Browsing by Subject "orgaaninen kemia"

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  • Muuronen, Mikko (Helsingin yliopisto, 2015)
    Understanding the electronic structure of a chemical system in detail is essential for describing its chemical reactivity. In the present work, quantum chemical methods are applied in combination with experimental studies to achieve such detailed mechanistic understanding of chemical systems. Understanding the basic theory behind computational methods is of importance when applying them to chemical problems. Therefore, the first part of this work provides an introduction to quantum chemical methods. The results of this work are published in four peer-reviewed publications. In each publication, the understanding of the chemical system has been obtained using a combination of experimental and quantum chemical studies. These include the design of a new-type of Au(III)-catalysts, and understanding mechanistic aspects related to a Au(III) catalytic cycle. We have also focused on understanding how the electronic structure of an alkyne affects the regioselectivity in the Pauson-Khand reaction. A computational model, which provides a qualitative and, to some extent, a quantitative prediction of regiochemical outcomes is presented.
  • Parikka, Kirsti (Helsingin yliopisto, 2007)
    The first synthesis of long chain 5-n-alkylresorcinols (C15-C25) in whole grains and whole grain products by a novel modification of Wittig reaction is described. 5-n-Alkylresorcinols are phenolic lipids that have various effects on biological systems, such as antioxidant activity and interaction with biological membranes. These compounds are considered as biomarkers of whole grain intake, which is connected with reduced risk of cardiovascular diseases and certain cancers. Novel hapten derivatives of 5-n-alkylresorcinols, potential compounds for immunoanalytical techniques, are prepared by the same procedure utilizing microwave catalysed aqueous Wittig reaction as the key step. The synthesised analogues are required by various analytical, metabolism and bioactivity investigations. Four alternative strategies for producing deuterium polylabelled 5-n-alkylresorcinols are explored. Ring-labelled D3-alkylresorcinols were synthesized by acidic H/D exchange. Side chain -labelled D4-derivative was prepared by a total synthesis approach utilizing D2 deuterogenation of a D2-alkene derivative, and deuterogenation of alkynes was investigated in another total synthesis approach. An -D3-labelled alkylresorcinol is isotopically pure and completely stable under all relevant conditions encountered during analytical work. The labelling of another phenolic component of whole grains was explored. The preparation of D3-ferulic acid and related compounds by way of selective methylation of the precursors is described. The deuterated compounds are useful as standards in the quantification of these natural products in various substances, such as food and human fluids. The pure 5-n-alkylresorcinol analogues prepared were used in in vitro experiments on alkylresorcinol antioxidant activity and antigenotoxicity. The in vitro experiments show that alkylresorcinols act as antioxidants, especially when incorporated into biological systems, but possess lower activity in chemical tests (FRAP and DPPH assay). Whole grain alkylresorcinols are shown for the first time to have a protective effect against copper induced oxidation of LDL, and H2O2 or genotoxic faecal water induced damage on HT29 cells.
  • Mäkelä, Valtteri (Helsingin yliopisto, 2016)
    NMR spectroscopy is an invaluable tool for structure elucidation in chemistry and molecular biology, which is able to provide unique information not easily obtained by other analytical methods. However, performing quantitative NMR experiments and mixture analysis is considerably less common due to constraints in sensitivity/resolution and the fact that NMR observes individual nuclei, not molecules. The advances in instrument design in the last 25 years have substantially increased the sensitivity of NMR spectrometers, diminishing the main weakness of NMR, while increases in field strength and ever more intricate experiments have improved the resolving power and expanded the attainable information. The minimal need for sample preparation and its non-specific nature make quantitative NMR suitable for many applications ranging from quality control to metabolome characterization. Furthermore, the development of automated sample changers and fully automated acquisition have made high-throughput NMR acquisition a more feasible and attractive, yet expensive, possibility. This work discusses the fundamental principles and limitations of quantitative liquid state NMR spectroscopy, and tries to put together a summary of its various aspects scattered across literature. Many of these more subtle features can be neglected in simple routine spectroscopy, but become important when extracting quantitative data and/or when trying to acquire and process vast amounts of spectra consistently. The original research presented in this thesis provides improved methods for data acquisition of quantitative 13C detected NMR spectra in the form of modified INEPT based experiments (Q-INEPT-CT and Q-INEPT-2D), while software tools for automated processing and analysis of NMR spectra are also presented (ImatraNMR and SimpeleNMR). The application of these tools is demonstrated in the analysis of complex hydrocarbon mixtures (base oils), plant extracts and blood plasma samples. The increased capability of NMR spectroscopy, the rising interest in metabolomics and for example the recent introduction of benchtop NMR spectrometers are likely to expand the future use of quantitative NMR in the analysis of complex mixtures. For this reason, the further development of robust, accurate and feasible analysis methods and tools is essential.
  • Pajunen, Taina (Helsingin yliopisto, 2009)
    The autoxidation of conjugated linoleic acid (CLA) is poorly understood in spite of increasing interest in the beneficial biological properties of CLA and growing consumption of CLA-rich foods. In this thesis, the autoxidation reactions of the two major CLA isomers, 9-cis,11-trans-octadecadienoic acid and 10-trans,12-cis-octadecadienoic acid, are investigated. The results contribute to an understanding of the early stages of the autoxidation of CLA methyl ester, and provide for the first time a means of producing and separating intact CLA methyl ester hydroperoxides as well as basic knowledge on lipid hydroperoxides and their hydroxy derivatives. Conjugated diene allylic monohydroperoxides were discovered as primary autoxidation products formed during autoxidation of CLA methyl esters in the presence and absence of α-tocopherol. This established that one of the autoxidation pathways of CLA methyl ester is the hydroperoxide pathway. Hydroperoxides were produced from the two major CLA methyl esters by taking advantage of the effect of α-tocopherol to promote hydroperoxide formation. The hydroperoxides were analysed and separated first as methyl hydroxyoctadecadienoates and then as intact hydroperoxides by HPLC. The isolated products were characterized by UV, GC-MS, and NMR techniques. In the presence of a high amount of α-tocopherol, the autoxidation of CLA methyl ester yields six kinetically-controlled conjugated diene monohydroperoxides and is diastereoselective in favour of one particular geometric isomer as a pair of enantiomers. The primary autoxidation products produced from the two major CLA isomers include new positional isomers of conjugated diene monohydroperoxides, the 8-, 10-, 12-, and 14-hydroperoxyoctadecadienoates. Furthermore, two of these new positional isomers have an unusual structure for a cis,trans lipid hydroperoxide where the allylic methine carbon is adjacent to the cis instead of the usual trans double bond. The 1H and 13C NMR spectra of nine isomeric methyl hydroxyoctadecadienoates and of ten isomeric methyl hydroperoxyoctadecadienoates including the unusual cis,trans hydroperoxides, i.e. Me 8-OOH-9c,11t and Me 14-OOH-10t,12c, were fully assigned with the aid of 2D NMR spectroscopy. The assigned NMR data enabled determination of the effects of the hydroxyl and hydroperoxyl groups on the carbon chemical shifts of CLA isomers, identification of diagnostic signals, and determination of chemical shift differences of the olefinic resonances that may help with the assignment of structure to as yet unknown lipid hydroperoxides either as hydroxy derivatives or as intact hydroperoxides. A mechanism for the hydroperoxide pathway of CLA autoxidation in the presence of a high amount of α-tocopherol was proposed based on the characterized primary products, their relative distribution, and theoretical calculations. This is an important step forward in CLA research, where exact mechanisms for the autoxidation of CLA have not been presented before. Knowledge of these hydroperoxide formation steps is of crucial importance for understanding the subsequent steps and the different pathways of the autoxidation of CLA. Moreover, a deeper understanding of the autoxidation mechanisms is required for ensuring the safety of CLA-rich foods. Knowledge of CLA oxidation and how it differs from the oxidation of nonconjugated polyunsaturated fatty acids may also be the key to understanding the biological mechanisms of CLA activity.
  • von Pfaler, Carl Constantin (Frenckell, 1844)
  • Hoikkala, Antti (Helsingin yliopisto, 2016)
    Isoflavonoid phytoestrogens are secondary plant metabolites, which structurally or functionally resemble 17β-estradiol and they originally received attention due to breeding problems affecting ewes grazing on subterranean clover. Later research of phytoestrogens has been focusing on the possible beneficial effects as oestrogen agonists or anti-estrogens. Due to their health promoting effects, the knowledge of the occurrence of isoflavonoids and their metabolites in food and biological fluids as well as the better understanding of their metabolic pathways have been the main aspects in the research field. The literature review introduces the biological significance of isoflavonoids in plants along with various analytical techniques used for the determination of these compounds in biological matrices. This is followed by a discussion of the isoflavone metabolism in humans, rodents, and ruminants. The experimental part focuses on the synthetic methods used for the preparation of the isoflavonoids, and on four studies in which they were used. In the first two studies cow milk was analysed. It was shown that commercial organic cow milk contains high levels of equol along with much lower levels of the other isoflavonoids typically found in milk and milk products. The levels of equol detected in organic milk were significantly higher than the levels found in normal milk which corresponds to the fodder that the cows are fed. In the following study five Finnish Ayrshire cows were subjected to a red clover rich diet in order to study the metabolism of the isoflavones futher. Equol and a hitherto unquantifed metabolite, 3 ,7-dihydroxyisoflavan was detected and quantitatively measured in milk samples. In another study, the metabolisation of genistein fatty acid ester was studied after (oral or parenteral) administration to adult female rhesus monkeys. It turned that levels of genistein fatty acid ester levels depended of the form of administration, and it may be possible to introduce intact genistein ester molecules into plasma by parenteral, but not oral administration. The last study, focuses on the metabolism of the soy isoflavones daidzein, genistein, and glycitein in humans. After oral administration of these isoflavones through ingestion of soy enriched food, daily urine samples of the volunteers were analysed. This led to identification of several metabolites and to the proposal of the metabolic pathways of the isoflavones ingested.
  • Pohjoispää, Monika (Helsingin yliopisto, 2014)
    Lignans are naturally occurring compounds, polyphenolic secondary plant and mammalian metabolites. Due to their ubiquitous presence and biological activity, lignans have attracted the interest of scientists from different areas, like nutrition scientists, pharmaceutical researchers and synthetic chemists. The research is very active, and the number of lignan related publications has proliferated. Lignans vary widely in the structure, and the present work focuses mainly on the (hydroxy)lignano-­9,9’­‐lactones, their rearranged products, and 9,9’-­epoxylignanes. The literature review introduces the stereochemistry and assignment of the absolute configuration of these lignans. In addition, stable isotope labelling of lignans is reviewed. The experimental part is focused on deuteration of lignans and rearrangement and stereochemistry studies. The deuteration reaction utilising acidic H/D exchange within the lignan skeleton was investigated. The relative reactivity of various aromatic sites, the stability of deuterium labels and the isotopic purity of the labelled compounds were examined. Experimental observations and results were compared to computational studies. Several stable, isotopically pure polydeuterated lignano-­9,9’-lactones and 9,9’-­epoxylignanes were synthesised. Alongside the deuteration experiments unexpected reactivity in eletrophilic aromatic deuteration of methylenedioxy substituted compounds was observed and further studied. In addition to deuteration, the stereochemistry of certain rearranged lignanolactones was a central subject of this study. Our findings allowed to clarify some mechanistical aspects of the rearrangement reactions of 7’-­hydroxylignano-­9,9’-­lactones and revise certain disputable structural data in the literature. Furthermore, the X-­ray structures of 7’-hydroxylignano-­9,9’-­lactones and rearranged 9’-hydroxylignano-­9,7’-­lactones were obtained for the first time.
  • Oksanen, Esko (Helsingin yliopisto, 2009)
    Inorganic pyrophosphatases (PPases, EC hydrolyse pyrophosphate in a reaction that provides the thermodynamic 'push' for many reactions in the cell, including DNA and protein synthesis. Soluble PPases can be classified into two families that differ completely in both sequence and structure. While Family I PPases are found in all kingdoms, family II PPases occur only in certain prokaryotes. The enzyme from baker's yeast (Saccharomyces cerevisiae) is very well characterised both kinetically and structurally, but the exact mechanism has remained elusive. The enzyme uses divalent cations as cofactors; in vivo the metal is magnesium. Two metals are permanently bound to the enzyme, while two come with the substrate. The reaction cycle involves the activation of the nucleophilic oxygen and allows different pathways for product release. In this thesis I have solved the crystal structures of wild type yeast PPase and seven active site variants in the presence of the native cofactor magnesium. These structures explain the effects of the mutations and have allowed me to describe each intermediate along the catalytic pathway with a structure. Although establishing the ʻchoreographyʼ of the heavy atoms is an important step in understanding the mechanism, hydrogen atoms are crucial for the mechanism. The most unambiguous method to determine the positions of these hydrogen atoms is neutron crystallography. In order to determine the neutron structure of yeast PPase I perdeuterated the enzyme and grew large crystals of it. Since the crystals were not stable at ambient temperature, a cooling device was developed to allow neutron data collection. In order to investigate the structural changes during the reaction in real time by time-resolved crystallography a photolysable substrate precursor is needed. I synthesised a candidate molecule and characterised its photolysis kinetics, but unfortunately it is hydrolysed by both yeast and Thermotoga maritima PPases. The mechanism of Family II PPases is subtly different from Family I. The native metal cofactor is manganese instead of magnesium, but the metal activation is more complex because the metal ions that arrive with the substrate are magnesium different from those permanently bound to the enzyme. I determined the crystal structures of wild type Bacillus subtilis PPase with the inhibitor imidodiphosphate and an inactive H98Q variant with the substrate pyrophosphate. These structures revealed a new trimetal site that activates the nucleophile. I also determined that the metal ion sites were partially occupied by manganese and iron using anomalous X- ray scattering.
  • Heinonen, Satu-Maarit (Helsingin yliopisto, 2006)
    Epidemiological studies have associated high soy intake with a lowered risk for certain hormone-dependent diseases, such as breast and prostate cancers, osteoporosis, and cardiovascular disease. Soy is a rich source of isoflavones, diphenolic plant compounds that have been shown to possess several biological activities. Soy is not part of the traditional Western diet, but many dietary supplements are commercially available in order to provide the proposed beneficial health effects of isoflavones without changing the original diet. These supplements are usually manufactured from extracts of soy or red clover, which is another important source of isoflavones. However, until recently, detailed studies of the metabolism of these compounds in humans have been lacking. The aim of this study was to identify urinary metabolites of isoflavones originating from soy or red clover using gas chromatography - mass spectrometry (GC-MS). To examine metabolism, soy and red clover supplementation studies with human volunteers were carried out. In addition, the metabolism of isoflavones was investigated in vitro by identification of metabolites formed during a 24-h fermentation of pure isoflavones with a human fecal inoculum. Qualitative methods for identification and analysis of isoflavone metabolites in urine and fecal fermentation samples by GC-MS were developed. Moreover, a detailed investigation of fragmentation of isoflavonoids in electron ionization mass spectrometry (EIMS) was carried out by means of synthetic reference compounds and deuterated trimethylsilyl derivatives. After isoflavone supplementation, 18 new metabolites of isoflavones were identified in human urine samples. The most abundant urinary metabolites of soy isoflavones daidzein, genistein, and glycitein were found to be the reduced metabolites, i.e. analogous isoflavanones, a-methyldeoxybenzoins, and isoflavans. Metabolites having additional hydroxyl and/or methoxy substituents, or their reduced analogs, were also identified. The main metabolites of red clover isoflavones formononetin and biochanin A were identified as daidzein and genistein. In addition, reduced and hydroxylated metabolites of formononetin and biochanin A were identified; however, they occurred at much lower levels in urine samples than daidzein or genistein or their reduced metabolites. The results of this study show that the metabolism of isoflavones is diverse. More studies are needed to determine whether the new isoflavonoid metabolites identified here have biological activities that contribute to the proposed beneficial effects of isoflavones on human health. Another task is to develop validated quantitative methods to determine the actual levels of isoflavones and their metabolites in biological matrices in order to assess the role of isoflavones in prevention of chronic diseases.
  • Fager-Jokela, Erika (Helsingin yliopisto, 2015)
    The Pauson-Khand reaction (PKR) is a very efficient method of synthesising cyclopentenones. In the reaction, an alkene, an alkyne and carbon monoxide combine to form a cyclopentenone ring, mediated or catalysed by a transition metal complex in one pot. In the cyclisation, three new carbon-carbon bonds are created. This thesis concentrates on the intermolecular variant of a cobalt(0)-mediated Pauson-Khand reaction. The development of intermolecular cyclisation has been slow over the past decade, due to the lack of reactive alkenes and the lack of regioselectivity for substituted alkynes. Despite the publication of numerous studies, the electronic effects involved are not yet completely understood. In this study, our purpose was to gain a greater understanding of the interplay between steric and electronic factors in determining the regioselectivity of the Pauson-Khand reaction. The electronic guidance regarding the alkyne regioselectivity of the Pauson-Khand reaction was studied with both conjugated aromatic alkynes and non-conjugated propargylic alkynes. It was demonstrated that, in the absence of steric effects, alkyne polarisation dictates the regiochemical selectivity of PKR. In conjugated systems, like diarylalkynes, Hammett values can be utilised in estimation of the polarisation of the alkyne. With nonconjugated alkynes, on the other hand, electronegativity of the substituent group designates the major regioisomer, as the charge differences are created via inductive effect. In addition to investigating regioselectivity, additive-free methods for promotion of Pauson-Khand reaction were developed and utilised, and Pauson-Khand reaction was applied in the synthesis of estrone E-ring extension. With microwaves (MW) used in promotion, the heat was effectively transferred to the reaction, saving energy and time without affecting the selectivity of the reaction.
  • Hakala, Ullastiina (Helsingin yliopisto, 2009)
    The use of ionic liquids in chemical research has gained considerable interest and activity in recent years. Due to their unique and varied physicochemical properties, in comparison to molecular solvents, the potential applications for ionic liquids are enormous. The use of microwave irradiation, as a powerful dielectric heating technique, in synthetic organic chemistry has been known since 1986. Since then, it has gained significant recognition for its research and application in both academia and industry. The use of either ionic liquids or microwave irradiation in synthetic organic chemistry has been known to afford improved, alternative or complimentary selectivities, in comparison to traditional processes. In this study, the use of ionic liquids as solvents, co-solvents and catalytic media was explored in Friedel-Crafts, deuterolabelling and O-demethylation reactions. Alternative methods for the production of a variety of aromatic ketones using the Friedel-Crafts acylation methodology were investigated using ionic liquid catalyst or ionic liquid acidic additive systems. The disclosed methods, i.e. metal bistriflamides and chloroindate ionic liquids systems, possessed good catalytic activity in the synthesis of typical benzophenones. These catalytic systems were also recyclable. Microwave irradiation was found to be useful in the synthesis of various polyhydroxydeoxybenzoins and arylpropanones as synthetic precursors to naturally occurring or potentially bioactive compounds. Under optimized condition, the reaction occurred in only four minutes using systems such as [bmim][NTf2]/HNTf2 and [bmim][BF4]/BF3·OEt2. Naturally occurring polyphenols, such as isoflavones, can possess various types of biological or pharmacological activity. In particular, some are noted for their beneficial effects on human health. Isotopically labelled analogues of polyphenols are valuable as analytical standards in the quantification of these compounds from biological matrices. A new strategy for deuterolabelling of polyphenols was developed using ionic liquids as co-solvents and 35% DCl/D2O, as a cheap deuterium source, under microwave irradiation. Under these conditions, perdeuterated compounds were achieved in short reaction times, in high isotopic purity and in excellent yields. An O-demethylation reaction was developed, using an ionic liquid reaction medium with BBr3 for the deprotection of a variety methyl protected polyphenolic compounds, such as isoflavons and lignans. This deprotection procedure was found to be very practical as the reaction occurred under mild reaction conditions and in short reaction times. The isolation and purification steps were particularly straightforward and high yielding, in comparison to traditional methods.
  • Kavakka, Jari (Helsingin yliopisto, 2010)
    Photosynthesis is a chemical process in which the energy of the light quanta is transformed into chemical energy. Chlorophyll (Chl) molecules play a key role in photosynthesis; they function in the antennae systems and in the photosynthetic reaction center where the primary charge separation (CS) takes place. Bio-inspired mimicry of the CS is an essential unit in dye-sensitized solar cells. Aim of this study was to design and develop electron donor-acceptor (EDA) pairs from Chls and fullerenes (C60) or carbon nanotubes (CNT). The supramolecular approach was chosen, as long synthetic sequences required by the covalent approach lead to long reaction schemes and low yields. Here, a π-interaction between soluble CNTs and Chl was used in EDA construction. Also, a beta-face selective two-point bound Chl-C60 EDA was introduced. In addition, the photophysical properties of the supramolecular EDA dyads were analyzed. In organic chemistry, nuclear magnetic resonance (NMR) spectroscopy is the most vital analytical technique in use. Multi-dimensional NMR experiments have enabled a structural analysis of complex natural products and proteins. However, in mixture analysis NMR is still facing difficulties. In many cases overlapping signals can t be resolved even with the help of multi-dimensional experiments. In this work, an NMR tool based on simple host-guest chemistry between analytes and macromolecules was developed. Diffusion ordered NMR spectroscopy (DOSY) measures the mobilities of compounds in an NMR sample. In a liquid state NMR sample, each of the analytes has a characteristic diffusion coefficient, which is proportional to the size of the analyte. With normal DOSY experiment, provided that the diffusion coefficients of the analytes differ enough, individual spectra of analytes can be extracted. When similar sized analytes differ chemically, an additive can be introduced into the sample. Since macromolecules in a liquid state NMR sample can be considered practically stationary, even faint supramolecular interaction can change the diffusion coefficient of the analyte sufficiently for a successful resolution in DOSY. In this thesis, polyvinylpyrrolidone and polyethyleneglycol enhanced DOSY NMR techniques, which enable mixture analysis of similar in size but chemically differing natural products, are introduced.
  • Karkola, Sampo (Helsingin yliopisto, 2009)
    Breast cancer is the most common cancer in women in the western countries. Approximately two-thirds of breast cancer tumours are hormone dependent, requiring estrogens to grow. Estrogens are formed in the human body via a multistep route starting from cholesterol. The final steps in the biosynthesis include the CYP450 aromatase enzyme, converting the male hormones androgens (preferred substrate androstenedione ASD) into estrogens(estrone E1), and the 17beta-HSD1 enzyme, converting the biologically less active E1 into the active hormone 17beta-hydroxyestradiol E2. E2 is bound to the nuclear estrogen receptors causing a cascade of biochemical reactions leading to cell proliferation in normal tissue, and to tumour growth in cancer tissue. Aromatase and 17beta-HSD1 are expressed in or near the breast tumour, locally providing the tissue with estrogens. One approach in treating hormone dependent breast tumours is to block the local estrogen production by inhibiting these two enzymes. Aromatase inhibitors are already on the market in treating breast cancer, despite the lack of an experimentally solved structure. The structure of 17beta-HSD1, on the other hand, has been solved, but no commercial drugs have emerged from the drug discovery projects reported in the literature. Computer-assisted molecular modelling is an invaluable tool in modern drug design projects. Modelling techniques can be used to generate a model of the target protein and to design novel inhibitors for them even if the target protein structure is unknown. Molecular modelling has applications in predicting the activities of theoretical inhibitors and in finding possible active inhibitors from a compound database. Inhibitor binding at atomic level can also be studied with molecular modelling. To clarify the interactions between the aromatase enzyme and its substrate and inhibitors, we generated a homology model based on a mammalian CYP450 enzyme, rabbit progesterone 21-hydroxylase CYP2C5. The model was carefully validated using molecular dynamics simulations (MDS) with and without the natural substrate ASD. Binding orientation of the inhibitors was based on the hypothesis that the inhibitors coordinate to the heme iron, and were studied using MDS. The inhibitors were dietary phytoestrogens, which have been shown to reduce the risk for breast cancer. To further validate the model, the interactions of a commercial breast cancer drug were studied with MDS and ligand–protein docking. In the case of 17beta-HSD1, a 3D QSAR model was generated on the basis of MDS of an enzyme complex with active inhibitor and ligand–protein docking, employing a compound library synthesised in our laboratory. Furthermore, four pharmacophore hypotheses with and without a bound substrate or an inhibitor were developed and used in screening a commercial database of drug-like compounds. The homology model of aromatase showed stable behaviour in MDS and was capable of explaining most of the results from mutagenesis studies. We were able to identify the active site residues contributing to the inhibitor binding, and explain differences in coordination geometry corresponding to the inhibitory activity. Interactions between the inhibitors and aromatase were in agreement with the mutagenesis studies reported for aromatase. Simulations of 17beta-HSD1 with inhibitors revealed an inhibitor binding mode with hydrogen bond interactions previously not reported, and a hydrophobic pocket capable of accommodating a bulky side chain. Pharmacophore hypothesis generation, followed by virtual screening, was able to identify several compounds that can be used in lead compound generation. The visualisation of the interaction fields from the QSAR model and the pharmacophores provided us with novel ideas for inhibitor development in our drug discovery project.
  • Koskela, Outi (Helsingin yliopisto, 2009)
    Proteins are complex biomacromolecules playing fundamental roles in the physiological processes of all living organisms. They function as structural units, enzymes, transporters, process regulators, and signal transducers. Defects in protein functions often derive from genetic mutations altering the protein structure, and impairment of essential protein functions manifests itself as pathological conditions. Proteins operate through interactions, and all protein functions depend on protein structure. In order to understand biological mechanisms at the molecular level, one has to know the structures of the proteins involved. This thesis covers structural and functional characterization of human filamins. Filamins are actin-binding and -bundling proteins that have numerous interaction partners. In addition to their actin-organizing functions, filamins are also known to have roles in cell adhesion and locomotion, and to participate in the logistics of cell membrane receptors, and in the coordination of intracellular signaling pathways. Filamin mutations in humans induce severe pathological conditions affecting the brain, bones, limbs, and the cardiovascular system. Filamins are large modular proteins composed of an N-terminal actin-binding domain and 24 consecutive immunoglobulin-like domains (IgFLNs). Nuclear magnetic resonance (NMR) spectroscopy is a versatile method of gaining insight into protein structure, dynamics and interactions. NMR spectroscopy was employed in this thesis to study the atomic structure and interaction mechanisms of C-terminal IgFLNs, which are known to house the majority of the filamin interaction sites. The structures of IgFLN single-domains 17 and 23 and IgFLN domain pairs 16-17 and 18-19 were determined using NMR spectroscopy. The structures of domain pairs 16 17 and 18 19 both revealed novel domain domain interaction modes of IgFLNs. NMR titrations were employed to characterize the interactions of filamins with glycoprotein Ibα, FilGAP, integrin β7 and dopamine receptors. Domain packing of IgFLN domain sextet 16 21 was further characterized using residual dipolar couplings and NMR relaxation analysis. This thesis demonstrates the versatility and potential of NMR spectroscopy in structural and functional studies of multi-domain proteins.
  • Helmig, Detlev; Guenther, Alex; Hueber, Jacques; Daly, Ryan; Wang, Wei; Park, Jeong-Hoo; Liikanen, Anssi; Praplan, Arnaud P. (Copernicus Publications, 2022)
    Atmospheric measurement techniques
    Previous research on atmospheric chemistry in the forest environment has shown that the total reactivity from biogenic volatile organic compound (BVOC) emissions is not well considered in forest chemistry models. One possible explanation for this discrepancy is the unawareness and neglect of reactive biogenic emissions that have eluded common monitoring methods. This question motivated the development of a total ozone reactivity monitor (TORM) for the direct determination of the reactivity of foliage emissions. Emission samples drawn from a vegetation branch enclosure experiment are mixed with a known and controlled amount of ozone (resulting in, e.g., 100 ppb of ozone) and directed through a temperature-controlled glass flow reactor to allow reactive biogenic emissions to react with ozone during the approximately 2 min residence time in the reactor. The ozone reactivity is determined from the difference in the ozone mole fraction before and after the reaction vessel. An inherent challenge of the experiment is the influence of changing water vapor in the sample air on the ozone signal. Sample air was drawn through Nafion dryers to mitigate the water vapor interference, and a commercial UV absorption ozone monitor was modified to directly determine the ozone differential with one instrument. These two modifications significantly reduced interferences from water vapor and errors associated with the determination of the reacted ozone as the difference from two individual measurements, resulting in a much improved and sensitive determination of the ozone reactivity. This paper provides a detailed description of the measurement design, the instrument apparatus, and its characterization. Examples and results from field deployments demonstrate the applicability and usefulness of the TORM.
  • Leikoski, Tuomo (Helsingin yliopisto, 2014)
    Formation of carbon carbon bonds constitutes the basis of synthetic organic chemistry. The growing demand of safer and environmentally friendlier processes, combined with continuing need for more efficient and selective reactions, has given challenges to industrial and fundamental academic research. The objective of this thesis was to develop novel ways to perform important carbon carbon bond-forming reactions on solid support. Of special focus were palladium- and copper-catalysed reactions of unsaturated amines. Polymer-bound propargylamine and allylamine were arylated successfully by the palladium-catalysed Sonogashira and Heck reaction, respectively. Additionally, allenes were produced in the Crabbé homologation of polymer-bound propargylamine, where copper acetylide is acting as an intermediate. All of these reactions would give rise to biologically interesting molecules: 1,3-arylaminopropanes after hydrogenation of the Sonogashira and Heck products and nitrogen-containing allenes by the Crabbé reaction. By varying the aryl iodide in solution, a series of arylated propargylamines and allylamines were synthesised and isolated as their acetamides. From the polymer-bound propargylamine, various allene amides were obtained after N-acylation followed by the Crabbé reaction. It was also briefly explored if the arylation of propargylamine on solid-phase could be possible without expensive palladium via the Castro-Stephens reaction, using a polymer-bound copper acetylide and the aryl iodide in solution. However, attempts to perform the first Castro Stephens reaction on solid-phase failed. Free amines are problematic in the Sonogashira and Heck reactions, due to coordination with the palladium catalyst and nucleophilicity toward the allene in the Crabbé reaction. These incompatibilities were solved by using the resin linkers simultaneously as protecting groups for the amines: as carbamates in the Sonogashira and Heck reaction, and as N-acyltriazenes in the Crabbé reaction. For the Heck reaction, finding the right reaction conditions turned out to be particularly difficult, the additional challenges being the narrow temperature window and the need to avoid polyarylation. Nevertheless, a regioselective γ-arylation could be performed giving similar yields as in the Sonogashira studies. In summary, alternative methods to perform important carbon carbon bond-forming reactions on solid support were developed.
  • Karppanen, Jari (Helsingin yliopisto, 2008)
    Environmentally benign and economical methods for the preparation of industrially important hydroxy acids and diacids were developed. The carboxylic acids, used in polyesters, alkyd resins, and polyamides, were obtained by the oxidation of the corresponding alcohols with hydrogen peroxide or air catalyzed by sodium tungstate or supported noble metals. These oxidations were carried out using water as a solvent. The alcohols are also a useful alternative to the conventional reactants, hydroxyaldehydes and cycloalkanes. The oxidation of 2,2-disubstituted propane-1,3-diols with hydrogen peroxide catalyzed by sodium tungstate afforded 2,2-disubstituted 3-hydroxypropanoic acids and 1,1-disubstituted ethane-1,2-diols as products. A computational study of the Baeyer-Villiger rearrangement of the intermediate 2,2-disubstituted 3-hydroxypropanals gave in-depth data of the mechanism of the reaction. Linear primary diols having chain length of at least six carbons were easily oxidized with hydrogen peroxide to linear dicarboxylic acids catalyzed by sodium tungstate. The Pt/C catalyzed air oxidation of 2,2-disubstituted propane-1,3-diols and linear primary diols afforded the highest yield of the corresponding hydroxy acids, while the Pt, Bi/C catalyzed oxidation of the diols afforded the highest yield of the corresponding diacids. The mechanism of the promoted oxidation was best described by the ensemble effect, and by the formation of a complex of the hydroxy and the carboxy groups of the hydroxy acids with bismuth atoms. The Pt, Bi/C catalyzed air oxidation of 2-substituted 2-hydroxymethylpropane-1,3-diols gave 2-substituted malonic acids by the decarboxylation of the corresponding triacids. Activated carbon was the best support and bismuth the most efficient promoter in the air oxidation of 2,2-dialkylpropane-1,3-diols to diacids. In oxidations carried out in organic solvents barium sulfate could be a valuable alternative to activated carbon as a non-flammable support. In the Pt/C catalyzed air oxidation of 2,2-disubstituted propane-1,3-diols to 2,2-disubstituted 3-hydroxypropanoic acids the small size of the 2-substituents enhanced the rate of the oxidation. When the potential of platinum of the catalyst was not controlled, the highest yield of the diacids in the Pt, Bi/C catalyzed air oxidation of 2,2-dialkylpropane-1,3-diols was obtained in the regime of mass transfer. The most favorable pH of the reaction mixture of the promoted oxidation was 10. The reaction temperature of 40°C prevented the decarboxylation of the diacids.
  • Lahtinen, Maarit (Helsingin yliopisto, 2013)
    Laccases (EC, benzenediol: oxygen oxidoreductase) are multicopper oxidases that can catalyze the oxidation of several, mainly different phenolic but also some inorganic substrates. Laccases selectively catalyze the one-electron oxidation of a phenolic substrate to a phenoxy radical, which can react further in non-enzymatic radical reactions. The phenolic subunits of lignin, one of the major components of wood, are natural substrates of laccases. In the presence of suitable small molecules, mediators, laccases can also catalyze the oxidation of the etherified (i.e. non-phenolic) subunits of lignin. The aim of this research is to increase the knowledge on the direct reactions of laccases and lignin, without mediators. Recently, this area has begun to garner increasing general interest as a result of the biorefinery concept, which aims to produce valuable raw material from sustainable resources. In addition, the most recent development of laccase mediators has been focusing on lignin-based phenolic molecules, which links these two areas, the laccase-mediator system and reactions without the mediator, directly to each other. Monomeric and dimeric lignin model compounds were used to evaluate the reactions and reactivity with laccases. Many of the model compounds represented the most common linkage-type in lignin, the beta-O-4 structure; thus, more efficient ways to synthesize these types of compounds were developed. Further, the oxidizabilities of the compounds, revealed by cyclic voltammetry, and the oxidation rates using the low- and the high-redox potential laccases from M. albomyces and T. hirsuta were compared in view of the theory that the reaction rate is dependent on the redox potential difference between the substrate and the laccase. However, it was found that the redox potential difference could not entirely explain the preferences of the studied laccases. The reaction products from the lignin model compounds were mainly formed as a result of 5-5 coupling and oxidation of the benzylic hydroxyl group to an aldehyde. The analysis was also performed as a function of time; for guaiacylic products the 5-5 coupling was the preferred reaction and these products were formed first. One model compound, vanillyl alcohol, was used to examine the effect of pH, enzyme dosage and temperature, all of which affected the product distribution. The observed predominating product was the 5-5 dimer, although according to computational evaluation, vanillin was the thermodynamically favored product, with a difference of 5.6 kcal mol-1. The transition states leading to the products seemed to affect the observed product distribution. In addition, the calculated pKa-values suggested that at the used pH range (4.5 7.5), rearomatization of the quinone intermediates could occur through deprotonation rather than through protonation. Finally, the M. albomyces laccase was tested in the presence of 1-allyl-3-methylimidazolium chloride, [Amim]Cl; an ionic liquid able to dissolve lignin. An expected decrease in enzyme activity was also found experimentally. The monolignol coniferyl alcohol was polymerized further, as expected, but the chemical structure of the formed dehydropolymer (DHP) was also affected by the presence of [Amim]Cl.
  • Setälä, Harri (Helsingin yliopisto, 2008)
    Dimeric phenolic compounds lignans and dilignols form in the so-called oxidative coupling reaction of phenols. Enzymes such as peroxidases and lac-cases catalyze the reaction using hydrogen peroxide or oxygen respectively as oxidant generating phenoxy radicals which couple together according to certain rules. In this thesis, the effects of the structures of starting materials mono-lignols and the effects of reaction conditions such as pH and solvent system on this coupling mechanism and on its regio- and stereoselectivity have been studied. After the primary coupling of two phenoxy radicals a very reactive quinone me-thide intermediate is formed. This intermediate reacts quickly with a suitable nucleophile which can be, for example, an intramolecular hydroxyl group or another nucleophile such as water, methanol, or a phenolic compound in the reaction system. This reaction is catalyzed by acids. After the nucleophilic addi-tion to the quinone methide, other hydrolytic reactions, rearrangements, and elimination reactions occur leading finally to stable dimeric structures called lignans or dilignols. Similar reactions occur also in the so-called lignification process when monolignol (or dilignol) reacts with the growing lignin polymer. New kinds of structures have been observed in this thesis. The dimeric com-pounds with so-called spirodienone structure have been observed to form both in the dehydrodimerization of methyl sinapate and in the beta-1-type cross-coupling reaction of two different monolignols. This beta-1-type dilignol with a spirodienone structure was the first synthetized and published dilignol model compound, and at present, it has been observed to exist as a fundamental construction unit in lignins. The enantioselectivity of the oxidative coupling reaction was also studied for obtaining enantiopure lignans and dilignols. A rather good enantioselectivity was obtained in the oxidative coupling reaction of two monolignols with chiral auxiliary substituents using peroxidase/H2O2 as an oxidation system. This observation was published as one of the first enantioselective oxidative coupling reaction of phenols. Pure enantiomers of lignans were also obtained by using chiral cryogenic chromatography as a chiral resolution technique. This technique was shown to be an alternative route to prepare enantiopure lignans or lignin model compounds in a preparative scale.
  • Nikkonen, Taru (Helsingin yliopisto, 2015)
    In photosynthetic systems, chlorophylls have a vital role in converting the energy of light into chemical energy. The absorption by antenna pigments and subsequent excitation energy transfer to the reaction centre, where charge separation processes take place, result in an electrochemical potential which is utilized in carbohydrate production. The structural properties of the chlorophylls as well as supramolecular interactions, mutual distances and orientations in their natural environment, determine the function of each pigment. The aim of this doctoral thesis was to mimic photosynthetic systems and to develop chlorophyll-based structures and materials for artificial photosynthetic applications. The literature review of this thesis will concentrate on the structural, photophysical, and supramolecular properties of chlorophyll derivatives. Their functions in natural environments and their potential use in artificial light-harvesting assemblies will be thoroughly discussed. The focus of the literature review will be solely on biomimetic systems that are built by the supramolecular approach. In addition to chlorophyll (chlorin) assemblies, supramolecular systems of some important chlorophyll analogues (e.g., porphyrins) are presented. The experimental part of this thesis is based on publications I-IV. Chlorophylls were separated from green algae and modified synthetically to achieve the desired photophysical and structural/supramolecular properties. In the first part of this thesis, the energy transferring antenna structure was designed utilizing a polymer, poly(4-vinylpyridine) (P4VP), to which Zn chlorin pigments were bound noncovalently through metal-ligand axial coordination. The investigation of the assemblies revealed tight coordination both in solution and solid state films. The absorptive and emitting regimes of the solid state Zn chlorin-P4VP assemblies with variable doping levels were determined. In another part of this thesis, a series of covalently linked chlorin dimers were synthesized and their intramolecular folding abilities were investigated using both spectroscopic and theoretical techniques. It was proven that chlorin dimers fold into a C2-symmetric structure via hydrogen bonding when the linker has a suitable length. To be exact, the folding was shown to be favored with 4-10 carbon atom linkers, of which the carbon linker with a 6-atom backbone was the most optimal. As a continuation of the work, the electron donating chlorin dimer was attached to an electron acceptor, fullerene, to give a chlorin dimer−azafulleroid. The experimental spectroscopical studies and theoretical investigations showed that the chlorin dimer−azafulleroid undergoes conformational switching depending on the polarity of the media. In nonpolar media, the hydrogen bonded folded dimer is present, while in polar media the two hydrophopic chlorins wrap around the azafulleroid. The photophysical studies indicated that the lifetime of photoinduced charge separation is longer in the folded conformation having similarities to the natural photosynthetic reaction centre special pair, that is, the self-assembled chlorophyll dimer that performs the primary electron transfer step in photosynthesis. Strong electron donors, such as ferrocene, Fe(η5-C5H5)2, and ruthenocene, Ru(η5-C5H5)2, are often utilized as electron donors in donor-acceptor pairs or conjugated to electron donors to achieve improved charge transfer properties with electron donating moieties. For the first time, metallocene-appended (either [Fe(η5-C5H5)(η5-C5H4)] or [Ru(η5-C5Me5)(η5-C5H4)]) chlorin derivatives were synthesized. The resulting metallocene-chlorins oxidized spontaneously under air to give certain oxidation products depending on the type of metallocene attached to the aromatic chlorin macrocycle. The oxidized metallocene-chlorins were characterized by steady-state and time-resolved absorption and emission spectroscopy.