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Low-energy (5-20 eV) electron-induced single and double strand breaks in well-defined DNA sequences
(2022)
Ionizing radiation is used in cancer radiation therapy to effectively damage the DNA of tumors. The main damage is due to generation of highly reactive secondary species such as low-energy electrons (LEEs). The accurate quantification of DNA radiation damage of well-defined DNA target sequences in terms of absolute cross sections for LEE-induced DNA strand breaks is possible by the DNA origami technique; however, to date, it is possible only for DNA single strands. In the present work DNA double strand breaks in the DNA sequence 5 '-d(CAC)4/5 ' d(GTG)4 are compared with DNA single strand breaks in the oligonucleotides 5 '-d(CAC)4 and 5 '-d(GTG)4 upon irradiation with LEEs in the energy range from 5 to 20 eV. A maximum of strand break cross section was found around 7 and 10 eV independent of the DNA sequence, indicating that dissociative electron attachment is the underlying mechanism of strand breakage and confirming previous studies using plasmid DNA.
During the last decades, therapeutical proteins have risen to great significance in the pharmaceutical industry. As non-human proteins that are introduced into the human body cause a distinct immune system reaction that triggers their rapid clearance, most newly approved protein pharmaceuticals are shielded by modification with synthetic polymers to significantly improve their blood circulation time. All such clinically approved protein-polymer conjugates contain polyethylene glycol (PEG) and its conjugation is denoted as PEGylation. However, many patients develop anti-PEG antibodies which cause a rapid clearance of PEGylated molecules upon repeated administration. Therefore, the search for alternative polymers that can replace PEG in therapeutic applications has become important. In addition, although the blood circulation time is significantly prolonged, the therapeutic activity of some conjugates is decreased compared to the unmodified protein. The reason is that these conjugates are formed by the traditional conjugation method that addresses the protein's lysine side chains. As proteins have many solvent exposed lysines, this results in a somewhat uncontrolled attachment of polymer chains, leading to a mixture of regioisomers, with some of them eventually affecting the therapeutic performance.
This thesis investigates a novel method for ligating macromolecules in a site-specific manner, using enzymatic catalysis. Sortase A is used as the enzyme: It is a well-studied transpeptidase which is able to catalyze the intermolecular ligation of two peptides. This process is commonly referred to as sortase-mediated ligation (SML). SML constitutes an equilibrium reaction, which limits product yield. Two previously reported methods to overcome this major limitation were tested with polymers without using an excessive amount of one reactant.
Specific C- or N-terminal peptide sequences (recognition sequence and nucleophile) as part of the protein are required for SML. The complementary peptide was located at the polymer chain end. Grafting-to was used to avoid damaging the protein during polymerization. To be able to investigate all possible combinations (protein-recognition sequence and nucleophile-protein as well as polymer-recognition sequence and nucleophile-polymer) all necessary building blocks were synthesized. Polymerization via reversible deactivation radical polymerization (RDRP) was used to achieve a narrow molecular weight distribution of the polymers, which is required for therapeutic use.
The synthesis of the polymeric building blocks was started by synthesizing the peptide via automated solid-phase peptide synthesis (SPPS) to avoid post-polymerization attachment and to enable easy adaptation of changes in the peptide sequence. To account for the different functionalities (free N- or C-terminus) required for SML, different linker molecules between resin and peptide were used.
To facilitate purification, the chain transfer agent (CTA) for reversible addition-fragmentation chain-transfer (RAFT) polymerization was coupled to the resin-immobilized recognition sequence peptide. The acrylamide and acrylate-based monomers used in this thesis were chosen for their potential to replace PEG.
Following that, surface-initiated (SI) ATRP and RAFT polymerization were attempted, but failed. As a result, the newly developed method of xanthate-supported photo-iniferter (XPI) RAFT polymerization in solution was used successfully to obtain a library of various peptide-polymer conjugates with different chain lengths and narrow molar mass distributions.
After peptide side chain deprotection, these constructs were used first to ligate two polymers via SML, which was successful but revealed a limit in polymer chain length (max. 100 repeat units). When utilizing equimolar amounts of reactants, the use of Ni2+ ions in combination with a histidine after the recognition sequence to remove the cleaved peptide from the equilibrium maximized product formation with conversions of up to 70 %.
Finally, a model protein and a nanobody with promising properties for therapeutical use were biotechnologically modified to contain the peptide sequences required for SML. Using the model protein for C- or N-terminal SML with various polymers did not result in protein-polymer conjugates. The reason is most likely the lack of accessibility of the protein termini to the enzyme. Using the nanobody for C-terminal SML, on the other hand, was successful. However, a similar polymer chain length limit was observed as in polymer-polymer SML. Furthermore, in case of the synthesis of protein-polymer conjugates, it was more effective to shift the SML equilibrium by using an excess of polymer than by employing the Ni2+ ion strategy.
Overall, the experimental data from this work provides a good foundation for future research in this promising field; however, more research is required to fully understand the potential and limitations of using SML for protein-polymer synthesis. In future, the method explored in this dissertation could prove to be a very versatile pathway to obtain therapeutic protein-polymer conjugates that exhibit high activities and long blood circulation times.
In precision agriculture, the estimation of soil parameters via sensors and the creation of nutrient maps are a prerequisite for farmers to take targeted measures such as spatially resolved fertilization. In this work, 68 soil samples uniformly distributed over a field near Bonn are investigated using laser-induced breakdown spectroscopy (LIBS). These investigations include the determination of the total contents of macro- and micronutrients as well as further soil parameters such as soil pH, soil organic matter (SOM) content, and soil texture. The applied LIBS instruments are a handheld and a platform spectrometer, which potentially allows for the single-point measurement and scanning of whole fields, respectively. Their results are compared with a high-resolution lab spectrometer. The prediction of soil parameters was based on multivariate methods. Different feature selection methods and regression methods like PLS, PCR, SVM, Lasso, and Gaussian processes were tested and compared. While good predictions were obtained for Ca, Mg, P, Mn, Cu, and silt content, excellent predictions were obtained for K, Fe, and clay content. The comparison of the three different spectrometers showed that although the lab spectrometer gives the best results, measurements with both field spectrometers also yield good results. This allows for a method transfer to the in-field measurements.
Efficient Removal of Tetracycline and Bisphenol A from Water with a New Hybrid Clay/TiO₂ Composite
(2023)
New TiO₂ hybrid composites were prepared fromkaolinclay, predried and carbonized biomass, and titanium tetraisopropoxideand explored for tetracycline (TET) and bisphenol A (BPA) removalfrom water. Overall, the removal rate is 84% for TET and 51% for BPA.The maximum adsorption capacities (q (m))are 30 and 23 mg/g for TET and BPA, respectively. These capacitiesare far greater than those obtained for unmodified TiO2. Increasing the ionic strength of the solution does not change theadsorption capacity of the adsorbent. pH changes only slightly changeBPA adsorption, while a pH > 7 significantly reduces the adsorptionof TET on the material. The Brouers-Sotolongo fractal modelbest describes the kinetic data for both TET and BPA adsorption, predictingthat the adsorption process occurs via a complex mechanism involvingvarious forces of attraction. Temkin and Freundlich isotherms, whichbest fit the equilibrium adsorption data for TET and BPA, respectively,suggest that adsorption sites are heterogeneous in nature. Overall,the composite materials are much more effective for TET removal fromaqueous solution than for BPA. This phenomenon is assigned to a differencein the TET/adsorbent interactions vs the BPA/adsorbent interactions:the decisive factor appears to be favorable electrostatic interactionsfor TET yielding a more effective TET removal.
Graphene is well-knownfor its unique combination of electricaland mechanical properties. However, its vanishing band gap limitsthe use of graphene in microelectronics. Covalent functionalizationof graphene has been a common approach to address this critical issueand introduce a band gap. In this Article, we systematically analyzethe functionalization of single-layer graphene (SLG) and bilayer graphene(BLG) with methyl (CH3) using periodic density functionaltheory (DFT) at the PBE+D3 level of theory. We also include a comparisonof methylated single-layer and bilayer graphene, as well as a discussionof different methylation options (radicalic, cationic, and anionic).For SLG, methyl coverages ranging from 1/8 to 1/1, (i.e.,the fully methylated analogue of graphane) are considered. We findthat up to a coverage theta of 1/2, graphene readily accepts CH3, with neighbor CH3 groups preferring trans positions. Above theta = 1/2, the tendency to accept further CH3 weakens and the lattice constant increases. The band gapbehaves less regularly, but overall it increases with increasing methylcoverage. Thus, methylated graphene shows potential for developingband gap-tuned microelectronics devices and may offer further functionalizationoptions. To guide in the interpretation of methylation experiments,vibrational signatures of various species are characterized by normal-modeanalysis (NMA), their vibrational density of states (VDOS), and infrared(IR) spectra, the latter two are obtained from ab initio moleculardynamics (AIMD) in combination with a velocity-velocity autocorrelationfunction (VVAF) approach.
Geometry, 11B, 13C chemical shifts and the spatial magnetic properties (Through-Space NMR Shieldings -TSNMRS) of both cations and anions of boron-trapped N-heterocyclic carbenes (NHCs) and cyclic (alkyl)(amino)carbenes (CAACs) and of the corresponding diborane/diborene/diboryne dis-carbene adducts have been calculated using the GIAO perturbation method employing the nucleus independent chemical shift (NICS) concept; the TSNMRS results are visualized as iso-chemical-shielding surfaces (ICSS) of various size and direction. The ICSS of the TSNMRS (actually the anisotropy effects measurable in 1H NMR spectroscopy) are employed to qualify and quantify the present multiple bond character of the Carbene-Boron bond in the trapped NHCs and CAACs. Results are confirmed by bond length and 11B/13C chemical shift variations. Thus the partial multiple bond character of the Carbene-Boron bond cannot be expressed by the arrow of weak, much longer dative bonds and should be omitted as in other covalent lone pair-it or triel bonds. & COPY; 2023 Elsevier Ltd. All rights reserved.
High-solid-content polystyrene and polyvinyl acetate dispersions of polymer particles with a 50 nm to 500 nm mean particle diameter and 12-55% (w/w) solid content have been produced via emulsion polymerization and characterized regarding their optical and physical properties. Both systems have been analyzed with common particle-size-measuring techniques like dynamic light scattering (DLS) and static light scattering (SLS) and compared to inline particle size distribution (PSD) measurements via photon density wave (PDW) spectroscopy in undiluted samples. It is shown that particle size measurements of undiluted polystyrene dispersions are in good agreement between analysis methods. However, for polyvinyl acetate particles, size determination is challenging due to bound water in the produced polymer. For the first time, water-swelling factors were determined via an iterative approach of PDW spectroscopy error (X-2) minimization. It is shown that water-swollen particles can be analyzed in high-solid-content solutions and their physical properties can be assumed to determine the refractive index, density, and volume fraction in dispersion. It was found that assumed water swelling improved the reduced scattering coefficient fit by PDW spectroscopy by up to ten times and particle size determination was refined and enabled. Particle size analysis of the water-swollen particles agreed well with offline-based state-of-the-art techniques.
In recent years, due to its great promise in boosting the energy density of lithium batteries for future energy storage, research on the Li metal anode, as an alternative to the graphite anode in Li-ion batteries, has gained significant momentum. However, the practical use of Li metal anodes has been plagued by unstable Li (re)deposition and poor cyclability. Although tremendous efforts have been devoted to the stabilization of Li metal anodes, the mechanisms of electrochemical (re-)deposition/dissolution of Li and solid-electrolyte-interphase (SEI) formation remain elusive. This article highlights the recent mechanistic understandings and observations of Li deposition/dissolution and SEI formation achieved from advanced characterization techniques and simulation methods, and discusses major limitations and open questions in these processes. In particular, the authors provide their perspectives on advanced and emerging/potential methods for obtaining new insights into these questions. In addition, they give an outlook into cutting-edge interdisciplinary research topics for Li metal anodes. It pushes beyond the current knowledge and is expected to accelerate development toward a more in-depth and comprehensive understanding, in order to guide future research on Li metal anodes toward practical application.
Die vorliegende Arbeit thematisiert die Synthese und die Polymerisation von Monomeren auf der Basis nachwachsender Rohstoffe wie zum Beispiel in Gewürzen und ätherischen Ölen enthaltenen kommerziell verfügbaren Phenylpropanoiden (Eugenol, Isoeugenol, Zimtalkohol, Anethol und Estragol) und des Terpenoids Myrtenol sowie ausgehend von der Rinde einer Birke (Betula pendula) und der Korkeiche (Quercus suber). Ausgewählte Phenylpropanoide (Eugenol, Isoeugenol und Zimtalkohol) und das Terpenoid Myrtenol wurden zunächst in den jeweiligen Laurylester überführt und anschließend das olefinische Strukturelement epoxidiert, wobei 4 neue (2-Methoxy-4-(oxiran-2-ylmethyl)phenyldodecanoat, 2-Methoxy-4-(3-methyl-oxiran-2-yl)phenyldodecanoat, (3-Phenyloxiran-2-yl)methyldodecanoat, (7,7-Dimethyl-3-oxatricyclo[4.1.1.02,4]octan-2-yl)methyldodecanoat) und 2 bereits bekannte monofunktionelle Epoxide (2-(4-Methoxybenzyl)oxiran und 2-(4-Methoxyphenyl)-3-methyloxiran) erhalten wurden, die mittels 1H-NMR-, 13C-NMR- und FT-IR-Spektroskopie sowie mit DSC untersucht wurden. Die Photo-DSC Untersuchung der Epoxidmonomere in einer kationischen Photopolymerisation bei 40 °C ergab die maximale Polymerisationsgeschwindigkeit (Rpmax: 0,005 s-1 bis 0,038 s-1) sowie die Zeit (tmax: 13 s bis 26 s) bis zum Erreichen des Rpmax-Wertes und führte zu flüssigen Oligomeren, deren zahlenmittlerer Polymerisationsgrad mit 3 bis 6 mittels GPC bestimmt wurde. Die Umsetzung von 2-Methoxy-4-(oxiran-2-ylmethyl)phenyldodecanoat mit Methacrylsäure ergab ein Isomerengemisch (2-Methoxy-4-(2-hydroxy-3-(methacryloyloxy)propyl)phenyldodecanoat und 2-Methoxy-4-(2-(methacryl-oyloxy)-3-hydroxypropyl)phenyldodecanoat), das mittels Photo-DSC in einer freien radikalischen Photopolymerisation untersucht wurde (Rpmax: 0,105 s-1 und tmax: 5 s), die zu festen in Chloroform unlöslichen Polymeren führte.
Aus Korkpulver und gemahlener Birkenrinde wurden selektiv 2 kristalline ω-Hydroxyfettsäuren (9,10-Epoxy-18-hydroxyoctadecansäure und 22-Hydroxydocosansäure) isoliert. Die kationische Photopolymerisation der 9,10-Epoxy-18-hydroxyoctadecansäure ergab einen nahezu farblosen transparenten und bei Raumtemperatur elastischen Film, welcher ein Anwendungspotential für Oberflächenbeschichtungen hat. Aus der Reaktion von 9,10-Epoxy-18-hydroxyoctadecansäure mit Methacrylsäure wurde ein bei Raumtemperatur flüssiges Gemisch aus zwei Konstitutionsisomeren (9,18-Dihydroxy-10-(methacryloyloxy)octadecansäure und 9-(Methacryloyloxy)-10,18-dihydroxyoctadecansäure) erhalten (Tg: -60 °C). Die radikalische Photopolymerisation dieser Konstitutionsisomere wurde ebenfalls mittels Photo-DSC untersucht (Rpmax: 0,098 s-1 und tmax: 3,8 s). Die Reaktion von 22-Hydroxydocosansäure mit Methacryloylchlorid ergab die kristalline 22-(Methacryloyloxy)docosansäure, welche ebenfalls in einer radikalischen Photopolymerisation mittels Photo-DSC untersucht wurde (Rpmax: 0,023 s-1 und tmax: 9,6 s).
Die mittels AIBN in Dimethylsulfoxid initiierte Homopolymerisation der 22-(Methacryloyloxy)docosansäure und der Isomerengemische bestehend aus 2-Methoxy-4-(2-hydroxy-3-(methacryloyloxy)propyl)phenyldodecanoat und 2-Methoxy-4-(2-(methacryl-oyloxy)-3-hydroxypropyl)phenyldodecanoat sowie aus 9,18-Dihydroxy-10-(methacryloy-loxy)octadecansäure und 9-(Methacryloyloxy)-10,18-dihydroxyoctadecansäure ergab feste lösliche Polymere, die mittels 1H-NMR- und FT-IR-Spektroskopie, GPC (Poly(2-methoxy-4-(2-hydroxy-3-(methacryloyloxy)propyl)phenyldodecanoat / 2-methoxy-4-(2-(methacryloyloxy)-3-hydroxypropyl)phenyldodecanoat): Pn = 94) und DSC (Poly(2-methoxy-4-(2-hydroxy-3-(methacryloyloxy)propyl)phenyldodecanoat / 2-methoxy-4-(2-(methacryloyloxy)-3-hydroxypropyl)phenyldodecanoat): Tg: 52 °C; Poly(9,18-dihydroxy-10-(methacryloyloxy)-octadecansäure / 9-(methacryloyloxy)-10,18-dihydroxyoctadecansäure): Tg: 10 °C; Poly(22-(methacryloyloxy)docosansäure): Tm: 74,1 °C, wobei der Schmelzpunkt mit dem des Photopolymers (Tm = 76,8 °C) vergleichbar ist) charakterisiert wurden.
Das bereits bekannte Monomer 4-(4-Methacryloyloxyphenyl)butan-2-on wurde ausgehend von 4-(4-Hydroxyphenyl)butan-2-on hergestellt, welches aus Birkenrinde gewonnen werden kann, und unter identischen Bedingungen für einen Vergleich mit den neuen Monomeren polymerisiert. Die freie radikalische Polymerisation führte zu Poly(4-(4-methacryloyloxyphenyl)butan-2-on) (Pn: 214 und Tg: 83 °C). Neben der Homopolymerisation wurde eine statistische Copolymerisation des Isomerengemisches 2-Methoxy-4-(2-hydroxy-3-(methacryl-oyloxy)propyl)phenyldodecanoat / 2-Methoxy-4-(2-(methacryloyloxy)-3-hydroxypropyl)-phenyldodecanoat mit 4-(4-Methacryloyloxyphenyl)butan-2-on untersucht, wobei ein äquimolarer Einsatz der Ausgangsmonomere zu einem Anstieg der Ausbeute, der Molmassenverteilung und der Dispersität des Copolymers (Tg: 44 °C) führte. Die unter Verwendung von Diethylcarbonat als „grünes“ Lösungsmittel mittels AIBN initiierten freien radikalischen Homopolymerisationen von 4-(4-Methacryloyloxyphenyl)butan-2-on und von Laurylmethacrylat ergaben vergleichbare Polymerisationsgrade der Homopolymere (Pn: 150), welche jedoch aufgrund ihrer Strukturunterschiede deutlich unterschiedliche Glasübergangstemperaturen hatten (Poly(4-(4-methacryloyloxyphenyl)butan-2-on): Tg: 70 °C, Poly(laurylmethacrylat) Tg: -49 °C. Eine statistische Copolymerisation äquimolarer Stoffmengen der beiden Monomere in Diethylcarbonat führte bei einer Polymerisationszeit von 60 Minuten zu einem leicht bevorzugten Einbau des 4-(4-Methacryloyloxyphenyl)butan-2-on in das Copolymer (Tg: 17 °C). Copolymerisationsdiagramme für die freien radikalischen Copolymerisationen von 4-(4-Methacryloyloxyphenyl)butan-2-on mit n-Butylmethacrylat beziehungsweise 2-(Dimethylamino)ethylmethacrylat (t: 20 min bis 60 min; Molenbrüche (X) für 4-(4-Methacryloyloxyphenyl)butan-2-on: 0,2; 0,4; 0,6 und 0,8) zeigten ein nahezu ideales azeotropes Copolymerisationsverhalten, obwohl ein leicht bevorzugter Einbau von 4-(4-Methacryloyloxyphenyl)butan-2-on in das jeweilige Copolymer beobachtet wurde. Dabei korreliert ein Anstieg der Ausbeute und der Glasübergangstemperatur der erhaltenen Copolymere mit einem zunehmenden Gehalt an 4-(4-Methacryloyloxyphenyl)butan-2-on im Reaktionsgemisch. Die unter Einsatz der modifizierten Gibbs-DiMarzio-Gleichung berechneten Glasübergangstemperaturen der Copolymere stimmten mit den gemessenen Werten gut überein. Das ist eine gute Ausgangsbasis für die Bestimmung der Glasübergangstemperatur eines Copolymers mit einer beliebigen Zusammensetzung.