The research work reported in the thesis deals with the development of dynamic covalent systems and their applications in evaluation and screening of protein-ligands and enzyme inhibitors, as well as in synthetic methodologies. The thesis is divided into four parts as described below. In part one, synthetic methodologies to access 3-functionalized phthalides and 3-thioisoindolinones using the concept of cascade reactions are demonstrated. Efficient syntheses of the target products are designed and performed in one-pot process under mild reaction conditions.  In part two, phosphine-catalyzed disulfide metathesis for the generation of dynamic carbohydrate system in aqueous solution is demonstrated. In the presence of biological target (Concanavalin A), the optimal dynamic ligand is successfully identified in situ by the 1H STD-NMR spectroscopy. In part three, lipase-catalyzed resolutions of dynamic reversible systems using reversible cyanohydrin and hemithioacetal reactions in one-pot processes are demonstrated. The dynamic systems are generated under thermodynamic control in organic solution and subsequently resolved by lipase-mediated resolution under kinetic control. The resolution processes resulted in the lipase-selected substrates with high structural and stereochemical specificities. In the last part, dynamic fragment-based strategy is presented using β-galactosidase as a model target enzyme. Based on our previous study, the best dynamic inhibitor of β-galactosidase was identified using 1H STD-NMR technique from dynamic hemithioacetal systems. The structure of the dynamic inhibitor is tailored by fragment linking and optimization processes. The designed inhibitor structures are then synthesized and tested for inhibition activities against β-galactosidase. / QC 20110526

This thesis deals with the development and application of new synthetic methodology in organic chemistry. The first part describes the development of a new protocol for the synthesis of 3-pyrrolines by means of a microwave-assisted ring-expansion reaction of 2-vinylaziridines. In addition, this methodology is implemented as a key-step in a formal total synthesis of the antibiotic (-)-anisomycin. In the second part, a new methodology for the synthesis of arylglycines from Weinreb amides is described. In this procedure, a Grignard reagent is added to the iminium ion formed from the Weinreb amide upon treatment with a base. When a chiral amide is used, the nucleophilic addition proceeds with high diastereoselectivity. Finally, an easy and straightforward synthesis of α-amino amides via a base-mediated rearrangement of modified Weinreb amides into N,O-acetals is presented. Subsequent arylation, alkylation, alkenylation or alkynylation of this intermediate affords the corresponding α-amino amides in excellent yields. Furthermore, a more generalized protocol for the α-arylation of Weinreb amides lacking an α-amino moiety is also discussed. / QC 20100719

Proteins are the most abundant biomolecules within a cell and are involved in all biochemical cellular processes ultimately determining cellular function. Therefore, to develop a complete understanding of cellular processes, obtaining knowledge about protein function and interaction at a molecular level is critical. Consequently, the investigation of proteins in their native environment or in partially purified mixtures is a major endeavour in modern life sciences. Due to their high chemical similarity, the inherent problem of studying proteins in complex mixtures is to specifically differentiate one protein of interest from the bulk of other proteins. Site-specific protein functionalisation strategies have become an indispensable tool in biochemical- and cell biology studies. This thesis presents the development of a new enzymatic site-specific protein functionalisation strategy that is based on the reversible covalent phosphocholination of short amino acid sequences in intact proteins. A synthetic strategy has been established that allows access to functionalised CDP-choline derivatives carrying fluorescent reporter groups, affinity tags or bioorthogonal handles. These CDP-choline derivatives serve as co-substrates for the bacterial phosphocholinating enzyme AnkX from Legionella pneumophila, which transfers a phosphocholine moiety to the switch II region of its native target protein Rab1b during infection. We identified the octapeptide sequence TITSSYYR as the minimum recognition sequence required to direct the AnkX catalysed phosphocholination and demonstrated the functionalisation of proteins of interest carrying this recognition tag at the N- or C-terminus as well as in internal loop regions. Moreover, this covalent modification can be hydrolytically reversed by the action of the Legionella enzyme Lem3, which makes the labeling strategy the first example of a covalent and reversible approach that is fully orthogonal to current existing methodologies. Thus, the here presented protein functionalisation approach holds the potential to increase the scope of possible labeling strategies in complex biological systems. In addition to the labeling of tagged target proteins, a CDP-choline derivative equipped with a biotin affinity-tag was synthesised and used in pull-down experiments to investigate the substrate scope of AnkX and to elucidate the role of protein phosphocholination during Legionella pneumophila infection. / Proteiner utgör huvudbeståndsdelen av alla biomolekyler i en cell. Dessa är involverade i alla cellulära processer som bestämmer cellens egenskaper. För att förstå de cellulära processerna är det nödvändigt att förstå proteinernas funktion på molekylär nivå. Att studera proteiner i deras naturliga omgivning, det vill säga inuti en cell eller i ett cellextrakt, är en stor utmaning i dagens livsvetenskaper. Eftersom proteiner är kemiskt lika varandra så är det svårt att skilja ett från tusentals andra. Att specifikt märka proteiner för att skilja ut dem från bakgrunden har blivit ett viktigt arbetssätt i modern biokemi och cellbiologi. Avhandlingen beskriver utvecklandet av en ny metod för reversibel och kovalent enzymatisk märkning baserat på fosfokolinering/defosfokolinering av en kort aminosyrasekvens i intakta proteiner. En syntesmetod för att framställa onaturliga CDP-kolinderivat har etablerats vilket tillåter oss att framställa CDP-kolin som bär en funktionalitet, vilket kan vara ett färgämne eller en affinitetstagg. Dessa onaturliga CDP-kolinderivat accepteras som co-substrat av enzymet AnkX från Legionella pneumophila vilket transfererar den funktionaliserade delen av CDP-kolinderivatet till en kort aminosyrasekvens baserad på AnkX’s naturliga substrat vid infektion, det lilla GTPaset Rab1. Under avhandlingsarbetets gång identifierades den kortaste aminosyrasekvensen som känns igen av AnkX, endast de åtta aminosyrorna TITSSYYR är nödvändiga för igenkänning av AnkX. Dessa åtta aminosyror kan genetiskt infogas i början, slutet eller mitt i ett protein för igenkänning och funktionalisering via AnkX och våra syntetiska CDP-kolinderivat. Vid Legionellainfektion i eukaryota celler klyvs fosfokolineringen efter en viss tid, eftersom Legionella pneumophila producerar ett fosfodiesteras, Lem3, som tar bort de fosfokolineringar som AnkX har installerat när de inte längre behövs. Vi har använt Lem3 för att ta bort märkning i sekvensen TITSS(PC)YYR, vilket gör vår strategi helt reversibel. Vi har kunnat demonstrera att AnkX-Lem3 systemet accepterar ett brett spektrum av CDP-kolinderivat, vilket gör metoden till den första av sitt slag, eftersom den är fullt reversibel. Vi har vidare undersökt vilka proteiner AnkX reagerar med inuti celler, vi använde oss av ett CDP-kolinderivat funktionaliserat med biotin, vilket har tillåtit oss att fiska ut alla de proteiner som fosfokolineras av AnkX. Förutom de små GTPaserna i Rab-familjen så identifierade vi även IMPDH2, ett enzym som reglerar det hastighetsbestämmande steget i syntesen av guanosin-nukleotider. Detta är mycket intressant, eftersom det leder till frågan ifall Legionella pneumophila manipulerar sin värdcell genom att förändra mängden GTP i förhållande till ATP.

Palladium-catalysed carbonylative multicomponent reactions have proven useful for the synthesis of structurally diverse compounds. Carbon monoxide serves as an atom-efficient, one-carbon building block, which allows for further structural elaboration of the carbonyl compound. By varying the components of the carbonylative multicomponent reaction, considerable product diversity can readily be attained. However, due to the reluctance to use toxic CO gas, considerable efforts have been directed at exploring non-gaseous approaches. The work described in this thesis has mainly focused on the development of palladium(0)-catalysed, carbonylative multicomponent synthetic methodology, using the non-gaseous CO source molybdenum hexacarbonyl, in the synthesis of heterocycles and other biologically relevant functional groups. The first part of this work describes the development of a non-gaseous carbonylative Sonogashira cross-coupling of bifunctional ortho-iodoanilines and terminal alkynes. Where 4-quinolones were synthesised via a carbonylation/cyclisation sequence. Using a similar synthetic strategy, three different N-cyanobenzamide intermediates were prepared by palladium-catalysed carbonylative couplings of various aryl halides and bromides and cyanamide. The formed intermediates provided a basis for further chemical transformations. First, ortho-iodoanilines were carbonylatively coupled with cyanamide and subsequently cyclised to yield heterocyclic 2-aminoquinazolinones. Next, building on those findings, the same synthetic strategy was applied to ortho-halophenols to provide a highly convenient domino carbonylation/cyclisation method for the preparation of benzoxazinones. The developed method was used to evaluate the efficiency of various non-gaseous CO sources. Third, the palladium-catalysed carbonylative synthesis of N-cyanobenzamides, was used to produce biologically relevant N-acylguanidines with considerable product diversity. Finally, one of the developed carbonylative methodologies was used in the preparation of potential NDH-2 inhibitors based on a quinolinyl pyrimidine scaffold. The prepared compounds were biologically evaluated in terms of inhibition of oxidoreductase NDH-2 and antibacterial activity on Gram-negative bacteria, S. aureus and Mtb. The biological evaluation revealed that some of the quinolinyl pyrimidines exerted inhibitory activity on the NDH-2 enzyme and possessed antibacterial properties. The work described in this thesis has been devoted to the development of non-gaseous one-pot, multicomponent carbonylation/cyclisation and carbonylation/amination reactions. The described methods offer highly attractive synthetic strategies that can be of great value to synthetic and medicinal chemists.

Palladium-catalyzed reactions have become one of the most important tools in modern organic chemistry due to its ability to catalyze the formation of new carbon-carbon bonds. The aim of the work presented in this thesis was to develop new palladium(II)-catalyzed addition reactions. In this work, cyanamides were investigated as a new substrate to give aryl amidines as products. The first protocol developed employed aryltrifluoroborates as the aryl partner, and the insertion of the aryl group into un-, mono-, and di-substituted cyanamides was successful for a wide variety of aryltrifluoroborates. An alternative method of generating the necessary intermediate for insertion into the cyanamide is the decarboxylative formation of aryl-palladium from aryl carboxylic acids. A protocol was developed for this reaction, but was unfortunately limited to a small number of ortho-substituted electron-rich aryl carboxylic acids. The mechanism was investigated by the means of DFT calculations and ESI-MS studies, and the rate-determining step was suggested to be the 1,2-carbopalladation based upon those results. A translation of the batch protocol to continuous-flow conditions was also demonstrated. The ideal method of generating the aryl-palladium species is by C-H bond activation, and this approach was demonstrated with indoles, giving a variety of 3-amidinoindoles as products. The mechanism was investigated by DFT calculations and a plausible catalytic cycle was proposed. A continuous-flow application of a desulfitative palladium(II)-catalyzed addition to nitriles to give ketones was developed. In addition, different reactor materials were evaluated in the microwave heated reactor cavity. Thus the reaction was shown to proceed with microwave heating in a borosilicate glass and an aluminum oxide reactor, and also in conditions mimicking conventional heating in a silicon carbide reactor. Finally, a protocol was developed for the convenient synthesis of sodium aryl sulfinates from Grignard and lithium reagents using a solid sulfur dioxide source as a safe alternative to the gas. The products of this protocol can be used as aryl-palladium precursors by a desulfitative process.

In the adaptation to the oxidative environment on earth, metals played a crucial role for the evolution of life. The presence of metals also allowed access to advanced functions due to their unique coordination sphere and reactivity. This thesis focused on exploiting these unique properties for further development of the field of dynamic chemistry – a field in which adaptation plays a central role as well. The first part of the thesis aimed to create a better understanding of multivalent effects in carbohydrate-lectin interactions. By reversible ligand coordination to zinc ions one of the nanoplatforms, the Borromean rings, could be selectively obtained. After carbohydrate functionalization the binding events were monitored by quartz crystal microbalance technology and compared to glycosylated fullerenes and dodecaamide cages. Overall, this investigation indicated that statistical and polyelectrolyte effects play a considerable role in the observed multivalent effects. The second part of the thesis aimed to design and synthesize a new catalyst for application in aqueous olefin metathesis. This afforded a ruthenium based catalyst that was applied in the self- and cross-metathesis of highly functionalized substrates, such as carbohydrates. In addition, it was shown that addition of a small amount of acetic acid prevented undesired double bond isomerization. The last part of the thesis aimed to explore new methods to discover transition metal catalysts. Dynamic exchange of directing groups generated a pool of potential substrates for C-H activation. Combining this pool of substrates with a pool of potential catalysts resulted in amplification of a reactive substrate/metal combination. By iterative deconvolution in combination with mass spectrometry, this “intermediate” could be identified from the mixture, proving applicability of this alternative approach to catalyst discovery. / <p>QC 20170809</p>

Organic electrode materials represent an intriguing alternative to their inorganic counterparts due to their sustainable and environmental-friendly properties. Their plastic character allows for the realization of light-weight, versatile and disposable devices for energy storage. Conducting redox polymers (CRPs) are one type of the organic electrode materials involved, which consist of a π-conjugated polymer backbone and covalently attached redox units, the so-called pendant. The polymer backbone can provide conductivity while it is oxidized or reduced (i. e., p- or n-doped) and the concurrent redox chemistry of the pendant provides charge capacity. The combination of these two components enables CRPs to provide both high charge capacity and high power capability. This dyad polymeric framework provides a solution to the two main problems associated with organic electrode materials based on small molecules: the dissolution of the active material in the electrolyte, and the sluggish charge transport within the material. This thesis introduces a general synthetic strategy to obtain the monomeric CRPs building blocks, followed by electrochemical polymerization to afford the active CRPs material. The choice of pendant and of polymer backbone depends on the potential match between these two components, i.e. the redox reaction of the pendant and the doping of backbone occurring within the same potential region. In the thesis, terephthalate and polythiophene were selected as the pendant and polymer backbone respectively, to get access to low potential CRPs. It was found that the presence of a non-conjugated linker between polymer backbone and pendant is essential for the polymerizability of the monomers as well as for the preservation of individual redox activities. The resulting CRPs exhibited fast charge transport within the polymer film and low activation barriers for charge propagation. These low potential CRPs were designed as the anode materials for energy storage applications. The combination of redox active pendant as charge carrier and a conductive polymer backbone reveals new insights into the requirements of organic matter based electrical energy storage materials.

An ionic liquid (IL) is a salt, which usually is in the liquid state at normal temperature and pressure. The properties of ILs can be adjusted for various processes and applications by choosing different combinations of ions. Similar to other salts, ILs contain only ions with positive (cations) and negative (anions) charges in equal proportions. However, to prevent solidification, ions in ionic liquids usually contain bulky organic chemical groups, which, apart from electrostatic interactions, promote other types of interactions between ions, such as: (i) van-der-Waals interactions; (ii) hydrogen bonding; (iii) - stacking, etc., depending on the particular chemical structure of the ions. All these interactions, in combination, may lead to formation of specific microstructures in ILs, which may vary with temperature caused by changing thermal rotational and translational energies of the ions. Ions in these microstructures may have preferential orientations relative to each other, maintain anisotropic properties similar to those in liquid crystals or, in some specific cases, may even separate into microscopically organised liquid phases. Therefore, the dynamics of ILs may also be dependent on their microstructure. In many practical applications ionic liquids are placed on surfaces or in confinements. Solid surfaces introduce extra forces, which may be specific to the charge of the ions or/and to functional groups in the ILs. The geometry and interactions of ions in confinements or/and pores of materials may also disrupt specific bulk microstructures of ILs. Both confinement effects and interactions of ions with surfaces are manifested in the translational dynamics of the ions. One of the most direct and informative methods to study translational dynamics of ILs is pulse-field-gradient nuclear magnetic resonance (PFG-NMR).In this thesis the results of PFG-NMR studies on a few classes of ILs are reported: (i) the historically “standard” (since Walden’s discovery in 1914) ionic liquid, the ethylammonium nitrate (EAN) and (ii) halogen-free orthoborate-based phosphonium, imidazolium and pyrrolidinium ILs with varied structure and lengths of alkyl chains in cations, and varied structures of orthoborate anions. These ILs were studied in bulk at different temperatures, and also in confinements, such as between parallel glass and Teflon plates and in mesoporous Vycor glass. It was found that diffusion coefficients of cations and anions in EAN, phosphonium and pyrrolidinium orthoborate ILs in bulk are different, but according to the standard Stocks-Einstein model, they correspond to diffusion of ions in homogeneous liquids. A change in the chemical structure of one of the ions results in a change in both the diffusion coefficient of the oppositely charged ion and the activation energy of diffusion for both ions in an IL. Similar effects were observed from the chemical shifts and diffusion coefficients measured by NMR for imidazolium orthoborate ILs dissolved in polyethylene glycol solutions, in which imidazolium cations strongly interact with PEG molecules, further affecting the diffusion of orthoborate anions via electrostatic interactions. A liquid-liquid phase separation was suggested for a few phosphonium and pyrrolidinium bis(mandelato)borate ILs, in which a divergence of diffusion coefficients and activation energies of diffusion for cations and anions was detected at temperatures below ca 50 °C. In addition, a free-volume theory was invoked to explain the dependences of density of ILs on the alkyl chain length in cations.It was also found that for a phosphonium bis(salicylato)borate IL confined in 4 nm mesoporous Vycor glass the diffusion coefficients of ions increase by a factor of 35! This phenomenon was explained by the dynamic heterogeneity of this IL in micropores and empty voids of the Vycor glass. For EAN IL in confinements between glass and Teflon plates, the diffusion of ethylammonium cations and nitrate anions is significantly anisotropic, i.e. slower in the direction of the normal to the plates and faster along the plates compared to diffusion of the ions in bulk. A plausible explanation of this PFG NMR data is that EAN forms layers near polar and non-polar solid surfaces. A similar phenomenon, to a lesser extent, was also observed for phosphonium cations of bis(mandelato)borate, bis(salicylato)borate and bis(oxalato)borate confined between glass plates. The results of these studies may have implications in modeling tribological performance, i.e., friction and wear reduction for contact pairs of different materials lubricated by various classes of ionic liquids. / För godkännande; 2016; 20160420 (andfil)

This thesis deals with the development of new reaction methodology as well as stereochemical investigations. The first part concerns the investigation of 1,2- and merged 1,2- and 1,3- asymmetric induction in Mukaiyama aldol additions to α-heteroatom and α,β- heteroatom substituted aldehydes respectively. In particular, the unexpected 1,2-syn selectivity obtained in the addition of sterically hindered nucleophiles to α-chloroaldehydes is examined, and an explanation for the observed stereochemical trends is proposed. The second part describes the development of a novel entry to α-amino-β- hydroxy esters by a 1,3-dipolar cycloaddition reaction of aldehydes and azomethine ylides, generated by thermolysis of aziridines. The third part deals with our efforts to develop a novel entry to vicinal all- carbon quaternary centers, based on an intramolecular domino Heck- carbonylation reaction using tetrasubstituted olefins. / QC 20120611

This thesis is about sustainability within chemistry, the so-called, green chemistry. With this work  I seek to combine green chemistry with sustainable  development  and find methods for teaching green chemistry in a laboratory environement.  I have designed  and tested two labs with ingredients of green  chemistry and sustainable development in my study. I wanted to determine if my design model  leads to conception for the students. The students have through forms and interviews declared their perspective on the education and their conception. In a laboratory environment the pros of a laboratory way of work should be recognized. Pre- and post-work puts the lab in a context. The students understand the concepts better if they are allowed to test their knowledge in a discussion. The teachers role in the discussion should be to lift the level of the discussion by controlling the conversation and in a constructiveway contribute to making the discussion move forward whenever necessary. / Denna uppsats behandar hållbarhet inom kemi, den så kallade gröna kemin. Med arbetet söker jag förena grön kemi med hållbar utveckling och hitta metoder för att undervisa grön kemi i en laborativ miljö. I undersökningen har jag designat och testat två laborationer med inslag av grön kemi och hållbar utveckling. Jag ville undersöka om undervisningsmodellen leder till en begreppsutveckling hos studenter och elever. Studenterna/eleverna har genom enkäter och intervjuer uttalat sig om dels sina egna kunskaper och dels om undervisningens inslag och dess bidrag till deras begreppsutveckling. I ett laborativt sammanhang bör fördelarna med ett laborativt arbetssätt utnyttjas. Förarbete och efterarbete ger laborationen ett sammanhang. Studenten/eleven förstår begreppen bättre om de får testa sina kunskaper i en diskussion. Lärarens roll i diskussionen bör vara att lyfta diskussionsnivån genom att styra samtalet och på ett konstruktivt sätt bidra till att föra diskussionen framåt när det är nödvändigt.