35 resultados para hydrogen-bond catalysis

em Doria (National Library of Finland DSpace Services) - National Library of Finland, Finland


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This thesis is based on computational chemistry studies on lignans, focusing on the naturally occurring lignan hydroxymatairesinol (HMR) (Papers I II) and on TADDOL-like conidendrin-based chiral 1,4-diol ligands (LIGNOLs) (Papers III V). A complete quantum chemical conformational analysis on HMR was previously conducted by Dr. Antti Taskinen. In the works reported in this thesis, HMR was further studied by classical molecular dynamics (MD) simulations in aqueous solution including torsional angle analysis, quantum chemical solvation e ect study by the COnductorlike Screening MOdel (COSMO), and hydrogen bond analysis (Paper I), as well as from a catalytic point of view including protonation and deprotonation studies at di erent levels of theory (Paper II). The computational LIGNOL studies in this thesis constitute a multi-level deterministic structural optimization of the following molecules: 1,1-diphenyl (2Ph), two diastereomers of 1,1,4-triphenyl (3PhR, 3PhS), 1,1,4,4-tetraphenyl (4Ph) and 1,1,4,4-tetramethyl (4Met) 1,4-diol (Paper IV) and a conformational solvation study applying MD and COSMO (Paper V). Furthermore, a computational study on hemiketals in connection with problems in the experimental work by Docent Patrik Eklund's group synthesizing the LIGNOLs based on natural products starting from HMR, is shortly described (Paper III).

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Modifiering av metallytor med starkt adsorberade kirala organiska molekyler är eventuellt den mest relevanta teknik man vet i dag för att skapa kirala ytor. Den kan utnyttjas i katalytisk produktion av enantiomeriskt rena kirala föreningar som behövs t.ex. som läkemedel och aromkemikalier. Trots många fördelar av asymmetrisk heterogen katalys jämfört med andra sätt för att få kirala föreningar, har den ändå inte blivit ett allmänt verktyg för storskaliga tillämpningar. Detta beror t.ex. på brist på djupare kunskaper i katalytiska reaktionsmekanismer och ursprunget för asymmetrisk induktion. I denna studie användes molekylmodelleringstekniker för att studera asymmetriska, heterogena katalytiska system, speciellt hydrering av prokirala karbonylföreningar till motsvarande kirala alkoholer på cinchona-alkaloidmodifierade Pt-katalysatorer. 1-Fenyl-1,2-propandion (PPD) och några andra föreningar, som innehåller en prokiral C=O-grupp, användes som reaktanter. Konformationer av reaktanter och cinchona-alkaloider (som kallas modifierare) samt vätebundna 1:1-komplex mellan dem studerades i gas- och lösningsfas med metoder som baserar sig på vågfunktionsteori och täthetsfunktionalteori (DFT). För beräkningen av protonaffiniteter användes också högst noggranna kombinationsmetoder såsom G2(MP2). Den relativa populationen av modifierarnas konformationer varierade som funktion av modifieraren, dess protonering och lösningsmedlet. Flera reaktant–modifierareinteraktionsgeometrier beaktades. Slutsatserna på riktning av stereoselektivitet baserade sig på den relativa termodynamiska stabiliteten av de diastereomeriska reaktant–modifierare-komplexen samt energierna hos π- och π*-orbitalerna i den reaktiva karbonylgruppen. Adsorption och reaktioner på Pt(111)-ytan betraktades med DFT. Regioselektivitet i hydreringen av PPD och 2,3-hexandion kunde förklaras med molekyl–yta-interaktioner. Storleken och formen av klustret använt för att beskriva Pt-ytan inverkade inte bara på adsorptionsenergierna utan också på de relativa stabiliteterna av olika adsorptionsstrukturer av en molekyl. Populationerna av modifierarnas konformationer i gas- och lösningsfas korrelerade inte med populationerna på Pt-ytan eller med enantioselektiviteten i hydreringen av PPD på Pt–cinchona-katalysatorer. Vissa modifierares konformationer och reaktant–modifierare-interaktionsgeometrier var stabila bara på metallytan. Teoretiskt beräknade potentialenergiprofiler för hydrering av kirala α-hydroxiketoner på Pt implicerade preferens för parvis additionsmekanism för väte och selektiviteter i harmoni med experimenten. De uppnådda resultaten ökar uppfattningen om kirala heterogena katalytiska system och kunde därför utnyttjas i utvecklingen av nya, mera aktiva och selektiva kirala katalysatorer.

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RNA is essential for all living organisms. It has important roles in protein synthesis, controlling gene expression as well as catalyzing biological reactions. Chemically RNA is a very stable molecule, although in biological systems many agents catalyze the cleavage of RNA, such as naturally occurring enzymes and ribozymes. Much effort has been put in the last decades in developing highly active artificial ribonucleases since such molecules could have potential in the therapeutic field and provide tools for molecular biology. Several potential catalysts have emerged, but usually detailed cleavage mechanism remains unresolved. This thesis is aimed at clarifying mechanistic details of the cleavage and isomerization of RNA by using simpler nucleoside models of RNA. The topics in the experimental part cover three different studies, one concerning the mechanism of catalysis by large ribozymes, one dealing with the reactivity of modified and unmodified RNA oligonucleotides and one showing an efficient catalysis of the cleavage and isomerization of an RNA phosphodiester bond by a dinuclear metal ion complex. A review of the literature concerning stabilization of the phosphorane intermediate of the hydrolysis and isomerization of RNA phosphodiester bond is first presented. The results obtained in the experimental work followed by mechanistic interpretations are introduced in the second part of the thesis. Especially the significance of hydrogen bonding interactions is discussed.

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The development of new technologies to supplement fossil resources has led to a growing interest in the utilization of alternative routes. Biomass is a rich renewable feedstock for producing fine chemicals, polymers, and a variety of commodities replacing petroleumderived chemicals. Transformation of biomass into diverse valuable chemicals is the key concept of a biorefinery. Catalytic conversion of biomass, which reduces the use of toxic chemicals is one of the important approaches to improve the profitability of biorefineries. Utilization of gold catalysts allows conducting reactions under environmentally-friendly conditions, with a high catalytic activity and selectivity. Gold-catalyzed valorization of several biomass-derived compounds as an alternative approach to the existing technologies was studied in this work. Isomerization of linoleic acid via double bond migration towards biologically active conjugated linoleic acid isomers (CLA) was investigated. The activity and selectivity of various gold catalysts towards cis-9,trans-11-CLA and trans-10,cis-12-CLA were investigated in a semi-batch reactor, showing that the yield of the desired products varied, depending on the catalyst support. The structure sensitivity in the selective oxidation of arabinose was demonstrated using a series of gold catalysts with different Au cluster sizes in a shaker reactor operating in a semibatch mode. The gas-phase selective oxidation of ethanol was studied and the influence of the catalyst support on the catalytic performance was investigated. The selective oxidation of the lignan hydroxymatairesinol (HMR), extracted from the Norway spruce (Picea abies) knots, to the lignan oxomatairesinol (oxoMAT) was extensively investigated. The influence of the reaction conditions and catalyst properties on the yield of oxoMAT was evaluated. In particular, the structure sensitivity of the reaction was demonstrated. The catalyst deactivation and regeneration procedures were studied. The reaction kinetics and mechanism were advanced.

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The evolution of our society is impossible without a constant progress in life-important areas such as chemical engineering and technology. Innovation, creativity and technology are three main components driving the progress of chemistry further towards a sustainable society. Biomass, being an attractive renewable feedstock for production of fine chemicals, energy-rich materials and even transportation fuels, captures progressively new positions in the area of chemical technology. Knowledge of heterogeneous catalysis and chemical technology applied to transformation of biomass-derived substances will open doors for a sustainable economy and facilitates the discovery of novel environmentally-benign processes which probably will replace existing technologies in the era of biorefinary. Aqueous-phase reforming (APR) is regarded as a promising technology for production of hydrogen and liquids fuels from biomass-derived substances such as C3-C6 polyols. In the present work, aqueous-phase reforming of glycerol, xylitol and sorbitol was investigated in the presence of supported Pt catalysts. The catalysts were deposited on different support materials, including Al2O3, TiO2 and carbons. Catalytic measurements were performed in a laboratory-scale continuous fixedbed reactor. An advanced analytical approach was developed in order to identify reaction products and reaction intermediates in the APR of polyols. The influence of the substrate structure on the product formation and selectivity in the APR reaction was also investigated, showing that the yields of the desired products varied depending on the substrate chain length. Additionally, the influence of bioethanol additive in the APR of glycerol and sorbitol was studied. A reaction network was advanced explaining the formation of products and key intermediates. The structure sensitivity in the aqueous-phase reforming reaction was demonstrated using a series of platinum catalysts supported on carbon with different Pt cluster sizes in the continuous fixed-bed reactor. Furthermore, a correlation between texture physico-chemical properties of the catalysts and catalytic data was established. The effect of the second metal (Re, Cu) addition to Pt catalysts was investigated in the APR of xylitol showing a superior hydrocarbon formation on PtRe bimetallic catalysts compared to monometallic Pt. On the basis of the experimental data obtained, mathematical modeling of the reaction kinetics was performed. The developed model was proven to successfully describe experimental data on APR of sorbitol with good accuracy.

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Ydinvoimalaitokset on suunniteltu ja rakennettu niin, että niillä on kyky selviytyä erilaisista käyttöhäiriöistä ja onnettomuuksista ilman laitoksen vahingoittumista sekä väestön ja ympäristön vaarantumista. On erittäin epätodennäköistä, että ydinvoimalaitosonnettomuus etenee reaktorisydämen vaurioitumiseen asti, minkä seurauksena sydänmateriaalien hapettuminen voi tuottaa vetyä. Jäädytyspiirin rikkoutumisen myötä vety saattaa kulkeutua ydinvoimalaitoksen suojarakennukseen, jossa se voi muodostaa palavan seoksen ilman hapen kanssa ja palaa tai jopa räjähtää. Vetypalosta aiheutuvat lämpötila- ja painekuormitukset vaarantavat suojarakennuksen eheyden ja suojarakennuksen sisällä olevien turvajärjestelmien toimivuuden, joten tehokas ja luotettava vedynhallintajärjestelmä on tarpeellinen. Passiivisia autokatalyyttisiä vetyrekombinaattoreita käytetäänyhä useammissa Euroopan ydinvoimaitoksissa vedynhallintaan. Nämä rekombinaattorit poistavat vetyä katalyyttisellä reaktiolla vedyn reagoidessa katalyytin pinnalla hapen kanssa muodostaen vesihöyryä. Rekombinaattorit ovat täysin passiivisiaeivätkä tarvitse ulkoista energiaa tai operaattoritoimintaa käynnistyäkseen taitoimiakseen. Rekombinaattoreiden käyttäytymisen tutkimisellatähdätään niiden toimivuuden selvittämiseen kaikissa mahdollisissa onnettomuustilanteissa, niiden suunnittelun optimoimiseen sekä niiden optimaalisen lukumäärän ja sijainnin määrittämiseen suojarakennuksessa. Suojarakennuksen mallintamiseen käytetään joko keskiarvoistavia ohjelmia (Lumped parameter (LP) code), moniulotteisia virtausmalliohjelmia (Computational Fluid Dynamics, CFD) tai näiden yhdistelmiä. Rekombinaattoreiden mallintaminen on toteutettu näissä ohjelmissa joko kokeellisella, teoreettisella tai yleisellä (eng. Global Approach) mallilla. Tämä diplomityö sisältää tulokset TONUS OD-ohjelman sisältämän Siemens FR90/1-150 rekombinaattorin mallin vedynkulutuksen tarkistuslaskuista ja TONUS OD-ohjelmalla suoritettujen laskujen tulokset Siemens rekombinaattoreiden vuorovaikutuksista. TONUS on CEA:n (Commissariat à 1'En¬ergie Atomique) kehittämä LP (OD) ja CFD -vetyanalyysiohjelma, jota käytetään vedyn jakautumisen, palamisenja detonaation mallintamiseen. TONUS:sta käytetään myös vedynpoiston mallintamiseen passiivisilla autokatalyyttisillä rekombinaattoreilla. Vedynkulutukseen vaikuttavat tekijät eroteltiin ja tutkittiin yksi kerrallaan. Rekombinaattoreiden vuorovaikutuksia tutkittaessa samaan tilavuuteen sijoitettiin eri kokoisia ja eri lukumäärä rekombinaattoreita. Siemens rekombinaattorimalli TONUS OD-ohjelmassa laskee vedynkulutuksen kuten oletettiin ja tulokset vahvistavat TONUS OD-ohjelman fysikaalisen laskennan luotettavuuden. Mahdollisia paikallisia jakautumia tutkitussa tilavuudessa ei voitu havaita LP-ohjelmalla, koska se käyttäälaskennassa suureiden tilavuuskeskiarvoja. Paikallisten jakautumien tutkintaan tarvitaan CFD -laskentaohjelma.

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Minimizing the risks of an investment portfolio but not in the favour of expected returns is one of the key interests of an investor. Typically, portfolio diversification is achieved using two main strategies: investing in different classes of assets thought to have little or negative correlations or investing in similar classes of assets in multiple markets through international diversification. This study investigates integration of the Russian financial markets in the time period of January 1, 2003 to December 28, 2007 using daily data. The aim is to test the intra-country and cross-country integration of the Russian stock and bond markets between seven countries. Our test methodology for the short-run dynamics testing is the vector autoregressive model (VAR) and for the long-run cointegration testing we use the Johansen cointegration test which is an extension to VAR. The empirical results of this study show that the Russian stock and bond markets are not integrated in the long-run either at intra-country or cross-country level which means that the markets are relatively segmented. The short-run dynamics are also relatively low. This implies a presence of potential gains from diversification.

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Prediction of the stock market valuation is a common interest to all market participants. Theoretically sound market valuation can be achieved by discounting future earnings of equities to present. Competing valuation models seek to find variables that affect the equity market valuation in a way that the market valuation can be explained and also variables that could be used to predict market valuation. In this paper we test the contemporaneous relationship between stock prices, forward looking earnings and long-term government bond yields. We test this so-called Fed model in a long- and short-term time series analysis. In order to test the dynamics of the relationship, we use the cointegration framework. The data used in this study spans over four decades of various market conditions between 1964-2007, using data from United States. The empirical results of our analysis do not give support for the Fed model. We are able to show that the long-term government bonds do not play statistically significant role in this relationship. The effect of forward earnings yield on the stock market prices is significant and thus we suggest the use of standard valuation ratios when trying to predict the future paths of equity prices. Also, changes in the long-term government bond yields do not have significant short-term impact on stock prices.

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In this thesis three experiments with atomic hydrogen (H) at low temperatures T<1 K are presented. Experiments were carried out with two- (2D) and three-dimensional (3D) H gas, and with H atoms trapped in solid H2 matrix. The main focus of this work is on interatomic interactions, which have certain specific features in these three systems considered. A common feature is the very high density of atomic hydrogen, the systems are close to quantum degeneracy. Short range interactions in collisions between atoms are important in gaseous H. The system of H in H2 differ dramatically because atoms remain fixed in the H2 lattice and properties are governed by long-range interactions with the solid matrix and with H atoms. The main tools in our studies were the methods of magnetic resonance, with electron spin resonance (ESR) at 128 GHz being used as the principal detection method. For the first time in experiments with H in high magnetic fields and at low temperatures we combined ESR and NMR to perform electron-nuclear double resonance (ENDOR) as well as coherent two-photon spectroscopy. This allowed to distinguish between different types of interactions in the magnetic resonance spectra. Experiments with 2D H gas utilized the thermal compression method in homogeneous magnetic field, developed in our laboratory. In this work methods were developed for direct studies of 3D H at high density, and for creating high density samples of H in H2. We measured magnetic resonance line shifts due to collisions in the 2D and 3D H gases. First we observed that the cold collision shift in 2D H gas composed of atoms in a single hyperfine state is much smaller than predicted by the mean-field theory. This motivated us to carry out similar experiments with 3D H. In 3D H the cold collision shift was found to be an order of magnitude smaller for atoms in a single hyperfine state than that for a mixture of atoms in two different hyperfine states. The collisional shifts were found to be in fair agreement with the theory, which takes into account symmetrization of the wave functions of the colliding atoms. The origin of the small shift in the 2D H composed of single hyperfine state atoms is not yet understood. The measurement of the shift in 3D H provides experimental determination for the difference of the scattering lengths of ground state atoms. The experiment with H atoms captured in H2 matrix at temperatures below 1 K originated from our work with H gas. We found out that samples of H in H2 were formed during recombination of gas phase H, enabling sample preparation at temperatures below 0.5 K. Alternatively, we created the samples by electron impact dissociation of H2 molecules in situ in the solid. By the latter method we reached highest densities of H atoms reported so far, 3.5(5)x1019 cm-3. The H atoms were found to be stable for weeks at temperatures below 0.5 K. The observation of dipolar interaction effects provides a verification for the density measurement. Our results point to two different sites for H atoms in H2 lattice. The steady-state nuclear polarizations of the atoms were found to be non-thermal. The possibility for further increase of the impurity H density is considered. At higher densities and lower temperatures it might be possible to observe phenomena related to quantum degeneracy in solid.

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A set of models in Aspen plus was built to simulate the direct synthesis process of hydrogen peroxide in a micro-reactor system. This process model can be used to carry out material balance calculation under various experimental conditions. Three thermodynamic property methods were compared by calculating gas solubility and Uniquac-RK method was finally selected for process model. Two different operation modes with corresponding operation conditions were proposed as the starting point of future experiments. Simulations for these two modes were carried out to get the information of material streams. Moreover, some hydrodynamic parameters such as gas/liquid superficial velocity, gas holdup were also calculated with improved process model. These parameters proved the proposed experimental conditions reasonable to some extent. The influence of operation conditions including temperature, pressure and circulation ratio was analyzed for the first operation mode, where pure oxygen was fed into dissolving tank and hydrogen-carbon dioxide mixture was fed into microreactor directly. The preferred operation conditions for the system are low temperature (2°C) and high pressure (30 bar) in dissolving tank. High circulation ratio might be good in the sense that more oxygen could be dissolved and fed into reactor for reactions, but meanwhile hydrodynamics of microreactor should be considered. Furthermore, more operation conditions of reactor gas/liquid feeds in both of two operation modes were proposed to provide guidance for future experiment design and corresponding hydrodynamic parameters were also calculated. Finally, safety issue was considered from thermodynamic point of view and there is no explosion danger at given experimental plan since the released reaction heat will not cause solvent vaporization inside the microchannels. The improvement of process model still needs further study based on the future experimental results.

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Inorganic pyrophosphatases (PPases) are essential enzymes for every living cell. PPases provide the necessary thermodynamic pull for many biosynthetic reactions by hydrolyzing pyrophosphate. There are two types of PPases: integral membrane-bound and soluble enzymes. The latter type is divided into two non-homologous protein families, I and II. Family I PPases are present in all kingdoms of life, whereas family II PPases are only found in prokaryotes, including archae. Family I PPases, particularly that from Saccharomyces cerevisiae, are among the most extensively characterized phosphoryl transfer enzymes. In the present study, we have solved the structures of wild-type and seven active site variants of S. cerevisiae PPase bound to its natural metal cofactor, magnesium ion. These structures have facilitated derivation of the complete enzyme reaction scheme for PPase, fulfilling structures of all the reaction intermediates. The main focus in this study was on a novel subfamily of family II PPases (CBSPPase) containing a large insert formed by two CBS domains and a DRTGG domain within the catalytic domain. The CBS domain (named after cystathionine beta-synthase in which it was initially identified) usually occurs as tandem pairs with two or four copies in many proteins in all kingdoms of life. The structure formed by a pair of CBS domains is also known as a Bateman domain. CBS domains function as regulatory units, with adenylate ligands as the main effectors. The DRTGG domain (designated based on its most conserved residues) occurs less frequently and only in prokaryotes. Often, the domain co-exists with CBS domains, but its function remains unknown. The key objective of the current study was to explore the structural rearrangements in the CBS domains induced by regulatory adenylate ligands and their functional consequences. Two CBS-PPases were investigated, one from Clostridium perfringens (cpCBS-PPase) containing both CBS and DRTGG domains in its regulatory region and the other from Moorella thermoacetica (mt CBS-PPase) lacking the DRTGG domain. We additionally constructed a separate regulatory region of cpCBS-PPase (cpCBS). Both full-length enzymes and cpCBS formed homodimers. Two structures of the regulatory region of cpCBS-PPase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate, were solved. The structures were significantly different, providing information on the structural pathway from bound adenylates to the interface between the regulatory and catalytic parts. To our knowledge, these are the first reported structures of a regulated CBS enzyme, which reveal large conformational changes upon regulator binding. The activator-bound structure was more open, consistent with the different thermostabilities of the activator- and inhibitor-bound forms of cpCBS-PPase. The results of the functional studies on wild-type and variant CBS-PPases provide support for inferences made on the basis of structural analyses. Moreover, these findings indicate that CBS-PPase activity is highly sensitive to adenine nucleotide distribution between AMP, ADP and ATP, and hence to the energy level of the cell. CBS-PPase activity is markedly inhibited at low energy levels, allowing PPi energy to be used for cell survival instead of being converted into heat.

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The purpose of this study was to simulate and to optimize integrated gasification for combine cycle (IGCC) for power generation and hydrogen (H2) production by using low grade Thar lignite coal and cotton stalk. Lignite coal is abundant of moisture and ash content, the idea of addition of cotton stalk is to increase the mass of combustible material per mass of feed use for the process, to reduce the consumption of coal and to increase the cotton stalk efficiently for IGCC process. Aspen plus software is used to simulate the process with different mass ratios of coal to cotton stalk and for optimization: process efficiencies, net power generation and H2 production etc. are considered while environmental hazard emissions are optimized to acceptance level. With the addition of cotton stalk in feed, process efficiencies started to decline along with the net power production. But for H2 production, it gave positive result at start but after 40% cotton stalk addition, H2 production also started to decline. It also affects negatively on environmental hazard emissions and mass of emissions/ net power production increases linearly with the addition of cotton stalk in feed mixture. In summation with the addition of cotton stalk, overall affects seemed to negative. But the effect is more negative after 40% cotton stalk addition so it is concluded that to get maximum process efficiencies and high production less amount of cotton stalk addition in feed is preferable and the maximum level of addition is estimated to 40%. Gasification temperature should keep lower around 1140 °C and prefer technique for studied feed in IGCC is fluidized bed (ash in dry form) rather than ash slagging gasifier

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Den snart 200 år gamla vetenskapsgrenen organisk synteskemi har starkt bidragit till moderna samhällens välfärd. Ett av flaggskeppen för den organiska synteskemin är utvecklingen och produktionen av nya läkemedel och speciellt de aktiva substanserna däri. Därmed är det viktigt att utveckla nya syntesmetoder, som kan tillämpas vid framställningen av farmaceutiskt relevanta målstrukturer. I detta sammanhang är den ultimata målsättningen dock inte endast en lyckad syntes av målmolekylen, utan det är allt viktigare att utveckla syntesrutter som uppfyller kriterierna för den hållbara utvecklingen. Ett av de centralaste verktygen som en organisk kemist har till förfogande i detta sammanhang är katalys, eller mera specifikt möjligheten att tillämpa olika katalytiska reaktioner vid framställning av komplexa målstrukturer. De motsvarande industriella processerna karakteriseras av hög effektivitet och minimerad avfallsproduktion, vilket naturligtvis gynnar den kemiska industrin samtidigt som de negativa miljöeffekterna minskas avsevärt. I denna doktorsavhandling har nya syntesrutter för produktion av finkemikalier med farmaceutisk relevans utvecklats genom att kombinera förhållandevis enkla transformationer till nya reaktionssekvenser. Alla reaktionssekvenser som diskuteras i denna avhandling påbörjades med en metallförmedlad allylering av utvalda aldehyder eller aldiminer. De erhållna produkterna innehållende en kol-koldubbelbindning med en närliggande hydroxyl- eller aminogrupp modifierades sedan vidare genom att tillämpa välkända katalytiska reaktioner. Alla syntetiserade molekyler som presenteras i denna avhandling karakteriseras som finkemikalier med hög potential vid farmaceutiska tillämpningar. Utöver detta tillämpades en mängd olika katalytiska reaktioner framgångsrikt vid syntes av dessa molekyler, vilket i sin tur förstärker betydelsen för de katalytiska verktygen i organiska kemins verktygslåda.