Creating new carbon-carbon bonds is one of the most important and challenging reactions in organic synthesis. Metal-catalyzed cross-coupling reactions have emerged as one of the preferred methods of producing new carbon-carbon bonds, and this work led to the 2010 Nobel Prize in Chemistry. This thesis was aimed at expanding the current research in the area of metal-catalyzed cross-coupling reactions to include new applications with dithiolane and dithiane protecting groups. 1,3-Dithiolane and 1,3-dithiane derivatives are particularly interesting molecules in that they can be deprotonated by a strong base to form anions, which can then be used for carbon-carbon bond synthesis. This thesis describes the investigation into the use of dithiolanes and dithianes in metal-catalyzed cross-coupling reactions, as well as some of the challenges faced in performing this sulfur-based chemistry.

Creating new carbon-carbon bonds is one of the most important and challenging reactions in organic synthesis. Metal-catalyzed cross-coupling reactions have emerged as one of the preferred methods of producing new carbon-carbon bonds, and this work led to the 2010 Nobel Prize in Chemistry. This thesis was aimed at expanding the current research in the area of metal-catalyzed cross-coupling reactions to include new applications with dithiolane and dithiane protecting groups. 1,3-Dithiolane and 1,3-dithiane derivatives are particularly interesting molecules in that they can be deprotonated by a strong base to form anions, which can then be used for carbon-carbon bond synthesis. This thesis describes the investigation into the use of dithiolanes and dithianes in metal-catalyzed cross-coupling reactions, as well as some of the challenges faced in performing this sulfur-based chemistry.

abstract: Reductive dechlorination by members of the bacterial genus Dehalococcoides is a common and cost-effective avenue for in situ bioremediation of sites contaminated with the chlorinated solvents, trichloroethene (TCE) and perchloroethene (PCE). The overarching goal of my research was to address some of the challenges associated with bioremediation timeframes by improving the rates of reductive dechlorination and the growth of Dehalococcoides in mixed communities. Biostimulation of contaminated sites or microcosms with electron donor fails to consistently promote dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), even when the presence of Dehalococcoides is confirmed. Supported by data from microcosm experiments, I showed that the stalling at cis-DCE is due a H2 competition in which components of the soil or sediment serve as electron acceptors for competing microorganisms. However, once competition was minimized by providing selective enrichment techniques, I illustrated how to obtain both fast rates and high-density Dehalococcoides using three distinct enrichment cultures. Having achieved a heightened awareness of the fierce competition for electron donor, I then identified bicarbonate (HCO3-) as a potential H2 sink for reductive dechlorination. HCO3- is the natural buffer in groundwater but also the electron acceptor for hydrogenotrophic methanogens and homoacetogens, two microbial groups commonly encountered with Dehalococcoides. By testing a range of concentrations in batch experiments, I showed that methanogens are favored at low HCO3 and homoacetogens at high HCO3-. The high HCO3- concentrations increased the H2 demand which negatively affected the rates and extent of dechlorination. By applying the gained knowledge on microbial community management, I ran the first successful continuous stirred-tank reactor (CSTR) at a 3-d hydraulic retention time for cultivation of dechlorinating cultures. I demonstrated that using carefully selected conditions in a CSTR, cultivation of Dehalococcoides at short retention times is feasible, resulting in robust cultures capable of fast dechlorination. Lastly, I provide a systematic insight into the effect of high ammonia on communities involved in dechlorination of chloroethenes. This work documents the potential use of landfill leachate as a substrate for dechlorination and an increased tolerance of Dehalococcoides to high ammonia concentrations (2 g L-1 NH4+-N) without loss of the ability to dechlorinate TCE to ethene. / Dissertation/Thesis / Ph.D. Microbiology 2013

Microbial respiration can be highly diverse and adaptable, with many bacteria able to respond to changes in their environment promptly and efficiently. The regulation of respiratory enzymes by highly responsive and precise transcriptional regulators confers distinct advantage for survival in sometimes harsh and extreme conditions. The organohalide-respiring bacterium Desulfitobacterium hafniense DCB-2 is able to utilise a wide range of electron acceptors and respiratory processes through tight regulation of respiratory machinery. An example of this tight regulation of respiratory machinery can been seen by biochemical analysis of the CRP-FNR-type transcriptional regulator family CprK, of which five are present in the strain. CprK1 is able to sense the presence of the physiological ligand, 3-chloro-4-hydroxyphenylacetic acid (CHPA), of reductive dehalogenase CprA1 with nM affinity. In this work we demonstrate that CprK1 is able to distinguish between the chlorinated CprA1 substrate CHPA and the non-chlorinated product 4-hydroxyphenylacetic acid (HPA) by ‘pKa interrogation’ of the 4-hydroxy moiety and by the atomic radius of the ortho-moiety. Through the use of in vitro biophysical and in vivo transcriptional response assays, we show that CprK1 is able to sense a number of halogenated phenols, including phenylacetic acids and nitrophenols. We also demonstrate that a 4-hydroxyl group is essential for CprK1 activation. In Chapter 4, an attempt to modify the effector sensitivity of CprK1 is performed by site-specific and random mutagenesis, and mutant selection assays are developed. We show that CprK1 is highly resistant to effector specificity modifications, with seemingly minor or conservative amino acid changes removing CprK1’s ability to initiate transcription. In Chapter 5, the CprK1 paralogue, CprK4 from D. hafniense DCB-2 is characterised by in vitro biophysical and in vivo transcriptional response assays in order to assess its potential as a biosensor. We show that CprK4 is able to bind cis-regulatory DNA elements dehaloboxes 7 and 10 in the absence of effector by Surface Plasmon Resonance (SPR) protein array; however, we were unable to identify its effectors reliably. Due to the unknown nature of CprK4’s effector, it is still unclear whether CprK4 could be a valuable biosensor.

Solar cells based on organohalide perovskites (PSCs) have made rapid progress in recent years and are a promising emerging technology. An important next evolutionary step for PSCs is their up-scaling to commercially relevant dimensions. The main challenges in scaling PSCs to be compatible with current c-Si cells are related to the limited conductivity of the transparent electrode, and the processing of a uniform and defect-free organohalide perovskite layer over large areas. In this work we present a generic and simple approach to realizing efficient solution-processed, monolithic solar cells based on methylammonium lead iodide (CH₃NH₃PbI₃). Our devices have an aperture area of 25 cm² without relying on an interconnected strip design, therefore reducing the complexity of the fabrication process and enhancing compatibility with the c-Si cell geometry. We utilize simple aluminum grid lines to increase the conductivity of the transparent electrode. These grid lines were exposed to an UV-ozone plasma to grow a thin aluminum oxide layer. This dramatically improves the wetting and film forming of the organohalide perovskite junction on top of the lines, reducing the probability of short circuits between the grid and the top electrode. The best devices employing these modified grids achieved power conversion efficiencies of up to 6.8%.