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Harnessing the immune system is a powerful tool in chemical biology and is the focus of cancer immunotherapy. Often, this is accomplished through monoclonal antibodies which recognize and recruit immune effector cells to an over-expressed cancer antigen presented at the cancer cell surface. More recently, there has been great interest in developing small molecule therapeutics which replicate this, but with lower developmental costs, greater modularity, and improved tumor penetration. One such class of therapeutics are bifunctional molecules known as antibody recruiting molecules, which form molecular bridges between two targets, i.e., a cancer receptor and antibody. Limitations in ternary complex formation between bifunctional molecules and their two binding targets has presented the need for increasing residence time at key junctions. Demonstrated here is the development of a covalent proximity-induction approach which leverages molecular recognition to drive an electrophilic warhead near a nucleophile within a target antibody binding site. Subsequent irreversible labeling reprograms these antibodies with tumor binding handles in situ for enhanced tumor opsonization and immune clearance mechanisms. This was accomplished by equipping a viral peptide epitope with a sulfur (VI) fluoride exchange electrophile to irreversibly label anti-herpes simplex virus (HSV) antibodies. Using the aryl sulfonyl fluoride warhead, we demonstrate fast and selective labeling for both model monoclonal antibodies, as well as natural polyclonal anti-HSV antibodies. Covalently reprogrammed antibodies elicited superior potency at both lower concentrations and with cell lines having lower antigen presentation. This proof of concept has broad applicability in developing covalent bifunctional molecules for bridging one or more protein:protein interactions. / Dissertation / Master of Science (MSc)

As countries pledge their commitment to a net-zero future, much of the previously forgotten climate change research were revitalized by efforts from both governmental and private sectors. In particular, the utilization of lignocellulosic materials saw a special spotlight in research interest for its abundance and its carbon removal capability during photosynthesis. The initial effort in mimicking enzymatic active sites of β-glucosidase will be explored. The crystalline covalent organic frameworks (COFs) allowed for the introduction of a variety of noncovalent interactions, which enhanced the adsorption and the catalytic activity against cellobiose and its glycosidic bonds. The physical processes associated with this reaction, such as the kinetics, equilibrium, and activation energies, will be closely examined and compared with existing standard materials and comparable advanced catalysts. In addition, several variants of COFs were synthesized to explore the effect of various noncovalent interactions with cellobiose. A radical-bearing COF was synthesized and characterized. The stability of this radical was examined by electron paramagnetic resonance spectroscopy (EPR) and its oxidative capability tested with model lignin and alcoholic compounds. The reaction products are monitored and identified using gas chromatography-mass spectroscopy (GC-MS). An oxidative coupling of phenol was explored, and its initial results are presented in chapter 5.

Molecularly imprinted polymers (MIPs) have been compared to natural antibodies in that they can specifically bind target compounds in a similar way that antibodies specifically bind to an antigen. The attraction of the MIPs technology is the ease of creating binding elements which are relatively cheap compared with the process of isolating natural antibodies. In this research monoterpenes, such as α-terpineol, were chosen to be the model compounds for investigating the molecular imprinting of small, poorly functionalised organic compounds. The conventional non-covalent approach was mainly used to synthesise these MIPs, but the sacrificial-spacer semi-covalent approach was also investigated. A less widely used method, porogen-imprinting - a variant of non-covalent imprinting - was adapted for α-terpineol. The latter novel terpene MIP appeared to specifically bind α-terpineol, by hydrogen bonding, so the polymer was characterised in detail. The main parameters which were altered for preparing non-covalent MIPs included the template (α-terpineol, (-)-menthol or trans-terpin); the functional monomer (methacrylic acid, 2-hydroxyethyl methacrylate, bilirubin and phenol [for the semi-covalent MIP]); the cross-linking monomer (ethylene glycol dimethacrylate, divinylbenzene and trimethylolpropane trimethacrylate); and also the polymerisation method (block or precipitation polymerisation). The binding specificity and cross-reactivity for all the polymers were tested using a liquid batch-binding setup. The batch-binding setup required the detection of analyte that was not bound in order to calculate by difference the fraction of analyte bound to the polymer. Initially the terpenes were to be detected by a colorimetric method; however attempts to make the method sensitive and reliable were not successful. In comparison, gas chromatography was more reliable for the detection of terpenes and was used for the experiments presented in this thesis. 1H-NMR studies of the interaction between α-terpineol and acetic acid (as a non-polymerisable analogue of methacrylic acid) were investigated as a basis for understanding the binding to the carboxyl functional group moiety employed in many of the non-covalent MIPs that were made. The interaction between (-)-menthol and phenol was also investigated because the phenol moiety was employed in the semi-covalent MIP. Only selected MIPs, which appeared to specifically bind the template, were physically characterised. This included optimising the batch-binding parameters, scanning electron microscopy imaging, surface area and pore radius analysis and in some cases Fourier transform-infrared spectroscopy of the polymers.

Le développement du photovoltaïque organique(OPV), passe à la fois par des progrès technologiques et par l’élaboration de nouveaux matériaux photoactifs. Au sein des dispositifs se trouvent en général deux types de semi-conducteurs organiques, l’un accepteur d’électrons,l’autre donneur.Au cours de ce travail, différentes stratégies de rigidification par pontage covalent ont été appliquées à trois familles de donneurs moléculaires afin d’en étudier l’impact sur leurs propriétés électroniques. Dans un premier temps, deux séries de dérivés pontés du quaterthiophène substitué en positions terminales par des groupements dicyanovinyles ont été synthétisées. La présence d’un pont méthylène au niveau du bithiophène central induit un décalage du spectre d’absorption vers les faibles énergies en élevant le niveau HOMO de la molécule. Leur potentiel comme matériaux donneurs a, par la suite, été évalué au sein de dispositifs solaires. Ainsi, selon la longueur des chaînes alkyles introduites sur le pont, des rendements de photoconversion de 2% à 3,4% sont atteints en cellules bicouches. Puis, dans un second temps, l’utilisation de l’hétérocycle rigide thiéno[2,3-b]indole a permis de concevoir la plus petite molécule push-pull à atteindre 1%d’efficacité. Un rendement de 3,1% est obtenu lorsque le système conjugué est étendu d’une unité thiophène. Enfin, un donneur moléculaire construit autour d’un dithién-2-yldicyanoéthylène ponté, fonctionnalisé en périphérie par des unités triphénylamine, conduit à des cellules moins performantes (0,3%) que son homologue non ponté (1,1%). / The development of the so-called organic photovoltaics (OPVs) still requires technological as well as chemical advances through the elaboration of new photoactive materials. Active layer of devices is typically composed of two organic semiconductors, one electron-acceptor and one electron-donor respectively. During this work, rigidification by covalent bridging was applied to three different kinds of molecular donors to assess its impact on the materials electronic properties. First, two series of covalently bridged dicyanovinyl(DCV) end-capped quaterthiophene derivatives have been synthesized. A methylene bridge on the central bithiophene unit leads to a significant bathochromic shift of the absorption spectrum associated with a raising of the HOMO level. Their potential as donor material has been evaluated in solar cells. Power conversion efficiencies ranging from 2% to 3.4% can be achieved in bilayers structures according to the length of the alkyl chains introduced on the bridged bithiophene moiety. Then, the use of a rigid thieno[2,3-b]indoleheterocycle allowed us to design, synthesize and characterize the smallest push-pull molecule able to reach 1% efficiency. It is worth noting that extending the conjugation length of this molecule by adding one thiophene unit leads to an increase of the efficiency up to 3.1%. Finally, a molecular donor built from a bridged dithienyldicyanoethylene core functionalized at both sides by a triphenylamine unit was studied and led to less efficient OPV cells (0.3%) than its unbridged counterpart (1.1%).

Les Métallo Protéases Matricielles (MMP) en tant qu'endopeptidases à zinc ont une large gamme de fonctions biologiques allant du remodelage tissulaire à la modulation de la réponse cellulaire. Une modification de leur activité protéolytique est souvent associée à de nombreux désordres biologiques. In vivo, ces protéases sont soumises à de nombreuses modifications post-traductionnelles. Elles sont sécrétées sous formes latentes à l'extérieur des cellules pour être ensuite transformées en forme fonctionnelles. Ces dernières sont ensuite inhibées par des inhibiteurs endogènes. En raison de leur sécrétion dans l’espace extra cellulaire, les MMP sous formes actives ont longtemps été considérées comme de simples ciseaux moléculaires capable de dégrader uniquement la matrice extracellulaire. Cependant, le remodelage tissulaire ne constitue pas la fonction unique et encore moins la fonction principale de ces enzymes. Elles peuvent en effet cliver une grande variété de substrats non matriciels et à ce titre sont impliquées dans la progression tumorale, l'immunité et l'inflammation. Pour ajouter une complexité supplémentaire à la biologie des MMP, il a été récemment montré que certaines MMP ont une localisation intracellulaire associée à des fonctions non protéolytiques. Ces observations, mais aussi celles montrant que ces protease participent à la progression de la maladie alors que d'autres ont une fonction protectrice, soulignent la nécessité de mieux documenter leur activation spatiale et temporelle dans divers contextes biologiques.Le profilage protéique basé sur l'activité vise à analyser l'état fonctionnel des protéines dans des échantillons biologiques complexes. À cette fin, des sondes basées sur l'activité (ABP), qui réagissent avec les enzymes en s’appuyant sur leur mécanisme catalytique, ont été développées pour la détection d’enzymes sous formes actives, notamment dans le cas des protéases à sérine et à cystéine. Une sonde basée sur l’activité (ABP) est classiquement composée : i) d’un groupement réactif conduisant à la modification covalente de résidus au sein du site actif de l’enzyme, ii) d’un motif de liaison imposant la sélectivité au groupement réactif et iii) d’un groupement rapporteur permettant la détection des enzymes ciblées. Cette approche ne s’applique toutefois pas aux MMP, pour lesquelles il n’existe pas de résidus nucléophiles conservés au sein du site actif. À cet égard, tous les ABP ciblant les MMP comportent un groupement photo activable qui, sous irradiation UV, favorise la formation du complexe covalent. De telles sondes photo sensibles ont permis de détecter les MMP sous leurs formes actives dans des tissus et des fluides, mais pas chez les animaux vivants au sein desquels l’étape de photo-activation ne peut être réalisé.Dans ce contexte, en nous appuyant sur un contexte structural favorable et en exploitant la chimie de l'acyl imidazole (LDAI) dirigée par un ligand, nous avons identifié une nouvelle série de sondes capables de modifier de manière covalente les MMP sans recourir à la photo-activation. Nous avons ainsi validé la capacité de ces sondes à marquer de manière sélective et efficace la MMP12 humaine in vitro et dans des protéomes complexes. Dans ce dernier cas, jusqu’à 50ng de hMMP12 correspondant à 0,05% du protéome total peuvent être détectés. Nous avons également déterminé l'identité de l’unique résidu modifié de façon covalente au sein du site actif de la hMMP-12 et vérifié que cette modification avait peu d'impact sur l’activité protéolytique de cette dernière. Nous avons démontré que cette approche permettait de détecter des MMP endogènes. Enfin, nous avons étendu cette stratégie de marquage à un panel plus large de MMP.En développant la première stratégie de marquage des formes actives de MMP «sans photo-activation», il semble maintenant possible d’envisager la détection de ces enzymes à la fois dans les protéomes complexes et in vivo. / Matrix MetalloProteases (MMPs) as zinc endopeptidases have a wide range of biological functions, and changes in their proteolytic activity underlie many biological disorders. Since their proteolytic activity has to be tightly controlled to prevent tissue destruction, theses proteases are subjected to numerous posttranslational modifications in vivo. They are secreted under latent forms outside of the cells, and are subsequently processed into their functional form that can be further inhibited by endogenous inhibitors. Due to their delineated area of activation, MMP active forms have long been considered for their unique ability to degrade extracellular substrates. However, turnover and breakdown of the extracellular matrix are neither the sole nor the main function of MMPs. These enzymes can indeed process a wide variety of non-matrix substrates and are involved in the regulation of multiple aspects of tumor progression, immunity and inflammation. To add further complexity to MMPs biology, some members within the family were recently reported to have intracellular localization associated to non-proteolytic functions. These observations but also those evidencing that some MMPs participate in disease progression while others have a protective function, stress the need to better document their spatial and temporal activation in various biological contexts.Activity-based protein profiling (ABPP) aims to analyze the functional state of proteins within complex biological samples. To this purpose, activity-based probes (ABPs) that react with enzymes in a mechanism-based manner have been successfully developed for the profiling of several enzymes including serine and cysteine proteases. A typical Activity-Based probe (ABP) is composed of i) a reactive warhead, which reacts in a covalent manner with enzyme active site residues, ii) a targeting moiety that imposes selectivity upon the reactive group and iii) a detectable group for subsequent analyses. This approach is not applicable to MMPs, which lack a targetable nucleophile involved in the catalysis. In this respect, all ABPs directed to MMPs are affinity-based probes (AfBPs) containing within their structure a photo cross-linking group that promotes the formation of a covalent complex upon UV-irradiation. Such photoactivatable probes have been successfully developed for the detection of MMPs under their active forms in fluids and tissue extracts, but not in living animals where the photo-activation step is not feasible.By relying on a favorable structural context and by exploiting the ligand-directed acyl imidazole (LDAI) chemistry, we have identified a novel series of AfBPs capable of covalently modifying matrix metalloproteases without making use of photo-activation. These active-site-directed probes whose structure was derived from that of a MMP12 selective inhibitor harbored a reactive acyl imidazole in their P3' position. They demonstrated their labelling specificity in vitro by covalently modifying a single Lysine residue within the MMP-12 S3' region. We also showed that these probes only targeted functional states of hMMP-12 and spared forms whose active site was occluded either by a synthetic or a natural inhibitor. We have validated the ability of these chemical probes to efficiently label human MMP12 in complex proteomes. In this case, down to 50 ng of hMMP12 corresponding to 0.05% of the whole proteome can be labelled and detected by in-gel fluorescence analysis. We demonstrated that this approach also allowed detecting endogenous MMPs secreted by stimulated-macrophages. In addition, by modifying the nature of the targeting moiety, we have extended this affinity-labeling approach to six other MMPs.By developing the first “photo activation-free” strategy to covalently modify active forms of MMPs, the unresolved proteomic profiling of native MMPs should be now accessible both in complex proteomes and in preclinical model in which MMPs are potential relevant targets.

Thesis advisor: Jianmin Gao / Covalent drugs present a unique situation in the clinical world. Formation of a covalent bond between a drug molecule and its target protein can lead to significant increases in a number of desirable traits such as residence time, potency, and efficacy of a drug. From a kinetic perspective, the formation of a covalent bond between a drug and its target functionally eliminates the dissociation rate (koff) of the compound, ensuring that the compound will stay engaged with its target. However, development of covalent drugs has been met with caution and concern, as an irreversible covalent bond forming on the wrong target can have disastrous results, so specificity is of the utmost importance. One option for increasing specificity is by linking a covalent binding electrophile, or warhead, to a peptide. Peptide-based therapeutics have already been shown to serve as effective protein-targeting modalities with high specificity, a specificity that would greatly benefit covalent drugs. Phage display is a powerful technique for the discovery of selective peptides which utilizes the screening of vast libraries of randomized peptides to identify strong binders. This technology has been used to discover a large number of protein-targeting peptides, but also a smaller number of cyclic, covalent binding peptides that function as enzymatic inhibitors. Herein, this study aimed to explore the idea of adding covalent-binding functionality to phage libraries in novel ways and expand upon the scope of proteins that can be targeted with phage libraries containing covalent libraries. We sought to develop a mechanistic and chemical understanding of the interactions between bacteriophage and chemical warheads to best understand both the limits and the potential of this technology. In order to best understand the relationship between chemical warhead and phage particle, a model system was developed based on the M13KE pIII protein. It was found that the extracellular N-terminal domains of this protein could be expressed and purified in low yields in bacterial cells and that these domains would behave similarly in solution as in the membrane of the M13KE bacteriophage. With this protein in hand, experiments previously performed using small, cysteine containing peptides, could be performed on a full protein to mimic the phage labeling environment. This protein was used to identify efficient cysteine crosslinkers, most notably dichloroacetone (DCA) and bis-chlorooxime (BCO). The pIII protein system was then used to study the viability of bifunctional warhead molecules containing a covalent warhead and a cysteine crosslinker. Based on preliminary analyses with the pIII protein, aryl sulfonyl fluoride was chosen as a novel warhead candidate that warranted further pursuit. Kinetic NMR studies verified that aryl sulfonyl fluoride was capable of forming covalent bonds with phenols under phage labeling conditions. Labeling experiments analyzed with LC/MS seemed to indicate a degradation of the warhead. However, as the source of the degradation was not able to be determined, it was decided that various affinity assays would be used to identify if phage could be labeled with an aryl sulfonyl fluoride-DCA conjugate. Both streptavidin-bead pulldown assays and ELISA assays were used, however both assays yielded results that could not conclusively verify the integrity of the warhead. During phage labeling experiments, a phenomenon was noted that phage titers after modification showed a 2-3 order of magnitude drop in phage count. Covalent modification of phage beyond what is intended could have troubling consequences for all covalent phage libraries, and so a more in-depth approach was taken to identify and better understand phage toxicity as it relates to covalent warheads. As a model, a well-studied diazaborine-mediated warhead with a slow dissociation rate was selected and used in a range of phage toxicity screenings. Despite statistical fluctuations between trials, toxicity screenings using this warhead served to highlight a unique concern for bifunctional covalent warheads. A concentration-dependent toxicity can be seen in phage incubated with bifunctional small molecules that is not present when incubated with the monofunctional equivalents. The presence of this toxicity even towards a phage with no free thiols highlights a unique challenge of off-target labeling within phage particles that, if solved, could provide the next significant step towards developing novel covalent phage libraries. / Thesis (MS) — Boston College, 2022. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

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Biological systems have the incredible ability to accomplish uncommon chemical transformations with supreme delicacy. Many of those chemical transformations take place within the pocket of enzymes, which provide unique micro environment. From the quest of better understanding and to mimic such complex biological systems chemists have developed their own prototypes having well-defined cavity. To this end, in last few years many aesthetically elegant 3D discrete architectures have been devised by employing noncovalent interactions especially metal-ligand co-ordination and hydrogen bonding. Conversely, architectures based on purely covalent interactions are relatively limited in number, owing to the laborious traditional covalent synthesis, which involves multi-step synthetic protocols and irreversible covalent bond formations. Nevertheless, in recent times by utilizing dynamic covalent chemistry (DCC) several such organic 3D discrete ensembles have been developed with ease and efficiency from simple and easily accessible building blocks. Interestingly in most of such cases imine condensation reaction has been utilized due to easy formation and cleavage of the imine bonds in an efficient and reversible manner. However, it is quite surprising that even though the dynamic nature of imine bonds has been well established; self-sorting/self-selection process has been overlooked in organic cage systems. Self-sorting in biological realm is a well-established synthetic protocol. DNA double helix formation via hydrogen bonding between the complimentary base pairs is probably the best known example of biological self-sorting. Self-sorting process has the ability to discriminate self from non-self to achieve highly ordered architectures from within a random reaction mixture. The credit of self-sorting/self-selection process goes to the hidden ‘molecular instructions’ encrypted within the complimentary building blocks. The foremost objective of the present thesis work is to implement the self-sorting/self-selection protocol in organic cage formation by harnessing the dynamic imine chemistry. During the course of the investigation it has been observed that non-covalent interaction especially hydrogen bonding could manipulate the outcome of such a process. Besides that, selective formation of a single isomer of an organic cage from a reaction mixture of an unsymmetrical aldehyde and a flexible amine has been successfully achieved by simply fine tuning the geometric features (shape and size) of the reacting aldehyde. Such three-dimensional cages are well appreciated by the scientific community owing to their potential applications in anion sensing, catalysis and gas storage/separation. However, they have not been explored as sensors for nitroaromatic explosives. Therefore, at this juncture several fluorescent organic cages have been synthesized and their potential application as chemosensor for the nitroaromatics has been tested. Moreover, a new synthetic protocol has been introduced for the post-synthetic modification of organic cages. Chapter 1 covers a brief introduction about dynamic covalent chemistry with main emphasis on dynamic imine chemistry and its use in covalent cage synthesis. Moreover, this chapter accounts the very recent applications of such cage compounds in various fields such as a pours material for gas storage/separation, a molecular host for the stabilization of reactive species and for the recognition of ions or molecules. Chapter 2 describes first time ever achieved self-sorting process in three-dimensional purely organic cages. First of all, four different [3+2] cages were synthesized by treating two different triamines with two different dialdehydes separately, by employing dynamic imine chemistry. The formation of desired cages was ascertained by various spectroscopic techniques. When a mixture of all the four components (two aldehydes and two amines) was subjected to reaction, only two cages were found to form (Scheme 1) out of several equally probable possibilities, which suggest a high-fidelity self-recognition. The issue of partner preferences was further verified by transforming a non-self-sorted cage into a self-sorted cage by treating the former with appropriate triamine or dialdehyde. For an in-depth understanding on this subject, theoretical calculations (gas phase DFT) were carried out, which suggested that observed self-sorting is a thermodynamically governed process. Scheme 1. Self-sorting in organic imine cages through partner preferences. Chapter 3 focuses that supramolecular interaction especially hydrogen-boding could be a possible way to direct a self-sorting process operating in imine based organic cage systems. It is a well-accepted fact that in most of the cases self-sorting process operates owing to the difference in geometric features (shape and size) of the competing building blocks. Thus increasing similarity in geometric features would create the situation more complex. It is anticipated that in such circumstances H-bonding could have a decisive role in partner selection. In order to investigate this, four different dialdehydes (A, B, C and D) having similar geometric background were synthesized. These aldehydes upon treatment with flexible amine X were found to form three nanosocpic [3+2] organic cages (aldehyde C gave insoluble uncharacterized material). When a one-pot reaction of triamine X with mixture of all the four aldehydes was carried out, selective formation of cage B3X2 was observed (Scheme 2). Conversely, the same reaction in absence of aldehyde B resulted in the formation of mixture of products. Theoretical and experimental studies fully support the fact that the presence of hydroxyl moiety adjacent to the formyl group in aldehyde B has the key role in selective formation of cage B3X2 from a complex reaction mixture, in which there are numerous equally probable possibilities. Such remarkable selection was further examined by converting a non-hydroxy (non-preferred) cage into hydroxy cage B3X2 (preferred) by treating the former with aldehyde B. The role of the H-bond in self-sorting process of two dialdehydes and two triamines has been established. Furthermore, the possibility of cage–to- cage transformation through imine bond metathesis has also been addressed. Scheme 2. H-bond directed 15-fold (2+3) incomplete self-sorting in organic imine cages. Chapter 4 presents the investigation on the formation of single isomeric species of a [3+2] oligoimine cage from a reaction mixture of an unsymmetrical dialdehyde and a flexible triamine. So far, most of the reported organic cages are derived by symmetric building units. Asymmetric building blocks for the construction of such organic architectures are not the desirable choices, as they could lead to form mixture of isomeric cages. However, the asymmetric building blocks might form selectively one isomer only under the thermodynamic bias, which prefers the formation of one isomer over the other (s). In order to understand the factors that can direct such a process, three asymmetric dialdehydes (A, B and C) were synthesized and their reaction with a flexible amine X was carried out. Experimental outcomes suggested a striking difference in the abilities of isomer selection between aldehydes A/B and C. In case of aldehyde A/B selective formation of one oligoimine cage was observed, whereas aldehyde C led to form two isomeric oligoimine cages (Scheme 3). Experimental and theoretical findings have pointed out that the geometric features (shape and size) of the aldehyde play a decisive role in such isomer selection process. Scheme 3. Shape and size directed self-selection in organic imine cages. Part A of Chapter 5 describes the synthesis and characterization of a fluorescent organic cage compound and its application as a sensor for the detection of explosive picric acid (PA). Picric acid is known to be as explosive as trinitrotoluene (TNT) and one of the principle constituents of many unexplored landmines. Though there are several fluorescent polymers, metal-organic frameworks and small molecule based sensors have been devised in last few years but very little attention has been given towards selective and sensitive detection of picric acid. In this context desired organic cage compound 4 was synthesized by employing imine condensation between 4,4-diformyltriphenylamine (1) with 1,3,5-tris(aminomethyl)-2,4,6-trimethylbenzene (2) followed by reduction of the imine bonds (Scheme 4). This fluorescent nature of the cage in both the solid and solution has been utilized for the detection of nitroaromatic compounds (NACs). Among the various NACs tested it has been found that PA induces highest quenching of the initial fluorescence intensity of the cage solution. Furthermore, this cage has the ability to discriminate PA from other nitrophenolic compounds, such as 2,4-dinitrophenol (DNP) and 4-nitrophenol. In addition to solution phase detection cage 4 has also been successfully utilized for the solid phase detection of PA. The experimental results demonstrates that high sensitivity of the cage towards PA is attributed to the stronger ground state complex formation between the cage and PA as well as excitation v energy transfer (EET) process from protonated cage to the picrate. This represents the first report of a cage compound as a sensor for nitroaromatic compounds. Scheme 4. Synthesis of a fluorescent organic cage for the selective detection of picric acid. Part B of Chapter 5 reports a new synthetic methodology to decorate covalent organic cages post-synthetically, based on one-pot copper(I) catalyzed A3 coupling. A3-coupling is a three-component reaction between formaldehyde, secondary amine and terminal alkyne. In the present study selected organic cage 4 is furnished with six secondary amine moieties and thus it was allowed to react with 6 equiv. of formaldehyde and 6 equiv. of terminal alkyne in presence of CuI as a catalyst (Scheme 5). By employing this synthetic strategy parent cage 4 has been modified to cages 5a-c with appendages phenyl-, xylyl- and napthyl-actylenes. The resulting decorated cages were characterized by multinuclear NMR (1H and 13C), MALDI-TOF and FTIR spectroscopy. All the post-synthetically decorated cages were found to be fluorescent in nature and thus in v order to explore their potential use as a chemosensor for nitroaromatic compounds, cage 5a was tested. Experimental findings have suggested high selectivity of the cage towards nitroaromatic compounds. Interestingly, among the various nitroaromatics tested it has been observed that the cage is more sensitivity towards nitrophenolic compounds, whereas among the various nitrophenols tested, picric acid induced highest quenching. Scheme 5. Post-synthetic modification of an organic cage via cu+ catalyzed A3 coupling.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: ß-Galactosidase of Escherichia coli is the equivalent of lactase in humans and has the ability to bind and hydrolyse lactose. Lactase de ciency is a common phenomenon present in almost 70% of the world's population. This has resulted in greater than before demands on the food processing industry to develop a method that will allow for the hydrolysis of the disaccharide lactose in milk but will also allow for the removal of the remaining active enzyme. In this thesis, a new method, that is bio-speci c and well characterized for the removal of lactose from a lactose containing solution, is described. The E537D mutated version of ß-Galactosidase, which has a much lower activity compared to the wildtype and is able to bio-speci cally bind lactose for longer periods, was covalently immobilised to commercially available magnetic nanoparticles (fl uidMAG-Amine) via two coupling strategies. Glutaraldehyde is a cross-linking agent that reacts with amine groups, while N- (3-Dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC) is a coupling agent that activates carboxylic groups. These agents are widely used for the coupling of biomolecules to solid supports. The covalently coupled fluidMAG-E537D ß-Galactosidase particles were characterized regarding retained enzymatic activity and ability to bind and physically remove lactose from a lactose containing solution by applying an external magnetic eld, after lactose binding, to the enzyme-particle complex in solution. Each component aimed at yielding this functionally immobilised enzyme complex was studied and optimized to contribute to the development of this novel technique, which is a ordable and simple, for the removal of lactose from solution for the ultimate production of lactose free milk. Results indicated the glutaraldehyde method of ß-Gal cross-linking to fluidMAG-Amine to be the preferred strategy since it allowed an increased carrier capacity of protein to the particles. The glutaraldehyde cross-linked protein also exhibited a two-fold higher activity than the EDC coupled protein. Furthermore, the glutaraldehyde cross-linked fluidMAG-E537D ß-Gal was able to physically remove 34 % of the lactose from a 0.2 nmol/L lactose in solution. This, therefore, con rmed the potential use of this novel technique in the food processing industry. / AFRIKAANSE OPSOMMING: ß-Galaktosidase vanaf Escherichia coli is dieselfde as laktase in mense en beskik oor die vermoë om laktose te bind en te hidroliseer. 'n Gebrek aan laktase kom algemeen voor en ongeveer 70 % van die wêreldbevolking ly hieraan. Laasgenoemde het daartoe gelei dat daar meer druk as vantevore op die voedselproduksie industrie is om 'n metode te ontwikkel waarmee die hidrolise van die disakkaried laktose in melk moontlik sal wees asook die verwydering van die oorblywende aktiewe ensiem. In hierdie tesis word 'n nuwe metode beskryf wat biospesi ek en goed gekarakteriseer is vir die verwydering van laktose vanuit 'n laktose bevattende oplossing. Die E537D gemuteerde weergawe van ß-Galaktosidase, wat beskik oor 'n baie laer aktiwiteit as die wildetipe asook die vermoë om laktose biospesi ek vir langer periodes te bind, is kovalent geïmmobiliseer op kommersieel beskikbare magnetiese nanopartikels (fluidMAG-Amine) via twee koppelingsstrategieë. Glutaraldehied is 'n kruisbindingsagent wat met amino groepe reageer, terwyl EDC 'n koppelingsagent is wat karboksie groepe aktiveer. Hierdie agente word algemeen gebruik vir die binding van biomolekules aan soliede matrikse. Die kovalent gekoppelde fluidMAG-E537D ß-Galaktosidase partikels is gekarakteriseer met betrekking tot behoue ensimatiese aktiwiteit en vermoë om laktose te bind en sies te verwyder vanuit 'n oplossing wat laktose bevat deur 'n eksterne magneetveld op die ensiem-partikel kompleks in oplossing toe te pas, nadat die binding van laktose plaasgevind het. Elke komponent van hierdie funksioneel geïmmobiliseerde ensiemkomplekse is ondersoek en geoptimaliseer met die doel om by te dra tot die ontwikkeling van 'n nuwe tegniek wat bekostigbaar en eenvoudig is vir die verwydering van laktose vanuit 'n oplossing vir die uiteindelike gebruik in die produksie van laktose-vrye melk. Resultate het getoon dat die glutaraldehied metode van ß-Gal kruisbinding op fluidMAG-Amine verkies word aangesien dit 'n verhoogde draerkapasiteit van proteïene op die partikels moontlik maak. Die glutaraldehied gekoppelde proteïene beskik ook oor twee keer meer aktiwiteit as die EDC gekoppelde proteïene. Die glutaraldehied gekoppelde fluidMAG-E537D ß -Gal kon 34 % van die laktose teenwoordig in 'n 0.2 nmol/L laktose oplossing sies verwyder. Hierdie het dus die potensiële gebruik van hierdie nuwe metode in die voedselproduksie industrie bevestig.