molecular compounds.
Nucleic acids are one of the important classes of biomolecules together with carbohydrates, proteins and lipids. Both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are most well known for their respective roles in the storage and expression of genetic information.
Over the course of the last decades, nucleic acids with a variety of other functions have been discovered in biological organisms or created artificially. Examples of these functional nucleic acids are riboswitches, aptamers and ribozymes. In order to gain information regarding their function, several analytical methods can be used.
Electron paramagnetic resonance (EPR) spectroscopy is one of several techniques which can be used to study nucleic acid structure and dynamics. However, EPR spectroscopy requires unpaired electrons and because nucleic acids themselves are not paramagnetic, the incorporation of spin labels which carry a radical is necessary.
Here, three new spin labels for the analysis of nucleic acids by EPR spectroscopy are presented. All of them share two important design features. First, the paramagnetic center is located at a nitroxide, flanked by ethyl groups to prevent nitroxide degradation, for example during solid phase synthesis. Furthermore, they were designed with rigidity as an important quality, in order to be useful for applications like pulsed electron double resonance (PELDOR) spectroscopy, where independent motion of the spin labels relative to the macromolecule has a noticeable negative effect on the precision of the measurements.
Benzi-spin is a spin label which differs from most previous examples of rigid spin labels in that rather than being based on a canonical nucleoside, with a specific base pairing partner, it is supposed to be a universal nucleoside which is sufficiently rigid for EPR measurements when placed opposite to a number of different nucleosides. Benzi-spin was successfully incorporated into a 20 nt oligonucleotide and its base pairing behavior with seven different nucleosides was examined by UV/VIS thermal denaturation and continuous wave (CW) EPR experiments. The results show only minor differences between the different nucleosides, thus confirming the ability of benzi-spin to act as a universally applicable spin label.
Lumi-spin is derived from lumichrome. It features a rigid scaffold, as well as a free 2'-hydroxy group, which should make it well suited for PELDOR experiments once it is incorporated into RNA oligonucleotides.
EÇr is based on the Ç family of spin labels, which contains the most well known rigid spin labels for nucleic acids to this day. It is essentially a version of EÇm with a free 2'-hydroxy group. It was converted to triphosphate EÇrTP and used for primer extension experiments to test the viability of enzymatic incorporation of rigid spin labels into oligonucleotides as an alternative to solid-phase synthesis. Incorporation into DNA by Therminator III DNA polymerase in both single-nucleotide and full-length primer extensions was achieved.
All three of these spin labels represent further additions to the expanding toolbox of EPR spectroscopy on nucleic acids and might prove valuable for future research.
Sphingolipids, including ceramides, are a diverse group of structurally related lipids composed of a sphingoid base backbone coupled to a fatty acid side chain and modified terminal hydroxyl group. Recently, it has been shown that sphingolipids show antimicrobial activity against a broad range of pathogenic microorganisms. The antimicrobial mechanism, however, remains so far elusive. Here, we introduce 'click-AT-CLEM', a labeling technique for correlated light and electron microscopy (CLEM) based on the super-resolution array tomography (srAT) approach and bio-orthogonal click chemistry for imaging of azido-tagged sphingolipids to directly visualize their interaction with the model Gram-negative bacterium Neisseria meningitidis at subcellular level. We observed ultrastructural damage of bacteria and disruption of the bacterial outer membrane induced by two azido-modified sphingolipids by scanning electron microscopy and transmission electron microscopy. Click-AT-CLEM imaging and mass spectrometry clearly revealed efficient incorporation of azido-tagged sphingolipids into the outer membrane of Gram-negative bacteria as underlying cause of their antimicrobial activity.
Zwei Arten helikal-chiraler Verbindungen mit einem oder zwei Boratomen wurden nach einem modularen Ansatz synthetisiert. Die Bildung der helikalen Strukturen erfolgte durch Einführung von Bor in flexible Biaryl- bzw. Triaryl-Vorstufen, hergestellt aus kleinen achiralen Bausteinen. Die durchgehend ortho-fusionierten Azabora[7]helicene zeichnen sich dabei durch außergewöhnliche Konfigurationsstabilität, blaue oder grüne Fluoreszenz in Lösung mit Quantenausbeuten (Φ\(_{fl}\)) von 18–24 %, grüne oder gelbe Emission im Festkörper (Φ\(_{fl}\) bis zu 23 %) und starke chiroptische Resonanz mit großen Anisotropiefaktoren von bis zu 1.12×10\(^{-2}\) aus. Azabora[9]helicene, aufgebaut aus winkelförmig sowie linear angeordneten Ringen, sind blaue Emitter mit Φ\(_{fl}\) von bis zu 47 % in CH\(_{2}\)Cl\(_{2}\) und 25 % im Festkörper. DFT-Rechnungen zeigen, dass ihre P-M-Interkonversion über einen komplexeren Weg verläuft als im Fall von H1. Röntgenstrukturanalyse von Einkristallen zeigt deutliche Unterschiede in der Packungsanordnung von Methyl- und Phenylderivaten auf. Die Moleküle werden als Primärstrukturen verlängerter Helices vorgeschlagen.
Durch stetige Entwicklung der Mikroskopiemethoden in den letzten Jahrzehnten ist es nun möglich Strukturen und Abläufe in biologischen Systemen detaillierter darzustellen als mit der von Abbe entdeckten maximalen Auflösungsgrenze. Oft werden dabei Fluoreszenzmarker benutzt, welche die unsichtbare Welt der Mikrobiologie und deren biochemische Prozesse illuminieren. Diese werden entweder durch Expression, wie z.B. das grün fluoreszierende Protein (GFP), in das zu untersuchende Objekt eingebracht oder durch klassische Markierungsmethoden mithilfe von fluoreszierenden Immunkonjugaten installiert. Jedoch gewinnt eine alternative Strategie, die von der interdisziplinären Zusammenarbeit zwischen Chemikern, Physikern und Biologen profitiert, immer mehr an Bedeutung – die bioorthogonale Click-Chemie. Sie ermöglicht eine effiziente Fluoreszenzmarkierung der biologischen Strukturen unter minimalem Eingriff in die Abläufe der Zelle. Dazu müssen allerdings sowohl Farbstoffe als auch die biologisch aktiven Substanzen chemisch modifiziert werden, da nur dadurch die Bioorthogonalität gewährleistet werden kann.
Mittlerweile existiert eine breite Palette an fluoreszierenden Farbstoffen, die das komplette sichtbare Spektrum abdecken und sich für diverse Mikroskopiemethoden eignen. Allerdings gibt es zwei Farbstoffklassen, die sich aus der gesamten Fülle abheben und sich für hochauflösende bildgebende Experimente auf Einzelmolekülebene eignen. Zum einen ist es die Farbstofffamilie der Cyanine und insbesondere der wasserlöslichen Pentamethincyanine, die reversibel und kontrolliert zum Photoschalten animiert werden können und in der stochastisch optischen Rekonstruktionsmikroskopie Anwendung finden. Zum anderen ist es die Gruppe, der Rhodamine und Fluoresceine, die zu Xanthenfarbstoffen gehören und sich durch gute photophysikalische Eigenschaften auszeichnen.
Trotz der Beliebtheit stellt ihre Darstellung immer noch eine Herausforderung dar und limitiert deren Einsatz. Deshalb war es notwendig im Rahmen der vorliegenden Arbeit Möglichkeiten zur Syntheseoptimierung beider Farbstoffklassen zu finden, damit diese im Folgenden weiterentwickelt und an die biologische Fragestellung angepasst werden können. Die Arbeit unterteilt sich deshalb in Relation an die oben genannten Farbstoffklassen in zwei Bereiche. Im ersten Teil wurden Projekte basierend auf den wasserlöslichen Pentamethincyaninen behandelt. Im zweiten Teil beschäftigte sich die Arbeit mit Projekten, die auf Xanthen-Farbstoffen aufbauen.
As viruses are obligatory intracellular parasites, any step during their life cycle strictly depends on successful interaction with their particular host cells. In particular, their interaction with cellular membranes is of crucial importance for most steps in the viral replication cycle. Such interactions are initiated by uptake of viral particles and subsequent trafficking to intracellular compartments to access their replication compartments which provide a spatially confined environment concentrating viral and cellular components, and subsequently, employ cellular membranes for assembly and exit of viral progeny. The ability of viruses to actively modulate lipid composition such as sphingolipids (SLs) is essential for successful completion of the viral life cycle. In addition to their structural and biophysical properties of cellular membranes, some sphingolipid (SL) species are bioactive and as such, take part in cellular signaling processes involved in regulating viral replication. It is especially due to the progress made in tools to study accumulation and dynamics of SLs, which visualize their compartmentalization and identify interaction partners at a cellular level, as well as the availability of genetic knockout systems, that the role of particular SL species in the viral replication process can be analyzed and, most importantly, be explored as targets for therapeutic intervention.
A highly sensitive short-wave infrared (SWIR, λ > 1000 nm) organic photodiode (OPD) is described based on a well-organized nanocrystalline bulk-heterojunction (BHJ) active layer composed of a dicyanovinyl-functionalized squaraine dye (SQ-H) donor material in combination with PC\(_{61}\)BM. Through thermal annealing, dipolar SQ-H chromophores self-assemble in a nanoscale structure with intermolecular charge transfer mediated coupling, resulting in a redshifted and narrow absorption band at 1040 nm as well as enhanced charge carrier mobility. The optimized OPD exhibits an external quantum efficiency (EQE) of 12.3% and a full-width at half-maximum of only 85 nm (815 cm\(^{-1}\)) at 1050 nm under 0 V, which is the first efficient SWIR OPD based on J-type aggregates. Photoplethysmography application for heart-rate monitoring is successfully demonstrated on flexible substrates without applying reverse bias, indicating the potential of OPDs based on short-range coupled dye aggregates for low-power operating wearable applications.
A bis(squaraine) dye equipped with alkyl and oligoethyleneglycol chains was synthesized by connecting two dicyanomethylene substituted squaraine dyes with a phenylene spacer unit. The aggregation behavior of this bis(squaraine) was investigated in non-polar toluene/tetrachloroethane (98:2) solvent mixture, which revealed competing cooperative self-assembly pathways into two supramolecular polymorphs with entirely different packing structures and UV/Vis/NIR absorption properties. The self-assembly pathway can be controlled by the cooling rate from a heated solution of the monomers. For both polymorphs, quasi-equilibrium conditions between monomers and the respective aggregates can be established to derive thermodynamic parameters and insights into the self-assembly mechanisms. AFM measurements revealed a nanosheet structure with a height of 2 nm for the thermodynamically more stable polymorph and a tubular nanorod structure with a helical pitch of 13 nm and a diameter of 5 nm for the kinetically favored polymorph. Together with wide angle X-ray scattering measurements, packing models were derived: the thermodynamic polymorph consists of brick-work type nanosheets that exhibit red-shifted absorption bands as typical for J-aggregates, while the nanorod polymorph consists of eight supramolecular polymer strands of the bis(squaraine) intertwined to form a chimney-type tubular structure. The absorption of this aggregate covers a large spectral range from 550 to 875 nm, which cannot be rationalized by the conventional exciton theory. By applying the Essential States Model and considering intermolecular charge transfer, the aggregate spectrum was adequately reproduced, revealing that the broad absorption spectrum is due to pronounced donor-acceptor overlap within the bis(squaraine) nanorods. The latter is also responsible for the pronounced bathochromic shift observed for the nanosheet structure as a result of the slip-stacked arranged squaraine chromophores.
Interactions between proteins and carbohydrates with larger biomacromolecules, e.g., lectins, are usually examined using self-assembled monolayers on target gold surfaces as a simplified model measuring setup. However, most of those measuring setups are either limited to a single substrate or do not allow for control over ligand distance and spacing. Here, we develop a synthetic strategy, consisting of a cascade of a thioesterification, native chemical ligation (NCL) and thiol-ene reaction, in order to create three-component polymer conjugates with a defined double bioactivation at the chain end. The target architecture is the vicinal attachment of two biomolecule residues to the α telechelic end point of a polymer and a thioether group at the ω chain end for fixating the conjugate to a gold sensor chip surface. As proof-of-principle studies for affinity measurements, we demonstrate the interaction between covalently bound mannose and ConA in surface acoustic wave (SAW) and surface plasmon resonance (SPR) experiments.
In the course of this work, a total of three photocatalytically active dyads for proton reduction could be synthesized together with the associated individual components. Two of them, D1 and D2, comprised a [Ru(bpy)3]2+ photosensitizer and D3 an [Ir(ppy)2bpy]+ photosensitizer. A Ppyr3-substituted propyldithiolate [FeFe] complex was used as catalyst in all systems. The absorption spectroscopic and electrochemical investigations showed that an inner-dyadic electronic coupling is effectively prevented in the dyads due to conjugation blockers within the bridging units used. The photocatalytic investigations exhibited that all dyad containing two-component systems (2CS) showed a significantly worse performance than the corresponding bimolecular three-component systems (3CS). Transient absorption spectroscopy showed that the 2CS behave very similarly to the associated multicomponent systems during photocatalysis. The electron that was intended for the intramolecular transfer from the photosensitizer unit to the catalyst unit within the dyads remains at the photosensitizer for a relatively long time, analogous to the 3CS and despite the covalently bound catalyst. It is therefore assumed that this intramolecular electron transfer is likely to be hindered as a result of the weak electronic coupling caused by the bridge units used. Instead, the system bypasses this through an intermolecular transfer to other dyad molecules in the immediate vicinity. In addition, with the help of emission quenching experiments and electrochemical investigations, it could be clearly concluded that all investigated systems proceed via the reductive quenching mechanism during photocatalysis.
The most important stereodynamic feature of carbo[n]helicenes is the interconversion of their enantiomers. The Gibbs activation energy (ΔG≠(T)) of this process, which determines the rate of enantiomerization, dictates the configurational stability of [n]helicenes. High values of ΔG≠(T) are required for applications of functional chiral molecules incorporating [n]helicenes or helicene substructures. This minireview provides an overview of the mechanism, recent developments, and factors affecting the enantiomerization of [n]helicenes, which will accelerate the design process of configurationally stable functional chiral molecules based on helicene substructures. Additionally, this minireview addresses the misconception and irregularities in the recent literature on how the terms “racemization” and “enantiomerization” are used as well as how the activation parameters are calculated for [n]helicenes and related compounds.
We investigated the folding kinetics of G‐quadruplex (G4) structures by comparing the K\(^{+}\)‐induced folding of an RNA G4 derived from the human telomeric repeat‐containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real‐time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off‐pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with \(^{19}\)F bound to C2′ in arabino configuration adopt exclusively anti conformations for χ. These fluoro‐modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively.
A series of perylene bisimide (PBI) dyes bearing various aryl substituents in 1,6,7,12 bay positions has been synthesized by Suzuki cross-coupling reaction. These molecules exhibit an exceptionally large and conformationally fixed twist angle of the PBI π-core due to the high steric congestion imparted by the aryl substituents in bay positions. Single crystal X-ray analyses of phenyl-, naphthyl- and pyrenyl-functionalized PBIs reveal interlocked π-π-stacking motifs, leading to conformational chirality and the possibility for the isolation of enantiopure atropoisomers by semipreparative HPLC. The interlocked arrangement endows these molecules with substantial racemization barriers of about 120 kJ mol\(^{−1}\) for the tetraphenyl- and tetra-2-naphthyl-substituted derivatives, which is among the highest racemization barriers for axially chiral PBIs. Variable temperature NMR studies reveal the presence of a multitude of up to fourteen conformational isomers in solution that are interconverted via smaller activation barriers of about 65 kJ mol\(^{−1}\). The redox and optical properties of these core-twisted PBIs have been characterized by cyclic voltammetry, UV/Vis/NIR and fluorescence spectroscopy and their respective atropo-enantiomers were further characterized by circular dichroism (CD) and circular polarized luminescence (CPL) spectroscopy.
Photocatalytic water oxidation is a promising process for the production of solar fuels and the elucidation of factors that influence this process is of high significance. Thus, we have studied in detail light‐driven water oxidation with a trinuclear Ru(bda) (bda: 2,2’‐bipyridine‐6,6’‐dicarboxylate) macrocycle MC3 and its highly water soluble derivative m‐CH\(_2\)NMe\(_2\)‐MC3 using a series of ruthenium tris(bipyridine) complexes as photosensitizers under varied reaction conditions. Our investigations showed that the catalytic activities of these Ru macrocycles are significantly affected by the choice of photosensitizer (PS) and reaction media, in addition to buffer concentration, light intensity and concentration of the sensitizer. Our steady‐state and transient spectroscopic studies revealed that the photocatalytic performance of trinuclear Ru(bda) macrocycles is not limited by their intrinsic catalytic activities but rather by the efficiency of photogeneration of oxidant PS\(^+\) and its ability to act as an oxidizing agent to the catalysts as both are strongly dependent on the choice of photosensitizer and the amount of employed organic co‐solvent.
A Calix[4]arene‐Based Cyclic Dinuclear Ruthenium Complex for Light‐Driven Catalytic Water Oxidation
(2021)
A cyclic dinuclear ruthenium(bda) (bda: 2,2’‐bipyridine‐6,6’‐dicarboxylate) complex equipped with oligo(ethylene glycol)‐functionalized axial calix[4]arene ligands has been synthesized for homogenous catalytic water oxidation. This novel Ru(bda) macrocycle showed significantly increased catalytic activity in chemical and photocatalytic water oxidation compared to the archetype mononuclear reference [Ru(bda)(pic)\(_2\)]. Kinetic investigations, including kinetic isotope effect studies, disclosed a unimolecular water nucleophilic attack mechanism of this novel dinuclear water oxidation catalyst (WOC) under the involvement of the second coordination sphere. Photocatalytic water oxidation with this cyclic dinuclear Ru complex using [Ru(bpy)\(_3\)]Cl\(_2\) as a standard photosensitizer revealed a turnover frequency of 15.5 s\(^{−1}\) and a turnover number of 460. This so far highest photocatalytic performance reported for a Ru(bda) complex underlines the potential of this water‐soluble WOC for artificial photosynthesis.
A highly strained covalent organic cage compound was synthesized from hexahydroxy tribenzotriquinacene (TBTQ) and a meta-terphenyl-based diboronic acid with an additional benzoic acid substituent in 2’-position. Usually, a 120° bite angle in the unsubstituted ditopic linker favors the formation of a [4+6] cage assembly. Here, the introduction of the benzoic acid group is shown to lead to a perfectly preorganized circular hydrogen-bonding array in the cavity of a trigonal-bipyramidal [2+3] cage, which energetically overcompensates the additional strain energy caused by the larger mismatch in bite angles for the smaller assembly. The strained cage compound was analyzed by mass spectrometry and \(^{1}\)H, \(^{13}\)C and DOSY NMR spectroscopy. DFT calculations revealed the energetic contribution of the hydrogen-bonding template to the cage stability. Furthermore, molecular dynamics simulations on early intermediates indicate an additional kinetic effect, as hydrogen bonding also preorganizes and rigidifies small oligomers to facilitate the exclusive formation of smaller and more strained macrocycles and cages.
Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.
Modular frameworks featuring well-defined pore structures in microscale domains establish tailor-made porous materials. For open molecular solids however, maintaining long-range order after desolvation is inherently challenging, since packing is usually governed by only a few supramolecular interactions. Here we report on two series of nanocubes obtained by co-condensation of two different hexahydroxy tribenzotriquinacenes (TBTQs) and benzene-1,4-diboronic acids (BDBAs) with varying linear alkyl chains in 2,5-position. n-Butyl groups at the apical position of the TBTQ vertices yielded soluble model compounds, which were analyzed by mass spectrometry and NMR spectroscopy. In contrast, methyl-substituted cages spontaneously crystallized as isostructural and highly porous solids with BET surface areas and pore volumes of up to 3426 m\(^2\) g\(^{-1}\) and 1.84 cm\(^3\) g\(^{-1}\). Single crystal X-ray diffraction and sorption measurements revealed an intricate cubic arrangement of alternating micro- and mesopores in the range of 0.97–2.2 nm that are fine-tuned by the alkyl substituents at the BDBA linker.
A protecting group strategy was employed to synthesise a series of indolenine squaraine dye oligomers up to the nonamer. The longer oligomers show a distinct solvent dependence of the absorption spectra, that is, either a strong blue shift or a strong red shift of the lowest energy bands in the near infrared spectral region. This behaviour is explained by exciton coupling theory as being due to H- or J-type coupling of transition moments. The H-type coupling is a consequence of a helix folding in solvents with a small Hansen dispersity index. DOSY NMR, small angle neutron scattering (SANS), quantum chemical and force field calculations agree upon a helix structure with an unusually large pitch and open voids that are filled with solvent molecules, thereby forming a kind of clathrate. The thermodynamic parameters of the folding process were determined by temperature dependent optical absorption spectra.
In this communication, we demonstrate a novel approach to prepare a discrete dimer of chiral phthalocyanine (Pc) by exploiting the flexible molecular geometry of helicenes, which enables structural interlocking and strong aggregation tendency of Pcs. Synthesized [7]helicene-Pc hybrid molecular structure, zinc-[7]helicenocyanine (Zn-7HPc), exclusively forms a stable dimeric pair consisting of two homochiral molecules. The dimerization constants were estimated to be as high as 8.96×10\(^6\) M\(^{−1}\) and 3.42×107 M\(^{−1}\) in THF and DMSO, respectively, indicating remarkable stability of dimer. In addition, Zn\(^{-7}\)HPc exhibited chiral self-sorting behavior, which resulted in preferential formation of a homochiral dimer also in the racemic sample. Two phthalocyanine subunits in the dimeric form strongly communicate with each other as revealed by a large comproportionation constant and observation of an IV-CT band for the thermodynamically stable mixed-valence state.
Molnupiravir is an orally available antiviral drug candidate currently in phase III trials for the treatment of patients with COVID-19. Molnupiravir increases the frequency of viral RNA mutations and impairs SARS-CoV-2 replication in animal models and in humans. Here, we establish the molecular mechanisms underlying molnupiravir-induced RNA mutagenesis by the viral RNA-dependent RNA polymerase (RdRp). Biochemical assays show that the RdRp uses the active form of molnupiravir, β-d-\(N^4\)-hydroxycytidine (NHC) triphosphate, as a substrate instead of cytidine triphosphate or uridine triphosphate. When the RdRp uses the resulting RNA as a template, NHC directs incorporation of either G or A, leading to mutated RNA products. Structural analysis of RdRp–RNA complexes that contain mutagenesis products shows that NHC can form stable base pairs with either G or A in the RdRp active center, explaining how the polymerase escapes proofreading and synthesizes mutated RNA. This two-step mutagenesis mechanism probably applies to various viral polymerases and can explain the broad-spectrum antiviral activity of molnupiravir.
Deracemization describes the conversion of a racemic mixture of a chiral molecule into an enantioenriched mixture or an enantiopure compound without structural modifications. Herein, we report an inherently chiral perylene bisimide (PBI) cyclophane whose chiral pocket is capable of transforming a racemic mixture of [5]‐helicene into an enantioenriched mixture with an enantiomeric excess of 66 %. UV/Vis and fluorescence titration studies reveal this cyclophane host composed of two helically twisted PBI dyes has high binding affinities for the respective homochiral carbohelicene guests, with outstanding binding constants of up to 3.9×10\(^{10}\) m\(^{-1}\) for [4]‐helicene. 2D NMR studies and single‐crystal X‐ray analysis demonstrate that the observed strong and enantioselective binding of homochiral carbohelicenes and the successful template‐catalyzed deracemization of [5]‐helicene can be explained by the enzyme‐like perfect shape complementarity of the macrocyclic supramolecular host.
Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.
Molecular functionality can be often directly attributed to given properties of the electronic wavefunction. Analogous to the potential energy surface, these properties can be represented as a function of the nuclear coordinates, giving rise to molecular “functional landscapes.” However, so far there has been no possibility for their systematic investigation. This perspective aims to discuss the development of new theoretical methods based on the multistate extension of the metadynamics approach, employing electronic collective variables. This emerging methodology allows to explore functional landscapes and to gain a deeper understanding of the structure–function relation in molecules and complex molecular systems in the ground and excited electronic state.
To circumvent time-consuming clinical trials, testing whether existing drugs are effective inhibitors of SARS-CoV-2, has led to the discovery of Remdesivir. We decided to follow this path and screened approved medications "off-label" against SARS-CoV-2. Fluoxetine inhibited SARS-CoV-2 at a concentration of 0.8 mu g/ml significantly in these screenings, and the EC50 was determined with 387 ng/ml. Furthermore, Fluoxetine reduced viral infectivity in precision-cut human lung slices showing its activity in relevant human tissue targeted in severe infections. Fluoxetine treatment resulted in a decrease in viral protein expression. Fluoxetine is a racemate consisting of both stereoisomers, while the S-form is the dominant serotonin reuptake inhibitor. We found that both isomers show similar activity on the virus, indicating that the R-form might specifically be used for SARS-CoV-2 treatment. Fluoxetine inhibited neither Rabies virus, human respiratory syncytial virus replication nor the Human Herpesvirus 8 or Herpes simplex virus type 1 gene expression, indicating that it acts virus-specific. Moreover, since it is known that Fluoxetine inhibits cytokine release, we see the role of Fluoxetine in the treatment of SARS-CoV-2 infected patients of risk groups.
Two dipolar merocyanines consisting of the same π‐conjugated chromophore but different alkyl substituents adopt very different packing arrangements in their respective solid state with either H‐ or J‐type exciton coupling, leading to ultranarrow absorption bands at 477 and 750 nm, respectively, due to exchange narrowing. The social self‐sorting behavior of these push‐pull chromophores in their mixed thin films is evaluated and the impact on morphology as well as opto‐electronical properties is determined. The implementation of this well‐tuned two‐component material with tailored optical features allows to optimize planar heterojunction organic photodiodes with fullerene (C\(_{60}\)) with either dual or single wavelength selectivity in the blue and NIR spectral range with ultranarrow bandwidths of only 11 nm (200 cm\(^{-1}\)) and an external quantum efficiency of up to 18% at 754 nm under 0 V bias. The application of these photodiodes as low‐power consuming heart rate monitors is demonstrated by a reflectance‐mode photoplethysmography (PPG) sensor.
Tribenzotriquinacene (TBTQ) is a polycyclic aromatic framework with a particularly rigid, C3v symmetrical, bowl-shaped core bearing three mutually fused indane wings. It has been discussed as a defect center for a nanographene by Kuck and colleagues. Therefore, extended TBTQ structures are promising models for saturated defect structures in graphene and graphene like molecules and could be used to investigate the role of defects for the electronic properties of graphene. With this motivation, three different pi-extended TBTQ derivatives have been synthesized in this work. Several different Scholl reaction conditions were tried to obtain fully annulated product of hexaphenyl substituted TBTQ. The desired benzannulated TBTQ derivative could not be obtained due to unfavourable electron density in the respective positions of the molecule and increased reactivity of the bay position of the precursor. As an another method for benzannulation is the on-surface synthesis of graphene flakes and can be carried out using electron beams e.g. in a tunneling microscope (STM). According to our previous research, the parent system TBTQ and centro-methyl TBTQ on silver and gold surfaces showed that the gas phase deposition of these molecules gives rise to the formation of highly ordered two-dimensional assemblies with unique structural features. This shows the feasibility for the formation of defective graphene networks starting from the parent structures. Therefore, the same deposition technique was used to deposit Me-TBTQ(OAc)3Ph6, and investigate the molecular self-assembly properties directly on the surface of Cu (111). In summary, the substrate temperature dependent self-assembly of Me-TBTQ(OAc)3Ph6 molecules on Cu(111), shows the following evolution of orientations. At room temperature, molecules form dimers, which construct a higher-coverage honeycomb lattice. Furthermore, one of the acetyl group located in the bay positions of the TBTQ core is cleaved and the remaining two induce the metal-molecule interaction. It was presumed that by increasing the temperature to 393 K, the remaining acetyl and methyl groups would beeliminated from the molecular structure.In addition, the smaller TBTQ-Ph6 molecules preferably lie flat on Cu(111) crystal and allowing the molecules to settle into a C3-symmetry and form a dense hexagonal structure.
Es wurde eine Vielzahl neuer, flüssigkristalliner Phthalocyanin-Sternmesogene synthetisiert. Die Struktur-Eigenschaftsbeziehungen und die thermotropen Eigenschaften neuer Phthalocyanin-Sternmesogene mit Freiraum sowie von sterisch überfrachteten Verbindungen wurden insbesondere hinsichtlich der Freiraumfüllung untersucht. Diesbezüglich wurde ein neuer supramolekularer, freiraumfüllender "Klick-Prozess" zwischen einem Molekül mit Freiraum und einem sterisch überfrachteten Molekül mit vier Fullerenen beobachtet. Die photophysikalischen Eigenschaften wurden zudem insbesondere im Hinblick auf die Anwendung für die Organische Photovoltaik untersucht.
In terms of the need of environmentally benign renewable and storable energy sources, splitting of water into hydrogen and oxygen by using sunlight is a promising approach. Hereby, water oxidation catalysts (WOCs) are required to perform the water oxidation comprising the transfer of four electrons to provide the reducing equivalents for producing hydrogen. The class of Ru(bda) (bda = 2,2'-bipyridine-6,6'-dicarboxylate) catalysts has proven to be efficient for this reaction.
In this thesis, ligand exchange processes in Ru(bda) complexes have been analyzed and the formation of multinuclear macrocyclic WOCs was studied. Based on the knowledge acquired by these studies, new multinuclear cyclic Ru(bda) complexes have been synthesized and their catalytic efficiencies in homogeneous water oxidation have been investigated. Going one step further for setting up functional devices, molecular WOCs have been immobilized on conducting or semiconducting supporting materials. Direct anchoring on carbon nanotubes generated a promising materials for further applications.
Vom Monomer zum Polymer: Iterative Synthese und optische Spektroskopie von Squarain-Oligomeren
(2022)
Mittels einer Schutzgruppenstrategie wurden Squarain-basierte monodisperse Oligomere synthetisiert. Die lösungsmittelabhängigen Konformationen (Random Coil vs. Helix) wie auch der Faltungsprozess der Homooligomere wurden mittels optischer Spektroskopie, verschiedener NMR-Experimenten, Kleinwinkelneutronenstreuungsexperimenten sowie quantenchemischen Berechnungen näher beleuchtet. Die optisch-spektroskopischen Beobachtungen wurden mithilfe der Exzitonenkopplungstheorie und einer Orientierungs- und Winkelabhängigkeit der Übergangsdipolmomente der Oligomere erklärt. Der hohe Windungsabstand der helikalen Konformation führt zu einer Interkalation von Lösungsmittel, wodurch eine Art Klathrat gebildet wird. Zusätzlich wurden mittels eines Frenkel-Exzitonenmodells die Absorptions- und Fluoreszenzspektren modelliert. Es konnten die Exzitonendelokalisationslängen abgeschätzt und die Auswirkung der energetischen und strukturellen Unordnungen auf die Absorptions- und Fluoreszenzspektren bestimmt werden. Die Absorptionsspektren werden vorwiegend durch strukturelle Unordnungen verbreitert, die Fluoreszenzspektren dagegen von energetischen Übergangsenergieabweichungen.
Weiterhin wurden auch alternierende Squarain-Cooligomere synthetisiert und mittels optischer Spektroskopie untersucht. Es wurde, abhängig von dem gewählten Lösungsmittel, eine Verschiebung der Hauptbande beobachtet, was durch einen Random Coil vs. helikale-/schlaufenartige Konformation erklärt wird. Gestützt wurde dies mittels quantenchemischen Berechnungen der jeweiligen Konformationen.
Abschließend wurden alternierende Squarain-Copolymere synthetisiert, in verschiedenen Größen aufgetrennt und mittels optischer Spektroskopie untersucht. Mittels EEI2D-Experimenten wurde die Exzitonendynamik in Abhängigkeit von der Kettenlänge eingehender untersucht. Hierbei wird eine steigende, aber relativ abnehmende Kohärenzlänge bestimmt, die Auswirkungen auf die Exzitonendynamik hat. Der Exzitonentransport weist erst wellenförmiges und dann subdiffuses Verhalten auf.
Synthese einer Bibliothek von Aminosäure-basierten Oligopeptid-Amphiphilen mittels Festphasensynthese, deren kovalente Knüpfung an einen nukleophilen Kern zu C3-symmetrischen Sternmesogenen und die Analyse der Einflüsse der verwendeten Aminosäuren auf die Sekundärstruktur des synthetisierten Moleküls.
Nucleic acids are not only one of the most important classes of macromolecules in biochemistry but also a promising platform for the defined arrangement of chromophores. Thanks to their precise organization by directional polar and hydrophobic interactions, oligonucleotides can be exploited as suitable templates for multichromophore assemblies with predictable properties. To expand the toolbox of emissive, base pairing nucleobase analogs several barbituric acid merocyanine (BAM) chromophores with tunable spectroscopic properties were synthesized and incorporated into RNA, DNA and glycol nucleic acid (GNA) oligonucleotides. A multitude of duplexes containing up to ten BAM chromophores was obtained and analysis by spectroscopic methods revealed the presence of dipolarly coupled merocyanine aggregates with properties
strongly dependent on the chromophore orientation toward each other and the backbone conformation. These characteristics were exploited for various applications such as FRET pair formation and polymerase chain reaction (PCR) experiments. The observed formation of higher-order aggregates implies future applications of these new oligonucleotide-chromophore systems as light-harvesting DNA nanomaterials. Besides oligonucleotide templated covalent assembly of chromophores also non-covalent nucleic acid-chromophore complexes are a broad field of research. Among these, fluorogenic RNA aptamers are of special interest with the most versatile ones based on derivatives of the GFP chromophore hydroxybenzylidene imidazolone (HBI). Therefore, new HBI-derived chromophores with an expanded conjugated system and an additional exocyclic amino group for an enhanced binding affinity were synthesized and analyzed in complex with the Chili aptamer. Among these, structurally new fluorogenes with strong fluorescence activation upon binding to Chili were identified which are promising for further derivatization and application as color-switching sensor devices for example.
A series of donor-acceptor macrocyclic architectures comprising oligothiophene strands that connect the imide positions of a perylene bisimide have been synthesized via a platinum-mediated cross-coupling strategy. The target structures were characterized by steady-state UV/Vis absorption, fluorescence and transient absorption spectroscopy, as well as cyclic and differential pulse voltammetry. Crystal structure analysis of the macrocycles revealed insights into the bridge arrangements. The properties of the macrocyclic bridges were compared to linear oligothiophene reference compounds which itself exhibited an unusual electrochemical effect.
Inspired by the proficiency of natural enzymes, mimicking of nanoenvironments for precise substrate preorganisation is a promising strategy in catalyst design. However, artificial examples of enzyme-like activation of H\(_2\)O molecules for the challenging oxidative water splitting reaction are hardly explored. Here, we introduce a mononuclear Ru(bda) complex (M1, bda: 2,2’-bipyridine-6,6’-dicarboxylate) equipped with a bipyridine-functionalized ligand to preorganize H\(_2\)O molecules in front of the metal center as in enzymatic clefts. The confined pocket of M1 accelerates chemically driven water oxidation at pH 1 by facilitating a water nucleophilic attack pathway with a remarkable turnover frequency of 140 s\(^{−1}\) that is comparable to the oxygen-evolving complex of photosystem II. Single crystal X-ray analysis of M1 under catalytic conditions allowed the observation of a 7th H\(_2\)O ligand directly coordinated to a RuIII center. Via a well-defined hydrogen-bonding network, another H\(_2\)O substrate is preorganized for the crucial O–O bond formation via nucleophilic attack.
The West African liana Ancistrocladus abbreviatus is a rich source of structurally most diverse naphthylisoquinoline alkaloids. From its roots, a series of four novel representatives, named ancistrobrevolines A–D (14–17) have now been isolated, displaying an unprecedented heterocyclic ring system, where the usual isoquinoline entity is replaced by a ring-contracted isoindolinone part. Their constitutions were elucidated by 1D and 2D NMR and HR-ESI-MS. The absolute configurations at the chiral axis and at the stereogenic center were assigned by using experimental and computational electronic circular dichroism (ECD) investigations and a ruthenium-mediated oxidative degradation, respectively. For the biosynthetic origin of the isoindolinones from ‘normal’ naphthyltetrahydroisoquinolines, a hypothetic pathway is presented. It involves oxidative decarboxylation steps leading to a ring contraction by a benzilic acid rearrangement. Ancistrobrevolines A (14) and B (15) were found to display moderate cytotoxic effects (up to 72%) against MCF-7 breast and A549 lung cancer cells and to reduce the formation of spheroids (mammospheres) in the breast cancer cell line.
Modified nucleotides in tRNAs are important determinants of folding, structure and function. Here we identify METTL8 as a mitochondrial matrix protein and active RNA methyltransferase responsible for installing m\(^3\)C\(_{32}\) in the human mitochondrial (mt-)tRNA\(^{Thr}\) and mt-tRNA\(^{Ser(UCN)}\). METTL8 crosslinks to the anticodon stem loop (ASL) of many mt-tRNAs in cells, raising the question of how methylation target specificity is achieved. Dissection of mttRNA recognition elements revealed U\(_{34}\)G\(_{35}\) and t\(^6\)A\(_{37}\)/(ms\(^2\))i\(^6\)A\(_{37}\), present concomitantly only in the ASLs of the two substrate mt-tRNAs, as key determinants for METTL8-mediated methylation of C\(_{32}\). Several lines of evidence demonstrate the influence of U\(_{34}\), G\(_{35}\), and the m\(^3\)C\(_{32}\) and t\(^6\)A\(_{37}\)/(ms\(^2\))i\(^6\)A\(_{37}\) modifications in mt-tRNA\(^{Thr/Ser(UCN)}\) on the structure of these mt-tRNAs. Although mt-tRNA\(^{Thr/Ser(UCN)}\) lacking METTL8-mediated m\(^3\)C\(_{32}\) are efficiently aminoacylated and associate with mitochondrial ribosomes, mitochondrial translation is mildly impaired by lack of METTL8. Together these results define the cellular targets of METTL8 and shed new light on the role of m\(^3\)C\(_{32}\) within mt-tRNAs.
In π-conjugated organic photovoltaic materials, an excimer state has been generally regarded as a trap state which hinders efficient excitation energy transport. But despite wide investigations of the excimer for overcoming the undesirable energy loss, the understanding of the relationship between the structure of the excimer in stacked organic compounds and its properties remains elusive. Here, we present the landscape of structural dynamics from the excimer formation to its relaxation in a co-facially stacked archetypical perylene bisimide folda-dimer using ultrafast time-domain Raman spectroscopy. We directly captured vibrational snapshots illustrating the ultrafast structural evolution triggering the excimer formation along the interchromophore coordinate on the complex excited-state potential surfaces and following evolution into a relaxed excimer state. Not only does this work showcase the ultrafast structural dynamics necessary for the excimer formation and control of excimer characteristics but also provides important criteria for designing the π-conjugated organic molecules.
Herein we devise and execute a new synthesis of a pristine boron-doped nanographene. Our target boron-doped nanographene was designed based on DFT calculations to possess a low LUMO energy level and a narrow band gap derived from its precise geometry and B-doping arrangement. Our synthesis of this target, a doubly B-doped hexabenzopentacene (B\(_{2}\)-HBP), employs six net C−H borylations of an alkene, comprising consecutive hydroboration/electrophilic borylation/dehydrogenation and BBr\(_{3}\)/AlCl\(_{3}\)/2,6-dichloropyridine-mediated C−H borylation steps. As predicted by our calculations, B\(_{2}\)-HBP absorbs strongly in the visible region and emits in the NIR up to 1150 nm in o-dichlorobenzene solutions. Furthermore, B\(_{2}\)-HBP possesses a very low LUMO level, showing two reversible reductions at −1.00 V and −1.17 V vs. Fc\(^{+}\)/Fc. Our methodology is surprisingly selective despite its implementation of unfunctionalized precursors and offers a new approach to the synthesis of pristine B-doped polycyclic aromatic hydrocarbons.
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.
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.
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.
Many dyes suffer from fast non-radiative decay pathways, thereby showing only short-lived excited states and weak photoluminescence. Here we show a pronounced fluorescence enhancement for a weakly fluorescent merocyanine (MC) dye by being co-facially stacked to other dyes in hetero-folda-trimer architectures. By means of fluorescence spectroscopy (lifetime, quantum yield) the fluorescence enhancement was explained by the rigidification of the emitting chromophore in the defined foldamer architecture and the presence of a non-forbidden lowest exciton state in H-coupled hetero-aggregates. This folding-induced fluorescence enhancement (FIFE) for specific sequences of π-stacked dyes points at a viable strategy toward improved fluorophores that relates to the approach used by nature in the green fluorescent protein (GFP).
RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the site-specific synthesis of 1-methyladenosine (m\(^1\)A) in RNA, using O\(^6\)-methylguanine (m\(^6\)G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 Å, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m1A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution.
RNA-cleaving deoxyribozymes have found broad application as useful tools for RNA biochemistry. However, tedious in vitro selection procedures combined with laborious characterization of individual candidate catalysts hinder the discovery of novel catalytic motifs. Here, we present a new high-throughput sequencing method, DZ-seq, which directly measures activity and localizes cleavage sites of thousands of deoxyribozymes. DZ-seq exploits A-tailing followed by reverse transcription with an oligo-dT primer to capture the cleavage status and sequences of both deoxyribozyme and RNA substrate. We validated DZ-seq by conventional analytical methods and demonstrated its utility by discovery of novel deoxyribozymes that allow for cleaving challenging RNA targets or the analysis of RNA modification states.
The objective of this thesis was the synthesis and characterisation of two linear multifunctional PEG-alternatives for bioconjugation and hydrogel formation: i) Hydrophilic acrylate based copolymers containing peptide binding units and ii) hydrophilic polyether based copolymers containing different functional groups for a physical crosslinking.
In section 3.1 the successful synthesis of water soluble and linear acrylate based polymers containing oligo(ethylene glycol) methyl ether acrylate with either linear thioester functional 2-hydroxyethyl acrylate, thiolactone acrylamide, or vinyl azlactone via the living radical polymerisation technique Reversible Addition Fragmentation Chain Transfer (RAFT) and via free-radical polymerisation is described. The obtained polymers were characterized via GPC, 1H NMR, IR and RAMAN spectroscopy.
The RAFT end group was found to be difficult to remove from these short polymer chains and accordingly underwent the undesired side reaction aminolysis with the peptide during the conjugation studies. Besides that, polymers without RAFT end groups did not show any binding of the peptide at the thioester groups, which can be improved in future by using higher reactant concentrations and higher amount of binding units at the polymer. Polymers containing the highly reactive azlactone group showed a peptide binding of 19 %, but unfortunately this function also underwent spontaneous hydrolysis before the peptide could even be bound. In all cases, oligo(ethylene glycol) methyl ether acrylate was used with a relatively high molecular weight (Mn = 480 Da) was used, which eventually was efficiently shielding the introduced binding units from the added peptide. In future, a shorter monomer with Mn = 300 Da or less or hydrophilic N,N’-dialkyl acrylamide based polymers with less steric hindrance could be used to improve this bioconjugation system. Additionally, the amount of monomers containing peptide binding units in the polymer can be increased and have an additional spacer to achieve higher loading efficiency.
The water soluble, linear and short polyether based polymers, so called polyglycidols, were successfully synthesized and modified as described in section 3.2. The obtained polymers were characterized using GPC, 1H NMR, 31P{1H} NMR, IR, and RAMAN spectroscopy. The allyl groups which were present up to 20 % were used for radical induced thiol-ene chemistry for the introduction of functional groups intended for the formation of the physically crosslinking hydrogels. For the positively charged polymers, first a chloride group had to be introduced for the subsequent nucleophilic substitution with the imidazolium compound. There, degrees of modifications were found in the range 40-97 % due to the repulsion forces of the charges, decreased concentration of active chloride groups, and limiting solution concentrations of the polymer for this reaction. For the negatively charged polymers, first a protected phosphonamide moiety was introduced with a deprotection step afterwards showing 100 % conversion for all reactions. Preliminary hydrogel tests did not show a formation of a three-dimensional network of the polymer chains which was attributed to the short backbone length of the used polymers, but the gained knowledge about the synthetic routes for the modification of the polymer was successfully transferred to longer linear polyglycidols. The same applies to the introduction of electron rich and electron poor compounds showing π-π stacking interactions by UV-vis spectroscopy.
Finally, long linear polyglycidyl ethers were synthesised successfully up to molecular weights of Mn ~ 30 kDa in section 3.3, which was also proven by GPC, 1H NMR, IR and RAMAN spectroscopy. This applies to the homopolymerisation of ethoxyethyl glycidyl ether, allyl glycidyl ether and their copolymerisation with an amount of the allyl compound ~ 10 %. Attempts for higher molecular weights up to 100 kDa showed an uncontrolled polymerisation behaviour and eventually can be improved in future by choosing a lower initiation temperature. Also, the allyl side groups were modified via radical induced thiol-ene chemistry to obtain positively charged functionalities via imidazolium moieties (85 %) and negatively charged functionalities via phosphonamide moieties (100 %) with quantitative degree of modifications. Hydrogel tests have still shown a remaining solution by using long linear polyglycidols carrying negative charges with long/short linear polyglycidols carrying positive charges. The addition of calcium chloride led to a precipitate of the polymer instead of a three-dimensional network formation representing a too high concentration of ions and therefore shielding water molecules with prevention from dissolving the polymer. These systems can be improved by tuning the polymers structure like longer polymer chains, longer spacer between polymer backbone and charge, and higher amount of functional groups.
The objective of the thesis was partly reached containing detailed investigated synthetic routes for the design and characterisation of functional polymers which could be used in future with improvements for bioconjugation and hydrogel formation tests.
The synthesis and characterization of laterally extended azabora[5]‐, ‐[6]‐ and ‐[7]helicenes, assembled from N‐heteroaromatic and dibenzo[g,p]chrysene building blocks is described. Formally, the π‐conjugated systems of the pristine azaborole helicenes were enlarged with a phenanthrene unit leading to compounds with large Stokes shifts, significantly enhanced luminescence quantum yields (Φ) and dissymmetry factors (g\(_{lum}\)). The beneficial effect on optical properties was also observed for helical elongation. The combined contributions of lateral and helical extensions resulted in a compound showing green emission with Φ of 0.31 and |g\(_{lum}\)| of 2.2×10\(^{−3}\), highest within the series of π‐extended azaborahelicenes and superior to emission intensity and chiroptical response of its non‐extended congener. This study shows that helical and lateral extensions of π‐conjugated systems are viable strategies to improve features of azaborole helicenes. In addition, single crystal X‐ray analysis of configurationally stable [6]‐ and ‐[7]helicenes was used to provide insight into their packing arrangements.
Designing highly efficient purely organic phosphors at room temperature remains a challenge because of fast non-radiative processes and slow intersystem crossing (ISC) rates. The majority of them emit only single component phosphorescence. Herein, we have prepared 3 isomers (o, m, p-bromophenyl)-bis(2,6-dimethylphenyl)boranes. Among the 3 isomers (o-, m- and p-BrTAB) synthesized, the ortho-one is the only one which shows dual phosphorescence, with a short lifetime of 0.8 ms and a long lifetime of 234 ms in the crystalline state at room temperature. Based on theoretical calculations and crystal structure analysis of o-BrTAB, the short lifetime component is ascribed to the T\(^M_1\) state of the monomer which emits the higher energy phosphorescence. The long-lived, lower energy phosphorescence emission is attributed to the T\(^A_1\) state of an aggregate, with multiple intermolecular interactions existing in crystalline o-BrTAB inhibiting nonradiative decay and stabilizing the triplet states efficiently.
Boric acid (BA) has been used as a transparent glass matrix for optical materials for over 100 years. However, recently, apparent room-temperature phosphorescence (RTP) from BA (crystalline and powder states) was reported (Zheng et al., Angew. Chem. Int. Ed. 2021, 60, 9500) when irradiated at 280 nm under ambient conditions. We suspected that RTP from their BA sample was induced by an unidentified impurity. Our experimental results show that pure BA synthesized from B(OMe)\(_{3}\) does not luminesce in the solid state when irradiated at 250–400 nm, while commercial BA indeed (faintly) luminesces. Our theoretical calculations show that neither individual BA molecules nor aggregates would absorb light at >175 nm, and we observe no absorption of solid pure BA experimentally at >200 nm. Therefore, it is not possible for pure BA to be excited at >250 nm even in the solid state. Thus, pure BA does not display RTP, whereas trace impurities can induce RTP.
RNA molecules play diverse roles in biological systems. Post-transcriptional RNA modifications and dynamic structures enhance the functional diversity of RNA. A prerequisite for studying their biological significance is the availability of reliable methods for the detection of RNA modifications and structures. Several promising approaches have been developed in the last few decades; however, efficient, and versatile tools are still required to study the dynamic features of RNA. This thesis focuses on the development of nucleic acid catalysts as a tool to address the current needs in studying RNA. The major part of this thesis aimed at the development of deoxyribozymes as a tool for the detection of RNA modifications. Using in vitro selection from a random DNA library, we found deoxyribozymes that are sensitive to N 6 -isopentenyladenosine (i6A), a native tRNA modification and structural analogue of m6A. The in vitro evolution identified three classes of DNA enzymes: AA, AB08, and AC17 DNAzymes that showed distinct response to i6A modification and showed strong discrimination between structural analogues, i.e., m6A and i6A. In the continuation of the project, we attempted to develop RNA-cleaving deoxyribozymes that differentially respond to monomethylated cytidine isomers, 3-methylcytidine (m3C), N4 - methylcytidine (m4C), and 5-methylcytidine (m5C). Several deoxyribozymes were identified from in vitro selection, which are selective for a specific methylated cytidine isomer. The characterization of AL112, AM101, AN05, and AK104 catalysts confirmed the successful evolution of modification-specific and general deoxyribozymes that showed a broad substrate scope. In order to accelerate the DNAzymes discovery, a high throughput sequencing method (DZ-seq) was established that directly quantifies the RNA cleavage activity and cleavage site from deep sequencing data. The libraries contained information about cleavage status, cleavage site and sequence of deoxyribozymes and RNA substrate. The fraction cleaved (FC) data obtained from Dz-seq was validated for a subset of deoxyribozmes using conventional gel based kinetic assay and showed a good linear correlation (R2 = 0.91). Dz-seq possesses a great potential for the discovery of novel deoxyribozymes for the analysis of various RNA modifications in the future. The second objective of the current study was the development of structure-specific RNA labeling ribozymes. Here, we attempted to develop ribozymes that targets RNA of interest by structure-specific interaction rather than base-pairing and focused on a specific RNA G-quadruplex as the target. Two subsequent selection experiments led to the identification of the adenylyltransferase ribozymes AO10.2 and AR9. The partial characterization of these catalysts showed that A010.2 was unable to recognize intact BCL2 structure, but it turned out as the first reported trans-active ribozyme that efficiently labeled uridine in a defined substrate RNA hybridized to the ribozyme. The other ribozyme AR9 was shown to serve as a trans-active, self-labeling ribozyme that catalyzed adenylyl transferase reaction in the presence of the intact BCL2 sequence. Based on these preliminary findings, we envision that AR9 could potentially serve as a reporter RNA by self-labeling in the presence of an RNA G-quadruplex. However, both AO10.2 and AR9 still require more detailed characterization for their potential applications.
A series of bis‐(4’‐pyridylethynyl)arenes (arene=benzene, tetrafluorobenzene, and anthracene) were synthesized and their bis‐N‐methylpyridinium compounds were investigated as a class of π‐extended methyl viologens. Their structures were determined by single crystal X‐ray diffraction, and their photophysical and electrochemical properties (cyclic voltammetry), as well as their interactions with DNA/RNA were investigated. The dications showed bathochromic shifts in emission compared to the neutral compounds. The neutral compounds showed very small Stokes shifts, which are a little larger for the dications. All of the compounds showed very short fluorescence lifetimes (<4 ns). The neutral compound with an anthracene core has a quantum yield of almost unity. With stronger acceptors, the analogous bis‐N‐methylpyridinium compound showed a larger two‐photon absorption cross‐section than its neutral precursor. All of the dicationic compounds interact with DNA/RNA; while the compounds with benzene and tetrafluorobenzene cores bind in the grooves, the one with an anthracene core intercalates as a consequence of its large, condensed aromatic linker moiety, and it aggregates within the polynucleotide when in excess over DNA/RNA. Moreover, all cationic compounds showed highly specific CD spectra upon binding to ds‐DNA/RNA, attributed to the rare case of forcing the planar, achiral molecule into a chiral rotamer, and negligible toxicity toward human cell lines at ≤10 μM concentrations. The anthracene‐analogue exhibited intracellular accumulation within lysosomes, preventing its interaction with cellular DNA/RNA. However, cytotoxicity was evident at 1 μM concentration upon exposure to light, due to singlet oxygen generation within cells. These multi‐faceted features, in combination with its two‐photon absorption properties, suggest it to be a promising lead compound for development of novel light‐activated theranostic agents.
Although a broad variety of classes of bioactive compounds have already been isolated from seaweeds of the genus Dictyota, most different species are still chemically and biologically unexplored. Dictyota species are well-known brown seaweeds belonging to the Dictyotaceae (Phaeophyta). The phytochemical composition within the genus Dictyota has recently received considerable interest, and a vast array of components, including diterpenes, sesquiterepenes, sterols, amino acids, as well as saturated and polyunsaturated fatty acids, have been characterized. The contribution of these valued metabolites to the biological potential, which includes anti-proliferative, anti-microbial, antiviral, antioxidant, anti-inflammatory, and anti-hyperpigmentation activities, of the genus Dictyota has also been explored. Therefore, this is the most comprehensive review, focusing on the published literature relevant to the chemically and pharmacologically diverse biopharmaceuticals isolated from different species of the genus Dictyota during the period from 1976 to now.
Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, - stacking and hydrogen-bonding interactions. The realized supramolecular motifs include hydrogenbonded BAM–adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.
Three novel tetracationic bis‐triarylboranes with 3,4‐ethylenedioxythiophene (EDOT) linkers, and their neutral precursors, showed significant red‐shifted absorption and emission compared to their thiophene‐containing analogues, with one of the EDOT‐derivatives emitting in the NIR region. Only the EDOT‐linked trixylylborane tetracation was stable in aqueous solution, indicating that direct attachment of a thiophene or even 3‐methylthiophene to the boron atom is insufficient to provide hydrolytic stability in aqueous solution. Further comparative analysis of the EDOT‐linked trixylylborane tetracation and its bis‐thiophene analogue revealed efficient photo‐induced singlet oxygen production, with the consequent biological implications. Thus, both analogues bind strongly to ds‐DNA and BSA, very efficiently enter living human cells, accumulate in several different cytoplasmic organelles with no toxic effect but, under intense visible light irradiation, they exhibit almost instantaneous and very strong cytotoxic effects, presumably attributed to singlet oxygen production. Thus, both compounds are intriguing theranostic agents, whose intracellular and probably intra‐tissue location can be monitored by strong fluorescence, allowing switching on of the strong bioactivity by well‐focused visible light.
Utilizing Pd‐catalyzed [5+2] annulation a series of heptagon‐extended corannulenes could be synthesized from a borinic acid precursor furnished by C−H borylation strategy. Single‐crystal X‐ray analysis revealed the presence of two conformational enantiomers crystallizing in a racemic mixture. Through their embedded five‐ and seven‐membered rings these polycyclic aromatic hydrocarbons (PAHs) exhibit both negative and positive curvature and UV/Vis/NIR absorption spectroscopy as well as cyclic voltammetry experiments provided insights into the influence of larger flanking aromatic systems and electron‐donating substituents encompassing the heptagonal ring. Through [5+2] annulation of acenaphthylene an azulene‐containing PAH with intriguing optoelectronical properties including a very small bandgap and absorption over the whole visible spectrum could be obtained. Theoretical calculations were employed to elucidate the long‐wavelength absorption and aromaticity.
Arene‐fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane‐perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π‐stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene‐fluoroarene‐programmed assembly of DNA.
Water‐soluble multinuclear complexes based on ruthenium 2,2′‐bipyridine‐6,6′‐dicarboxylate (bda) and ditopic bipyridine linker units are investigated in three‐component visible light‐driven water oxidation catalysis. Systematic studies revealed a strong enhancement of the catalytic efficiency in the absence of organic co‐solvents and with increasing oligomer length. In‐depth kinetic and morphological investigations suggest that the enhanced performance is induced by the self‐assembly of linear Ru(bda) oligomers into aggregated superstructures. The obtained turnover frequencies (up to 14.9 s\(^{−1}\)) and turnover numbers (more than 1000) per ruthenium center are the highest reported so far for Ru(bda)‐based photocatalytic water oxidation systems.
Dye–dye interactions affect the optical and electronic properties in organic semiconductor films of light harvesting and detecting optoelectronic applications. This review elaborates how to tailor these properties of organic semiconductors for organic solar cells (OSCs) and organic photodiodes (OPDs). While these devices rely on similar materials, the demands for their optical properties are rather different, the former requiring a broad absorption spectrum spanning from the UV over visible up to the near‐infrared region and the latter an ultra‐narrow absorption spectrum at a specific, targeted wavelength. In order to design organic semiconductors satisfying these demands, fundamental insights on the relationship of optical properties are provided depending on molecular packing arrangement and the resultant electronic coupling thereof. Based on recent advancements in the theoretical understanding of intermolecular interactions between slip‐stacked dyes, distinguishing classical J‐aggregates with predominant long‐range Coulomb coupling from charge transfer (CT)‐mediated or ‐coupled J‐aggregates, whose red‐shifts are primarily governed by short‐range orbital interactions, is suggested. Within this framework, the relationship between aggregate structure and functional properties of representative classes of dye aggregates is analyzed for the most advanced OSCs and wavelength‐selective OPDs, providing important insights into the rational design of thin‐film optoelectronic materials.