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    Synthesis and Characterization of Nanoporous Resin Particles for Water Purification

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    Through progressive industrialization and the relentless consumption of natural raw materials, man is exerting a negative influence on his habitat. In particular, water as the basis of life and almost all processes of our economy is contaminated by various pollutants due to excessive use and insufficient purification. Here, oxyanions, heavy metal ions and organic pollutants pose a high risk to aquatic habitats and ultimately to humans. Due to insufficient removal, they also contribute to the loss of non-renewable raw materials for industrial cycles. Due to a mostly low effect concentration and potential interactions with diverse living organisms, the removal of many contaminants is extremely important to avoid further altering existing ecosystems. Adsorption represents an energy-efficient method of removal using adsorbents suitable for this purpose. Highly cross-linked resin polymers such as poly(melamine-co-formaldehyde) (PMF) with its excellent chemical resistance, high number of functional groups and ease of preparation, represent promising starting points for adsorbents. This dissertation describes the colloidal aqueous synthesis of nanoporous resin particles (e.g. PMF) by templating with SiO2 nanoparticles (SiO2 NPs), which are subsequently used to adsorb water pollutants. An overall goal of this work consists of elucidating the mechanism for particle and pore formation by systematically varying various synthesis parameters. Electron microscopy, N2-soprtion and particle size measurement are used to analyze the morphology, size and pore structure of the particles. Comprehensive investigations thus allow to determine the influence of each tested synthesis parameter on these properties. A very important goal, especially for future large-scale applicability, is the colloidal production of uniform particles, which have both a high ordered porosity and particle diameters in the range of a few micrometers. This enables an application as a fixed-bed adsorber that can be flowed through. This goal is closely linked to the mechanistic elucidation of pore and particle formation in the synthesis. The prepared nanoporous PMF particles were tested for various adsorption applications after their characterization. In order to obtain a comprehensive picture of the applicability of PMF particles, experiments with oxyanions, with pharmaceuticals as representatives of organic pollutants and with heavy metal ions will be carried out respectively. On the one hand, these experiments will focus on investigating the adsorption performance and mechanism of PMF with the respective pollutant. On the other hand, the influence of the changed porosity on the adsorption mechanism is investigated by using different particles of a varied synthesis parameter. Sulfate and phosphate ions were investigated in the oxyanion class. Extremely high separation rates were demonstrated for both ions, significantly outperforming previous commercially available materials. In experiments concerning a potential selective adsorption and thus separation of both species, the PMF/SiO2 hybrid particles, in which the template had not yet been removed, showed a selective sulfate adsorption. The immobilization of heavy metal ions was analyzed with special focus on the simultaneous separation of the Cu2+ ions and respective anions used here. Investigations of the adsorbent after the adsorption experiments by means of electron microscopy, X-ray scattering and electron spin resonance spectroscopy elucidated the adsorption mechanism, which had been insufficiently analyzed so far. Here, adsorption and surface-induced precipitation were identified as partially separate subprocesses, both of which are responsible for the separation of both metal and anions from solution. In adsorption experiments with the monovalent ions nitrate and chloride, a two-step uptake process was identified, which was mathematically described for the first time via a new adsorption isotherm. In the scope of organic water pollutants, the separation of the pharmaceutical diclofenac is being tested. In particular, the adsorption of pharmaceuticals is an urgent issue due to their low effect concentration and ubiquity in surface and tap waters. Pharmaceutical separation using PMF has hardly been investigated worldwide despite its promising properties. In these experiments, particles templated with SiO2 NPs of different sizes and stabilized in different ways were tested. This resulted in pore systems that varied from each other especially in their accessibility of the pore system and in the diameter of the connecting channels between the main cavities. These characteristics significantly affected the adsorption capacity and separation rates in low concentration range. A final goal is to synthesize a resin network that uses an equally highly functional triazine-based monomer instead of melamine. The monomer 2,4,6-tris(2,4,6-trihydroxyphenyl)-1,3,5-triazine (3PT) possesses nine hydroxyl groups each, whereby a polymer based on it should exhibit strongly modified adsorption properties compared to PMF. This monomer was used in an aqueous polymerization analogous to PMF to produce a previously unknown polymer network, which was designated P(3PT-F). Here, templating was omitted because the newly prepared material already exhibited intrinsic nanoporosity due to the size of the 3PT monomer. In subsequent adsorption experiments, very high separation rates were demonstrated for the toxic metal ions Pb2+, Cd2+ and Ni2+. In realistic initial concentrations, the contamination was reduced to drinking water quality in each case. P(3PT-F) also showed highly selective removal of Pb2+ over the common ions Ca2+, Mg2+, K+ and Fe2+. As fundamental evidence, reusability was also demonstrated by complete desorption with dilute HCl and subsequent re-adsorption without significant reduction in capacity. Overall, starting from the fundamental study of PMF particle synthesis, a more general understanding of aqueous dispersion polymerization of hydrophobic resins was first derived and templating with hydrophilic SiO2 NPs was implemented. With the help of understanding the particle growth processes and interactions responsible for templating, the properties of the resulting particles could be controlled. Subsequently, the influence of the changed porosity in particular on the separation performance could be investigated in the adsorption studies. In addition, it was possible to analyze which interactions PMF enters into with the respective pollutant types. By replacing the monomer melamine with a hydroxyl-containing monomer, a novel resin polymer could be produced. With its altered porosity and reactivity, this can now serve as a new starting point for adsorption experiments with strongly altered adsorption performance, e.g. towards heavy metal ions.:Abstract 1 Kurzfassung 5 List of Publications 9 First-Author Publications 9 Co-Author Publications 10 Patent 12 Conference Proceedings 12 Oral Presentations 12 Poster 12 List of Figures 13 Mesoporous Poly(Melamine-co-Formaldehyde) Particles for Efficient and Selective Phosphate and Sulfate Removal: 14 Tuning the Pore Structure of Templated Mesoporous Poly(melamine-co-formaldehyde) Particles toward Diclofenac Removal: 15 Adsorption vs. Surface Precipitation of Cu²+ onto Porous Poly(melamine-co-formaldehyde) Particles: 16 SiO2 Nanospheres as Surfactant and Template in Aqueous Dispersion Polymerizations Yielding Nanoporous Resin Particles: 18 Waterborne Phenolic, Triazine-Based Porous Polymer Particles for the Removal of Nickel, Cadmium, and Lead Ions: 19 List of Tables 21 Mesoporous Poly(Melamine-co-Formaldehyde) Particles for Efficient and Selective Phosphate and Sulfate Removal: 21 Tuning the Pore Structure of Templated Mesoporous Poly(melamine-co-formaldehyde) Particles toward Diclofenac Removal: 21 Adsorption vs. Surface Precipitation of Cu²+ onto Porous Poly(melamine-co-formaldehyde) Particles: 22 SiO2 Nanospheres as Surfactant and Template in Aqueous Dispersion Polymerizations Yielding Nanoporous Resin Particles: 22 Waterborne Phenolic, Triazine-Based Porous Polymer Particles for the Removal of Nickel, Cadmium, and Lead Ions: 23 Abbreviations 25 Symbols 26 1. Introduction 1 2. Objectives and Experimental Design 5 3. Scientific Background 11 3.1. Poly(melamine-co-formaldehyde) 11 3.1.1. Polymerization Mechanism 11 3.1.2. Synthesis Strategies for the Preparation of Porous PMF Particles. 13 3.1.3. Fields of Application of PMF 13 3.2. Adsorption 15 3.2.1. Adsorption Isotherms and Mathematical Modeling 16 3.3. Surface Precipitation 20 4. Fundamentals of Instrumental Analytics 23 4.1. Gas Sorption Measurements 23 4.1.1. Determination of Pore Sizes 26 4.1.2. Determination of Specific Surface Area 27 4.2. Transmission Electron Microscopy 29 4.3. Inductively Coupled Plasma Optical Emission Spectroscopy 31 Results and Discussion 33 Chapter Overview 33 5. Mesoporous Poly(Melamine-co-Formaldehyde) Particles for Efficient and Selective Phosphate and Sulfate Removal 37 Graphical Abstract 37 Abstract 37 1. Introduction 38 2. Results and Discussion 39 2.1. Synthesis and Characterization of the PMF Particles 40 2.2. Sorption Experiments 47 3. Materials and Methods 54 3.1. Materials 54 3.2. Methods 54 3.3. Synthesis of the PMF Particles 56 3.4. Water Treatment Experiments 57 4. Conclusions 59 6. Tuning the Pore Structure of Templated Mesoporous Poly(melamine-co-formaldehyde) Particles toward Diclofenac Removal 65 Graphical Abstract 65 Abstract 65 1. Introduction 66 2. Materials 68 3. Methods 68 3.1. Synthesis of the PMF particles 70 3.2. Water treatment experiments with diclofenac solution 72 3.3. Theoretical model 72 3. Results and Discussion 73 3.1. Synthesis and characterization of the PMF particles 74 3.2. Adsorption of Pharmaceutics 80 4. Conclusion 84 7. Adsorption vs. Surface Precipitation of Cu²+ onto Porous Poly(melamine-co-formaldehyde) Particles 89 Graphical Abstract 89 Abstract 89 1. Introduction 90 2. Materials and methods 91 2.1. Materials 91 2.2. Synthesis of the Poly(melamine-co-formaldehyde) particles 92 2.3. Methods 93 2.4. Water treatment experiments 96 3. Results and discussion 97 3.1. Synthesis and characterization of the PMF particles 98 3.2. Cu2+ uptake experiments 102 3.3. Mechanism for Cu2+ and Anion Removal 115 3.4. Investigation of other heavy metal salts 116 4. Conclusions 117 8. SiO₂ Nanospheres as Surfactant and Template in Aqueous Dispersion Polymerizations Yielding Nanoporous Resin Particles 121 Graphical Abstract 121 Abstract 121 1. Introduction 122 2. Materials and methods 123 2.1. Materials 123 2.2. Methods 124 2.3. Synthesis of the PMF particles 125 2.4. Water treatment experiments 128 2.5. Theoretical model 129 3. Results and Discussion 132 3.1. PMF-Std 133 3.2. Influence of the reaction mixture composition 136 3.3. Variation of the process parameters 140 3.4. Conclusion on the templating mechanism for PMF-Std 146 3.5. Acquiring µm-sized porous PMF particles for adsorption application 149 3.6. Adsorption experiments with K2Cr2O7 solution 151 4. Conclusion 155 9. Waterborne Phenolic, Triazine-Based Porous Polymer Particles for the Removal of Nickel, Cadmium, and Lead Ions 161 Graphical Abstract 161 Abstract 161 1. Introduction 162 2. Materials and methods 163 2.1. Materials 163 2.2. Synthesis 164 2.3. Characterization 166 2.4. Batch adsorption experiments 169 2.5. Calculation and theoretical models 170 3. Results and discussion 172 3.1. Synthesis and characterization of the polymer particles 172 3.2. Adsorption experiments with Ni2+, Cd2+, and Pb2+ onto P(3PT-F)-3L 178 4. Conclusions 184 10. Conclusion and Outlook 191 Contribution to Publications 197 Mesoporous Poly(Melamine-co-Formaldehyde) Particles for Efficient and Selective Phosphate and Sulfate Removal 197 Tuning the Pore Structure of Templated Mesoporous Poly(melamine-co-formaldehyde) Particles toward Diclofenac Removal 198 Adsorption vs. Surface Precipitation of Cu²+ onto Porous Poly(melamine-co-formaldehyde) Particles 199 SiO₂ Nanospheres as Surfactant and Template in Aqueous Dispersion Polymerizations Yielding Nanoporous Resin Particles 200 Waterborne Phenolic, Triazine-Based Porous Polymer Particles for the Removal of Nickel, Cadmium, and Lead Ions 201 Danksagung 203 Appendix 205 References 207 Eidesstattliche Versicherung 217Durch fortschreitende Industrialisierung und den schonungslosen Verbrauch natürlicher Rohstoffe übt der Mensch negativen Einfluss auf seinen Lebensraum aus. Insbesondere Wasser als Grundlage des Lebens und fast aller Prozesse unserer Wirtschaft wird durch eine übermäßige Nutzung und unzureichende Reinigung mit diversen Schadstoffen kontaminiert. Hierbei stellen Oxyanionen, Schwermetallionen und organische Schadstoffe ein hohes Risiko für aquatische Lebensräume und letztendlich auch den Menschen dar. Durch unzureichende Entfernung tragen sie außerdem zum Verlust nicht-erneuerbarer Rohstoffe für industrielle Kreisläufe bei. Durch eine meist geringe Effektkonzentration und potentielle Wechselwirkungen mit diversen Lebewesen ist die Entfernung vieler Verunreinigungen extrem wichtig, um bestehende Ökosysteme nicht weiter zu verändern. Adsorption stellt eine energieeffiziente Methode zur Entfernung dieser Schadstoffe durch hierfür geeignete Adsorbentien dar. Hochgradig vernetzte Harzpolymere wie Poly(melamin-co-formaldehyd) (PMF) stellen mit ihrer sehr hohen chemischen Beständigkeit, einer hohen Zahl funktioneller Gruppen und einfachen Herstellbarkeit einen vielversprechenden Ausgangspunkt für Adsorbentien dar. Diese Dissertation beschreibt die kolloidale, wässrige Synthese nanoporöser Harzpartikel (z. B. PMF) durch eine Templatierung mit SiO2 Nanopartikeln (SiO2 NPs), welche anschließend zur Adsorption von Wasserschadstoffen eingesetzt werden. Ein übergeordnetes Ziel dieser Arbeit besteht aus der Aufklärung des Mechanismus zur Partikel- und Porenbildung durch systematische Variation verschiedener Syntheseparameter. Mittels Elektronenmikroskopie, N2-Sorption und Partikelgrößenmessung wird die Morphologie, Größe und Porenstruktur der Partikel analysiert. Umfassende Untersuchungen ermöglichen somit, den Einfluss der einzelnen getesteten Syntheseparameter auf diese Eigenschaften zu bestimmen. Ein sehr wichtiges Ziel, besonders für eine zukünftige großtechnische Anwendbarkeit, ist dabei die kolloidale Herstellung uniformer Partikel, welche sowohl eine hohe geordnete Porosität als auch Partikeldurchmesser im Bereich einiger Mikrometer aufweisen. Dies ermöglicht einen Einsatz als durchströmbaren Festbett-Adsorber. Dieses Ziel ist eng mit der mechanistischen Aufklärung der Poren- und Partikelbildung in der Synthese verknüpft. Die hergestellten nanoporösen PMF-Partikel wurden nach ihrer Charakterisierung für verschiedene Adsorptionsanwendungen getestet. Um ein umfassendes Bild über die Einsetzbarkeit von PMF-Partikeln zu erhalten, sollen jeweils Versuche mit Oxyanionen, mit Schwermetallionen und mit Pharmazeutika als Vertreter organischer Schadstoffe durchgeführt werden. Bei diesen Versuchen steht zum einen die Untersuchung der Adsorptionsleistung und des Adsorptionsmechanismus des jeweiligen Schadstoffes an PMF im Vordergrund. Zum anderen wird durch die Verwendung verschiedener Partikel, bei welchen ein einzelner Syntheseparameter variiert wurde, der Einfluss der veränderten Porosität auf den Adsorptionsmechanismus untersucht. Sulfat- und Phosphationen wurden in der Klasse der Oxyanionen untersucht. Für beide Ionen wurden extrem hohe Abtrennraten nachgewiesen, welche bisherige kommerziell erhältliche Materialien signifikant übertraf. In Versuchen hinsichtlich einer potentiellen selektiven Adsorption und somit Trennung beider Spezies, zeigten die PMF/SiO2-Hybridpartikel, bei welchen das Templat noch nicht entfernt wurde, eine selektive Sulfatadsorption. Die Immobilisierung von Schwermetallionen wurde mit besonderem Fokus auf die gleichzeitig auftretende Abtrennung der dafür verwendeten Cu2+-Ionen und jeweiliger Anionen analysiert. Durch Untersuchungen des Adsorbens nach den Adsorptionsversuchen mittels Elektronenmikroskopie, Röntgenstreuung und Elektronenspinresonanz-Spektroskopie wurde der bisher unzureichend analysierte Adsorptionsmechanismus aufgeklärt. Hierbei wurden Adsorption und oberflächeninduzierte Fällung als separate Teilprozesse identifiziert, welche beide jeweils für die Abscheidung von sowohl Metall- als auch Anionen aus der Lösung verantwortlich sind. Bei Adsorptionsversuchen mit den einwertigen Ionen Nitrat und Chlorid wurde ein zweistufiger Prozess identifiziert, welcher erstmals über eine neue Adsorptionsisotherme mathematisch beschrieben wurde. Im Bereich organischer Wasserschadstoffe wird die Abtrennung des Pharmazeutikums Diclofenac getestet. Insbesondere die Adsorption von Pharmazeutika stellt aufgrund von deren geringen Effektkonzentration und Allgegenwärtigkeit in Oberflächen- und Leitungswässern ein dringliches Thema dar. Die Pharmazeutika-Abtrennung mittels PMF wurde trotz seiner vielversprechenden Eigenschaften weltweit bisher kaum untersucht. Im Rahmen dieser Versuche wurden Partikel getestet, welche mit unterschiedlich großen und unterschiedlich stabilisierten SiO2 NPs templatiert wurden. Dadurch entstanden Porensysteme, die besonders in derer Zugänglichkeit ihres Porensystems und in dem Durchmesser der Verbindungskanäle zwischen den Hauptkavitäten voneinander variierten. Diese Eigenschaften wirkten sich signifikant auf die Adsorptionskapazität und die Abtrennraten im niedrigen Konzentrationsbereich aus. Ein abschließendes Ziel ist die Synthese eines Harznetzwerkes, welches statt Melamin auf einem ebenso hochfunktionellen, triazinbasierten Monomer basiert. Das Monomer 2,4,6-Tris(2,4,6-trihydroxyphenyl)-1,3,5-triazin (3PT) besitzt jeweils neun Hydroxylgruppen, wodurch ein darauf basierendes Polymer stark veränderte Adsorptionseigenschaften gegenüber PMF aufweisen soll. Mit diesem Monomer wurde in einer analog zu PMF durchgeführten wässrigen Polymerisation ein bisher unbekanntes Polymernetzwerk hergestellt, welches als P(3PT-F) bezeichnet wurde. Hierbei wurde auf Templatierung verzichtet, da das neu hergestellte Material bereits intrinsische Nanoporosität durch die Größe des verwendeten 3PT-Monomers aufwies. In anschließenden Adsorptionsversuchen wurden sehr hohe Abtrennraten für die toxischen Metallion Pb2+, Cd2+ und Ni2+ nachgewiesen. In realistischen Ausgangskonzentrationen wurde die Kontamination mit diesen Ionen jeweils auf Trinkwasserqualität reduziert. P(3PT-F) zeigte außerdem eine sehr selektive Abtrennung von Pb2+ gegenüber den häufig vorkommenden Ionen Ca2+, Mg2+, K+ und Fe2+. Als grundlegender Beweis konnte eine Wiederverwendbarkeit durch die vollständige Desorption mit verdünnter HCl gezeigt werden und eine anschließende erneute Adsorption ohne signifikante Verringerung der Kapazität. Insgesamt wurde ausgehend von der grundlegenden Untersuchung der PMF-Partikelsynthese erst ein generelleres Verständnis der wässrigen Dispersionspolymerisation hydrophober Harze abgeleitet und die Templatierung mit hydrophilen SiO2 NPs implementiert. Mithilfe des Verständnisses der Partikelwachstumsprozesse und der Wechselwirkungen, welche für die Templatierung verantwortlich sind, konnten die Eigenschaften der entstehenden Partikel gesteuert werden. Im Rahmen der Adsorptionsuntersuchungen konnte anschließend der Einfluss insbesondere der veränderten Porosität auf die Abtrennleistung untersucht werden. Außerdem konnte analysiert werden, welche Wechselwirkungen PMF mit den jeweiligen Schadstoffarten eingeht. Durch den Austausch des Monomers Melamin gegen das hydroxylhaltiges Monomer 3PT konnte ein neuartiges Harzpolymer hergestellt werden. Dieses kann mit seiner veränderten Porosität und Reaktivität nun als neuer Ausgangspunkt für Adsorptionsexperimente mit stark veränderter Adsorptionsleistung z. B. gegenüber Schwermetallionen dienen.:Abstract 1 Kurzfassung 5 List of Publications 9 First-Author Publications 9 Co-Author Publications 10 Patent 12 Conference Proceedings 12 Oral Presentations 12 Poster 12 List of Figures 13 Mesoporous Poly(Melamine-co-Formaldehyde) Particles for Efficient and Selective Phosphate and Sulfate Removal: 14 Tuning the Pore Structure of Templated Mesoporous Poly(melamine-co-formaldehyde) Particles toward Diclofenac Removal: 15 Adsorption vs. Surface Precipitation of Cu²+ onto Porous Poly(melamine-co-formaldehyde) Particles: 16 SiO2 Nanospheres as Surfactant and Template in Aqueous Dispersion Polymerizations Yielding Nanoporous Resin Particles: 18 Waterborne Phenolic, Triazine-Based Porous Polymer Particles for the Removal of Nickel, Cadmium, and Lead Ions: 19 List of Tables 21 Mesoporous Poly(Melamine-co-Formaldehyde) Particles for Efficient and Selective Phosphate and Sulfate Removal: 21 Tuning the Pore Structure of Templated Mesoporous Poly(melamine-co-formaldehyde) Particles toward Diclofenac Removal: 21 Adsorption vs. Surface Precipitation of Cu²+ onto Porous Poly(melamine-co-formaldehyde) Particles: 22 SiO2 Nanospheres as Surfactant and Template in Aqueous Dispersion Polymerizations Yielding Nanoporous Resin Particles: 22 Waterborne Phenolic, Triazine-Based Porous Polymer Particles for the Removal of Nickel, Cadmium, and Lead Ions: 23 Abbreviations 25 Symbols 26 1. Introduction 1 2. Objectives and Experimental Design 5 3. Scientific Background 11 3.1. Poly(melamine-co-formaldehyde) 11 3.1.1. Polymerization Mechanism 11 3.1.2. Synthesis Strategies for the Preparation of Porous PMF Particles. 13 3.1.3. Fields of Application of PMF 13 3.2. Adsorption 15 3.2.1. Adsorption Isotherms and Mathematical Modeling 16 3.3. Surface Precipitation 20 4. Fundamentals of Instrumental Analytics 23 4.1. Gas Sorption Measurements 23 4.1.1. Determination of

    Elucidation of novel biosynthetic pathways for the discovery of cyclodipeptide derivatives from Streptomyces species

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    Cyclodipeptides (CDPs) with a 2,5-diketopiperazine (DKP) as central core occur ubiquitously in living organisms, from simple bacteria and fungi to more complex ones like plants and animals. They display various biological and pharmacological effects, including antibiotic, antifungal, and antiproliferative activities. In microorganisms, CDPs are usually synthesized by one of the two distinct enzyme families, nonribosomal peptide synthetases (NRPSs), mainly occurring in fungi, or cyclodipeptide synthases (CDPSs), commonly found in bacteria. NRPS for CDP formation are comparably large (~2500 amino acids), bi-modular enzymes, using free amino acids as substrates. CDPSs on the other hand are smaller (200 – 300 amino acids) and require activated amino acyl tRNAs for peptide bond formation. In general, the formation of the DKP ring increases the stability of CDPs against proteolysis compared to their acyclic counterparts. This enables a variety of intriguing modifications carried out by tailoring enzymes. Their genetic information often lies in direct neighborhood to that of backbone enzymes, like CDPSs, arranged in biosynthetic gene clusters (BGCs). In CDPS-associated pathways, tailoring enzymes comprise cyclodipeptide oxidases (CDOs), cytochrome P450 (P450) enzymes, FeII/2-oxoglutarate dependent (FeII/2-OG) oxidases, as well as methyl- (MTs) and prenyltransferases (PTs). In this thesis, eight of such BGCs from Streptomyces species were identified using genome mining and elucidated by a combination of heterologous expression and biochemical analyses. In the first project, a BGC from Streptomyces cinnamoneus consisting of five genes was chosen for detailed investigation and termed gtm gene cluster. It codes for four enzymes, i.e. a CDPS (GtmA), a CDO (GtmBC), a P450 enzyme (GtmD), and a FeII/2-OG oxidase (GtmE). The genes were cloned in different combinations into the replicative pPWW50A vector for heterologous expression in Streptomyces albus J1074 (S. albus). Investigation using LC-MS and NMR spectroscopy revealed that GtmA synthesizes cyclo-L-Trp-L-Met, GtmBC installs a double bond at the methionine residue of the DKP, GtmD transfers a guanine onto the tryptophan moiety, and GtmE forms a second double bond at another side of the DKP. Together, this cascade results in the formation of the novel secondary metabolite guatrypmethine C. As the second dehydrogenation by GtmE displayed a novel reaction for FeII/2-OG oxidases in CDPS-dependent pathways, it was further characterized biochemically using the recombinant protein. It was proven that GtmE indeed catalyzes the conversion of the precursor guatrypmethine A to the pathway end product guatrypmethine C. No efficient conversion of the stable isomer guatrypmethine B was observed by GtmE. This experimental finding was further supported by quantum chemical calculations using density functional theory. In the second project, in cooperation with Dr. Jing Liu, a widely distributed two-gene locus, gymAB, was identified in 47 different actinobacteria. It comprises the genes gymA and gymB, coding for a CDPS and a P450 oxidase, respectively. The latter is closely related to CYP121, an essential enzyme for the viability of Mycobacterium tuberculosis. Six representative Streptomyces species were selected for functional elucidation of these BGCs. In analogy to the first project, their genes were cloned into pPWW50A and overexpressed in S. albus. Analyses of the cultural extracts by LC-MS in combination with NMR spectroscopy of the purified compounds showed that all six CDPSs produce cyclo-L-Tyr-L-Tyr (cYY) as major product. Subsequently, the P450 oxidases catalyze two different kind of reactions – either the formation of an intramolecular C-C bond within cYY resulting in mycocyclosin, or the intermolecular transfer of the nucleobases guanine or hypoxanthine, leading to the formation of the novel secondary metabolites guatyromycine A and B, respectively. The reactions catalyzed by GymBs were confirmed with biochemical assays using recombinant proteins of all six candidates. As the intramolecular coupling is the same reaction performed by CYP121 from Mycobacterium tuberculosis, the corresponding gene cluster was also expressed heterologously in the same manner. However, CYP121 merely catalyzes the formation of mycocyclosin, indicating that GymBs might have evolved from CYP121 and slightly changed during evolution. In the third project, I contributed to the elucidation of a BGC from Streptomyces aurantiacus, coding for the CDPS SasA, the PT SasB, and the MT SasC. It was proven that the sasABC gene cluster is responsible for the formation of streptoazine C. The involved PT SasB catalyzes two regular prenylations at both tryptophan residues within cyclo-L-Trp-L-Trp. By incubation with other CDPs and dehydrogenated CDPs, it was shown that SasB possesses a broad substrate flexibility and can convert at least eight other CDP derivatives efficiently

    Advantages of multi-dimensional biasing in accelerated dynamics: application to the calculation of the acid pKapK_a for acetic acid

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    The use of accelerated sampling methods such as metadynamics has shown significant advantage in calculations that involve infrequent events, which would otherwise require sampling a prohibitive number of configurations to determine, e.g., difference in free energies between two or more chemically distinct states such as in the calculation of acid dissociation constants KaK_a. In this case, the most common method is to bias the system via a single collective variable (CV) representing the coordination numbercoordination~number of the proton donor group, which yields results in reasonable agreement with experiments. Here we study the deprotonation of acetic acid using the reactive force field ReaxFF and observe a significant dependence of KaK_a on the simulation box size when biasing only the coordination number CV, which is due to incomplete sampling of the deprotonated state for small simulation systems, and inefficient sampling for larger ones. Incorporating a second CV representing the distance between the H3_3O+^+ cation and the acetate anion results in a substantially more efficient sampling both accelerating the dynamics and virtually eliminating the computational box size dependence.Comment: 22 pages, 9 figure

    Successive Ring Expansion (SuRE) in the synthesis of medium sized ring and macrocycle libraries

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    This thesis describes the development of new methodologies to synthesize different medium sized rings and macrocycles, either using Successive Ring Expansion (SuRE) reactions or SuRE-like reactions. In Chapter 2, new N-acylation conditions had been developed for lactams that cannot easily ring expand using previously reported Nacylation conditions. In Chapter 3, SuRE reactions were utilised to synthesize the 15-membered macrocyclic core of natural products Solomonamides and a series of analogues. Chapter 4 describes the development of a conjugate addition/ring expansion (CARE) cascade reaction, which allows the synthesis of diverse functionalized medium sized rings and macrocycles. In Chapter 5, two new ring expansion protocols (nitro reduction method and conjugate addition method) to access medium sized and macrocyclic sulfonamides are described. Chapter 6 describes the ring expansion study of P=O containing molecules, which showed quite different reactivity comparing to normal SuRE reaction. Chapter 7 describes a SuRE strategy to synthesize medium sized and macrocyclic aza sugars

    MULTISCALE MOLECULAR MODELING STUDIES OF THE DYNAMICS AND CATALYTIC MECHANISMS OF IRON(II)- AND ZINC(II)-DEPENDENT METALLOENZYMES

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    Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps collagen degradation. Chapter 2 investigates the substrate selectivity and dynamics on the enzyme-substrate complexes of DNA repair enzymes, AlkB and FTO. Chapter 3 unravels the mechanisms and effects of dynamics on the demethylation of 3-methylcytosine substrate by AlkB and AlkBH2 enzymes. The results imply that the nature of DNA and conformational dynamics influence the electronic structure of the iron center during demethylation. Chapter 4 delineates how second-coordination and long-range residue mutations affect the oxidation of 5-methylcytosine substrate to 5-hydroxymethylcytosine by TET2 enzyme. The results reveal that mutations affect DNA binding/interactions and the energetic contributions of residues stabilizing key catalytic species. Chapter 5 describes the reparation of unnatural alkylated substrates by TET2, their effects on second-coordination interactions and long-range correlated motions in TET2. The study reveals that post-hydroxylation reactions occur in aqueous solution outside the enzyme environment. Chapter 6 establishes how applying external electric fields (EEFs) enhances specificity of KDM4E for C—H over N—H activation during dimethylated arginine substrate demethylation. The results reveal that applying positive EEFs parallel to Fe=O bond enhances C—H activation rate, while inhibiting the N—H one. Chapter 7 addresses the formation of catalytically competent MMP-1·THP complex of MMP-1. The studies reveal the role of MMP-1’s catalytic domain a-helices, the linker, and changes in coordination states of catalytic Zn(II) during the transition. Overall, the presented results contribute to the in-depth understanding of the fundamental mechanisms of the studied enzymes and provide a background for developing enzyme-specific inhibitors against the associated disorders and diseases

    Heterocyclic Compounds from Marine Organisms

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    Marine drugs have drawn considerable attention due to their significant biological and pharmacological properties, such as antimicrobial or antibacterial activities and antitumor effects, among others. The frequent occurrence of heterocyclic motifs in the structure of many of these targets has revealed the key role of these units as promising pharmacophores. In this Special Issue we have gathered several original papers which highlight the isolation, structural elucidation and biological essays of newly isolated heterocyclic marine drugs, as well as reviews which give an overview of the isolation, synthesis and pharmacological activities of different classes of marine heterocycles

    Heterogeneous vanadium Schiff base complexes in catalytic oxidation reactions

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    The chemistry of Schiff base has received remarkable attention in different applications, both organic synthesis and industries. Over the past few years many reports have been on the synthesis, characterization and application of vanadium Schiff base complexes. However, heterogeneous vanadium Schiff base catalysts are active for various oxidation reactions, making catalytic oxidation of hydrocarbons a great interest. This review summarizes the recent development of organic substrate oxidation with heterogeneous vanadium Schiff base catalysts
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