Sulfoxides as an intramolecular sulfenylating agent for indoles and diverse applications of the sulfide-sulfoxide redox cycle in organic chemistry

This dissertation involves study of various aspects of sulfoxide chemistry. Specifically designed t-butyl and propanenitrile sulfoxides tethered to indole-2-carboxamide were used as a source of intramolecular sulfenylating agents to synthesize novel indolo[3,2-b]-1-5-benzothiazepinones which are structurally analogous to the other biologically active benzothiazepinones. This study reveals that the intramolecular cyclization of sulfoxide follows an electrophilic sulfenylation (Sulfoxide Electrophilic Sulfenylation, SES) reaction pathway. Evidence of the absence of sulfenic acid as a transient reactive intermediate in such intramolecular cyclization is also provided. In another study, sulfoxide was used as a “protecting group” of thioether to synthesize 8-membered, indole substituted, thiazocine-2-acetic acid derivative via Ring Closing Metathesis (RCM). Protection (oxidation) of inert (to RCM) sulfide to sulfoxide followed by RCM produced cyclized product in good yields. Deprotection (reduction) of sulfoxide was achieved using Lawessons Reagent (L.R.). Application of the sulfide-sulfoxide redox cycle to solve the existing difficulties in using RCM methodology to thioethers is illustrated. A new design of a “molecular brake”, based on the sulfide-sulfoxide redox cycle is described. N-Ar rotation in simple isoindolines is controlled by the oxidation state of the proximate sulfur atom. Sulfide [S(II)] shows “free” [brake OFF] N-Ar rotation whereas sulfoxide displayed hindered [brake ON] N-Ar rotation. The semi-empirical molecular orbital (PM3) calculations revealed concerted pyramidalization of amidic nitrogen with N-Ar rotation.

Synthesis, structure, and stability of metal-organic frameworks

Metal-organic frameworks (MOFs) obtained much attention because of their unusual structures and properties as well as their potential applications. This dissertation research was focused on (1) the effects of synthesis conditions on the structures of MOFs, (2) the thermal stability of MOFs, (3) pressure-induced amorphization, and (4) the effect of high-valent ions on the structure of a MOF. This research demonstrated that the crystal structure of MOF-5 could be controlled by drying solvents. If the vacuum solvent is dimethylformamide (DMF), the crystal structure of MOF-5 is tetragonal. In contrast, if the DMF is displaced by CH2Cl2 before the vacuum, the obtained MOF-5 occupies a cubic structure. Furthermore, it was found that the tetragonal MOF-5 exhibited a mediate surface area (300-1000 m2/g). The surface area of tetragonal MOF-5 is also dependent on Zn(NO3)2/H2BDC (H2BDC: terephthalic acid) molar ratios used for its synthesis. The optimum ratio is 1.38, at which synthesized tetragonal MOF-5 exhibits the highest crystallinity and surface area (1297 m2/g). The thermal stability and decomposition of MOF-5 were systematically investigated. The thermal decomposition of cubic and tetragonal MOF-5s resulted in the same products: CO2, benzene, amorphous carbon, and crystal ZnO. The thermal decomposition is due to breaking carboxylic bridges between benzene rings and Zn4O clusters. Identifying structural relationships between crystalline and noncrystalline states is of fundamental interest in materials research. Currently, amorphization of solid materials at ambient temperature requires an ultra-high pressure (several GPa). However, this research demonstrated that MOF-5 and IRMOF-8 can be irreversibly amorphized at ambient temperature by employing a low compressing pressure of 3.5 MPa, which is 100 times lower than that required for amorphization of other solids. Furthermore, the pressure-induced amorphization (PIA) of MOFs is strongly dependent on the changeability of bond angles. If the geometric structure of a MOF can allow bond angles to be changed without breaking bonds, it can easily be amorphized by compression. This can explain why MOF-5 and IRMOF-8 can easily be amorphized via compression than Cu-BTC. It is generally recognized that zeolitic imidazolate frameworks (ZIFs) occupy much higher stability than other types of MOFs. The representative of ZIFs is Zn(2-methylimidazole)2 (ZIF-8) exhibiting high-decomposition temperature and high chemical resistance to various solvents. However, so far, it is still unknown whether the high stability of ZIF-8 can be challenged by ions, which is important for its modification by doping ions. In this research, we performed aqueous salt solution treatment on ZIF-8, and the results showed that anions (Cl¯ and NO3¯) in a solution exhibited no effect on the crystal structure of ZIF-8. However, the effect of cations (in a solution) on structure of ZIF-8 strongly depends on the cation valences. The univalent metal cations showed no effect on the structure of ZIF-8, whereas the bivalent or higher-valent metal cations caused the collapse of ZIF-8 crystal structure. Therefore, structure stability of ZIF-8 is considered when it is subjected to the application, in which high-valent metal cations are involved.

Aza-Michael addition of amines to activated alkenes catalyzed by Silica supported perchloric acid under a solvent-free condition

An efficient aza-Michael addition of amines to a series of ,-unsaturated ketones, carboxylic esters, nitriles and chalcones has been carried out using perchloric acid supported over silica gel (HClO4-SiO2) at room temperature in high yields under solvent-free reaction conditions.

A versatile proline/alanine transporter in the unicellular pathogen Leishmania donovani regulates amino acid homoeostasis and osmotic stress responses

Unlike all other organisms, parasitic protozoa of the family Trypanosomatidae maintain a large cellular pool of proline that, together with the alanine pool, serve as alternative carbon sources as well as reservoirs of organic osmolytes. These reflect adaptation to their insect vectors whose haemolymphs are exceptionally rich in the two amino acids. In the present study we identify and characterize a new neutral amino acid transporter, LdAAP24, that translocates proline and alanine across the Leishmania donovani plasma membrane. This transporter fulfils multiple functions: it is the sole supplier for the intracellular pool of proline and contributes to the alanine pool; it is essential for cell volume regulation after osmotic stress; and it regulates the transport and homoeostasis of glutamate and arginine, none of which are its substrates. Notably, we provide evidence that proline and alanine exhibit different roles in the parasitic response to hypotonic shock; alanine affects swelling, whereas proline influences the rate of volume recovery. On the basis of our data we suggest that LdAAP24 plays a key role in parasite adaptation to its varying environments in host and vector, a phenomenon essential for successful parasitism.

Arsenic and selenium mobilisation from organic matter treated mine spoil with and without inorganic fertilisation

Organic matter amendments are applied to contaminated soil to provide a better habitat for re-vegetation and remediation, and olive mill waste compost (OMWC) has been described as a promising material for this aim. We report here the results of an incubation experiment carried out in flooded conditions to study its influence in As and metal solubility in a trace elements contaminated soil. NPK fertilisation and especially organic amendment application resulted in increased As, Se and Cu concentrations in pore water. Independent of the amendment, dimethylarsenic acid (DMA) was the most abundant As species in solution. The application of OMWC increased pore water dissolved organic-carbon (DOC) concentrations, which may explain the observed mobilisation of As, Cu and Se; phosphate added in NPK could also be in part responsible of the mobilisation caused in As. Therefore, the application of soil amendments in mine soils may be particularly problematic in flooded systems.

Fluorinated olefinic peptide nucleic acid: synthesis and pairing properties with complementary DNA

The fluorinated olefinic peptide nucleic acid (F-OPA) system was designed as a peptide nucleic acid (PNA) analogue in which the base carrying amide moiety was replaced by an isostructural and isoelectrostatic fluorinated C-C double bond, locking the nucleobases in one of the two possible rotameric forms. By comparison of the base-pairing properties of this analogue with its nonfluorinated analogue OPA and PNA, we aimed at a closer understanding of the role of this amide function in complementary DNA recognition. Here we present the synthesis of the F-OPA monomer building blocks containing the nucleobases A, T, and G according to the MMTr/Acyl protecting group scheme. Key steps are a selective desymmetrization of the double bond in the monomer precursor via lactonization as well as a highly regioselective Mitsunobu reaction for the introduction of the bases. PNA decamers containing single F-OPA mutations and fully modified F-OPA decamers and pentadecamers containing the bases A and T were synthesized by solid-phase peptide chemistry, and their hybridization properties with complementary parallel and antiparallel DNA were assessed by UV melting curves and CD spectroscopic methods. The stability of the duplexes formed by the decamers containing single (Z)-F-OPA modifications with parallel and antiparallel DNA was found to be strongly dependent on their position in the sequence with T(m) values ranging from +2.4 to -8.1 degrees C/modification as compared to PNA. Fully modified F-OPA decamers and pentadecamers were found to form parallel duplexes with complementary DNA with reduced stability compared to PNA or OPA. An asymmetric F-OPA pentadecamer was found to form a stable self-complex (T(m) approximately 65 degrees C) of unknown structure. The generally reduced affinity to DNA may therefore be due to an increased propensity for self-aggregation

High affinity amino acid transporters specifically expressed in xylem parenchyma and developing seeds of Arabidopsis

Arabidopsis amino acid transporters (AAPs) show individual temporal and spatial expression patterns. A new amino acid transporter, AAP8 was isolated by reverse transcription-PCR. Growth and transport assays in comparison to AAP1-5 characterize AAP8 and AAP6 as high affinity amino acid transport systems from Arabidopsis. Histochemical promoter-beta-glucuronidase (GUS) studies identified AAP6 expression in xylem parenchyma, cells requiring high affinity transport due to the low amino acid concentration in xylem sap. AAP6 may thus function in uptake of amino acids from xylem. Histochemical analysis of AAP8 revealed stage-dependent expression in siliques and developing seeds. Thus AAP8 is probably responsible for import of organic nitrogen into developing seeds. The only missing transporter of the family AAP7 was nonfunctional in yeast with respect to amino acid transport, and expression was not detectable. Therefore, AAP6 and -8 are the only members of the family able to transport aspartate with physiologically relevant affinity. AAP1, -6 and -8 are the closest AAP paralogs. Although AAP1 and AAP8 originate from a duplicated region on chromosome I, biochemical properties and expression pattern diverged. Overlapping substrate specificities paired with individual properties and expression patterns point to specific functions of each of the AAP genes in nitrogen distribution rather than to mere redundancy.

Deoxynucleoside triphosphates bearing histamine, carboxylic acid, and hydroxyl residues--synthesis and biochemical characterization.

Modified nucleoside triphosphates (dA(Hs)TP, dU(POH)TP, and dC(Val)TP) bearing imidazole, hydroxyl, and carboxylic acid residues connected to the purine and pyrimidine bases through alkyne linkers were prepared. These modified dN*TPs were excellent substrates for various DNA polymerases in primer extension reactions. Moreover, the combined use of terminal deoxynucleotidyl transferase (TdT) and the modified dNTPs led to efficient tailing reactions that rival those of natural counterparts. Finally, the triphosphates were tolerated by polymerases under PCR conditions, and the ensuing modified oligonucleotides served as templates for the regeneration of unmodified DNA. Thus, these modified dN*TPs are fully compatible with in vitro selection methods and can be used to develop artificial peptidases based on DNA.

Protein profiling of organic stone matrix and urine from dogs with urolithiasis

Two-thirds of the organic matrix in urinary stones consists of proteins. Their relationship to calculogenesis remains controversial with regard to their effect as inhibitors or promoters during stone formation. The purpose of the present study was to determine the differences in peptide and protein pattern between the urine of stone formers (n = 23) and control dogs (n = 12), as well as between organic matrix of different urinary stones (struvite n = 11, calcium oxalate n = 8, uric acid n = 4) using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. Specific differences in protein and peptide profiles were found in the organic matrix of different mineral compositions. Characteristic differences were also found in urinary peptide and protein pattern especially in molecular masses below 20 kDa between affected and healthy dogs. Based on the obtained molecular masses they were in some cases tentatively identified as proteins that are known to be involved in stone formation in humans. The study shows that in dogs, specific-urinary peptides and proteins might be associated with urolithiasis. It indicates the importance to further characterize those proteins for possible diagnostic purposes in prognosis and therapy

The influence of physical state on shikimic acid ozonolysis: a case for in situ microspectroscopy

Atmospheric soluble organic aerosol material can become solid or semi-solid. Due to increasing viscosity and decreasing diffusivity, this can impact important processes such as gas uptake and reactivity within aerosols containing such substances. This work explores the dependence of shikimic acid ozonolysis on humidity and thereby viscosity. Shikimic acid, a proxy for oxygenated reactive organic material, reacts with O3 in a Criegee-type reaction. We used an environmental microreactor embedded in a scanning transmission X-ray microscope (STXM) to probe this oxidation process. This technique facilitates in situ measurements with single micron-sized particles and allows to obtain near-edge X-ray absorption fine structure (NEXAFS) spectra with high spatial resolution. Thus, the chemical evolution of the interior of the particles can be followed under reaction conditions. The experiments show that the overall degradation rate of shikimic acid is depending on the relative humidity in a way that is controlled by the decreasing diffusivity of ozone with decreasing humidity. This decreasing diffusivity is most likely linked to the increasing viscosity of the shikimic acid–water mixture. The degradation rate was also depending on particle size, most congruent with a reacto-diffusion limited kinetic case where the reaction progresses only in a shallow layer within the bulk. No gradient in the shikimic acid concentration was observed within the bulk material at any humidity indicating that the diffusivity of shikimic acid is still high enough to allow its equilibration throughout the particles on the timescale of hours at higher humidity and that the thickness of the oxidized layer under dry conditions, where the particles are solid, is beyond the resolution of STXM.

Seasonal variation of high-molecular-weight compounds in the water-soluble fraction of organic urban aerosols

Aerosol samples were collected in Zurich, Switzerland, at an urban background site and were analyzed with size exclusion chromatography (SEC) and laser/desorption ionization mass spectrometry (LDI-MS) for water-soluble organic compounds with high molecular weight. Daily samples were collected during two campaigns in winter and summer, for 1 month each. The concentration of high-molecular-weight compounds (humic-like substances (HULIS)) was between 0.4 and 4 μg/m3 in winter and summer. The most intense signals in the LDI-MS mass spectra were measured between m/z150 and 500, comparing well with the mode of the two main high mass peaks determined with SEC corresponding to masses between 200 and 600 Da. For the maximum molecular weight, however, different results were obtained by the two techniques: whereas a maximum molecular weight between 1300 and 3300 Da was found with SEC, hardly any peaks above m/z700 were measured with LDI-MS. During summer the maximum molecular weight of HULIS (determined with SEC) correlates positively with several parameters such as ozone and increased temperature indicative of enhanced atmospheric photo-oxidation. The HULIS concentration also correlates positively with the oxalic acid concentration in the particles. This suggests that HULIS are generated by secondary processes in summer. The lack of such correlations during winter suggests that other sources and processes might be important during colder seasons.

Organic geochemistry of sediments from North Alex Mud Vulcano

Hydrocarbon seeps are ubiquitous at gas-prone Cenozoic deltas such as the Nile Deep Sea Fan (NDSF) where seepage into the bottom water has been observed at several mud volcanoes (MVs) including North Alex MV (NAMV). Here we investigated the sources of hydrocarbon gases and sedimentary organic matter together with biomarkers of microbial activity at four locations of NAMV to constrain how venting at the seafloor relates to the generation of hydrocarbon gases in deeper sediments. At the centre, high upward flux of hot (70 °C) hydrocarbon-rich fluids is indicated by an absence of biomarkers of Anaerobic Oxidation of Methane (AOM) and nearly constant methane (CH4) concentration depth-profile. The presence of lipids of incompatible thermal maturities points to mixing between early-mature petroleum and immature organic matter, indicating that shallow mud has been mobilized by the influx of deep-sourced hydrocarbon-rich fluids. Methane is enriched in the heavier isotopes, with values of d13C ~-46.6 per mil VPDB and dD ~-228 per mil VSMOW, and is associated with high amounts of heavier homologues (C2+) suggesting a co-genetic origin with the petroleum. On the contrary at the periphery, a lower but sustained CH4 flux is indicated by deeper sulphate-methane transition zones and the presence of 13C-depleted biomarkers of AOM, consistent with predominantly immature organic matter. Values of d13C-CH4 ~-60 per mil VPDB and decreased concentrations of 13C-enriched C2+ are typical of mixed microbial CH4 and biodegraded thermogenic gas from Plio-Pleistocene reservoirs of the region. The maturity of gas condensate migrated from pre-Miocene sources into Miocene reservoirs of the Western NDSF is higher than that of the gas vented at the centre of NAMV, supporting the hypothesis that it is rather released from the degradation of oil in Neogene reservoirs. Combined with the finding of hot pore water and petroleum at the centre, our results suggest that clay mineral dehydration of Neogene sediments, which takes place posterior to reservoir filling, may contribute to intense gas generation at high sedimentation rate deltas.