The epigenetic post-translational modifications (PTMs) of histone proteins are numerous and have an important role in regulating cellular development. Molecular recognition elements that can bind directly to epigenetic PTMs have previously been developed. The most synthetically accessible of these are a family of molecules called monoaryl-trisulfonate calix[4]arenes. The initial goal of this thesis was to develop research tools consisting of these asymmetrically-derivatized calixarenes immobilized onto a solid resin for the purpose of enrichment of PTM-bearing species. Seven novel resin-immobilized calixarene reagents were created and employed in batch-wise pulldown experiments, as well as chromatographic separations. These experiments produced mixed results: poor efficacy was demonstrated in batch-binding experiments but total separation of certain PTM bearing peptides was achieved in a chromatographic approach. During these studies, a subset of these calixarenes were found to undergo self-association in water in a fashion not previously observed for calixarenes. Secondary goals of the thesis were to create new examples of this self-associating motif, and to characterize and develop structure-function relationships for their assemblies. Eight new self-associating calixarenes were developed and characterized extensively by 1H NMR, isothermal titration calorimetry (ITC), and X-ray crystallography. Self-association was shown to be enthalpically driven with Kd values ranging from 1-20 mM. The dimeric assembly behaviours were remarkably consistent across many different family members, and were shown to persist even in highly competitive media like mock blood and urine. This system represents a novel class of ordered calixarenes assemblies that operate in biological media. / Graduate / 2016-12-23

Following an introoduction on calixarene chemistry and their metal-ion complexes including some of their applications, the aims of the work are described. Thus, the first part of this thesis concerns the detemination of the standard enthalpies of solution, sH°, of new lithium and sodiimi 1:1 electrolytes based on eth p=tert-butycalix[4]arene tetraethanoate containing various anions in acetonitrile at 298.15 K. Using these data in conjunction with previously reported sH° values for the free metal-ion salts and the ligand and standard enthalpies of complexation, cH°H° of allcali-metal cations (Li+ and Na+) and the calix[4]arene ester in the same solvent, standard enthalpies of coordination, coordH° referred to the process in which the reactants and the product are in the solid stated were calculated. The anion effect on the coordination process was determined. The second part of this thesis is related to an investigation on the solution properties of pyridinocalix[4]arenes and their metal-ion complexes. Transfer Gibbs energies of geometrical isomers of pyridinocalix[4]arenes from acetonitrile to various solvents reflect that these ligands undergo selective solvation in the various solvents but these cannot be correlated with any single solvent property. The complexing ability of 5,11,17,23 - tetra - tert - butyl[25,26,27,28 - tetrakis (2-pyridyhnethyl) oxy]- calix[4]arene for metal cations was investigated by a variety of techniques. Thus 1H NMR studies were performed to obtain information about the active sites of the ligand in its interaction with metal cations. Conductance measurements were used to establish the composition of the metal-ion complexes in dipolar aprotic media. Potentiometric and calorimetric measurements were performed to derive the thermodynamics associated with the complexation process in acetonitrile and benzonitrile. Based on stability constant data, two metal-ion complexes were isolated. The crystal structure of the sodium and acetonitrile complex of 5,11,17,23- tetra- tert- butyl[25,26,27,28 - tetrakis (2-pyiidylmethyl)oxy] calix[4] arene solved by X-ray diffraction studies shows three different complexes in the lattice, two sited on a fourfold axis and a third one on a twofold axis where all ligands exhibit a 'cone' conformation and the sodium ion is encapsulated in their hydrophilic pockets with their hydrophobic cavities filled with an acetonitrile molecule. The crystal structure of the 1:1 monoacetonitrile and silver complex of the 2-pyridyl derivative with the perchlorate ion as the counter ion shows the macrocycle sited on a fourfold symmetry axis. The presence of acetonitrile in the hydrophobic cavity of the ligand is also found. The silver cation is encapsulated in the hydrophilic cavity through the ethereal oxygens and the pyridinic nitrogens. Conclusions and suggestions for furthur research in this area are given.

This thesis concerns the thermodynamics of macrocycles and their metal cation complexes in non-aqueous media and these are discussed under two main headings, i) Thermodynamics of Alkali-Metal Cations and Macrocycles in Solution and in the Solid State. Thermodynamic parameters of complexation for alkali-metal cations and macrocycles (18-crown-6 and ethyl p-tert-butylcalix(6)arene hexanoate) in benzo-nitrile at 298.15 K are first reported. These data are compared with those previously reported for cryptand 222 and these cations in this solvent. A 'peak' selectivity for potassium is observed for the complexation of the calix(6)arene ester with alkali metal cations. The process is enthalpy controlled with an exothermic maximum for the potassium cation. Thermodynamic data of complexation are characterised by a lower enthalpic stability and a more favourable entropy (except for K+) than corresponding data involving cryptand 222 or indeed 18-crown-6. Standard enthalpies of solution, DeltasH0, of macrocycles and their sodium and potassium salts in benzonitrile measured calorimetrically are discussed in relation to (i) data for the uncomplexed salts and (ii) previously reported data for sodium and potassium cryptate salts in various solvents. Enthalpies of coordination, DeltacoordH0, for eighteen systems involving sodium and potassium coronates, cryptates and calix(6)arenates are derived and whenever possible these are discussed on the basis of (i) available X-ray crystallographic data and (ii) the anion effect on the coordination process. ii) Thermodynamics of Lower Rim Calix(4)arene Derivatives with the Silver Cation in Different Media at 298.15 K. The DeltasH0 values of p-tert-butyl(bis-diethylamine-bis-methysulphanyl) calix(4)arene (EATCalix4) in various solvents at 298.15 K are reported. Transfer parameters from acetonitrile to other solvents are calculated. The interaction of EATCalix4 and the silver cation was investigated by 1H NMR in deuterated acetonitrile at 298 K showing that the ligand hosts the metal cation through interaction with the different donor atoms (O, N, S). Conductimetric titrations indicate that the stoichiometry of the complex is 1:1. The thermodynamics of complexation of EATCalix4 and silver in six solvents at 298.15 K is reported. The DeltasH0 values of the free and the complex silver perchlorate salts have been also measured in various solvents and these have been combined with DeltacH0 data to derive the DeltacoordH0 of this system. A few representative examples about the use of coordination data are given. The medium effect on the complexation process is assessed in terms of DeltatG0, DeltatH0 and DeltatS0 of the reactants and the product from acetonitrile to the appropriate solvent. The relevance of analysing the solvation changes that these species undergo upon complexation is emphasised.

In this thesis, different approaches in synthesizing molecular resist are examined, and structure-property relations for the molecular resist properties are studied. This allows for design of resists that could be studied further as either negative or positive tone resists in photolithography. A series of compounds having different number of acrylate moiety, and different backbones were investigated for photoresist application. Thermal curing of acrylate compounds in organic solvent was also examined. Film shrinkage, as well as auto-polymerization was observed for these compounds that make them unsuitable as photoresist material. Furthermore, calix[4]resorcinarenes (C4MR) was chosen as backbone, and the functional groups was selected as oxetane and epoxy. Full functionalized C4MR compounds with oxetane, epoxy and allyl were synthesized. Variable-temperature NMR of C4MR-8Allyl was studied in order to get a better understanding of the structure’s conformers. Energy barrier of exchange (ΔG#) was determined from coalescence temperatures, and was 57.4 KJ/mol for aromatic and vinyl hydrogens and 62.1 KJ/mol for allylic hydrogens.

Die Uranspeziation in ausgewählten Sicker- und Grubenwässern des ehemaligen Uranbergbaus wurde mittels spektroskopischer Methoden (TRLFS, LIPAS) untersucht. Deren Kenntnis in Abhängigkeit vom pH-Wert ermöglicht die Optimierung der Uranabtrennung mittels uranophiler Calixarene. Mittels Flüssig-Flüssig-Extraktion wurde gezeigt, dass COOH-derivatisierte Calix[6]arene als effektive Extraktionsmittel für die selektive Uranylabtrennung aus umweltrelevanten Wässern bei pH-Werten größer 4 geeignet sind und für Praxisanwendungen eingesetzt werden können. Extraktionskonstanten wurden bestimmt. Die durch Fixierung dieser Calixarenderivate auf Polyester dargestellten calixarenmodifizierten Vliese sind in der Lage Uranylionen aus synthetischen Grubenwässern in Anwesenheit von Konkurrenzionen abzutrennen. Die Untersuchungen zur Reversibilität der Uranbindung an calixarenausgerüsteten Polyestervliesen haben gezeigt, dass eine fast vollständige Regenerierung der calixarenmodifizierten Vliese mittels verdünnter Mineralsäuren möglich ist. Die regenerierten textilen Filtermaterialien können für weitere Uranabtrennungszyklen eingesetzt werden. Nach Auswahl geeigneter Calixarenderivate ist eine Übertragung des entwickelten Abtrennungsprinzipes auf weitere Actinide (z.B. Np, Pu) bzw. Schwermetall-Kontaminanten (z.B. As, Cd, Pb) möglich.

The covalent modifications to the histone 2A, 2B, 3, and 4 N-terminal tails that affect gene expression have been deemed the “Histone Code.” Mis-regulation of these signalling pathways is of great interest as are important in human disease. A variety of peptides containing post-translationally modified histone 3 and 4 sequences were read using a supramolecular sensor array approach, where two or three sensors gave a unique response for each analyte when compared to others. These sequences were chosen to determine what type of modifications could be read (phosphorylation, acetylation, methylation) and if this type of array would be suitable for reading analytes on which antibodies—the leading technology—typically perform poorly. It was found that three sensors, which operate in neutral aqueous solution, were able to discriminate 16 different histone analytes. Additionally, it was shown that this array could report simultaneously on both concentration and the identities of histone analytes. / Graduate

Role of N-methylated lysines (K) and arginines (R) was underappreciated for a long time before the turn of the century. With the help of new emerging technologies, their crucial role in chromatin regulation was established and now their mention when discussing gene regulation is almost a given. Despite this, much about how they contribute to the cellular chemistry is still to be discovered. There is a major gap in current knowledge base due to an incomplete list of possible lysine and arginine methylation sites. This is because of their low copy number inside the cell which makes it difficult to detect them. New methylation sites are being added every day. This thesis aims to provide a solution to this problem by establishing methods that can help detect N-methylated lysines and argnines that are present in really low quantity inside the cell. The work is influenced by a previously established fact that p-sulfonatocalix[4]arene binds methylated lysine over unmethylated ones. We have first attempted to improve this native affinity by decorating the calix[4]arene skeleton with different substituents. To this effect, we have developed methods for regioselective functionalization of calix[4]arene scaffold and then studied their effect on its binding profile against a set of test peptides derived from proteins found in vivo. We then demonstrate a proof-of-concept enrichment method using selected molecules from our inventory. We use these calix[4]arene based molecules as a stationary phase modifier in a chromatography setup and then show that it can separate peptides based on presence of N-methylated lysines and arginines. We propose that introduction of such a method would improve the visibility of low level N-methylated peptides by removing the bulk of back ground unmethylated analytes and thus improving their signal strength. Finally, we establish the utility of this method by showing that more N-methylated lysines are detected from a real-world proteomics sample prepared using our enrichment method. This work opens new avenues for use of supramolecular chemistry in proteomics studies. We believe that this thesis is a confident demonstration that host-guest chemistry can help expand the existing knowledge about bimolecular processes found in vivo and must be explored further. / Graduate / 2021-12-23

Die Uranspeziation in ausgewählten Sicker- und Grubenwässern des ehemaligen Uranbergbaus wurde mittels spektroskopischer Methoden (TRLFS, LIPAS) untersucht. Deren Kenntnis in Abhängigkeit vom pH-Wert ermöglicht die Optimierung der Uranabtrennung mittels uranophiler Calixarene. Mittels Flüssig-Flüssig-Extraktion wurde gezeigt, dass COOH-derivatisierte Calix[6]arene als effektive Extraktionsmittel für die selektive Uranylabtrennung aus umweltrelevanten Wässern bei pH-Werten größer 4 geeignet sind und für Praxisanwendungen eingesetzt werden können. Extraktionskonstanten wurden bestimmt. Die durch Fixierung dieser Calixarenderivate auf Polyester dargestellten calixarenmodifizierten Vliese sind in der Lage Uranylionen aus synthetischen Grubenwässern in Anwesenheit von Konkurrenzionen abzutrennen. Die Untersuchungen zur Reversibilität der Uranbindung an calixarenausgerüsteten Polyestervliesen haben gezeigt, dass eine fast vollständige Regenerierung der calixarenmodifizierten Vliese mittels verdünnter Mineralsäuren möglich ist. Die regenerierten textilen Filtermaterialien können für weitere Uranabtrennungszyklen eingesetzt werden. Nach Auswahl geeigneter Calixarenderivate ist eine Übertragung des entwickelten Abtrennungsprinzipes auf weitere Actinide (z.B. Np, Pu) bzw. Schwermetall-Kontaminanten (z.B. As, Cd, Pb) möglich.

The receptor dimers that mediate bacterial chemotaxis form high-order signaling complexes with CheW and the kinase CheA. From the packing arrangement in two crystal structures of different receptor cytoplasmic fragments, two different models have been proposed for receptor signaling arrays: the trimers-of-dimers and hedgerow models. We identified an interdimer distance that differs substantially in the two models, labeled the atoms defining this distance through isotopic enrichment, and measured it with 13C-19F REDOR. This was done in two types of receptor samples: first, isolated bacterial membranes containing overexpressed, intact receptor, and second, soluble receptor fragments reconstituted into kinase-active signaling complexes. In both cases, the distance found was not compatible with the receptor dimer−dimer contacts observed in the trimers-of-dimers or in the hedgerow models. Comparisons of simulated and observed REDOR dephasing were used to deduce a closest-approach distance at this interface, which provides a constraint for the possible arrangements of kinase-competent receptor assemblies. An alternate model of receptor signaling is proposed, which reconciles this result with existing structural and biochemical data. Additionally, two advances to solid-state NMR methodology are described. The first is a set of strategies to protect protein samples against degradation by solid-state NMR analysis. Biochemical and spectroscopic techniques are prescribed to identify and isolate specific challenges to protein stability, allowing them to be addressed individually. For this purpose a new pulse sequence (Thermal Calibration Under Pulseload, or TCUP) is employed, which allows sample temperature to be measured with exceptional time resolution. The second NMR advance describes the creation and characterization of a 13C-19F REDOR distance-calibration standard. The inclusion compound of 4-fluorotoluene and tert-butylcalix[4]arene was used for this purpose. The compound is easily synthesized from commercially available materials, and provides a long, isolated 13C-19F distance of 4.1 Å. Dynamics within the compound allow direct observation of 19F resonances without 1H-decoupling, and provide exceptionally sharp 13C resonances; these characteristics speed the routine setup of REDOR experiments. Both methodological developments were important to performing accurate distance measurements on functionally relevant chemotaxis signaling complexes; they also pave the way for making similar measurements in other proteins of interest.

No description available.