Doctor of Philosophy / Department of Chemistry / Ryszard J. Jankowiak / This dissertation reports the low temperature frequency domain spectroscopic study of three different natural pigment protein complexes and one artificial antenna system. The main focus of this work is to better understand electronic structure, excitation energy transfer (EET), and electron transfer (ET) dynamics in these systems that could have impact on achieving higher efficiency in future artificial solar cells. In the first part of this dissertation, electronic structure and EET pathways in isolated intact CP43 prime protein complex, which is isolated from Cyanobacterium synechocystis PCC 6803 grown under iron stressed conditions, are investigated using low-temperature absorption, fluorescence, fluorescence excitation, and hole-burning (HB) spectroscopies. This work suggests that, in analogy to the CP43 complex of PSII core, CP43 prime possesses two quasi-degenerate low energy states, A prime and B prime. The various low-temperature optical spectra are fitted considering an uncorrelated EET model. This work suggests that for optimal energy transfer from CP43 prime to PSI, the A prime and B prime state chlorophylls belonging to each CP43 prime should face towards the PSI core. The second part of dissertation reports the photochemical HB study on novel Zinc bacterial reaction center (Zn-RC) from Rhodobacter sphaeroides and its β-mutant (Zn-β-RC). This study shows that ET in the two samples is similar; however, the quantum efficiency of charge separation in the mutant decreases by 60 %. This finding suggests that the coordination state of the HA site zinc bacteriochlorophyll does not tune the active branch ET. Simultaneous fits of various optical spectra using experimentally determined inhomogeneity provides more reliable electron phonon coupling parameters for the P870 state of both RC samples. In the last part of this dissertation, EET in a novel artificial antenna system (ethynyl linked chlorophyll trefoil, ChlT1) is investigated. EET time in ChlT1 is ~2 ps. ChlT1 in MTHF/ethanol glass forms four different types of aggregates, A1-A4. The EET time in A1 and A2 type aggregates slows down only by a factor of 5 and 7, respectively. This study suggests that ChlT1 and its aggregates can be used as efficient antenna systems in designing organic solar cells.

In this thesis, topics in chemical hazard and risk assessment are explored through the use of multimedia mass balance models and high-throughput chemical property prediction methods. Chemical hazard metrics, as calculated by environmental fate and transport simulations, are investigated to determine the validity of two common simplifying assumptions in the underlying models; the use of octanol as a surrogate for organic matter and the use of environmental parameters that do not vary in time. A major finding is that the use of these common simplifying assumptions in multimedia mass balance models has little effect on chemical risk assessment, provided that chemicals are ranked relative to each other rather than a predetermined cutoff value. Chemical properties relevant to hazard and risk are collected, and applied in a large-scale chemical hazard assessment to derive a short list of potential Arctic contaminants. Several further data needs are identified; these are widely applicable and easily calculable metrics for chemical biodegradation, toxicity and emissions. A new method of predicting chemical properties is presented to assist in meeting these data needs. The method automatically creates predictive, quantitative relationships between the structures and properties of chemicals that are comparable to similar relationships created with expert judgement.

In this thesis, topics in chemical hazard and risk assessment are explored through the use of multimedia mass balance models and high-throughput chemical property prediction methods. Chemical hazard metrics, as calculated by environmental fate and transport simulations, are investigated to determine the validity of two common simplifying assumptions in the underlying models; the use of octanol as a surrogate for organic matter and the use of environmental parameters that do not vary in time. A major finding is that the use of these common simplifying assumptions in multimedia mass balance models has little effect on chemical risk assessment, provided that chemicals are ranked relative to each other rather than a predetermined cutoff value. Chemical properties relevant to hazard and risk are collected, and applied in a large-scale chemical hazard assessment to derive a short list of potential Arctic contaminants. Several further data needs are identified; these are widely applicable and easily calculable metrics for chemical biodegradation, toxicity and emissions. A new method of predicting chemical properties is presented to assist in meeting these data needs. The method automatically creates predictive, quantitative relationships between the structures and properties of chemicals that are comparable to similar relationships created with expert judgement.

The accumulation of polychlorinated biphenyls (PCBs) into humans was described using CoZMoMAN, a mechanistic multimedia fate and transport model coupled to a human food chain model. Model results demonstrated that concentration-age relationships for population cross-sections and individuals over time are not equivalent and that, under steady-state conditions, the lipid-normalized concentration of PCBs in an individual does not monotonically increase with age. By considering the decades-long emission history of PCBs in the model simulations, it was shown that an individual’s concentration mostly depends upon when she/he was born relative to the peak in emissions. Similarly, the two most influential factors controlling the shape of cross-sectional concentration-age trends obtained in human biomonitoring studies are the time lapse between the peak in emissions and sample collection and chemical elimination half-life. As a result, it should be possible to deduce information on these two factors from the shape of cross-sectional concentration-age trend. Reproductive behaviours (parity, age at birth, breastfeeding) were shown to potentially have a significant impact on exposure (and can contribute substantially to the observed variability in biomonitoring studies) though the mother’s reproductive history has a greater influence on the prenatal and postnatal exposures of her children than it does on her own cumulative lifetime exposure. A case study of the influence of dietary transitions in a hypothetical Arctic community demonstrated that dietary transitions are an important factor underlying the variability in PCB body burdens within and between subpopulations in addition to partially explaining the observed temporal trends. Comparison of PCB partitioning to various lipid materials suggested that 1) triolein is a good surrogate for human storage lipids; 2) liposomes are not an appropriate surrogate for human storage tissues; and 3) that partitioning into human MCF-7 cells is dominated by the storage lipids rather than by membrane lipids. Finally, a new bioenergetically-balanced bioaccumulation (3B) fish model is presented. Comparison of results from the 3B model with that of existing models revealed that feeding and growth rates used by previous fish bioaccumulation models were not bioenergetically consistent. Differences in biomagnification factors with fish size and temperature as a result of differing energetic requirements demonstrated the importance of the assumptions regarding growth rate and feeding rate.

Information regarding the structure and function of living tissues and cells is instrumental to the advancement of cell biology and biophysics. Nonlinear optical microscopy can provide such information, but only certain biological structures generate nonlinear optical signals. Therefore, structural specificity can be achieved by introducing labels for nonlinear optical microscopy. Few studies exist in the literature about labels that facilitate harmonic generation, coined "harmonophores". This thesis consists of the first major investigation of harmonophores for third harmonic generation (THG) microscopy. Carotenoids and chlorophylls were investigated as potential harmonophores. Their nonlinear optical properties were studied by the THG ratio technique. In addition, a tunable refractometer was built in order to determine their second hyperpolarizability (γ). At 830 nm excitation wavelength, carotenoids and chlorophylls were found to have large negative γ values however, at 1028 nm, the sign of γ reversed for carotenoids and remained negative for chlorophylls. Consequently, at 1028 nm wavelength, THG signal is canceled with mixtures of carotenoids and chlorophylls. Furthermore, when such molecules are covalently bonded as dyads or interact within photosynthetic pigment-protein complexes, it is found that additive effects with the γ values still play a role, however, the overall γ value is also influenced by the intra-pigment and inter-pigment interaction. The nonlinear optical properties of aggregates containing chlorophylls and carotenoids were the target of subsequent investigations. Carotenoid aggregates were imaged with polarization-dependent second harmonic generation and THG microscopy. Both techniques revealed crystallographic information pertaining to H and J aggregates and β-carotene crystalline aggregates found in orange carrot. In order to demonstrate THG enhancement due to labeling, cultured cells were labeled with carotenoid incorporated liposomes. In addition, Drosophila melanogaster larvae muscle as well as keratin structures in the hair cortex were labeled with β-carotene. Polarization-dependent THG studies may be particularly useful in understanding the structural organization that occurs within biological structures containing carotenoids and chlorophylls such as photosynthetic pigment-protein complexes and carotenoid aggregates in plants and alga. Further, artificial labeling with carotenoids and chlorophylls may be useful in clinical applications since they are nontoxic, nutritionally valuable, and they can aid in visualizing structural changes in cellular components.

Anatase titanium dioxide was synthesized using a hydrothermal treatment of bis(ammonium lactato) titanium dihydroxide (ALT) under a variety conditions. Heating the precursor produces highly crystalline particles that do not undergo a crystal phase transition upon calcination; however, it does remove a layer of surface adsorbed lactate. Three titanium-polyelectrolyte composites (PAA, PAH, and PEI) were formed through electrostatic polymer chain collapse. In order to gain a measure of the relative photo-activity of these various samples the interaction and de-colouration of methylene blue (MB) was investigated. The composite particles were not active whereas the non-composite titanium dioxide and solution phase PAA were individually active. MB was found to form dimers with anionic PAA through electrostatic interaction; however, there was no difference in the de-colouration rate of these dimers versus the monomers. Finally, it was found that pre-irradiating the polyelectrolyte prior to combining with MB decreases the de-colouration rate.

A new portable flow tube technique, the Toronto Photo-Oxidation Tube v2.0 was developed and characterized to explore its potential to control and monitor the OH-initiated formation and chemical aging of secondary organic aerosol (SOA) in-situ. The first study investigated the different operational parameters of this flow tube technique. TPOT v2.0 can generate oxidizing conditions equivalent to ambient OH exposures of 2.3 – 10.8 days. The transmission efficiency of a model organic aerosol indicated negligible losses in the oxidation tube. Differences in the residence time distribution curves measured for a gas and model organic aerosol showed that particles were subjected to approximately half of the OH exposure compared to gases. The second study examined the capacity of the TPOT technique to generate secondary aerosols due to OH oxidation. High aerosol yield was observed for H2SO4 particles, whereas a low aerosol yield was observed for α-pinene SOA.

As of 2010, cancer remains the leading cause of death in Canada, and second in the United States of America. This is despite decades of research into development of chemotherapeutics and diagnostics. A number of major challenges have prevented new discoveries from translating into a reduction in mortality rates. One challenge is the poor efficiency with which anti-cancer agents (diagnostic contrast agents and therapeutics) reach deregulated cells in the body. Therefore, development of new methods and technologies for improving efficiency of delivery has been a focus of research. Nanoparticles are leading candidates for improving the efficiency of delivery because they can act as payload vehicles for anti-cancer agents, because it is possible to mediate their interaction with biological systems and thus their pharmaockinetics, and because they can exploit inherent vulnerabilities of tumours. This thesis describes the results from a series of research projects designed to progress our understanding of how nanoparticles behave in vivo, and how their design can be optimized to improve tumour targeting.

Anatase titanium dioxide was synthesized using a hydrothermal treatment of bis(ammonium lactato) titanium dihydroxide (ALT) under a variety conditions. Heating the precursor produces highly crystalline particles that do not undergo a crystal phase transition upon calcination; however, it does remove a layer of surface adsorbed lactate. Three titanium-polyelectrolyte composites (PAA, PAH, and PEI) were formed through electrostatic polymer chain collapse. In order to gain a measure of the relative photo-activity of these various samples the interaction and de-colouration of methylene blue (MB) was investigated. The composite particles were not active whereas the non-composite titanium dioxide and solution phase PAA were individually active. MB was found to form dimers with anionic PAA through electrostatic interaction; however, there was no difference in the de-colouration rate of these dimers versus the monomers. Finally, it was found that pre-irradiating the polyelectrolyte prior to combining with MB decreases the de-colouration rate.

A new portable flow tube technique, the Toronto Photo-Oxidation Tube v2.0 was developed and characterized to explore its potential to control and monitor the OH-initiated formation and chemical aging of secondary organic aerosol (SOA) in-situ. The first study investigated the different operational parameters of this flow tube technique. TPOT v2.0 can generate oxidizing conditions equivalent to ambient OH exposures of 2.3 – 10.8 days. The transmission efficiency of a model organic aerosol indicated negligible losses in the oxidation tube. Differences in the residence time distribution curves measured for a gas and model organic aerosol showed that particles were subjected to approximately half of the OH exposure compared to gases. The second study examined the capacity of the TPOT technique to generate secondary aerosols due to OH oxidation. High aerosol yield was observed for H2SO4 particles, whereas a low aerosol yield was observed for α-pinene SOA.