<p>Molecular recognition via noncovalent interactions plays a key role in many biological processes such as antigen-antibody interactions, protein folding, the bonding and catalytic transformation of substrates by enzymes, etc. Amongst these noncovalent interactions, electrostatic interactions, hydrogen bonding, π-π interactions, and metal-to-ligand bonding are the most prominent. Exploring noncovalent interactions in host-guest systems that range from small hydrocarbon systems to more complex systems is the main motivation of this thesis. The present study involves the design, synthesis and characterization of clip-shaped molecules as host structures, and an examination of their binding properties with a variety of guests using NMR spectroscopy. </p><p>Several clips with a hydrocarbon or glycoluril backbone were synthesized. The binding of cations to small, hydrocarbon-based clips suggests that binding is enhanced by the rigidity and cooperativity between the two sidewalls of the clip. Binding is also very much dependant on the solvent properties. </p><p>Glycoluril-based clips built with aromatic sidewalls provide a deep cavity for binding guest molecules. The binding properties of these hosts were studied with several guests such as cations, Lewis acids and Lewis bases. Lewis basic binding sites in the acenaphthene-terminated clip were dominating in guest binding. Complexation-induced conformational changes in the wall-to-wall distance were observed for this clip.</p><p>In contrast, for a porphyrin-terminated clip with metal centers, very strong binding to a series of Lewis basic guests of various sizes into the clip cavity was observed. Conformational locking of guests with long alkyl chains was achieved, suggesting that, this clip could be useful as a potential molecular tool for the structural characterization of acyclic molecules with several stereogenic centers. This porphyrin clip was also shown to bind substituted fullerenes in the cavity.</p>

<p>This thesis describes the design and synthesis of molecules with potential roles in biomedicine, with an emphasis on molecular recognition in complex biological environments. The first chapter describes the synthesis and evaluation of compounds for use in nuclide therapy. Carboranes are frequently used in the development of drugs for Boron Neutron Capture Therapy. New routes for monohydroxylation at the B and C atoms of <i>p</i>-carborane have been developed. The Suzuki-Miyaura reaction has been applied to the cross-coupling of <i>bis</i>(neopentyl glycolato)diboron or <i>bis</i>(pinacolato)diboron and 2-I-<i>p</i>-carborane. The synthesized derivatives are important intermediates in the synthesis of a number of potentially biologically active carborane-containing molecules.</p><p>The DNA intercalator doxorubicin has been functionalized to enable ¹²⁵I labelling. The aim of combining the DNA intercalator with ¹²⁵I was to achieve high delivery of cytotoxic radiation to the nucleus. The DNA-binding ability and cellular uptake of the synthesized compounds have been evaluated. One of the compounds bound strongly to DNA and had similar cellular uptake as daunorubicin, which makes the compound very interesting for further biological evaluation.</p><p>The second chapter describes the use of polypeptide conjugates to broaden our knowledge of molecular recognition. The polypeptides consist of 42 amino acids each and are designed to fold into helix-loop-helix motifs that dimerize due to their amphiphilic character. The polypeptides are combined with a variety of small organic molecules. The incorporation of small aromatic molecules to influence the structure and dynamics of a polypeptide has been investigated. By attaching a dansyl group to the side chain of a lysine residue, the dynamics of the protein’s hydrophobic core where affected to such a degree that a native-like fold was formed. The polypeptide conjugates have also been used to study the binding and recognition of native proteins. High-affinity binders for chitinases and acetylcholine esterase have been developed and evaluated.</p>

This thesis describes the design and synthesis of molecules with potential roles in biomedicine, with an emphasis on molecular recognition in complex biological environments. The first chapter describes the synthesis and evaluation of compounds for use in nuclide therapy. Carboranes are frequently used in the development of drugs for Boron Neutron Capture Therapy. New routes for monohydroxylation at the B and C atoms of p-carborane have been developed. The Suzuki-Miyaura reaction has been applied to the cross-coupling of bis(neopentyl glycolato)diboron or bis(pinacolato)diboron and 2-I-p-carborane. The synthesized derivatives are important intermediates in the synthesis of a number of potentially biologically active carborane-containing molecules. The DNA intercalator doxorubicin has been functionalized to enable 125I labelling. The aim of combining the DNA intercalator with 125I was to achieve high delivery of cytotoxic radiation to the nucleus. The DNA-binding ability and cellular uptake of the synthesized compounds have been evaluated. One of the compounds bound strongly to DNA and had similar cellular uptake as daunorubicin, which makes the compound very interesting for further biological evaluation. The second chapter describes the use of polypeptide conjugates to broaden our knowledge of molecular recognition. The polypeptides consist of 42 amino acids each and are designed to fold into helix-loop-helix motifs that dimerize due to their amphiphilic character. The polypeptides are combined with a variety of small organic molecules. The incorporation of small aromatic molecules to influence the structure and dynamics of a polypeptide has been investigated. By attaching a dansyl group to the side chain of a lysine residue, the dynamics of the protein’s hydrophobic core where affected to such a degree that a native-like fold was formed. The polypeptide conjugates have also been used to study the binding and recognition of native proteins. High-affinity binders for chitinases and acetylcholine esterase have been developed and evaluated.

Artificial systems involving water oxidation and solar cells are promising ways for the conversion of solar energy into fuels and electricity. These systems usually consist of a photosensitizer, an electron donor and / or an electron acceptor. This thesis deals with the synthesis and photoinduced electron transfer of several donor-sensitizer-acceptor supramolecular systems. The first part of this thesis describes the synthesis and properties of two novel dinuclear ruthenium complexes as electron donors to mimic the donor side reaction of Photosystem II. These two Ru2 complexes were then covalently linked to ruthenium trisbipyridine and the properties of the resulting trinuclear complexes were studied by cyclic voltammetry and transient absorption spectroscopy. The second part presents the synthesis and photoinduced electron transfer of covalently linked donor-sensitizer supramolecular systems in the presence of TiO2 as electron acceptors. Electron donors are tyrosine, phenol and their derivatives, and dinuclear ruthenium complexes. Intramolecular electron transfer from the donor to the oxidized sensitizer was observed by transient absorption spectroscopy after light excitation of the Ru(bpy)32+ moiety. The potential applications of Ru2-based electron donors in artificial systems for water oxidation and solar cells are discussed. In the final part, the photoinduced interfacial electron transfer in the systems based on carotenoids and TiO2 is studied. Carotenoids are shown to act as both sensitizers and electron donors, which could be used in artificial systems to mimic the electron transfer chain in natural photosynthesis.

This thesis deals with synthetically modified chiral molecules and their application in asymmetric catalysis. The first part of the thesis describes the use of commercially available chiral diamine ligands in the iridium catalyzed transfer hydrogenation of aromatic ketones. The chiral diamine ligands were mixed with an appropriate transition-metal complex, which after addition of suitable base provided a chiral transition metal complex capable of reducing a range of different aromatic ketones in high yields and enantioselectivities. The developed methodology constitutes a cost effective and readily available procedure for transfer hydrogenation reactions. The following chapters in the thesis are completely devoted to rational design of small organic molecules acting as catalyst in various organocatalytic transformations. Organocatalytic methodology, represent a new and complementary approach to asymmetric organic synthesis, as compared to e.g. transition metal based methodology. Advantages of this methodology typically include mild and less stringent reaction conditions. This, in combination with the lack of toxic transition metal by-products, makes the process more environmentally benign; the organocatalytic methodology, therefore represent a promising approach towards implementation of green chemistry in organic synthesis. Despite this promise, typical drawbacks of the current methodology are long reaction times and the need for high catalyst loadings. Thus, a large demand exists for enhancing reactivity and increasing selectivity in organocatalytic reactions. The present thesis describes several efforts where we have tried to rationally design improved catalysts for various enantioselective organocata-lytic reactions. First, a structurally modified L-proline, incorporating a 1H-tetrazolic acid, was synthesized and evaluated in the direct asymmetric organocatalytic aldol reaction. As shown in Paper II, the catalyst displayed very high reactivity and subsequent studies were initiated in order to rationalize the reactivity enhancement (Paper III). Delightfully, the design principle of a 1H-tetrazolic acid as replacement for a carboxylic acid has since been widely used in the community, including our own efforts in organocatalytic asymmetric cyclopropanations (Paper V)and Diels-Alder reactions (Paper VII). Novel catalysts, including other functionalizations, were also designed for organocatalytic asymmetric addition of nitroalkanes to α,β-unsaturated aldehydes (Paper IV) and for cyclopropanations (Paper VI).

Quantum chemical studies on lowcoordinated group 14-16 compounds have been performed. This thesis focuses particularly on silenes influenced by reverse Siδ-=Cδ+ bond polarization. Hypercoordinated carbon compounds are also studied. The geometries from calculations with several common computationally inexpensive methods have been tested against high level CCSD/cc-pVTZ geometries for a series of substituted silenes. Hybrid HF/DFT methods performed best among the inexpensive methods tested for silenes. Heavy alkenes strongly influenced by reverse polarization are found to have less exothermic dimerization energies for both head-to-head and head-to-tail dimerizations, and to have higher activation energies for water addition than naturally polarized heavy alkenes. We also investigated solvated lithium, magnesium and potassium silenolates and found that lithium and magnesium ions coordinate preferably to O, giving their SiC bond some double bond character. Reverse polarized 2-siloxy-, 2-thiosiloxy-, and 2-(N-sila-N-methyl)-silenes could according to calculations be formed thermolytically from the corresponding tetrasilanes as transient species. It was, however, found that silenes highly influenced by π-conjugative reverse polarization have low barriers for the back-reaction, and thus these silenes are more difficult to form as stable species than naturally polarized silenes. It is also found that conjugated 1-siladienes, formed by electrocyclic ring-opening of 1-silacyclobut-2-enes, which are highly influenced by π-conjugative reverse polarization, have higher barriers for electrocyclization back to starting material than naturally polarized 1-siladienes. It is found that CHe54+, CHe64+, CNe54+, and CNe64+ are the closest carbon analogs of SiH5-, SiH62-, SiF5- and SiF62-, respectively. However, due to their exothermic dissociation reaction, these very high-lying local minima will be impossible to reach experimentally.

Structure-based drug design and combinatorial chemistry play important roles in the search for new drugs, and both these elements of medicinal chemistry were included in the present studies. This thesis outlines the synthesis of protease inhibitors against thrombin and the HCV NS3 protease, as well as the synthesis of a combinatorial library using solid phase chemistry.In the current work potent thrombin inhibitors were generated based on the D-Phe-Pro-Arg motif incorporating cyclopentene and cyclohexene scaffolds that were synthesized by ring-closing metathesis chemistry. A structure-activity relationship study was carried out using the crystallographic results for one of the inhibitors co-crystallized with thrombin. HCV NS3 protease inhibitors comprising the proline bioisostere 4-hydroxy-cyclopent-2-ene-1,2-dicarbboxylic acid were synthesized displaying low nanomolar activity. The stereochemistry and regiochemistry of the scaffolds were determined by NOESY and HMBC spectra, respectively. The final diastereomeric target compounds were isolated and annotated by applying TOCSY and ROESY NMR experiments. Furthermore, a 4-phenyl-2-carboxypiperazine targeted combinatorial chemistry library was synthesized to be used early in the lead discovery phase. This was done using a scaffold that was synthesized by palladiumcatalyzed aromatic amination chemistry and subsequently derivatized with eight electrophiles and ten nucleophiles.

The research described in this thesis is directed toward the efficient, enantioselective synthesis of chiral products that have useful functionality. This goal was pursued through catalytic asymmetric hydrogenation, a reaction class that selectively introduces one or two stereocenters into a molecule in an atom-efficient step. This reaction uses a small amount (often &lt;1 mol%) of a chiral catalyst to impart stereoselectivity to the product formed. Though catalytic asymmetric hydrogenation is not a new reaction type, there remain many substrate classes for which it is ineffective. The present thesis describes efforts to extend the reaction to some of these substrates classes. Some of the products synthesized in these studies may eventually find use as building blocks for the production of chiral pharmaceuticals, agrochemicals, or flavouring or colouring agents. However, the primary and immediate aim of this thesis was to develop and demonstrate new catalysts that are rapid and effective in the asymmetric hydrogenation of a broad range of compounds. Paper I describes the design and construction of two new, related chiral iridium compounds that are catalysts for asymmetric hydrogenation. They each contain an N,P-donating phosphinooxazoline ligand that is held together by a rigid bicyclic unit. One of these iridium compounds catalyzed the asymmetric hydrogenation of acyclic aryl imines, often with very good enantioselectivities. This is particularly notable because acyclic imines are difficult to reduce with useful enantioselectivity. The second catalyst was useful for the asymmetric hydrogenation of two aryl olefins. In Paper II, the class of catalysts introduced into Paper I is expanded to include many more related compounds, and these are also applied to the asymmetric hydrogenation of prochiral imines and olefins. By studying a range of related catalysts that differ in a single attribute, we were able to probe how different parts of the catalyst affect the yield and selectivity of the hydrogenation reactions. Whereas iridium catalysts had been applied to the asymmetric hydrogenation of imines and largely unfunctionalized olefins prior to this work (with varied degrees of success), they had not been used to reduce fluoroolefins. Their hydrogenation, which is discussed in Paper III, was complicated by concomitant defluorination to yield non-halogenated alkanes. To combat this problem, several iridium-based hydrogenation catalysts were applied to the reaction. Two catalysts stood out for their ability to produce chiral fluoroalkanes in good enantioselectivity while minimizing the defluorination reaction, and one of these bore a phosphinooxazoline ligand of the type described in Papers I and II. Enol phosphinates are another class of olefins that had not previously been subjected to iridium-catalyzed asymmetric hydrogenation. They do, however, constitute an attractive substrate class, because the product chiral alkyl phosphinates can be transformed into chiral alcohols or chiral phosphines with no erosion of enantiopurity. Iridium complexes of the phosphinooxazoline ligands described in Papers I and II were extremely effective catalysts for the asymmetric hydrogenation of enol phosphinates. They produced alkyl phosphinates from di- and trisubstituted enol phosphinate, β-ketoester-derived enol phosphinates, and even purely alkyl-substituted enol phopshinates, in very high yields and enantioselectivities.

Despite the unfavorable pharmacokinetic properties associated with peptides, they are still of great interest in drug development due to a multitude of interesting biological functions. The development of peptidomimetics strives to maintain or improve the biological activity of a peptide concurrently with removing the unwanted properties. This thesis describes two synthetic approaches to peptidomimetics with particular emphasis on secondary structure mimetics. First the design, synthesis and evaluation of two beta-turn mimetics incorporated in the endorphin Leu-enkephalin is presented. The beta-turn mimetics were stabilized by replacement of the intramolecular hydrogen bond with an ethylene bridge, and the amide bond between Tyr and Gly was replaced with an ether linkage. Linear analogues of the two mimetics were also synthesized. The peptidomimetics and their linear analogues were evaluated in a competitive binding assay at two opiate receptors, my and delta. One of the cyclized beta-turn mimetics was found to be a delta receptor antagonist with an IC50 value of 160 nM. Second a synthetic strategy to a beta-strand mimetic using 2-fluoro-4-iodopyridine as scaffold is described. The synthesis involved a Grignard exchange reaction on the pyridine scaffold using an amino acid derivative as electrophile followed by an SNAr reaction using an amine as nucleophile. The synthesis of a tripeptidomimetic of Leu-Gly-Gly and attempts to introduce chiral building blocks at the C-terminal, as well as studies towards elongated mimetics are presented. Two additional studies deal with the synthesis of two classes of potential thrombin inhibitors based on the pyridine scaffold. The first class contain pyridine as central fragment (P2 residue) substituted with a para-amidinobenzylamine group as P1 residue and various benzoyl groups as P3 residues. Three potential thrombin inhibitors were synthesized and found to be microM inhibitors in an enzymatic assay. In the second class, the pyridine ring serves as P3 residue. This class also lacks a strongly basic group in the P1 position. A small library of eight compounds were synthesized and evaluated in the enzymatic assay. Unfortunately, these compounds lacked inhibitory activity.

This thesis describes the development of new synthetic methodologies for preparation of bioactive interesting compounds, e.g. substituted pyridines, piperidines or piparazines. Thesecompounds are synthesized from commercially available, cheap and easily prepared reagents, videlicet the reaction between Grignard reagents and heterocyclic N-oxides.  The first part of this thesis deals with an improvement for synthesis of dienal-oximes and substituted pyridines. This was accomplished by a rapid addition of Grignard reagents to pyridine N-oxides at rt. yielding a diverse set of substituted dienal-oximes. During these studies, it was observed that the obtained dienal-oxmies are prone to ring-close upon heating. By taking advantage of this, a practical synthesis of substituted pyridines was developed. In the second part, an ortho-metalation of pyridine N-oxides using Grignard reagents is discussed. The method can be used for incorporation of a range of different electrophiles, including aldehydes, ketones and halogens. Furthermore, the importance for incorporation of halogens are exemplified through a Suzuki–Miyaura coupling reaction of 2-iodo pyridine N-oxides and different boronic acids. Later it was discovered that if the reaction temperature is kept below -20 °C, the undesired ringopening can be avoided. Thus, the synthesis of 2,3-dihydropyridine N-oxide, by reacting Grignard reagents with pyridine N-oxides at -40 °C followed by sequential addition of aldehyde or ketone, was accomplished. The reaction provides complete regio- and stereoselectivity yielding trans-2,3-dihydropyridine N-oxides in good yields. These intermediate products could then be used for synthesis of either substituted piperidines, by reduction, or reacted in a Diels–Alder cycloaddtion to give the aza-bicyclo compound. In the last part of this thesis, the discovered reactivity for pyridine N-oxides, is applied on pyrazine N-oxides in effort to synthesize substituted piperazines. These substances are obtained by the reaction of Grignard reagents and pyrazine N-oxides at -78 °C followed by reduction and protection, using a one-pot procedure. The product, a protected piperazine, that easily can be orthogonally deprotected, allowing synthetic modifications at either nitrogens in a fast and step efficient manner. Finally, an enantioselective procedure using a combination of PhMgCl and (-)-sparteine is discussed, giving opportunity for a stereoselective synthesis of substituted piperazines.